fix links

DESCRIPTION

@@ -94,7 +94,7 @@ Description: Fit Bayesian generalized (non-)linear multivariate multilevel model
 LazyData: true
 NeedsCompilation: no
 License: GPL-2
-URL: https://github.com/paul-buerkner/brms, https://discourse.mc-stan.org/, https://paul-buerkner.github.io/brms/
+URL: https://github.com/paul-buerkner/brms, https://discourse.mc-stan.org/, https://paulbuerkner.com/brms/
 BugReports: https://github.com/paul-buerkner/brms/issues
 Additional_repositories:
     https://stan-dev.r-universe.dev/

R/conditional_effects.R

@@ -97,16 +97,18 @@
 #'   If \code{NULL} (default), \code{ncol} is computed internally based
 #'   on the number of rows of \code{conditions}.
 #' @param points Logical. Indicates if the original data points should be added
-#'   via \code{\link{geom_jitter}}. Default is \code{FALSE}. Can be controlled
-#'   globally via the \code{brms.plot_points} option. Note that only those data
-#'   points will be added that match the specified conditions defined in
-#'   \code{conditions}. For categorical predictors, the conditions have to match
-#'   exactly. For numeric predictors, argument \code{select_points} is used to
-#'   determine, which points do match a condition.
+#'   via \code{\link[ggplot2:geom_jitter]{geom_jitter}}. Default is
+#'   \code{FALSE}. Can be controlled globally via the \code{brms.plot_points}
+#'   option. Note that only those data points will be added that match the
+#'   specified conditions defined in \code{conditions}. For categorical
+#'   predictors, the conditions have to match exactly. For numeric predictors,
+#'   argument \code{select_points} is used to determine, which points do match a
+#'   condition.
 #' @param rug Logical. Indicates if a rug representation of predictor values
-#'   should be added via \code{\link{geom_rug}}. Default is \code{FALSE}.
-#'   Depends on \code{select_points} in the same way as \code{points} does. Can
-#'   be controlled globally via the \code{brms.plot_rug} option.
+#'   should be added via \code{\link[ggplot2:geom_rug]{geom_rug}}. Default is
+#'   \code{FALSE}. Depends on \code{select_points} in the same way as
+#'   \code{points} does. Can be controlled globally via the \code{brms.plot_rug}
+#'   option.
 #' @param mean Logical. Only relevant for spaghetti plots.
 #'   If \code{TRUE} (the default), display the mean regression
 #'   line on top of the regression lines for each sample.
@@ -118,30 +120,30 @@
 #'   Either \code{"contour"} or \code{"raster"}.
 #' @param line_args Only used in plots of continuous predictors:
 #'   A named list of arguments passed to
-#'   \code{\link{geom_smooth}}.
+#'   \code{\link[ggplot2:geom_smooth]{geom_smooth}}.
 #' @param cat_args Only used in plots of categorical predictors:
 #'   A named list of arguments passed to
-#'   \code{\link{geom_point}}.
+#'   \code{\link[ggplot2:geom_point]{geom_point}}.
 #' @param errorbar_args Only used in plots of categorical predictors:
 #'   A named list of arguments passed to
-#'   \code{\link{geom_errorbar}}.
+#'   \code{\link[ggplot2:geom_errorbar]{geom_errorbar}}.
 #' @param surface_args Only used in surface plots:
 #'   A named list of arguments passed to
-#'   \code{\link{geom_contour}} or
-#'   \code{\link{geom_raster}}
+#'   \code{\link[ggplot2:geom_contour]{geom_contour}} or
+#'   \code{\link[ggplot2:geom_raster]{geom_raster}}
 #'   (depending on argument \code{stype}).
 #' @param spaghetti_args Only used in spaghetti plots:
 #'   A named list of arguments passed to
-#'   \code{\link{geom_smooth}}.
+#'   \code{\link[ggplot2:geom_smooth]{geom_smooth}}.
 #' @param point_args Only used if \code{points = TRUE}:
 #'   A named list of arguments passed to
-#'   \code{\link{geom_jitter}}.
+#'   \code{\link[ggplot2:geom_jitter]{geom_jitter}}.
 #' @param rug_args Only used if \code{rug = TRUE}:
 #'   A named list of arguments passed to
-#'   \code{\link{geom_rug}}.
-#' @param facet_args Only used if if multiple condtions are provided:
+#'   \code{\link[ggplot2:geom_rug]{geom_rug}}.
+#' @param facet_args Only used if if multiple conditions are provided:
 #'   A named list of arguments passed to
-#'   \code{\link{facet_wrap}}.
+#'   \code{\link[ggplot2:facet_wrap]{facet_wrap}}.
 #'
 #' @return An object of class \code{'brms_conditional_effects'} which is a
 #'   named list with one data.frame per effect containing all information
@@ -154,7 +156,7 @@
 #'   rows).
 #'
 #'   The corresponding \code{plot} method returns a named
-#'   list of \code{\link{ggplot}} objects, which can be further
+#'   list of \code{\link[ggplot2:ggplot]{ggplot}} objects, which can be further
 #'   customized using the \pkg{ggplot2} package.
 #'
 #' @details When creating \code{conditional_effects} for a particular predictor
@@ -170,7 +172,8 @@
 #'
 #'   To fully change colors of the created plots, one has to amend both
 #'   \code{scale_colour} and \code{scale_fill}. See
-#'   \code{\link{scale_colour_grey}} or \code{\link{scale_colour_gradient}} for
+#'   \code{\link[ggplot2:scale_color_grey]{scale_colour_grey}} or
+#'   \code{\link[ggplot2:scale_color_gradient]{scale_colour_gradient}} for
 #'   more details.
 #'
 #' @examples

R/priors.R

@@ -2073,7 +2073,7 @@ eval_dirichlet <- function(prior, len = NULL, env = NULL) {
 #'
 #' Piironen J. & Vehtari A. (2017). On the Hyperprior Choice for the Global
 #' Shrinkage Parameter in the Horseshoe Prior. Artificial Intelligence and
-#' Statistics. \url{https://arxiv.org/pdf/1610.05559v1.pdf}
+#' Statistics. \url{https://arxiv.org/pdf/1610.05559v1}
 #'
 #' Piironen, J., and Vehtari, A. (2017). Sparsity information and regularization
 #' in the horseshoe and other shrinkage priors. Electronic Journal of
@@ -2182,11 +2182,11 @@ horseshoe <- function(df = 1, scale_global = 1, df_global = 1,
 #' Zhang, Y. D., Naughton, B. P., Bondell, H. D., & Reich, B. J. (2020).
 #' Bayesian regression using a prior on the model fit: The R2-D2 shrinkage
 #' prior. Journal of the American Statistical Association.
-#' \url{https://arxiv.org/pdf/1609.00046.pdf}
+#' \url{https://arxiv.org/pdf/1609.00046}
 #'
 #' Aguilar J. E. & Bürkner P. C. (2022). Intuitive Joint Priors for Bayesian
 #' Linear Multilevel Models: The R2D2M2 prior. ArXiv preprint.
-#' \url{https://arxiv.org/pdf/2208.07132.pdf}
+#' \url{https://arxiv.org/pdf/2208.07132}
 #'
 #' @seealso \code{\link{set_prior}}
 #'

README.Rmd

@@ -58,8 +58,8 @@ predictive checks, cross-validation, and Bayes factors.
 
 * [Introduction to brms](https://doi.org/10.18637/jss.v080.i01) (Journal of Statistical Software)
 * [Advanced multilevel modeling with brms](https://journal.r-project.org/archive/2018/RJ-2018-017/index.html) (The R Journal)
-* [Website](https://paul-buerkner.github.io/brms/) (Website of brms with documentation and vignettes)
-* [Blog posts](https://paul-buerkner.github.io/software/brms-blogposts.html) (List of blog posts about brms)
+* [Website](https://paulbuerkner.com/brms/) (Website of brms with documentation and vignettes)
+* [Blog posts](http://paulbuerkner.com/software/brms-blogposts.html) (List of blog posts about brms)
 * [Ask a question](https://discourse.mc-stan.org/) (Stan Forums on Discourse)
 * [Open an issue](https://github.com/paul-buerkner/brms/issues) (GitHub issues for bug reports and feature requests)
 

README.md

@@ -39,10 +39,10 @@ with posterior predictive checks, cross-validation, and Bayes factors.
 -   [Advanced multilevel modeling with
     brms](https://journal.r-project.org/archive/2018/RJ-2018-017/index.html)
     (The R Journal)
--   [Website](https://paul-buerkner.github.io/brms/) (Website of brms
+-   [Website](https://paulbuerkner.com/brms/) (Website of brms
     with documentation and vignettes)
 -   [Blog
-    posts](https://paul-buerkner.github.io/software/brms-blogposts.html)
+    posts](http://paulbuerkner.com/software/brms-blogposts.html)
     (List of blog posts about brms)
 -   [Ask a question](https://discourse.mc-stan.org/) (Stan Forums on
     Discourse)