Add a type = "cloglog" for log minus log survival plots (#195)

* Adding a type = "cloglog" to tidysurvfit() and ggsurvfit() to plot log minus log survival curves

* Add documentation for cloglog

* Solve undefined global functions and variables

* Correct visible binding

* doc update

* doc update

* updates

* more updates

* Update R-CMD-check.yaml

* Update NEWS.md

* Update NEWS.md

* Update DESCRIPTION

* more updates

---------

Co-authored-by: Daniel Sjoberg <danield.sjoberg@gmail.com>

.github/workflows/R-CMD-check.yaml

@@ -25,16 +25,14 @@ jobs:
           - {os: macOS-latest,   r: 'release'}
 
           - {os: windows-latest, r: 'release'}
-          # Use 3.6 to trigger usage of RTools35
-          - {os: windows-latest, r: '3.6'}
 
           # Use older ubuntu to maximise backward compatibility
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
           - {os: ubuntu-latest,   r: 'oldrel-2'}
           - {os: ubuntu-latest,   r: 'oldrel-3'}
-          # - {os: ubuntu-latest,   r: 'oldrel-4'}
+          - {os: ubuntu-latest,   r: 'oldrel-4'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ggsurvfit
 Title: Flexible Time-to-Event Figures
-Version: 1.0.0.9002
+Version: 1.0.0.9003
 Authors@R: c(
     person("Daniel D.", "Sjoberg", , "danield.sjoberg@gmail.com", role = c("aut", "cre", "cph"),
            comment = c(ORCID = "0000-0003-0862-2018")),

NEWS.md

@@ -1,15 +1,17 @@
 # ggsurvfit (development version)
 
-* For multi-state models created with `survfit()`, the y-axis label is now "Probability in State". (#205)
-
-* Updated legend position syntax to account for changes in {ggplot2} v3.5.0.
+* We now allow for negative follow-up times in `tidy_survfit()` (and subsequently `ggsurvfit()`). When negative follow-up times are present users should specify `survfit(start.time)` and we print a note to this effect when not set. (#192) 
 
 * The `tidy_survfit()` (and subsequently `ggsurvfit()`) now honor the `survfit(start.time)` if specified. (#192)
 
-* We now allow for negative follow-up times in `tidy_survfit()` (and subsequently `ggsurvfit()`). When negative follow-up times are present users should specify `survfit(start.time)` and we print a note to this effect when not set. (#192) 
+* Updated legend position syntax to account for changes in {ggplot2} v3.5.0.
 
 * As of {survival} v3.6-4, the number censored are now returned as a matrix for multi-state models (i.e. competing risks models). The `tidy_survfit()` function has been updated to account for this new structure and the minimum version of {survival} has been increased to the latest version. (#199)
 
+* For non-competing risks multi-state models created with `survfit()`, the y-axis label is now "Probability in State". (#205)
+
+* Added the "`cloglog`" transformation option to `ggsurvfit(type)` and `tidy_survfit(type)`. (#194)
+
 # ggsurvfit 1.0.0
 
 * By default, a model plot created with `ggsurvfit()` or `ggcuminc()` uses the color aesthetic to plot curves by the stratifying variable(s), and further, `ggcuminc()` uses the linetype aesthetic for plots that contain multiple outcomes (i.e. competing events). We now introduce the global option `"ggsurvfit.switch-color-linetype"` to switch these defaults, giving users more flexibility over the output figures. Furthermore, when the `linetype_aes=` argument is called in a situation when it does not apply, it will be silently ignored (previously, an error message _may_ have been thrown). (#166)

R/ggcuminc.R

@@ -15,7 +15,7 @@
 #'
 #' @section Details:
 #'
-#' *Why do we not use `cmprsk::cuminc()`?*
+#' *Why not use `cmprsk::cuminc()`?*
 #'
 #' The implementation of `cmprsk::cuminc()` does not provide the data required
 #' to construct the risk table. Moreover, the `tidycmprsk::cuminc()` has a

R/tidy_survfit.R

@@ -12,13 +12,14 @@
 #' @param type type of statistic to report.
 #' Available for Kaplan-Meier estimates only.
 #' Default is `"survival"`.
-#' Must be one of the following:
+#' Must be one of the following or a function:
 #' ```{r, echo = FALSE}
 #' dplyr::tribble(
 #'   ~type,          ~transformation,
 #'   '`"survival"`', '`x`',
 #'   '`"risk"`',     '`1 - x`',
 #'   '`"cumhaz"`',   '`-log(x)`',
+#'   '`"cloglog"`',   '`log(-log(x))`',
 #' ) %>%
 #' knitr::kable()
 #' ```
@@ -31,7 +32,7 @@
 #'   tidy_survfit()
 tidy_survfit <- function(x,
                          times = NULL,
-                         type = c("survival", "risk", "cumhaz")) {
+                         type = c("survival", "risk", "cumhaz", "cloglog")) {
   # check inputs ---------------------------------------------------------------
   if (!inherits(x, "survfit")) {
     cli_abort(c("!" = "Argument {.code x} must be class {.cls survfit}.",
@@ -180,13 +181,14 @@ tidy_survfit <- function(x,
              risk = function(y) 1 - y,
              # survfit object contains an estimate for Cumhaz and SE based on Nelson-Aalen with or without correction for ties
              # However, no CI is calculated automatically. For plotting, the MLE estimator is used for convenience.
-             cumhaz = function(y) -log(y)
+             cumhaz = function(y) -log(y),
+             cloglog = function(y) log(-log(y))
       )
   } else {
     .transfun <- type
   }
   if (!rlang::is_function(.transfun)) {
-    cli_abort("The {.var type} argument must be one of {.val {c('survival', 'risk', 'cumhaz')}}, or a function.")
+    cli_abort("The {.var type} argument must be one of {.val {c('survival', 'risk', 'cumhaz', 'cloglog')}}, or a function.")
   }
 
   # transform estimates --------------------------------------------------------
@@ -218,6 +220,7 @@ tidy_survfit <- function(x,
             !is.null(.env$survfit$transitions) ~ "Probability in State",
           rlang::is_string(.env$type) && .env$type %in% "risk" ~ "Risk",
           rlang::is_string(.env$type) && .env$type %in% "cumhaz" ~ "Cumulative Hazard",
+          rlang::is_string(.env$type) && .env$type %in% "cloglog" ~ "Log Minus Log Survival",
           TRUE ~ rlang::expr_deparse(.transfun)
         )
     )
@@ -347,7 +350,8 @@ tidy_survfit <- function(x,
              "survival" = "decreasing",
              "cuminc" = "increasing",
              "risk" = "increasing",
-             "cumhaz" = "increasing"
+             "cumhaz" = "increasing",
+             "cloglog" = "increasing"
       )
   }
   else {