Review of Joanna testing (#361)

* Review of Joanna testing

estimate_cuminc
--------------
- Initialize data argument
- focus on arguments that are required for ADaM eg confint can be defined through ... Tidycmprisk should deal with confint variations
- add more informative messages
- Do we want to add an overall strata? We can put Overall instead of 1 inside the formula and then add a column strat99= Overall
- %||% is not defined. When strata is NULL then the formula becomes ...... ~ NULL in the final object without any error => used ifelse statement

testing
-------
- we need to focus on what the wrapper is doing, not on what the tidycmprisk function
 -- test arguments
 -- test excecuting surrounding the main function
 -- do not test how the main function works
- downstream processing of this object needs to be tested in the respective test files, not in the estimate function
- we expect tidycmprisk to do the heavy lifting and testing on the final object. We only verify wether the wrapper does not change the object. If it do

* Re-build README.Rmd

* review updates

* Update _pkgdown.yml

* adding `visR::` prefix in examples

* review updates from call

* Re-build README.Rmd

* update for conf.int

* Re-build README.Rmd

* redocument

Co-authored-by: shaesen2 <shaesen2@its.jnj.com>
Co-authored-by: GitHub Actions <actions@github.com>
Co-authored-by: Daniel Sjoberg <danield.sjoberg@gmail.com>

.gitignore

@@ -2,7 +2,6 @@
 /notebooks/libs
 /notebooks/*.html
 .Rproj.user
-visR.Rproj
 .Rbuildignore
 inst/doc
 .Rhistory

DESCRIPTION

@@ -83,7 +83,7 @@ Suggests:
     rmarkdown,
     rsconnect,
     shiny,
-    gt (>= 0.1.0),
+    gt (>= 0.3.0),
     forcats,
     testthat (>= 2.1.0),
     data.table,

R/estimate_KM.R

@@ -123,11 +123,11 @@ estimate_KM <- function(
 
 # Remove NA from the analysis --------------------------------------------
 
-  data <- as.data.frame(data)%>%
-    tidyr::drop_na(AVAL, CNSR, strata)
+  data <- as.data.frame(data) %>%
+    tidyr::drop_na(AVAL, CNSR)
 
   if (!is.null(strata)){
-    data <- data%>%
+    data <- data %>%
       tidyr::drop_na(any_of({{strata}}))
   }
 

R/estimate_cuminc.R

@@ -7,7 +7,7 @@
 #' Column must be a factor and the first level indicates censoring, the
 #' next level is the outcome of interest, and the remaining levels are the
 #' competing events. Default is `"CNSR"`
-#' @param conf.int Confidence internal level. Default is 0.95.
+#' @param conf.int Confidence internal level. Default is 0.95. Parameter is passed to `tidycmprsk::cuminc(conf.level=)`
 #' @param ... Additional argument passed to `tidycmprsk::cuminc()`
 #' @inheritParams estimate_KM
 #' @inheritParams visr
@@ -20,29 +20,66 @@
 #' @export
 #'
 #' @examples
-#' estimate_cuminc(
-#'   tidycmprsk::trial,
-#'   strata = "trt",
-#'   CNSR = "death_cr",
-#'   AVAL = "ttdeath"
-#' ) %>%
-#'   visr() %>%
-#'   add_CI() %>%
-#'   add_risktable(statlist = c("n.risk", "cum.event"))
-
-estimate_cuminc <- function(data
+#' cuminc <-
+#'   visR::estimate_cuminc(
+#'     data = tidycmprsk::trial,
+#'     strata = "trt",
+#'     CNSR = "death_cr",
+#'     AVAL = "ttdeath"
+#'   )
+#' cuminc
+#'
+#' cuminc %>%
+#'   visR::visr() %>%
+#'   visR::add_CI() %>%
+#'   visR::add_risktable(statlist = c("n.risk", "cum.event"))
+
+estimate_cuminc <- function( data = NULL
                             ,strata = NULL
                             ,CNSR = "CNSR"
                             ,AVAL = "AVAL"
                             ,conf.int = 0.95
                             ,...) {
-  # check for installation of tidycmprsk package
+
+
+  # check for installation of tidycmprsk package -------------------------
   rlang::check_installed("tidycmprsk", version = "0.1.1")
   dots <- rlang::dots_list(...)
 
-  # checking/prepping inputs ---------------------------------------------------
-  strata <- strata %||% "1" %>% paste(collapse = " + ")
+  # Validate data --------------------------------------------------------
+  if (is.null(data)) stop(paste0("Data can't be NULL."))
+  if (!is.numeric(conf.int)) stop(paste0("conf.int needs to be numeric."))
+  if (!(0 <= conf.int & conf.int <= 1)) stop(paste0("conf.int needs to between 0 and 1."))
+
+  # Validate columns -----------------------------------------------------
+  reqcols <- c(strata, CNSR, AVAL)
+
+  if (! all(reqcols %in% colnames(data))){
+    stop(paste0("Following columns are missing from `data`: ", paste(setdiff(reqcols, colnames(data)), collapse = " "), "."))
+  }
+
+  if (! is.numeric(data[[AVAL]])){
+    stop("Analysis variable (AVAL) is not numeric.")
+  }
+
+  if (! is.factor(data[[CNSR]])){
+    stop("Censor variable (CNSR) is not a factor")
+  }
+
+  # Remove NA from the analysis ------------------------------------------
+
+  data <- data %>%
+    tidyr::drop_na(AVAL, CNSR)
+
+  if (!is.null(strata)){
+    data <- data %>%
+      tidyr::drop_na(any_of({{strata}}))
+  }
+
+  # Ensure the presence of at least one strata ---------------------------
+  strata <- ifelse(is.null(strata), 1, strata %>% paste(collapse = " + "))
 
+  # cuminc ---------------------------------------------------------------
   cuminc <-
     tidycmprsk::cuminc(
       formula = stats::as.formula(paste0("survival::Surv(", AVAL, ", ", CNSR, ") ~ ", strata)),

R/utils_visr.R

@@ -6,16 +6,15 @@
 #'
 #' @return List of \code{ggplot} with equal width.
 #'
-#' @references \url{https://stackoverflow.com/questions/26159495/align-multiple-ggplot-
-#'                  graphs-with-and-without-legends}
+#' @references \url{https://stackoverflow.com/questions/26159495}
 #'
 #' @examples
 #' \donttest{
 #'
 #' ## create 2 graphs
 #' p1 <- ggplot2::ggplot(adtte, ggplot2::aes(x = as.numeric(AGE), fill = "Age")) +
 #'   ggplot2::geom_histogram(bins = 15)
-#'   
+#'
 #' p2 <- ggplot2::ggplot(adtte, ggplot2::aes(x = as.numeric(AGE))) +
 #'  ggplot2::geom_histogram(bins = 15)
 #'

README.md

@@ -44,7 +44,7 @@ coverage](https://codecov.io/gh/openpharma/visR/branch/develop/graph/badge.svg)]
 [![pkgdown](https://github.com/openpharma/visR/actions/workflows/makedocs.yml/badge.svg)](https://github.com/openpharma/visR/actions/workflows/makedocs.yml)
 [![CRAN
 status](https://www.r-pkg.org/badges/version/visR)](https://CRAN.R-project.org/package=visR)
-<a href=https://github.com/pharmaR/riskmetric><img src=https://img.shields.io/badge/riskmetric-0.53-green></img></a>
+<a href=https://github.com/pharmaR/riskmetric><img src=https://img.shields.io/badge/riskmetric-0.52-green></img></a>
 <!-- badges: end -->
 
 ## Installation
@@ -109,11 +109,13 @@ Please note that the `visR` project is released with a [Contributor Code
 of Conduct](CODE_OF_CONDUCT.md). By contributing to this project, you
 agree to abide by its terms. Thank you to all contributors:
 
+[@AlexandraP-21](https://github.com/AlexandraP-21),
 [@ardeeshany](https://github.com/ardeeshany),
 [@bailliem](https://github.com/bailliem),
 [@ddsjoberg](https://github.com/ddsjoberg),
 [@epijim](https://github.com/epijim),
 [@gdario](https://github.com/gdario),
+[@joanacmbarros](https://github.com/joanacmbarros),
 [@lcomm](https://github.com/lcomm),
 [@prabhushanmup](https://github.com/prabhushanmup),
 [@rebecca-albrecht](https://github.com/rebecca-albrecht),

_pkgdown.yml

@@ -11,6 +11,8 @@ authors:
     href: "https://www.linkedin.com/in/stevenhaesendonckx/"
   James Black:
     href: "https://www.epijim.uk/"
+  Daniel D. Sjoberg:
+    href: "https://www.danieldsjoberg.com/"
 
 development:
   mode: auto