From 8ca6702db107623aad758d2031fd3ffcb90d6046 Mon Sep 17 00:00:00 2001 From: Max Turgeon Date: Tue, 6 Aug 2024 16:23:50 -0400 Subject: [PATCH] address CRAN check issues --- .Rbuildignore | 1 - CRAN-SUBMISSION | 6 +++--- DESCRIPTION | 4 ++-- NEWS.md | 5 +++++ R/plot_methods.R | 18 +++++++++--------- man/popTime.Rd | 18 +++++++++--------- 6 files changed, 28 insertions(+), 24 deletions(-) diff --git a/.Rbuildignore b/.Rbuildignore index 22a67f4d..3b67c25b 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -9,7 +9,6 @@ ^risksets\.R$ ^visreg\.R$ ^vignettes\/bmtcrr\.csv$ -^inst\/doc\/.*md$ ^casebase\.Rproj$ ^_config\.yml$ ^test\.rds$ diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index 69f2ffc4..ddc39d70 100644 --- a/CRAN-SUBMISSION +++ b/CRAN-SUBMISSION @@ -1,4 +1,4 @@ -Version: 0.10.4 -Date: 2024-02-01 15:52:26 UTC +Version: 0.10.5 +Date: 2024-04-09 21:24:52 UTC SHA: - 7d788b4dded3ebf18611a16f75340d3fa7a5bdba + fecef524e8d1a52504b4714dbd12352250cd1eab diff --git a/DESCRIPTION b/DESCRIPTION index 2a0c15dc..8d7a0a2f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: casebase Type: Package Title: Fitting Flexible Smooth-in-Time Hazards and Risk Functions via Logistic and Multinomial Regression -Version: 0.10.5 -Date: 2024-04-09 +Version: 0.10.6 +Date: 2024-08-06 Authors@R: c( person("Sahir", "Bhatnagar", , "sahir.bhatnagar@gmail.com", role = c("aut", "cre"), comment = "https://sahirbhatnagar.com/"), diff --git a/NEWS.md b/NEWS.md index 72f3c6c3..0e144200 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +# casebase 0.10.6 + +* Fix build directory WARNING. +* Fix cross-reference NOTE. + # casebase 0.10.5 * Skip tests when R is compiled against ATLAS BLAS diff --git a/R/plot_methods.R b/R/plot_methods.R index 83fef2cd..dba0884a 100644 --- a/R/plot_methods.R +++ b/R/plot_methods.R @@ -13,14 +13,14 @@ #' @param add.competing.event Logical indicating if the competing event should #' be added to the plot. Default: FALSE #' @param casebase.theme Logical indication if the casebase theme be used. The -#' casebase theme uses \code{\link{theme_minimal}}. Default: TRUE. +#' casebase theme uses [ggplot2::theme_minimal()]. Default: TRUE. #' @param ribbon.params A list containing arguments that are passed to -#' \code{\link{geom_ribbon}} which is used to plot the +#' [ggplot2::geom_ribbon()] which is used to plot the #' population-time area. These arguments will override the function defaults. #' For example, you can set \code{ribbon.params = list(colour = 'green')} if #' you want the area to be green. #' @param case.params,base.params,competing.params A list containing arguments -#' that are passed to \code{\link{geom_point}} which is used to plot +#' that are passed to [ggplot2::geom_point()] which is used to plot #' the case series, base series, competing events. These arguments will #' override the function defaults. For example, you can set \code{case.params #' = list(size = 1.5)} if you want to increase the point size for the case @@ -29,20 +29,20 @@ #' \code{color.params} and \code{fill.params} arguments, if you want to change #' the color of the points. #' @param color.params A list containing arguments that are passed to -#' \code{\link{scale_color_manual}} which is used to plot the legend. +#' [ggplot2::scale_color_manual()] which is used to plot the legend. #' Only used if \code{legend=TRUE}. These arguments will override the function #' defaults. Use this argument if you want to change the color of the points. #' See examples for more details. #' @param fill.params A list containing arguments that are passed to -#' \code{\link{scale_fill_manual}} which is used to plot the legend. +#' [ggplot2::scale_fill_manual()] which is used to plot the legend. #' Only used if \code{legend=TRUE}. These arguments will override the function #' defaults. Use this argument if you want to change the color of the points. #' See examples for more details. #' @param theme.params A list containing arguments that are passed to -#' \code{\link{theme}}. For example \code{theme.params = +#' [ggplot2::theme()]. For example \code{theme.params = #' list(legend.position = 'none')}. #' @param facet.params A list containing arguments that are passed to -#' \code{\link{facet_wrap}} which is used to create facet plots. Only +#' [ggplot2::facet_wrap()] which is used to create facet plots. Only #' used if plotting exposure stratified population time plots. These arguments #' will override the function defaults. #' @param ratio If \code{add.base.series=TRUE}, integer, giving the ratio of the @@ -102,8 +102,8 @@ #' @importFrom ggplot2 scale_colour_manual element_blank facet_wrap #' @importFrom ggplot2 theme xlab ylab #' @seealso -#' \link{geom_point},\link{geom_ribbon},\link{theme}, -#' \link{scale_colour_manual}, \link{scale_fill_manual}, +#' [ggplot2::geom_point()],[ggplot2::geom_ribbon()],[ggplot2::theme()], +#' [ggplot2::scale_colour_manual()], [ggplot2::scale_fill_manual()], #' \link{sampleCaseBase} #' @examples #' # change color of points diff --git a/man/popTime.Rd b/man/popTime.Rd index dc71af32..15ad2a17 100644 --- a/man/popTime.Rd +++ b/man/popTime.Rd @@ -57,16 +57,16 @@ to the plot. Default: FALSE} be added to the plot. Default: FALSE} \item{casebase.theme}{Logical indication if the casebase theme be used. The -casebase theme uses \code{\link{theme_minimal}}. Default: TRUE.} +casebase theme uses \code{\link[ggplot2:ggtheme]{ggplot2::theme_minimal()}}. Default: TRUE.} \item{ribbon.params}{A list containing arguments that are passed to -\code{\link{geom_ribbon}} which is used to plot the +\code{\link[ggplot2:geom_ribbon]{ggplot2::geom_ribbon()}} which is used to plot the population-time area. These arguments will override the function defaults. For example, you can set \code{ribbon.params = list(colour = 'green')} if you want the area to be green.} \item{case.params, base.params, competing.params}{A list containing arguments -that are passed to \code{\link{geom_point}} which is used to plot +that are passed to \code{\link[ggplot2:geom_point]{ggplot2::geom_point()}} which is used to plot the case series, base series, competing events. These arguments will override the function defaults. For example, you can set \code{case.params = list(size = 1.5)} if you want to increase the point size for the case @@ -76,23 +76,23 @@ points. Doing so will result in unexpected results for the legend. See the the color of the points.} \item{color.params}{A list containing arguments that are passed to -\code{\link{scale_color_manual}} which is used to plot the legend. +\code{\link[ggplot2:scale_manual]{ggplot2::scale_color_manual()}} which is used to plot the legend. Only used if \code{legend=TRUE}. These arguments will override the function defaults. Use this argument if you want to change the color of the points. See examples for more details.} \item{fill.params}{A list containing arguments that are passed to -\code{\link{scale_fill_manual}} which is used to plot the legend. +\code{\link[ggplot2:scale_manual]{ggplot2::scale_fill_manual()}} which is used to plot the legend. Only used if \code{legend=TRUE}. These arguments will override the function defaults. Use this argument if you want to change the color of the points. See examples for more details.} \item{theme.params}{A list containing arguments that are passed to -\code{\link{theme}}. For example \code{theme.params = +\code{\link[ggplot2:theme]{ggplot2::theme()}}. For example \code{theme.params = list(legend.position = 'none')}.} \item{facet.params}{A list containing arguments that are passed to -\code{\link{facet_wrap}} which is used to create facet plots. Only +\code{\link[ggplot2:facet_wrap]{ggplot2::facet_wrap()}} which is used to create facet plots. Only used if plotting exposure stratified population time plots. These arguments will override the function defaults.} @@ -264,8 +264,8 @@ popTimeData <- popTime(data = bmtcrr, time = "ftime", exposure = "D") attr(popTimeData, "exposure") } \seealso{ -\link{geom_point},\link{geom_ribbon},\link{theme}, -\link{scale_colour_manual}, \link{scale_fill_manual}, +\code{\link[ggplot2:geom_point]{ggplot2::geom_point()}},\code{\link[ggplot2:geom_ribbon]{ggplot2::geom_ribbon()}},\code{\link[ggplot2:theme]{ggplot2::theme()}}, +\code{\link[ggplot2:scale_manual]{ggplot2::scale_colour_manual()}}, \code{\link[ggplot2:scale_manual]{ggplot2::scale_fill_manual()}}, \link{sampleCaseBase} \code{\link{plot.popTime}}