added figures for paper

ComPlat · Oct 24, 2024 · cb11202 · cb11202
1 parent 84b45ec
commit cb11202
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Showing 36 changed files with 642 additions and 456 deletions.
diff --git a/Paper/DBA_5_different_seeds.RData b/Paper/DBA_5_different_seeds.RData
diff --git a/Paper/DBA_10_different_seeds.RData → ...eterVariance/DBA_10_different_seeds.RData b/Paper/DBA_10_different_seeds.RData → ...eterVariance/DBA_10_different_seeds.RData
diff --git a/Paper/FigNr1.pdf → Paper/DecentFitParameterVariance/FigNr1.pdf b/Paper/FigNr1.pdf → Paper/DecentFitParameterVariance/FigNr1.pdf
diff --git a/Paper/FigNr1.png → Paper/DecentFitParameterVariance/FigNr1.png b/Paper/FigNr1.png → Paper/DecentFitParameterVariance/FigNr1.png
diff --git a/Paper/FigNr1_Run_Simulations.R → ...arameterVariance/FigNr1_Run_Simulations.R b/Paper/FigNr1_Run_Simulations.R → ...arameterVariance/FigNr1_Run_Simulations.R
@@ -29,7 +29,7 @@ gda <- function() {
   )
 
   # NOTE: data var column [M]
-  data <- readLines("GDA.txt")
+  data <- readLines("../GDA.txt")
   var <- lapply(data, function(x) {
     strsplit(x, split = "\t")[[1]][1]
   }) |> unlist()
@@ -77,7 +77,7 @@ dba <- function() {
   )
 
   # NOTE: data var column [M]
-  data <- readLines("DBA.txt")
+  data <- readLines("../DBA.txt")
   var <- lapply(data, function(x) {
     strsplit(x, split = "\t")[[1]][1]
   }) |> unlist()
@@ -128,7 +128,7 @@ ida <- function() {
   )
 
   # NOTE: data var column [M]
-  data <- readLines("IDA.txt")
+  data <- readLines("../IDA.txt")
   var <- lapply(data, function(x) {
     strsplit(x, split = "\t")[[1]][1]
   }) |> unlist()

diff --git a/Paper/FigNr1_Visualisation.R → ...tParameterVariance/FigNr1_Visualisation.R b/Paper/FigNr1_Visualisation.R → ...tParameterVariance/FigNr1_Visualisation.R
@@ -164,10 +164,10 @@ p_param <- ggdraw(p_param) +
   )
 
 p <- plot_grid(p_signal, p_param, nrow = 2)
-ggsave("FigNr1.pdf", p,
+ggsave("../FigNr1.pdf", p,
   width = 8, height = 8 * 2 / 3
 )
-ggsave("FigNr1.png", p,
+ggsave("../FigNr1.png", p,
   width = 8, height = 8 * 2 / 3,
   bg = "white", dpi = 800
 )
diff --git a/Paper/GDA_10_different_seeds.RData → ...eterVariance/GDA_10_different_seeds.RData b/Paper/GDA_10_different_seeds.RData → ...eterVariance/GDA_10_different_seeds.RData
diff --git a/Paper/IDA_10_different_seeds.RData → ...eterVariance/IDA_10_different_seeds.RData b/Paper/IDA_10_different_seeds.RData → ...eterVariance/IDA_10_different_seeds.RData
diff --git a/Paper/Rplots.pdf → Paper/DecentFitParameterVariance/Rplots.pdf b/Paper/Rplots.pdf → Paper/DecentFitParameterVariance/Rplots.pdf
diff --git a/Paper/ForwardTest/Rplots.pdf b/Paper/ForwardTest/Rplots.pdf
diff --git a/Paper/ForwardTest/forward.R b/Paper/ForwardTest/forward.R
diff --git a/Paper/IDA_5_different_seeds.RData b/Paper/IDA_5_different_seeds.RData
diff --git a/Paper/MeasurementVariance/MeasurementVariance.R b/Paper/MeasurementVariance/MeasurementVariance.R
@@ -0,0 +1,152 @@
+dba <- function() {
+  lowerBounds <- c(
+    kHD = 0,
+    I0 = 0,
+    IHD = 0,
+    ID = 0
+  )
+  upperBounds <- c(
+    kHD = 10^7,
+    I0 = 10^5,
+    IHD = 10^8,
+    ID = 10^7
+  )
+  additionalParameters <- c(
+    dye = 151 * 10^-6
+  )
+  tsf::batch("dba_dye_const",
+    lowerBounds, upperBounds,
+    path = "../DBA.txt",
+    additionalParameters,
+    ngen = 1000,
+    num_rep = 5, num_cores = 4,
+    errorThreshold = 0.6
+  )
+}
+res <- dba()
+save(res, file = "dba.RData")
+
+ida <- function() {
+  lowerBounds <- c(
+    kG = 0,
+    I0 = 0,
+    IHD = 0,
+    ID = 0
+  )
+  upperBounds <- c(
+    kG = 10^10,
+    I0 = 10^2,
+    IHD = 10^10,
+    ID = 10^10
+  )
+  additionalParameters <- c(
+    host = 4.3 * 10^-6,
+    dye = 6 * 10^-6,
+    kHD = 1.7E07
+  )
+
+  tsf::batch("ida",
+    lowerBounds, upperBounds,
+    path = "../IDA.txt",
+    additionalParameters,
+    ngen = 1000,
+    num_rep = 5, num_cores = 4,
+    errorThreshold = 0.6
+  )
+}
+res <- ida()
+save(res, file = "ida.RData")
+
+
+
+gda <- function() {
+  lowerBounds <- c(
+    kG = 10,
+    I0 = 0,
+    IHD = 0,
+    ID = 0
+  )
+  upperBounds <- c(
+    kG = 10^9,
+    I0 = 700,
+    IHD = 10^9,
+    ID = 10^9
+  )
+  additionalParameters <- c(
+    host = 103 * 10^-6,
+    guest = 1050 * 10^-6,
+    kHD = 2431.14
+  )
+
+  tsf::batch("gda",
+    lowerBounds, upperBounds,
+    path = "../GDA.txt",
+    additionalParameters,
+    ngen = 1000,
+    num_rep = 5, num_cores = 4,
+    errorThreshold = 0.6
+  )
+}
+res <- gda()
+save(res, file = "gda.RData")
+
+
+dba <- function() {
+  lowerBounds <- c(
+    kHD = 0,
+    I0 = 0,
+    IHD = 0,
+    ID = 0
+  )
+  upperBounds <- c(
+    kHD = 10^7,
+    I0 = 10^5,
+    IHD = 10^8,
+    ID = 10^7
+  )
+  additionalParameters <- c(
+    dye = 151 * 10^-6
+  )
+  tsf::batch("dba_dye_const",
+    lowerBounds, upperBounds,
+    path = "../DBA.txt",
+    additionalParameters,
+    ngen = 1000,
+    num_rep = 5, num_cores = 4,
+    errorThreshold = 0.6
+  )
+}
+res <- dba()
+save(res, file = "dba.RData")
+
+
+ida <- function() {
+  lowerBounds <- c(
+    kG = 0,
+    I0 = 0,
+    IHD = 0,
+    ID = 0
+  )
+  upperBounds <- c(
+    kG = 10^10,
+    I0 = 10^2,
+    IHD = 10^10,
+    ID = 10^10
+  )
+  additionalParameters <- c(
+    host = 4.3 * 10^-6,
+    dye = 6 * 10^-6,
+    kHD = 1.7E07
+  )
+
+  tsf::batch("ida",
+    lowerBounds, upperBounds,
+    path = "../IDA.txt",
+    additionalParameters,
+    ngen = 1000,
+    num_rep = 5, num_cores = 4,
+    errorThreshold = 0.6
+  )
+}
+res <- ida()
+save(res, file = "ida.RData")