theme_classic2 removed #217

kassambara · Jun 7, 2017 · c538f36 · c538f36
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commit c538f36
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Showing 19 changed files with 22 additions and 29 deletions.
diff --git a/R/ggcoxadjustedcurves.R b/R/ggcoxadjustedcurves.R
@@ -16,7 +16,7 @@ NULL
 #'@param individual.curves if TRUE then all individual predicted survival curves will be plotted
 #'@param curve.size,curve.alpha size and alpha for individual survival curves
 #'@param ylab y axis label.
-#'@param ggtheme function, ggplot2 theme name. Default value is \link{theme_classic2}.
+#'@param ggtheme function, ggplot2 theme name.
 #'  Allowed values include ggplot2 official themes: see \code{\link[ggplot2]{theme}}.
 #'@inheritParams ggpubr::ggpar
 #'@param ... further arguments passed to the function \code{\link[ggpubr]{ggpar}} for customizing the plot.

diff --git a/R/ggcoxfunctional.R b/R/ggcoxfunctional.R
@@ -20,7 +20,7 @@ NULL
 #'@param title the title of the final \link{grob} (\code{top} in \link{arrangeGrob})
 #'@param caption the caption of the final \link{grob} (\code{bottom} in \link{arrangeGrob})
 #'@param point.col,point.size,point.shape,point.alpha color, size, shape and visibility to be used for points.
-#'@param ggtheme function, ggplot2 theme name. Default value is \link{theme_classic2}.
+#'@param ggtheme function, ggplot2 theme name.
 #'  Allowed values include ggplot2 official themes: see \code{\link[ggplot2]{theme}}.
 #'@param ... further arguments passed to the function \code{\link[ggpubr]{ggpar}} for customizing the plot.
 #'@return Returns an object of class \code{ggcoxfunctional} which is a list of ggplots.

diff --git a/R/ggcoxzph.R b/R/ggcoxzph.R
@@ -13,7 +13,7 @@
 #'  are produced in turn for each variable of a model.
 #'@param point.col,point.size,point.shape,point.alpha color, size, shape and visibility to be used for points.
 #'@param caption the caption of the final \link{grob} (\code{bottom} in \link{arrangeGrob})
-#'@param ggtheme function, ggplot2 theme name. Default value is \link{theme_classic2}.
+#'@param ggtheme function, ggplot2 theme name.
 #'  Allowed values include ggplot2 official themes: see \code{\link[ggplot2]{theme}}.
 #'@param ... further arguments passed to either the print() function or to the \code{\link[ggpubr]{ggpar}} function for customizing the plot (see Details section).
 #'@details \strong{Customizing the plots}: The plot can be easily

diff --git a/R/ggsurvevents.R b/R/ggsurvevents.R
@@ -5,7 +5,7 @@
 #' @param data a dataset for predictions. If not supplied then data will be extracted from `fit` object.
 #' @param type one of \code{c("cumulative", "radius", "fraction")}. \code{"cumulative"} stands for cumulative number of events, \code{"radius"} stands for number of events within a given radius,
 #' @param normalized if \code{TRUE} relative number of events is presented,
-#' @param ggtheme function, ggplot2 theme name. Default value is theme_classic2. Allowed values include ggplot2 official themes: see theme.
+#' @param ggtheme function, ggplot2 theme name.  Allowed values include ggplot2 official themes: see theme.
 #' @param censored.on.top is TRUE then censored events are on the top
 #' @param palette the color palette to be used for coloring of significant variables.
 #' @param ... other graphical parameters to be passed to the function \link[ggpubr]{ggpar}.

diff --git a/R/surv_cutpoint.R b/R/surv_cutpoint.R
@@ -181,13 +181,13 @@ print.surv_cutpoint <- function(x, ...){
 
 
 #' @param ggtheme function, ggplot2 theme name. Default value is
-#'   \link{theme_classic2}. Allowed values include ggplot2 official themes. see
+#'   \link{theme_classic}. Allowed values include ggplot2 official themes. see
 #'   ?ggplot2::ggtheme.
 #' @param bins Number of bins for histogram. Defaults to 30.
 #' @method plot surv_cutpoint
 #' @rdname surv_cutpoint
 #' @export
-plot.surv_cutpoint <- function(x, variables = NULL, ggtheme = theme_classic2(), bins = 30, ...)
+plot.surv_cutpoint <- function(x, variables = NULL, ggtheme = theme_classic(), bins = 30, ...)
   {
 
   if(!inherits(x, "surv_cutpoint"))
@@ -271,7 +271,7 @@ print.plot_surv_cutpoint <- function(x, ..., newpage = TRUE){
 # Helper function
 # %%%%%%%%%%%%%%%%%%%%%
 
-.ggpar <- function(p, ggtheme = theme_classic2(),...){
+.ggpar <- function(p, ggtheme = theme_classic(),...){
   argmt <- list(...)
   p <- ggpubr::ggpar(p, ggtheme = ggtheme,...)
   if(is.null(argmt$font.x)) p <- p + theme(axis.text.x = element_text(face = "plain"))

diff --git a/docs/reference/ggcoxadjustedcurves.html b/docs/reference/ggcoxadjustedcurves.html
diff --git a/docs/reference/ggcoxfunctional.html b/docs/reference/ggcoxfunctional.html
diff --git a/docs/reference/ggcoxzph.html b/docs/reference/ggcoxzph.html
diff --git a/docs/reference/ggsurvevents.html b/docs/reference/ggsurvevents.html
diff --git a/docs/reference/ggsurvplot_list-6.png b/docs/reference/ggsurvplot_list-6.png
diff --git a/docs/reference/ggsurvplot_list.html b/docs/reference/ggsurvplot_list.html
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/reference/surv_cutpoint-7.png b/docs/reference/surv_cutpoint-7.png
diff --git a/docs/reference/surv_cutpoint.html b/docs/reference/surv_cutpoint.html
diff --git a/man/ggcoxadjustedcurves.Rd b/man/ggcoxadjustedcurves.Rd
diff --git a/man/ggcoxfunctional.Rd b/man/ggcoxfunctional.Rd
diff --git a/man/ggcoxzph.Rd b/man/ggcoxzph.Rd
diff --git a/man/ggsurvevents.Rd b/man/ggsurvevents.Rd
diff --git a/man/surv_cutpoint.Rd b/man/surv_cutpoint.Rd