diff --git a/.lintr b/.lintr new file mode 100644 index 0000000..738dc13 --- /dev/null +++ b/.lintr @@ -0,0 +1,5 @@ + +linters: linters_with_defaults( + object_name_linter = NULL, + commented_code_linter = NULL + ) diff --git a/MTT/R/lc50.r b/MTT/R/lc50.r index 0f24096..648dcf6 100644 --- a/MTT/R/lc50.r +++ b/MTT/R/lc50.r @@ -1,12 +1,13 @@ +# FIX: the names abs, conc, names are mandatory fix this errorClass <- R6::R6Class("errorClass", public = list( error_message = NULL, object = NULL, initialize = function(error_message = NULL) { - self$error_message = error_message + self$error_message <- error_message }, isNull = function() { - if(is.null(self$error_message)) { + if (is.null(self$error_message)) { return(TRUE) } return(FALSE) @@ -14,110 +15,116 @@ errorClass <- R6::R6Class("errorClass", ) ) -shapenumber <- function (my.number) { +shapenumber <- function(my.number) { if (is.finite(my.number)) { - my.result <- signif(my.number,3) - } else { + my.result <- signif(my.number, 3) + } else { my.result <- NA - } - return (my.result) + } + return(my.result) } -#calculates the robust 68th percentile of the residuals -#adapted from Motulsky HJ, Brown RE, BMC Bioinformatics 2006, 7:123 -robust_68_percentile <- function (residuals) { +# calculates the robust 68th percentile of the residuals +# adapted from Motulsky HJ, Brown RE, BMC Bioinformatics 2006, 7:123 +robust_68_percentile <- function(residuals) { res <- abs(residuals) res_sorted <- sort(res) - res_percentiles <- (seq(1:length(res_sorted))/length(res_sorted))*100 + res_percentiles <- (seq(1:length(res_sorted)) / length(res_sorted)) * 100 index <- min(which(res_percentiles > 68.25)) - x <- c(res_percentiles[index-1],res_percentiles[index]) - y <- c(res_sorted[index-1],res_sorted[index]) - m <- lm(y~x) + x <- c(res_percentiles[index - 1], res_percentiles[index]) + y <- c(res_sorted[index - 1], res_sorted[index]) + m <- lm(y ~ x) x <- c(68.25) y <- predict(m, as.data.frame(x)) return(y) } -#calculates the robust standard deviation of the residuals (RSDR) with correction for degrees of freedom -#adapted from Motulsky HJ, Brown RE, BMC Bioinformatics 2006, 7:123 +# calculates the robust standard deviation of the residuals (RSDR) with correction for degrees of freedom +# adapted from Motulsky HJ, Brown RE, BMC Bioinformatics 2006, 7:123 robust_standard_deviation_residuals <- function(residuals, number_of_coefficients_fitted) { my_residuals <- as.numeric(residuals) my_residuals <- na.omit(residuals) - N <- length(my_residuals) #the number of data points fitted - K <- number_of_coefficients_fitted #for ic50, 4 coefficients are fitted - result <- robust_68_percentile(residuals) * N/(N-K) - return (result) + N <- length(my_residuals) # the number of data points fitted + K <- number_of_coefficients_fitted # for ic50, 4 coefficients are fitted + result <- robust_68_percentile(residuals) * N / (N - K) + return(result) } -#false discovery rate (FDR) approach, returns a T/F vector for selection of valid data points -#adapted from Motulsky HJ, Brown RE, BMC Bioinformatics 2006, 7:123 +# false discovery rate (FDR) approach, returns a T/F vector for selection of valid data points +# adapted from Motulsky HJ, Brown RE, BMC Bioinformatics 2006, 7:123 false_discovery_rate <- function(res) { - N <- length(res) - Q <- 0.01 #Q=1% - K <- 4 #number of coefficients in the fitted LL.4 model - R <- robust_standard_deviation_residuals(res,K) #the robust standard deviation of the residuals + N <- length(res) + Q <- 0.01 # Q=1% + K <- 4 # number of coefficients in the fitted LL.4 model + R <- robust_standard_deviation_residuals(res, K) # the robust standard deviation of the residuals id <- seq(1:length(res)) - df <- data.frame(id,res) + df <- data.frame(id, res) df$res_abs <- abs(df$res) - df <- df[order(df$res_abs),] + df <- df[order(df$res_abs), ] df$i <- seq(1:N) df$i_fraction <- df$i / N - df$alpha <- Q*(N-(df$i-1))/N + df$alpha <- Q * (N - (df$i - 1)) / N df$t <- df$res_abs / R - df$P <- dt(df$t, N-K) + df$P <- dt(df$t, N - K) df$include <- ifelse(df$P < df$alpha & df$i_fraction >= 0.7, FALSE, TRUE) df2 <- df[order(df$id), ] - return (df2$include) + return(df2$include) } check_fit <- function(model, min_conc, max_conc, min_abs, max_abs, substance_name) { - if(model$fit$convergence != TRUE) return(errorClass$new(paste(substance_name, - "Model did not converge"))) - b <- coefficients(model)[1] #Hill coefficient - c <- coefficients(model)[2] #asymptote 1 - d <- coefficients(model)[3] #asymptote 2 - e <- coefficients(model)[4] #IC50 - RSE <- summary(model)$rseMat[1] #residual standard error estimated + if (model$fit$convergence != TRUE) { + return(errorClass$new(paste( + substance_name, + "Model did not converge" + ))) + } + b <- coefficients(model)[1] # Hill coefficient + c <- coefficients(model)[2] # asymptote 1 + d <- coefficients(model)[3] # asymptote 2 + e <- coefficients(model)[4] # IC50 + RSE <- summary(model)$rseMat[1] # residual standard error estimated Response_lowestdose_predicted <- predict(model, data.frame(concentration = min_conc), se.fit = FALSE)[1] Response_highestdose_predicted <- predict(model, data.frame(concentration = max_conc), se.fit = FALSE)[1] Response_difference <- 100 * abs(Response_lowestdose_predicted - Response_highestdose_predicted) HillCoefficient <- b - IC50_relative <- e - pIC50 <- -log10(e/1000000) + IC50_relative <- e + pIC50 <- -log10(e / 1000000) Problems <- "" if (Response_difference < 25) { Problems <- paste(Problems, "Response Difference lower than 25%", collapse = " , ") - } else if(IC50_relative > max_conc) { + } else if (IC50_relative > max_conc) { Problems <- paste(Problems, "IC50 larger than highest measured concentration", collapse = " , ") - } else if(IC50_relative < min_conc) { + } else if (IC50_relative < min_conc) { Problems <- paste(Problems, "IC50 lower than lowest measured concentration", collapse = " , ") - } - + } + confidence_interval <- confint(model, parm = c("e"), level = 0.95) - IC50_relative_lower <- confidence_interval[1] + IC50_relative_lower <- confidence_interval[1] IC50_relative_higher <- confidence_interval[2] p_value <- noEffect(model)[3] Response_lowestdose_predicted <- shapenumber(Response_lowestdose_predicted) Response_highestdose_predicted <- shapenumber(Response_highestdose_predicted) - HillCoefficient <- shapenumber(HillCoefficient) + HillCoefficient <- shapenumber(HillCoefficient) IC50_relative <- shapenumber(IC50_relative) IC50_relative_lower <- shapenumber(IC50_relative_lower) IC50_relative_higher <- shapenumber(IC50_relative_higher) - pIC50 <- shapenumber( -log10(IC50_relative/1000000)) + pIC50 <- shapenumber(-log10(IC50_relative / 1000000)) p_value <- shapenumber(p_value) - ylim_low = 0 - ylim_high = 125 + ylim_low <- 0 + ylim_high <- 125 if (min_abs < ylim_low) ylim_low <- min_abs if (max_abs > ylim_high) ylim_high <- max_abs - outvar <- data.frame(name = substance_name, - Response_lowestdose_predicted = Response_lowestdose_predicted, - Response_highestdose_predicted = Response_highestdose_predicted, - HillCoefficient = HillCoefficient, - asymptote_one = c, asymptote_two = d, - IC50_relative = IC50_relative, IC50_relative_lower = IC50_relative_lower, - IC50_relative_higher = IC50_relative_higher, pIC50 = pIC50, - RSE = RSE, p_value = p_value, Problems = Problems) - return (outvar) + outvar <- data.frame( + name = substance_name, + Response_lowestdose_predicted = Response_lowestdose_predicted, + Response_highestdose_predicted = Response_highestdose_predicted, + HillCoefficient = HillCoefficient, + asymptote_one = c, asymptote_two = d, + IC50_relative = IC50_relative, IC50_relative_lower = IC50_relative_lower, + IC50_relative_higher = IC50_relative_higher, pIC50 = pIC50, + RSE = RSE, p_value = p_value, Problems = Problems + ) + return(outvar) } drawplot <- function(df, abs_col, conc_col, model, valid_points, title, @@ -127,16 +134,18 @@ drawplot <- function(df, abs_col, conc_col, model, valid_points, title, grid <- seq(min_conc, max_conc, 0.1) plotFct <- (model$curve)[[1]] res <- plotFct(grid) - data <- data.frame(abs = res, - conc = grid) + data <- data.frame( + abs = res, + conc = grid + ) data_measured <- data.frame(conc = df[, conc_col], abs = df[, abs_col]) p <- ggplot() + - geom_boxplot(data = data_measured, aes(x = conc, y = abs*100, group = conc)) + - geom_line(data = data, aes(x = conc, y = abs*100)) + - xlab("Concentration [µM]") + - ylab("Viability [%]") + - ggtitle(title) - + geom_boxplot(data = data_measured, aes(x = conc, y = abs * 100, group = conc)) + + geom_line(data = data, aes(x = conc, y = abs * 100)) + + xlab("Concentration [µM]") + + ylab("Viability [%]") + + ggtitle(title) + max_conc <- max(df[, conc_col]) + 10 min_conc <- -10 xmin <- IC50_relative - IC50_relative_lower @@ -147,29 +156,35 @@ drawplot <- function(df, abs_col, conc_col, model, valid_points, title, yrange <- ymax - ymin butt_height <- yrange * 0.1 ymedian <- median(df[, abs_col]) * 100 - if (xmin > min_conc && xmax < max_conc ) { - p <- p + geom_errorbarh(aes(xmin = xmin, - xmax = xmax, y = ymedian), - colour = "darkred", end = "butt", height = butt_height) + if (xmin > min_conc && xmax < max_conc) { + p <- p + geom_errorbarh( + aes( + xmin = xmin, + xmax = xmax, y = ymedian + ), + colour = "darkred", end = "butt", height = butt_height + ) } else { p <- p + labs(caption = "Confidence intervall not in conc. range") + theme(plot.caption = element_text(color = "darkred", face = "italic", size = 7)) - } + } } else { p <- p + labs(caption = "Confidence intervall could not be calculated") + theme(plot.caption = element_text(color = "darkred", face = "italic", size = 7)) } - + return(p) } ic50_internal <- function(df, abs, conc, title) { - model <- drm(abs ~ conc, data = df , fct = LL.4(), robust = "median") + model <- drm(abs ~ conc, data = df, fct = LL.4(), robust = "median") valid_points <- false_discovery_rate(residuals(model)) - model <- drm(abs ~ conc, data = df , subset = valid_points, start = model$coefficients, fct = LL.4(), robust = "mean") + model <- drm(abs ~ conc, data = df, subset = valid_points, start = model$coefficients, fct = LL.4(), robust = "mean") res <- check_fit(model, min(df[, conc]), max(df[, conc]), min(df[, abs]), max(df[, abs]), title) - p <- drawplot(df, abs, conc, model, valid_points, title, res$IC50_relative, - res$IC50_relative_lower, res$IC50_relative_higher) + p <- drawplot( + df, abs, conc, model, valid_points, title, res$IC50_relative, + res$IC50_relative_lower, res$IC50_relative_higher + ) return(list(res, p)) } @@ -178,10 +193,10 @@ drawplotOnlyRawData <- function(df, abs_col, conc_col, title) { max_conc <- max(df[, conc_col]) data_measured <- data.frame(conc = df[, conc_col], abs = df[, abs_col]) p <- ggplot() + - geom_boxplot(data = data_measured, aes(x = conc, y = abs*100, group = conc)) + + geom_boxplot(data = data_measured, aes(x = conc, y = abs * 100, group = conc)) + xlab("Concentration [µM]") + ylab("Viability [%]") + - ggtitle(title) + ggtitle(title) return(p) } @@ -203,50 +218,49 @@ drawplotOnlyRawData <- function(df, abs_col, conc_col, title) { ic50 <- function(df, abs_col, conc_col, substance_name_col, negative_identifier, positive_identifier) { substances <- unique(df$names) - if(!(negative_identifier %in% substances)) { + if (!(negative_identifier %in% substances)) { return(errorClass$new("the string for the negative control was not found!")) } - if(!(positive_identifier %in% substances)) { + if (!(positive_identifier %in% substances)) { return(errorClass$new("the string for the positive control was not found!")) } substances <- substances[substances != negative_identifier] - substances <- substances[substances != positive_identifier] - if(length(substances) < 1) { + substances <- substances[substances != positive_identifier] + if (length(substances) < 1) { return(errorClass$new("The data for compounds seems to be missing")) } - if(!is.numeric(df[, abs_col])) { - return(errorClass$new("The absorbance data is not numerical")) + if (!is.numeric(df[, abs_col])) { + return(errorClass$new("The absorbance data is not numerical")) } temp_conc <- df[, conc_col] temp_conc[temp_conc == negative_identifier] <- -1 temp_conc[temp_conc == positive_identifier] <- -2 temp_conc <- as.numeric(temp_conc) - if(any(is.na(temp_conc))) { - return(errorClass$new("The concentration data cannot be converted to numerical")) + if (any(is.na(temp_conc))) { + return(errorClass$new("The concentration data cannot be converted to numerical")) } df[, conc_col] <- temp_conc - if(!is.numeric(df[, conc_col])) { - return(errorClass$new("The concentration data is not numerical")) + if (!is.numeric(df[, conc_col])) { + return(errorClass$new("The concentration data is not numerical")) } - neg_mean <- mean(df[df[ , substance_name_col] == negative_identifier, abs_col]) - pos_mean <- mean(df[df[ , substance_name_col] == positive_identifier, abs_col]) + neg_mean <- mean(df[df[, substance_name_col] == negative_identifier, abs_col]) + pos_mean <- mean(df[df[, substance_name_col] == positive_identifier, abs_col]) df[, abs_col] <- (df[, abs_col] - pos_mean) / neg_mean res <- list() - for(i in seq_along(substances)) { + for (i in seq_along(substances)) { df_temp <- df[df$names == substances[i], ] - m <- tryCatch({ - m <- ic50_internal(df_temp, abs_col, conc_col, substances[i]) - }, - error = function(err) { - retval <- errorClass$new(paste("A warning occurred: ", conditionMessage(err))) - retval$object <- drawplotOnlyRawData(df_temp, abs_col, conc_col, substances[i]) - return(retval) - }) + m <- tryCatch( + { + m <- ic50_internal(df_temp, abs_col, conc_col, substances[i]) + }, + error = function(err) { + retval <- errorClass$new(paste("A warning occurred: ", conditionMessage(err))) + retval$object <- drawplotOnlyRawData(df_temp, abs_col, conc_col, substances[i]) + return(retval) + } + ) res[[i]] <- m } - + return(res) } - - - diff --git a/bs/.development/Distris.html b/bs/.development/000Distris.html similarity index 95% rename from bs/.development/Distris.html rename to bs/.development/000Distris.html index a74a88b..cb54e2b 100644 --- a/bs/.development/Distris.html +++ b/bs/.development/000Distris.html @@ -57,16 +57,16 @@ - - - - - - - - - - + + + + + + + + + + @@ -175,7 +175,7 @@

Plott
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
-

+

diff --git a/bs/.development/Distris.qmd b/bs/.development/000Distris.qmd similarity index 100% rename from bs/.development/Distris.qmd rename to bs/.development/000Distris.qmd diff --git a/bs/.development/Distris_files/figure-html/plot-histogram-1.png b/bs/.development/000Distris_files/figure-html/plot-histogram-1.png similarity index 100% rename from bs/.development/Distris_files/figure-html/plot-histogram-1.png rename to bs/.development/000Distris_files/figure-html/plot-histogram-1.png diff --git a/bs/.development/Regression_files/libs/bootstrap/bootstrap-icons.css b/bs/.development/000Distris_files/libs/bootstrap/bootstrap-icons.css similarity index 100% rename from bs/.development/Regression_files/libs/bootstrap/bootstrap-icons.css rename to bs/.development/000Distris_files/libs/bootstrap/bootstrap-icons.css diff --git a/bs/.development/Regression_files/libs/bootstrap/bootstrap-icons.woff b/bs/.development/000Distris_files/libs/bootstrap/bootstrap-icons.woff similarity index 100% rename from bs/.development/Regression_files/libs/bootstrap/bootstrap-icons.woff rename to bs/.development/000Distris_files/libs/bootstrap/bootstrap-icons.woff diff --git a/bs/.development/Distris_files/libs/bootstrap/bootstrap.min.css b/bs/.development/000Distris_files/libs/bootstrap/bootstrap.min.css similarity index 100% rename from bs/.development/Distris_files/libs/bootstrap/bootstrap.min.css rename to bs/.development/000Distris_files/libs/bootstrap/bootstrap.min.css diff --git a/bs/.development/Regression_files/libs/bootstrap/bootstrap.min.js b/bs/.development/000Distris_files/libs/bootstrap/bootstrap.min.js similarity index 100% rename from bs/.development/Regression_files/libs/bootstrap/bootstrap.min.js rename to bs/.development/000Distris_files/libs/bootstrap/bootstrap.min.js diff --git a/bs/.development/Distris_files/libs/clipboard/clipboard.min.js b/bs/.development/000Distris_files/libs/clipboard/clipboard.min.js similarity index 100% rename from bs/.development/Distris_files/libs/clipboard/clipboard.min.js rename to bs/.development/000Distris_files/libs/clipboard/clipboard.min.js diff --git a/bs/.development/Regression_files/libs/quarto-html/anchor.min.js b/bs/.development/000Distris_files/libs/quarto-html/anchor.min.js similarity index 100% rename from bs/.development/Regression_files/libs/quarto-html/anchor.min.js rename to bs/.development/000Distris_files/libs/quarto-html/anchor.min.js diff --git a/bs/.development/Regression_files/libs/quarto-html/popper.min.js b/bs/.development/000Distris_files/libs/quarto-html/popper.min.js similarity index 100% rename from bs/.development/Regression_files/libs/quarto-html/popper.min.js rename to bs/.development/000Distris_files/libs/quarto-html/popper.min.js diff --git a/bs/.development/Regression_files/libs/quarto-html/quarto-syntax-highlighting.css b/bs/.development/000Distris_files/libs/quarto-html/quarto-syntax-highlighting.css similarity index 100% rename from bs/.development/Regression_files/libs/quarto-html/quarto-syntax-highlighting.css rename to bs/.development/000Distris_files/libs/quarto-html/quarto-syntax-highlighting.css diff --git a/bs/.development/Regression_files/libs/quarto-html/quarto.js b/bs/.development/000Distris_files/libs/quarto-html/quarto.js similarity index 100% rename from bs/.development/Regression_files/libs/quarto-html/quarto.js rename to bs/.development/000Distris_files/libs/quarto-html/quarto.js diff --git a/bs/.development/Distris_files/libs/quarto-html/tippy.css b/bs/.development/000Distris_files/libs/quarto-html/tippy.css similarity index 100% rename from bs/.development/Distris_files/libs/quarto-html/tippy.css rename to bs/.development/000Distris_files/libs/quarto-html/tippy.css diff --git a/bs/.development/Distris_files/libs/quarto-html/tippy.umd.min.js b/bs/.development/000Distris_files/libs/quarto-html/tippy.umd.min.js similarity index 100% rename from bs/.development/Distris_files/libs/quarto-html/tippy.umd.min.js rename to bs/.development/000Distris_files/libs/quarto-html/tippy.umd.min.js diff --git a/bs/.development/001ConvergenceAndCentralLimitTheorem.R b/bs/.development/001ConvergenceAndCentralLimitTheorem.R new file mode 100644 index 0000000..f668d50 --- /dev/null +++ b/bs/.development/001ConvergenceAndCentralLimitTheorem.R @@ -0,0 +1,45 @@ +# Mean +mean_exp <- function(n) { + x <- rexp(n, 1) + return(mean(x)) +} +n <- seq(1, 10^4, by = 10) +ms <- lapply(n, mean_exp) +plot(n, ms) + +# Variance +var_exp <- function(n) { + x <- rexp(n, 1) + return(sd(x)) +} +n <- seq(1, 10^4, by = 10) +vs <- lapply(n, var_exp) +plot(n, vs) + + +# Central Limit Theorem Simulation +sample_means <- function(sample_size, n_samples) { + replicate(n_samples, mean(rexp(sample_size, rate = 10))) +} +sample_sizes <- c(5, 30, 100, 1000, 10000, 10^5) +n_samples <- 10000 + +clt_data <- lapply(sample_sizes, function(size) { + data.frame( + x = 1:n_samples, + mean = sample_means(size, n_samples), + sample_size = factor(size) + ) +}) + +library(ggplot2) +library(cowplot) + +p_fct <- function(df) { + ggplot(df) + + geom_histogram(aes(x = mean, y = ..density..), bins = 50, fill = "lightblue") + + geom_density(aes(x = mean), color = "darkred", size = 1.5) +} +plot_list <- lapply(clt_data, p_fct) + +plot_grid(plotlist = plot_list, ncol = 2, labels = "AUTO") diff --git a/bs/.development/001ECDF.html b/bs/.development/001ECDF.html new file mode 100644 index 0000000..c766ae7 --- /dev/null +++ b/bs/.development/001ECDF.html @@ -0,0 +1,422 @@ + + + + + + + + + +Empircial cumulative distribution function + + + + + + + + + + + + + + + + + + + +
+ +
+ +
+
+

Empircial cumulative distribution function

+
+ + + +
+ + + + +
+ + +
+ +
+

Calculation of empirical cumulative distribution function (ECDF)

+
+
n <- 20
+randoms <- runif(n, 1, 10)
+how_often <- sample.int(3, n, replace = TRUE)
+sample <- numeric(sum(how_often))
+counter <- 1
+for (i in 1:n) {
+  sample[counter:(counter + how_often[i] - 1)] <- rep(randoms[i], how_often[i])
+  counter <- counter + how_often[i]
+}
+sample <- sort(sample)
+unique_sample <- unique(sample)
+total_observations <- length(sample)
+ecdf <- sapply(unique_sample, function(x) {
+  sum(sample <= x) / total_observations
+})
+ecdf
+
+
 [1] 0.04761905 0.11904762 0.14285714 0.21428571 0.26190476 0.33333333
+ [7] 0.40476190 0.47619048 0.52380952 0.57142857 0.64285714 0.69047619
+[13] 0.71428571 0.78571429 0.80952381 0.83333333 0.90476190 0.92857143
+[19] 0.95238095 1.00000000
+
+
df <- data.frame(x = unique_sample, y = ecdf)
+library(ggplot2)
+ggplot(data = df, aes(x = x, y = y)) +
+  geom_step() +
+  geom_label(aes(label = round(x, 2)))
+
+

+
+
+
    +
  • If the ECDF value is F_n(5) = 0.5

  • +
  • it means 50% of the sample values are less than or equal to 5.

  • +
  • The CDF corresponds to a theoretical probability distribution (e.g. normal, exponential).

  • +
  • It is the integral of the probability density function (PDF)

  • +
  • PDF are the d-functions in R

  • +
  • CDF are the p-functions in R

  • +
  • The q-functions in R compute the quantiles of a distribution.

  • +
  • They are the inverse of the CDF.

  • +
  • In simple terms, the quantile tells you the value of x

  • +
  • below which a proportion p of the data lies.

  • +
+
+
+

Empirical quantiles and qqunif plot

+
+
n <- 200
+randoms <- runif(n, 1, 10)
+how_often <- sample.int(3, n, replace = TRUE)
+sample <- numeric(sum(how_often))
+counter <- 1
+for (i in 1:n) {
+  sample[counter:(counter + how_often[i] - 1)] <- rep(randoms[i], how_often[i])
+  counter <- counter + how_often[i]
+}
+sample <- sort(sample)
+n <- length(sample)
+
+ps <- seq(0, 1, 0.1)
+qq <- data.frame(
+  empirical = numeric(length(ps)),
+  theoretical = numeric(length(ps))
+)
+for (i in 1:length(ps)) {
+  # i = p * (n + 1)
+  idx <- ps[i] * (n + 1)
+  if (floor(idx) == 0) {
+    idx <- 1
+  } else if (ceiling(idx) >= n) {
+    idx <- n
+  }
+  qq$empirical[i] <- (sample[ceiling(idx)] + sample[floor(idx)] ) / 2
+  qq$theoretical[i] <- qunif(p = ps[i], min = 1, max = 10)
+}
+plot(qq$theoretical, qq$empirical)
+abline(0, 1, col = "red", lty = 2)
+
+

+
+
+
+ +
+ + +
+ + + + \ No newline at end of file diff --git a/bs/.development/ECDF.R b/bs/.development/001ECDF.qmd similarity index 64% rename from bs/.development/ECDF.R rename to bs/.development/001ECDF.qmd index e4e2331..d705889 100644 --- a/bs/.development/ECDF.R +++ b/bs/.development/001ECDF.qmd @@ -1,5 +1,12 @@ -# Calculation of empirical cumulative distribution function (ECDF) +--- +title: "Empircial cumulative distribution function" +output: html_document # Use `output: quarto::html` for Quarto +--- + +## Calculation of empirical cumulative distribution function (ECDF) + +```{r ecdf calculation} n <- 20 randoms <- runif(n, 1, 10) how_often <- sample.int(3, n, replace = TRUE) @@ -22,21 +29,25 @@ library(ggplot2) ggplot(data = df, aes(x = x, y = y)) + geom_step() + geom_label(aes(label = round(x, 2))) +``` -# If the ECDF value is F_n(5) = 0.5 -# it means 50% of the sample values are less than or equal to 5. -# The CDF corresponds to a theoretical probability distribution (e.g. normal, exponential). -# It is the integral of the probability density function (PDF) -# PDF are the d-functions in R -# CDF are the p-functions in R -# The q-functions in R compute the quantiles of a distribution. -# They are the inverse of the CDF. -# In simple terms, the quantile tells you the value of x -# below which a proportion p of the data lies. +- If the ECDF value is F_n(5) = 0.5 +- it means 50% of the sample values are less than or equal to 5. +- The CDF corresponds to a theoretical probability distribution (e.g. normal, exponential). +- It is the integral of the probability density function (PDF) -# Empirical quantiles -n <- 20 +- PDF are the d-functions in R +- CDF are the p-functions in R +- The q-functions in R compute the quantiles of a distribution. +- They are the inverse of the CDF. +- In simple terms, the quantile tells you the value of x +- below which a proportion p of the data lies. + +## Empirical quantiles and qqunif plot + +```{r qqunif} +n <- 200 randoms <- runif(n, 1, 10) how_often <- sample.int(3, n, replace = TRUE) sample <- numeric(sum(how_often)) @@ -66,3 +77,5 @@ for (i in 1:length(ps)) { } plot(qq$theoretical, qq$empirical) abline(0, 1, col = "red", lty = 2) +``` + diff --git a/bs/.development/001ECDF_files/figure-html/ecdf calculation-1.png b/bs/.development/001ECDF_files/figure-html/ecdf calculation-1.png new file mode 100644 index 0000000..0f94fa0 Binary files /dev/null and b/bs/.development/001ECDF_files/figure-html/ecdf calculation-1.png differ diff --git a/bs/.development/001ECDF_files/figure-html/qqunif-1.png b/bs/.development/001ECDF_files/figure-html/qqunif-1.png new file mode 100644 index 0000000..ee2d11e Binary files /dev/null and b/bs/.development/001ECDF_files/figure-html/qqunif-1.png differ diff --git a/bs/.development/Regression_linear_model_files/libs/bootstrap/bootstrap-icons.css b/bs/.development/001ECDF_files/libs/bootstrap/bootstrap-icons.css similarity index 100% rename from bs/.development/Regression_linear_model_files/libs/bootstrap/bootstrap-icons.css rename to bs/.development/001ECDF_files/libs/bootstrap/bootstrap-icons.css diff --git a/bs/.development/Regression_linear_model_files/libs/bootstrap/bootstrap-icons.woff b/bs/.development/001ECDF_files/libs/bootstrap/bootstrap-icons.woff similarity index 100% rename from bs/.development/Regression_linear_model_files/libs/bootstrap/bootstrap-icons.woff rename to bs/.development/001ECDF_files/libs/bootstrap/bootstrap-icons.woff diff --git a/bs/.development/Regression_files/libs/bootstrap/bootstrap.min.css b/bs/.development/001ECDF_files/libs/bootstrap/bootstrap.min.css similarity index 100% rename from bs/.development/Regression_files/libs/bootstrap/bootstrap.min.css rename to bs/.development/001ECDF_files/libs/bootstrap/bootstrap.min.css diff --git a/bs/.development/Regression_linear_model_files/libs/bootstrap/bootstrap.min.js b/bs/.development/001ECDF_files/libs/bootstrap/bootstrap.min.js similarity index 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from bs/.development/Regression_linear_model_files/libs/quarto-html/popper.min.js rename to bs/.development/001ECDF_files/libs/quarto-html/popper.min.js diff --git a/bs/.development/Regression_linear_model_files/libs/quarto-html/quarto-syntax-highlighting.css b/bs/.development/001ECDF_files/libs/quarto-html/quarto-syntax-highlighting.css similarity index 100% rename from bs/.development/Regression_linear_model_files/libs/quarto-html/quarto-syntax-highlighting.css rename to bs/.development/001ECDF_files/libs/quarto-html/quarto-syntax-highlighting.css diff --git a/bs/.development/Regression_linear_model_files/libs/quarto-html/quarto.js b/bs/.development/001ECDF_files/libs/quarto-html/quarto.js similarity index 100% rename from bs/.development/Regression_linear_model_files/libs/quarto-html/quarto.js rename to bs/.development/001ECDF_files/libs/quarto-html/quarto.js diff --git a/bs/.development/Regression_files/libs/quarto-html/tippy.css b/bs/.development/001ECDF_files/libs/quarto-html/tippy.css similarity index 100% rename from bs/.development/Regression_files/libs/quarto-html/tippy.css rename to bs/.development/001ECDF_files/libs/quarto-html/tippy.css diff --git a/bs/.development/Regression_files/libs/quarto-html/tippy.umd.min.js b/bs/.development/001ECDF_files/libs/quarto-html/tippy.umd.min.js similarity index 100% rename from bs/.development/Regression_files/libs/quarto-html/tippy.umd.min.js rename to bs/.development/001ECDF_files/libs/quarto-html/tippy.umd.min.js diff --git a/bs/.development/002Likelihood.html b/bs/.development/002Likelihood.html new file mode 100644 index 0000000..0737cbd --- /dev/null +++ b/bs/.development/002Likelihood.html @@ -0,0 +1,436 @@ + + + + + + + + + +Exploring Likelihood in R + + + + + + + + + + + + + + + + + + + +
+ +
+ +
+
+

Exploring Likelihood in R

+
+ + + +
+ + + + +
+ + +
+ +
+

Likelihood of a Dataset

+

Likelihood refers to how probable a specific set of data is under a given model. It quantifies the models ability to explain the observed data. Maximizing the likelihood helps estimate the parameters that make the observed data most probable (used in maximum likelihood estimation).

+
+

fitdistr and AIC

+
    +
  • fitdistr (in MASS package): Fits a distribution to data by estimating its parameters using maximum likelihood estimation. It’s useful for modeling and checking which distribution best matches your data.
  • +
  • AIC (Akaike Information Criterion): Measures the relative quality of statistical models, balancing model fit and complexity. A lower AIC indicates a model that better explains the data with fewer parameters.
  • +
+
+
library(FAwR)
+
+
Loading required package: MASS
+
+
+
Loading required package: lattice
+
+
+
Loading required package: glpkAPI
+
+
+
using GLPK version 5.0
+
+
library(ggplot2)
+library(MASS)
+data(gutten)
+hist(gutten$dbh.cm)
+
+

+
+
fit_norm <- fitdistr(gutten$dbh.cm, "normal")
+fit_norm
+
+
      mean          sd    
+  20.7820833   10.5987949 
+ ( 0.3059609) ( 0.2163470)
+
+
likelihood <- prod(
+  dnorm(gutten$dbh.cm,
+  mean = fit_norm$estimate[1],
+  sd = fit_norm$estimate[2])
+) # Cannot be calculated like this by a computer --> is 0
+likelihood <- sum(
+  log(
+    dnorm(gutten$dbh.cm,
+      mean = fit_norm$estimate[1],
+      sd = fit_norm$estimate[2])
+  )
+)
+likelihood
+
+
[1] -4535.615
+
+
logLik(fit_norm)
+
+
'log Lik.' -4535.615 (df=2)
+
+
AIC(fit_norm)
+
+
[1] 9075.229
+
+
BIC(fit_norm)
+
+
[1] 9085.409
+
+
# log normal
+fit_lognorm <- fitdistr(gutten$dbh.cm, "lognormal")
+fit_lognorm
+
+
    meanlog       sdlog   
+  2.82767051   0.77740010 
+ (0.02244161) (0.01586861)
+
+
likelihood <- sum(
+  log(
+    dnorm(gutten$dbh.cm,
+      mean = fit_lognorm$estimate[1],
+      sd = fit_lognorm$estimate[2])
+  )
+)
+likelihood
+
+
[1] -Inf
+
+
logLik(fit_lognorm)
+
+
'log Lik.' -4793.771 (df=2)
+
+
AIC(fit_lognorm)
+
+
[1] 9591.541
+
+
BIC(fit_lognorm)
+
+
[1] 9601.722
+
+
+
+
+ +
+ + +
+ + + + \ No newline at end of file diff --git a/bs/.development/002Likelihood.qmd b/bs/.development/002Likelihood.qmd new file mode 100644 index 0000000..528cb9e --- /dev/null +++ b/bs/.development/002Likelihood.qmd @@ -0,0 +1,60 @@ +--- +title: "Exploring Likelihood in R" +output: html_document # Use `output: quarto::html` for Quarto +--- + +## Likelihood of a Dataset +Likelihood refers to how probable a specific set of data is under a given model. +It quantifies the models ability to explain the observed data. +Maximizing the likelihood helps estimate the parameters that make the observed data +most probable (used in maximum likelihood estimation). + +### fitdistr and AIC +- fitdistr (in MASS package): Fits a distribution to data by estimating + its parameters using maximum likelihood estimation. + It's useful for modeling and checking which distribution best matches your data. +- AIC (Akaike Information Criterion): Measures the relative quality + of statistical models, balancing model fit and complexity. A lower AIC + indicates a model that better explains the data with fewer parameters. + +```{r Likelihood} +library(FAwR) +library(ggplot2) +library(MASS) +data(gutten) +hist(gutten$dbh.cm) +fit_norm <- fitdistr(gutten$dbh.cm, "normal") +fit_norm +likelihood <- prod( + dnorm(gutten$dbh.cm, + mean = fit_norm$estimate[1], + sd = fit_norm$estimate[2]) +) # Cannot be calculated like this by a computer --> is 0 +likelihood <- sum( + log( + dnorm(gutten$dbh.cm, + mean = fit_norm$estimate[1], + sd = fit_norm$estimate[2]) + ) +) +likelihood +logLik(fit_norm) +AIC(fit_norm) +BIC(fit_norm) + +# log normal +fit_lognorm <- fitdistr(gutten$dbh.cm, "lognormal") +fit_lognorm +likelihood <- sum( + log( + dnorm(gutten$dbh.cm, + mean = fit_lognorm$estimate[1], + sd = fit_lognorm$estimate[2]) + ) +) +likelihood +logLik(fit_lognorm) +AIC(fit_lognorm) +BIC(fit_lognorm) +``` + diff --git a/bs/.development/Regression_linear_model_files/figure-html/Likelihood-1.png b/bs/.development/002Likelihood_files/figure-html/Likelihood-1.png similarity index 100% rename from bs/.development/Regression_linear_model_files/figure-html/Likelihood-1.png rename to bs/.development/002Likelihood_files/figure-html/Likelihood-1.png diff --git a/bs/.development/Distris_files/libs/bootstrap/bootstrap-icons.css b/bs/.development/002Likelihood_files/libs/bootstrap/bootstrap-icons.css similarity index 95% rename from bs/.development/Distris_files/libs/bootstrap/bootstrap-icons.css rename to bs/.development/002Likelihood_files/libs/bootstrap/bootstrap-icons.css index 285e444..94f1940 100644 --- a/bs/.development/Distris_files/libs/bootstrap/bootstrap-icons.css +++ b/bs/.development/002Likelihood_files/libs/bootstrap/bootstrap-icons.css @@ -1,14 +1,8 @@ -/*! - * Bootstrap Icons v1.11.1 (https://icons.getbootstrap.com/) - * Copyright 2019-2023 The Bootstrap Authors - * Licensed under MIT (https://github.com/twbs/icons/blob/main/LICENSE) - */ - @font-face { font-display: block; font-family: "bootstrap-icons"; src: -url("./bootstrap-icons.woff?2820a3852bdb9a5832199cc61cec4e65") format("woff"); +url("./bootstrap-icons.woff?2ab2cbbe07fcebb53bdaa7313bb290f2") format("woff"); } .bi::before, @@ -447,6 +441,7 @@ url("./bootstrap-icons.woff?2820a3852bdb9a5832199cc61cec4e65") format("woff"); .bi-cloud-fog2::before { content: "\f2a2"; } .bi-cloud-hail-fill::before { content: "\f2a3"; } .bi-cloud-hail::before { content: "\f2a4"; } +.bi-cloud-haze-1::before { content: "\f2a5"; } .bi-cloud-haze-fill::before { content: "\f2a6"; } .bi-cloud-haze::before { content: "\f2a7"; } .bi-cloud-haze2-fill::before { content: "\f2a8"; } @@ -1442,16 +1437,21 @@ url("./bootstrap-icons.woff?2820a3852bdb9a5832199cc61cec4e65") format("woff"); .bi-dpad::before { content: "\f687"; } .bi-ear-fill::before { content: "\f688"; } .bi-ear::before { content: "\f689"; } +.bi-envelope-check-1::before { content: "\f68a"; } .bi-envelope-check-fill::before { content: "\f68b"; } .bi-envelope-check::before { content: "\f68c"; } +.bi-envelope-dash-1::before { content: "\f68d"; } .bi-envelope-dash-fill::before { content: "\f68e"; } .bi-envelope-dash::before { content: "\f68f"; } +.bi-envelope-exclamation-1::before { content: "\f690"; } .bi-envelope-exclamation-fill::before { content: "\f691"; } .bi-envelope-exclamation::before { content: "\f692"; } .bi-envelope-plus-fill::before { content: "\f693"; } .bi-envelope-plus::before { content: "\f694"; } +.bi-envelope-slash-1::before { content: "\f695"; } .bi-envelope-slash-fill::before { content: "\f696"; } .bi-envelope-slash::before { content: "\f697"; } +.bi-envelope-x-1::before { content: "\f698"; } .bi-envelope-x-fill::before { content: "\f699"; } .bi-envelope-x::before { content: "\f69a"; } .bi-explicit-fill::before { content: "\f69b"; } @@ -1461,6 +1461,8 @@ url("./bootstrap-icons.woff?2820a3852bdb9a5832199cc61cec4e65") format("woff"); .bi-list-columns-reverse::before { content: "\f69f"; } .bi-list-columns::before { content: "\f6a0"; } .bi-meta::before { content: "\f6a1"; } +.bi-mortorboard-fill::before { content: "\f6a2"; } +.bi-mortorboard::before { content: "\f6a3"; } .bi-nintendo-switch::before { content: "\f6a4"; } .bi-pc-display-horizontal::before { content: "\f6a5"; } .bi-pc-display::before { content: "\f6a6"; } @@ -1479,6 +1481,7 @@ url("./bootstrap-icons.woff?2820a3852bdb9a5832199cc61cec4e65") format("woff"); .bi-send-check::before { content: "\f6b3"; } .bi-send-dash-fill::before { content: "\f6b4"; } .bi-send-dash::before { content: "\f6b5"; } +.bi-send-exclamation-1::before { content: "\f6b6"; } .bi-send-exclamation-fill::before { content: "\f6b7"; } .bi-send-exclamation::before { content: "\f6b8"; } .bi-send-fill::before { content: "\f6b9"; } @@ -1490,6 +1493,7 @@ url("./bootstrap-icons.woff?2820a3852bdb9a5832199cc61cec4e65") format("woff"); .bi-send-x::before { content: "\f6bf"; } .bi-send::before { content: "\f6c0"; } .bi-steam::before { content: "\f6c1"; } +.bi-terminal-dash-1::before { content: "\f6c2"; } .bi-terminal-dash::before { content: "\f6c3"; } .bi-terminal-plus::before { content: "\f6c4"; } .bi-terminal-split::before { content: "\f6c5"; } @@ -1519,6 +1523,7 @@ url("./bootstrap-icons.woff?2820a3852bdb9a5832199cc61cec4e65") format("woff"); .bi-usb-symbol::before { content: "\f6dd"; } .bi-usb::before { content: "\f6de"; } .bi-boombox-fill::before { content: "\f6df"; } +.bi-displayport-1::before { content: "\f6e0"; } .bi-displayport::before { content: "\f6e1"; } .bi-gpu-card::before { content: "\f6e2"; } .bi-memory::before { content: "\f6e3"; } @@ -1531,6 +1536,8 @@ url("./bootstrap-icons.woff?2820a3852bdb9a5832199cc61cec4e65") format("woff"); .bi-pci-card::before { content: "\f6ea"; } .bi-router-fill::before { content: "\f6eb"; } .bi-router::before { content: "\f6ec"; } +.bi-ssd-fill::before { content: "\f6ed"; } +.bi-ssd::before { content: "\f6ee"; } .bi-thunderbolt-fill::before { content: "\f6ef"; } .bi-thunderbolt::before { content: "\f6f0"; } .bi-usb-drive-fill::before { content: "\f6f1"; } @@ -1637,6 +1644,7 @@ url("./bootstrap-icons.woff?2820a3852bdb9a5832199cc61cec4e65") format("woff"); .bi-filetype-pdf::before { content: "\f756"; } .bi-filetype-php::before { content: "\f757"; } .bi-filetype-png::before { content: "\f758"; } +.bi-filetype-ppt-1::before { content: "\f759"; } .bi-filetype-ppt::before { content: "\f75a"; } .bi-filetype-psd::before { content: "\f75b"; } .bi-filetype-py::before { content: "\f75c"; } @@ -1652,6 +1660,7 @@ url("./bootstrap-icons.woff?2820a3852bdb9a5832199cc61cec4e65") format("woff"); .bi-filetype-txt::before { content: "\f766"; } .bi-filetype-wav::before { content: "\f767"; } .bi-filetype-woff::before { content: "\f768"; } +.bi-filetype-xls-1::before { content: "\f769"; } .bi-filetype-xls::before { content: "\f76a"; } .bi-filetype-xml::before { content: "\f76b"; } .bi-filetype-yml::before { content: "\f76c"; } @@ -1694,38 +1703,56 @@ url("./bootstrap-icons.woff?2820a3852bdb9a5832199cc61cec4e65") format("woff"); .bi-filetype-json::before { content: "\f791"; } .bi-filetype-pptx::before { content: "\f792"; } .bi-filetype-xlsx::before { content: "\f793"; } +.bi-1-circle-1::before { content: "\f794"; } +.bi-1-circle-fill-1::before { content: "\f795"; } .bi-1-circle-fill::before { content: "\f796"; } .bi-1-circle::before { content: "\f797"; } .bi-1-square-fill::before { content: "\f798"; } .bi-1-square::before { content: "\f799"; } +.bi-2-circle-1::before { content: "\f79a"; } +.bi-2-circle-fill-1::before { content: "\f79b"; } .bi-2-circle-fill::before { content: "\f79c"; } .bi-2-circle::before { content: "\f79d"; } .bi-2-square-fill::before { content: "\f79e"; } .bi-2-square::before { content: "\f79f"; } +.bi-3-circle-1::before { content: "\f7a0"; } +.bi-3-circle-fill-1::before { content: "\f7a1"; } .bi-3-circle-fill::before { content: "\f7a2"; } .bi-3-circle::before { content: "\f7a3"; } .bi-3-square-fill::before { content: "\f7a4"; } .bi-3-square::before { content: "\f7a5"; } +.bi-4-circle-1::before { content: "\f7a6"; } +.bi-4-circle-fill-1::before { content: "\f7a7"; } .bi-4-circle-fill::before { content: "\f7a8"; } .bi-4-circle::before { content: "\f7a9"; } .bi-4-square-fill::before { content: "\f7aa"; } .bi-4-square::before { content: "\f7ab"; } +.bi-5-circle-1::before { content: "\f7ac"; } +.bi-5-circle-fill-1::before { content: "\f7ad"; } .bi-5-circle-fill::before { content: "\f7ae"; } .bi-5-circle::before { content: "\f7af"; } .bi-5-square-fill::before { content: "\f7b0"; } .bi-5-square::before { content: "\f7b1"; } +.bi-6-circle-1::before { content: "\f7b2"; } +.bi-6-circle-fill-1::before { content: "\f7b3"; } .bi-6-circle-fill::before { content: "\f7b4"; } .bi-6-circle::before { content: "\f7b5"; } .bi-6-square-fill::before { content: "\f7b6"; } .bi-6-square::before { content: "\f7b7"; } +.bi-7-circle-1::before { content: "\f7b8"; } +.bi-7-circle-fill-1::before { content: "\f7b9"; } .bi-7-circle-fill::before { content: "\f7ba"; } .bi-7-circle::before { content: "\f7bb"; } .bi-7-square-fill::before { content: "\f7bc"; } .bi-7-square::before { content: "\f7bd"; } +.bi-8-circle-1::before { content: "\f7be"; } +.bi-8-circle-fill-1::before { content: "\f7bf"; } .bi-8-circle-fill::before { content: "\f7c0"; } .bi-8-circle::before { content: "\f7c1"; } .bi-8-square-fill::before { content: "\f7c2"; } .bi-8-square::before { content: "\f7c3"; } +.bi-9-circle-1::before { content: "\f7c4"; } +.bi-9-circle-fill-1::before { content: "\f7c5"; } .bi-9-circle-fill::before { content: "\f7c6"; } .bi-9-circle::before { content: "\f7c7"; } .bi-9-square-fill::before { content: "\f7c8"; } @@ -1744,6 +1771,8 @@ url("./bootstrap-icons.woff?2820a3852bdb9a5832199cc61cec4e65") format("woff"); .bi-browser-edge::before { content: "\f7d5"; } .bi-browser-firefox::before { content: "\f7d6"; } .bi-browser-safari::before { content: "\f7d7"; } +.bi-c-circle-1::before { content: "\f7d8"; } +.bi-c-circle-fill-1::before { content: "\f7d9"; } .bi-c-circle-fill::before { content: "\f7da"; } .bi-c-circle::before { content: "\f7db"; } .bi-c-square-fill::before { content: "\f7dc"; } @@ -1754,6 +1783,8 @@ url("./bootstrap-icons.woff?2820a3852bdb9a5832199cc61cec4e65") format("woff"); .bi-car-front::before { content: "\f7e1"; } .bi-cassette-fill::before { content: "\f7e2"; } .bi-cassette::before { content: "\f7e3"; } +.bi-cc-circle-1::before { content: "\f7e4"; } +.bi-cc-circle-fill-1::before { content: "\f7e5"; } .bi-cc-circle-fill::before { content: "\f7e6"; } .bi-cc-circle::before { content: "\f7e7"; } .bi-cc-square-fill::before { content: "\f7e8"; } @@ -1772,6 +1803,8 @@ url("./bootstrap-icons.woff?2820a3852bdb9a5832199cc61cec4e65") format("woff"); .bi-filetype-sql::before { content: "\f7f5"; } .bi-fire::before { content: "\f7f6"; } .bi-google-play::before { content: "\f7f7"; } +.bi-h-circle-1::before { content: "\f7f8"; } +.bi-h-circle-fill-1::before { content: "\f7f9"; } .bi-h-circle-fill::before { content: "\f7fa"; } .bi-h-circle::before { content: "\f7fb"; } .bi-h-square-fill::before { content: "\f7fc"; } @@ -1780,6 +1813,8 @@ url("./bootstrap-icons.woff?2820a3852bdb9a5832199cc61cec4e65") format("woff"); .bi-lungs-fill::before { content: "\f7ff"; } .bi-lungs::before { content: "\f800"; } .bi-microsoft-teams::before { content: "\f801"; } +.bi-p-circle-1::before { content: "\f802"; } +.bi-p-circle-fill-1::before { content: "\f803"; } .bi-p-circle-fill::before { content: "\f804"; } .bi-p-circle::before { content: "\f805"; } .bi-p-square-fill::before { content: "\f806"; } @@ -1788,6 +1823,8 @@ url("./bootstrap-icons.woff?2820a3852bdb9a5832199cc61cec4e65") format("woff"); .bi-pass::before { content: "\f809"; } .bi-prescription::before { content: "\f80a"; } .bi-prescription2::before { content: "\f80b"; } +.bi-r-circle-1::before { content: "\f80c"; } +.bi-r-circle-fill-1::before { content: "\f80d"; } .bi-r-circle-fill::before { content: "\f80e"; } .bi-r-circle::before { content: "\f80f"; } .bi-r-square-fill::before { content: "\f810"; } @@ -1979,100 +2016,3 @@ url("./bootstrap-icons.woff?2820a3852bdb9a5832199cc61cec4e65") format("woff"); .bi-sina-weibo::before { content: "\f8ca"; } .bi-tencent-qq::before { content: "\f8cb"; } .bi-wikipedia::before { content: "\f8cc"; } -.bi-alphabet-uppercase::before { content: "\f2a5"; } -.bi-alphabet::before { content: "\f68a"; } -.bi-amazon::before { content: "\f68d"; } -.bi-arrows-collapse-vertical::before { content: "\f690"; } -.bi-arrows-expand-vertical::before { content: "\f695"; } -.bi-arrows-vertical::before { content: "\f698"; } -.bi-arrows::before { content: "\f6a2"; } -.bi-ban-fill::before { content: "\f6a3"; } -.bi-ban::before { content: "\f6b6"; } -.bi-bing::before { content: "\f6c2"; } -.bi-cake::before { content: "\f6e0"; } -.bi-cake2::before { content: "\f6ed"; } -.bi-cookie::before { content: "\f6ee"; } -.bi-copy::before { content: "\f759"; } -.bi-crosshair::before { content: 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t?t:{}},a(K,t,Y),t}_handleSwipe(){const t=Math.abs(this.touchDeltaX);if(t<=40)return;const e=t/this.touchDeltaX;this.touchDeltaX=0,e&&this._slide(e>0?J:Z)}_addEventListeners(){this._config.keyboard&&j.on(this._element,"keydown.bs.carousel",(t=>this._keydown(t))),"hover"===this._config.pause&&(j.on(this._element,"mouseenter.bs.carousel",(t=>this.pause(t))),j.on(this._element,"mouseleave.bs.carousel",(t=>this.cycle(t)))),this._config.touch&&this._touchSupported&&this._addTouchEventListeners()}_addTouchEventListeners(){const t=t=>this._pointerEvent&&("pen"===t.pointerType||"touch"===t.pointerType),e=e=>{t(e)?this.touchStartX=e.clientX:this._pointerEvent||(this.touchStartX=e.touches[0].clientX)},i=t=>{this.touchDeltaX=t.touches&&t.touches.length>1?0:t.touches[0].clientX-this.touchStartX},n=e=>{t(e)&&(this.touchDeltaX=e.clientX-this.touchStartX),this._handleSwipe(),"hover"===this._config.pause&&(this.pause(),this.touchTimeout&&clearTimeout(this.touchTimeout),this.touchTimeout=setTimeout((t=>this.cycle(t)),500+this._config.interval))};V.find(".carousel-item img",this._element).forEach((t=>{j.on(t,"dragstart.bs.carousel",(t=>t.preventDefault()))})),this._pointerEvent?(j.on(this._element,"pointerdown.bs.carousel",(t=>e(t))),j.on(this._element,"pointerup.bs.carousel",(t=>n(t))),this._element.classList.add("pointer-event")):(j.on(this._element,"touchstart.bs.carousel",(t=>e(t))),j.on(this._element,"touchmove.bs.carousel",(t=>i(t))),j.on(this._element,"touchend.bs.carousel",(t=>n(t))))}_keydown(t){if(/input|textarea/i.test(t.target.tagName))return;const e=tt[t.key];e&&(t.preventDefault(),this._slide(e))}_getItemIndex(t){return this._items=t&&t.parentNode?V.find(".carousel-item",t.parentNode):[],this._items.indexOf(t)}_getItemByOrder(t,e){const i=t===Q;return v(this._items,e,i,this._config.wrap)}_triggerSlideEvent(t,e){const i=this._getItemIndex(t),n=this._getItemIndex(V.findOne(nt,this._element));return j.trigger(this._element,"slide.bs.carousel",{relatedTarget:t,direction:e,from:n,to:i})}_setActiveIndicatorElement(t){if(this._indicatorsElement){const e=V.findOne(".active",this._indicatorsElement);e.classList.remove(it),e.removeAttribute("aria-current");const i=V.find("[data-bs-target]",this._indicatorsElement);for(let e=0;e{j.trigger(this._element,et,{relatedTarget:o,direction:d,from:s,to:r})};if(this._element.classList.contains("slide")){o.classList.add(h),u(o),n.classList.add(c),o.classList.add(c);const t=()=>{o.classList.remove(c,h),o.classList.add(it),n.classList.remove(it,h,c),this._isSliding=!1,setTimeout(f,0)};this._queueCallback(t,n,!0)}else n.classList.remove(it),o.classList.add(it),this._isSliding=!1,f();a&&this.cycle()}_directionToOrder(t){return[J,Z].includes(t)?m()?t===Z?G:Q:t===Z?Q:G:t}_orderToDirection(t){return[Q,G].includes(t)?m()?t===G?Z:J:t===G?J:Z:t}static carouselInterface(t,e){const i=st.getOrCreateInstance(t,e);let{_config:n}=i;"object"==typeof e&&(n={...n,...e});const s="string"==typeof e?e:n.slide;if("number"==typeof e)i.to(e);else if("string"==typeof s){if(void 0===i[s])throw new TypeError(`No method named "${s}"`);i[s]()}else n.interval&&n.ride&&(i.pause(),i.cycle())}static jQueryInterface(t){return this.each((function(){st.carouselInterface(this,t)}))}static dataApiClickHandler(t){const e=n(this);if(!e||!e.classList.contains("carousel"))return;const i={...U.getDataAttributes(e),...U.getDataAttributes(this)},s=this.getAttribute("data-bs-slide-to");s&&(i.interval=!1),st.carouselInterface(e,i),s&&st.getInstance(e).to(s),t.preventDefault()}}j.on(document,"click.bs.carousel.data-api","[data-bs-slide], [data-bs-slide-to]",st.dataApiClickHandler),j.on(window,"load.bs.carousel.data-api",(()=>{const t=V.find('[data-bs-ride="carousel"]');for(let e=0,i=t.length;et===this._element));null!==s&&o.length&&(this._selector=s,this._triggerArray.push(e))}this._initializeChildren(),this._config.parent||this._addAriaAndCollapsedClass(this._triggerArray,this._isShown()),this._config.toggle&&this.toggle()}static get Default(){return rt}static get NAME(){return ot}toggle(){this._isShown()?this.hide():this.show()}show(){if(this._isTransitioning||this._isShown())return;let t,e=[];if(this._config.parent){const t=V.find(ut,this._config.parent);e=V.find(".collapse.show, .collapse.collapsing",this._config.parent).filter((e=>!t.includes(e)))}const i=V.findOne(this._selector);if(e.length){const n=e.find((t=>i!==t));if(t=n?pt.getInstance(n):null,t&&t._isTransitioning)return}if(j.trigger(this._element,"show.bs.collapse").defaultPrevented)return;e.forEach((e=>{i!==e&&pt.getOrCreateInstance(e,{toggle:!1}).hide(),t||H.set(e,"bs.collapse",null)}));const n=this._getDimension();this._element.classList.remove(ct),this._element.classList.add(ht),this._element.style[n]=0,this._addAriaAndCollapsedClass(this._triggerArray,!0),this._isTransitioning=!0;const s=`scroll${n[0].toUpperCase()+n.slice(1)}`;this._queueCallback((()=>{this._isTransitioning=!1,this._element.classList.remove(ht),this._element.classList.add(ct,lt),this._element.style[n]="",j.trigger(this._element,"shown.bs.collapse")}),this._element,!0),this._element.style[n]=`${this._element[s]}px`}hide(){if(this._isTransitioning||!this._isShown())return;if(j.trigger(this._element,"hide.bs.collapse").defaultPrevented)return;const t=this._getDimension();this._element.style[t]=`${this._element.getBoundingClientRect()[t]}px`,u(this._element),this._element.classList.add(ht),this._element.classList.remove(ct,lt);const e=this._triggerArray.length;for(let t=0;t{this._isTransitioning=!1,this._element.classList.remove(ht),this._element.classList.add(ct),j.trigger(this._element,"hidden.bs.collapse")}),this._element,!0)}_isShown(t=this._element){return t.classList.contains(lt)}_getConfig(t){return(t={...rt,...U.getDataAttributes(this._element),...t}).toggle=Boolean(t.toggle),t.parent=r(t.parent),a(ot,t,at),t}_getDimension(){return this._element.classList.contains("collapse-horizontal")?"width":"height"}_initializeChildren(){if(!this._config.parent)return;const t=V.find(ut,this._config.parent);V.find(ft,this._config.parent).filter((e=>!t.includes(e))).forEach((t=>{const e=n(t);e&&this._addAriaAndCollapsedClass([t],this._isShown(e))}))}_addAriaAndCollapsedClass(t,e){t.length&&t.forEach((t=>{e?t.classList.remove(dt):t.classList.add(dt),t.setAttribute("aria-expanded",e)}))}static jQueryInterface(t){return this.each((function(){const e={};"string"==typeof t&&/show|hide/.test(t)&&(e.toggle=!1);const 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e=t.ownerDocument;return e&&e.defaultView||window}return t}function $t(t){return t instanceof Wt(t).Element||t instanceof Element}function zt(t){return t instanceof Wt(t).HTMLElement||t instanceof HTMLElement}function qt(t){return"undefined"!=typeof ShadowRoot&&(t instanceof Wt(t).ShadowRoot||t instanceof ShadowRoot)}const Ft={name:"applyStyles",enabled:!0,phase:"write",fn:function(t){var e=t.state;Object.keys(e.elements).forEach((function(t){var i=e.styles[t]||{},n=e.attributes[t]||{},s=e.elements[t];zt(s)&&Rt(s)&&(Object.assign(s.style,i),Object.keys(n).forEach((function(t){var e=n[t];!1===e?s.removeAttribute(t):s.setAttribute(t,!0===e?"":e)})))}))},effect:function(t){var e=t.state,i={popper:{position:e.options.strategy,left:"0",top:"0",margin:"0"},arrow:{position:"absolute"},reference:{}};return Object.assign(e.elements.popper.style,i.popper),e.styles=i,e.elements.arrow&&Object.assign(e.elements.arrow.style,i.arrow),function(){Object.keys(e.elements).forEach((function(t){var 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Q="x"===y?mt:bt,G="x"===y?gt:_t,Z=E[w],J=Z+g[Q],tt=Z-g[G],et=oe(f?ne(J,K):J,Z,f?ie(tt,X):tt);E[w]=et,C[w]=et-Z}}e.modifiersData[n]=C}},requiresIfExists:["offset"]};function Me(t,e,i){void 0===i&&(i=!1);var n=zt(e);zt(e)&&function(t){var e=t.getBoundingClientRect();e.width,t.offsetWidth,e.height,t.offsetHeight}(e);var s,o,r=Gt(e),a=Vt(t),l={scrollLeft:0,scrollTop:0},c={x:0,y:0};return(n||!n&&!i)&&(("body"!==Rt(e)||we(r))&&(l=(s=e)!==Wt(s)&&zt(s)?{scrollLeft:(o=s).scrollLeft,scrollTop:o.scrollTop}:ve(s)),zt(e)?((c=Vt(e)).x+=e.clientLeft,c.y+=e.clientTop):r&&(c.x=ye(r))),{x:a.left+l.scrollLeft-c.x,y:a.top+l.scrollTop-c.y,width:a.width,height:a.height}}function He(t){var e=new Map,i=new Set,n=[];function s(t){i.add(t.name),[].concat(t.requires||[],t.requiresIfExists||[]).forEach((function(t){if(!i.has(t)){var n=e.get(t);n&&s(n)}})),n.push(t)}return t.forEach((function(t){e.set(t.name,t)})),t.forEach((function(t){i.has(t.name)||s(t)})),n}var Be={placement:"bottom",modifiers:[],strategy:"absolute"};function Re(){for(var t=arguments.length,e=new Array(t),i=0;ij.on(t,"mouseover",d))),this._element.focus(),this._element.setAttribute("aria-expanded",!0),this._menu.classList.add(Je),this._element.classList.add(Je),j.trigger(this._element,"shown.bs.dropdown",t)}hide(){if(c(this._element)||!this._isShown(this._menu))return;const t={relatedTarget:this._element};this._completeHide(t)}dispose(){this._popper&&this._popper.destroy(),super.dispose()}update(){this._inNavbar=this._detectNavbar(),this._popper&&this._popper.update()}_completeHide(t){j.trigger(this._element,"hide.bs.dropdown",t).defaultPrevented||("ontouchstart"in document.documentElement&&[].concat(...document.body.children).forEach((t=>j.off(t,"mouseover",d))),this._popper&&this._popper.destroy(),this._menu.classList.remove(Je),this._element.classList.remove(Je),this._element.setAttribute("aria-expanded","false"),U.removeDataAttribute(this._menu,"popper"),j.trigger(this._element,"hidden.bs.dropdown",t))}_getConfig(t){if(t={...this.constructor.Default,...U.getDataAttributes(this._element),...t},a(Ue,t,this.constructor.DefaultType),"object"==typeof t.reference&&!o(t.reference)&&"function"!=typeof t.reference.getBoundingClientRect)throw new TypeError(`${Ue.toUpperCase()}: Option "reference" provided type "object" without a required "getBoundingClientRect" method.`);return t}_createPopper(t){if(void 0===Fe)throw new TypeError("Bootstrap's dropdowns require Popper (https://popper.js.org)");let e=this._element;"parent"===this._config.reference?e=t:o(this._config.reference)?e=r(this._config.reference):"object"==typeof this._config.reference&&(e=this._config.reference);const i=this._getPopperConfig(),n=i.modifiers.find((t=>"applyStyles"===t.name&&!1===t.enabled));this._popper=qe(e,this._menu,i),n&&U.setDataAttribute(this._menu,"popper","static")}_isShown(t=this._element){return t.classList.contains(Je)}_getMenuElement(){return V.next(this._element,ei)[0]}_getPlacement(){const t=this._element.parentNode;if(t.classList.contains("dropend"))return ri;if(t.classList.contains("dropstart"))return ai;const e="end"===getComputedStyle(this._menu).getPropertyValue("--bs-position").trim();return t.classList.contains("dropup")?e?ni:ii:e?oi:si}_detectNavbar(){return null!==this._element.closest(".navbar")}_getOffset(){const{offset:t}=this._config;return"string"==typeof t?t.split(",").map((t=>Number.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_getPopperConfig(){const t={placement:this._getPlacement(),modifiers:[{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"offset",options:{offset:this._getOffset()}}]};return"static"===this._config.display&&(t.modifiers=[{name:"applyStyles",enabled:!1}]),{...t,..."function"==typeof this._config.popperConfig?this._config.popperConfig(t):this._config.popperConfig}}_selectMenuItem({key:t,target:e}){const i=V.find(".dropdown-menu .dropdown-item:not(.disabled):not(:disabled)",this._menu).filter(l);i.length&&v(i,e,t===Ye,!i.includes(e)).focus()}static jQueryInterface(t){return this.each((function(){const e=hi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}static clearMenus(t){if(t&&(2===t.button||"keyup"===t.type&&"Tab"!==t.key))return;const e=V.find(ti);for(let i=0,n=e.length;ie+t)),this._setElementAttributes(di,"paddingRight",(e=>e+t)),this._setElementAttributes(ui,"marginRight",(e=>e-t))}_disableOverFlow(){this._saveInitialAttribute(this._element,"overflow"),this._element.style.overflow="hidden"}_setElementAttributes(t,e,i){const n=this.getWidth();this._applyManipulationCallback(t,(t=>{if(t!==this._element&&window.innerWidth>t.clientWidth+n)return;this._saveInitialAttribute(t,e);const s=window.getComputedStyle(t)[e];t.style[e]=`${i(Number.parseFloat(s))}px`}))}reset(){this._resetElementAttributes(this._element,"overflow"),this._resetElementAttributes(this._element,"paddingRight"),this._resetElementAttributes(di,"paddingRight"),this._resetElementAttributes(ui,"marginRight")}_saveInitialAttribute(t,e){const i=t.style[e];i&&U.setDataAttribute(t,e,i)}_resetElementAttributes(t,e){this._applyManipulationCallback(t,(t=>{const i=U.getDataAttribute(t,e);void 0===i?t.style.removeProperty(e):(U.removeDataAttribute(t,e),t.style[e]=i)}))}_applyManipulationCallback(t,e){o(t)?e(t):V.find(t,this._element).forEach(e)}isOverflowing(){return this.getWidth()>0}}const pi={className:"modal-backdrop",isVisible:!0,isAnimated:!1,rootElement:"body",clickCallback:null},mi={className:"string",isVisible:"boolean",isAnimated:"boolean",rootElement:"(element|string)",clickCallback:"(function|null)"},gi="show",_i="mousedown.bs.backdrop";class bi{constructor(t){this._config=this._getConfig(t),this._isAppended=!1,this._element=null}show(t){this._config.isVisible?(this._append(),this._config.isAnimated&&u(this._getElement()),this._getElement().classList.add(gi),this._emulateAnimation((()=>{_(t)}))):_(t)}hide(t){this._config.isVisible?(this._getElement().classList.remove(gi),this._emulateAnimation((()=>{this.dispose(),_(t)}))):_(t)}_getElement(){if(!this._element){const t=document.createElement("div");t.className=this._config.className,this._config.isAnimated&&t.classList.add("fade"),this._element=t}return this._element}_getConfig(t){return(t={...pi,..."object"==typeof t?t:{}}).rootElement=r(t.rootElement),a("backdrop",t,mi),t}_append(){this._isAppended||(this._config.rootElement.append(this._getElement()),j.on(this._getElement(),_i,(()=>{_(this._config.clickCallback)})),this._isAppended=!0)}dispose(){this._isAppended&&(j.off(this._element,_i),this._element.remove(),this._isAppended=!1)}_emulateAnimation(t){b(t,this._getElement(),this._config.isAnimated)}}const vi={trapElement:null,autofocus:!0},yi={trapElement:"element",autofocus:"boolean"},wi=".bs.focustrap",Ei="backward";class Ai{constructor(t){this._config=this._getConfig(t),this._isActive=!1,this._lastTabNavDirection=null}activate(){const{trapElement:t,autofocus:e}=this._config;this._isActive||(e&&t.focus(),j.off(document,wi),j.on(document,"focusin.bs.focustrap",(t=>this._handleFocusin(t))),j.on(document,"keydown.tab.bs.focustrap",(t=>this._handleKeydown(t))),this._isActive=!0)}deactivate(){this._isActive&&(this._isActive=!1,j.off(document,wi))}_handleFocusin(t){const{target:e}=t,{trapElement:i}=this._config;if(e===document||e===i||i.contains(e))return;const n=V.focusableChildren(i);0===n.length?i.focus():this._lastTabNavDirection===Ei?n[n.length-1].focus():n[0].focus()}_handleKeydown(t){"Tab"===t.key&&(this._lastTabNavDirection=t.shiftKey?Ei:"forward")}_getConfig(t){return t={...vi,..."object"==typeof t?t:{}},a("focustrap",t,yi),t}}const Ti="modal",Oi="Escape",Ci={backdrop:!0,keyboard:!0,focus:!0},ki={backdrop:"(boolean|string)",keyboard:"boolean",focus:"boolean"},Li="hidden.bs.modal",xi="show.bs.modal",Di="resize.bs.modal",Si="click.dismiss.bs.modal",Ni="keydown.dismiss.bs.modal",Ii="mousedown.dismiss.bs.modal",Pi="modal-open",ji="show",Mi="modal-static";class Hi extends B{constructor(t,e){super(t),this._config=this._getConfig(e),this._dialog=V.findOne(".modal-dialog",this._element),this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._isShown=!1,this._ignoreBackdropClick=!1,this._isTransitioning=!1,this._scrollBar=new fi}static get Default(){return Ci}static get NAME(){return Ti}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||this._isTransitioning||j.trigger(this._element,xi,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._isAnimated()&&(this._isTransitioning=!0),this._scrollBar.hide(),document.body.classList.add(Pi),this._adjustDialog(),this._setEscapeEvent(),this._setResizeEvent(),j.on(this._dialog,Ii,(()=>{j.one(this._element,"mouseup.dismiss.bs.modal",(t=>{t.target===this._element&&(this._ignoreBackdropClick=!0)}))})),this._showBackdrop((()=>this._showElement(t))))}hide(){if(!this._isShown||this._isTransitioning)return;if(j.trigger(this._element,"hide.bs.modal").defaultPrevented)return;this._isShown=!1;const t=this._isAnimated();t&&(this._isTransitioning=!0),this._setEscapeEvent(),this._setResizeEvent(),this._focustrap.deactivate(),this._element.classList.remove(ji),j.off(this._element,Si),j.off(this._dialog,Ii),this._queueCallback((()=>this._hideModal()),this._element,t)}dispose(){[window,this._dialog].forEach((t=>j.off(t,".bs.modal"))),this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}handleUpdate(){this._adjustDialog()}_initializeBackDrop(){return new bi({isVisible:Boolean(this._config.backdrop),isAnimated:this._isAnimated()})}_initializeFocusTrap(){return new Ai({trapElement:this._element})}_getConfig(t){return t={...Ci,...U.getDataAttributes(this._element),..."object"==typeof t?t:{}},a(Ti,t,ki),t}_showElement(t){const e=this._isAnimated(),i=V.findOne(".modal-body",this._dialog);this._element.parentNode&&this._element.parentNode.nodeType===Node.ELEMENT_NODE||document.body.append(this._element),this._element.style.display="block",this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.scrollTop=0,i&&(i.scrollTop=0),e&&u(this._element),this._element.classList.add(ji),this._queueCallback((()=>{this._config.focus&&this._focustrap.activate(),this._isTransitioning=!1,j.trigger(this._element,"shown.bs.modal",{relatedTarget:t})}),this._dialog,e)}_setEscapeEvent(){this._isShown?j.on(this._element,Ni,(t=>{this._config.keyboard&&t.key===Oi?(t.preventDefault(),this.hide()):this._config.keyboard||t.key!==Oi||this._triggerBackdropTransition()})):j.off(this._element,Ni)}_setResizeEvent(){this._isShown?j.on(window,Di,(()=>this._adjustDialog())):j.off(window,Di)}_hideModal(){this._element.style.display="none",this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._isTransitioning=!1,this._backdrop.hide((()=>{document.body.classList.remove(Pi),this._resetAdjustments(),this._scrollBar.reset(),j.trigger(this._element,Li)}))}_showBackdrop(t){j.on(this._element,Si,(t=>{this._ignoreBackdropClick?this._ignoreBackdropClick=!1:t.target===t.currentTarget&&(!0===this._config.backdrop?this.hide():"static"===this._config.backdrop&&this._triggerBackdropTransition())})),this._backdrop.show(t)}_isAnimated(){return this._element.classList.contains("fade")}_triggerBackdropTransition(){if(j.trigger(this._element,"hidePrevented.bs.modal").defaultPrevented)return;const{classList:t,scrollHeight:e,style:i}=this._element,n=e>document.documentElement.clientHeight;!n&&"hidden"===i.overflowY||t.contains(Mi)||(n||(i.overflowY="hidden"),t.add(Mi),this._queueCallback((()=>{t.remove(Mi),n||this._queueCallback((()=>{i.overflowY=""}),this._dialog)}),this._dialog),this._element.focus())}_adjustDialog(){const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._scrollBar.getWidth(),i=e>0;(!i&&t&&!m()||i&&!t&&m())&&(this._element.style.paddingLeft=`${e}px`),(i&&!t&&!m()||!i&&t&&m())&&(this._element.style.paddingRight=`${e}px`)}_resetAdjustments(){this._element.style.paddingLeft="",this._element.style.paddingRight=""}static jQueryInterface(t,e){return this.each((function(){const i=Hi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===i[t])throw new TypeError(`No method named "${t}"`);i[t](e)}}))}}j.on(document,"click.bs.modal.data-api",'[data-bs-toggle="modal"]',(function(t){const e=n(this);["A","AREA"].includes(this.tagName)&&t.preventDefault(),j.one(e,xi,(t=>{t.defaultPrevented||j.one(e,Li,(()=>{l(this)&&this.focus()}))}));const i=V.findOne(".modal.show");i&&Hi.getInstance(i).hide(),Hi.getOrCreateInstance(e).toggle(this)})),R(Hi),g(Hi);const Bi="offcanvas",Ri={backdrop:!0,keyboard:!0,scroll:!1},Wi={backdrop:"boolean",keyboard:"boolean",scroll:"boolean"},$i="show",zi=".offcanvas.show",qi="hidden.bs.offcanvas";class Fi extends B{constructor(t,e){super(t),this._config=this._getConfig(e),this._isShown=!1,this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._addEventListeners()}static get NAME(){return Bi}static get Default(){return Ri}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||j.trigger(this._element,"show.bs.offcanvas",{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._element.style.visibility="visible",this._backdrop.show(),this._config.scroll||(new fi).hide(),this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.classList.add($i),this._queueCallback((()=>{this._config.scroll||this._focustrap.activate(),j.trigger(this._element,"shown.bs.offcanvas",{relatedTarget:t})}),this._element,!0))}hide(){this._isShown&&(j.trigger(this._element,"hide.bs.offcanvas").defaultPrevented||(this._focustrap.deactivate(),this._element.blur(),this._isShown=!1,this._element.classList.remove($i),this._backdrop.hide(),this._queueCallback((()=>{this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._element.style.visibility="hidden",this._config.scroll||(new fi).reset(),j.trigger(this._element,qi)}),this._element,!0)))}dispose(){this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}_getConfig(t){return t={...Ri,...U.getDataAttributes(this._element),..."object"==typeof t?t:{}},a(Bi,t,Wi),t}_initializeBackDrop(){return new bi({className:"offcanvas-backdrop",isVisible:this._config.backdrop,isAnimated:!0,rootElement:this._element.parentNode,clickCallback:()=>this.hide()})}_initializeFocusTrap(){return new Ai({trapElement:this._element})}_addEventListeners(){j.on(this._element,"keydown.dismiss.bs.offcanvas",(t=>{this._config.keyboard&&"Escape"===t.key&&this.hide()}))}static jQueryInterface(t){return this.each((function(){const e=Fi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t]||t.startsWith("_")||"constructor"===t)throw new TypeError(`No method named "${t}"`);e[t](this)}}))}}j.on(document,"click.bs.offcanvas.data-api",'[data-bs-toggle="offcanvas"]',(function(t){const e=n(this);if(["A","AREA"].includes(this.tagName)&&t.preventDefault(),c(this))return;j.one(e,qi,(()=>{l(this)&&this.focus()}));const i=V.findOne(zi);i&&i!==e&&Fi.getInstance(i).hide(),Fi.getOrCreateInstance(e).toggle(this)})),j.on(window,"load.bs.offcanvas.data-api",(()=>V.find(zi).forEach((t=>Fi.getOrCreateInstance(t).show())))),R(Fi),g(Fi);const Ui=new Set(["background","cite","href","itemtype","longdesc","poster","src","xlink:href"]),Vi=/^(?:(?:https?|mailto|ftp|tel|file|sms):|[^#&/:?]*(?:[#/?]|$))/i,Ki=/^data:(?:image\/(?:bmp|gif|jpeg|jpg|png|tiff|webp)|video\/(?:mpeg|mp4|ogg|webm)|audio\/(?:mp3|oga|ogg|opus));base64,[\d+/a-z]+=*$/i,Xi=(t,e)=>{const i=t.nodeName.toLowerCase();if(e.includes(i))return!Ui.has(i)||Boolean(Vi.test(t.nodeValue)||Ki.test(t.nodeValue));const n=e.filter((t=>t instanceof RegExp));for(let t=0,e=n.length;t{Xi(t,r)||i.removeAttribute(t.nodeName)}))}return n.body.innerHTML}const Qi="tooltip",Gi=new Set(["sanitize","allowList","sanitizeFn"]),Zi={animation:"boolean",template:"string",title:"(string|element|function)",trigger:"string",delay:"(number|object)",html:"boolean",selector:"(string|boolean)",placement:"(string|function)",offset:"(array|string|function)",container:"(string|element|boolean)",fallbackPlacements:"array",boundary:"(string|element)",customClass:"(string|function)",sanitize:"boolean",sanitizeFn:"(null|function)",allowList:"object",popperConfig:"(null|object|function)"},Ji={AUTO:"auto",TOP:"top",RIGHT:m()?"left":"right",BOTTOM:"bottom",LEFT:m()?"right":"left"},tn={animation:!0,template:'',trigger:"hover focus",title:"",delay:0,html:!1,selector:!1,placement:"top",offset:[0,0],container:!1,fallbackPlacements:["top","right","bottom","left"],boundary:"clippingParents",customClass:"",sanitize:!0,sanitizeFn:null,allowList:{"*":["class","dir","id","lang","role",/^aria-[\w-]*$/i],a:["target","href","title","rel"],area:[],b:[],br:[],col:[],code:[],div:[],em:[],hr:[],h1:[],h2:[],h3:[],h4:[],h5:[],h6:[],i:[],img:["src","srcset","alt","title","width","height"],li:[],ol:[],p:[],pre:[],s:[],small:[],span:[],sub:[],sup:[],strong:[],u:[],ul:[]},popperConfig:null},en={HIDE:"hide.bs.tooltip",HIDDEN:"hidden.bs.tooltip",SHOW:"show.bs.tooltip",SHOWN:"shown.bs.tooltip",INSERTED:"inserted.bs.tooltip",CLICK:"click.bs.tooltip",FOCUSIN:"focusin.bs.tooltip",FOCUSOUT:"focusout.bs.tooltip",MOUSEENTER:"mouseenter.bs.tooltip",MOUSELEAVE:"mouseleave.bs.tooltip"},nn="fade",sn="show",on="show",rn="out",an=".tooltip-inner",ln=".modal",cn="hide.bs.modal",hn="hover",dn="focus";class un extends B{constructor(t,e){if(void 0===Fe)throw new TypeError("Bootstrap's tooltips require Popper (https://popper.js.org)");super(t),this._isEnabled=!0,this._timeout=0,this._hoverState="",this._activeTrigger={},this._popper=null,this._config=this._getConfig(e),this.tip=null,this._setListeners()}static get Default(){return tn}static get NAME(){return Qi}static get Event(){return en}static get DefaultType(){return Zi}enable(){this._isEnabled=!0}disable(){this._isEnabled=!1}toggleEnabled(){this._isEnabled=!this._isEnabled}toggle(t){if(this._isEnabled)if(t){const e=this._initializeOnDelegatedTarget(t);e._activeTrigger.click=!e._activeTrigger.click,e._isWithActiveTrigger()?e._enter(null,e):e._leave(null,e)}else{if(this.getTipElement().classList.contains(sn))return void this._leave(null,this);this._enter(null,this)}}dispose(){clearTimeout(this._timeout),j.off(this._element.closest(ln),cn,this._hideModalHandler),this.tip&&this.tip.remove(),this._disposePopper(),super.dispose()}show(){if("none"===this._element.style.display)throw new Error("Please use show on visible elements");if(!this.isWithContent()||!this._isEnabled)return;const t=j.trigger(this._element,this.constructor.Event.SHOW),e=h(this._element),i=null===e?this._element.ownerDocument.documentElement.contains(this._element):e.contains(this._element);if(t.defaultPrevented||!i)return;"tooltip"===this.constructor.NAME&&this.tip&&this.getTitle()!==this.tip.querySelector(an).innerHTML&&(this._disposePopper(),this.tip.remove(),this.tip=null);const n=this.getTipElement(),s=(t=>{do{t+=Math.floor(1e6*Math.random())}while(document.getElementById(t));return t})(this.constructor.NAME);n.setAttribute("id",s),this._element.setAttribute("aria-describedby",s),this._config.animation&&n.classList.add(nn);const o="function"==typeof this._config.placement?this._config.placement.call(this,n,this._element):this._config.placement,r=this._getAttachment(o);this._addAttachmentClass(r);const{container:a}=this._config;H.set(n,this.constructor.DATA_KEY,this),this._element.ownerDocument.documentElement.contains(this.tip)||(a.append(n),j.trigger(this._element,this.constructor.Event.INSERTED)),this._popper?this._popper.update():this._popper=qe(this._element,n,this._getPopperConfig(r)),n.classList.add(sn);const l=this._resolvePossibleFunction(this._config.customClass);l&&n.classList.add(...l.split(" ")),"ontouchstart"in document.documentElement&&[].concat(...document.body.children).forEach((t=>{j.on(t,"mouseover",d)}));const c=this.tip.classList.contains(nn);this._queueCallback((()=>{const t=this._hoverState;this._hoverState=null,j.trigger(this._element,this.constructor.Event.SHOWN),t===rn&&this._leave(null,this)}),this.tip,c)}hide(){if(!this._popper)return;const t=this.getTipElement();if(j.trigger(this._element,this.constructor.Event.HIDE).defaultPrevented)return;t.classList.remove(sn),"ontouchstart"in document.documentElement&&[].concat(...document.body.children).forEach((t=>j.off(t,"mouseover",d))),this._activeTrigger.click=!1,this._activeTrigger.focus=!1,this._activeTrigger.hover=!1;const e=this.tip.classList.contains(nn);this._queueCallback((()=>{this._isWithActiveTrigger()||(this._hoverState!==on&&t.remove(),this._cleanTipClass(),this._element.removeAttribute("aria-describedby"),j.trigger(this._element,this.constructor.Event.HIDDEN),this._disposePopper())}),this.tip,e),this._hoverState=""}update(){null!==this._popper&&this._popper.update()}isWithContent(){return Boolean(this.getTitle())}getTipElement(){if(this.tip)return this.tip;const t=document.createElement("div");t.innerHTML=this._config.template;const e=t.children[0];return this.setContent(e),e.classList.remove(nn,sn),this.tip=e,this.tip}setContent(t){this._sanitizeAndSetContent(t,this.getTitle(),an)}_sanitizeAndSetContent(t,e,i){const n=V.findOne(i,t);e||!n?this.setElementContent(n,e):n.remove()}setElementContent(t,e){if(null!==t)return o(e)?(e=r(e),void(this._config.html?e.parentNode!==t&&(t.innerHTML="",t.append(e)):t.textContent=e.textContent)):void(this._config.html?(this._config.sanitize&&(e=Yi(e,this._config.allowList,this._config.sanitizeFn)),t.innerHTML=e):t.textContent=e)}getTitle(){const t=this._element.getAttribute("data-bs-original-title")||this._config.title;return this._resolvePossibleFunction(t)}updateAttachment(t){return"right"===t?"end":"left"===t?"start":t}_initializeOnDelegatedTarget(t,e){return e||this.constructor.getOrCreateInstance(t.delegateTarget,this._getDelegateConfig())}_getOffset(){const{offset:t}=this._config;return"string"==typeof t?t.split(",").map((t=>Number.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_resolvePossibleFunction(t){return"function"==typeof t?t.call(this._element):t}_getPopperConfig(t){const e={placement:t,modifiers:[{name:"flip",options:{fallbackPlacements:this._config.fallbackPlacements}},{name:"offset",options:{offset:this._getOffset()}},{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"arrow",options:{element:`.${this.constructor.NAME}-arrow`}},{name:"onChange",enabled:!0,phase:"afterWrite",fn:t=>this._handlePopperPlacementChange(t)}],onFirstUpdate:t=>{t.options.placement!==t.placement&&this._handlePopperPlacementChange(t)}};return{...e,..."function"==typeof this._config.popperConfig?this._config.popperConfig(e):this._config.popperConfig}}_addAttachmentClass(t){this.getTipElement().classList.add(`${this._getBasicClassPrefix()}-${this.updateAttachment(t)}`)}_getAttachment(t){return Ji[t.toUpperCase()]}_setListeners(){this._config.trigger.split(" ").forEach((t=>{if("click"===t)j.on(this._element,this.constructor.Event.CLICK,this._config.selector,(t=>this.toggle(t)));else if("manual"!==t){const e=t===hn?this.constructor.Event.MOUSEENTER:this.constructor.Event.FOCUSIN,i=t===hn?this.constructor.Event.MOUSELEAVE:this.constructor.Event.FOCUSOUT;j.on(this._element,e,this._config.selector,(t=>this._enter(t))),j.on(this._element,i,this._config.selector,(t=>this._leave(t)))}})),this._hideModalHandler=()=>{this._element&&this.hide()},j.on(this._element.closest(ln),cn,this._hideModalHandler),this._config.selector?this._config={...this._config,trigger:"manual",selector:""}:this._fixTitle()}_fixTitle(){const t=this._element.getAttribute("title"),e=typeof this._element.getAttribute("data-bs-original-title");(t||"string"!==e)&&(this._element.setAttribute("data-bs-original-title",t||""),!t||this._element.getAttribute("aria-label")||this._element.textContent||this._element.setAttribute("aria-label",t),this._element.setAttribute("title",""))}_enter(t,e){e=this._initializeOnDelegatedTarget(t,e),t&&(e._activeTrigger["focusin"===t.type?dn:hn]=!0),e.getTipElement().classList.contains(sn)||e._hoverState===on?e._hoverState=on:(clearTimeout(e._timeout),e._hoverState=on,e._config.delay&&e._config.delay.show?e._timeout=setTimeout((()=>{e._hoverState===on&&e.show()}),e._config.delay.show):e.show())}_leave(t,e){e=this._initializeOnDelegatedTarget(t,e),t&&(e._activeTrigger["focusout"===t.type?dn:hn]=e._element.contains(t.relatedTarget)),e._isWithActiveTrigger()||(clearTimeout(e._timeout),e._hoverState=rn,e._config.delay&&e._config.delay.hide?e._timeout=setTimeout((()=>{e._hoverState===rn&&e.hide()}),e._config.delay.hide):e.hide())}_isWithActiveTrigger(){for(const t in this._activeTrigger)if(this._activeTrigger[t])return!0;return!1}_getConfig(t){const e=U.getDataAttributes(this._element);return Object.keys(e).forEach((t=>{Gi.has(t)&&delete e[t]})),(t={...this.constructor.Default,...e,..."object"==typeof t&&t?t:{}}).container=!1===t.container?document.body:r(t.container),"number"==typeof t.delay&&(t.delay={show:t.delay,hide:t.delay}),"number"==typeof t.title&&(t.title=t.title.toString()),"number"==typeof t.content&&(t.content=t.content.toString()),a(Qi,t,this.constructor.DefaultType),t.sanitize&&(t.template=Yi(t.template,t.allowList,t.sanitizeFn)),t}_getDelegateConfig(){const t={};for(const e in this._config)this.constructor.Default[e]!==this._config[e]&&(t[e]=this._config[e]);return t}_cleanTipClass(){const t=this.getTipElement(),e=new RegExp(`(^|\\s)${this._getBasicClassPrefix()}\\S+`,"g"),i=t.getAttribute("class").match(e);null!==i&&i.length>0&&i.map((t=>t.trim())).forEach((e=>t.classList.remove(e)))}_getBasicClassPrefix(){return"bs-tooltip"}_handlePopperPlacementChange(t){const{state:e}=t;e&&(this.tip=e.elements.popper,this._cleanTipClass(),this._addAttachmentClass(this._getAttachment(e.placement)))}_disposePopper(){this._popper&&(this._popper.destroy(),this._popper=null)}static jQueryInterface(t){return this.each((function(){const e=un.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}}g(un);const fn={...un.Default,placement:"right",offset:[0,8],trigger:"click",content:"",template:''},pn={...un.DefaultType,content:"(string|element|function)"},mn={HIDE:"hide.bs.popover",HIDDEN:"hidden.bs.popover",SHOW:"show.bs.popover",SHOWN:"shown.bs.popover",INSERTED:"inserted.bs.popover",CLICK:"click.bs.popover",FOCUSIN:"focusin.bs.popover",FOCUSOUT:"focusout.bs.popover",MOUSEENTER:"mouseenter.bs.popover",MOUSELEAVE:"mouseleave.bs.popover"};class gn extends un{static get Default(){return fn}static get NAME(){return"popover"}static get Event(){return mn}static get DefaultType(){return pn}isWithContent(){return this.getTitle()||this._getContent()}setContent(t){this._sanitizeAndSetContent(t,this.getTitle(),".popover-header"),this._sanitizeAndSetContent(t,this._getContent(),".popover-body")}_getContent(){return this._resolvePossibleFunction(this._config.content)}_getBasicClassPrefix(){return"bs-popover"}static jQueryInterface(t){return this.each((function(){const e=gn.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}}g(gn);const _n="scrollspy",bn={offset:10,method:"auto",target:""},vn={offset:"number",method:"string",target:"(string|element)"},yn="active",wn=".nav-link, .list-group-item, .dropdown-item",En="position";class An extends B{constructor(t,e){super(t),this._scrollElement="BODY"===this._element.tagName?window:this._element,this._config=this._getConfig(e),this._offsets=[],this._targets=[],this._activeTarget=null,this._scrollHeight=0,j.on(this._scrollElement,"scroll.bs.scrollspy",(()=>this._process())),this.refresh(),this._process()}static get Default(){return bn}static get NAME(){return _n}refresh(){const t=this._scrollElement===this._scrollElement.window?"offset":En,e="auto"===this._config.method?t:this._config.method,n=e===En?this._getScrollTop():0;this._offsets=[],this._targets=[],this._scrollHeight=this._getScrollHeight(),V.find(wn,this._config.target).map((t=>{const s=i(t),o=s?V.findOne(s):null;if(o){const t=o.getBoundingClientRect();if(t.width||t.height)return[U[e](o).top+n,s]}return null})).filter((t=>t)).sort(((t,e)=>t[0]-e[0])).forEach((t=>{this._offsets.push(t[0]),this._targets.push(t[1])}))}dispose(){j.off(this._scrollElement,".bs.scrollspy"),super.dispose()}_getConfig(t){return(t={...bn,...U.getDataAttributes(this._element),..."object"==typeof t&&t?t:{}}).target=r(t.target)||document.documentElement,a(_n,t,vn),t}_getScrollTop(){return this._scrollElement===window?this._scrollElement.pageYOffset:this._scrollElement.scrollTop}_getScrollHeight(){return this._scrollElement.scrollHeight||Math.max(document.body.scrollHeight,document.documentElement.scrollHeight)}_getOffsetHeight(){return this._scrollElement===window?window.innerHeight:this._scrollElement.getBoundingClientRect().height}_process(){const t=this._getScrollTop()+this._config.offset,e=this._getScrollHeight(),i=this._config.offset+e-this._getOffsetHeight();if(this._scrollHeight!==e&&this.refresh(),t>=i){const t=this._targets[this._targets.length-1];this._activeTarget!==t&&this._activate(t)}else{if(this._activeTarget&&t0)return this._activeTarget=null,void this._clear();for(let e=this._offsets.length;e--;)this._activeTarget!==this._targets[e]&&t>=this._offsets[e]&&(void 0===this._offsets[e+1]||t`${e}[data-bs-target="${t}"],${e}[href="${t}"]`)),i=V.findOne(e.join(","),this._config.target);i.classList.add(yn),i.classList.contains("dropdown-item")?V.findOne(".dropdown-toggle",i.closest(".dropdown")).classList.add(yn):V.parents(i,".nav, .list-group").forEach((t=>{V.prev(t,".nav-link, .list-group-item").forEach((t=>t.classList.add(yn))),V.prev(t,".nav-item").forEach((t=>{V.children(t,".nav-link").forEach((t=>t.classList.add(yn)))}))})),j.trigger(this._scrollElement,"activate.bs.scrollspy",{relatedTarget:t})}_clear(){V.find(wn,this._config.target).filter((t=>t.classList.contains(yn))).forEach((t=>t.classList.remove(yn)))}static jQueryInterface(t){return this.each((function(){const e=An.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}}j.on(window,"load.bs.scrollspy.data-api",(()=>{V.find('[data-bs-spy="scroll"]').forEach((t=>new An(t)))})),g(An);const Tn="active",On="fade",Cn="show",kn=".active",Ln=":scope > li > .active";class xn extends B{static get NAME(){return"tab"}show(){if(this._element.parentNode&&this._element.parentNode.nodeType===Node.ELEMENT_NODE&&this._element.classList.contains(Tn))return;let t;const e=n(this._element),i=this._element.closest(".nav, .list-group");if(i){const e="UL"===i.nodeName||"OL"===i.nodeName?Ln:kn;t=V.find(e,i),t=t[t.length-1]}const s=t?j.trigger(t,"hide.bs.tab",{relatedTarget:this._element}):null;if(j.trigger(this._element,"show.bs.tab",{relatedTarget:t}).defaultPrevented||null!==s&&s.defaultPrevented)return;this._activate(this._element,i);const o=()=>{j.trigger(t,"hidden.bs.tab",{relatedTarget:this._element}),j.trigger(this._element,"shown.bs.tab",{relatedTarget:t})};e?this._activate(e,e.parentNode,o):o()}_activate(t,e,i){const n=(!e||"UL"!==e.nodeName&&"OL"!==e.nodeName?V.children(e,kn):V.find(Ln,e))[0],s=i&&n&&n.classList.contains(On),o=()=>this._transitionComplete(t,n,i);n&&s?(n.classList.remove(Cn),this._queueCallback(o,t,!0)):o()}_transitionComplete(t,e,i){if(e){e.classList.remove(Tn);const t=V.findOne(":scope > .dropdown-menu .active",e.parentNode);t&&t.classList.remove(Tn),"tab"===e.getAttribute("role")&&e.setAttribute("aria-selected",!1)}t.classList.add(Tn),"tab"===t.getAttribute("role")&&t.setAttribute("aria-selected",!0),u(t),t.classList.contains(On)&&t.classList.add(Cn);let n=t.parentNode;if(n&&"LI"===n.nodeName&&(n=n.parentNode),n&&n.classList.contains("dropdown-menu")){const e=t.closest(".dropdown");e&&V.find(".dropdown-toggle",e).forEach((t=>t.classList.add(Tn))),t.setAttribute("aria-expanded",!0)}i&&i()}static jQueryInterface(t){return this.each((function(){const e=xn.getOrCreateInstance(this);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}}j.on(document,"click.bs.tab.data-api",'[data-bs-toggle="tab"], [data-bs-toggle="pill"], [data-bs-toggle="list"]',(function(t){["A","AREA"].includes(this.tagName)&&t.preventDefault(),c(this)||xn.getOrCreateInstance(this).show()})),g(xn);const Dn="toast",Sn="hide",Nn="show",In="showing",Pn={animation:"boolean",autohide:"boolean",delay:"number"},jn={animation:!0,autohide:!0,delay:5e3};class Mn extends B{constructor(t,e){super(t),this._config=this._getConfig(e),this._timeout=null,this._hasMouseInteraction=!1,this._hasKeyboardInteraction=!1,this._setListeners()}static get DefaultType(){return Pn}static get Default(){return jn}static get NAME(){return 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98% rename from bs/.development/Distris_files/libs/quarto-html/quarto-syntax-highlighting.css rename to bs/.development/002Likelihood_files/libs/quarto-html/quarto-syntax-highlighting.css index b30ce57..d9fd98f 100644 --- a/bs/.development/Distris_files/libs/quarto-html/quarto-syntax-highlighting.css +++ b/bs/.development/002Likelihood_files/libs/quarto-html/quarto-syntax-highlighting.css @@ -85,7 +85,6 @@ code span.st { code span.cf { color: #003B4F; - font-weight: bold; font-style: inherit; } @@ -194,7 +193,6 @@ code span.dv { code span.kw { color: #003B4F; - font-weight: bold; font-style: inherit; } diff --git a/bs/.development/Distris_files/libs/quarto-html/quarto.js b/bs/.development/002Likelihood_files/libs/quarto-html/quarto.js similarity index 96% rename from bs/.development/Distris_files/libs/quarto-html/quarto.js rename to bs/.development/002Likelihood_files/libs/quarto-html/quarto.js index 39e6869..c3935c7 100644 --- a/bs/.development/Distris_files/libs/quarto-html/quarto.js +++ b/bs/.development/002Likelihood_files/libs/quarto-html/quarto.js @@ -9,7 +9,7 @@ const layoutMarginEls = () => { // Find any conflicting margin elements and add margins to the // top to prevent overlap const marginChildren = window.document.querySelectorAll( - ".column-margin.column-container > *, .margin-caption, .aside" + ".column-margin.column-container > * " ); let lastBottom = 0; @@ -18,14 +18,25 @@ const layoutMarginEls = () => { // clear the top margin so we recompute it marginChild.style.marginTop = null; const top = marginChild.getBoundingClientRect().top + window.scrollY; + console.log({ + childtop: marginChild.getBoundingClientRect().top, + scroll: window.scrollY, + top, + lastBottom, + }); if (top < lastBottom) { - const marginChildStyle = window.getComputedStyle(marginChild); - const marginBottom = parseFloat(marginChildStyle["marginBottom"]); - const margin = lastBottom - top + marginBottom; + const margin = lastBottom - top; marginChild.style.marginTop = `${margin}px`; } const styles = window.getComputedStyle(marginChild); const marginTop = parseFloat(styles["marginTop"]); + + console.log({ + top, + height: marginChild.getBoundingClientRect().height, + marginTop, + total: top + marginChild.getBoundingClientRect().height + marginTop, + }); lastBottom = top + marginChild.getBoundingClientRect().height + marginTop; } } @@ -35,15 +46,7 @@ window.document.addEventListener("DOMContentLoaded", function (_event) { // Recompute the position of margin elements anytime the body size changes if (window.ResizeObserver) { const resizeObserver = new window.ResizeObserver( - throttle(() => { - layoutMarginEls(); - if ( - window.document.body.getBoundingClientRect().width < 990 && - isReaderMode() - ) { - quartoToggleReader(); - } - }, 50) + throttle(layoutMarginEls, 50) ); resizeObserver.observe(window.document.body); } @@ -94,7 +97,7 @@ window.document.addEventListener("DOMContentLoaded", function (_event) { if (link.href.indexOf("#") !== -1) { const anchor = link.href.split("#")[1]; const heading = window.document.querySelector( - `[data-anchor-id="${anchor}"]` + `[data-anchor-id=${anchor}]` ); if (heading) { // Add the class @@ -134,10 +137,8 @@ window.document.addEventListener("DOMContentLoaded", function (_event) { window.innerHeight + window.pageYOffset >= window.document.body.offsetHeight ) { - // This is the no-scroll case where last section should be the active one sectionIndex = 0; } else { - // This finds the last section visible on screen that should be made active sectionIndex = [...sections].reverse().findIndex((section) => { if (section) { return window.pageYOffset >= section.offsetTop - sectionMargin; @@ -319,7 +320,6 @@ window.document.addEventListener("DOMContentLoaded", function (_event) { for (const child of el.children) { child.style.opacity = 0; child.style.overflow = "hidden"; - child.style.pointerEvents = "none"; } nexttick(() => { @@ -361,7 +361,6 @@ window.document.addEventListener("DOMContentLoaded", function (_event) { const clone = child.cloneNode(true); clone.style.opacity = 1; - clone.style.pointerEvents = null; clone.style.display = null; toggleContents.append(clone); } @@ -436,7 +435,6 @@ window.document.addEventListener("DOMContentLoaded", function (_event) { for (const child of el.children) { child.style.opacity = 1; child.style.overflow = null; - child.style.pointerEvents = null; } const placeholderEl = window.document.getElementById( @@ -744,7 +742,6 @@ window.document.addEventListener("DOMContentLoaded", function (_event) { // Process the collapse state if this is an UL if (el.tagName === "UL") { if (tocOpenDepth === -1 && depth > 1) { - // toc-expand: false el.classList.add("collapse"); } else if ( depth <= tocOpenDepth || @@ -763,9 +760,10 @@ window.document.addEventListener("DOMContentLoaded", function (_event) { }; // walk the TOC and expand / collapse any items that should be shown + if (tocEl) { - updateActiveLink(); walk(tocEl, 0); + updateActiveLink(); } // Throttle the scroll event and walk peridiocally @@ -784,10 +782,6 @@ window.document.addEventListener("DOMContentLoaded", function (_event) { window.addEventListener( "resize", throttle(() => { - if (tocEl) { - updateActiveLink(); - walk(tocEl, 0); - } if (!isReaderMode()) { hideOverlappedSidebars(); } diff --git a/bs/.development/Regression_linear_model_files/libs/quarto-html/tippy.css b/bs/.development/002Likelihood_files/libs/quarto-html/tippy.css similarity index 100% rename from bs/.development/Regression_linear_model_files/libs/quarto-html/tippy.css rename to bs/.development/002Likelihood_files/libs/quarto-html/tippy.css diff --git a/bs/.development/Regression_linear_model_files/libs/quarto-html/tippy.umd.min.js b/bs/.development/002Likelihood_files/libs/quarto-html/tippy.umd.min.js similarity index 100% rename from bs/.development/Regression_linear_model_files/libs/quarto-html/tippy.umd.min.js rename to bs/.development/002Likelihood_files/libs/quarto-html/tippy.umd.min.js diff --git a/bs/.development/Regression_linear_model.html b/bs/.development/003LinearModel.html similarity index 57% rename from bs/.development/Regression_linear_model.html rename to bs/.development/003LinearModel.html index a71e6af..8eb9597 100644 --- a/bs/.development/Regression_linear_model.html +++ b/bs/.development/003LinearModel.html @@ -7,7 +7,7 @@ -Exploring Probability Distributions in R +generalized linear model in R - - - - - - - - - - + + + + + + + + + + @@ -81,7 +81,7 @@
-

Exploring Probability Distributions in R

+

generalized linear model in R

@@ -96,108 +96,9 @@

Exploring Probability Distributions in R

-
-

Likelihood of a Dataset

-

Likelihood refers to how probable a specific set of data is under a given model. It quantifies the model�s ability to explain the observed data. Maximizing the likelihood helps estimate the parameters that make the observed data most probable (used in maximum likelihood estimation).

-
-

fitdistr and AIC

-
    -
  • fitdistr (in MASS package): Fits a distribution to data by estimating its parameters using maximum likelihood estimation. It’s useful for modeling and checking which distribution best matches your data.
  • -
  • AIC (Akaike Information Criterion): Measures the relative quality of statistical models, balancing model fit and complexity. A lower AIC indicates a model that better explains the data with fewer parameters.
  • -
-
-
library(FAwR)
-
-
Loading required package: MASS
-
-
-
Loading required package: lattice
-
-
-
Loading required package: glpkAPI
-
-
-
using GLPK version 5.0
-
-
library(ggplot2)
-library(MASS)
-data(gutten)
-hist(gutten$dbh.cm)
-
-

-
-
fit_norm <- fitdistr(gutten$dbh.cm, "normal")
-fit_norm
-
-
      mean          sd    
-  20.7820833   10.5987949 
- ( 0.3059609) ( 0.2163470)
-
-
likelihood <- prod(
-  dnorm(gutten$dbh.cm,
-  mean = fit_norm$estimate[1],
-  sd = fit_norm$estimate[2])
-) # Cannot be calculated like this by a computer --> is 0
-likelihood <- sum(
-  log(
-    dnorm(gutten$dbh.cm,
-      mean = fit_norm$estimate[1],
-      sd = fit_norm$estimate[2])
-  )
-)
-likelihood
-
-
[1] -4535.615
-
-
logLik(fit_norm)
-
-
'log Lik.' -4535.615 (df=2)
-
-
AIC(fit_norm)
-
-
[1] 9075.229
-
-
BIC(fit_norm)
-
-
[1] 9085.409
-
-
# log normal
-fit_lognorm <- fitdistr(gutten$dbh.cm, "lognormal")
-fit_lognorm
-
-
    meanlog       sdlog   
-  2.82767051   0.77740010 
- (0.02244161) (0.01586861)
-
-
likelihood <- sum(
-  log(
-    dnorm(gutten$dbh.cm,
-      mean = fit_lognorm$estimate[1],
-      sd = fit_lognorm$estimate[2])
-  )
-)
-likelihood
-
-
[1] -Inf
-
-
logLik(fit_lognorm)
-
-
'log Lik.' -4793.771 (df=2)
-
-
AIC(fit_lognorm)
-
-
[1] 9591.541
-
-
BIC(fit_lognorm)
-
-
[1] 9601.722
-
-
-
-

Regression i.e. generalized linear models

-

A regression describes the quantitative relationship between one or more predictor variables and a response variable. Here a distribution is again fitted to the measured data. However, a predictor effects certain parameters of the distribution. For example, we have three factors in our dataset: genotype, time and treatment. Moreover, we want to predict the CO2 uptake rate (our response variable). Furthermore, we assume normally distributed values. CO2uptake ~ N(µ = a + bgenotype + ctime + d*treatment, �)

+

A regression describes the quantitative relationship between one or more predictor variables and a response variable. Here a distribution is again fitted to the measured data. However, a predictor effects certain parameters of the distribution. For example, we have three factors in our dataset: genotype, time and treatment. Moreover, we want to predict the CO2 uptake rate (our response variable). Furthermore, we assume normally distributed values. CO2uptake ~ N(µ = a + bgenotype + ctime + d*treatment, ρ)

@@ -422,8 +325,8 @@

5. Estimate Varia \hat{\sigma}^2 = \frac{\sum \hat{\epsilon}_i^2}{n - p} \] where \(p\) is the number of estimated parameters (e.g., \(p = 2\) for intercept and slope).

-
design_matrix <- model.matrix(sizes ~ sex, data = df)
-head(design_matrix)
+
design_matrix <- model.matrix(sizes ~ sex, data = df)
+head(design_matrix)
  (Intercept) sexM
 1           1    0
@@ -433,7 +336,7 @@ 

5. Estimate Varia 5 1 0 6 1 0

-
tail(design_matrix)
+
tail(design_matrix)
      (Intercept) sexM
 19995           1    1
@@ -443,23 +346,23 @@ 

5. Estimate Varia 19999 1 1 20000 1 1

-
beta_hat <- solve(t(design_matrix) %*% design_matrix) %*% t(design_matrix) %*% df$sizes
-beta_hat
+
beta_hat <- solve(t(design_matrix) %*% design_matrix) %*% t(design_matrix) %*% df$sizes
+beta_hat
                 [,1]
-(Intercept) 170.02331
-sexM         11.88137
+(Intercept) 169.94919 +sexM 12.12533
-
cat(
-  "Model: which considers the sex\n",
-  "y = N(µ = a*F + b*M, �)\n"
-)
+
cat(
+  "Model: which considers the sex\n",
+  "y = N(µ = a*F + b*M, ρ)\n"
+)
Model: which considers the sex
- y = N(µ = a*F + b*M, �)
+ y = N(µ = a*F + b*M, ρ)
-
m <- glm(sizes ~ sex, data = df, family = "gaussian")
-summary(m)
+
m <- glm(sizes ~ sex, data = df, family = "gaussian")
+summary(m)

 Call:
@@ -467,31 +370,31 @@ 

5. Estimate Varia Coefficients: Estimate Std. Error t value Pr(>|t|) -(Intercept) 170.02331 0.05018 3388.2 <2e-16 *** -sexM 11.88137 0.07097 167.4 <2e-16 *** +(Intercept) 169.94919 0.05010 3392.0 <2e-16 *** +sexM 12.12533 0.07086 171.1 <2e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 -(Dispersion parameter for gaussian family taken to be 25.18066) +(Dispersion parameter for gaussian family taken to be 25.10343) - Null deviance: 1209397 on 19999 degrees of freedom -Residual deviance: 503563 on 19998 degrees of freedom -AIC: 121283 + Null deviance: 1237137 on 19999 degrees of freedom +Residual deviance: 502018 on 19998 degrees of freedom +AIC: 121222 Number of Fisher Scoring iterations: 2

-
sum(residuals(m)^2) / (nrow(df) - 2)
+
sum(residuals(m)^2) / (nrow(df) - 2)
-
[1] 25.18066
-
-
# Calc residuals
-# NOTE: Is beta_hat[1] + beta_hat[2] * df$sizes but in addition sex is considered
-y_hat <- design_matrix %*% beta_hat 
-residuals <- df$sizes - y_hat
-variance <- sum(residuals^2) / (nrow(df) - 2)
-variance
+
[1] 25.10343
+
+
# Calc residuals
+# NOTE: Is beta_hat[1] + beta_hat[2] * df$sizes but in addition sex is considered
+y_hat <- design_matrix %*% beta_hat 
+residuals <- df$sizes - y_hat
+variance <- sum(residuals^2) / (nrow(df) - 2)
+variance
-
[1] 25.18066
+
[1] 25.10343

diff --git a/bs/.development/Regression_linear_model.qmd b/bs/.development/003LinearModel.qmd similarity index 75% rename from bs/.development/Regression_linear_model.qmd rename to bs/.development/003LinearModel.qmd index 3af6b75..ebb9ae7 100644 --- a/bs/.development/Regression_linear_model.qmd +++ b/bs/.development/003LinearModel.qmd @@ -1,63 +1,8 @@ --- -title: "Exploring Probability Distributions in R" +title: "generalized linear model in R" output: html_document # Use `output: quarto::html` for Quarto --- -## Likelihood of a Dataset -Likelihood refers to how probable a specific set of data is under a given model. -It quantifies the modelâ��s ability to explain the observed data. -Maximizing the likelihood helps estimate the parameters that make the observed data -most probable (used in maximum likelihood estimation). - -### fitdistr and AIC -- fitdistr (in MASS package): Fits a distribution to data by estimating - its parameters using maximum likelihood estimation. - It's useful for modeling and checking which distribution best matches your data. -- AIC (Akaike Information Criterion): Measures the relative quality - of statistical models, balancing model fit and complexity. A lower AIC - indicates a model that better explains the data with fewer parameters. - -```{r Likelihood} -library(FAwR) -library(ggplot2) -library(MASS) -data(gutten) -hist(gutten$dbh.cm) -fit_norm <- fitdistr(gutten$dbh.cm, "normal") -fit_norm -likelihood <- prod( - dnorm(gutten$dbh.cm, - mean = fit_norm$estimate[1], - sd = fit_norm$estimate[2]) -) # Cannot be calculated like this by a computer --> is 0 -likelihood <- sum( - log( - dnorm(gutten$dbh.cm, - mean = fit_norm$estimate[1], - sd = fit_norm$estimate[2]) - ) -) -likelihood -logLik(fit_norm) -AIC(fit_norm) -BIC(fit_norm) - -# log normal -fit_lognorm <- fitdistr(gutten$dbh.cm, "lognormal") -fit_lognorm -likelihood <- sum( - log( - dnorm(gutten$dbh.cm, - mean = fit_lognorm$estimate[1], - sd = fit_lognorm$estimate[2]) - ) -) -likelihood -logLik(fit_lognorm) -AIC(fit_lognorm) -BIC(fit_lognorm) -``` - ## Regression i.e. generalized linear models A regression describes the quantitative relationship between @@ -67,7 +12,7 @@ However, a predictor effects certain parameters of the distribution. For example, we have three factors in our dataset: genotype, time and treatment. Moreover, we want to predict the CO2 uptake rate (our response variable). Furthermore, we assume normally distributed values. -CO2uptake ~ N(µ = a + b*genotype + c*time + d*treatment, Ï�) +CO2uptake ~ N(µ = a + b*genotype + c*time + d*treatment, ρ) ### The link function/scala Often distributions have only a certain interval in which they @@ -86,6 +31,8 @@ knitr::kable(df) ```{r Regressions} +library(ggplot2) +library(MASS) df <- data.frame(sizes = c(rnorm(10000, mean = 170, sd = 5), rnorm(10000, mean = 182, sd = 5)), sex = rep(c("F", "M"), each = 10000)) p1 <- ggplot(df, aes(x = sizes, colour = sex)) + @@ -102,7 +49,7 @@ cat( summary(m) cat( "Model: which considers the sex\n", - "y = N(µ = a*F + b*M, Ï�)\n" + "y = N(µ = a*F + b*M, ρ)\n" ) m <- glm(sizes ~ sex, data = df, family = "gaussian") summary(m) @@ -226,7 +173,7 @@ beta_hat <- solve(t(design_matrix) %*% design_matrix) %*% t(design_matrix) %*% d beta_hat cat( "Model: which considers the sex\n", - "y = N(µ = a*F + b*M, Ï�)\n" + "y = N(µ = a*F + b*M, ρ)\n" ) m <- glm(sizes ~ sex, data = df, family = 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this._config.reference&&(e=this._config.reference);const i=this._getPopperConfig(),n=i.modifiers.find((t=>"applyStyles"===t.name&&!1===t.enabled));this._popper=qe(e,this._menu,i),n&&U.setDataAttribute(this._menu,"popper","static")}_isShown(t=this._element){return t.classList.contains(Je)}_getMenuElement(){return V.next(this._element,ei)[0]}_getPlacement(){const t=this._element.parentNode;if(t.classList.contains("dropend"))return ri;if(t.classList.contains("dropstart"))return ai;const e="end"===getComputedStyle(this._menu).getPropertyValue("--bs-position").trim();return t.classList.contains("dropup")?e?ni:ii:e?oi:si}_detectNavbar(){return null!==this._element.closest(".navbar")}_getOffset(){const{offset:t}=this._config;return"string"==typeof t?t.split(",").map((t=>Number.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_getPopperConfig(){const t={placement:this._getPlacement(),modifiers:[{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"offset",options:{offset:this._getOffset()}}]};return"static"===this._config.display&&(t.modifiers=[{name:"applyStyles",enabled:!1}]),{...t,..."function"==typeof this._config.popperConfig?this._config.popperConfig(t):this._config.popperConfig}}_selectMenuItem({key:t,target:e}){const i=V.find(".dropdown-menu .dropdown-item:not(.disabled):not(:disabled)",this._menu).filter(l);i.length&&v(i,e,t===Ye,!i.includes(e)).focus()}static jQueryInterface(t){return this.each((function(){const e=hi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}static clearMenus(t){if(t&&(2===t.button||"keyup"===t.type&&"Tab"!==t.key))return;const e=V.find(ti);for(let i=0,n=e.length;ie+t)),this._setElementAttributes(di,"paddingRight",(e=>e+t)),this._setElementAttributes(ui,"marginRight",(e=>e-t))}_disableOverFlow(){this._saveInitialAttribute(this._element,"overflow"),this._element.style.overflow="hidden"}_setElementAttributes(t,e,i){const n=this.getWidth();this._applyManipulationCallback(t,(t=>{if(t!==this._element&&window.innerWidth>t.clientWidth+n)return;this._saveInitialAttribute(t,e);const s=window.getComputedStyle(t)[e];t.style[e]=`${i(Number.parseFloat(s))}px`}))}reset(){this._resetElementAttributes(this._element,"overflow"),this._resetElementAttributes(this._element,"paddingRight"),this._resetElementAttributes(di,"paddingRight"),this._resetElementAttributes(ui,"marginRight")}_saveInitialAttribute(t,e){const i=t.style[e];i&&U.setDataAttribute(t,e,i)}_resetElementAttributes(t,e){this._applyManipulationCallback(t,(t=>{const i=U.getDataAttribute(t,e);void 0===i?t.style.removeProperty(e):(U.removeDataAttribute(t,e),t.style[e]=i)}))}_applyManipulationCallback(t,e){o(t)?e(t):V.find(t,this._element).forEach(e)}isOverflowing(){return this.getWidth()>0}}const pi={className:"modal-backdrop",isVisible:!0,isAnimated:!1,rootElement:"body",clickCallback:null},mi={className:"string",isVisible:"boolean",isAnimated:"boolean",rootElement:"(element|string)",clickCallback:"(function|null)"},gi="show",_i="mousedown.bs.backdrop";class bi{constructor(t){this._config=this._getConfig(t),this._isAppended=!1,this._element=null}show(t){this._config.isVisible?(this._append(),this._config.isAnimated&&u(this._getElement()),this._getElement().classList.add(gi),this._emulateAnimation((()=>{_(t)}))):_(t)}hide(t){this._config.isVisible?(this._getElement().classList.remove(gi),this._emulateAnimation((()=>{this.dispose(),_(t)}))):_(t)}_getElement(){if(!this._element){const t=document.createElement("div");t.className=this._config.className,this._config.isAnimated&&t.classList.add("fade"),this._element=t}return this._element}_getConfig(t){return(t={...pi,..."object"==typeof t?t:{}}).rootElement=r(t.rootElement),a("backdrop",t,mi),t}_append(){this._isAppended||(this._config.rootElement.append(this._getElement()),j.on(this._getElement(),_i,(()=>{_(this._config.clickCallback)})),this._isAppended=!0)}dispose(){this._isAppended&&(j.off(this._element,_i),this._element.remove(),this._isAppended=!1)}_emulateAnimation(t){b(t,this._getElement(),this._config.isAnimated)}}const vi={trapElement:null,autofocus:!0},yi={trapElement:"element",autofocus:"boolean"},wi=".bs.focustrap",Ei="backward";class Ai{constructor(t){this._config=this._getConfig(t),this._isActive=!1,this._lastTabNavDirection=null}activate(){const{trapElement:t,autofocus:e}=this._config;this._isActive||(e&&t.focus(),j.off(document,wi),j.on(document,"focusin.bs.focustrap",(t=>this._handleFocusin(t))),j.on(document,"keydown.tab.bs.focustrap",(t=>this._handleKeydown(t))),this._isActive=!0)}deactivate(){this._isActive&&(this._isActive=!1,j.off(document,wi))}_handleFocusin(t){const{target:e}=t,{trapElement:i}=this._config;if(e===document||e===i||i.contains(e))return;const n=V.focusableChildren(i);0===n.length?i.focus():this._lastTabNavDirection===Ei?n[n.length-1].focus():n[0].focus()}_handleKeydown(t){"Tab"===t.key&&(this._lastTabNavDirection=t.shiftKey?Ei:"forward")}_getConfig(t){return t={...vi,..."object"==typeof t?t:{}},a("focustrap",t,yi),t}}const Ti="modal",Oi="Escape",Ci={backdrop:!0,keyboard:!0,focus:!0},ki={backdrop:"(boolean|string)",keyboard:"boolean",focus:"boolean"},Li="hidden.bs.modal",xi="show.bs.modal",Di="resize.bs.modal",Si="click.dismiss.bs.modal",Ni="keydown.dismiss.bs.modal",Ii="mousedown.dismiss.bs.modal",Pi="modal-open",ji="show",Mi="modal-static";class Hi extends B{constructor(t,e){super(t),this._config=this._getConfig(e),this._dialog=V.findOne(".modal-dialog",this._element),this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._isShown=!1,this._ignoreBackdropClick=!1,this._isTransitioning=!1,this._scrollBar=new fi}static get Default(){return Ci}static get NAME(){return Ti}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||this._isTransitioning||j.trigger(this._element,xi,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._isAnimated()&&(this._isTransitioning=!0),this._scrollBar.hide(),document.body.classList.add(Pi),this._adjustDialog(),this._setEscapeEvent(),this._setResizeEvent(),j.on(this._dialog,Ii,(()=>{j.one(this._element,"mouseup.dismiss.bs.modal",(t=>{t.target===this._element&&(this._ignoreBackdropClick=!0)}))})),this._showBackdrop((()=>this._showElement(t))))}hide(){if(!this._isShown||this._isTransitioning)return;if(j.trigger(this._element,"hide.bs.modal").defaultPrevented)return;this._isShown=!1;const t=this._isAnimated();t&&(this._isTransitioning=!0),this._setEscapeEvent(),this._setResizeEvent(),this._focustrap.deactivate(),this._element.classList.remove(ji),j.off(this._element,Si),j.off(this._dialog,Ii),this._queueCallback((()=>this._hideModal()),this._element,t)}dispose(){[window,this._dialog].forEach((t=>j.off(t,".bs.modal"))),this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}handleUpdate(){this._adjustDialog()}_initializeBackDrop(){return new bi({isVisible:Boolean(this._config.backdrop),isAnimated:this._isAnimated()})}_initializeFocusTrap(){return new Ai({trapElement:this._element})}_getConfig(t){return t={...Ci,...U.getDataAttributes(this._element),..."object"==typeof t?t:{}},a(Ti,t,ki),t}_showElement(t){const e=this._isAnimated(),i=V.findOne(".modal-body",this._dialog);this._element.parentNode&&this._element.parentNode.nodeType===Node.ELEMENT_NODE||document.body.append(this._element),this._element.style.display="block",this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.scrollTop=0,i&&(i.scrollTop=0),e&&u(this._element),this._element.classList.add(ji),this._queueCallback((()=>{this._config.focus&&this._focustrap.activate(),this._isTransitioning=!1,j.trigger(this._element,"shown.bs.modal",{relatedTarget:t})}),this._dialog,e)}_setEscapeEvent(){this._isShown?j.on(this._element,Ni,(t=>{this._config.keyboard&&t.key===Oi?(t.preventDefault(),this.hide()):this._config.keyboard||t.key!==Oi||this._triggerBackdropTransition()})):j.off(this._element,Ni)}_setResizeEvent(){this._isShown?j.on(window,Di,(()=>this._adjustDialog())):j.off(window,Di)}_hideModal(){this._element.style.display="none",this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._isTransitioning=!1,this._backdrop.hide((()=>{document.body.classList.remove(Pi),this._resetAdjustments(),this._scrollBar.reset(),j.trigger(this._element,Li)}))}_showBackdrop(t){j.on(this._element,Si,(t=>{this._ignoreBackdropClick?this._ignoreBackdropClick=!1:t.target===t.currentTarget&&(!0===this._config.backdrop?this.hide():"static"===this._config.backdrop&&this._triggerBackdropTransition())})),this._backdrop.show(t)}_isAnimated(){return this._element.classList.contains("fade")}_triggerBackdropTransition(){if(j.trigger(this._element,"hidePrevented.bs.modal").defaultPrevented)return;const{classList:t,scrollHeight:e,style:i}=this._element,n=e>document.documentElement.clientHeight;!n&&"hidden"===i.overflowY||t.contains(Mi)||(n||(i.overflowY="hidden"),t.add(Mi),this._queueCallback((()=>{t.remove(Mi),n||this._queueCallback((()=>{i.overflowY=""}),this._dialog)}),this._dialog),this._element.focus())}_adjustDialog(){const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._scrollBar.getWidth(),i=e>0;(!i&&t&&!m()||i&&!t&&m())&&(this._element.style.paddingLeft=`${e}px`),(i&&!t&&!m()||!i&&t&&m())&&(this._element.style.paddingRight=`${e}px`)}_resetAdjustments(){this._element.style.paddingLeft="",this._element.style.paddingRight=""}static jQueryInterface(t,e){return this.each((function(){const i=Hi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===i[t])throw new TypeError(`No method named "${t}"`);i[t](e)}}))}}j.on(document,"click.bs.modal.data-api",'[data-bs-toggle="modal"]',(function(t){const e=n(this);["A","AREA"].includes(this.tagName)&&t.preventDefault(),j.one(e,xi,(t=>{t.defaultPrevented||j.one(e,Li,(()=>{l(this)&&this.focus()}))}));const i=V.findOne(".modal.show");i&&Hi.getInstance(i).hide(),Hi.getOrCreateInstance(e).toggle(this)})),R(Hi),g(Hi);const Bi="offcanvas",Ri={backdrop:!0,keyboard:!0,scroll:!1},Wi={backdrop:"boolean",keyboard:"boolean",scroll:"boolean"},$i="show",zi=".offcanvas.show",qi="hidden.bs.offcanvas";class Fi extends B{constructor(t,e){super(t),this._config=this._getConfig(e),this._isShown=!1,this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._addEventListeners()}static get NAME(){return Bi}static get Default(){return Ri}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||j.trigger(this._element,"show.bs.offcanvas",{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._element.style.visibility="visible",this._backdrop.show(),this._config.scroll||(new fi).hide(),this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.classList.add($i),this._queueCallback((()=>{this._config.scroll||this._focustrap.activate(),j.trigger(this._element,"shown.bs.offcanvas",{relatedTarget:t})}),this._element,!0))}hide(){this._isShown&&(j.trigger(this._element,"hide.bs.offcanvas").defaultPrevented||(this._focustrap.deactivate(),this._element.blur(),this._isShown=!1,this._element.classList.remove($i),this._backdrop.hide(),this._queueCallback((()=>{this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._element.style.visibility="hidden",this._config.scroll||(new fi).reset(),j.trigger(this._element,qi)}),this._element,!0)))}dispose(){this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}_getConfig(t){return t={...Ri,...U.getDataAttributes(this._element),..."object"==typeof t?t:{}},a(Bi,t,Wi),t}_initializeBackDrop(){return new bi({className:"offcanvas-backdrop",isVisible:this._config.backdrop,isAnimated:!0,rootElement:this._element.parentNode,clickCallback:()=>this.hide()})}_initializeFocusTrap(){return new Ai({trapElement:this._element})}_addEventListeners(){j.on(this._element,"keydown.dismiss.bs.offcanvas",(t=>{this._config.keyboard&&"Escape"===t.key&&this.hide()}))}static jQueryInterface(t){return this.each((function(){const e=Fi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t]||t.startsWith("_")||"constructor"===t)throw new TypeError(`No method named "${t}"`);e[t](this)}}))}}j.on(document,"click.bs.offcanvas.data-api",'[data-bs-toggle="offcanvas"]',(function(t){const e=n(this);if(["A","AREA"].includes(this.tagName)&&t.preventDefault(),c(this))return;j.one(e,qi,(()=>{l(this)&&this.focus()}));const i=V.findOne(zi);i&&i!==e&&Fi.getInstance(i).hide(),Fi.getOrCreateInstance(e).toggle(this)})),j.on(window,"load.bs.offcanvas.data-api",(()=>V.find(zi).forEach((t=>Fi.getOrCreateInstance(t).show())))),R(Fi),g(Fi);const Ui=new Set(["background","cite","href","itemtype","longdesc","poster","src","xlink:href"]),Vi=/^(?:(?:https?|mailto|ftp|tel|file|sms):|[^#&/:?]*(?:[#/?]|$))/i,Ki=/^data:(?:image\/(?:bmp|gif|jpeg|jpg|png|tiff|webp)|video\/(?:mpeg|mp4|ogg|webm)|audio\/(?:mp3|oga|ogg|opus));base64,[\d+/a-z]+=*$/i,Xi=(t,e)=>{const i=t.nodeName.toLowerCase();if(e.includes(i))return!Ui.has(i)||Boolean(Vi.test(t.nodeValue)||Ki.test(t.nodeValue));const n=e.filter((t=>t instanceof RegExp));for(let t=0,e=n.length;t{Xi(t,r)||i.removeAttribute(t.nodeName)}))}return n.body.innerHTML}const Qi="tooltip",Gi=new Set(["sanitize","allowList","sanitizeFn"]),Zi={animation:"boolean",template:"string",title:"(string|element|function)",trigger:"string",delay:"(number|object)",html:"boolean",selector:"(string|boolean)",placement:"(string|function)",offset:"(array|string|function)",container:"(string|element|boolean)",fallbackPlacements:"array",boundary:"(string|element)",customClass:"(string|function)",sanitize:"boolean",sanitizeFn:"(null|function)",allowList:"object",popperConfig:"(null|object|function)"},Ji={AUTO:"auto",TOP:"top",RIGHT:m()?"left":"right",BOTTOM:"bottom",LEFT:m()?"right":"left"},tn={animation:!0,template:'',trigger:"hover focus",title:"",delay:0,html:!1,selector:!1,placement:"top",offset:[0,0],container:!1,fallbackPlacements:["top","right","bottom","left"],boundary:"clippingParents",customClass:"",sanitize:!0,sanitizeFn:null,allowList:{"*":["class","dir","id","lang","role",/^aria-[\w-]*$/i],a:["target","href","title","rel"],area:[],b:[],br:[],col:[],code:[],div:[],em:[],hr:[],h1:[],h2:[],h3:[],h4:[],h5:[],h6:[],i:[],img:["src","srcset","alt","title","width","height"],li:[],ol:[],p:[],pre:[],s:[],small:[],span:[],sub:[],sup:[],strong:[],u:[],ul:[]},popperConfig:null},en={HIDE:"hide.bs.tooltip",HIDDEN:"hidden.bs.tooltip",SHOW:"show.bs.tooltip",SHOWN:"shown.bs.tooltip",INSERTED:"inserted.bs.tooltip",CLICK:"click.bs.tooltip",FOCUSIN:"focusin.bs.tooltip",FOCUSOUT:"focusout.bs.tooltip",MOUSEENTER:"mouseenter.bs.tooltip",MOUSELEAVE:"mouseleave.bs.tooltip"},nn="fade",sn="show",on="show",rn="out",an=".tooltip-inner",ln=".modal",cn="hide.bs.modal",hn="hover",dn="focus";class un extends B{constructor(t,e){if(void 0===Fe)throw new TypeError("Bootstrap's tooltips require Popper (https://popper.js.org)");super(t),this._isEnabled=!0,this._timeout=0,this._hoverState="",this._activeTrigger={},this._popper=null,this._config=this._getConfig(e),this.tip=null,this._setListeners()}static get Default(){return tn}static get NAME(){return Qi}static get Event(){return en}static get DefaultType(){return Zi}enable(){this._isEnabled=!0}disable(){this._isEnabled=!1}toggleEnabled(){this._isEnabled=!this._isEnabled}toggle(t){if(this._isEnabled)if(t){const e=this._initializeOnDelegatedTarget(t);e._activeTrigger.click=!e._activeTrigger.click,e._isWithActiveTrigger()?e._enter(null,e):e._leave(null,e)}else{if(this.getTipElement().classList.contains(sn))return void this._leave(null,this);this._enter(null,this)}}dispose(){clearTimeout(this._timeout),j.off(this._element.closest(ln),cn,this._hideModalHandler),this.tip&&this.tip.remove(),this._disposePopper(),super.dispose()}show(){if("none"===this._element.style.display)throw new Error("Please use show on visible elements");if(!this.isWithContent()||!this._isEnabled)return;const t=j.trigger(this._element,this.constructor.Event.SHOW),e=h(this._element),i=null===e?this._element.ownerDocument.documentElement.contains(this._element):e.contains(this._element);if(t.defaultPrevented||!i)return;"tooltip"===this.constructor.NAME&&this.tip&&this.getTitle()!==this.tip.querySelector(an).innerHTML&&(this._disposePopper(),this.tip.remove(),this.tip=null);const n=this.getTipElement(),s=(t=>{do{t+=Math.floor(1e6*Math.random())}while(document.getElementById(t));return t})(this.constructor.NAME);n.setAttribute("id",s),this._element.setAttribute("aria-describedby",s),this._config.animation&&n.classList.add(nn);const o="function"==typeof this._config.placement?this._config.placement.call(this,n,this._element):this._config.placement,r=this._getAttachment(o);this._addAttachmentClass(r);const{container:a}=this._config;H.set(n,this.constructor.DATA_KEY,this),this._element.ownerDocument.documentElement.contains(this.tip)||(a.append(n),j.trigger(this._element,this.constructor.Event.INSERTED)),this._popper?this._popper.update():this._popper=qe(this._element,n,this._getPopperConfig(r)),n.classList.add(sn);const l=this._resolvePossibleFunction(this._config.customClass);l&&n.classList.add(...l.split(" ")),"ontouchstart"in document.documentElement&&[].concat(...document.body.children).forEach((t=>{j.on(t,"mouseover",d)}));const c=this.tip.classList.contains(nn);this._queueCallback((()=>{const t=this._hoverState;this._hoverState=null,j.trigger(this._element,this.constructor.Event.SHOWN),t===rn&&this._leave(null,this)}),this.tip,c)}hide(){if(!this._popper)return;const t=this.getTipElement();if(j.trigger(this._element,this.constructor.Event.HIDE).defaultPrevented)return;t.classList.remove(sn),"ontouchstart"in document.documentElement&&[].concat(...document.body.children).forEach((t=>j.off(t,"mouseover",d))),this._activeTrigger.click=!1,this._activeTrigger.focus=!1,this._activeTrigger.hover=!1;const e=this.tip.classList.contains(nn);this._queueCallback((()=>{this._isWithActiveTrigger()||(this._hoverState!==on&&t.remove(),this._cleanTipClass(),this._element.removeAttribute("aria-describedby"),j.trigger(this._element,this.constructor.Event.HIDDEN),this._disposePopper())}),this.tip,e),this._hoverState=""}update(){null!==this._popper&&this._popper.update()}isWithContent(){return Boolean(this.getTitle())}getTipElement(){if(this.tip)return this.tip;const t=document.createElement("div");t.innerHTML=this._config.template;const e=t.children[0];return this.setContent(e),e.classList.remove(nn,sn),this.tip=e,this.tip}setContent(t){this._sanitizeAndSetContent(t,this.getTitle(),an)}_sanitizeAndSetContent(t,e,i){const n=V.findOne(i,t);e||!n?this.setElementContent(n,e):n.remove()}setElementContent(t,e){if(null!==t)return o(e)?(e=r(e),void(this._config.html?e.parentNode!==t&&(t.innerHTML="",t.append(e)):t.textContent=e.textContent)):void(this._config.html?(this._config.sanitize&&(e=Yi(e,this._config.allowList,this._config.sanitizeFn)),t.innerHTML=e):t.textContent=e)}getTitle(){const t=this._element.getAttribute("data-bs-original-title")||this._config.title;return this._resolvePossibleFunction(t)}updateAttachment(t){return"right"===t?"end":"left"===t?"start":t}_initializeOnDelegatedTarget(t,e){return e||this.constructor.getOrCreateInstance(t.delegateTarget,this._getDelegateConfig())}_getOffset(){const{offset:t}=this._config;return"string"==typeof t?t.split(",").map((t=>Number.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_resolvePossibleFunction(t){return"function"==typeof t?t.call(this._element):t}_getPopperConfig(t){const e={placement:t,modifiers:[{name:"flip",options:{fallbackPlacements:this._config.fallbackPlacements}},{name:"offset",options:{offset:this._getOffset()}},{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"arrow",options:{element:`.${this.constructor.NAME}-arrow`}},{name:"onChange",enabled:!0,phase:"afterWrite",fn:t=>this._handlePopperPlacementChange(t)}],onFirstUpdate:t=>{t.options.placement!==t.placement&&this._handlePopperPlacementChange(t)}};return{...e,..."function"==typeof this._config.popperConfig?this._config.popperConfig(e):this._config.popperConfig}}_addAttachmentClass(t){this.getTipElement().classList.add(`${this._getBasicClassPrefix()}-${this.updateAttachment(t)}`)}_getAttachment(t){return Ji[t.toUpperCase()]}_setListeners(){this._config.trigger.split(" ").forEach((t=>{if("click"===t)j.on(this._element,this.constructor.Event.CLICK,this._config.selector,(t=>this.toggle(t)));else if("manual"!==t){const e=t===hn?this.constructor.Event.MOUSEENTER:this.constructor.Event.FOCUSIN,i=t===hn?this.constructor.Event.MOUSELEAVE:this.constructor.Event.FOCUSOUT;j.on(this._element,e,this._config.selector,(t=>this._enter(t))),j.on(this._element,i,this._config.selector,(t=>this._leave(t)))}})),this._hideModalHandler=()=>{this._element&&this.hide()},j.on(this._element.closest(ln),cn,this._hideModalHandler),this._config.selector?this._config={...this._config,trigger:"manual",selector:""}:this._fixTitle()}_fixTitle(){const t=this._element.getAttribute("title"),e=typeof this._element.getAttribute("data-bs-original-title");(t||"string"!==e)&&(this._element.setAttribute("data-bs-original-title",t||""),!t||this._element.getAttribute("aria-label")||this._element.textContent||this._element.setAttribute("aria-label",t),this._element.setAttribute("title",""))}_enter(t,e){e=this._initializeOnDelegatedTarget(t,e),t&&(e._activeTrigger["focusin"===t.type?dn:hn]=!0),e.getTipElement().classList.contains(sn)||e._hoverState===on?e._hoverState=on:(clearTimeout(e._timeout),e._hoverState=on,e._config.delay&&e._config.delay.show?e._timeout=setTimeout((()=>{e._hoverState===on&&e.show()}),e._config.delay.show):e.show())}_leave(t,e){e=this._initializeOnDelegatedTarget(t,e),t&&(e._activeTrigger["focusout"===t.type?dn:hn]=e._element.contains(t.relatedTarget)),e._isWithActiveTrigger()||(clearTimeout(e._timeout),e._hoverState=rn,e._config.delay&&e._config.delay.hide?e._timeout=setTimeout((()=>{e._hoverState===rn&&e.hide()}),e._config.delay.hide):e.hide())}_isWithActiveTrigger(){for(const t in this._activeTrigger)if(this._activeTrigger[t])return!0;return!1}_getConfig(t){const e=U.getDataAttributes(this._element);return Object.keys(e).forEach((t=>{Gi.has(t)&&delete e[t]})),(t={...this.constructor.Default,...e,..."object"==typeof t&&t?t:{}}).container=!1===t.container?document.body:r(t.container),"number"==typeof t.delay&&(t.delay={show:t.delay,hide:t.delay}),"number"==typeof t.title&&(t.title=t.title.toString()),"number"==typeof t.content&&(t.content=t.content.toString()),a(Qi,t,this.constructor.DefaultType),t.sanitize&&(t.template=Yi(t.template,t.allowList,t.sanitizeFn)),t}_getDelegateConfig(){const t={};for(const e in this._config)this.constructor.Default[e]!==this._config[e]&&(t[e]=this._config[e]);return t}_cleanTipClass(){const t=this.getTipElement(),e=new 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mode 100644 index 0000000..d9fd98f --- /dev/null +++ b/bs/.development/003LinearModel_files/libs/quarto-html/quarto-syntax-highlighting.css @@ -0,0 +1,203 @@ +/* quarto syntax highlight colors */ +:root { + --quarto-hl-ot-color: #003B4F; + --quarto-hl-at-color: #657422; + --quarto-hl-ss-color: #20794D; + --quarto-hl-an-color: #5E5E5E; + --quarto-hl-fu-color: #4758AB; + --quarto-hl-st-color: #20794D; + --quarto-hl-cf-color: #003B4F; + --quarto-hl-op-color: #5E5E5E; + --quarto-hl-er-color: #AD0000; + --quarto-hl-bn-color: #AD0000; + --quarto-hl-al-color: #AD0000; + --quarto-hl-va-color: #111111; + --quarto-hl-bu-color: inherit; + --quarto-hl-ex-color: inherit; + --quarto-hl-pp-color: #AD0000; + --quarto-hl-in-color: #5E5E5E; + --quarto-hl-vs-color: #20794D; + --quarto-hl-wa-color: #5E5E5E; + --quarto-hl-do-color: #5E5E5E; + --quarto-hl-im-color: #00769E; + --quarto-hl-ch-color: #20794D; + --quarto-hl-dt-color: #AD0000; + --quarto-hl-fl-color: #AD0000; + --quarto-hl-co-color: #5E5E5E; + --quarto-hl-cv-color: #5E5E5E; + --quarto-hl-cn-color: #8f5902; + --quarto-hl-sc-color: #5E5E5E; + --quarto-hl-dv-color: #AD0000; + --quarto-hl-kw-color: #003B4F; +} + +/* other quarto variables */ +:root { + --quarto-font-monospace: SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace; +} + +pre > code.sourceCode > span { + color: #003B4F; +} + +code span { + color: #003B4F; +} + +code.sourceCode > span { + color: #003B4F; +} + +div.sourceCode, +div.sourceCode pre.sourceCode { + color: #003B4F; +} + +code span.ot { + color: #003B4F; + font-style: inherit; +} + +code span.at { + color: #657422; + font-style: inherit; +} + +code span.ss { + color: #20794D; + font-style: inherit; +} + +code span.an { + color: #5E5E5E; + font-style: inherit; +} + +code span.fu { + color: #4758AB; + font-style: inherit; +} + +code span.st { + color: #20794D; + font-style: inherit; +} + +code span.cf { + color: #003B4F; + font-style: inherit; +} + +code span.op { + color: #5E5E5E; + font-style: inherit; +} + +code span.er { + color: #AD0000; + font-style: inherit; +} + +code span.bn { + color: #AD0000; + font-style: inherit; +} + +code span.al { + color: #AD0000; + font-style: inherit; +} + +code span.va { + color: #111111; + font-style: inherit; +} + +code span.bu { + font-style: inherit; +} + +code span.ex { + font-style: inherit; +} + +code span.pp { + color: #AD0000; + font-style: inherit; +} + +code span.in { + color: #5E5E5E; + font-style: inherit; +} + +code span.vs { + color: #20794D; + font-style: inherit; +} + +code span.wa { + color: #5E5E5E; + font-style: italic; +} + +code span.do { + color: #5E5E5E; + font-style: italic; +} + +code span.im { + color: #00769E; + font-style: inherit; +} + +code span.ch { + color: #20794D; + font-style: inherit; +} + +code span.dt { + color: #AD0000; + font-style: inherit; +} + +code span.fl { + color: #AD0000; + font-style: inherit; +} + +code span.co { + color: #5E5E5E; + font-style: inherit; +} + +code span.cv { + color: #5E5E5E; + font-style: italic; +} + +code span.cn { + color: #8f5902; + font-style: inherit; +} + +code span.sc { + color: #5E5E5E; + font-style: inherit; +} + +code span.dv { + color: #AD0000; + font-style: inherit; +} + +code span.kw { + color: #003B4F; + font-style: inherit; +} + +.prevent-inlining { + content: " { + // Find any conflicting margin elements and add margins to the + // top to prevent overlap + const marginChildren = window.document.querySelectorAll( + ".column-margin.column-container > * " + ); + + let lastBottom = 0; + for (const marginChild of marginChildren) { + if (marginChild.offsetParent !== null) { + // clear the top margin so we recompute it + marginChild.style.marginTop = null; + const top = marginChild.getBoundingClientRect().top + window.scrollY; + console.log({ + childtop: marginChild.getBoundingClientRect().top, + scroll: window.scrollY, + top, + lastBottom, + }); + if (top < lastBottom) { + const margin = lastBottom - top; + marginChild.style.marginTop = `${margin}px`; + } + const styles = window.getComputedStyle(marginChild); + const marginTop = parseFloat(styles["marginTop"]); + + console.log({ + top, + height: marginChild.getBoundingClientRect().height, + marginTop, + total: top + marginChild.getBoundingClientRect().height + marginTop, + }); + lastBottom = top + marginChild.getBoundingClientRect().height + marginTop; + } + } +}; + +window.document.addEventListener("DOMContentLoaded", function (_event) { + // Recompute the position of margin elements anytime the body size changes + if (window.ResizeObserver) { + const resizeObserver = new window.ResizeObserver( + throttle(layoutMarginEls, 50) + ); + resizeObserver.observe(window.document.body); + } + + const tocEl = window.document.querySelector('nav.toc-active[role="doc-toc"]'); + const sidebarEl = window.document.getElementById("quarto-sidebar"); + const leftTocEl = window.document.getElementById("quarto-sidebar-toc-left"); + const marginSidebarEl = window.document.getElementById( + "quarto-margin-sidebar" + ); + // function to determine whether the element has a previous sibling that is active + const prevSiblingIsActiveLink = (el) => { + const sibling = el.previousElementSibling; + if (sibling && sibling.tagName === "A") { + return sibling.classList.contains("active"); + } else { + return false; + } + }; + + // fire slideEnter for bootstrap tab activations (for htmlwidget resize behavior) + function fireSlideEnter(e) { + const event = window.document.createEvent("Event"); + event.initEvent("slideenter", true, true); + window.document.dispatchEvent(event); + } + const tabs = window.document.querySelectorAll('a[data-bs-toggle="tab"]'); + tabs.forEach((tab) => { + tab.addEventListener("shown.bs.tab", fireSlideEnter); + }); + + // fire slideEnter for tabby tab activations (for htmlwidget resize behavior) + document.addEventListener("tabby", fireSlideEnter, false); + + // Track scrolling and mark TOC links as active + // get table of contents and sidebar (bail if we don't have at least one) + const tocLinks = tocEl + ? [...tocEl.querySelectorAll("a[data-scroll-target]")] + : []; + const makeActive = (link) => tocLinks[link].classList.add("active"); + const removeActive = (link) => tocLinks[link].classList.remove("active"); + const removeAllActive = () => + [...Array(tocLinks.length).keys()].forEach((link) => removeActive(link)); + + // activate the anchor for a section associated with this TOC entry + tocLinks.forEach((link) => { + link.addEventListener("click", () => { + if (link.href.indexOf("#") !== -1) { + const anchor = link.href.split("#")[1]; + const heading = window.document.querySelector( + `[data-anchor-id=${anchor}]` + ); + if (heading) { + // Add the class + heading.classList.add("reveal-anchorjs-link"); + + // function to show the anchor + const handleMouseout = () => { + heading.classList.remove("reveal-anchorjs-link"); + heading.removeEventListener("mouseout", handleMouseout); + }; + + // add a function to clear the anchor when the user mouses out of it + heading.addEventListener("mouseout", handleMouseout); + } + } + }); + }); + + const sections = tocLinks.map((link) => { + const target = link.getAttribute("data-scroll-target"); + if (target.startsWith("#")) { + return window.document.getElementById(decodeURI(`${target.slice(1)}`)); + } else { + return window.document.querySelector(decodeURI(`${target}`)); + } + }); + + const sectionMargin = 200; + let currentActive = 0; + // track whether we've initialized state the first time + let init = false; + + const updateActiveLink = () => { + // The index from bottom to top (e.g. reversed list) + let sectionIndex = -1; + if ( + window.innerHeight + window.pageYOffset >= + window.document.body.offsetHeight + ) { + sectionIndex = 0; + } else { + sectionIndex = [...sections].reverse().findIndex((section) => { + if (section) { + return window.pageYOffset >= section.offsetTop - sectionMargin; + } else { + return false; + } + }); + } + if (sectionIndex > -1) { + const current = sections.length - sectionIndex - 1; + if (current !== currentActive) { + removeAllActive(); + currentActive = current; + makeActive(current); + if (init) { + window.dispatchEvent(sectionChanged); + } + init = true; + } + } + }; + + const inHiddenRegion = (top, bottom, hiddenRegions) => { + for (const region of hiddenRegions) { + if (top <= region.bottom && bottom >= region.top) { + return true; + } + } + return false; + }; + + const categorySelector = "header.quarto-title-block .quarto-category"; + const activateCategories = (href) => { + // Find any categories + // Surround them with a link pointing back to: + // #category=Authoring + try { + const categoryEls = window.document.querySelectorAll(categorySelector); + for (const categoryEl of categoryEls) { + const categoryText = categoryEl.textContent; + if (categoryText) { + const link = `${href}#category=${encodeURIComponent(categoryText)}`; + const linkEl = window.document.createElement("a"); + linkEl.setAttribute("href", link); + for (const child of categoryEl.childNodes) { + linkEl.append(child); + } + categoryEl.appendChild(linkEl); + } + } + } catch { + // Ignore errors + } + }; + function hasTitleCategories() { + return window.document.querySelector(categorySelector) !== null; + } + + function offsetRelativeUrl(url) { + const offset = getMeta("quarto:offset"); + return offset ? offset + url : url; + } + + function offsetAbsoluteUrl(url) { + const offset = getMeta("quarto:offset"); + const baseUrl = new URL(offset, window.location); + + const projRelativeUrl = url.replace(baseUrl, ""); + if (projRelativeUrl.startsWith("/")) { + return projRelativeUrl; + } else { + return "/" + projRelativeUrl; + } + } + + // read a meta tag value + function getMeta(metaName) { + const metas = window.document.getElementsByTagName("meta"); + for (let i = 0; i < metas.length; i++) { + if (metas[i].getAttribute("name") === metaName) { + return metas[i].getAttribute("content"); + } + } + return ""; + } + + async function findAndActivateCategories() { + const currentPagePath = offsetAbsoluteUrl(window.location.href); + const response = await fetch(offsetRelativeUrl("listings.json")); + if (response.status == 200) { + return response.json().then(function (listingPaths) { + const listingHrefs = []; + for (const listingPath of listingPaths) { + const pathWithoutLeadingSlash = listingPath.listing.substring(1); + for (const item of listingPath.items) { + if ( + item === currentPagePath || + item === currentPagePath + "index.html" + ) { + // Resolve this path against the offset to be sure + // we already are using the correct path to the listing + // (this adjusts the listing urls to be rooted against + // whatever root the page is actually running against) + const relative = offsetRelativeUrl(pathWithoutLeadingSlash); + const baseUrl = window.location; + const resolvedPath = new URL(relative, baseUrl); + listingHrefs.push(resolvedPath.pathname); + break; + } + } + } + + // Look up the tree for a nearby linting and use that if we find one + const nearestListing = findNearestParentListing( + offsetAbsoluteUrl(window.location.pathname), + listingHrefs + ); + if (nearestListing) { + activateCategories(nearestListing); + } else { + // See if the referrer is a listing page for this item + const referredRelativePath = offsetAbsoluteUrl(document.referrer); + const referrerListing = listingHrefs.find((listingHref) => { + const isListingReferrer = + listingHref === referredRelativePath || + listingHref === referredRelativePath + "index.html"; + return isListingReferrer; + }); + + if (referrerListing) { + // Try to use the referrer if possible + activateCategories(referrerListing); + } else if (listingHrefs.length > 0) { + // Otherwise, just fall back to the first listing + activateCategories(listingHrefs[0]); + } + } + }); + } + } + if (hasTitleCategories()) { + findAndActivateCategories(); + } + + const findNearestParentListing = (href, listingHrefs) => { + if (!href || !listingHrefs) { + return undefined; + } + // Look up the tree for a nearby linting and use that if we find one + const relativeParts = href.substring(1).split("/"); + while (relativeParts.length > 0) { + const path = relativeParts.join("/"); + for (const listingHref of listingHrefs) { + if (listingHref.startsWith(path)) { + return listingHref; + } + } + relativeParts.pop(); + } + + return undefined; + }; + + const manageSidebarVisiblity = (el, placeholderDescriptor) => { + let isVisible = true; + let elRect; + + return (hiddenRegions) => { + if (el === null) { + return; + } + + // Find the last element of the TOC + const lastChildEl = el.lastElementChild; + + if (lastChildEl) { + // Converts the sidebar to a menu + const convertToMenu = () => { + for (const child of el.children) { + child.style.opacity = 0; + child.style.overflow = "hidden"; + } + + nexttick(() => { + const toggleContainer = window.document.createElement("div"); + toggleContainer.style.width = "100%"; + toggleContainer.classList.add("zindex-over-content"); + toggleContainer.classList.add("quarto-sidebar-toggle"); + toggleContainer.classList.add("headroom-target"); // Marks this to be managed by headeroom + toggleContainer.id = placeholderDescriptor.id; + toggleContainer.style.position = "fixed"; + + const toggleIcon = window.document.createElement("i"); + toggleIcon.classList.add("quarto-sidebar-toggle-icon"); + toggleIcon.classList.add("bi"); + toggleIcon.classList.add("bi-caret-down-fill"); + + const toggleTitle = window.document.createElement("div"); + const titleEl = window.document.body.querySelector( + placeholderDescriptor.titleSelector + ); + if (titleEl) { + toggleTitle.append( + titleEl.textContent || titleEl.innerText, + toggleIcon + ); + } + toggleTitle.classList.add("zindex-over-content"); + toggleTitle.classList.add("quarto-sidebar-toggle-title"); + toggleContainer.append(toggleTitle); + + const toggleContents = window.document.createElement("div"); + toggleContents.classList = el.classList; + toggleContents.classList.add("zindex-over-content"); + toggleContents.classList.add("quarto-sidebar-toggle-contents"); + for (const child of el.children) { + if (child.id === "toc-title") { + continue; + } + + const clone = child.cloneNode(true); + clone.style.opacity = 1; + clone.style.display = null; + toggleContents.append(clone); + } + toggleContents.style.height = "0px"; + const positionToggle = () => { + // position the element (top left of parent, same width as parent) + if (!elRect) { + elRect = el.getBoundingClientRect(); + } + toggleContainer.style.left = `${elRect.left}px`; + toggleContainer.style.top = `${elRect.top}px`; + toggleContainer.style.width = `${elRect.width}px`; + }; + positionToggle(); + + toggleContainer.append(toggleContents); + el.parentElement.prepend(toggleContainer); + + // Process clicks + let tocShowing = false; + // Allow the caller to control whether this is dismissed + // when it is clicked (e.g. sidebar navigation supports + // opening and closing the nav tree, so don't dismiss on click) + const clickEl = placeholderDescriptor.dismissOnClick + ? toggleContainer + : toggleTitle; + + const closeToggle = () => { + if (tocShowing) { + toggleContainer.classList.remove("expanded"); + toggleContents.style.height = "0px"; + tocShowing = false; + } + }; + + // Get rid of any expanded toggle if the user scrolls + window.document.addEventListener( + "scroll", + throttle(() => { + closeToggle(); + }, 50) + ); + + // Handle positioning of the toggle + window.addEventListener( + "resize", + throttle(() => { + elRect = undefined; + positionToggle(); + }, 50) + ); + + window.addEventListener("quarto-hrChanged", () => { + elRect = undefined; + }); + + // Process the click + clickEl.onclick = () => { + if (!tocShowing) { + toggleContainer.classList.add("expanded"); + toggleContents.style.height = null; + tocShowing = true; + } else { + closeToggle(); + } + }; + }); + }; + + // Converts a sidebar from a menu back to a sidebar + const convertToSidebar = () => { + for (const child of el.children) { + child.style.opacity = 1; + child.style.overflow = null; + } + + const placeholderEl = window.document.getElementById( + placeholderDescriptor.id + ); + if (placeholderEl) { + placeholderEl.remove(); + } + + el.classList.remove("rollup"); + }; + + if (isReaderMode()) { + convertToMenu(); + isVisible = false; + } else { + // Find the top and bottom o the element that is being managed + const elTop = el.offsetTop; + const elBottom = + elTop + lastChildEl.offsetTop + lastChildEl.offsetHeight; + + if (!isVisible) { + // If the element is current not visible reveal if there are + // no conflicts with overlay regions + if (!inHiddenRegion(elTop, elBottom, hiddenRegions)) { + convertToSidebar(); + isVisible = true; + } + } else { + // If the element is visible, hide it if it conflicts with overlay regions + // and insert a placeholder toggle (or if we're in reader mode) + if (inHiddenRegion(elTop, elBottom, hiddenRegions)) { + convertToMenu(); + isVisible = false; + } + } + } + } + }; + }; + + const tabEls = document.querySelectorAll('a[data-bs-toggle="tab"]'); + for (const tabEl of tabEls) { + const id = tabEl.getAttribute("data-bs-target"); + if (id) { + const columnEl = document.querySelector( + `${id} .column-margin, .tabset-margin-content` + ); + if (columnEl) + tabEl.addEventListener("shown.bs.tab", function (event) { + const el = event.srcElement; + if (el) { + const visibleCls = `${el.id}-margin-content`; + // walk up until we find a parent tabset + let panelTabsetEl = el.parentElement; + while (panelTabsetEl) { + if (panelTabsetEl.classList.contains("panel-tabset")) { + break; + } + panelTabsetEl = panelTabsetEl.parentElement; + } + + if (panelTabsetEl) { + const prevSib = panelTabsetEl.previousElementSibling; + if ( + prevSib && + prevSib.classList.contains("tabset-margin-container") + ) { + const childNodes = prevSib.querySelectorAll( + ".tabset-margin-content" + ); + for (const childEl of childNodes) { + if (childEl.classList.contains(visibleCls)) { + childEl.classList.remove("collapse"); + } else { + childEl.classList.add("collapse"); + } + } + } + } + } + + layoutMarginEls(); + }); + } + } + + // Manage the visibility of the toc and the sidebar + const marginScrollVisibility = manageSidebarVisiblity(marginSidebarEl, { + id: "quarto-toc-toggle", + titleSelector: "#toc-title", + dismissOnClick: true, + }); + const sidebarScrollVisiblity = manageSidebarVisiblity(sidebarEl, { + id: "quarto-sidebarnav-toggle", + titleSelector: ".title", + dismissOnClick: false, + }); + let tocLeftScrollVisibility; + if (leftTocEl) { + tocLeftScrollVisibility = manageSidebarVisiblity(leftTocEl, { + id: "quarto-lefttoc-toggle", + titleSelector: "#toc-title", + dismissOnClick: true, + }); + } + + // Find the first element that uses formatting in special columns + const conflictingEls = window.document.body.querySelectorAll( + '[class^="column-"], [class*=" column-"], aside, [class*="margin-caption"], [class*=" margin-caption"], [class*="margin-ref"], [class*=" margin-ref"]' + ); + + // Filter all the possibly conflicting elements into ones + // the do conflict on the left or ride side + const arrConflictingEls = Array.from(conflictingEls); + const leftSideConflictEls = arrConflictingEls.filter((el) => { + if (el.tagName === "ASIDE") { + return false; + } + return Array.from(el.classList).find((className) => { + return ( + className !== "column-body" && + className.startsWith("column-") && + !className.endsWith("right") && + !className.endsWith("container") && + className !== "column-margin" + ); + }); + }); + const rightSideConflictEls = arrConflictingEls.filter((el) => { + if (el.tagName === "ASIDE") { + return true; + } + + const hasMarginCaption = Array.from(el.classList).find((className) => { + return className == "margin-caption"; + }); + if (hasMarginCaption) { + return true; + } + + return Array.from(el.classList).find((className) => { + return ( + className !== "column-body" && + !className.endsWith("container") && + className.startsWith("column-") && + !className.endsWith("left") + ); + }); + }); + + const kOverlapPaddingSize = 10; + function toRegions(els) { + return els.map((el) => { + const boundRect = el.getBoundingClientRect(); + const top = + boundRect.top + + document.documentElement.scrollTop - + kOverlapPaddingSize; + return { + top, + bottom: top + el.scrollHeight + 2 * kOverlapPaddingSize, + }; + }); + } + + let hasObserved = false; + const visibleItemObserver = (els) => { + let visibleElements = [...els]; + const intersectionObserver = new IntersectionObserver( + (entries, _observer) => { + entries.forEach((entry) => { + if (entry.isIntersecting) { + if (visibleElements.indexOf(entry.target) === -1) { + visibleElements.push(entry.target); + } + } else { + visibleElements = visibleElements.filter((visibleEntry) => { + return visibleEntry !== entry; + }); + } + }); + + if (!hasObserved) { + hideOverlappedSidebars(); + } + hasObserved = true; + }, + {} + ); + els.forEach((el) => { + intersectionObserver.observe(el); + }); + + return { + getVisibleEntries: () => { + return visibleElements; + }, + }; + }; + + const rightElementObserver = visibleItemObserver(rightSideConflictEls); + const leftElementObserver = visibleItemObserver(leftSideConflictEls); + + const hideOverlappedSidebars = () => { + marginScrollVisibility(toRegions(rightElementObserver.getVisibleEntries())); + sidebarScrollVisiblity(toRegions(leftElementObserver.getVisibleEntries())); + if (tocLeftScrollVisibility) { + tocLeftScrollVisibility( + toRegions(leftElementObserver.getVisibleEntries()) + ); + } + }; + + window.quartoToggleReader = () => { + // Applies a slow class (or removes it) + // to update the transition speed + const slowTransition = (slow) => { + const manageTransition = (id, slow) => { + const el = document.getElementById(id); + if (el) { + if (slow) { + el.classList.add("slow"); + } else { + el.classList.remove("slow"); + } + } + }; + + manageTransition("TOC", slow); + manageTransition("quarto-sidebar", slow); + }; + const readerMode = !isReaderMode(); + setReaderModeValue(readerMode); + + // If we're entering reader mode, slow the transition + if (readerMode) { + slowTransition(readerMode); + } + highlightReaderToggle(readerMode); + hideOverlappedSidebars(); + + // If we're exiting reader mode, restore the non-slow transition + if (!readerMode) { + slowTransition(!readerMode); + } + }; + + const highlightReaderToggle = (readerMode) => { + const els = document.querySelectorAll(".quarto-reader-toggle"); + if (els) { + els.forEach((el) => { + if (readerMode) { + el.classList.add("reader"); + } else { + el.classList.remove("reader"); + } + }); + } + }; + + const setReaderModeValue = (val) => { + if (window.location.protocol !== "file:") { + window.localStorage.setItem("quarto-reader-mode", val); + } else { + localReaderMode = val; + } + }; + + const isReaderMode = () => { + if (window.location.protocol !== "file:") { + return window.localStorage.getItem("quarto-reader-mode") === "true"; + } else { + return localReaderMode; + } + }; + let localReaderMode = null; + + const tocOpenDepthStr = tocEl?.getAttribute("data-toc-expanded"); + const tocOpenDepth = tocOpenDepthStr ? Number(tocOpenDepthStr) : 1; + + // Walk the TOC and collapse/expand nodes + // Nodes are expanded if: + // - they are top level + // - they have children that are 'active' links + // - they are directly below an link that is 'active' + const walk = (el, depth) => { + // Tick depth when we enter a UL + if (el.tagName === "UL") { + depth = depth + 1; + } + + // It this is active link + let isActiveNode = false; + if (el.tagName === "A" && el.classList.contains("active")) { + isActiveNode = true; + } + + // See if there is an active child to this element + let hasActiveChild = false; + for (child of el.children) { + hasActiveChild = walk(child, depth) || hasActiveChild; + } + + // Process the collapse state if this is an UL + if (el.tagName === "UL") { + if (tocOpenDepth === -1 && depth > 1) { + el.classList.add("collapse"); + } else if ( + depth <= tocOpenDepth || + hasActiveChild || + prevSiblingIsActiveLink(el) + ) { + el.classList.remove("collapse"); + } else { + el.classList.add("collapse"); + } + + // untick depth when we leave a UL + depth = depth - 1; + } + return hasActiveChild || isActiveNode; + }; + + // walk the TOC and expand / collapse any items that should be shown + + if (tocEl) { + walk(tocEl, 0); + updateActiveLink(); + } + + // Throttle the scroll event and walk peridiocally + window.document.addEventListener( + "scroll", + throttle(() => { + if (tocEl) { + updateActiveLink(); + walk(tocEl, 0); + } + if (!isReaderMode()) { + hideOverlappedSidebars(); + } + }, 5) + ); + window.addEventListener( + "resize", + throttle(() => { + if (!isReaderMode()) { + hideOverlappedSidebars(); + } + }, 10) + ); + hideOverlappedSidebars(); + highlightReaderToggle(isReaderMode()); +}); + +// grouped tabsets +window.addEventListener("pageshow", (_event) => { + function getTabSettings() { + const data = localStorage.getItem("quarto-persistent-tabsets-data"); + if (!data) { + localStorage.setItem("quarto-persistent-tabsets-data", "{}"); + return {}; + } + if (data) { + return JSON.parse(data); + } + } + + function setTabSettings(data) { + localStorage.setItem( + "quarto-persistent-tabsets-data", + JSON.stringify(data) + ); + } + + function setTabState(groupName, groupValue) { + const data = getTabSettings(); + data[groupName] = groupValue; + setTabSettings(data); + } + + function toggleTab(tab, active) { + const tabPanelId = tab.getAttribute("aria-controls"); + const tabPanel = document.getElementById(tabPanelId); + if (active) { + tab.classList.add("active"); + tabPanel.classList.add("active"); + } else { + tab.classList.remove("active"); + tabPanel.classList.remove("active"); + } + } + + function toggleAll(selectedGroup, selectorsToSync) { + for (const [thisGroup, tabs] of Object.entries(selectorsToSync)) { + const active = selectedGroup === thisGroup; + for (const tab of tabs) { + toggleTab(tab, active); + } + } + } + + function findSelectorsToSyncByLanguage() { + const result = {}; + const tabs = Array.from( + document.querySelectorAll(`div[data-group] a[id^='tabset-']`) + ); + for (const item of tabs) { + const div = item.parentElement.parentElement.parentElement; + const group = div.getAttribute("data-group"); + if (!result[group]) { + result[group] = {}; + } + const selectorsToSync = result[group]; + const value = item.innerHTML; + if (!selectorsToSync[value]) { + selectorsToSync[value] = []; + } + selectorsToSync[value].push(item); + } + return result; + } + + function setupSelectorSync() { + const selectorsToSync = findSelectorsToSyncByLanguage(); + Object.entries(selectorsToSync).forEach(([group, tabSetsByValue]) => { + Object.entries(tabSetsByValue).forEach(([value, items]) => { + items.forEach((item) => { + item.addEventListener("click", (_event) => { + setTabState(group, value); + toggleAll(value, selectorsToSync[group]); + }); + }); + }); + }); + return selectorsToSync; + } + + const selectorsToSync = setupSelectorSync(); + for (const [group, selectedName] of Object.entries(getTabSettings())) { + const selectors = selectorsToSync[group]; + // it's possible that stale state gives us empty selections, so we explicitly check here. + if (selectors) { + toggleAll(selectedName, selectors); + } + } +}); + +function throttle(func, wait) { + let waiting = false; + return function () { + if (!waiting) { + func.apply(this, arguments); + waiting = true; + setTimeout(function () { + waiting = false; + }, wait); + } + }; +} + +function nexttick(func) { + return setTimeout(func, 0); +} diff --git a/bs/.development/003LinearModel_files/libs/quarto-html/tippy.css b/bs/.development/003LinearModel_files/libs/quarto-html/tippy.css new file mode 100644 index 0000000..e6ae635 --- /dev/null +++ b/bs/.development/003LinearModel_files/libs/quarto-html/tippy.css @@ -0,0 +1 @@ +.tippy-box[data-animation=fade][data-state=hidden]{opacity:0}[data-tippy-root]{max-width:calc(100vw - 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b/bs/.development/004GeneralisedLinearModel.html similarity index 67% rename from bs/.development/Regression.html rename to bs/.development/004GeneralisedLinearModel.html index fda1343..f8894fe 100644 --- a/bs/.development/Regression.html +++ b/bs/.development/004GeneralisedLinearModel.html @@ -57,16 +57,16 @@ - - - - - - - - - - + + + + + + + + + + @@ -96,12 +96,27 @@

Regression: maximum likelihood by hand

-
-

Maximum likelihood estimation

+
+

Regression & Maximum likelihood estimation

We calculate for each entry of the response variable the probability that this value is taken from a distribution with specific parameters. For example we can calculate the probability that a value \(y_i\) is taken from a poisson distribution with a specific mean \(\lambda\). This calculation is in R done via \(dpois(y_i, lambda)\). Afterwards the values are logaritmized and summed up. This sum is called log-likelihood. The goal is to maximize this sum.

-
data(InsectSprays)
-summary(InsectSprays)
+
library(FAwR)
+
+
Loading required package: MASS
+
+
+
Loading required package: lattice
+
+
+
Loading required package: glpkAPI
+
+
+
using GLPK version 5.0
+
+
library(ggplot2)
+library(MASS)
+data(InsectSprays)
+summary(InsectSprays)
     count       spray 
  Min.   : 0.00   A:12  
@@ -111,7 +126,7 @@ 

Maximum likelihood estimation

3rd Qu.:14.25 E:12 Max. :26.00 F:12
-
head(InsectSprays)
+
head(InsectSprays)
  count spray
 1    10     A
@@ -121,20 +136,20 @@ 

Maximum likelihood estimation

5 14 A 6 12 A
-
predictors <- InsectSprays$spray
-m <- data.frame(letters = toupper(letters[1:7]), values = 1:7)
-predictors <- m[predictors, "values"]
-response <- InsectSprays$count
-ll <- function(params) {
-  sum(
-    dpois(
-      InsectSprays$count,
-      lambda = exp(params[1] + params[2]*predictors), log = TRUE
-    )
-  )
-}
-op <- optim(par = c(1, 0.1), fn = ll, control = list(fnscale = -1), hessian = TRUE)
-op
+
predictors <- InsectSprays$spray
+m <- data.frame(letters = toupper(letters[1:7]), values = 1:7)
+predictors <- m[predictors, "values"]
+response <- InsectSprays$count
+ll <- function(params) {
+  sum(
+    dpois(
+      InsectSprays$count,
+      lambda = exp(params[1] + params[2]*predictors), log = TRUE
+    )
+  )
+}
+op <- optim(par = c(1, 0.1), fn = ll, control = list(fnscale = -1), hessian = TRUE)
+op
$par
 [1]  2.47560089 -0.06587347
@@ -157,53 +172,53 @@ 

Maximum likelihood estimation

[1,] -684.0493 -2263.103 [2,] -2263.1029 -9466.483
-
# Standard errors of the parameters
-sqrt(diag(solve(-op$hessian)))
+
# Standard errors of the parameters
+sqrt(diag(solve(-op$hessian)))
[1] 0.08361806 0.02247758
-
# z values of the parameters
-z_values <- op$par / sqrt(diag(solve(-op$hessian)))
-z_values
+
# z values of the parameters
+z_values <- op$par / sqrt(diag(solve(-op$hessian)))
+z_values
[1] 29.60606 -2.93063
-
# calculate critical value of the t distribution. -2 because two parameters are optimized
-critical_values <- qt(0.05,
-    df = length(response) - 2,
-    lower.tail = FALSE
-  ) # Significant as the critical value is smaller than the t values
-critical_values
+
# calculate critical value of the t distribution. -2 because two parameters are optimized
+critical_values <- qt(0.05,
+    df = length(response) - 2,
+    lower.tail = FALSE
+  ) # Significant as the critical value is smaller than the t values
+critical_values
[1] 1.666914
-
# p values
-2 * (1 - pnorm(abs(z_values)))
+
# p values
+2 * (1 - pnorm(abs(z_values)))
[1] 0.000000000 0.003382749
-
# Anova
-# Null model
-null_ll <- function(params) {
-  sum(dpois(InsectSprays$count, lambda = exp(params[1]), log = TRUE))
-}
-op_null <- optim(par = c(1), fn = null_ll, control = list(fnscale = -1), hessian = TRUE)
+
# Anova
+# Null model
+null_ll <- function(params) {
+  sum(dpois(InsectSprays$count, lambda = exp(params[1]), log = TRUE))
+}
+op_null <- optim(par = c(1), fn = null_ll, control = list(fnscale = -1), hessian = TRUE)
Warning in optim(par = c(1), fn = null_ll, control = list(fnscale = -1), : one-dimensional optimization by Nelder-Mead is unreliable:
 use "Brent" or optimize() directly
-
null_loglik <- -op_null$value  # Negative log-likelihood of the null model
-# Full model
-full_loglik <- -op$value  # Negative log-likelihood of the full model
-# LRT statistic
-lr_stat <- 2 * (null_loglik - full_loglik)
-p_value_lr <- 1 - pchisq(lr_stat, 1) # df = 1
-p_value_lr
+
null_loglik <- -op_null$value  # Negative log-likelihood of the null model
+# Full model
+full_loglik <- -op$value  # Negative log-likelihood of the full model
+# LRT statistic
+lr_stat <- 2 * (null_loglik - full_loglik)
+p_value_lr <- 1 - pchisq(lr_stat, 1) # df = 1
+p_value_lr
[1] 0.003336856
-
m <- glm(response ~ predictors, family = poisson)
-m
+
m <- glm(response ~ predictors, family = poisson)
+m

 Call:  glm(formula = response ~ predictors, family = poisson)
@@ -216,7 +231,7 @@ 

Maximum likelihood estimation

Null Deviance: 409 Residual Deviance: 400.4 AIC: 670.7
-
summary(m)
+
summary(m)

 Call:
@@ -237,7 +252,7 @@ 

Maximum likelihood estimation

Number of Fisher Scoring iterations: 5
-
anova(m, test = "Chisq")
+
anova(m, test = "Chisq")
Analysis of Deviance Table
 
diff --git a/bs/.development/Regression.qmd b/bs/.development/004GeneralisedLinearModel.qmd
similarity index 95%
rename from bs/.development/Regression.qmd
rename to bs/.development/004GeneralisedLinearModel.qmd
index ef57cf6..a93c4f4 100644
--- a/bs/.development/Regression.qmd
+++ b/bs/.development/004GeneralisedLinearModel.qmd
@@ -3,7 +3,7 @@ title: "Regression: maximum likelihood by hand"
 output: html_document
 ---
 
-# Maximum likelihood estimation
+# Regression & Maximum likelihood estimation
 
 We calculate for each entry of the response variable the probability that this value
 is taken from a distribution with specific parameters. For example we can calculate the
@@ -13,6 +13,9 @@ This sum is called log-likelihood. The goal is to maximize this sum.
 
 
 ```{r Data, include = TRUE}
+library(FAwR)
+library(ggplot2)
+library(MASS)
 data(InsectSprays)
 summary(InsectSprays)
 head(InsectSprays)
diff --git a/bs/.development/004GeneralisedLinearModel_files/libs/bootstrap/bootstrap-icons.css b/bs/.development/004GeneralisedLinearModel_files/libs/bootstrap/bootstrap-icons.css
new file mode 100644
index 0000000..94f1940
--- /dev/null
+++ b/bs/.development/004GeneralisedLinearModel_files/libs/bootstrap/bootstrap-icons.css
@@ -0,0 +1,2018 @@
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diff --git a/bs/.development/004GeneralisedLinearModel_files/libs/bootstrap/bootstrap-icons.woff b/bs/.development/004GeneralisedLinearModel_files/libs/bootstrap/bootstrap-icons.woff
new file mode 100644
index 0000000..18d21d4
Binary files /dev/null and b/bs/.development/004GeneralisedLinearModel_files/libs/bootstrap/bootstrap-icons.woff differ
diff --git a/bs/.development/004GeneralisedLinearModel_files/libs/bootstrap/bootstrap.min.css b/bs/.development/004GeneralisedLinearModel_files/libs/bootstrap/bootstrap.min.css
new file mode 100644
index 0000000..a87b434
--- /dev/null
+++ b/bs/.development/004GeneralisedLinearModel_files/libs/bootstrap/bootstrap.min.css
@@ -0,0 +1,10 @@
+/*!
+ * Bootstrap v5.1.3 (https://getbootstrap.com/)
+ * Copyright 2011-2021 The Bootstrap Authors
+ * Copyright 2011-2021 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)
+ */:root{--bs-blue: #0d6efd;--bs-indigo: #6610f2;--bs-purple: #6f42c1;--bs-pink: #d63384;--bs-red: #dc3545;--bs-orange: #fd7e14;--bs-yellow: #ffc107;--bs-green: #198754;--bs-teal: #20c997;--bs-cyan: #0dcaf0;--bs-white: #ffffff;--bs-gray: #6c757d;--bs-gray-dark: #343a40;--bs-gray-100: #f8f9fa;--bs-gray-200: #e9ecef;--bs-gray-300: #dee2e6;--bs-gray-400: #ced4da;--bs-gray-500: #adb5bd;--bs-gray-600: #6c757d;--bs-gray-700: #495057;--bs-gray-800: #343a40;--bs-gray-900: #212529;--bs-default: #dee2e6;--bs-primary: #0d6efd;--bs-secondary: #6c757d;--bs-success: #198754;--bs-info: #0dcaf0;--bs-warning: #ffc107;--bs-danger: #dc3545;--bs-light: #f8f9fa;--bs-dark: #212529;--bs-default-rgb: 222, 226, 230;--bs-primary-rgb: 13, 110, 253;--bs-secondary-rgb: 108, 117, 125;--bs-success-rgb: 25, 135, 84;--bs-info-rgb: 13, 202, 240;--bs-warning-rgb: 255, 193, 7;--bs-danger-rgb: 220, 53, 69;--bs-light-rgb: 248, 249, 250;--bs-dark-rgb: 33, 37, 41;--bs-white-rgb: 255, 255, 255;--bs-black-rgb: 0, 0, 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Be={placement:"bottom",modifiers:[],strategy:"absolute"};function Re(){for(var t=arguments.length,e=new Array(t),i=0;ij.on(t,"mouseover",d))),this._element.focus(),this._element.setAttribute("aria-expanded",!0),this._menu.classList.add(Je),this._element.classList.add(Je),j.trigger(this._element,"shown.bs.dropdown",t)}hide(){if(c(this._element)||!this._isShown(this._menu))return;const t={relatedTarget:this._element};this._completeHide(t)}dispose(){this._popper&&this._popper.destroy(),super.dispose()}update(){this._inNavbar=this._detectNavbar(),this._popper&&this._popper.update()}_completeHide(t){j.trigger(this._element,"hide.bs.dropdown",t).defaultPrevented||("ontouchstart"in document.documentElement&&[].concat(...document.body.children).forEach((t=>j.off(t,"mouseover",d))),this._popper&&this._popper.destroy(),this._menu.classList.remove(Je),this._element.classList.remove(Je),this._element.setAttribute("aria-expanded","false"),U.removeDataAttribute(this._menu,"popper"),j.trigger(this._element,"hidden.bs.dropdown",t))}_getConfig(t){if(t={...this.constructor.Default,...U.getDataAttributes(this._element),...t},a(Ue,t,this.constructor.DefaultType),"object"==typeof t.reference&&!o(t.reference)&&"function"!=typeof t.reference.getBoundingClientRect)throw new TypeError(`${Ue.toUpperCase()}: Option "reference" provided type "object" without a required "getBoundingClientRect" method.`);return t}_createPopper(t){if(void 0===Fe)throw new TypeError("Bootstrap's dropdowns require Popper (https://popper.js.org)");let e=this._element;"parent"===this._config.reference?e=t:o(this._config.reference)?e=r(this._config.reference):"object"==typeof this._config.reference&&(e=this._config.reference);const i=this._getPopperConfig(),n=i.modifiers.find((t=>"applyStyles"===t.name&&!1===t.enabled));this._popper=qe(e,this._menu,i),n&&U.setDataAttribute(this._menu,"popper","static")}_isShown(t=this._element){return t.classList.contains(Je)}_getMenuElement(){return V.next(this._element,ei)[0]}_getPlacement(){const t=this._element.parentNode;if(t.classList.contains("dropend"))return ri;if(t.classList.contains("dropstart"))return ai;const e="end"===getComputedStyle(this._menu).getPropertyValue("--bs-position").trim();return t.classList.contains("dropup")?e?ni:ii:e?oi:si}_detectNavbar(){return null!==this._element.closest(".navbar")}_getOffset(){const{offset:t}=this._config;return"string"==typeof t?t.split(",").map((t=>Number.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_getPopperConfig(){const t={placement:this._getPlacement(),modifiers:[{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"offset",options:{offset:this._getOffset()}}]};return"static"===this._config.display&&(t.modifiers=[{name:"applyStyles",enabled:!1}]),{...t,..."function"==typeof this._config.popperConfig?this._config.popperConfig(t):this._config.popperConfig}}_selectMenuItem({key:t,target:e}){const i=V.find(".dropdown-menu .dropdown-item:not(.disabled):not(:disabled)",this._menu).filter(l);i.length&&v(i,e,t===Ye,!i.includes(e)).focus()}static jQueryInterface(t){return this.each((function(){const e=hi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}static clearMenus(t){if(t&&(2===t.button||"keyup"===t.type&&"Tab"!==t.key))return;const e=V.find(ti);for(let i=0,n=e.length;ie+t)),this._setElementAttributes(di,"paddingRight",(e=>e+t)),this._setElementAttributes(ui,"marginRight",(e=>e-t))}_disableOverFlow(){this._saveInitialAttribute(this._element,"overflow"),this._element.style.overflow="hidden"}_setElementAttributes(t,e,i){const n=this.getWidth();this._applyManipulationCallback(t,(t=>{if(t!==this._element&&window.innerWidth>t.clientWidth+n)return;this._saveInitialAttribute(t,e);const s=window.getComputedStyle(t)[e];t.style[e]=`${i(Number.parseFloat(s))}px`}))}reset(){this._resetElementAttributes(this._element,"overflow"),this._resetElementAttributes(this._element,"paddingRight"),this._resetElementAttributes(di,"paddingRight"),this._resetElementAttributes(ui,"marginRight")}_saveInitialAttribute(t,e){const i=t.style[e];i&&U.setDataAttribute(t,e,i)}_resetElementAttributes(t,e){this._applyManipulationCallback(t,(t=>{const i=U.getDataAttribute(t,e);void 0===i?t.style.removeProperty(e):(U.removeDataAttribute(t,e),t.style[e]=i)}))}_applyManipulationCallback(t,e){o(t)?e(t):V.find(t,this._element).forEach(e)}isOverflowing(){return this.getWidth()>0}}const pi={className:"modal-backdrop",isVisible:!0,isAnimated:!1,rootElement:"body",clickCallback:null},mi={className:"string",isVisible:"boolean",isAnimated:"boolean",rootElement:"(element|string)",clickCallback:"(function|null)"},gi="show",_i="mousedown.bs.backdrop";class bi{constructor(t){this._config=this._getConfig(t),this._isAppended=!1,this._element=null}show(t){this._config.isVisible?(this._append(),this._config.isAnimated&&u(this._getElement()),this._getElement().classList.add(gi),this._emulateAnimation((()=>{_(t)}))):_(t)}hide(t){this._config.isVisible?(this._getElement().classList.remove(gi),this._emulateAnimation((()=>{this.dispose(),_(t)}))):_(t)}_getElement(){if(!this._element){const t=document.createElement("div");t.className=this._config.className,this._config.isAnimated&&t.classList.add("fade"),this._element=t}return this._element}_getConfig(t){return(t={...pi,..."object"==typeof t?t:{}}).rootElement=r(t.rootElement),a("backdrop",t,mi),t}_append(){this._isAppended||(this._config.rootElement.append(this._getElement()),j.on(this._getElement(),_i,(()=>{_(this._config.clickCallback)})),this._isAppended=!0)}dispose(){this._isAppended&&(j.off(this._element,_i),this._element.remove(),this._isAppended=!1)}_emulateAnimation(t){b(t,this._getElement(),this._config.isAnimated)}}const vi={trapElement:null,autofocus:!0},yi={trapElement:"element",autofocus:"boolean"},wi=".bs.focustrap",Ei="backward";class Ai{constructor(t){this._config=this._getConfig(t),this._isActive=!1,this._lastTabNavDirection=null}activate(){const{trapElement:t,autofocus:e}=this._config;this._isActive||(e&&t.focus(),j.off(document,wi),j.on(document,"focusin.bs.focustrap",(t=>this._handleFocusin(t))),j.on(document,"keydown.tab.bs.focustrap",(t=>this._handleKeydown(t))),this._isActive=!0)}deactivate(){this._isActive&&(this._isActive=!1,j.off(document,wi))}_handleFocusin(t){const{target:e}=t,{trapElement:i}=this._config;if(e===document||e===i||i.contains(e))return;const n=V.focusableChildren(i);0===n.length?i.focus():this._lastTabNavDirection===Ei?n[n.length-1].focus():n[0].focus()}_handleKeydown(t){"Tab"===t.key&&(this._lastTabNavDirection=t.shiftKey?Ei:"forward")}_getConfig(t){return t={...vi,..."object"==typeof t?t:{}},a("focustrap",t,yi),t}}const Ti="modal",Oi="Escape",Ci={backdrop:!0,keyboard:!0,focus:!0},ki={backdrop:"(boolean|string)",keyboard:"boolean",focus:"boolean"},Li="hidden.bs.modal",xi="show.bs.modal",Di="resize.bs.modal",Si="click.dismiss.bs.modal",Ni="keydown.dismiss.bs.modal",Ii="mousedown.dismiss.bs.modal",Pi="modal-open",ji="show",Mi="modal-static";class Hi extends B{constructor(t,e){super(t),this._config=this._getConfig(e),this._dialog=V.findOne(".modal-dialog",this._element),this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._isShown=!1,this._ignoreBackdropClick=!1,this._isTransitioning=!1,this._scrollBar=new fi}static get Default(){return Ci}static get NAME(){return Ti}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||this._isTransitioning||j.trigger(this._element,xi,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._isAnimated()&&(this._isTransitioning=!0),this._scrollBar.hide(),document.body.classList.add(Pi),this._adjustDialog(),this._setEscapeEvent(),this._setResizeEvent(),j.on(this._dialog,Ii,(()=>{j.one(this._element,"mouseup.dismiss.bs.modal",(t=>{t.target===this._element&&(this._ignoreBackdropClick=!0)}))})),this._showBackdrop((()=>this._showElement(t))))}hide(){if(!this._isShown||this._isTransitioning)return;if(j.trigger(this._element,"hide.bs.modal").defaultPrevented)return;this._isShown=!1;const t=this._isAnimated();t&&(this._isTransitioning=!0),this._setEscapeEvent(),this._setResizeEvent(),this._focustrap.deactivate(),this._element.classList.remove(ji),j.off(this._element,Si),j.off(this._dialog,Ii),this._queueCallback((()=>this._hideModal()),this._element,t)}dispose(){[window,this._dialog].forEach((t=>j.off(t,".bs.modal"))),this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}handleUpdate(){this._adjustDialog()}_initializeBackDrop(){return new bi({isVisible:Boolean(this._config.backdrop),isAnimated:this._isAnimated()})}_initializeFocusTrap(){return new Ai({trapElement:this._element})}_getConfig(t){return t={...Ci,...U.getDataAttributes(this._element),..."object"==typeof t?t:{}},a(Ti,t,ki),t}_showElement(t){const e=this._isAnimated(),i=V.findOne(".modal-body",this._dialog);this._element.parentNode&&this._element.parentNode.nodeType===Node.ELEMENT_NODE||document.body.append(this._element),this._element.style.display="block",this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.scrollTop=0,i&&(i.scrollTop=0),e&&u(this._element),this._element.classList.add(ji),this._queueCallback((()=>{this._config.focus&&this._focustrap.activate(),this._isTransitioning=!1,j.trigger(this._element,"shown.bs.modal",{relatedTarget:t})}),this._dialog,e)}_setEscapeEvent(){this._isShown?j.on(this._element,Ni,(t=>{this._config.keyboard&&t.key===Oi?(t.preventDefault(),this.hide()):this._config.keyboard||t.key!==Oi||this._triggerBackdropTransition()})):j.off(this._element,Ni)}_setResizeEvent(){this._isShown?j.on(window,Di,(()=>this._adjustDialog())):j.off(window,Di)}_hideModal(){this._element.style.display="none",this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._isTransitioning=!1,this._backdrop.hide((()=>{document.body.classList.remove(Pi),this._resetAdjustments(),this._scrollBar.reset(),j.trigger(this._element,Li)}))}_showBackdrop(t){j.on(this._element,Si,(t=>{this._ignoreBackdropClick?this._ignoreBackdropClick=!1:t.target===t.currentTarget&&(!0===this._config.backdrop?this.hide():"static"===this._config.backdrop&&this._triggerBackdropTransition())})),this._backdrop.show(t)}_isAnimated(){return this._element.classList.contains("fade")}_triggerBackdropTransition(){if(j.trigger(this._element,"hidePrevented.bs.modal").defaultPrevented)return;const{classList:t,scrollHeight:e,style:i}=this._element,n=e>document.documentElement.clientHeight;!n&&"hidden"===i.overflowY||t.contains(Mi)||(n||(i.overflowY="hidden"),t.add(Mi),this._queueCallback((()=>{t.remove(Mi),n||this._queueCallback((()=>{i.overflowY=""}),this._dialog)}),this._dialog),this._element.focus())}_adjustDialog(){const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._scrollBar.getWidth(),i=e>0;(!i&&t&&!m()||i&&!t&&m())&&(this._element.style.paddingLeft=`${e}px`),(i&&!t&&!m()||!i&&t&&m())&&(this._element.style.paddingRight=`${e}px`)}_resetAdjustments(){this._element.style.paddingLeft="",this._element.style.paddingRight=""}static jQueryInterface(t,e){return this.each((function(){const i=Hi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===i[t])throw new TypeError(`No method named "${t}"`);i[t](e)}}))}}j.on(document,"click.bs.modal.data-api",'[data-bs-toggle="modal"]',(function(t){const e=n(this);["A","AREA"].includes(this.tagName)&&t.preventDefault(),j.one(e,xi,(t=>{t.defaultPrevented||j.one(e,Li,(()=>{l(this)&&this.focus()}))}));const i=V.findOne(".modal.show");i&&Hi.getInstance(i).hide(),Hi.getOrCreateInstance(e).toggle(this)})),R(Hi),g(Hi);const Bi="offcanvas",Ri={backdrop:!0,keyboard:!0,scroll:!1},Wi={backdrop:"boolean",keyboard:"boolean",scroll:"boolean"},$i="show",zi=".offcanvas.show",qi="hidden.bs.offcanvas";class Fi extends B{constructor(t,e){super(t),this._config=this._getConfig(e),this._isShown=!1,this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._addEventListeners()}static get NAME(){return Bi}static get Default(){return Ri}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||j.trigger(this._element,"show.bs.offcanvas",{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._element.style.visibility="visible",this._backdrop.show(),this._config.scroll||(new fi).hide(),this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.classList.add($i),this._queueCallback((()=>{this._config.scroll||this._focustrap.activate(),j.trigger(this._element,"shown.bs.offcanvas",{relatedTarget:t})}),this._element,!0))}hide(){this._isShown&&(j.trigger(this._element,"hide.bs.offcanvas").defaultPrevented||(this._focustrap.deactivate(),this._element.blur(),this._isShown=!1,this._element.classList.remove($i),this._backdrop.hide(),this._queueCallback((()=>{this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._element.style.visibility="hidden",this._config.scroll||(new fi).reset(),j.trigger(this._element,qi)}),this._element,!0)))}dispose(){this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}_getConfig(t){return t={...Ri,...U.getDataAttributes(this._element),..."object"==typeof t?t:{}},a(Bi,t,Wi),t}_initializeBackDrop(){return new bi({className:"offcanvas-backdrop",isVisible:this._config.backdrop,isAnimated:!0,rootElement:this._element.parentNode,clickCallback:()=>this.hide()})}_initializeFocusTrap(){return new Ai({trapElement:this._element})}_addEventListeners(){j.on(this._element,"keydown.dismiss.bs.offcanvas",(t=>{this._config.keyboard&&"Escape"===t.key&&this.hide()}))}static jQueryInterface(t){return this.each((function(){const e=Fi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t]||t.startsWith("_")||"constructor"===t)throw new TypeError(`No method named "${t}"`);e[t](this)}}))}}j.on(document,"click.bs.offcanvas.data-api",'[data-bs-toggle="offcanvas"]',(function(t){const e=n(this);if(["A","AREA"].includes(this.tagName)&&t.preventDefault(),c(this))return;j.one(e,qi,(()=>{l(this)&&this.focus()}));const i=V.findOne(zi);i&&i!==e&&Fi.getInstance(i).hide(),Fi.getOrCreateInstance(e).toggle(this)})),j.on(window,"load.bs.offcanvas.data-api",(()=>V.find(zi).forEach((t=>Fi.getOrCreateInstance(t).show())))),R(Fi),g(Fi);const Ui=new Set(["background","cite","href","itemtype","longdesc","poster","src","xlink:href"]),Vi=/^(?:(?:https?|mailto|ftp|tel|file|sms):|[^#&/:?]*(?:[#/?]|$))/i,Ki=/^data:(?:image\/(?:bmp|gif|jpeg|jpg|png|tiff|webp)|video\/(?:mpeg|mp4|ogg|webm)|audio\/(?:mp3|oga|ogg|opus));base64,[\d+/a-z]+=*$/i,Xi=(t,e)=>{const i=t.nodeName.toLowerCase();if(e.includes(i))return!Ui.has(i)||Boolean(Vi.test(t.nodeValue)||Ki.test(t.nodeValue));const n=e.filter((t=>t instanceof RegExp));for(let t=0,e=n.length;t{Xi(t,r)||i.removeAttribute(t.nodeName)}))}return n.body.innerHTML}const Qi="tooltip",Gi=new Set(["sanitize","allowList","sanitizeFn"]),Zi={animation:"boolean",template:"string",title:"(string|element|function)",trigger:"string",delay:"(number|object)",html:"boolean",selector:"(string|boolean)",placement:"(string|function)",offset:"(array|string|function)",container:"(string|element|boolean)",fallbackPlacements:"array",boundary:"(string|element)",customClass:"(string|function)",sanitize:"boolean",sanitizeFn:"(null|function)",allowList:"object",popperConfig:"(null|object|function)"},Ji={AUTO:"auto",TOP:"top",RIGHT:m()?"left":"right",BOTTOM:"bottom",LEFT:m()?"right":"left"},tn={animation:!0,template:'',trigger:"hover focus",title:"",delay:0,html:!1,selector:!1,placement:"top",offset:[0,0],container:!1,fallbackPlacements:["top","right","bottom","left"],boundary:"clippingParents",customClass:"",sanitize:!0,sanitizeFn:null,allowList:{"*":["class","dir","id","lang","role",/^aria-[\w-]*$/i],a:["target","href","title","rel"],area:[],b:[],br:[],col:[],code:[],div:[],em:[],hr:[],h1:[],h2:[],h3:[],h4:[],h5:[],h6:[],i:[],img:["src","srcset","alt","title","width","height"],li:[],ol:[],p:[],pre:[],s:[],small:[],span:[],sub:[],sup:[],strong:[],u:[],ul:[]},popperConfig:null},en={HIDE:"hide.bs.tooltip",HIDDEN:"hidden.bs.tooltip",SHOW:"show.bs.tooltip",SHOWN:"shown.bs.tooltip",INSERTED:"inserted.bs.tooltip",CLICK:"click.bs.tooltip",FOCUSIN:"focusin.bs.tooltip",FOCUSOUT:"focusout.bs.tooltip",MOUSEENTER:"mouseenter.bs.tooltip",MOUSELEAVE:"mouseleave.bs.tooltip"},nn="fade",sn="show",on="show",rn="out",an=".tooltip-inner",ln=".modal",cn="hide.bs.modal",hn="hover",dn="focus";class un extends B{constructor(t,e){if(void 0===Fe)throw new TypeError("Bootstrap's tooltips require Popper (https://popper.js.org)");super(t),this._isEnabled=!0,this._timeout=0,this._hoverState="",this._activeTrigger={},this._popper=null,this._config=this._getConfig(e),this.tip=null,this._setListeners()}static get Default(){return tn}static get NAME(){return Qi}static get Event(){return en}static get DefaultType(){return Zi}enable(){this._isEnabled=!0}disable(){this._isEnabled=!1}toggleEnabled(){this._isEnabled=!this._isEnabled}toggle(t){if(this._isEnabled)if(t){const e=this._initializeOnDelegatedTarget(t);e._activeTrigger.click=!e._activeTrigger.click,e._isWithActiveTrigger()?e._enter(null,e):e._leave(null,e)}else{if(this.getTipElement().classList.contains(sn))return void this._leave(null,this);this._enter(null,this)}}dispose(){clearTimeout(this._timeout),j.off(this._element.closest(ln),cn,this._hideModalHandler),this.tip&&this.tip.remove(),this._disposePopper(),super.dispose()}show(){if("none"===this._element.style.display)throw new Error("Please use show on visible elements");if(!this.isWithContent()||!this._isEnabled)return;const t=j.trigger(this._element,this.constructor.Event.SHOW),e=h(this._element),i=null===e?this._element.ownerDocument.documentElement.contains(this._element):e.contains(this._element);if(t.defaultPrevented||!i)return;"tooltip"===this.constructor.NAME&&this.tip&&this.getTitle()!==this.tip.querySelector(an).innerHTML&&(this._disposePopper(),this.tip.remove(),this.tip=null);const n=this.getTipElement(),s=(t=>{do{t+=Math.floor(1e6*Math.random())}while(document.getElementById(t));return t})(this.constructor.NAME);n.setAttribute("id",s),this._element.setAttribute("aria-describedby",s),this._config.animation&&n.classList.add(nn);const o="function"==typeof this._config.placement?this._config.placement.call(this,n,this._element):this._config.placement,r=this._getAttachment(o);this._addAttachmentClass(r);const{container:a}=this._config;H.set(n,this.constructor.DATA_KEY,this),this._element.ownerDocument.documentElement.contains(this.tip)||(a.append(n),j.trigger(this._element,this.constructor.Event.INSERTED)),this._popper?this._popper.update():this._popper=qe(this._element,n,this._getPopperConfig(r)),n.classList.add(sn);const l=this._resolvePossibleFunction(this._config.customClass);l&&n.classList.add(...l.split(" ")),"ontouchstart"in document.documentElement&&[].concat(...document.body.children).forEach((t=>{j.on(t,"mouseover",d)}));const c=this.tip.classList.contains(nn);this._queueCallback((()=>{const t=this._hoverState;this._hoverState=null,j.trigger(this._element,this.constructor.Event.SHOWN),t===rn&&this._leave(null,this)}),this.tip,c)}hide(){if(!this._popper)return;const t=this.getTipElement();if(j.trigger(this._element,this.constructor.Event.HIDE).defaultPrevented)return;t.classList.remove(sn),"ontouchstart"in document.documentElement&&[].concat(...document.body.children).forEach((t=>j.off(t,"mouseover",d))),this._activeTrigger.click=!1,this._activeTrigger.focus=!1,this._activeTrigger.hover=!1;const e=this.tip.classList.contains(nn);this._queueCallback((()=>{this._isWithActiveTrigger()||(this._hoverState!==on&&t.remove(),this._cleanTipClass(),this._element.removeAttribute("aria-describedby"),j.trigger(this._element,this.constructor.Event.HIDDEN),this._disposePopper())}),this.tip,e),this._hoverState=""}update(){null!==this._popper&&this._popper.update()}isWithContent(){return Boolean(this.getTitle())}getTipElement(){if(this.tip)return this.tip;const t=document.createElement("div");t.innerHTML=this._config.template;const e=t.children[0];return this.setContent(e),e.classList.remove(nn,sn),this.tip=e,this.tip}setContent(t){this._sanitizeAndSetContent(t,this.getTitle(),an)}_sanitizeAndSetContent(t,e,i){const n=V.findOne(i,t);e||!n?this.setElementContent(n,e):n.remove()}setElementContent(t,e){if(null!==t)return o(e)?(e=r(e),void(this._config.html?e.parentNode!==t&&(t.innerHTML="",t.append(e)):t.textContent=e.textContent)):void(this._config.html?(this._config.sanitize&&(e=Yi(e,this._config.allowList,this._config.sanitizeFn)),t.innerHTML=e):t.textContent=e)}getTitle(){const t=this._element.getAttribute("data-bs-original-title")||this._config.title;return this._resolvePossibleFunction(t)}updateAttachment(t){return"right"===t?"end":"left"===t?"start":t}_initializeOnDelegatedTarget(t,e){return e||this.constructor.getOrCreateInstance(t.delegateTarget,this._getDelegateConfig())}_getOffset(){const{offset:t}=this._config;return"string"==typeof t?t.split(",").map((t=>Number.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_resolvePossibleFunction(t){return"function"==typeof t?t.call(this._element):t}_getPopperConfig(t){const e={placement:t,modifiers:[{name:"flip",options:{fallbackPlacements:this._config.fallbackPlacements}},{name:"offset",options:{offset:this._getOffset()}},{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"arrow",options:{element:`.${this.constructor.NAME}-arrow`}},{name:"onChange",enabled:!0,phase:"afterWrite",fn:t=>this._handlePopperPlacementChange(t)}],onFirstUpdate:t=>{t.options.placement!==t.placement&&this._handlePopperPlacementChange(t)}};return{...e,..."function"==typeof this._config.popperConfig?this._config.popperConfig(e):this._config.popperConfig}}_addAttachmentClass(t){this.getTipElement().classList.add(`${this._getBasicClassPrefix()}-${this.updateAttachment(t)}`)}_getAttachment(t){return Ji[t.toUpperCase()]}_setListeners(){this._config.trigger.split(" 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this._element.getAttribute("data-bs-original-title");(t||"string"!==e)&&(this._element.setAttribute("data-bs-original-title",t||""),!t||this._element.getAttribute("aria-label")||this._element.textContent||this._element.setAttribute("aria-label",t),this._element.setAttribute("title",""))}_enter(t,e){e=this._initializeOnDelegatedTarget(t,e),t&&(e._activeTrigger["focusin"===t.type?dn:hn]=!0),e.getTipElement().classList.contains(sn)||e._hoverState===on?e._hoverState=on:(clearTimeout(e._timeout),e._hoverState=on,e._config.delay&&e._config.delay.show?e._timeout=setTimeout((()=>{e._hoverState===on&&e.show()}),e._config.delay.show):e.show())}_leave(t,e){e=this._initializeOnDelegatedTarget(t,e),t&&(e._activeTrigger["focusout"===t.type?dn:hn]=e._element.contains(t.relatedTarget)),e._isWithActiveTrigger()||(clearTimeout(e._timeout),e._hoverState=rn,e._config.delay&&e._config.delay.hide?e._timeout=setTimeout((()=>{e._hoverState===rn&&e.hide()}),e._config.delay.hide):e.hide())}_isWithActiveTrigger(){for(const t in this._activeTrigger)if(this._activeTrigger[t])return!0;return!1}_getConfig(t){const e=U.getDataAttributes(this._element);return Object.keys(e).forEach((t=>{Gi.has(t)&&delete e[t]})),(t={...this.constructor.Default,...e,..."object"==typeof t&&t?t:{}}).container=!1===t.container?document.body:r(t.container),"number"==typeof t.delay&&(t.delay={show:t.delay,hide:t.delay}),"number"==typeof t.title&&(t.title=t.title.toString()),"number"==typeof t.content&&(t.content=t.content.toString()),a(Qi,t,this.constructor.DefaultType),t.sanitize&&(t.template=Yi(t.template,t.allowList,t.sanitizeFn)),t}_getDelegateConfig(){const t={};for(const e in this._config)this.constructor.Default[e]!==this._config[e]&&(t[e]=this._config[e]);return t}_cleanTipClass(){const t=this.getTipElement(),e=new RegExp(`(^|\\s)${this._getBasicClassPrefix()}\\S+`,"g"),i=t.getAttribute("class").match(e);null!==i&&i.length>0&&i.map((t=>t.trim())).forEach((e=>t.classList.remove(e)))}_getBasicClassPrefix(){return"bs-tooltip"}_handlePopperPlacementChange(t){const{state:e}=t;e&&(this.tip=e.elements.popper,this._cleanTipClass(),this._addAttachmentClass(this._getAttachment(e.placement)))}_disposePopper(){this._popper&&(this._popper.destroy(),this._popper=null)}static jQueryInterface(t){return this.each((function(){const e=un.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}}g(un);const fn={...un.Default,placement:"right",offset:[0,8],trigger:"click",content:"",template:''},pn={...un.DefaultType,content:"(string|element|function)"},mn={HIDE:"hide.bs.popover",HIDDEN:"hidden.bs.popover",SHOW:"show.bs.popover",SHOWN:"shown.bs.popover",INSERTED:"inserted.bs.popover",CLICK:"click.bs.popover",FOCUSIN:"focusin.bs.popover",FOCUSOUT:"focusout.bs.popover",MOUSEENTER:"mouseenter.bs.popover",MOUSELEAVE:"mouseleave.bs.popover"};class gn extends un{static get Default(){return fn}static get NAME(){return"popover"}static get Event(){return mn}static get DefaultType(){return pn}isWithContent(){return this.getTitle()||this._getContent()}setContent(t){this._sanitizeAndSetContent(t,this.getTitle(),".popover-header"),this._sanitizeAndSetContent(t,this._getContent(),".popover-body")}_getContent(){return this._resolvePossibleFunction(this._config.content)}_getBasicClassPrefix(){return"bs-popover"}static jQueryInterface(t){return this.each((function(){const 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t=this._scrollElement===this._scrollElement.window?"offset":En,e="auto"===this._config.method?t:this._config.method,n=e===En?this._getScrollTop():0;this._offsets=[],this._targets=[],this._scrollHeight=this._getScrollHeight(),V.find(wn,this._config.target).map((t=>{const s=i(t),o=s?V.findOne(s):null;if(o){const t=o.getBoundingClientRect();if(t.width||t.height)return[U[e](o).top+n,s]}return null})).filter((t=>t)).sort(((t,e)=>t[0]-e[0])).forEach((t=>{this._offsets.push(t[0]),this._targets.push(t[1])}))}dispose(){j.off(this._scrollElement,".bs.scrollspy"),super.dispose()}_getConfig(t){return(t={...bn,...U.getDataAttributes(this._element),..."object"==typeof t&&t?t:{}}).target=r(t.target)||document.documentElement,a(_n,t,vn),t}_getScrollTop(){return this._scrollElement===window?this._scrollElement.pageYOffset:this._scrollElement.scrollTop}_getScrollHeight(){return this._scrollElement.scrollHeight||Math.max(document.body.scrollHeight,document.documentElement.scrollHeight)}_getOffsetHeight(){return this._scrollElement===window?window.innerHeight:this._scrollElement.getBoundingClientRect().height}_process(){const t=this._getScrollTop()+this._config.offset,e=this._getScrollHeight(),i=this._config.offset+e-this._getOffsetHeight();if(this._scrollHeight!==e&&this.refresh(),t>=i){const t=this._targets[this._targets.length-1];this._activeTarget!==t&&this._activate(t)}else{if(this._activeTarget&&t0)return this._activeTarget=null,void this._clear();for(let e=this._offsets.length;e--;)this._activeTarget!==this._targets[e]&&t>=this._offsets[e]&&(void 0===this._offsets[e+1]||t`${e}[data-bs-target="${t}"],${e}[href="${t}"]`)),i=V.findOne(e.join(","),this._config.target);i.classList.add(yn),i.classList.contains("dropdown-item")?V.findOne(".dropdown-toggle",i.closest(".dropdown")).classList.add(yn):V.parents(i,".nav, .list-group").forEach((t=>{V.prev(t,".nav-link, .list-group-item").forEach((t=>t.classList.add(yn))),V.prev(t,".nav-item").forEach((t=>{V.children(t,".nav-link").forEach((t=>t.classList.add(yn)))}))})),j.trigger(this._scrollElement,"activate.bs.scrollspy",{relatedTarget:t})}_clear(){V.find(wn,this._config.target).filter((t=>t.classList.contains(yn))).forEach((t=>t.classList.remove(yn)))}static jQueryInterface(t){return this.each((function(){const e=An.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}}j.on(window,"load.bs.scrollspy.data-api",(()=>{V.find('[data-bs-spy="scroll"]').forEach((t=>new An(t)))})),g(An);const Tn="active",On="fade",Cn="show",kn=".active",Ln=":scope > li > .active";class xn extends B{static get NAME(){return"tab"}show(){if(this._element.parentNode&&this._element.parentNode.nodeType===Node.ELEMENT_NODE&&this._element.classList.contains(Tn))return;let t;const e=n(this._element),i=this._element.closest(".nav, .list-group");if(i){const e="UL"===i.nodeName||"OL"===i.nodeName?Ln:kn;t=V.find(e,i),t=t[t.length-1]}const s=t?j.trigger(t,"hide.bs.tab",{relatedTarget:this._element}):null;if(j.trigger(this._element,"show.bs.tab",{relatedTarget:t}).defaultPrevented||null!==s&&s.defaultPrevented)return;this._activate(this._element,i);const o=()=>{j.trigger(t,"hidden.bs.tab",{relatedTarget:this._element}),j.trigger(this._element,"shown.bs.tab",{relatedTarget:t})};e?this._activate(e,e.parentNode,o):o()}_activate(t,e,i){const n=(!e||"UL"!==e.nodeName&&"OL"!==e.nodeName?V.children(e,kn):V.find(Ln,e))[0],s=i&&n&&n.classList.contains(On),o=()=>this._transitionComplete(t,n,i);n&&s?(n.classList.remove(Cn),this._queueCallback(o,t,!0)):o()}_transitionComplete(t,e,i){if(e){e.classList.remove(Tn);const t=V.findOne(":scope > .dropdown-menu .active",e.parentNode);t&&t.classList.remove(Tn),"tab"===e.getAttribute("role")&&e.setAttribute("aria-selected",!1)}t.classList.add(Tn),"tab"===t.getAttribute("role")&&t.setAttribute("aria-selected",!0),u(t),t.classList.contains(On)&&t.classList.add(Cn);let n=t.parentNode;if(n&&"LI"===n.nodeName&&(n=n.parentNode),n&&n.classList.contains("dropdown-menu")){const e=t.closest(".dropdown");e&&V.find(".dropdown-toggle",e).forEach((t=>t.classList.add(Tn))),t.setAttribute("aria-expanded",!0)}i&&i()}static jQueryInterface(t){return this.each((function(){const e=xn.getOrCreateInstance(this);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}}j.on(document,"click.bs.tab.data-api",'[data-bs-toggle="tab"], [data-bs-toggle="pill"], [data-bs-toggle="list"]',(function(t){["A","AREA"].includes(this.tagName)&&t.preventDefault(),c(this)||xn.getOrCreateInstance(this).show()})),g(xn);const Dn="toast",Sn="hide",Nn="show",In="showing",Pn={animation:"boolean",autohide:"boolean",delay:"number"},jn={animation:!0,autohide:!0,delay:5e3};class Mn extends B{constructor(t,e){super(t),this._config=this._getConfig(e),this._timeout=null,this._hasMouseInteraction=!1,this._hasKeyboardInteraction=!1,this._setListeners()}static get DefaultType(){return Pn}static get Default(){return jn}static get NAME(){return Dn}show(){j.trigger(this._element,"show.bs.toast").defaultPrevented||(this._clearTimeout(),this._config.animation&&this._element.classList.add("fade"),this._element.classList.remove(Sn),u(this._element),this._element.classList.add(Nn),this._element.classList.add(In),this._queueCallback((()=>{this._element.classList.remove(In),j.trigger(this._element,"shown.bs.toast"),this._maybeScheduleHide()}),this._element,this._config.animation))}hide(){this._element.classList.contains(Nn)&&(j.trigger(this._element,"hide.bs.toast").defaultPrevented||(this._element.classList.add(In),this._queueCallback((()=>{this._element.classList.add(Sn),this._element.classList.remove(In),this._element.classList.remove(Nn),j.trigger(this._element,"hidden.bs.toast")}),this._element,this._config.animation)))}dispose(){this._clearTimeout(),this._element.classList.contains(Nn)&&this._element.classList.remove(Nn),super.dispose()}_getConfig(t){return t={...jn,...U.getDataAttributes(this._element),..."object"==typeof t&&t?t:{}},a(Dn,t,this.constructor.DefaultType),t}_maybeScheduleHide(){this._config.autohide&&(this._hasMouseInteraction||this._hasKeyboardInteraction||(this._timeout=setTimeout((()=>{this.hide()}),this._config.delay)))}_onInteraction(t,e){switch(t.type){case"mouseover":case"mouseout":this._hasMouseInteraction=e;break;case"focusin":case"focusout":this._hasKeyboardInteraction=e}if(e)return void this._clearTimeout();const i=t.relatedTarget;this._element===i||this._element.contains(i)||this._maybeScheduleHide()}_setListeners(){j.on(this._element,"mouseover.bs.toast",(t=>this._onInteraction(t,!0))),j.on(this._element,"mouseout.bs.toast",(t=>this._onInteraction(t,!1))),j.on(this._element,"focusin.bs.toast",(t=>this._onInteraction(t,!0))),j.on(this._element,"focusout.bs.toast",(t=>this._onInteraction(t,!1)))}_clearTimeout(){clearTimeout(this._timeout),this._timeout=null}static jQueryInterface(t){return this.each((function(){const e=Mn.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t](this)}}))}}return R(Mn),g(Mn),{Alert:W,Button:z,Carousel:st,Collapse:pt,Dropdown:hi,Modal:Hi,Offcanvas:Fi,Popover:gn,ScrollSpy:An,Tab:xn,Toast:Mn,Tooltip:un}}));
+//# sourceMappingURL=bootstrap.bundle.min.js.map
\ No newline at end of file
diff --git a/bs/.development/004GeneralisedLinearModel_files/libs/clipboard/clipboard.min.js b/bs/.development/004GeneralisedLinearModel_files/libs/clipboard/clipboard.min.js
new file mode 100644
index 0000000..1103f81
--- /dev/null
+++ b/bs/.development/004GeneralisedLinearModel_files/libs/clipboard/clipboard.min.js
@@ -0,0 +1,7 @@
+/*!
+ * clipboard.js v2.0.11
+ * https://clipboardjs.com/
+ *
+ * Licensed MIT © Zeno Rocha
+ */
+!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return b}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),r=n.n(e);function c(t){try{return document.execCommand(t)}catch(t){return}}var a=function(t){t=r()(t);return c("cut"),t};function o(t,e){var n,o,t=(n=t,o="rtl"===document.documentElement.getAttribute("dir"),(t=document.createElement("textarea")).style.fontSize="12pt",t.style.border="0",t.style.padding="0",t.style.margin="0",t.style.position="absolute",t.style[o?"right":"left"]="-9999px",o=window.pageYOffset||document.documentElement.scrollTop,t.style.top="".concat(o,"px"),t.setAttribute("readonly",""),t.value=n,t);return e.container.appendChild(t),e=r()(t),c("copy"),t.remove(),e}var f=function(t){var e=1.anchorjs-link,.anchorjs-link:focus{opacity:1}",u.sheet.cssRules.length),u.sheet.insertRule("[data-anchorjs-icon]::after{content:attr(data-anchorjs-icon)}",u.sheet.cssRules.length),u.sheet.insertRule('@font-face{font-family:anchorjs-icons;src:url(data:n/a;base64,AAEAAAALAIAAAwAwT1MvMg8yG2cAAAE4AAAAYGNtYXDp3gC3AAABpAAAAExnYXNwAAAAEAAAA9wAAAAIZ2x5ZlQCcfwAAAH4AAABCGhlYWQHFvHyAAAAvAAAADZoaGVhBnACFwAAAPQAAAAkaG10eASAADEAAAGYAAAADGxvY2EACACEAAAB8AAAAAhtYXhwAAYAVwAAARgAAAAgbmFtZQGOH9cAAAMAAAAAunBvc3QAAwAAAAADvAAAACAAAQAAAAEAAHzE2p9fDzz1AAkEAAAAAADRecUWAAAAANQA6R8AAAAAAoACwAAAAAgAAgAAAAAAAAABAAADwP/AAAACgAAA/9MCrQABAAAAAAAAAAAAAAAAAAAAAwABAAAAAwBVAAIAAAAAAAIAAAAAAAAAAAAAAAAAAAAAAAMCQAGQAAUAAAKZAswAAACPApkCzAAAAesAMwEJAAAAAAAAAAAAAAAAAAAAARAAAAAAAAAAAAAAAAAAAAAAQAAg//0DwP/AAEADwABAAAAAAQAAAAAAAAAAAAAAIAAAAAAAAAIAAAACgAAxAAAAAwAAAAMAAAAcAAEAAwAAABwAAwABAAAAHAAEADAAAAAIAAgAAgAAACDpy//9//8AAAAg6cv//f///+EWNwADAAEAAAAAAAAAAAAAAAAACACEAAEAAAAAAAAAAAAAAAAxAAACAAQARAKAAsAAKwBUAAABIiYnJjQ3NzY2MzIWFxYUBwcGIicmNDc3NjQnJiYjIgYHBwYUFxYUBwYGIwciJicmNDc3NjIXFhQHBwYUFxYWMzI2Nzc2NCcmNDc2MhcWFAcHBgYjARQGDAUtLXoWOR8fORYtLTgKGwoKCjgaGg0gEhIgDXoaGgkJBQwHdR85Fi0tOAobCgoKOBoaDSASEiANehoaCQkKGwotLXoWOR8BMwUFLYEuehYXFxYugC44CQkKGwo4GkoaDQ0NDXoaShoKGwoFBe8XFi6ALjgJCQobCjgaShoNDQ0NehpKGgobCgoKLYEuehYXAAAADACWAAEAAAAAAAEACAAAAAEAAAAAAAIAAwAIAAEAAAAAAAMACAAAAAEAAAAAAAQACAAAAAEAAAAAAAUAAQALAAEAAAAAAAYACAAAAAMAAQQJAAEAEAAMAAMAAQQJAAIABgAcAAMAAQQJAAMAEAAMAAMAAQQJAAQAEAAMAAMAAQQJAAUAAgAiAAMAAQQJAAYAEAAMYW5jaG9yanM0MDBAAGEAbgBjAGgAbwByAGoAcwA0ADAAMABAAAAAAwAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAABAAH//wAP) format("truetype")}',u.sheet.cssRules.length)),u=document.querySelectorAll("[id]"),t=[].map.call(u,function(A){return A.id}),i=0;i\]./()*\\\n\t\b\v\u00A0]/g,"-").replace(/-{2,}/g,"-").substring(0,this.options.truncate).replace(/^-+|-+$/gm,"").toLowerCase()},this.hasAnchorJSLink=function(A){var e=A.firstChild&&-1<(" "+A.firstChild.className+" ").indexOf(" anchorjs-link "),A=A.lastChild&&-1<(" "+A.lastChild.className+" ").indexOf(" anchorjs-link ");return e||A||!1}}});
+// @license-end
\ No newline at end of file
diff --git a/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/popper.min.js b/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/popper.min.js
new file mode 100644
index 0000000..2269d66
--- /dev/null
+++ b/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/popper.min.js
@@ -0,0 +1,6 @@
+/**
+ * @popperjs/core v2.11.4 - MIT License
+ */
+
+!function(e,t){"object"==typeof exports&&"undefined"!=typeof module?t(exports):"function"==typeof define&&define.amd?define(["exports"],t):t((e="undefined"!=typeof globalThis?globalThis:e||self).Popper={})}(this,(function(e){"use strict";function t(e){if(null==e)return window;if("[object Window]"!==e.toString()){var t=e.ownerDocument;return t&&t.defaultView||window}return e}function n(e){return e instanceof t(e).Element||e instanceof Element}function r(e){return e instanceof t(e).HTMLElement||e instanceof HTMLElement}function o(e){return"undefined"!=typeof ShadowRoot&&(e instanceof t(e).ShadowRoot||e instanceof ShadowRoot)}var i=Math.max,a=Math.min,s=Math.round;function f(e,t){void 0===t&&(t=!1);var n=e.getBoundingClientRect(),o=1,i=1;if(r(e)&&t){var a=e.offsetHeight,f=e.offsetWidth;f>0&&(o=s(n.width)/f||1),a>0&&(i=s(n.height)/a||1)}return{width:n.width/o,height:n.height/i,top:n.top/i,right:n.right/o,bottom:n.bottom/i,left:n.left/o,x:n.left/o,y:n.top/i}}function c(e){var n=t(e);return{scrollLeft:n.pageXOffset,scrollTop:n.pageYOffset}}function p(e){return e?(e.nodeName||"").toLowerCase():null}function u(e){return((n(e)?e.ownerDocument:e.document)||window.document).documentElement}function l(e){return f(u(e)).left+c(e).scrollLeft}function d(e){return t(e).getComputedStyle(e)}function h(e){var t=d(e),n=t.overflow,r=t.overflowX,o=t.overflowY;return/auto|scroll|overlay|hidden/.test(n+o+r)}function m(e,n,o){void 0===o&&(o=!1);var i,a,d=r(n),m=r(n)&&function(e){var t=e.getBoundingClientRect(),n=s(t.width)/e.offsetWidth||1,r=s(t.height)/e.offsetHeight||1;return 1!==n||1!==r}(n),v=u(n),g=f(e,m),y={scrollLeft:0,scrollTop:0},b={x:0,y:0};return(d||!d&&!o)&&(("body"!==p(n)||h(v))&&(y=(i=n)!==t(i)&&r(i)?{scrollLeft:(a=i).scrollLeft,scrollTop:a.scrollTop}:c(i)),r(n)?((b=f(n,!0)).x+=n.clientLeft,b.y+=n.clientTop):v&&(b.x=l(v))),{x:g.left+y.scrollLeft-b.x,y:g.top+y.scrollTop-b.y,width:g.width,height:g.height}}function v(e){var 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t=-1!==navigator.userAgent.toLowerCase().indexOf("firefox");if(-1!==navigator.userAgent.indexOf("Trident")&&r(e)&&"fixed"===d(e).position)return null;var n=g(e);for(o(n)&&(n=n.host);r(n)&&["html","body"].indexOf(p(n))<0;){var i=d(n);if("none"!==i.transform||"none"!==i.perspective||"paint"===i.contain||-1!==["transform","perspective"].indexOf(i.willChange)||t&&"filter"===i.willChange||t&&i.filter&&"none"!==i.filter)return n;n=n.parentNode}return null}(e)||n}var j="top",E="bottom",D="right",A="left",L="auto",P=[j,E,D,A],M="start",k="end",W="viewport",B="popper",H=P.reduce((function(e,t){return e.concat([t+"-"+M,t+"-"+k])}),[]),T=[].concat(P,[L]).reduce((function(e,t){return e.concat([t,t+"-"+M,t+"-"+k])}),[]),R=["beforeRead","read","afterRead","beforeMain","main","afterMain","beforeWrite","write","afterWrite"];function S(e){var t=new Map,n=new Set,r=[];function o(e){n.add(e.name),[].concat(e.requires||[],e.requiresIfExists||[]).forEach((function(e){if(!n.has(e)){var 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+
diff --git a/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/quarto-syntax-highlighting.css b/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/quarto-syntax-highlighting.css
new file mode 100644
index 0000000..d9fd98f
--- /dev/null
+++ b/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/quarto-syntax-highlighting.css
@@ -0,0 +1,203 @@
+/* quarto syntax highlight colors */
+:root {
+  --quarto-hl-ot-color: #003B4F;
+  --quarto-hl-at-color: #657422;
+  --quarto-hl-ss-color: #20794D;
+  --quarto-hl-an-color: #5E5E5E;
+  --quarto-hl-fu-color: #4758AB;
+  --quarto-hl-st-color: #20794D;
+  --quarto-hl-cf-color: #003B4F;
+  --quarto-hl-op-color: #5E5E5E;
+  --quarto-hl-er-color: #AD0000;
+  --quarto-hl-bn-color: #AD0000;
+  --quarto-hl-al-color: #AD0000;
+  --quarto-hl-va-color: #111111;
+  --quarto-hl-bu-color: inherit;
+  --quarto-hl-ex-color: inherit;
+  --quarto-hl-pp-color: #AD0000;
+  --quarto-hl-in-color: #5E5E5E;
+  --quarto-hl-vs-color: #20794D;
+  --quarto-hl-wa-color: #5E5E5E;
+  --quarto-hl-do-color: #5E5E5E;
+  --quarto-hl-im-color: #00769E;
+  --quarto-hl-ch-color: #20794D;
+  --quarto-hl-dt-color: #AD0000;
+  --quarto-hl-fl-color: #AD0000;
+  --quarto-hl-co-color: #5E5E5E;
+  --quarto-hl-cv-color: #5E5E5E;
+  --quarto-hl-cn-color: #8f5902;
+  --quarto-hl-sc-color: #5E5E5E;
+  --quarto-hl-dv-color: #AD0000;
+  --quarto-hl-kw-color: #003B4F;
+}
+
+/* other quarto variables */
+:root {
+  --quarto-font-monospace: SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace;
+}
+
+pre > code.sourceCode > span {
+  color: #003B4F;
+}
+
+code span {
+  color: #003B4F;
+}
+
+code.sourceCode > span {
+  color: #003B4F;
+}
+
+div.sourceCode,
+div.sourceCode pre.sourceCode {
+  color: #003B4F;
+}
+
+code span.ot {
+  color: #003B4F;
+  font-style: inherit;
+}
+
+code span.at {
+  color: #657422;
+  font-style: inherit;
+}
+
+code span.ss {
+  color: #20794D;
+  font-style: inherit;
+}
+
+code span.an {
+  color: #5E5E5E;
+  font-style: inherit;
+}
+
+code span.fu {
+  color: #4758AB;
+  font-style: inherit;
+}
+
+code span.st {
+  color: #20794D;
+  font-style: inherit;
+}
+
+code span.cf {
+  color: #003B4F;
+  font-style: inherit;
+}
+
+code span.op {
+  color: #5E5E5E;
+  font-style: inherit;
+}
+
+code span.er {
+  color: #AD0000;
+  font-style: inherit;
+}
+
+code span.bn {
+  color: #AD0000;
+  font-style: inherit;
+}
+
+code span.al {
+  color: #AD0000;
+  font-style: inherit;
+}
+
+code span.va {
+  color: #111111;
+  font-style: inherit;
+}
+
+code span.bu {
+  font-style: inherit;
+}
+
+code span.ex {
+  font-style: inherit;
+}
+
+code span.pp {
+  color: #AD0000;
+  font-style: inherit;
+}
+
+code span.in {
+  color: #5E5E5E;
+  font-style: inherit;
+}
+
+code span.vs {
+  color: #20794D;
+  font-style: inherit;
+}
+
+code span.wa {
+  color: #5E5E5E;
+  font-style: italic;
+}
+
+code span.do {
+  color: #5E5E5E;
+  font-style: italic;
+}
+
+code span.im {
+  color: #00769E;
+  font-style: inherit;
+}
+
+code span.ch {
+  color: #20794D;
+  font-style: inherit;
+}
+
+code span.dt {
+  color: #AD0000;
+  font-style: inherit;
+}
+
+code span.fl {
+  color: #AD0000;
+  font-style: inherit;
+}
+
+code span.co {
+  color: #5E5E5E;
+  font-style: inherit;
+}
+
+code span.cv {
+  color: #5E5E5E;
+  font-style: italic;
+}
+
+code span.cn {
+  color: #8f5902;
+  font-style: inherit;
+}
+
+code span.sc {
+  color: #5E5E5E;
+  font-style: inherit;
+}
+
+code span.dv {
+  color: #AD0000;
+  font-style: inherit;
+}
+
+code span.kw {
+  color: #003B4F;
+  font-style: inherit;
+}
+
+.prevent-inlining {
+  content: " {
+  // Find any conflicting margin elements and add margins to the
+  // top to prevent overlap
+  const marginChildren = window.document.querySelectorAll(
+    ".column-margin.column-container > * "
+  );
+
+  let lastBottom = 0;
+  for (const marginChild of marginChildren) {
+    if (marginChild.offsetParent !== null) {
+      // clear the top margin so we recompute it
+      marginChild.style.marginTop = null;
+      const top = marginChild.getBoundingClientRect().top + window.scrollY;
+      console.log({
+        childtop: marginChild.getBoundingClientRect().top,
+        scroll: window.scrollY,
+        top,
+        lastBottom,
+      });
+      if (top < lastBottom) {
+        const margin = lastBottom - top;
+        marginChild.style.marginTop = `${margin}px`;
+      }
+      const styles = window.getComputedStyle(marginChild);
+      const marginTop = parseFloat(styles["marginTop"]);
+
+      console.log({
+        top,
+        height: marginChild.getBoundingClientRect().height,
+        marginTop,
+        total: top + marginChild.getBoundingClientRect().height + marginTop,
+      });
+      lastBottom = top + marginChild.getBoundingClientRect().height + marginTop;
+    }
+  }
+};
+
+window.document.addEventListener("DOMContentLoaded", function (_event) {
+  // Recompute the position of margin elements anytime the body size changes
+  if (window.ResizeObserver) {
+    const resizeObserver = new window.ResizeObserver(
+      throttle(layoutMarginEls, 50)
+    );
+    resizeObserver.observe(window.document.body);
+  }
+
+  const tocEl = window.document.querySelector('nav.toc-active[role="doc-toc"]');
+  const sidebarEl = window.document.getElementById("quarto-sidebar");
+  const leftTocEl = window.document.getElementById("quarto-sidebar-toc-left");
+  const marginSidebarEl = window.document.getElementById(
+    "quarto-margin-sidebar"
+  );
+  // function to determine whether the element has a previous sibling that is active
+  const prevSiblingIsActiveLink = (el) => {
+    const sibling = el.previousElementSibling;
+    if (sibling && sibling.tagName === "A") {
+      return sibling.classList.contains("active");
+    } else {
+      return false;
+    }
+  };
+
+  // fire slideEnter for bootstrap tab activations (for htmlwidget resize behavior)
+  function fireSlideEnter(e) {
+    const event = window.document.createEvent("Event");
+    event.initEvent("slideenter", true, true);
+    window.document.dispatchEvent(event);
+  }
+  const tabs = window.document.querySelectorAll('a[data-bs-toggle="tab"]');
+  tabs.forEach((tab) => {
+    tab.addEventListener("shown.bs.tab", fireSlideEnter);
+  });
+
+  // fire slideEnter for tabby tab activations (for htmlwidget resize behavior)
+  document.addEventListener("tabby", fireSlideEnter, false);
+
+  // Track scrolling and mark TOC links as active
+  // get table of contents and sidebar (bail if we don't have at least one)
+  const tocLinks = tocEl
+    ? [...tocEl.querySelectorAll("a[data-scroll-target]")]
+    : [];
+  const makeActive = (link) => tocLinks[link].classList.add("active");
+  const removeActive = (link) => tocLinks[link].classList.remove("active");
+  const removeAllActive = () =>
+    [...Array(tocLinks.length).keys()].forEach((link) => removeActive(link));
+
+  // activate the anchor for a section associated with this TOC entry
+  tocLinks.forEach((link) => {
+    link.addEventListener("click", () => {
+      if (link.href.indexOf("#") !== -1) {
+        const anchor = link.href.split("#")[1];
+        const heading = window.document.querySelector(
+          `[data-anchor-id=${anchor}]`
+        );
+        if (heading) {
+          // Add the class
+          heading.classList.add("reveal-anchorjs-link");
+
+          // function to show the anchor
+          const handleMouseout = () => {
+            heading.classList.remove("reveal-anchorjs-link");
+            heading.removeEventListener("mouseout", handleMouseout);
+          };
+
+          // add a function to clear the anchor when the user mouses out of it
+          heading.addEventListener("mouseout", handleMouseout);
+        }
+      }
+    });
+  });
+
+  const sections = tocLinks.map((link) => {
+    const target = link.getAttribute("data-scroll-target");
+    if (target.startsWith("#")) {
+      return window.document.getElementById(decodeURI(`${target.slice(1)}`));
+    } else {
+      return window.document.querySelector(decodeURI(`${target}`));
+    }
+  });
+
+  const sectionMargin = 200;
+  let currentActive = 0;
+  // track whether we've initialized state the first time
+  let init = false;
+
+  const updateActiveLink = () => {
+    // The index from bottom to top (e.g. reversed list)
+    let sectionIndex = -1;
+    if (
+      window.innerHeight + window.pageYOffset >=
+      window.document.body.offsetHeight
+    ) {
+      sectionIndex = 0;
+    } else {
+      sectionIndex = [...sections].reverse().findIndex((section) => {
+        if (section) {
+          return window.pageYOffset >= section.offsetTop - sectionMargin;
+        } else {
+          return false;
+        }
+      });
+    }
+    if (sectionIndex > -1) {
+      const current = sections.length - sectionIndex - 1;
+      if (current !== currentActive) {
+        removeAllActive();
+        currentActive = current;
+        makeActive(current);
+        if (init) {
+          window.dispatchEvent(sectionChanged);
+        }
+        init = true;
+      }
+    }
+  };
+
+  const inHiddenRegion = (top, bottom, hiddenRegions) => {
+    for (const region of hiddenRegions) {
+      if (top <= region.bottom && bottom >= region.top) {
+        return true;
+      }
+    }
+    return false;
+  };
+
+  const categorySelector = "header.quarto-title-block .quarto-category";
+  const activateCategories = (href) => {
+    // Find any categories
+    // Surround them with a link pointing back to:
+    // #category=Authoring
+    try {
+      const categoryEls = window.document.querySelectorAll(categorySelector);
+      for (const categoryEl of categoryEls) {
+        const categoryText = categoryEl.textContent;
+        if (categoryText) {
+          const link = `${href}#category=${encodeURIComponent(categoryText)}`;
+          const linkEl = window.document.createElement("a");
+          linkEl.setAttribute("href", link);
+          for (const child of categoryEl.childNodes) {
+            linkEl.append(child);
+          }
+          categoryEl.appendChild(linkEl);
+        }
+      }
+    } catch {
+      // Ignore errors
+    }
+  };
+  function hasTitleCategories() {
+    return window.document.querySelector(categorySelector) !== null;
+  }
+
+  function offsetRelativeUrl(url) {
+    const offset = getMeta("quarto:offset");
+    return offset ? offset + url : url;
+  }
+
+  function offsetAbsoluteUrl(url) {
+    const offset = getMeta("quarto:offset");
+    const baseUrl = new URL(offset, window.location);
+
+    const projRelativeUrl = url.replace(baseUrl, "");
+    if (projRelativeUrl.startsWith("/")) {
+      return projRelativeUrl;
+    } else {
+      return "/" + projRelativeUrl;
+    }
+  }
+
+  // read a meta tag value
+  function getMeta(metaName) {
+    const metas = window.document.getElementsByTagName("meta");
+    for (let i = 0; i < metas.length; i++) {
+      if (metas[i].getAttribute("name") === metaName) {
+        return metas[i].getAttribute("content");
+      }
+    }
+    return "";
+  }
+
+  async function findAndActivateCategories() {
+    const currentPagePath = offsetAbsoluteUrl(window.location.href);
+    const response = await fetch(offsetRelativeUrl("listings.json"));
+    if (response.status == 200) {
+      return response.json().then(function (listingPaths) {
+        const listingHrefs = [];
+        for (const listingPath of listingPaths) {
+          const pathWithoutLeadingSlash = listingPath.listing.substring(1);
+          for (const item of listingPath.items) {
+            if (
+              item === currentPagePath ||
+              item === currentPagePath + "index.html"
+            ) {
+              // Resolve this path against the offset to be sure
+              // we already are using the correct path to the listing
+              // (this adjusts the listing urls to be rooted against
+              // whatever root the page is actually running against)
+              const relative = offsetRelativeUrl(pathWithoutLeadingSlash);
+              const baseUrl = window.location;
+              const resolvedPath = new URL(relative, baseUrl);
+              listingHrefs.push(resolvedPath.pathname);
+              break;
+            }
+          }
+        }
+
+        // Look up the tree for a nearby linting and use that if we find one
+        const nearestListing = findNearestParentListing(
+          offsetAbsoluteUrl(window.location.pathname),
+          listingHrefs
+        );
+        if (nearestListing) {
+          activateCategories(nearestListing);
+        } else {
+          // See if the referrer is a listing page for this item
+          const referredRelativePath = offsetAbsoluteUrl(document.referrer);
+          const referrerListing = listingHrefs.find((listingHref) => {
+            const isListingReferrer =
+              listingHref === referredRelativePath ||
+              listingHref === referredRelativePath + "index.html";
+            return isListingReferrer;
+          });
+
+          if (referrerListing) {
+            // Try to use the referrer if possible
+            activateCategories(referrerListing);
+          } else if (listingHrefs.length > 0) {
+            // Otherwise, just fall back to the first listing
+            activateCategories(listingHrefs[0]);
+          }
+        }
+      });
+    }
+  }
+  if (hasTitleCategories()) {
+    findAndActivateCategories();
+  }
+
+  const findNearestParentListing = (href, listingHrefs) => {
+    if (!href || !listingHrefs) {
+      return undefined;
+    }
+    // Look up the tree for a nearby linting and use that if we find one
+    const relativeParts = href.substring(1).split("/");
+    while (relativeParts.length > 0) {
+      const path = relativeParts.join("/");
+      for (const listingHref of listingHrefs) {
+        if (listingHref.startsWith(path)) {
+          return listingHref;
+        }
+      }
+      relativeParts.pop();
+    }
+
+    return undefined;
+  };
+
+  const manageSidebarVisiblity = (el, placeholderDescriptor) => {
+    let isVisible = true;
+    let elRect;
+
+    return (hiddenRegions) => {
+      if (el === null) {
+        return;
+      }
+
+      // Find the last element of the TOC
+      const lastChildEl = el.lastElementChild;
+
+      if (lastChildEl) {
+        // Converts the sidebar to a menu
+        const convertToMenu = () => {
+          for (const child of el.children) {
+            child.style.opacity = 0;
+            child.style.overflow = "hidden";
+          }
+
+          nexttick(() => {
+            const toggleContainer = window.document.createElement("div");
+            toggleContainer.style.width = "100%";
+            toggleContainer.classList.add("zindex-over-content");
+            toggleContainer.classList.add("quarto-sidebar-toggle");
+            toggleContainer.classList.add("headroom-target"); // Marks this to be managed by headeroom
+            toggleContainer.id = placeholderDescriptor.id;
+            toggleContainer.style.position = "fixed";
+
+            const toggleIcon = window.document.createElement("i");
+            toggleIcon.classList.add("quarto-sidebar-toggle-icon");
+            toggleIcon.classList.add("bi");
+            toggleIcon.classList.add("bi-caret-down-fill");
+
+            const toggleTitle = window.document.createElement("div");
+            const titleEl = window.document.body.querySelector(
+              placeholderDescriptor.titleSelector
+            );
+            if (titleEl) {
+              toggleTitle.append(
+                titleEl.textContent || titleEl.innerText,
+                toggleIcon
+              );
+            }
+            toggleTitle.classList.add("zindex-over-content");
+            toggleTitle.classList.add("quarto-sidebar-toggle-title");
+            toggleContainer.append(toggleTitle);
+
+            const toggleContents = window.document.createElement("div");
+            toggleContents.classList = el.classList;
+            toggleContents.classList.add("zindex-over-content");
+            toggleContents.classList.add("quarto-sidebar-toggle-contents");
+            for (const child of el.children) {
+              if (child.id === "toc-title") {
+                continue;
+              }
+
+              const clone = child.cloneNode(true);
+              clone.style.opacity = 1;
+              clone.style.display = null;
+              toggleContents.append(clone);
+            }
+            toggleContents.style.height = "0px";
+            const positionToggle = () => {
+              // position the element (top left of parent, same width as parent)
+              if (!elRect) {
+                elRect = el.getBoundingClientRect();
+              }
+              toggleContainer.style.left = `${elRect.left}px`;
+              toggleContainer.style.top = `${elRect.top}px`;
+              toggleContainer.style.width = `${elRect.width}px`;
+            };
+            positionToggle();
+
+            toggleContainer.append(toggleContents);
+            el.parentElement.prepend(toggleContainer);
+
+            // Process clicks
+            let tocShowing = false;
+            // Allow the caller to control whether this is dismissed
+            // when it is clicked (e.g. sidebar navigation supports
+            // opening and closing the nav tree, so don't dismiss on click)
+            const clickEl = placeholderDescriptor.dismissOnClick
+              ? toggleContainer
+              : toggleTitle;
+
+            const closeToggle = () => {
+              if (tocShowing) {
+                toggleContainer.classList.remove("expanded");
+                toggleContents.style.height = "0px";
+                tocShowing = false;
+              }
+            };
+
+            // Get rid of any expanded toggle if the user scrolls
+            window.document.addEventListener(
+              "scroll",
+              throttle(() => {
+                closeToggle();
+              }, 50)
+            );
+
+            // Handle positioning of the toggle
+            window.addEventListener(
+              "resize",
+              throttle(() => {
+                elRect = undefined;
+                positionToggle();
+              }, 50)
+            );
+
+            window.addEventListener("quarto-hrChanged", () => {
+              elRect = undefined;
+            });
+
+            // Process the click
+            clickEl.onclick = () => {
+              if (!tocShowing) {
+                toggleContainer.classList.add("expanded");
+                toggleContents.style.height = null;
+                tocShowing = true;
+              } else {
+                closeToggle();
+              }
+            };
+          });
+        };
+
+        // Converts a sidebar from a menu back to a sidebar
+        const convertToSidebar = () => {
+          for (const child of el.children) {
+            child.style.opacity = 1;
+            child.style.overflow = null;
+          }
+
+          const placeholderEl = window.document.getElementById(
+            placeholderDescriptor.id
+          );
+          if (placeholderEl) {
+            placeholderEl.remove();
+          }
+
+          el.classList.remove("rollup");
+        };
+
+        if (isReaderMode()) {
+          convertToMenu();
+          isVisible = false;
+        } else {
+          // Find the top and bottom o the element that is being managed
+          const elTop = el.offsetTop;
+          const elBottom =
+            elTop + lastChildEl.offsetTop + lastChildEl.offsetHeight;
+
+          if (!isVisible) {
+            // If the element is current not visible reveal if there are
+            // no conflicts with overlay regions
+            if (!inHiddenRegion(elTop, elBottom, hiddenRegions)) {
+              convertToSidebar();
+              isVisible = true;
+            }
+          } else {
+            // If the element is visible, hide it if it conflicts with overlay regions
+            // and insert a placeholder toggle (or if we're in reader mode)
+            if (inHiddenRegion(elTop, elBottom, hiddenRegions)) {
+              convertToMenu();
+              isVisible = false;
+            }
+          }
+        }
+      }
+    };
+  };
+
+  const tabEls = document.querySelectorAll('a[data-bs-toggle="tab"]');
+  for (const tabEl of tabEls) {
+    const id = tabEl.getAttribute("data-bs-target");
+    if (id) {
+      const columnEl = document.querySelector(
+        `${id} .column-margin, .tabset-margin-content`
+      );
+      if (columnEl)
+        tabEl.addEventListener("shown.bs.tab", function (event) {
+          const el = event.srcElement;
+          if (el) {
+            const visibleCls = `${el.id}-margin-content`;
+            // walk up until we find a parent tabset
+            let panelTabsetEl = el.parentElement;
+            while (panelTabsetEl) {
+              if (panelTabsetEl.classList.contains("panel-tabset")) {
+                break;
+              }
+              panelTabsetEl = panelTabsetEl.parentElement;
+            }
+
+            if (panelTabsetEl) {
+              const prevSib = panelTabsetEl.previousElementSibling;
+              if (
+                prevSib &&
+                prevSib.classList.contains("tabset-margin-container")
+              ) {
+                const childNodes = prevSib.querySelectorAll(
+                  ".tabset-margin-content"
+                );
+                for (const childEl of childNodes) {
+                  if (childEl.classList.contains(visibleCls)) {
+                    childEl.classList.remove("collapse");
+                  } else {
+                    childEl.classList.add("collapse");
+                  }
+                }
+              }
+            }
+          }
+
+          layoutMarginEls();
+        });
+    }
+  }
+
+  // Manage the visibility of the toc and the sidebar
+  const marginScrollVisibility = manageSidebarVisiblity(marginSidebarEl, {
+    id: "quarto-toc-toggle",
+    titleSelector: "#toc-title",
+    dismissOnClick: true,
+  });
+  const sidebarScrollVisiblity = manageSidebarVisiblity(sidebarEl, {
+    id: "quarto-sidebarnav-toggle",
+    titleSelector: ".title",
+    dismissOnClick: false,
+  });
+  let tocLeftScrollVisibility;
+  if (leftTocEl) {
+    tocLeftScrollVisibility = manageSidebarVisiblity(leftTocEl, {
+      id: "quarto-lefttoc-toggle",
+      titleSelector: "#toc-title",
+      dismissOnClick: true,
+    });
+  }
+
+  // Find the first element that uses formatting in special columns
+  const conflictingEls = window.document.body.querySelectorAll(
+    '[class^="column-"], [class*=" column-"], aside, [class*="margin-caption"], [class*=" margin-caption"], [class*="margin-ref"], [class*=" margin-ref"]'
+  );
+
+  // Filter all the possibly conflicting elements into ones
+  // the do conflict on the left or ride side
+  const arrConflictingEls = Array.from(conflictingEls);
+  const leftSideConflictEls = arrConflictingEls.filter((el) => {
+    if (el.tagName === "ASIDE") {
+      return false;
+    }
+    return Array.from(el.classList).find((className) => {
+      return (
+        className !== "column-body" &&
+        className.startsWith("column-") &&
+        !className.endsWith("right") &&
+        !className.endsWith("container") &&
+        className !== "column-margin"
+      );
+    });
+  });
+  const rightSideConflictEls = arrConflictingEls.filter((el) => {
+    if (el.tagName === "ASIDE") {
+      return true;
+    }
+
+    const hasMarginCaption = Array.from(el.classList).find((className) => {
+      return className == "margin-caption";
+    });
+    if (hasMarginCaption) {
+      return true;
+    }
+
+    return Array.from(el.classList).find((className) => {
+      return (
+        className !== "column-body" &&
+        !className.endsWith("container") &&
+        className.startsWith("column-") &&
+        !className.endsWith("left")
+      );
+    });
+  });
+
+  const kOverlapPaddingSize = 10;
+  function toRegions(els) {
+    return els.map((el) => {
+      const boundRect = el.getBoundingClientRect();
+      const top =
+        boundRect.top +
+        document.documentElement.scrollTop -
+        kOverlapPaddingSize;
+      return {
+        top,
+        bottom: top + el.scrollHeight + 2 * kOverlapPaddingSize,
+      };
+    });
+  }
+
+  let hasObserved = false;
+  const visibleItemObserver = (els) => {
+    let visibleElements = [...els];
+    const intersectionObserver = new IntersectionObserver(
+      (entries, _observer) => {
+        entries.forEach((entry) => {
+          if (entry.isIntersecting) {
+            if (visibleElements.indexOf(entry.target) === -1) {
+              visibleElements.push(entry.target);
+            }
+          } else {
+            visibleElements = visibleElements.filter((visibleEntry) => {
+              return visibleEntry !== entry;
+            });
+          }
+        });
+
+        if (!hasObserved) {
+          hideOverlappedSidebars();
+        }
+        hasObserved = true;
+      },
+      {}
+    );
+    els.forEach((el) => {
+      intersectionObserver.observe(el);
+    });
+
+    return {
+      getVisibleEntries: () => {
+        return visibleElements;
+      },
+    };
+  };
+
+  const rightElementObserver = visibleItemObserver(rightSideConflictEls);
+  const leftElementObserver = visibleItemObserver(leftSideConflictEls);
+
+  const hideOverlappedSidebars = () => {
+    marginScrollVisibility(toRegions(rightElementObserver.getVisibleEntries()));
+    sidebarScrollVisiblity(toRegions(leftElementObserver.getVisibleEntries()));
+    if (tocLeftScrollVisibility) {
+      tocLeftScrollVisibility(
+        toRegions(leftElementObserver.getVisibleEntries())
+      );
+    }
+  };
+
+  window.quartoToggleReader = () => {
+    // Applies a slow class (or removes it)
+    // to update the transition speed
+    const slowTransition = (slow) => {
+      const manageTransition = (id, slow) => {
+        const el = document.getElementById(id);
+        if (el) {
+          if (slow) {
+            el.classList.add("slow");
+          } else {
+            el.classList.remove("slow");
+          }
+        }
+      };
+
+      manageTransition("TOC", slow);
+      manageTransition("quarto-sidebar", slow);
+    };
+    const readerMode = !isReaderMode();
+    setReaderModeValue(readerMode);
+
+    // If we're entering reader mode, slow the transition
+    if (readerMode) {
+      slowTransition(readerMode);
+    }
+    highlightReaderToggle(readerMode);
+    hideOverlappedSidebars();
+
+    // If we're exiting reader mode, restore the non-slow transition
+    if (!readerMode) {
+      slowTransition(!readerMode);
+    }
+  };
+
+  const highlightReaderToggle = (readerMode) => {
+    const els = document.querySelectorAll(".quarto-reader-toggle");
+    if (els) {
+      els.forEach((el) => {
+        if (readerMode) {
+          el.classList.add("reader");
+        } else {
+          el.classList.remove("reader");
+        }
+      });
+    }
+  };
+
+  const setReaderModeValue = (val) => {
+    if (window.location.protocol !== "file:") {
+      window.localStorage.setItem("quarto-reader-mode", val);
+    } else {
+      localReaderMode = val;
+    }
+  };
+
+  const isReaderMode = () => {
+    if (window.location.protocol !== "file:") {
+      return window.localStorage.getItem("quarto-reader-mode") === "true";
+    } else {
+      return localReaderMode;
+    }
+  };
+  let localReaderMode = null;
+
+  const tocOpenDepthStr = tocEl?.getAttribute("data-toc-expanded");
+  const tocOpenDepth = tocOpenDepthStr ? Number(tocOpenDepthStr) : 1;
+
+  // Walk the TOC and collapse/expand nodes
+  // Nodes are expanded if:
+  // - they are top level
+  // - they have children that are 'active' links
+  // - they are directly below an link that is 'active'
+  const walk = (el, depth) => {
+    // Tick depth when we enter a UL
+    if (el.tagName === "UL") {
+      depth = depth + 1;
+    }
+
+    // It this is active link
+    let isActiveNode = false;
+    if (el.tagName === "A" && el.classList.contains("active")) {
+      isActiveNode = true;
+    }
+
+    // See if there is an active child to this element
+    let hasActiveChild = false;
+    for (child of el.children) {
+      hasActiveChild = walk(child, depth) || hasActiveChild;
+    }
+
+    // Process the collapse state if this is an UL
+    if (el.tagName === "UL") {
+      if (tocOpenDepth === -1 && depth > 1) {
+        el.classList.add("collapse");
+      } else if (
+        depth <= tocOpenDepth ||
+        hasActiveChild ||
+        prevSiblingIsActiveLink(el)
+      ) {
+        el.classList.remove("collapse");
+      } else {
+        el.classList.add("collapse");
+      }
+
+      // untick depth when we leave a UL
+      depth = depth - 1;
+    }
+    return hasActiveChild || isActiveNode;
+  };
+
+  // walk the TOC and expand / collapse any items that should be shown
+
+  if (tocEl) {
+    walk(tocEl, 0);
+    updateActiveLink();
+  }
+
+  // Throttle the scroll event and walk peridiocally
+  window.document.addEventListener(
+    "scroll",
+    throttle(() => {
+      if (tocEl) {
+        updateActiveLink();
+        walk(tocEl, 0);
+      }
+      if (!isReaderMode()) {
+        hideOverlappedSidebars();
+      }
+    }, 5)
+  );
+  window.addEventListener(
+    "resize",
+    throttle(() => {
+      if (!isReaderMode()) {
+        hideOverlappedSidebars();
+      }
+    }, 10)
+  );
+  hideOverlappedSidebars();
+  highlightReaderToggle(isReaderMode());
+});
+
+// grouped tabsets
+window.addEventListener("pageshow", (_event) => {
+  function getTabSettings() {
+    const data = localStorage.getItem("quarto-persistent-tabsets-data");
+    if (!data) {
+      localStorage.setItem("quarto-persistent-tabsets-data", "{}");
+      return {};
+    }
+    if (data) {
+      return JSON.parse(data);
+    }
+  }
+
+  function setTabSettings(data) {
+    localStorage.setItem(
+      "quarto-persistent-tabsets-data",
+      JSON.stringify(data)
+    );
+  }
+
+  function setTabState(groupName, groupValue) {
+    const data = getTabSettings();
+    data[groupName] = groupValue;
+    setTabSettings(data);
+  }
+
+  function toggleTab(tab, active) {
+    const tabPanelId = tab.getAttribute("aria-controls");
+    const tabPanel = document.getElementById(tabPanelId);
+    if (active) {
+      tab.classList.add("active");
+      tabPanel.classList.add("active");
+    } else {
+      tab.classList.remove("active");
+      tabPanel.classList.remove("active");
+    }
+  }
+
+  function toggleAll(selectedGroup, selectorsToSync) {
+    for (const [thisGroup, tabs] of Object.entries(selectorsToSync)) {
+      const active = selectedGroup === thisGroup;
+      for (const tab of tabs) {
+        toggleTab(tab, active);
+      }
+    }
+  }
+
+  function findSelectorsToSyncByLanguage() {
+    const result = {};
+    const tabs = Array.from(
+      document.querySelectorAll(`div[data-group] a[id^='tabset-']`)
+    );
+    for (const item of tabs) {
+      const div = item.parentElement.parentElement.parentElement;
+      const group = div.getAttribute("data-group");
+      if (!result[group]) {
+        result[group] = {};
+      }
+      const selectorsToSync = result[group];
+      const value = item.innerHTML;
+      if (!selectorsToSync[value]) {
+        selectorsToSync[value] = [];
+      }
+      selectorsToSync[value].push(item);
+    }
+    return result;
+  }
+
+  function setupSelectorSync() {
+    const selectorsToSync = findSelectorsToSyncByLanguage();
+    Object.entries(selectorsToSync).forEach(([group, tabSetsByValue]) => {
+      Object.entries(tabSetsByValue).forEach(([value, items]) => {
+        items.forEach((item) => {
+          item.addEventListener("click", (_event) => {
+            setTabState(group, value);
+            toggleAll(value, selectorsToSync[group]);
+          });
+        });
+      });
+    });
+    return selectorsToSync;
+  }
+
+  const selectorsToSync = setupSelectorSync();
+  for (const [group, selectedName] of Object.entries(getTabSettings())) {
+    const selectors = selectorsToSync[group];
+    // it's possible that stale state gives us empty selections, so we explicitly check here.
+    if (selectors) {
+      toggleAll(selectedName, selectors);
+    }
+  }
+});
+
+function throttle(func, wait) {
+  let waiting = false;
+  return function () {
+    if (!waiting) {
+      func.apply(this, arguments);
+      waiting = true;
+      setTimeout(function () {
+        waiting = false;
+      }, wait);
+    }
+  };
+}
+
+function nexttick(func) {
+  return setTimeout(func, 0);
+}
diff --git a/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/tippy.css b/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/tippy.css
new file mode 100644
index 0000000..e6ae635
--- /dev/null
+++ b/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/tippy.css
@@ -0,0 +1 @@
+.tippy-box[data-animation=fade][data-state=hidden]{opacity:0}[data-tippy-root]{max-width:calc(100vw - 10px)}.tippy-box{position:relative;background-color:#333;color:#fff;border-radius:4px;font-size:14px;line-height:1.4;white-space:normal;outline:0;transition-property:transform,visibility,opacity}.tippy-box[data-placement^=top]>.tippy-arrow{bottom:0}.tippy-box[data-placement^=top]>.tippy-arrow:before{bottom:-7px;left:0;border-width:8px 8px 0;border-top-color:initial;transform-origin:center top}.tippy-box[data-placement^=bottom]>.tippy-arrow{top:0}.tippy-box[data-placement^=bottom]>.tippy-arrow:before{top:-7px;left:0;border-width:0 8px 8px;border-bottom-color:initial;transform-origin:center bottom}.tippy-box[data-placement^=left]>.tippy-arrow{right:0}.tippy-box[data-placement^=left]>.tippy-arrow:before{border-width:8px 0 8px 8px;border-left-color:initial;right:-7px;transform-origin:center left}.tippy-box[data-placement^=right]>.tippy-arrow{left:0}.tippy-box[data-placement^=right]>.tippy-arrow:before{left:-7px;border-width:8px 8px 8px 0;border-right-color:initial;transform-origin:center right}.tippy-box[data-inertia][data-state=visible]{transition-timing-function:cubic-bezier(.54,1.5,.38,1.11)}.tippy-arrow{width:16px;height:16px;color:#333}.tippy-arrow:before{content:"";position:absolute;border-color:transparent;border-style:solid}.tippy-content{position:relative;padding:5px 9px;z-index:1}
\ No newline at end of file
diff --git a/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/tippy.umd.min.js b/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/tippy.umd.min.js
new file mode 100644
index 0000000..ca292be
--- /dev/null
+++ b/bs/.development/004GeneralisedLinearModel_files/libs/quarto-html/tippy.umd.min.js
@@ -0,0 +1,2 @@
+!function(e,t){"object"==typeof exports&&"undefined"!=typeof module?module.exports=t(require("@popperjs/core")):"function"==typeof define&&define.amd?define(["@popperjs/core"],t):(e=e||self).tippy=t(e.Popper)}(this,(function(e){"use strict";var t={passive:!0,capture:!0},n=function(){return document.body};function r(e,t,n){if(Array.isArray(e)){var r=e[t];return null==r?Array.isArray(n)?n[t]:n:r}return e}function o(e,t){var n={}.toString.call(e);return 0===n.indexOf("[object")&&n.indexOf(t+"]")>-1}function i(e,t){return"function"==typeof e?e.apply(void 0,t):e}function a(e,t){return 0===t?e:function(r){clearTimeout(n),n=setTimeout((function(){e(r)}),t)};var n}function s(e,t){var n=Object.assign({},e);return t.forEach((function(e){delete n[e]})),n}function u(e){return[].concat(e)}function c(e,t){-1===e.indexOf(t)&&e.push(t)}function p(e){return e.split("-")[0]}function f(e){return[].slice.call(e)}function l(e){return Object.keys(e).reduce((function(t,n){return void 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+
diff --git a/bs/.development/DiagnosticPlots.R b/bs/.development/DiagnosticPlots.R
deleted file mode 100644
index c0d6856..0000000
--- a/bs/.development/DiagnosticPlots.R
+++ /dev/null
@@ -1,181 +0,0 @@
-library(car)
-library(ggplot2)
-library(cowplot)
-
-diagnosticPlots <- function(df, formula) {
-  model <- lm(formula, data = df)
-  resids <- residuals(model)
-  fitted <- fitted(model)
-
-  # Identify influential points
-  p <- length(coef(model))
-  n <- length(resids)
-  leverage <- hatvalues(model)
-  cooks_dist <- cooks.distance(model)
-  high_leverage_threshold <- (2 * (p + 1)) / n
-  high_cooks_threshold <- 4 / n
-  influential_points <- which(
-    leverage > high_leverage_threshold | cooks_dist > high_cooks_threshold
-  )
-
-  # resids vs fitted
-  line_data <- lowess(fitted, resids) |> as.data.frame()
-  resids_fitted_df <- data.frame(fitted = fitted, residuals = resids, index = 1:n)
-  resids_vs_fitted <- ggplot(
-    data = resids_fitted_df,
-    aes(x = fitted, y = residuals)
-  ) +
-    geom_point() +
-    geom_hline(yintercept = 0,
-      linetype = "dashed",
-      color = "black",
-      size = 0.25
-    ) +
-    geom_line(
-      data = line_data,
-      aes(x = x, y = y)
-    ) +
-    geom_text(data = resids_fitted_df[influential_points, ],
-      aes(label = index),
-      vjust = -1,
-      color = "black",
-      size = 3) +
-    labs(
-      y = "Residuals", x = "Fitted values",
-      title = "Residuals vs Fitted values"
-    )
-
-  # qq norm plot
-  standardized_resids <- resids / sd(resids)
-  sqrt_resids <- sqrt(abs(standardized_resids))
-  ordered_resids <- sort(standardized_resids)
-  theoretical_quantiles <- qnorm((1:n) / (n + 1))
-  resids_quantiles_df <- data.frame(
-    quantiles = theoretical_quantiles, residuals = ordered_resids,
-    index = 1:n
-  )
-  slope <- sd(ordered_resids)
-  intercept <- mean(ordered_resids)
-  resids_vs_quantiles <- ggplot(
-    data = resids_quantiles_df,
-    aes(x = quantiles, y = residuals)
-  ) +
-    geom_point() +
-    geom_abline(
-      aes(
-        slope = slope,
-        intercept = intercept
-      )
-    ) +
-    geom_text(data = resids_quantiles_df[influential_points, ],
-      aes(label = index),
-      vjust = -1,
-      color = "black",
-      size = 3) +
-    labs(
-      y = "Standardized residuals", x = "Theoretical Quantiles",
-      title = "Q-Q Residuals"
-    )
-
-  # Manual Scale-Location Plot
-  line_data <- lowess(fitted, sqrt_resids) |> as.data.frame()
-  sqrt_resids_fitted_df <- data.frame(
-    fitted = fitted, residuals = sqrt_resids,
-    index = 1:n
-  )
-  sqrt_resids_vs_fitted <- ggplot(
-    data = sqrt_resids_fitted_df,
-    aes(x = fitted, y = residuals)
-  ) +
-    geom_point() +
-    geom_line(
-      data = line_data,
-      aes(x = x, y = y),
-      colour = "black"
-    ) +
-    geom_text(data = sqrt_resids_fitted_df[influential_points, ],
-      aes(label = index),
-      vjust = -1,
-      color = "black",
-      size = 3) +
-    labs(
-      y = expression(sqrt("Standardized residuals")),
-      x = "Fitted values",
-      title = "Scale-Location"
-    )
-
-  # Residuals vs Leverage
-  line_data <- lowess(leverage, standardized_resids) |> as.data.frame()
-  residuals_leverage_df <- data.frame(
-    residuals = standardized_resids, leverage = leverage,
-    index = 1:n
-  )
-  residuals_vs_leverage <- ggplot(
-    data = residuals_leverage_df,
-    aes(x = leverage, y = residuals)
-  ) +
-    geom_point() +
-    geom_line(
-      data = line_data,
-      aes(x = x, y = y)
-    ) +
-    geom_hline(yintercept = 0,
-      linetype = "dashed",
-      color = "black",
-      size = 0.25
-    ) +
-    geom_text(data = residuals_leverage_df[influential_points, ],
-      aes(label = index),
-      vjust = -1,
-      color = "black",
-      size = 3) +
-    labs(
-      y = "Standardized residuals", x = "Leverage",
-      title = "Residuals vs Leverage"
-    )
-
-  plot_grid(
-    resids_vs_fitted,
-    resids_vs_quantiles,
-    sqrt_resids_vs_fitted,
-    residuals_vs_leverage
-  )
-}
-
-df <- CO2
-f <- formula(uptake ~ conc)
-p <- diagnosticPlots(df, f)
-print(p)
-
-model <- lm(f, data = df)
-par(mfrow = c(3, 2))
-plot(model)
-plot(model, 4)
-
-CooksDistance <- function(df, formula) {
-  # https://rpubs.com/DragonflyStats/Cooks-Distance
-  model <- lm(formula, data = df)
-  cd <- cooks.distance(model)
-  cd <- data.frame(CooksDistance = cd,
-    Index = 1:length(cd))
-  n <- nrow(df)
-  # NOTE: number of predictors -1 (remove intercept via -1)
-  k <- length(coef(model)) - 1 
-  cutoff <- 4 / (n - k - 1)
-  ggplot(data = cd, aes(Index, CooksDistance)) +
-    geom_point() +
-    geom_line() +
-    geom_hline(yintercept = cutoff,
-      linetype = "dashed",
-      color = "black",
-      size = 0.25
-    ) +
-    geom_text(data = cd[cd$CooksDistance >= cutoff, ],
-      aes(label = Index),
-      vjust = -1,
-      color = "black",
-      size = 3)
-}
-
-CooksDistance(df, f)
-
diff --git a/bs/.development/Distris.R b/bs/.development/Distris.R
deleted file mode 100644
index 61b717f..0000000
--- a/bs/.development/Distris.R
+++ /dev/null
@@ -1,28 +0,0 @@
-dnorm(0.25, mean = 0, sd = 1)
-dnorm(0.5, mean = 0, sd = 1)
-dnorm(0.005, mean = 0, sd = 1)
-dnorm(5, mean = 0, sd = 1)
-dnorm(0.01, mean = 0, sd = 1)
-
-mean <- 0
-sd <- 1
-set.seed(123) # For reproducibility
-samples <- rnorm(1000, mean, sd)
-hist(samples,
-  breaks = 30, probability = TRUE, col = "lightgray",
-  main = "Histogram of Random Samples with PDF Overlay",
-  xlab = "x", ylab = "Density", ylim = c(0, 1.25)
-)
-
-x <- seq(-4, 4, length.out = 100)
-lines(x, dnorm(x, mean, sd), col = "blue", lwd = 2)
-
-x <- seq(-4, 4, length.out = 100)
-lines(x, pnorm(x, mean, sd), type = "l", lwd = 2, col = "red")
-
-lines(density(samples), col = "green", lwd = 2)
-
-legend("topright",
-  legend = c("PDF (dnorm)", "CDF (pnorm)", "Empirical Density", "Histogram of Samples"),
-  col = c("blue", "red", "green", "lightgray"), lwd = 2, fill = c(NA, NA, NA, "lightgray")
-)
diff --git a/bs/.development/Distris_files/figure-html/Likelihood-1.png b/bs/.development/Distris_files/figure-html/Likelihood-1.png
deleted file mode 100644
index 9609417..0000000
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diff --git a/bs/.development/Distris_files/figure-html/Regressions Continued-1.png b/bs/.development/Distris_files/figure-html/Regressions Continued-1.png
deleted file mode 100644
index 5990e36..0000000
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diff --git a/bs/.development/Distris_files/figure-html/Regressions-1.png b/bs/.development/Distris_files/figure-html/Regressions-1.png
deleted file mode 100644
index a6bcfd5..0000000
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diff --git a/bs/.development/Distris_files/figure-html/Regressions-2.png b/bs/.development/Distris_files/figure-html/Regressions-2.png
deleted file mode 100644
index 366e14a..0000000
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diff --git a/bs/.development/Distris_files/figure-html/plot-histogram-2.png b/bs/.development/Distris_files/figure-html/plot-histogram-2.png
deleted file mode 100644
index 9444f42..0000000
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diff --git a/bs/.development/Distris_files/libs/bootstrap/bootstrap-icons.woff b/bs/.development/Distris_files/libs/bootstrap/bootstrap-icons.woff
deleted file mode 100644
index dbeeb05..0000000
Binary files a/bs/.development/Distris_files/libs/bootstrap/bootstrap-icons.woff and /dev/null differ
diff --git a/bs/.development/Distris_files/libs/bootstrap/bootstrap.min.js b/bs/.development/Distris_files/libs/bootstrap/bootstrap.min.js
deleted file mode 100644
index e8f21f7..0000000
--- a/bs/.development/Distris_files/libs/bootstrap/bootstrap.min.js
+++ /dev/null
@@ -1,7 +0,0 @@
-/*!
-  * Bootstrap v5.3.1 (https://getbootstrap.com/)
-  * Copyright 2011-2023 The Bootstrap Authors (https://github.com/twbs/bootstrap/graphs/contributors)
-  * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)
-  */
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J,Z="x"===y?zt:Vt,tt="x"===y?Rt:qt,et=A[w],it="y"===w?"height":"width",nt=et+g[Z],st=et-g[tt],ot=-1!==[zt,Vt].indexOf(_),rt=null!=(J=null==x?void 0:x[w])?J:0,at=ot?nt:et-E[it]-T[it]-rt+O.altAxis,lt=ot?et+E[it]+T[it]-rt-O.altAxis:st,ct=f&&ot?function(t,e,i){var n=Ne(t,e,i);return n>i?i:n}(at,et,lt):Ne(f?at:nt,et,f?lt:st);A[w]=ct,k[w]=ct-et}e.modifiersData[n]=k}},requiresIfExists:["offset"]};function di(t,e,i){void 0===i&&(i=!1);var n,s,o=me(e),r=me(e)&&function(t){var e=t.getBoundingClientRect(),i=we(e.width)/t.offsetWidth||1,n=we(e.height)/t.offsetHeight||1;return 1!==i||1!==n}(e),a=Le(e),l=Te(t,r,i),c={scrollLeft:0,scrollTop:0},h={x:0,y:0};return(o||!o&&!i)&&(("body"!==ue(e)||Ue(a))&&(c=(n=e)!==fe(n)&&me(n)?{scrollLeft:(s=n).scrollLeft,scrollTop:s.scrollTop}:Xe(n)),me(e)?((h=Te(e,!0)).x+=e.clientLeft,h.y+=e.clientTop):a&&(h.x=Ye(a))),{x:l.left+c.scrollLeft-h.x,y:l.top+c.scrollTop-h.y,width:l.width,height:l.height}}function ui(t){var e=new Map,i=new Set,n=[];function s(t){i.add(t.name),[].concat(t.requires||[],t.requiresIfExists||[]).forEach((function(t){if(!i.has(t)){var n=e.get(t);n&&s(n)}})),n.push(t)}return t.forEach((function(t){e.set(t.name,t)})),t.forEach((function(t){i.has(t.name)||s(t)})),n}var fi={placement:"bottom",modifiers:[],strategy:"absolute"};function pi(){for(var t=arguments.length,e=new Array(t),i=0;iNumber.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_getPopperConfig(){const t={placement:this._getPlacement(),modifiers:[{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"offset",options:{offset:this._getOffset()}}]};return(this._inNavbar||"static"===this._config.display)&&(F.setDataAttribute(this._menu,"popper","static"),t.modifiers=[{name:"applyStyles",enabled:!1}]),{...t,...g(this._config.popperConfig,[t])}}_selectMenuItem({key:t,target:e}){const i=z.find(".dropdown-menu 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e=/input|textarea/i.test(t.target.tagName),i="Escape"===t.key,n=[Ei,Ti].includes(t.key);if(!n&&!i)return;if(e&&!i)return;t.preventDefault();const s=this.matches(Ii)?this:z.prev(this,Ii)[0]||z.next(this,Ii)[0]||z.findOne(Ii,t.delegateTarget.parentNode),o=qi.getOrCreateInstance(s);if(n)return t.stopPropagation(),o.show(),void o._selectMenuItem(t);o._isShown()&&(t.stopPropagation(),o.hide(),s.focus())}}N.on(document,Si,Ii,qi.dataApiKeydownHandler),N.on(document,Si,Pi,qi.dataApiKeydownHandler),N.on(document,Li,qi.clearMenus),N.on(document,Di,qi.clearMenus),N.on(document,Li,Ii,(function(t){t.preventDefault(),qi.getOrCreateInstance(this).toggle()})),m(qi);const Vi="backdrop",Ki="show",Qi=`mousedown.bs.${Vi}`,Xi={className:"modal-backdrop",clickCallback:null,isAnimated:!1,isVisible:!0,rootElement:"body"},Yi={className:"string",clickCallback:"(function|null)",isAnimated:"boolean",isVisible:"boolean",rootElement:"(element|string)"};class Ui extends H{constructor(t){super(),this._config=this._getConfig(t),this._isAppended=!1,this._element=null}static get Default(){return Xi}static get DefaultType(){return Yi}static get NAME(){return Vi}show(t){if(!this._config.isVisible)return void g(t);this._append();const e=this._getElement();this._config.isAnimated&&d(e),e.classList.add(Ki),this._emulateAnimation((()=>{g(t)}))}hide(t){this._config.isVisible?(this._getElement().classList.remove(Ki),this._emulateAnimation((()=>{this.dispose(),g(t)}))):g(t)}dispose(){this._isAppended&&(N.off(this._element,Qi),this._element.remove(),this._isAppended=!1)}_getElement(){if(!this._element){const t=document.createElement("div");t.className=this._config.className,this._config.isAnimated&&t.classList.add("fade"),this._element=t}return this._element}_configAfterMerge(t){return t.rootElement=r(t.rootElement),t}_append(){if(this._isAppended)return;const t=this._getElement();this._config.rootElement.append(t),N.on(t,Qi,(()=>{g(this._config.clickCallback)})),this._isAppended=!0}_emulateAnimation(t){_(t,this._getElement(),this._config.isAnimated)}}const Gi=".bs.focustrap",Ji=`focusin${Gi}`,Zi=`keydown.tab${Gi}`,tn="backward",en={autofocus:!0,trapElement:null},nn={autofocus:"boolean",trapElement:"element"};class sn extends H{constructor(t){super(),this._config=this._getConfig(t),this._isActive=!1,this._lastTabNavDirection=null}static get Default(){return en}static get DefaultType(){return nn}static get NAME(){return"focustrap"}activate(){this._isActive||(this._config.autofocus&&this._config.trapElement.focus(),N.off(document,Gi),N.on(document,Ji,(t=>this._handleFocusin(t))),N.on(document,Zi,(t=>this._handleKeydown(t))),this._isActive=!0)}deactivate(){this._isActive&&(this._isActive=!1,N.off(document,Gi))}_handleFocusin(t){const{trapElement:e}=this._config;if(t.target===document||t.target===e||e.contains(t.target))return;const i=z.focusableChildren(e);0===i.length?e.focus():this._lastTabNavDirection===tn?i[i.length-1].focus():i[0].focus()}_handleKeydown(t){"Tab"===t.key&&(this._lastTabNavDirection=t.shiftKey?tn:"forward")}}const on=".fixed-top, .fixed-bottom, .is-fixed, .sticky-top",rn=".sticky-top",an="padding-right",ln="margin-right";class cn{constructor(){this._element=document.body}getWidth(){const t=document.documentElement.clientWidth;return Math.abs(window.innerWidth-t)}hide(){const t=this.getWidth();this._disableOverFlow(),this._setElementAttributes(this._element,an,(e=>e+t)),this._setElementAttributes(on,an,(e=>e+t)),this._setElementAttributes(rn,ln,(e=>e-t))}reset(){this._resetElementAttributes(this._element,"overflow"),this._resetElementAttributes(this._element,an),this._resetElementAttributes(on,an),this._resetElementAttributes(rn,ln)}isOverflowing(){return this.getWidth()>0}_disableOverFlow(){this._saveInitialAttribute(this._element,"overflow"),this._element.style.overflow="hidden"}_setElementAttributes(t,e,i){const n=this.getWidth();this._applyManipulationCallback(t,(t=>{if(t!==this._element&&window.innerWidth>t.clientWidth+n)return;this._saveInitialAttribute(t,e);const s=window.getComputedStyle(t).getPropertyValue(e);t.style.setProperty(e,`${i(Number.parseFloat(s))}px`)}))}_saveInitialAttribute(t,e){const i=t.style.getPropertyValue(e);i&&F.setDataAttribute(t,e,i)}_resetElementAttributes(t,e){this._applyManipulationCallback(t,(t=>{const i=F.getDataAttribute(t,e);null!==i?(F.removeDataAttribute(t,e),t.style.setProperty(e,i)):t.style.removeProperty(e)}))}_applyManipulationCallback(t,e){if(o(t))e(t);else for(const i of z.find(t,this._element))e(i)}}const hn=".bs.modal",dn=`hide${hn}`,un=`hidePrevented${hn}`,fn=`hidden${hn}`,pn=`show${hn}`,mn=`shown${hn}`,gn=`resize${hn}`,_n=`click.dismiss${hn}`,bn=`mousedown.dismiss${hn}`,vn=`keydown.dismiss${hn}`,yn=`click${hn}.data-api`,wn="modal-open",An="show",En="modal-static",Tn={backdrop:!0,focus:!0,keyboard:!0},Cn={backdrop:"(boolean|string)",focus:"boolean",keyboard:"boolean"};class On extends W{constructor(t,e){super(t,e),this._dialog=z.findOne(".modal-dialog",this._element),this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._isShown=!1,this._isTransitioning=!1,this._scrollBar=new cn,this._addEventListeners()}static get Default(){return Tn}static get DefaultType(){return Cn}static get NAME(){return"modal"}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||this._isTransitioning||N.trigger(this._element,pn,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._isTransitioning=!0,this._scrollBar.hide(),document.body.classList.add(wn),this._adjustDialog(),this._backdrop.show((()=>this._showElement(t))))}hide(){this._isShown&&!this._isTransitioning&&(N.trigger(this._element,dn).defaultPrevented||(this._isShown=!1,this._isTransitioning=!0,this._focustrap.deactivate(),this._element.classList.remove(An),this._queueCallback((()=>this._hideModal()),this._element,this._isAnimated())))}dispose(){N.off(window,hn),N.off(this._dialog,hn),this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}handleUpdate(){this._adjustDialog()}_initializeBackDrop(){return new Ui({isVisible:Boolean(this._config.backdrop),isAnimated:this._isAnimated()})}_initializeFocusTrap(){return new sn({trapElement:this._element})}_showElement(t){document.body.contains(this._element)||document.body.append(this._element),this._element.style.display="block",this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.scrollTop=0;const e=z.findOne(".modal-body",this._dialog);e&&(e.scrollTop=0),d(this._element),this._element.classList.add(An),this._queueCallback((()=>{this._config.focus&&this._focustrap.activate(),this._isTransitioning=!1,N.trigger(this._element,mn,{relatedTarget:t})}),this._dialog,this._isAnimated())}_addEventListeners(){N.on(this._element,vn,(t=>{"Escape"===t.key&&(this._config.keyboard?this.hide():this._triggerBackdropTransition())})),N.on(window,gn,(()=>{this._isShown&&!this._isTransitioning&&this._adjustDialog()})),N.on(this._element,bn,(t=>{N.one(this._element,_n,(e=>{this._element===t.target&&this._element===e.target&&("static"!==this._config.backdrop?this._config.backdrop&&this.hide():this._triggerBackdropTransition())}))}))}_hideModal(){this._element.style.display="none",this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._isTransitioning=!1,this._backdrop.hide((()=>{document.body.classList.remove(wn),this._resetAdjustments(),this._scrollBar.reset(),N.trigger(this._element,fn)}))}_isAnimated(){return this._element.classList.contains("fade")}_triggerBackdropTransition(){if(N.trigger(this._element,un).defaultPrevented)return;const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._element.style.overflowY;"hidden"===e||this._element.classList.contains(En)||(t||(this._element.style.overflowY="hidden"),this._element.classList.add(En),this._queueCallback((()=>{this._element.classList.remove(En),this._queueCallback((()=>{this._element.style.overflowY=e}),this._dialog)}),this._dialog),this._element.focus())}_adjustDialog(){const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._scrollBar.getWidth(),i=e>0;if(i&&!t){const t=p()?"paddingLeft":"paddingRight";this._element.style[t]=`${e}px`}if(!i&&t){const t=p()?"paddingRight":"paddingLeft";this._element.style[t]=`${e}px`}}_resetAdjustments(){this._element.style.paddingLeft="",this._element.style.paddingRight=""}static jQueryInterface(t,e){return this.each((function(){const i=On.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===i[t])throw new TypeError(`No method named "${t}"`);i[t](e)}}))}}N.on(document,yn,'[data-bs-toggle="modal"]',(function(t){const e=z.getElementFromSelector(this);["A","AREA"].includes(this.tagName)&&t.preventDefault(),N.one(e,pn,(t=>{t.defaultPrevented||N.one(e,fn,(()=>{a(this)&&this.focus()}))}));const i=z.findOne(".modal.show");i&&On.getInstance(i).hide(),On.getOrCreateInstance(e).toggle(this)})),R(On),m(On);const xn=".bs.offcanvas",kn=".data-api",Ln=`load${xn}${kn}`,Sn="show",Dn="showing",$n="hiding",In=".offcanvas.show",Nn=`show${xn}`,Pn=`shown${xn}`,Mn=`hide${xn}`,jn=`hidePrevented${xn}`,Fn=`hidden${xn}`,Hn=`resize${xn}`,Wn=`click${xn}${kn}`,Bn=`keydown.dismiss${xn}`,zn={backdrop:!0,keyboard:!0,scroll:!1},Rn={backdrop:"(boolean|string)",keyboard:"boolean",scroll:"boolean"};class qn extends W{constructor(t,e){super(t,e),this._isShown=!1,this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._addEventListeners()}static get Default(){return zn}static get DefaultType(){return Rn}static get NAME(){return"offcanvas"}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||N.trigger(this._element,Nn,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._backdrop.show(),this._config.scroll||(new cn).hide(),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.classList.add(Dn),this._queueCallback((()=>{this._config.scroll&&!this._config.backdrop||this._focustrap.activate(),this._element.classList.add(Sn),this._element.classList.remove(Dn),N.trigger(this._element,Pn,{relatedTarget:t})}),this._element,!0))}hide(){this._isShown&&(N.trigger(this._element,Mn).defaultPrevented||(this._focustrap.deactivate(),this._element.blur(),this._isShown=!1,this._element.classList.add($n),this._backdrop.hide(),this._queueCallback((()=>{this._element.classList.remove(Sn,$n),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._config.scroll||(new cn).reset(),N.trigger(this._element,Fn)}),this._element,!0)))}dispose(){this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}_initializeBackDrop(){const t=Boolean(this._config.backdrop);return new Ui({className:"offcanvas-backdrop",isVisible:t,isAnimated:!0,rootElement:this._element.parentNode,clickCallback:t?()=>{"static"!==this._config.backdrop?this.hide():N.trigger(this._element,jn)}:null})}_initializeFocusTrap(){return new sn({trapElement:this._element})}_addEventListeners(){N.on(this._element,Bn,(t=>{"Escape"===t.key&&(this._config.keyboard?this.hide():N.trigger(this._element,jn))}))}static jQueryInterface(t){return this.each((function(){const e=qn.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t]||t.startsWith("_")||"constructor"===t)throw new TypeError(`No method named "${t}"`);e[t](this)}}))}}N.on(document,Wn,'[data-bs-toggle="offcanvas"]',(function(t){const e=z.getElementFromSelector(this);if(["A","AREA"].includes(this.tagName)&&t.preventDefault(),l(this))return;N.one(e,Fn,(()=>{a(this)&&this.focus()}));const i=z.findOne(In);i&&i!==e&&qn.getInstance(i).hide(),qn.getOrCreateInstance(e).toggle(this)})),N.on(window,Ln,(()=>{for(const t of z.find(In))qn.getOrCreateInstance(t).show()})),N.on(window,Hn,(()=>{for(const t of z.find("[aria-modal][class*=show][class*=offcanvas-]"))"fixed"!==getComputedStyle(t).position&&qn.getOrCreateInstance(t).hide()})),R(qn),m(qn);const Vn={"*":["class","dir","id","lang","role",/^aria-[\w-]*$/i],a:["target","href","title","rel"],area:[],b:[],br:[],col:[],code:[],div:[],em:[],hr:[],h1:[],h2:[],h3:[],h4:[],h5:[],h6:[],i:[],img:["src","srcset","alt","title","width","height"],li:[],ol:[],p:[],pre:[],s:[],small:[],span:[],sub:[],sup:[],strong:[],u:[],ul:[]},Kn=new Set(["background","cite","href","itemtype","longdesc","poster","src","xlink:href"]),Qn=/^(?!javascript:)(?:[a-z0-9+.-]+:|[^&:/?#]*(?:[/?#]|$))/i,Xn=(t,e)=>{const i=t.nodeName.toLowerCase();return e.includes(i)?!Kn.has(i)||Boolean(Qn.test(t.nodeValue)):e.filter((t=>t instanceof RegExp)).some((t=>t.test(i)))},Yn={allowList:Vn,content:{},extraClass:"",html:!1,sanitize:!0,sanitizeFn:null,template:"
"},Un={allowList:"object",content:"object",extraClass:"(string|function)",html:"boolean",sanitize:"boolean",sanitizeFn:"(null|function)",template:"string"},Gn={entry:"(string|element|function|null)",selector:"(string|element)"};class Jn extends H{constructor(t){super(),this._config=this._getConfig(t)}static get Default(){return Yn}static get DefaultType(){return Un}static get NAME(){return"TemplateFactory"}getContent(){return Object.values(this._config.content).map((t=>this._resolvePossibleFunction(t))).filter(Boolean)}hasContent(){return this.getContent().length>0}changeContent(t){return this._checkContent(t),this._config.content={...this._config.content,...t},this}toHtml(){const t=document.createElement("div");t.innerHTML=this._maybeSanitize(this._config.template);for(const[e,i]of Object.entries(this._config.content))this._setContent(t,i,e);const e=t.children[0],i=this._resolvePossibleFunction(this._config.extraClass);return i&&e.classList.add(...i.split(" ")),e}_typeCheckConfig(t){super._typeCheckConfig(t),this._checkContent(t.content)}_checkContent(t){for(const[e,i]of Object.entries(t))super._typeCheckConfig({selector:e,entry:i},Gn)}_setContent(t,e,i){const n=z.findOne(i,t);n&&((e=this._resolvePossibleFunction(e))?o(e)?this._putElementInTemplate(r(e),n):this._config.html?n.innerHTML=this._maybeSanitize(e):n.textContent=e:n.remove())}_maybeSanitize(t){return this._config.sanitize?function(t,e,i){if(!t.length)return t;if(i&&"function"==typeof i)return i(t);const n=(new window.DOMParser).parseFromString(t,"text/html"),s=[].concat(...n.body.querySelectorAll("*"));for(const t of s){const i=t.nodeName.toLowerCase();if(!Object.keys(e).includes(i)){t.remove();continue}const n=[].concat(...t.attributes),s=[].concat(e["*"]||[],e[i]||[]);for(const e of n)Xn(e,s)||t.removeAttribute(e.nodeName)}return n.body.innerHTML}(t,this._config.allowList,this._config.sanitizeFn):t}_resolvePossibleFunction(t){return g(t,[this])}_putElementInTemplate(t,e){if(this._config.html)return e.innerHTML="",void e.append(t);e.textContent=t.textContent}}const Zn=new Set(["sanitize","allowList","sanitizeFn"]),ts="fade",es="show",is=".modal",ns="hide.bs.modal",ss="hover",os="focus",rs={AUTO:"auto",TOP:"top",RIGHT:p()?"left":"right",BOTTOM:"bottom",LEFT:p()?"right":"left"},as={allowList:Vn,animation:!0,boundary:"clippingParents",container:!1,customClass:"",delay:0,fallbackPlacements:["top","right","bottom","left"],html:!1,offset:[0,6],placement:"top",popperConfig:null,sanitize:!0,sanitizeFn:null,selector:!1,template:'',title:"",trigger:"hover focus"},ls={allowList:"object",animation:"boolean",boundary:"(string|element)",container:"(string|element|boolean)",customClass:"(string|function)",delay:"(number|object)",fallbackPlacements:"array",html:"boolean",offset:"(array|string|function)",placement:"(string|function)",popperConfig:"(null|object|function)",sanitize:"boolean",sanitizeFn:"(null|function)",selector:"(string|boolean)",template:"string",title:"(string|element|function)",trigger:"string"};class cs extends W{constructor(t,e){if(void 0===vi)throw new TypeError("Bootstrap's tooltips require Popper (https://popper.js.org)");super(t,e),this._isEnabled=!0,this._timeout=0,this._isHovered=null,this._activeTrigger={},this._popper=null,this._templateFactory=null,this._newContent=null,this.tip=null,this._setListeners(),this._config.selector||this._fixTitle()}static get Default(){return as}static get DefaultType(){return ls}static get NAME(){return"tooltip"}enable(){this._isEnabled=!0}disable(){this._isEnabled=!1}toggleEnabled(){this._isEnabled=!this._isEnabled}toggle(){this._isEnabled&&(this._activeTrigger.click=!this._activeTrigger.click,this._isShown()?this._leave():this._enter())}dispose(){clearTimeout(this._timeout),N.off(this._element.closest(is),ns,this._hideModalHandler),this._element.getAttribute("data-bs-original-title")&&this._element.setAttribute("title",this._element.getAttribute("data-bs-original-title")),this._disposePopper(),super.dispose()}show(){if("none"===this._element.style.display)throw new Error("Please use show on visible elements");if(!this._isWithContent()||!this._isEnabled)return;const t=N.trigger(this._element,this.constructor.eventName("show")),e=(c(this._element)||this._element.ownerDocument.documentElement).contains(this._element);if(t.defaultPrevented||!e)return;this._disposePopper();const i=this._getTipElement();this._element.setAttribute("aria-describedby",i.getAttribute("id"));const{container:n}=this._config;if(this._element.ownerDocument.documentElement.contains(this.tip)||(n.append(i),N.trigger(this._element,this.constructor.eventName("inserted"))),this._popper=this._createPopper(i),i.classList.add(es),"ontouchstart"in document.documentElement)for(const t of[].concat(...document.body.children))N.on(t,"mouseover",h);this._queueCallback((()=>{N.trigger(this._element,this.constructor.eventName("shown")),!1===this._isHovered&&this._leave(),this._isHovered=!1}),this.tip,this._isAnimated())}hide(){if(this._isShown()&&!N.trigger(this._element,this.constructor.eventName("hide")).defaultPrevented){if(this._getTipElement().classList.remove(es),"ontouchstart"in document.documentElement)for(const t of[].concat(...document.body.children))N.off(t,"mouseover",h);this._activeTrigger.click=!1,this._activeTrigger[os]=!1,this._activeTrigger[ss]=!1,this._isHovered=null,this._queueCallback((()=>{this._isWithActiveTrigger()||(this._isHovered||this._disposePopper(),this._element.removeAttribute("aria-describedby"),N.trigger(this._element,this.constructor.eventName("hidden")))}),this.tip,this._isAnimated())}}update(){this._popper&&this._popper.update()}_isWithContent(){return Boolean(this._getTitle())}_getTipElement(){return this.tip||(this.tip=this._createTipElement(this._newContent||this._getContentForTemplate())),this.tip}_createTipElement(t){const e=this._getTemplateFactory(t).toHtml();if(!e)return null;e.classList.remove(ts,es),e.classList.add(`bs-${this.constructor.NAME}-auto`);const i=(t=>{do{t+=Math.floor(1e6*Math.random())}while(document.getElementById(t));return t})(this.constructor.NAME).toString();return e.setAttribute("id",i),this._isAnimated()&&e.classList.add(ts),e}setContent(t){this._newContent=t,this._isShown()&&(this._disposePopper(),this.show())}_getTemplateFactory(t){return this._templateFactory?this._templateFactory.changeContent(t):this._templateFactory=new Jn({...this._config,content:t,extraClass:this._resolvePossibleFunction(this._config.customClass)}),this._templateFactory}_getContentForTemplate(){return{".tooltip-inner":this._getTitle()}}_getTitle(){return this._resolvePossibleFunction(this._config.title)||this._element.getAttribute("data-bs-original-title")}_initializeOnDelegatedTarget(t){return this.constructor.getOrCreateInstance(t.delegateTarget,this._getDelegateConfig())}_isAnimated(){return this._config.animation||this.tip&&this.tip.classList.contains(ts)}_isShown(){return this.tip&&this.tip.classList.contains(es)}_createPopper(t){const e=g(this._config.placement,[this,t,this._element]),i=rs[e.toUpperCase()];return 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if("manual"!==e){const t=e===ss?this.constructor.eventName("mouseenter"):this.constructor.eventName("focusin"),i=e===ss?this.constructor.eventName("mouseleave"):this.constructor.eventName("focusout");N.on(this._element,t,this._config.selector,(t=>{const e=this._initializeOnDelegatedTarget(t);e._activeTrigger["focusin"===t.type?os:ss]=!0,e._enter()})),N.on(this._element,i,this._config.selector,(t=>{const e=this._initializeOnDelegatedTarget(t);e._activeTrigger["focusout"===t.type?os:ss]=e._element.contains(t.relatedTarget),e._leave()}))}this._hideModalHandler=()=>{this._element&&this.hide()},N.on(this._element.closest(is),ns,this._hideModalHandler)}_fixTitle(){const t=this._element.getAttribute("title");t&&(this._element.getAttribute("aria-label")||this._element.textContent.trim()||this._element.setAttribute("aria-label",t),this._element.setAttribute("data-bs-original-title",t),this._element.removeAttribute("title"))}_enter(){this._isShown()||this._isHovered?this._isHovered=!0:(this._isHovered=!0,this._setTimeout((()=>{this._isHovered&&this.show()}),this._config.delay.show))}_leave(){this._isWithActiveTrigger()||(this._isHovered=!1,this._setTimeout((()=>{this._isHovered||this.hide()}),this._config.delay.hide))}_setTimeout(t,e){clearTimeout(this._timeout),this._timeout=setTimeout(t,e)}_isWithActiveTrigger(){return Object.values(this._activeTrigger).includes(!0)}_getConfig(t){const e=F.getDataAttributes(this._element);for(const t of Object.keys(e))Zn.has(t)&&delete e[t];return t={...e,..."object"==typeof t&&t?t:{}},t=this._mergeConfigObj(t),t=this._configAfterMerge(t),this._typeCheckConfig(t),t}_configAfterMerge(t){return t.container=!1===t.container?document.body:r(t.container),"number"==typeof t.delay&&(t.delay={show:t.delay,hide:t.delay}),"number"==typeof t.title&&(t.title=t.title.toString()),"number"==typeof t.content&&(t.content=t.content.toString()),t}_getDelegateConfig(){const t={};for(const[e,i]of Object.entries(this._config))this.constructor.Default[e]!==i&&(t[e]=i);return t.selector=!1,t.trigger="manual",t}_disposePopper(){this._popper&&(this._popper.destroy(),this._popper=null),this.tip&&(this.tip.remove(),this.tip=null)}static jQueryInterface(t){return this.each((function(){const e=cs.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}}m(cs);const hs={...cs.Default,content:"",offset:[0,8],placement:"right",template:'',trigger:"click"},ds={...cs.DefaultType,content:"(null|string|element|function)"};class us extends cs{static get Default(){return hs}static get DefaultType(){return ds}static get 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e=this._observableSections.get(t.target.hash);if(e){t.preventDefault();const i=this._rootElement||window,n=e.offsetTop-this._element.offsetTop;if(i.scrollTo)return void i.scrollTo({top:n,behavior:"smooth"});i.scrollTop=n}})))}_getNewObserver(){const t={root:this._rootElement,threshold:this._config.threshold,rootMargin:this._config.rootMargin};return new IntersectionObserver((t=>this._observerCallback(t)),t)}_observerCallback(t){const e=t=>this._targetLinks.get(`#${t.target.id}`),i=t=>{this._previousScrollData.visibleEntryTop=t.target.offsetTop,this._process(e(t))},n=(this._rootElement||document.documentElement).scrollTop,s=n>=this._previousScrollData.parentScrollTop;this._previousScrollData.parentScrollTop=n;for(const o of t){if(!o.isIntersecting){this._activeTarget=null,this._clearActiveClass(e(o));continue}const t=o.target.offsetTop>=this._previousScrollData.visibleEntryTop;if(s&&t){if(i(o),!n)return}else s||t||i(o)}}_initializeTargetsAndObservables(){this._targetLinks=new Map,this._observableSections=new Map;const t=z.find(bs,this._config.target);for(const e of t){if(!e.hash||l(e))continue;const t=z.findOne(decodeURI(e.hash),this._element);a(t)&&(this._targetLinks.set(decodeURI(e.hash),e),this._observableSections.set(e.hash,t))}}_process(t){this._activeTarget!==t&&(this._clearActiveClass(this._config.target),this._activeTarget=t,t.classList.add(_s),this._activateParents(t),N.trigger(this._element,ps,{relatedTarget:t}))}_activateParents(t){if(t.classList.contains("dropdown-item"))z.findOne(".dropdown-toggle",t.closest(".dropdown")).classList.add(_s);else for(const e of z.parents(t,".nav, .list-group"))for(const t of z.prev(e,ys))t.classList.add(_s)}_clearActiveClass(t){t.classList.remove(_s);const e=z.find(`${bs}.${_s}`,t);for(const t of e)t.classList.remove(_s)}static jQueryInterface(t){return this.each((function(){const e=Es.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t]||t.startsWith("_")||"constructor"===t)throw new TypeError(`No method named "${t}"`);e[t]()}}))}}N.on(window,gs,(()=>{for(const t of z.find('[data-bs-spy="scroll"]'))Es.getOrCreateInstance(t)})),m(Es);const Ts=".bs.tab",Cs=`hide${Ts}`,Os=`hidden${Ts}`,xs=`show${Ts}`,ks=`shown${Ts}`,Ls=`click${Ts}`,Ss=`keydown${Ts}`,Ds=`load${Ts}`,$s="ArrowLeft",Is="ArrowRight",Ns="ArrowUp",Ps="ArrowDown",Ms="Home",js="End",Fs="active",Hs="fade",Ws="show",Bs=":not(.dropdown-toggle)",zs='[data-bs-toggle="tab"], [data-bs-toggle="pill"], [data-bs-toggle="list"]',Rs=`.nav-link${Bs}, .list-group-item${Bs}, [role="tab"]${Bs}, ${zs}`,qs=`.${Fs}[data-bs-toggle="tab"], .${Fs}[data-bs-toggle="pill"], .${Fs}[data-bs-toggle="list"]`;class Vs extends W{constructor(t){super(t),this._parent=this._element.closest('.list-group, .nav, [role="tablist"]'),this._parent&&(this._setInitialAttributes(this._parent,this._getChildren()),N.on(this._element,Ss,(t=>this._keydown(t))))}static get NAME(){return"tab"}show(){const t=this._element;if(this._elemIsActive(t))return;const e=this._getActiveElem(),i=e?N.trigger(e,Cs,{relatedTarget:t}):null;N.trigger(t,xs,{relatedTarget:e}).defaultPrevented||i&&i.defaultPrevented||(this._deactivate(e,t),this._activate(t,e))}_activate(t,e){t&&(t.classList.add(Fs),this._activate(z.getElementFromSelector(t)),this._queueCallback((()=>{"tab"===t.getAttribute("role")?(t.removeAttribute("tabindex"),t.setAttribute("aria-selected",!0),this._toggleDropDown(t,!0),N.trigger(t,ks,{relatedTarget:e})):t.classList.add(Ws)}),t,t.classList.contains(Hs)))}_deactivate(t,e){t&&(t.classList.remove(Fs),t.blur(),this._deactivate(z.getElementFromSelector(t)),this._queueCallback((()=>{"tab"===t.getAttribute("role")?(t.setAttribute("aria-selected",!1),t.setAttribute("tabindex","-1"),this._toggleDropDown(t,!1),N.trigger(t,Os,{relatedTarget:e})):t.classList.remove(Ws)}),t,t.classList.contains(Hs)))}_keydown(t){if(![$s,Is,Ns,Ps,Ms,js].includes(t.key))return;t.stopPropagation(),t.preventDefault();const e=this._getChildren().filter((t=>!l(t)));let i;if([Ms,js].includes(t.key))i=e[t.key===Ms?0:e.length-1];else{const n=[Is,Ps].includes(t.key);i=b(e,t.target,n,!0)}i&&(i.focus({preventScroll:!0}),Vs.getOrCreateInstance(i).show())}_getChildren(){return z.find(Rs,this._parent)}_getActiveElem(){return this._getChildren().find((t=>this._elemIsActive(t)))||null}_setInitialAttributes(t,e){this._setAttributeIfNotExists(t,"role","tablist");for(const t of e)this._setInitialAttributesOnChild(t)}_setInitialAttributesOnChild(t){t=this._getInnerElement(t);const e=this._elemIsActive(t),i=this._getOuterElement(t);t.setAttribute("aria-selected",e),i!==t&&this._setAttributeIfNotExists(i,"role","presentation"),e||t.setAttribute("tabindex","-1"),this._setAttributeIfNotExists(t,"role","tab"),this._setInitialAttributesOnTargetPanel(t)}_setInitialAttributesOnTargetPanel(t){const e=z.getElementFromSelector(t);e&&(this._setAttributeIfNotExists(e,"role","tabpanel"),t.id&&this._setAttributeIfNotExists(e,"aria-labelledby",`${t.id}`))}_toggleDropDown(t,e){const i=this._getOuterElement(t);if(!i.classList.contains("dropdown"))return;const n=(t,n)=>{const s=z.findOne(t,i);s&&s.classList.toggle(n,e)};n(".dropdown-toggle",Fs),n(".dropdown-menu",Ws),i.setAttribute("aria-expanded",e)}_setAttributeIfNotExists(t,e,i){t.hasAttribute(e)||t.setAttribute(e,i)}_elemIsActive(t){return t.classList.contains(Fs)}_getInnerElement(t){return t.matches(Rs)?t:z.findOne(Rs,t)}_getOuterElement(t){return t.closest(".nav-item, .list-group-item")||t}static jQueryInterface(t){return this.each((function(){const e=Vs.getOrCreateInstance(this);if("string"==typeof t){if(void 0===e[t]||t.startsWith("_")||"constructor"===t)throw new TypeError(`No method named "${t}"`);e[t]()}}))}}N.on(document,Ls,zs,(function(t){["A","AREA"].includes(this.tagName)&&t.preventDefault(),l(this)||Vs.getOrCreateInstance(this).show()})),N.on(window,Ds,(()=>{for(const t of z.find(qs))Vs.getOrCreateInstance(t)})),m(Vs);const Ks=".bs.toast",Qs=`mouseover${Ks}`,Xs=`mouseout${Ks}`,Ys=`focusin${Ks}`,Us=`focusout${Ks}`,Gs=`hide${Ks}`,Js=`hidden${Ks}`,Zs=`show${Ks}`,to=`shown${Ks}`,eo="hide",io="show",no="showing",so={animation:"boolean",autohide:"boolean",delay:"number"},oo={animation:!0,autohide:!0,delay:5e3};class ro extends W{constructor(t,e){super(t,e),this._timeout=null,this._hasMouseInteraction=!1,this._hasKeyboardInteraction=!1,this._setListeners()}static get Default(){return oo}static get DefaultType(){return so}static get NAME(){return"toast"}show(){N.trigger(this._element,Zs).defaultPrevented||(this._clearTimeout(),this._config.animation&&this._element.classList.add("fade"),this._element.classList.remove(eo),d(this._element),this._element.classList.add(io,no),this._queueCallback((()=>{this._element.classList.remove(no),N.trigger(this._element,to),this._maybeScheduleHide()}),this._element,this._config.animation))}hide(){this.isShown()&&(N.trigger(this._element,Gs).defaultPrevented||(this._element.classList.add(no),this._queueCallback((()=>{this._element.classList.add(eo),this._element.classList.remove(no,io),N.trigger(this._element,Js)}),this._element,this._config.animation)))}dispose(){this._clearTimeout(),this.isShown()&&this._element.classList.remove(io),super.dispose()}isShown(){return this._element.classList.contains(io)}_maybeScheduleHide(){this._config.autohide&&(this._hasMouseInteraction||this._hasKeyboardInteraction||(this._timeout=setTimeout((()=>{this.hide()}),this._config.delay)))}_onInteraction(t,e){switch(t.type){case"mouseover":case"mouseout":this._hasMouseInteraction=e;break;case"focusin":case"focusout":this._hasKeyboardInteraction=e}if(e)return void this._clearTimeout();const i=t.relatedTarget;this._element===i||this._element.contains(i)||this._maybeScheduleHide()}_setListeners(){N.on(this._element,Qs,(t=>this._onInteraction(t,!0))),N.on(this._element,Xs,(t=>this._onInteraction(t,!1))),N.on(this._element,Ys,(t=>this._onInteraction(t,!0))),N.on(this._element,Us,(t=>this._onInteraction(t,!1)))}_clearTimeout(){clearTimeout(this._timeout),this._timeout=null}static jQueryInterface(t){return this.each((function(){const e=ro.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t](this)}}))}}return R(ro),m(ro),{Alert:Q,Button:Y,Carousel:xt,Collapse:Bt,Dropdown:qi,Modal:On,Offcanvas:qn,Popover:us,ScrollSpy:Es,Tab:Vs,Toast:ro,Tooltip:cs}})); -//# sourceMappingURL=bootstrap.bundle.min.js.map \ No newline at end of file diff --git a/bs/.development/Distris_files/libs/quarto-html/anchor.min.js b/bs/.development/Distris_files/libs/quarto-html/anchor.min.js deleted file mode 100644 index 5ac814d..0000000 --- a/bs/.development/Distris_files/libs/quarto-html/anchor.min.js +++ /dev/null @@ -1,9 +0,0 @@ -// @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&dn=expat.txt Expat -// -// AnchorJS - v5.0.0 - 2023-01-18 -// https://www.bryanbraun.com/anchorjs/ -// Copyright (c) 2023 Bryan Braun; Licensed MIT -// -// @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&dn=expat.txt Expat -!function(A,e){"use strict";"function"==typeof define&&define.amd?define([],e):"object"==typeof module&&module.exports?module.exports=e():(A.AnchorJS=e(),A.anchors=new 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t=e.state,n=e.name,r=t.rects.reference,o=t.rects.popper,i=t.modifiersData.preventOverflow,a=J(t,{elementContext:"reference"}),s=J(t,{altBoundary:!0}),f=ve(a,r),c=ve(s,o,i),p=ye(f),u=ye(c);t.modifiersData[n]={referenceClippingOffsets:f,popperEscapeOffsets:c,isReferenceHidden:p,hasPopperEscaped:u},t.attributes.popper=Object.assign({},t.attributes.popper,{"data-popper-reference-hidden":p,"data-popper-escaped":u})}},be=Z({defaultModifiers:[ee,te,oe,ie]}),xe=[ee,te,oe,ie,ae,le,he,me,ge],we=Z({defaultModifiers:xe});e.applyStyles=ie,e.arrow=me,e.computeStyles=oe,e.createPopper=we,e.createPopperLite=be,e.defaultModifiers=xe,e.detectOverflow=J,e.eventListeners=ee,e.flip=le,e.hide=ge,e.offset=ae,e.popperGenerator=Z,e.popperOffsets=te,e.preventOverflow=he,Object.defineProperty(e,"__esModule",{value:!0})})); - diff --git a/bs/.development/FormulaHelper.R b/bs/.development/FormulaHelper.R deleted file mode 100644 index a206f64..0000000 --- a/bs/.development/FormulaHelper.R +++ /dev/null @@ -1,18 +0,0 @@ -get_formula <- function(model) { - call <- model$call |> as.character() - e <- try( - { - as.formula(call[2]) - }, - silent = TRUE - ) - if (inherits(e, "try-error")) { - return(get(call[2]) |> knitr::kable()) - } else { - return(knitr::kable(call[2])) - } -} - -show <- function(model) { - knitr::kable(broom::tidy(model)) -} diff --git a/bs/.development/Regression_linear_model_files/figure-html/Regressions-1.png b/bs/.development/Regression_linear_model_files/figure-html/Regressions-1.png deleted file mode 100644 index 1afa818..0000000 Binary files a/bs/.development/Regression_linear_model_files/figure-html/Regressions-1.png and /dev/null differ diff --git a/bs/.development/Rplots.pdf b/bs/.development/Rplots.pdf deleted file mode 100644 index ea7f0ef..0000000 Binary files a/bs/.development/Rplots.pdf and /dev/null differ diff --git a/bs/.development/deploy.R b/bs/.development/deploy.R deleted file mode 100644 index 3cbafb4..0000000 --- a/bs/.development/deploy.R +++ /dev/null @@ -1,4 +0,0 @@ -setwd("/home/konrad/Documents/Biostats") - -shinylive::export("./bs/inst/serverless_app/", "docs") -httpuv::runStaticServer("docs/") diff --git a/bs/.development/minimalApp.R b/bs/.development/minimalApp.R deleted file mode 100644 index f233de6..0000000 --- a/bs/.development/minimalApp.R +++ /dev/null @@ -1,56 +0,0 @@ -library(shiny) - -ui <- fluidPage( - # JavaScript to initialize the popover with interactive content on click - tags$script(HTML(" - $(document).ready(function() { - // Initialize the popover on click instead of hover - $('#aovTest').popover({ - trigger: 'click', // Opens on click - html: true, - content: '', - placement: 'bottom' - }); - - // Set up click event for the button inside the popover - $(document).on('click', '#popoverBtn', function() { - Shiny.setInputValue('go_to_tab', 'infoTab'); - $('#aovTest').popover('hide'); // Hide the popover after clicking the button - }); - - // Close the popover if clicking outside of it - $(document).on('click', function(e) { - if (!$(e.target).closest('#aovTest').length) { - $('#aovTest').popover('hide'); - } - }); - }); - ")), - - # UI with tab layout - tabsetPanel( - id = "mainTabset", - tabPanel("Main", - # Action button with popover for interactive tooltip - actionButton( - "aovTest", "ANOVA" - ), - p("This is the Main tab.") - ), - tabPanel("Info", - value = "infoTab", # This is the ID to match in JavaScript - h3("ANOVA Information"), - p("Here are more details about ANOVA...") - ) - ) -) - -server <- function(input, output, session) { - # Observe the JavaScript input and update the selected tab - observeEvent(input$go_to_tab, { - updateTabsetPanel(session, "mainTabset", selected = input$go_to_tab) - }) -} - -shinyApp(ui, server) - diff --git a/bs/.development/remove_buttons.R b/bs/.development/remove_buttons.R deleted file mode 100644 index c62235b..0000000 --- a/bs/.development/remove_buttons.R +++ /dev/null @@ -1,55 +0,0 @@ -library(shiny) - -ui <- fluidPage( - titlePanel("Dynamic List with Remove Buttons"), - sidebarLayout( - sidebarPanel( - numericInput("num_input", "Enter a number:", value = 0), - actionButton("add_btn", "Add to List") - ), - mainPanel( - uiOutput("dynamic_list") - ) - ) -) - -server <- function(input, output, session) { - listValues <- reactiveVal(list()) - observeEvent(input$add_btn, { - current_list <- listValues() - new_item_name <- paste0("item_", length(current_list) + 1) - current_list[[new_item_name]] <- input$num_input - listValues(current_list) - }) - - # Dynamically render the list UI - output$dynamic_list <- renderUI({ - current_list <- listValues() - if (length(current_list) == 0) { - return("No items in the list.") - } - # Create UI elements for each item in the list - tagList(lapply(names(current_list), function(name) { - div( - style = "margin-bottom: 10px;", - span(paste(name, ":", current_list[[name]]), style = "margin-right: 10px;"), - actionButton(name, "Remove", class = "btn-danger btn-sm") - ) - })) - }) - - # Observe and handle remove buttons dynamically - observe({ - current_list <- listValues() - lapply(names(current_list), function(name) { - observeEvent(input[[name]], { - current_list <- listValues() - current_list[[name]] <- NULL # Remove the item - listValues(current_list) - }, ignoreInit = TRUE) - }) - }) -} - -shinyApp(ui, server) - diff --git a/bs/R/DoseResponse.R b/bs/R/DoseResponse.R index c156520..8c18ae5 100644 --- a/bs/R/DoseResponse.R +++ b/bs/R/DoseResponse.R @@ -17,8 +17,16 @@ DoseResponseSidebarUI <- function(id) { ), br(), uiOutput(NS(id, "substanceNamesUI")), - uiOutput(NS(id, "negIdentifierUI")), - uiOutput(NS(id, "posIdentifierUI")), + checkboxInput( + NS(id, "xTransform"), + label = "Log transform x-axis", + value = FALSE + ), + checkboxInput( + NS(id, "yTransform"), + label = "Log transform y-axis", + value = FALSE + ), actionButton(NS(id, "ic50"), "Conduct analysis") ) ) @@ -41,9 +49,13 @@ DoseResponseUI <- function(id) { tabPanel( "Results Plot", uiOutput(NS(id, "dropdown_plots")), - plotOutput(NS(id, "dr_result_plot")), + plotOutput( + NS(id, "dr_result_plot"), + click = NS(id, "plot_click") + ), actionButton(NS(id, "previousPage"), "Previous plot"), - actionButton(NS(id, "nextPage"), "Next plot") + actionButton(NS(id, "nextPage"), "Next plot"), + p("Click on the plot to mark outliers") ) ) ) @@ -56,10 +68,11 @@ DoseResponseServer <- function(id, data, listResults) { names = NULL, # For dropdown_plots overview_plots = NULL, currentPage = 1, - currentPageOverview = 1 + currentPageOverview = 1, + outliers = NULL ) - # Render names, conc and abs column + # Render names of substances output[["substanceNamesUI"]] <- renderUI({ req(!is.null(data$df)) req(is.data.frame(data$df)) @@ -81,52 +94,6 @@ DoseResponseServer <- function(id, data, listResults) { ) }) - output[["negIdentifierUI"]] <- renderUI({ - req(!is.null(data$df)) - req(is.data.frame(data$df)) - req(input$`substanceNames`) - choices <- unique(data$df[[input$substanceNames]]) - req(length(choices) >= 1) - tooltip <- "Select the name used for the negative control" - div( - tags$label( - "Dependent Variable", - class = "tooltip", - title = tooltip, - `data-toggle` = "tooltip" - ), - selectInput( - inputId = paste0("DOSERESPONSE-negIdentifier"), - label = "Name of the negative control", - choices = choices[1:length(choices)], - selected = NULL - ) - ) - }) - - output[["posIdentifierUI"]] <- renderUI({ - req(!is.null(data$df)) - req(is.data.frame(data$df)) - req(input$`substanceNames`) - choices <- unique(data$df[[input$substanceNames]]) - req(length(choices) >= 1) - tooltip <- "Select the name used for the positive control" - div( - tags$label( - "Dependent Variable", - class = "tooltip", - title = tooltip, - `data-toggle` = "tooltip" - ), - selectInput( - inputId = paste0("DOSERESPONSE-posIdentifier"), - label = "Name of the positive control", - choices = choices[1:length(choices)], - selected = NULL - ) - ) - }) - # Render split by group output[["open_split_by_group"]] <- renderUI({ actionButton(NS(id, "open_split_by_group"), @@ -206,15 +173,11 @@ DoseResponseServer <- function(id, data, listResults) { }) }) - drFct <- function() { + drFct <- function(reset_outliers = TRUE) { req(is.data.frame(data$df)) df <- data$df req(input$substanceNames) names <- input$substanceNames - req(input$negIdentifier) - neg <- input$negIdentifier - req(input$posIdentifier) - pos <- input$posIdentifier print_noti(!is.null(data$formula), "You have to set a formula") req(!is.null(data$formula)) r_vals$plots <- NULL # reset @@ -222,51 +185,73 @@ DoseResponseServer <- function(id, data, listResults) { r_vals$currentPage <- 1 # reset r_vals$overview_plots <- NULL # reset r_vals$currentPageOverview <- 1 # reset + if (reset_outliers) { + r_vals$outliers <- NULL + } + is_xlog <- input$xTransform + is_ylog <- input$yTransform f <- as.character(data$formula) + formula <- data$formula dep <- f[2] indep <- f[3] err <- NULL resDF <- NULL resPlot <- NULL - e <- try({ - check_ast(str2lang(indep), colnames(df)) - check_ast(str2lang(dep), colnames(df)) - res <- ic50(df, dep, indep, names, neg, pos) - stopifnot(!inherits(res, "errorClass")) - resDF <- lapply(res, function(x) { - if (inherits(x, "errorClass")) { - return(NULL) - } - return(x[[1]]) - }) - resDF <- resDF[!is.null(resDF)] - resDF <- resDF[!sapply(resDF, is.null)] - resDF <- Reduce(rbind, resDF) - resP <- lapply(res, function(x) { - if (inherits(x, "errorClass")) { - return(NULL) + e <- try( + { + check_formula(formula) + check_ast(str2lang(indep), colnames(df)) + check_ast(str2lang(dep), colnames(df)) + res <- ic50( + df, dep, + indep, names, r_vals$outliers, + is_xlog, is_ylog + ) + if (inherits(res, "errorClass")) { + stop(res$error_message) } - return(x[[2]]) - }) - resP <- resP[!is.null(resP)] - resP <- resP[!sapply(resP, is.null)] - r_vals$plots <- resP - r_vals$names <- resDF$name - resPlot <- resP - overviewPlots <- create_plot_pages(resPlot) - r_vals$overview_plots <- overviewPlots - }) + resDF <- lapply(res, function(x) { + if (inherits(x, "errorClass")) { + return(NULL) + } + return(x[[1]]) + }) + resDF <- resDF[!is.null(resDF)] + resDF <- resDF[!sapply(resDF, is.null)] + resDF <- Reduce(rbind, resDF) + resP <- lapply(res, function(x) { + if (inherits(x, "errorClass")) { + return(NULL) + } + return(x[[2]]) + }) + resP <- resP[!is.null(resP)] + resP <- resP[!sapply(resP, is.null)] + r_vals$plots <- resP + r_vals$names <- resDF$name + resPlot <- resP + overviewPlots <- create_plot_pages(resPlot) + r_vals$overview_plots <- overviewPlots + }, + silent = TRUE + ) if (inherits(e, "try-error")) { err <- conditionMessage(attr(e, "condition")) print_noti(FALSE, err) } else { listResults$curr_data <- new("doseResponse", df = resDF, p = resPlot) - listResults$curr_name <- paste("Test Nr", length(listResults$all_names) + 1, "Conducted dose response analysis") + listResults$curr_name <- paste( + "Test Nr", length(listResults$all_names) + 1, + "Conducted dose response analysis" + ) output$dr_result <- renderTable(resDF, digits = 6) listResults$counter <- listResults$counter + 1 new_result_name <- paste0("DoseResponseNr", listResults$counter) - listResults$all_data[[new_result_name]] <- new("doseResponse", df = resDF, p = resPlot) + listResults$all_data[[new_result_name]] <- new( + "doseResponse", + df = resDF, p = resPlot + ) exportTestValues( doseresponse_res = listResults$curr_data @@ -326,6 +311,47 @@ DoseResponseServer <- function(id, data, listResults) { } }) + observeEvent(input$plot_click, { + req(!is.null(input$plot_click)) + req(is.data.frame(data$df)) + print_noti(!is.null(data$formula), "You have to set a formula") + try({ + click <- input$plot_click + df <- data$df + indices <- which(df$names == r_vals$names[r_vals$currentPage]) + indices <- data.frame( + original_indices = indices, + new_indices = seq_along(indices) + ) + sub_df <- df[df$names == r_vals$names[r_vals$currentPage], ] + f <- as.character(data$formula) + formula <- data$formula + check_formula(formula) + dep <- f[2] + indep <- f[3] + x <- as.numeric(sub_df[, indep]) + y <- as.numeric(sub_df[, dep]) + x <- x[!is.na(x)] + y <- y[!is.na(y)] + distances <- sqrt((x - click$x)^2 + (y - click$y)^2) + nearest <- which.min(distances) + if (distances[nearest] < 0.1) { + nearest <- indices[indices$new_indices == nearest, "original_indices"] + if (nearest %in% r_vals$outliers) { + r_vals$outliers <- r_vals$outliers[r_vals$outliers != nearest] + } else { + r_vals$outliers <- c( + r_vals$outliers, + nearest + ) + } + old_current_page <- r_vals$currentPage + drFct(FALSE) + r_vals$currentPage <- old_current_page + } + }) + }) + # Display overview plots observe({ req(!is.null(r_vals$overview_plots)) diff --git a/bs/R/lc50.r b/bs/R/lc50.r index 3f95f3e..d15409b 100644 --- a/bs/R/lc50.r +++ b/bs/R/lc50.r @@ -3,10 +3,10 @@ errorClass <- R6::R6Class("errorClass", error_message = NULL, object = NULL, initialize = function(error_message = NULL) { - self$error_message = error_message + self$error_message <- error_message }, isNull = function() { - if(is.null(self$error_message)) { + if (is.null(self$error_message)) { return(TRUE) } return(FALSE) @@ -14,285 +14,365 @@ errorClass <- R6::R6Class("errorClass", ) ) -shapenumber <- function (my.number) { - if (is.finite(my.number)) { - my.result <- signif(my.number,3) - } else { - my.result <- NA - } - return (my.result) +shapenumber <- function(num) { + if (is.finite(num)) { + res <- signif(num) + } else { + res <- NA + } + return(res) } -#calculates the robust 68th percentile of the residuals -#adapted from Motulsky HJ, Brown RE, BMC Bioinformatics 2006, 7:123 -robust_68_percentile <- function (residuals) { +# calculates the robust 68th percentile of the residuals +# adapted from Motulsky HJ, Brown RE, BMC Bioinformatics 2006, 7:123 +robust_68_percentile <- function(residuals) { res <- abs(residuals) res_sorted <- sort(res) - res_percentiles <- (seq(1:length(res_sorted))/length(res_sorted))*100 - index <- min(which(res_percentiles > 68.25)) - x <- c(res_percentiles[index-1],res_percentiles[index]) - y <- c(res_sorted[index-1],res_sorted[index]) - m <- lm(y~x) - x <- c(68.25) + res_percentiles <- (seq_len(length(res_sorted)) / length(res_sorted)) + index <- min(which(res_percentiles > 0.6825)) + x <- c(res_percentiles[index - 1], res_percentiles[index]) + y <- c(res_sorted[index - 1], res_sorted[index]) + m <- lm(y ~ x) + x <- 0.6825 y <- predict(m, as.data.frame(x)) return(y) } -#calculates the robust standard deviation of the residuals (RSDR) with correction for degrees of freedom -#adapted from Motulsky HJ, Brown RE, BMC Bioinformatics 2006, 7:123 -robust_standard_deviation_residuals <- function(residuals, number_of_coefficients_fitted) { - my_residuals <- as.numeric(residuals) - my_residuals <- na.omit(residuals) - N <- length(my_residuals) #the number of data points fitted - K <- number_of_coefficients_fitted #for ic50, 4 coefficients are fitted - result <- robust_68_percentile(residuals) * N/(N-K) - return (result) +# calculates the robust standard deviation of the residuals (RSDR) +# with correction for degrees of freedom +# adapted from Motulsky HJ, Brown RE, BMC Bioinformatics 2006, 7:123 +# robust_standard_deviation_residuals = rsdr +rsdr <- function(residuals, number_of_coefficients_fitted) { + resids <- as.numeric(residuals) + resids <- na.omit(residuals) + N <- length(resids) + robust_68_percentile(residuals) * + N / (N - number_of_coefficients_fitted) } -#false discovery rate (FDR) approach, returns a T/F vector for selection of valid data points -#adapted from Motulsky HJ, Brown RE, BMC Bioinformatics 2006, 7:123 +# false discovery rate (FDR) approach, +# returns a T/F vector for selection of valid data points +# adapted from Motulsky HJ, Brown RE, BMC Bioinformatics 2006, 7:123 false_discovery_rate <- function(res) { - N <- length(res) - Q <- 0.01 #Q=1% - K <- 4 #number of coefficients in the fitted LL.4 model - R <- robust_standard_deviation_residuals(res,K) #the robust standard deviation of the residuals - id <- seq(1:length(res)) - df <- data.frame(id,res) + N <- length(res) + # Q=1% + Q <- 0.01 + # number of coefficients in the fitted LL.4 model + K <- 4 + R <- rsdr(res, K) + id <- seq_len(length(res)) + df <- data.frame(id, res) df$res_abs <- abs(df$res) - df <- df[order(df$res_abs),] + df <- df[order(df$res_abs), ] df$i <- seq(1:N) df$i_fraction <- df$i / N - df$alpha <- Q*(N-(df$i-1))/N + df$alpha <- Q * (N - (df$i - 1)) / N df$t <- df$res_abs / R - df$P <- dt(df$t, N-K) + df$P <- dt(df$t, N - K) df$include <- ifelse(df$P < df$alpha & df$i_fraction >= 0.7, FALSE, TRUE) df2 <- df[order(df$id), ] - return (df2$include) + return(df2$include) } -check_fit <- function(model, min_conc, max_conc, min_abs, max_abs, substance_name) { - if(model$fit$convergence != TRUE) return(errorClass$new(paste(substance_name, - "Model did not converge"))) - b <- coefficients(model)[1] #Hill coefficient - c <- coefficients(model)[2] #asymptote 1 - d <- coefficients(model)[3] #asymptote 2 - e <- coefficients(model)[4] #IC50 - RSE <- summary(model)$rseMat[1] #residual standard error estimated - Response_lowestdose_predicted <- predict(model, data.frame(concentration = min_conc), se.fit = FALSE)[1] - Response_highestdose_predicted <- predict(model, data.frame(concentration = max_conc), se.fit = FALSE)[1] - Response_difference <- 100 * abs(Response_lowestdose_predicted - Response_highestdose_predicted) +check_fit <- function(model, min_conc, max_conc, + min_abs, max_abs, substance_name) { + if (model$fit$convergence != TRUE) { + return(errorClass$new(paste( + substance_name, + "Model did not converge" + ))) + } + b <- coefficients(model)[1] # Hill coefficient + c <- coefficients(model)[2] # asymptote 1 + d <- coefficients(model)[3] # asymptote 2 + e <- coefficients(model)[4] # IC50 + RSE <- summary(model)$rseMat[1] # residual standard error estimated + Response_lowestdose_predicted <- predict( + model, data.frame(concentration = min_conc), + se.fit = FALSE + )[1] + Response_highestdose_predicted <- predict( + model, data.frame(concentration = max_conc), + se.fit = FALSE + )[1] + Response_difference <- abs( + Response_lowestdose_predicted - Response_highestdose_predicted + ) HillCoefficient <- b - IC50_relative <- e - pIC50 <- -log10(e/1000000) + IC50_relative <- e Problems <- "" - if (Response_difference < 25) { - Problems <- paste(Problems, "Response Difference lower than 25%", collapse = " , ") - } else if(IC50_relative > max_conc) { - Problems <- paste(Problems, "IC50 larger than highest measured concentration", collapse = " , ") - } else if(IC50_relative < min_conc) { - Problems <- paste(Problems, "IC50 lower than lowest measured concentration", collapse = " , ") - } - + if (Response_difference < 0.25) { + Problems <- paste(Problems, + "Response Difference lower than 25%", + collapse = " , " + ) + } else if (IC50_relative > max_conc) { + Problems <- paste(Problems, + "IC50 larger than highest measured concentration", + collapse = " , " + ) + } else if (IC50_relative < min_conc) { + Problems <- paste(Problems, + "IC50 lower than lowest measured concentration", + collapse = " , " + ) + } confidence_interval <- confint(model, parm = c("e"), level = 0.95) - IC50_relative_lower <- confidence_interval[1] + IC50_relative_lower <- confidence_interval[1] IC50_relative_higher <- confidence_interval[2] p_value <- noEffect(model)[3] Response_lowestdose_predicted <- shapenumber(Response_lowestdose_predicted) Response_highestdose_predicted <- shapenumber(Response_highestdose_predicted) - HillCoefficient <- shapenumber(HillCoefficient) + HillCoefficient <- shapenumber(HillCoefficient) IC50_relative <- shapenumber(IC50_relative) IC50_relative_lower <- shapenumber(IC50_relative_lower) IC50_relative_higher <- shapenumber(IC50_relative_higher) - pIC50 <- shapenumber( -log10(IC50_relative/1000000)) + pIC50 <- shapenumber(-log10(IC50_relative)) p_value <- shapenumber(p_value) - ylim_low = 0 - ylim_high = 125 - if (min_abs < ylim_low) ylim_low <- min_abs - if (max_abs > ylim_high) ylim_high <- max_abs - outvar <- data.frame(name = substance_name, - Response_lowestdose_predicted = Response_lowestdose_predicted, - Response_highestdose_predicted = Response_highestdose_predicted, - HillCoefficient = HillCoefficient, - asymptote_one = c, asymptote_two = d, - IC50_relative = IC50_relative, IC50_relative_lower = IC50_relative_lower, - IC50_relative_higher = IC50_relative_higher, pIC50 = pIC50, - RSE = RSE, p_value = p_value, Problems = Problems) - return (outvar) + outvar <- data.frame( + name = substance_name, + Response_lowestdose_predicted = Response_lowestdose_predicted, + Response_highestdose_predicted = Response_highestdose_predicted, + HillCoefficient = HillCoefficient, + asymptote_one = c, asymptote_two = d, + IC50_relative = IC50_relative, IC50_relative_lower = IC50_relative_lower, + IC50_relative_higher = IC50_relative_higher, pIC50 = pIC50, + RSE = RSE, p_value = p_value, Problems = Problems + ) + return(outvar) +} + +drawplotOnlyRawData <- function(df, abs_col, conc_col, title) { + data_measured <- data.frame(conc = df[, conc_col], abs = df[, abs_col]) + p <- ggplot() + + geom_boxplot( + data = data_measured, + aes(x = conc, y = abs, group = conc) + ) + + geom_point( + data = data_measured, + aes(x = conc, y = abs) + ) + + xlab("Concentration") + # Concentration in µM + ylab("Viability") + # Viaibility [%] + ggtitle(title) + return(p) +} + +addOutlierLayer <- function(df_outlier, abs_col, conc_col, p) { + if (nrow(df_outlier) == 0) { + return(p) + } + p <- p + + geom_point( + data = df_outlier, + aes( + x = df_outlier[, conc_col], + y = df_outlier[, abs_col], color = "Outlier" + ) + ) + + scale_color_manual( + name = "", + values = "darkorange" + ) } drawplot <- function(df, abs_col, conc_col, model, valid_points, title, - IC50_relative, IC50_relative_lower, IC50_relative_higher) { + IC50_relative, IC50_relative_lower, IC50_relative_higher, + df_outlier) { min_conc <- min(df[, conc_col]) max_conc <- max(df[, conc_col]) grid <- seq(min_conc, max_conc, 0.1) plotFct <- (model$curve)[[1]] res <- plotFct(grid) - data <- data.frame(abs = res, - conc = grid) - data_measured <- data.frame(conc = df[, conc_col], abs = df[, abs_col]) - p <- ggplot() + - geom_boxplot(data = data_measured, aes(x = conc, y = abs*100, group = conc)) + - geom_line(data = data, aes(x = conc, y = abs*100)) + - xlab("Concentration [µM]") + - ylab("Viability [%]") + - ggtitle(title) - - max_conc <- max(df[, conc_col]) + 10 - min_conc <- -10 + data <- data.frame( + abs = res, + conc = grid + ) + p <- drawplotOnlyRawData(df, abs_col, conc_col, title) + + geom_line(data = data, aes(x = conc, y = abs)) + p <- addOutlierLayer(df_outlier, abs_col, conc_col, p) + max_conc <- max(df[, conc_col]) + + 0.1 * (max(df[, conc_col]) - min(df[, conc_col])) + min_conc <- min(df[, conc_col]) - 0.1 * min(df[, conc_col]) xmin <- IC50_relative - IC50_relative_lower xmax <- IC50_relative + IC50_relative_higher - if (!is.na(xmin) & !is.na(xmax)) { - ymin <- min(df[, abs_col]) * 100 - ymax <- max(df[, abs_col]) * 100 + if (!is.na(xmin) && !is.na(xmax)) { + ymin <- min(df[, abs_col]) + ymax <- max(df[, abs_col]) yrange <- ymax - ymin butt_height <- yrange * 0.1 - ymedian <- median(df[, abs_col]) * 100 - if (xmin > min_conc && xmax < max_conc ) { - p <- p + geom_errorbarh(aes(xmin = xmin, - xmax = xmax, y = ymedian), - colour = "darkred", end = "butt", height = butt_height) + ymedian <- median(df[, abs_col]) + if (xmin > min_conc && xmax < max_conc) { + p <- p + geom_errorbarh( + aes( + xmin = xmin, + xmax = xmax, y = ymedian + ), + colour = "darkred", end = "butt", height = butt_height + ) } else { p <- p + labs(caption = "Confidence intervall not in conc. range") + - theme(plot.caption = element_text(color = "darkred", face = "italic", size = 7)) - } + theme( + plot.caption = + element_text(color = "darkred", face = "italic", size = 8) + ) + } } else { p <- p + labs(caption = "Confidence intervall could not be calculated") + - theme(plot.caption = element_text(color = "darkred", face = "italic", size = 7)) + theme( + plot.caption = + element_text(color = "darkred", face = "italic", size = 8) + ) } - + return(p) } -ic50_internal <- function(df, abs, conc, title) { - model <- drm(abs ~ conc, data = df , fct = LL.4(), robust = "median") +ic50_internal <- function(df, abs, conc, title, df_outlier) { + model <- drm(abs ~ conc, + data = df, fct = LL.4(), + robust = "median" + ) valid_points <- false_discovery_rate(residuals(model)) - model <- drm(abs ~ conc, data = df , subset = valid_points, start = model$coefficients, fct = LL.4(), robust = "mean") - res <- check_fit(model, min(df[, conc]), max(df[, conc]), min(df[, abs]), max(df[, abs]), title) - p <- drawplot(df, abs, conc, model, valid_points, title, res$IC50_relative, - res$IC50_relative_lower, res$IC50_relative_higher) + model <- drm(abs ~ conc, + data = df, + subset = valid_points, + start = model$coefficients, + fct = LL.4(), robust = "mean", + ) + res <- check_fit( + model, min(df[, conc]), + max(df[, conc]), min(df[, abs]), max(df[, abs]), title + ) + p <- drawplot( + df, abs, conc, model, valid_points, title, res$IC50_relative, + res$IC50_relative_lower, res$IC50_relative_higher, df_outlier + ) return(list(res, p)) } -drawplotOnlyRawData <- function(df, abs_col, conc_col, title) { - min_conc <- min(df[, conc_col]) - max_conc <- max(df[, conc_col]) - data_measured <- data.frame(conc = df[, conc_col], abs = df[, abs_col]) - p <- ggplot() + - geom_boxplot(data = data_measured, aes(x = conc, y = abs*100, group = conc)) + - xlab("Concentration [µM]") + - ylab("Viability [%]") + - ggtitle(title) - return(p) +check_dr_df <- function(df, abs_col, + conc_col, substance_name_col) { + if (!is.character(df[, substance_name_col]) && + !is.factor(df[, substance_name_col])) { + return(errorClass$new("The substance names are not character")) + } + substances <- unique(df[, substance_name_col]) + if (length(substances) < 1) { + return(errorClass$new("The data for compounds seems to be missing")) + } + if (!is.numeric(df[, abs_col])) { + return(errorClass$new("The absorbance data is not numerical")) + } + return(NULL) } -#' Calculates the ic50 values -#' @export -#' @import drc -#' @import ggplot2 -#' @param df a data.frame which contains all the data -#' @param abs_col the name of the column in df which contains the dependent variable -#' @param conc_col the name of the column in df which contains the different concentrations -#' @param substance_name_col the name of the column in df which contains the different names of the compounds -#' @param negative_identifier a character defining the name to identify the negative control within conc_col -#' @param positive_identifier a character defining the name to identify the positive control within conc_col -#' @return a list is returned containing the ic50 value the fitted plots and other parameters -#' @examples -#' path <- system.file("data", package = "MTT") -#' df <- read.csv(paste0(path, "/ExampleData.txt")) -#' ic50(df, "abs", "conc", "names", "neg", "pos") -ic50 <- function(df, abs_col, conc_col, substance_name_col, negative_identifier, positive_identifier) { - substances <- unique(df$names) - - if(!(negative_identifier %in% substances)) { - return(errorClass$new("the string for the negative control was not found!")) +transform_conc_dr <- function(conc_col) { + temp_conc <- as.numeric(conc_col) + if (all(is.na(temp_conc))) { + return(errorClass$new( + "The concentration data cannot be converted to numerical" + )) } - if(!(positive_identifier %in% substances)) { - return(errorClass$new("the string for the positive control was not found!")) + if (!is.numeric(temp_conc)) { + return(errorClass$new("The concentration data is not numerical")) } - substances <- substances[substances != negative_identifier] - substances <- substances[substances != positive_identifier] - if(length(substances) < 1) { - return(errorClass$new("The data for compounds seems to be missing")) + return(temp_conc) +} + +log_dr <- function(df, islog_x, islog_y) { + if (islog_x) { + df$conc <- log(df$conc) } - if(!is.numeric(df[, abs_col])) { - return(errorClass$new("The absorbance data is not numerical")) + if (islog_y) { + df$abs <- log(df$abs) } - temp_conc <- df[, conc_col] - temp_conc[temp_conc == negative_identifier] <- -1 - temp_conc[temp_conc == positive_identifier] <- -2 - temp_conc <- as.numeric(temp_conc) - if(any(is.na(temp_conc))) { - return(errorClass$new("The concentration data cannot be converted to numerical")) + return(df) +} + +#' @examples +#' path <- system.file("data", package = "MTT") +#' df <- read.csv(paste0(path, "/ExampleData.txt")) +#' ic50(df, "abs", "conc", "names", NULL, FALSE, FALSE) +ic50 <- function(df, abs_col, conc_col, + substance_name_col, outliers, + islog_x, islog_y) { + # Checks + err <- check_dr_df(df, abs_col, conc_col, substance_name_col) + if (inherits(err, "errorClass")) { + return(err) + } + substances <- unique(df[, substance_name_col]) + # Data preparation + temp_conc <- transform_conc_dr(df[, conc_col]) + if (inherits(temp_conc, "errorClass")) { + return(temp_conc) } df[, conc_col] <- temp_conc - if(!is.numeric(df[, conc_col])) { - return(errorClass$new("The concentration data is not numerical")) + df <- data.frame( + abs = df[, abs_col], + conc = df[, conc_col], + names = df[, substance_name_col] + ) + df <- log_dr(df, islog_x, islog_y) + df_outlier <- data.frame() + if (length(outliers) >= 1) { + df_outlier <- df[outliers, ] + df <- df[-outliers, ] } - neg_mean <- mean(df[df[ , substance_name_col] == negative_identifier, abs_col]) - pos_mean <- mean(df[df[ , substance_name_col] == positive_identifier, abs_col]) - df[, abs_col] <- (df[, abs_col] - pos_mean) / neg_mean + df <- df[!sapply(df$conc, is.na), ] res <- list() - for(i in seq_along(substances)) { + for (i in seq_along(substances)) { df_temp <- df[df$names == substances[i], ] - m <- tryCatch({ - m <- ic50_internal(df_temp, abs_col, conc_col, substances[i]) - }, - error = function(err) { - retval <- errorClass$new(paste("A warning occurred: ", conditionMessage(err))) - retval$object <- drawplotOnlyRawData(df_temp, abs_col, conc_col, substances[i]) - return(retval) - }) + df_temp_outlier <- df_outlier[df_outlier$names == substances[i], ] + m <- tryCatch( + { + m <- ic50_internal( + df_temp, + "abs", "conc", + substances[i], df_temp_outlier + ) + }, + error = function(err) { + retval <- errorClass$new( + paste("A warning occurred: ", conditionMessage(err)) + ) + retval$object <- drawplotOnlyRawData( + df_temp, "abs", "conc", substances[i] + ) + return(retval) + } + ) res[[i]] <- m } - return(res) } -report_plots <- function(ic50List) { - p3 <- ggdraw() + - draw_line(x = c(0, 1), y = c(0.5, 0.5), color = "black", size = 1) + - theme_void() - for(i in seq_along(ic50List)) { - if(is(ic50List[[i]], "errorClass")) { - p <- ic50List[[i]]$object - p <- p + - annotate("text", x = -Inf, y = -Inf, - hjust = -0.2, vjust = -1, label = ic50List[[i]]$error_message) - #print(p) - #print(p3) - next - } - p1 <- ic50List[[i]][[2]] - a <- ic50List[[i]][[1]] |> t() |> as.data.frame() - a <- data.frame(names = row.names(a), Predicition = a) - a[a$names == "Response_lowestdose_predicted", 1] <- "Response_lowestdose" - a[a$names == "Response_highestdose_predicted", 1] <- "Response_highestdose" - problem <- a[a$names == "Problems", 2] - a <- a[(a$names != "Problems") & (a$names != "name"), ] - p2 <- ggplot(a, aes(x = 0, y = factor(names), label = Prediction)) + - geom_line(size = 0) + - geom_text(position = position_nudge(x = -1.1), hjust = 0, size = 3) + - theme_minimal() + - theme(axis.text.x = element_blank(), - axis.ticks.x = element_blank(), - panel.grid.major.x = element_blank(), - panel.grid.minor.x = element_blank(), - panel.grid.major.y = element_blank(), - panel.grid.minor.y = element_blank(), - axis.title.x = element_blank(), - axis.title.y = element_blank(), - axis.text.y = element_text(hjust = 0, face = "bold"), - axis.line.y = element_line(), - plot.caption = element_text(hjust = 1, face = "italic", colour = "darkred", - size = 7) ) - if(problem != "") { - p2 <- p2 + labs(caption = paste("Note:", as.character(problem)) ) - } - - p <- ggdraw() + - draw_plot(p2, x = 0, y = 0, width = 0.5, height = 0.5) + - draw_plot(p1, x = 0.5, y = 0, width = 0.5, height = 0.5) - #print(p) - #print(p3) +df <- read.csv("/home/konrad/Documents/Biostats/test_data/Biostats_2.csv") +library(ggplot2) +library(drc) + +l <- ic50( + df, + "Activity_SpotTotalIntensity", + "concentration", "ColumnValues", + NULL, FALSE, TRUE +) +pf <- function(l, idx) { + p <- l[[idx]] + if (inherits(p, "errorClass")) { + print(p$error_message) + return(p$object) } + p[[2]] + scale_x_log10() } +pl <- lapply(1:20, function(i) pf(l, i)) +cowplot::plot_grid(plotlist = pl) +pl <- lapply(21:40, function(i) pf(l, i)) +cowplot::plot_grid(plotlist = pl) +pl <- lapply(41:60, function(i) pf(l, i)) +cowplot::plot_grid(plotlist = pl) + +rm(list = ls()) +head(df) diff --git a/test_data/Biostats_2.csv b/test_data/Biostats_2.csv new file mode 100644 index 0000000..2fa039b --- /dev/null +++ b/test_data/Biostats_2.csv @@ -0,0 +1,1537 @@ +"PlateId/Barcode","PlateNumber","WellId","Row","Column","Status","Zposition","ColumnValues","Activity_ValidObjectCount","Activity_SpotTotalAreaCh2","Activity_SpotTotalIntensity","concentration" +"CI027749",9,"A01",1,1,"Succeeded",0,"VC",8.525789764711348,0.3406659654724419,0.16658604957947248,100 +"CI027749",9,"A02",1,2,"Succeeded",0,"VC",-108.15836119623592,-2.964266375478498,-1.4578577235874632,100 +"CI027749",9,"A03",1,3,"Succeeded",0,"X5962",-47.03809164526354,2.88643403898541,2.6536483367042156,100 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