Prep CRAN submission

maraab23 · Sep 7, 2022 · a4f5f21 · a4f5f21
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diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,31 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: covr::codecov(quiet = FALSE)
+        shell: Rscript {0}
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ggseqplot
 Title: Render Sequence Plots using 'ggplot2'
-Version: 0.7.2.9020
+Version: 0.8.0
 Authors@R: 
   person("Marcel", "Raab", , "marcel.raab@gmail.com", role = c("aut", "cre"),
          comment = c(ORCID = "0000-0002-3097-1591"))
@@ -11,7 +11,7 @@ Description: A set of wrapper functions that mainly re-produces some of the
   with TraMineR::seqdef(). The package automates the reshaping and plotting 
   of sequence data. Resulting plots are of class 'ggplot', i.e. components 
   can be added and tweaked using '+' and regular 'ggplot2' functions. 
-URL: https://github.com/maraab23/ggseqplot
+URL: https://maraab23.github.io/ggseqplot/, https://github.com/maraab23/ggseqplot
 BugReports: https://github.com/maraab23/ggseqplot/issues
 Depends: 
     R (>= 4.1.0),

diff --git a/NEWS.md b/NEWS.md
@@ -1,20 +1,18 @@
-# ggseqplot
+# ggseqplot 0.8.0
 
-# ggseqplot 0.7.2.9020 <br><small>(development version)</small>
+* complete revision of `ggseqrfplot` after `{TraMineR}` release 2.2-5 
+  (special thanks to Gilbert Ritschard for the support)
+
+* added `{TraMineR}` as dependency 
 
-* complete revision of ggseqrfplot after TraMineR release 2.2-5
-* added TraMineR as dependency 
-* tests still need to be updated 
-
-# ggseqplot 0.7.2.9001 <br><small>(development version)</small>
-
-* the group argument now respects order of grouping variable when rendering faceted plots
-* updated tests
+* the group argument now respects order of grouping variable when rendering faceted plots 
+  (issue raised bv Lucille Mattijssen)
 
 # ggseqplot 0.7.2
 
 * fixed sorting issue for y-axis labels in grouped iplots
-* allow for additional facet_wrap arguments to change plot appearance 
+
+* allow for additional `facet_wrap` arguments to change plot appearance 
 
 # ggseqplot 0.7.1
 
@@ -24,8 +22,6 @@
 
 * Added option to break down dplots by state (`dissect`)
 
-# ggseqplot 0.6.2.9000 <br><small>(development version)</small>
-
 * Set minimum R version because of R's new pipe (#1, @cbrueffer)
 
 # ggseqplot 0.6.2

diff --git a/R/ggseqdplot.R b/R/ggseqdplot.R
@@ -66,8 +66,6 @@
 #' # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 #'
 #' # Examples from TraMineR::seqplot
-#'
-#' library(TraMineR)
 #' library(ggplot2)
 #'
 #' # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git a/R/ggseqeplot.R b/R/ggseqeplot.R
@@ -45,9 +45,6 @@
 #'
 #' # Examples from TraMineR::seqplot
 #'
-#' library(TraMineR)
-#' library(ggplot2)
-#'
 #' # actcal data set
 #' data(actcal)
 #'

diff --git a/R/ggseqfplot.R b/R/ggseqfplot.R
@@ -51,7 +51,6 @@
 #'
 #' # Examples from TraMineR::seqplot
 #'
-#' library(TraMineR)
 #' library(ggplot2)
 #'
 #' # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git a/R/ggseqiplot.R b/R/ggseqiplot.R
@@ -74,8 +74,6 @@
 #'
 #' # Examples from TraMineR::seqplot
 #'
-#' library(TraMineR)
-#'
 #' # actcal data set
 #' data(actcal)
 #'

diff --git a/R/ggseqmsplot.R b/R/ggseqmsplot.R
@@ -39,7 +39,6 @@
 #'
 #' # Examples from TraMineR::seqplot
 #'
-#' library(TraMineR)
 #' library(ggplot2)
 #'
 #' # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git a/R/ggseqmtplot.R b/R/ggseqmtplot.R
@@ -49,7 +49,6 @@
 #'
 #' # Examples from TraMineR::seqplot
 #'
-#' library(TraMineR)
 #' library(ggplot2)
 #'
 #' # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git a/R/ggseqrfplot.R b/R/ggseqrfplot.R
@@ -90,7 +90,8 @@
 #' At this point \code{ggseqrfplot} does not support a grouping option. For
 #' plotting multiple groups, I recommend to produce group specific seqrfobjects or
 #' plots and to arrange them in a common plot using \code{\link[patchwork]{patchwork}}.
-#'
+#' See Example 6 in the vignette for further details:
+#' \code{vignette("ggseqplot", package = "ggseqplot")}
 #'
 #' @return A relative frequency sequence plot using \code{\link[ggplot2]{ggplot}}.
 #' @export
@@ -102,11 +103,11 @@
 #'   \insertAllCited{}
 #'
 #' @examples
-#' ## From TraMineR::seqprf
-#' library(TraMineR)
+#' ## Load additional libraries
 #' library(patchwork)
 #' library(ggplot2)
 #'
+#' ## From TraMineR::seqprf
 #' ## Defining a sequence object with the data in columns 10 to 25
 #' ## (family status from age 15 to 30) in the biofam data set
 #' data(biofam)
@@ -178,29 +179,40 @@ ggseqrfplot <- function(seqdata = NULL,
     )
   }
 
+  if (!is.null(seqdata) & !inherits(seqdata, "stslist") & !inherits(seqdata, "seqrf") & inherits(seqrfobject, "seqrf")) {
+    usethis::ui_info(
+      "you specified {usethis::ui_code('seqdata')} which are not stored as sequence object
+     and a valid {usethis::ui_code('seqrfobject')}; the {usethis::ui_code('seqdata')};
+     as well as the potentially specified parameters
+     {usethis::ui_code(c('k', 'sortv', 'weighted', 'grp.meth', 'squared', 'pow'))}
+     will be ignored; the plot will be rendered for the {usethis::ui_field('seqrfobject')}"
+    )
+  }
+
   if (inherits(seqdata, "stslist") & !is.null(seqrfobject) & !inherits(seqrfobject, "seqrf")) {
     usethis::ui_info(
-      "you specified a {usethis::ui_code('seqrfobject')} & {usethis::ui_code('seqdata')};
+    "you specified a {usethis::ui_code('seqrfobject')} & {usethis::ui_code('seqdata')};
     the {usethis::ui_code('seqrfobject')} is not of class {usethis::ui_code('seqrf')} and will be ignored;
     the plot will be rendered for the {usethis::ui_field('seqdata')} if the other parameters are specified correctly"
     )
   }
 
-  if (!is.null(seqdata) & !inherits(seqdata, "stslist") & !inherits(seqdata, "seqrf")) {
+  if (!is.null(seqdata) & !inherits(seqdata, "stslist") & !inherits(seqdata, "seqrf") & !inherits(seqrfobject, "seqrf")) {
     stop(
-    "you specified seqdata which are not stored as sequence object;
-use 'TraMineR::seqdef' to create a sequence object of class 'stslist')"
+    "you specified seqdata which are not stored as sequence object and no valid seqrfobject;
+use 'TraMineR::seqdef' to create a sequence object of class 'stslist' or specify a valid seqrfobject)"
     )
   }
 
+
   if (!is.null(seqdata) & !inherits(seqdata, "stslist") & inherits(seqdata, "seqrf")) {
     stop(
     "you specified seqdata which are of class 'seqrf';
   probably you forgot to type 'seqrfobject = '"
     )
   }
 
-  if (is.null(seqrfobject) & !is.null(seqdata) & !inherits(seqdata, "stslist")) {
+  if (is.null(seqrfobject) & (is.null(seqdata) | !inherits(seqdata, "stslist"))) {
     stop(
       "no seqrfobject specified & seqdata are either not specified or not
   stored as sequence object; use 'TraMineR::seqdef' to create one"

diff --git a/R/ggseqrplot.R b/R/ggseqrplot.R
@@ -47,7 +47,6 @@
 #'   \insertAllCited{}
 #'
 #' @examples
-#' library(TraMineR)
 #' ## Defining a sequence object with the data in columns 10 to 25
 #' ## (family status from age 15 to 30) in the biofam data set
 #' data(biofam)

diff --git a/R/ggseqtrplot.R b/R/ggseqtrplot.R
@@ -43,8 +43,6 @@
 #'
 #' # Examples from TraMineR::seqplot
 #'
-#' library(TraMineR)
-#'
 #' # biofam data set
 #' data(biofam)
 #' # We use only a sample of 300 cases

diff --git a/R/rfplot.R b/R/rfplot.R