Merge pull request #458 from openpharma/457-release-v04-deprecating-f…

…unctions

Release v0.4

.Rbuildignore

@@ -21,3 +21,4 @@
 ^tests/testthat/_snaps$
 ^CRAN-SUBMISSION$
 ^revdep$
+^vignettes/interactive_tte_tutorial$

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 0.3.1
-Date: 2022-08-17 20:02:15 UTC
-SHA: 58605b99d1aaae107d6cccffe018717438e99e8f
+Version: 0.4.0
+Date: 2023-11-20 18:11:15 UTC
+SHA: 27b222093f72ed812a09055caecf1de1aae65658

DESCRIPTION

@@ -33,29 +33,32 @@ Imports:
     broom (>= 0.7.11),
     cowplot,
     dplyr (>= 1.0.0),
+    DT,
+    forcats,
     ggplot2,
+    graphics,
+    grDevices,
+    grid,
     gridExtra,
+    gt (>= 0.3.0),
     gtable,
     kableExtra,
+    knitr,
     lifecycle,
     rlang (>= 1.0.0),
+    stats,
     survival (>= 3.4-0),
-    tidyr (>= 1.0.0)
+    tibble,
+    tidycmprsk (>= 0.1.1),
+    tidyr (>= 1.0.0),
+    utils
 Suggests:
-    covr,
     data.table,
-    DT,
-    forcats,
-    gt (>= 0.3.0),
-    knitr,
+    ggpubr,
     learnr,
     rmarkdown,
-    rsconnect,
-    shiny,
     spelling,
     testthat (>= 2.1.0),
-    tibble,
-    tidycmprsk (>= 0.1.1),
     vdiffr
 VignetteBuilder: 
     knitr

R/visr.R

@@ -20,17 +20,19 @@
 #'   do a proposal.
 #' @param y_ticks Ticks for the y-axis. When not specified,
 #'   the default will do a proposal based on the `fun` argument.
+#'
 #' @param fun Function that represents the scale of the estimate.
 #'   The current options are:
-#'   \itemize{
-#'   \item{`surv`}{ is the survival probability. This is the default.}
-#'   \item{`log`}{ is log of the survival probability}
-#'   \item{`event`}{ is the failure probability}
-#'   \item{`cloglog`}{ is log(-log(survival probability))}
-#'   \item{`pct`}{ is survival as a percentage}
-#'   \item{`logpct`}{ is log survival as a percentage}
-#'   \item{`cumhaz`}{ is the cumulative hazard}
+#'   \tabular{ll}{
+#'   \code{surv} \tab is the survival probability. This is the default \cr
+#'   \code{log} \tab is log of the survival probability \cr
+#'   \code{event} \tab is the failure probability \cr
+#'   \code{cloglog} \tab is log(-log(survival probability)) \cr
+#'   \code{pct} \tab is survival as a percentage \cr
+#'   \code{logpct} \tab is log survival as a percentage \cr
+#'   \code{cumhaz} \tab is the cumulative hazard \cr
 #'   }
+#'
 #' @param legend_position Specifies the legend position in the plot.
 #'   Character values allowed are "top" "left" "bottom" "right".
 #'   Numeric coordinates are also allowed.

cran-comments.md

@@ -1,8 +1,9 @@
 ## Resubmission
 This is a resubmission. In this version I have:
 
-* Resolved a warning from a failing test - see update below, 
-* Updated DESCRIPTION file to require latest version of survival (>= 3.4-0).
+* added notes that we are deprecating `visr.survfit()` and `visr.tidycuminc()`, recommending the use of {ggsurvfit} instead.  
+* Minor edit to documentation in `vis.R` to remove a note due to an itemized list. 
+
 
 ## Test environments
 * Ubuntu 18.04 LTS (on github actions), devel, release, oldrel-1, oldrel-2, oldrel-3, oldrel-4
@@ -12,10 +13,27 @@ This is a resubmission. In this version I have:
 
 ## R CMD check results
 
-0 errors | 0 warnings | 0 note
-  Maintainer: 'Mark Baillie <[email protected]>'
-
-  New submission
-
-  Package was archived on CRAN
-
+There were no ERRORs or WARNINGs. 
+
+There are 2 NOTEs I am aware of. 
+
+1. One is only found on Windows (Server 2022, R-devel 64-bit): 
+
+```
+* checking for detritus in the temp directory ... NOTE
+Found the following files/directories:
+  'lastMiKTeXException'
+```
+
+As noted in [R-hub issue #503](https://github.com/r-hub/rhub/issues/503), this may be due to a bug/crash in MiKTeX and can likely be ignored.
+
+
+2. The second is 
+
+```
+* checking for non-standard things in the check directory ... NOTE
+Found the following files/directories:
+  ''NULL''
+```
+
+As noted in [R-hub issue #560](https://github.com/r-hub/rhub/issues/560), this seems to be an Rhub issue and hopefully be ignored.