diff --git a/.Rbuildignore b/.Rbuildignore index 18eb23d7..09986ac6 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -21,3 +21,4 @@ ^tests/testthat/_snaps$ ^CRAN-SUBMISSION$ ^revdep$ +^vignettes/interactive_tte_tutorial$ diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index e4217e43..5ec15a20 100644 --- a/CRAN-SUBMISSION +++ b/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 diff --git a/DESCRIPTION b/DESCRIPTION index 366443f9..422466df 100644 --- a/DESCRIPTION +++ b/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 diff --git a/R/visr.R b/R/visr.R index 10ca9d56..66f1b148 100644 --- a/R/visr.R +++ b/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. diff --git a/cran-comments.md b/cran-comments.md index 485e7114..43ededcf 100644 --- a/cran-comments.md +++ b/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 ' - - 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. diff --git a/man/visr.Rd b/man/visr.Rd index c2fef11f..3470e0f2 100644 --- a/man/visr.Rd +++ b/man/visr.Rd @@ -70,14 +70,14 @@ the default will do a proposal based on the \code{fun} argument.} \item{fun}{Function that represents the scale of the estimate. The current options are: -\itemize{ -\item{\code{surv}}{ is the survival probability. This is the default.} -\item{\code{log}}{ is log of the survival probability} -\item{\code{event}}{ is the failure probability} -\item{\code{cloglog}}{ is log(-log(survival probability))} -\item{\code{pct}}{ is survival as a percentage} -\item{\code{logpct}}{ is log survival as a percentage} -\item{\code{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 }} \item{legend_position}{Specifies the legend position in the plot.