From 021e406f40018b23727f6b75c1f2297e82cc1c7c Mon Sep 17 00:00:00 2001 From: Torsten Hothorn Date: Tue, 6 Apr 2021 10:58:09 +0200 Subject: [PATCH] url -> doi; speedup --- man/Family.Rd | 4 ++-- man/baselearners.Rd | 12 +++++++++++- man/cvrisk.Rd | 2 +- man/gamboost.Rd | 2 +- man/glmboost.Rd | 2 +- man/mboost_fit.Rd | 2 +- man/methods.Rd | 4 ++-- man/plot.Rd | 2 +- 8 files changed, 20 insertions(+), 10 deletions(-) diff --git a/man/Family.Rd b/man/Family.Rd index 8b29216..77acf2f 100644 --- a/man/Family.Rd +++ b/man/Family.Rd @@ -309,7 +309,7 @@ distribution approximation used in Ma and Huang (2005). Benjamin Hofner, Andreas Mayr, Nikolay Robinzonov and Matthias Schmid (2014). Model-based Boosting in R: A Hands-on Tutorial Using the R Package mboost. \emph{Computational Statistics}, \bold{29}, 3--35.\cr - \url{http://dx.doi.org/10.1007/s00180-012-0382-5} + \doi{10.1007/s00180-012-0382-5} Available as vignette via: \code{vignette(package = "mboost", "mboost_tutorial")} @@ -320,7 +320,7 @@ distribution approximation used in Ma and Huang (2005). Weinhold, L., S. Pechlivanis, S. Wahl, P. Hoffmann and M. Schmid (2016) A Statistical Model for the Analysis of Bounded Response Variables in DNA Methylation Studies. - \emph{BMC Bioinformatics}. 2016; 17: 480. \url{http://dx.doi.org/10.1186/s12859-016-1347-4} + \emph{BMC Bioinformatics}. 2016; 17: 480. \doi{10.1186/s12859-016-1347-4} } \seealso{\code{\link{mboost}} for the usage of \code{Family}s. See \code{\link{boost_family-class}} for objects resulting from a call to \code{Family}. } diff --git a/man/baselearners.Rd b/man/baselearners.Rd index 07c9108..a073844 100644 --- a/man/baselearners.Rd +++ b/man/baselearners.Rd @@ -620,16 +620,20 @@ bl1 \%O\% bl2 bspatial(x1, x2, knots = 12, center = TRUE, df = 1) mod1 <- gamboost(form1) + \dontrun{ plot(mod1) + } mod2 <- gamboost(form2) ## automated plot function: plot(mod2) ## plot sum of linear and smooth effects: - library(lattice) + library("lattice") df <- expand.grid(x1 = unique(x1), x2 = unique(x2)) df$pred <- predict(mod2, newdata = df) + \dontrun{ levelplot(pred ~ x1 * x2, data = df) + } ## specify radial basis function base-learner for spatial effect ## and use data-adaptive effective range (theta = NULL, see 'args') @@ -639,13 +643,17 @@ bl1 \%O\% bl2 form4 <- y ~ brad(x1, x2, knots = 50, args = list(theta = 0.4)) mod3 <- gamboost(form3) + \dontrun{ plot(mod3) + } dim(extract(mod3, what = "design", which = "brad")[[1]]) knots <- attr(extract(mod3, what = "design", which = "brad")[[1]], "knots") mod4 <- gamboost(form4) dim(extract(mod4, what = "design", which = "brad")[[1]]) + \dontrun{ plot(mod4) + } ### random intercept id <- factor(rep(1:10, each = 5)) @@ -696,8 +704,10 @@ bl1 \%O\% bl2 for (i in seq(along = levels(z))) with(nd[nd$z == i,], lines(x, pred_gam, col = z, lty = "dashed")) ### convenience function for plotting + \dontrun{ par(mfrow = c(1,3)) plot(mod_gam) + } ### remove intercept from base-learner diff --git a/man/cvrisk.Rd b/man/cvrisk.Rd index 9f48b02..46b199e 100644 --- a/man/cvrisk.Rd +++ b/man/cvrisk.Rd @@ -105,7 +105,7 @@ cv(weights, type = c("bootstrap", "kfold", "subsampling"), importance of knowing when to stop - a sequential stopping rule for component-wise gradient boosting. \emph{Methods of Information in Medicine}, \bold{51}, 178--186. \cr - DOI: \url{http://dx.doi.org/10.3414/ME11-02-0030} + DOI: \doi{10.3414/ME11-02-0030} } \seealso{\code{\link{AIC.mboost}} for diff --git a/man/gamboost.Rd b/man/gamboost.Rd index bbf7846..ae6ac11 100644 --- a/man/gamboost.Rd +++ b/man/gamboost.Rd @@ -107,7 +107,7 @@ gamboost(formula, data = list(), na.action = na.omit, weights = NULL, Benjamin Hofner, Andreas Mayr, Nikolay Robinzonov and Matthias Schmid (2014). Model-based Boosting in R: A Hands-on Tutorial Using the R Package mboost. \emph{Computational Statistics}, \bold{29}, 3--35.\cr - \url{http://dx.doi.org/10.1007/s00180-012-0382-5} + \doi{10.1007/s00180-012-0382-5} Available as vignette via: \code{vignette(package = "mboost", "mboost_tutorial")} } diff --git a/man/glmboost.Rd b/man/glmboost.Rd index a7c6258..1238ddb 100644 --- a/man/glmboost.Rd +++ b/man/glmboost.Rd @@ -80,7 +80,7 @@ Benjamin Hofner, Andreas Mayr, Nikolay Robinzonov and Matthias Schmid (2014). Model-based Boosting in R: A Hands-on Tutorial Using the R Package mboost. \emph{Computational Statistics}, \bold{29}, 3--35.\cr - \url{http://dx.doi.org/10.1007/s00180-012-0382-5} + \doi{10.1007/s00180-012-0382-5} Available as vignette via: \code{vignette(package = "mboost", "mboost_tutorial")} } diff --git a/man/mboost_fit.Rd b/man/mboost_fit.Rd index dec5965..2df63da 100644 --- a/man/mboost_fit.Rd +++ b/man/mboost_fit.Rd @@ -93,7 +93,7 @@ mboost_fit(blg, response, weights = rep(1, NROW(response)), offset = NULL, Benjamin Hofner, Andreas Mayr, Nikolay Robinzonov and Matthias Schmid (2014). Model-based Boosting in R: A Hands-on Tutorial Using the R Package mboost. \emph{Computational Statistics}, \bold{29}, 3--35.\cr - \url{http://dx.doi.org/10.1007/s00180-012-0382-5} + \doi{10.1007/s00180-012-0382-5} Available as vignette via: \code{vignette(package = "mboost", "mboost_tutorial")} diff --git a/man/methods.Rd b/man/methods.Rd index 8833379..d28d5ca 100644 --- a/man/methods.Rd +++ b/man/methods.Rd @@ -325,7 +325,7 @@ downstream.test(object, ...) Benjamin Hofner, Andreas Mayr, Nikolay Robinzonov and Matthias Schmid (2014). Model-based Boosting in R: A Hands-on Tutorial Using the R Package mboost. \emph{Computational Statistics}, \bold{29}, 3--35.\cr - \url{http://dx.doi.org/10.1007/s00180-012-0382-5} + \doi{10.1007/s00180-012-0382-5} Clifford M. Hurvich, Jeffrey S. Simonoff and Chih-Ling Tsai (1998), Smoothing parameter selection in nonparametric regression using @@ -348,7 +348,7 @@ downstream.test(object, ...) importance of knowing when to stop - a sequential stopping rule for component-wise gradient boosting. \emph{Methods of Information in Medicine}, \bold{51}, 178--186. \cr - DOI: \url{http://dx.doi.org/10.3414/ME11-02-0030} + DOI: \doi{10.3414/ME11-02-0030} } \seealso{ diff --git a/man/plot.Rd b/man/plot.Rd index 98f5545..e0b709b 100644 --- a/man/plot.Rd +++ b/man/plot.Rd @@ -114,7 +114,7 @@ Benjamin Hofner, Andreas Mayr, Nikolay Robinzonov and Matthias Schmid (2014). Model-based Boosting in R: A Hands-on Tutorial Using the R Package mboost. \emph{Computational Statistics}, \bold{29}, 3--35.\cr - \url{http://dx.doi.org/10.1007/s00180-012-0382-5} + \doi{10.1007/s00180-012-0382-5} } \seealso{ \code{\link{mboost_methods}} for further methods.