Merge pull request #163 from sahirbhatnagar/cran-0824

address CRAN check issues

.Rbuildignore

@@ -9,7 +9,6 @@
 ^risksets\.R$
 ^visreg\.R$
 ^vignettes\/bmtcrr\.csv$
-^inst\/doc\/.*md$
 ^casebase\.Rproj$
 ^_config\.yml$
 ^test\.rds$

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

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

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", , "[email protected]", role = c("aut", "cre"),
            comment = "https://sahirbhatnagar.com/"),

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

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