use roxytypes

Genentech · Aug 10, 2023 · 0701e38 · 0701e38
1 parent 67b2a0b
commit 0701e38
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Showing 18 changed files with 4,169 additions and 3,950 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -11,6 +11,7 @@ repos:
         additional_dependencies:
           - shiny
           - checkmate
+          - openpharma/roxytypes
       # codemeta must be above use-tidy-description when both are used
       # id: codemeta-description-updated
       - id: use-tidy-description

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -30,14 +30,19 @@ Suggests:
     reshape,
     testthat
 Imports:
-    checkmate
+    checkmate,
+    lifecycle
 VignetteBuilder:
     knitr
 Encoding: UTF-8
 Language: en-US
 LazyData: true
-Roxygen: list(markdown = TRUE)
+Roxygen:
+    list(markdown = TRUE, packages = "roxytypes")
 RoxygenNote: 7.2.3
+Config/Needs/documentation:
+    roxytypes
+Config/roxytypes: list(format = "({type}):\\cr {description}")
 Collate:
     'Phase1b-package.R'
     'betadiff.R'

diff --git a/NAMESPACE b/NAMESPACE
@@ -46,13 +46,14 @@ importFrom(graphics,par)
 importFrom(graphics,plot)
 importFrom(graphics,polygon)
 importFrom(graphics,title)
+importFrom(lifecycle,deprecated)
+importFrom(stats,acf)
 importFrom(stats,binom.test)
 importFrom(stats,dbeta)
 importFrom(stats,dbinom)
 importFrom(stats,integrate)
 importFrom(stats,optimize)
 importFrom(stats,pbeta)
-importFrom(stats,qlogis)
 importFrom(stats,quantile)
 importFrom(stats,rbeta)
 importFrom(stats,rbinom)

diff --git a/R/Phase1b-package.R b/R/Phase1b-package.R
@@ -8,5 +8,8 @@
 ##'
 ##' @import checkmate
 ##' @importFrom graphics plot hist
+##' @importFrom lifecycle deprecated
+##' @importFrom stats acf
+##'
 ##' @keywords package
 NULL
diff --git a/R/helpers.R b/R/helpers.R
@@ -58,16 +58,20 @@ is.probRange <- function(x,
 }
 
 
-##' The logit function
+##' The Logit Function
 ##'
-##' @param x vector of probabilities
-##' @return logit(x) calculates logit(x)=log(x/(1-x))
+##' @description `r lifecycle::badge("experimental")`
 ##'
-##' @importFrom stats qlogis
+##' This just calculates the logit.
+##'
+##' @typed x: numeric
+##'   probabilities to transform.
+##' @return The logit of `x`.
 ##'
 ##' @example examples/logit.R
 ##' @export
-##' @keywords programming
 logit <- function(x) {
+  assert_numeric(x)
+
   stats::qlogis(x)
 }