renv really is a love/hate relationship

.Rprofile

@@ -1,10 +0,0 @@
-options(
-  renv.settings.snapshot.type = "explicit",
-  renv.config.auto.snapshot = TRUE,
-  renv.config.pak.enabled = TRUE
-)
-source("renv/activate.R")
-
-if (interactive()) {
-  suppressMessages(require(usethis))
-}

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: stRoke
 Title: Clinical Stroke Research
-Version: 24.2.1
+Version: 24.10.1
 Authors@R: 
     person("Andreas Gammelgaard", "Damsbo", , "agdamsbo@clin.au.dk", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-7559-1154"))
@@ -17,7 +17,7 @@ BugReports: https://github.com/agdamsbo/stRoke/issues
 License: GPL-3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 LazyData: true
 Suggests:
     knitr,
@@ -25,7 +25,11 @@ Suggests:
     testthat,
     git2r,
     here,
-    spelling
+    spelling,
+    usethis,
+    pak,
+    roxygen2,
+    devtools
 Config/testthat/edition: 3
 Imports: 
     calendar,

NEWS.md

@@ -1,4 +1,4 @@
-# stRoke 24.2.1
+# stRoke 24.10.1
 
 ### Functions:
 
@@ -8,8 +8,12 @@
 
 * UPDATE: `add_padding()` updated to include option to add leading and/or tailing string with `lead` or `tail`.
 
+* Moving: The following functions are moved to `agdamsbo/project.aid` to focus on (stroke) trial related functions: `str_extract()`.
+
 * NEW: `mfi_calc()` calculates domain scores from the MFI questionnaire. Takes data frame of 20 ordered as the questionnaire. Default is to reverse questions with reverse scoring.
 
+Checks set up with `rhub` v2
+
 # stRoke 23.9.1
 
 ### Functions:

R/ci_plot.R

@@ -42,8 +42,8 @@ ci_plot <-
            title = NULL, 
            method = "auto") {
     
-    if (!method %in% c("auto", "model"))
+    if (!method %in% c("auto", "model")){
-      stop("Method has to either 'auto' or 'model'")
+      stop("Method has to either 'auto' or 'model'")}
     
     if (method == "auto") {
       if (!is.factor(ds[, y]))

R/ds2ical.R

@@ -1,3 +1,4 @@
+utils::globalVariables(c("DTSTART"))
 #' Convert data set to ical file
 #'
 #' @param data data set

R/generic_stroke.R

@@ -36,13 +36,13 @@ generic_stroke <-
       gtsummary::add_overall()
     
     x <- table(df[, c(group, score, strata)])
-    f1 <- rankinPlot::grottaBar(
+    f1 <- suppressWarnings(rankinPlot::grottaBar(
       x = x,
       groupName = group,
       scoreName = score,
       strataName = strata,
       colourScheme = "custom"
-    )
+    ))
     
     df[, score] <- factor(df[, score], ordered = TRUE)
     

R/mfi_calc.R

@@ -1,4 +1,5 @@
-#' Title
+utils::globalVariables(c("ndx"))
+#' Reverses relevant MFI subscores
 #'
 #' @param d data frame or tibble
 #' @param var numeric vector of indices of columns to reverse

R/str_extract.R

@@ -1,5 +1,7 @@
 #' Extract string based on regex pattern
 #' 
+#' DEPRECATION: moved to `agdamsbo/project.aid`
+#' 
 #' Use base::strsplit to 
 #' @param d vector of character strings
 #' @param pattern regex pattern to match

data-raw/cprs.R

@@ -5,4 +5,4 @@ usethis::use_data(cprs, overwrite = TRUE)
 cprs <- data.frame(cpr=sample(c("2310450637", "010115-4000", "0101896000",
                                 "010189-3000","300450-1030","010150-4021",
                                 "011085-AKE3","0101EJ-ATW3"),200,TRUE))
-save(cprs,file="cprs.rda")
+save(cprs,file="data/cprs.rda")

man/multi_rev.Rd

@@ -2,7 +2,7 @@
 % Please edit documentation in R/mfi_calc.R
 \name{multi_rev}
 \alias{multi_rev}
-\title{Title}
+\title{Reverses relevant MFI subscores}
 \usage{
 multi_rev(d, var)
 }
@@ -15,7 +15,7 @@ multi_rev(d, var)
 data.frame or tibble depending on input
 }
 \description{
-Title
+Reverses relevant MFI subscores
 }
 \examples{
 # rep_len(sample(1:5),length.out = 100) |> matrix(ncol=10) |> multi_rev(2:4)

man/str_extract.Rd

@@ -15,6 +15,9 @@ str_extract(d, pattern)
 vector of character strings
 }
 \description{
+DEPRECATION: moved to \code{agdamsbo/project.aid}
+}
+\details{
 Use base::strsplit to
 }
 \examples{

renv/.gitignore

@@ -1,7 +0,0 @@
-library/
-local/
-cellar/
-lock/
-python/
-sandbox/
-staging/

renv/settings.json

@@ -1,19 +0,0 @@
-{
-  "bioconductor.version": null,
-  "external.libraries": [],
-  "ignored.packages": [],
-  "package.dependency.fields": [
-    "Imports",
-    "Depends",
-    "LinkingTo"
-  ],
-  "ppm.enabled": null,
-  "ppm.ignored.urls": [],
-  "r.version": null,
-  "snapshot.type": "explicit",
-  "use.cache": true,
-  "vcs.ignore.cellar": true,
-  "vcs.ignore.library": true,
-  "vcs.ignore.local": true,
-  "vcs.manage.ignores": true
-}

stRoke.Rproj

@@ -15,4 +15,4 @@ LaTeX: pdfLaTeX
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
-PackageRoxygenize: rd,collate,namespace
+PackageRoxygenize: rd,collate,namespace,vignette

tests/spelling.R

@@ -1,3 +0,0 @@
-if(requireNamespace('spelling', quietly = TRUE))
-  spelling::spell_check_test(vignettes = TRUE, error = FALSE,
-                             skip_on_cran = TRUE)

tests/testthat/test-generic_stroke.R

@@ -2,12 +2,12 @@ test_that("generic_stroke() runs!", {
   iris$ord <-
     factor(sample(1:3, size = nrow(iris), replace = TRUE), ordered = TRUE)
   result <-
-    generic_stroke(
+    suppressMessages(generic_stroke(
       df = iris,
       group = "Species",
       score = "ord",
       variables = colnames(iris)[1:3]
-    )
+    ))
   expect_equal(length(result), 3)
   expect_equal(class(result), "list")
   expect_true("tbl_summary" %in% class(result[[1]]))