mirror of
https://github.com/agdamsbo/stRoke.git
synced 2024-11-21 12:30:23 +01:00
multiple updates and additions. see 'NEWS.md'
This commit is contained in:
parent
559f9dee4e
commit
6434165e20
10
DESCRIPTION
10
DESCRIPTION
@ -1,6 +1,6 @@
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Package: stRoke
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Title: Clinical Stroke Research
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Version: 24.2.1
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Version: 24.10.1
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Authors@R:
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person("Andreas Gammelgaard", "Damsbo", , "agdamsbo@clin.au.dk", role = c("aut", "cre"),
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comment = c(ORCID = "0000-0002-7559-1154"))
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@ -17,7 +17,7 @@ BugReports: https://github.com/agdamsbo/stRoke/issues
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License: GPL-3
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Encoding: UTF-8
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Roxygen: list(markdown = TRUE)
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RoxygenNote: 7.3.1
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RoxygenNote: 7.3.2
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LazyData: true
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Suggests:
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knitr,
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@ -25,7 +25,11 @@ Suggests:
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testthat,
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git2r,
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here,
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spelling
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spelling,
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usethis,
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pak,
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roxygen2,
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devtools
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Config/testthat/edition: 3
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Imports:
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calendar,
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6
NEWS.md
6
NEWS.md
@ -1,4 +1,4 @@
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# stRoke 24.2.1
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# stRoke 24.10.1
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### Functions:
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@ -8,8 +8,12 @@
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* UPDATE: `add_padding()` updated to include option to add leading and/or tailing string with `lead` or `tail`.
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* Moving: The following functions are moved to `agdamsbo/project.aid` to focus on (stroke) trial related functions: `str_extract()`.
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* 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.
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Checks set up with `rhub` v2
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# stRoke 23.9.1
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### Functions:
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@ -42,8 +42,8 @@ ci_plot <-
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title = NULL,
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method = "auto") {
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if (!method %in% c("auto", "model"))
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stop("Method has to either 'auto' or 'model'")
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if (!method %in% c("auto", "model")){
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stop("Method has to either 'auto' or 'model'")}
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if (method == "auto") {
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if (!is.factor(ds[, y]))
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@ -1,3 +1,4 @@
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utils::globalVariables(c("DTSTART"))
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#' Convert data set to ical file
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#'
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#' @param data data set
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@ -36,13 +36,13 @@ generic_stroke <-
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gtsummary::add_overall()
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x <- table(df[, c(group, score, strata)])
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f1 <- rankinPlot::grottaBar(
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f1 <- suppressWarnings(rankinPlot::grottaBar(
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x = x,
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groupName = group,
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scoreName = score,
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strataName = strata,
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colourScheme = "custom"
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)
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))
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df[, score] <- factor(df[, score], ordered = TRUE)
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@ -1,4 +1,5 @@
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#' Title
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utils::globalVariables(c("ndx"))
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#' Reverses relevant MFI subscores
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#'
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#' @param d data frame or tibble
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#' @param var numeric vector of indices of columns to reverse
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@ -1,5 +1,7 @@
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#' Extract string based on regex pattern
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#'
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#' DEPRECATION: moved to `agdamsbo/project.aid`
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#'
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#' Use base::strsplit to
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#' @param d vector of character strings
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#' @param pattern regex pattern to match
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@ -5,4 +5,4 @@ usethis::use_data(cprs, overwrite = TRUE)
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cprs <- data.frame(cpr=sample(c("2310450637", "010115-4000", "0101896000",
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"010189-3000","300450-1030","010150-4021",
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"011085-AKE3","0101EJ-ATW3"),200,TRUE))
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save(cprs,file="cprs.rda")
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save(cprs,file="data/cprs.rda")
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BIN
data/cprs.rda
BIN
data/cprs.rda
Binary file not shown.
@ -2,7 +2,7 @@
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% Please edit documentation in R/mfi_calc.R
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\name{multi_rev}
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\alias{multi_rev}
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\title{Title}
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\title{Reverses relevant MFI subscores}
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\usage{
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multi_rev(d, var)
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}
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@ -15,7 +15,7 @@ multi_rev(d, var)
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data.frame or tibble depending on input
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}
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\description{
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Title
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Reverses relevant MFI subscores
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}
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\examples{
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# rep_len(sample(1:5),length.out = 100) |> matrix(ncol=10) |> multi_rev(2:4)
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@ -15,6 +15,9 @@ str_extract(d, pattern)
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vector of character strings
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}
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\description{
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DEPRECATION: moved to \code{agdamsbo/project.aid}
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}
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\details{
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Use base::strsplit to
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}
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\examples{
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498
renv.lock
498
renv.lock
@ -1,6 +1,6 @@
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{
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{
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"Name": "CRAN",
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@ -11,9 +11,9 @@
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|
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|
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"R",
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"grDevices",
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@ -22,13 +22,13 @@
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"stats",
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"grDevices",
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@ -39,7 +39,7 @@
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"stats",
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|
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@ -63,18 +63,18 @@
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@ -83,17 +83,7 @@
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"jsonlite",
|
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"utils"
|
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@ -115,88 +105,23 @@
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|
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|
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|
||||
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|
||||
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|
||||
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|
||||
"generics",
|
||||
"glue",
|
||||
"lifecycle",
|
||||
"purrr",
|
||||
"rlang",
|
||||
"stringr",
|
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|
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"tidyr"
|
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|
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|
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|
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|
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|
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|
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|
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"labelled",
|
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"lifecycle",
|
||||
"purrr",
|
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|
||||
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
||||
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|
||||
"fastmap",
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||||
"grDevices",
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||||
"htmltools",
|
||||
"jquerylib",
|
||||
@ -207,56 +132,62 @@
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||||
"rlang",
|
||||
"sass"
|
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],
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|
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|
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|
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|
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@ -266,57 +197,35 @@
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"methods",
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|
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|
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@ -341,27 +250,15 @@
|
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],
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|
||||
"Requirements": [
|
||||
"R",
|
||||
"methods"
|
||||
"R"
|
||||
],
|
||||
"Hash": "daf4a1246be12c1fa8c7705a0935c1a0"
|
||||
"Hash": "6b567375113ceb7d9f800de4dd42218e"
|
||||
},
|
||||
"fansi": {
|
||||
"Package": "fansi",
|
||||
@ -377,17 +274,17 @@
|
||||
},
|
||||
"farver": {
|
||||
"Package": "farver",
|
||||
"Version": "2.1.1",
|
||||
"Version": "2.1.2",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "8106d78941f34855c440ddb946b8f7a5"
|
||||
"Hash": "680887028577f3fa2a81e410ed0d6e42"
|
||||
},
|
||||
"fastmap": {
|
||||
"Package": "fastmap",
|
||||
"Version": "1.1.1",
|
||||
"Version": "1.2.0",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "f7736a18de97dea803bde0a2daaafb27"
|
||||
"Hash": "aa5e1cd11c2d15497494c5292d7ffcc8"
|
||||
},
|
||||
"fontawesome": {
|
||||
"Package": "fontawesome",
|
||||
@ -401,32 +298,16 @@
|
||||
],
|
||||
"Hash": "c2efdd5f0bcd1ea861c2d4e2a883a67d"
|
||||
},
|
||||
"forcats": {
|
||||
"Package": "forcats",
|
||||
"Version": "1.0.0",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"cli",
|
||||
"glue",
|
||||
"lifecycle",
|
||||
"magrittr",
|
||||
"rlang",
|
||||
"tibble"
|
||||
],
|
||||
"Hash": "1a0a9a3d5083d0d573c4214576f1e690"
|
||||
},
|
||||
"fs": {
|
||||
"Package": "fs",
|
||||
"Version": "1.6.3",
|
||||
"Version": "1.6.4",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"methods"
|
||||
],
|
||||
"Hash": "47b5f30c720c23999b913a1a635cf0bb"
|
||||
"Hash": "15aeb8c27f5ea5161f9f6a641fafd93a"
|
||||
},
|
||||
"generics": {
|
||||
"Package": "generics",
|
||||
@ -441,7 +322,7 @@
|
||||
},
|
||||
"ggplot2": {
|
||||
"Package": "ggplot2",
|
||||
"Version": "3.4.4",
|
||||
"Version": "3.5.1",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
@ -462,22 +343,22 @@
|
||||
"vctrs",
|
||||
"withr"
|
||||
],
|
||||
"Hash": "313d31eff2274ecf4c1d3581db7241f9"
|
||||
"Hash": "44c6a2f8202d5b7e878ea274b1092426"
|
||||
},
|
||||
"glue": {
|
||||
"Package": "glue",
|
||||
"Version": "1.7.0",
|
||||
"Version": "1.8.0",
|
||||
"Source": "Repository",
|
||||
"Repository": "RSPM",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"methods"
|
||||
],
|
||||
"Hash": "e0b3a53876554bd45879e596cdb10a52"
|
||||
"Hash": "5899f1eaa825580172bb56c08266f37c"
|
||||
},
|
||||
"gt": {
|
||||
"Package": "gt",
|
||||
"Version": "0.10.1",
|
||||
"Version": "0.11.1",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
@ -503,13 +384,13 @@
|
||||
"vctrs",
|
||||
"xml2"
|
||||
],
|
||||
"Hash": "03009c105dfae79460b8eb9d8cf791e4"
|
||||
"Hash": "3170d1f0f45e531c241179ab57cd30bd"
|
||||
},
|
||||
"gtable": {
|
||||
"Package": "gtable",
|
||||
"Version": "0.3.4",
|
||||
"Version": "0.3.5",
|
||||
"Source": "Repository",
|
||||
"Repository": "RSPM",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"cli",
|
||||
@ -518,95 +399,53 @@
|
||||
"lifecycle",
|
||||
"rlang"
|
||||
],
|
||||
"Hash": "b29cf3031f49b04ab9c852c912547eef"
|
||||
"Hash": "e18861963cbc65a27736e02b3cd3c4a0"
|
||||
},
|
||||
"gtsummary": {
|
||||
"Package": "gtsummary",
|
||||
"Version": "1.7.2",
|
||||
"Version": "2.0.3",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"broom",
|
||||
"broom.helpers",
|
||||
"cards",
|
||||
"cli",
|
||||
"dplyr",
|
||||
"forcats",
|
||||
"glue",
|
||||
"gt",
|
||||
"knitr",
|
||||
"lifecycle",
|
||||
"purrr",
|
||||
"rlang",
|
||||
"stringr",
|
||||
"tibble",
|
||||
"tidyr",
|
||||
"vctrs"
|
||||
],
|
||||
"Hash": "08df7405a102e3f0bdf7a13a29e8c6ab"
|
||||
},
|
||||
"haven": {
|
||||
"Package": "haven",
|
||||
"Version": "2.5.4",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"cli",
|
||||
"cpp11",
|
||||
"forcats",
|
||||
"hms",
|
||||
"lifecycle",
|
||||
"methods",
|
||||
"readr",
|
||||
"rlang",
|
||||
"tibble",
|
||||
"tidyselect",
|
||||
"vctrs"
|
||||
],
|
||||
"Hash": "9171f898db9d9c4c1b2c745adc2c1ef1"
|
||||
"Hash": "cd4d593e8ce0ad4e5c2c0acc50ce7330"
|
||||
},
|
||||
"highr": {
|
||||
"Package": "highr",
|
||||
"Version": "0.10",
|
||||
"Version": "0.11",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"xfun"
|
||||
],
|
||||
"Hash": "06230136b2d2b9ba5805e1963fa6e890"
|
||||
},
|
||||
"hms": {
|
||||
"Package": "hms",
|
||||
"Version": "1.1.3",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"lifecycle",
|
||||
"methods",
|
||||
"pkgconfig",
|
||||
"rlang",
|
||||
"vctrs"
|
||||
],
|
||||
"Hash": "b59377caa7ed00fa41808342002138f9"
|
||||
"Hash": "d65ba49117ca223614f71b60d85b8ab7"
|
||||
},
|
||||
"htmltools": {
|
||||
"Package": "htmltools",
|
||||
"Version": "0.5.7",
|
||||
"Version": "0.5.8.1",
|
||||
"Source": "Repository",
|
||||
"Repository": "RSPM",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"base64enc",
|
||||
"digest",
|
||||
"ellipsis",
|
||||
"fastmap",
|
||||
"grDevices",
|
||||
"rlang",
|
||||
"utils"
|
||||
],
|
||||
"Hash": "2d7b3857980e0e0d0a1fd6f11928ab0f"
|
||||
"Hash": "81d371a9cc60640e74e4ab6ac46dcedc"
|
||||
},
|
||||
"htmlwidgets": {
|
||||
"Package": "htmlwidgets",
|
||||
@ -627,7 +466,7 @@
|
||||
"Package": "isoband",
|
||||
"Version": "0.2.7",
|
||||
"Source": "Repository",
|
||||
"Repository": "RSPM",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"grid",
|
||||
"utils"
|
||||
@ -646,13 +485,13 @@
|
||||
},
|
||||
"jsonlite": {
|
||||
"Package": "jsonlite",
|
||||
"Version": "1.8.8",
|
||||
"Version": "1.8.9",
|
||||
"Source": "Repository",
|
||||
"Repository": "RSPM",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"methods"
|
||||
],
|
||||
"Hash": "e1b9c55281c5adc4dd113652d9e26768"
|
||||
"Hash": "4e993b65c2c3ffbffce7bb3e2c6f832b"
|
||||
},
|
||||
"juicyjuice": {
|
||||
"Package": "juicyjuice",
|
||||
@ -666,7 +505,7 @@
|
||||
},
|
||||
"knitr": {
|
||||
"Package": "knitr",
|
||||
"Version": "1.45",
|
||||
"Version": "1.48",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
@ -678,7 +517,7 @@
|
||||
"xfun",
|
||||
"yaml"
|
||||
],
|
||||
"Hash": "1ec462871063897135c1bcbe0fc8f07d"
|
||||
"Hash": "acf380f300c721da9fde7df115a5f86f"
|
||||
},
|
||||
"labeling": {
|
||||
"Package": "labeling",
|
||||
@ -691,26 +530,9 @@
|
||||
],
|
||||
"Hash": "b64ec208ac5bc1852b285f665d6368b3"
|
||||
},
|
||||
"labelled": {
|
||||
"Package": "labelled",
|
||||
"Version": "2.12.0",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"dplyr",
|
||||
"haven",
|
||||
"lifecycle",
|
||||
"rlang",
|
||||
"stringr",
|
||||
"tidyr",
|
||||
"vctrs"
|
||||
],
|
||||
"Hash": "1ec27c624ece6c20431e9249bd232797"
|
||||
},
|
||||
"lattice": {
|
||||
"Package": "lattice",
|
||||
"Version": "0.22-5",
|
||||
"Version": "0.22-6",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
@ -721,13 +543,13 @@
|
||||
"stats",
|
||||
"utils"
|
||||
],
|
||||
"Hash": "7c5e89f04e72d6611c77451f6331a091"
|
||||
"Hash": "cc5ac1ba4c238c7ca9fa6a87ca11a7e2"
|
||||
},
|
||||
"lifecycle": {
|
||||
"Package": "lifecycle",
|
||||
"Version": "1.0.4",
|
||||
"Source": "Repository",
|
||||
"Repository": "RSPM",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"cli",
|
||||
@ -761,7 +583,7 @@
|
||||
},
|
||||
"markdown": {
|
||||
"Package": "markdown",
|
||||
"Version": "1.12",
|
||||
"Version": "1.13",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
@ -770,7 +592,7 @@
|
||||
"utils",
|
||||
"xfun"
|
||||
],
|
||||
"Hash": "765cf53992401b3b6c297b69e1edb8bd"
|
||||
"Hash": "074efab766a9d6360865ad39512f2a7e"
|
||||
},
|
||||
"memoise": {
|
||||
"Package": "memoise",
|
||||
@ -812,18 +634,18 @@
|
||||
},
|
||||
"munsell": {
|
||||
"Package": "munsell",
|
||||
"Version": "0.5.0",
|
||||
"Version": "0.5.1",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"colorspace",
|
||||
"methods"
|
||||
],
|
||||
"Hash": "6dfe8bf774944bd5595785e3229d8771"
|
||||
"Hash": "4fd8900853b746af55b81fda99da7695"
|
||||
},
|
||||
"nlme": {
|
||||
"Package": "nlme",
|
||||
"Version": "3.1-164",
|
||||
"Version": "3.1-166",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
@ -833,7 +655,7 @@
|
||||
"stats",
|
||||
"utils"
|
||||
],
|
||||
"Hash": "a623a2239e642806158bc4dc3f51565d"
|
||||
"Hash": "ccbb8846be320b627e6aa2b4616a2ded"
|
||||
},
|
||||
"pillar": {
|
||||
"Package": "pillar",
|
||||
@ -862,30 +684,6 @@
|
||||
],
|
||||
"Hash": "01f28d4278f15c76cddbea05899c5d6f"
|
||||
},
|
||||
"prettyunits": {
|
||||
"Package": "prettyunits",
|
||||
"Version": "1.2.0",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R"
|
||||
],
|
||||
"Hash": "6b01fc98b1e86c4f705ce9dcfd2f57c7"
|
||||
},
|
||||
"progress": {
|
||||
"Package": "progress",
|
||||
"Version": "1.2.3",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"R6",
|
||||
"crayon",
|
||||
"hms",
|
||||
"prettyunits"
|
||||
],
|
||||
"Hash": "f4625e061cb2865f111b47ff163a5ca6"
|
||||
},
|
||||
"purrr": {
|
||||
"Package": "purrr",
|
||||
"Version": "1.0.2",
|
||||
@ -925,13 +723,13 @@
|
||||
},
|
||||
"reactR": {
|
||||
"Package": "reactR",
|
||||
"Version": "0.5.0",
|
||||
"Version": "0.6.1",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"htmltools"
|
||||
],
|
||||
"Hash": "c9014fd1a435b2d790dd506589cb24e5"
|
||||
"Hash": "b8e3d93f508045812f47136c7c44c251"
|
||||
},
|
||||
"reactable": {
|
||||
"Package": "reactable",
|
||||
@ -948,53 +746,30 @@
|
||||
],
|
||||
"Hash": "6069eb2a6597963eae0605c1875ff14c"
|
||||
},
|
||||
"readr": {
|
||||
"Package": "readr",
|
||||
"Version": "2.1.5",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"R6",
|
||||
"cli",
|
||||
"clipr",
|
||||
"cpp11",
|
||||
"crayon",
|
||||
"hms",
|
||||
"lifecycle",
|
||||
"methods",
|
||||
"rlang",
|
||||
"tibble",
|
||||
"tzdb",
|
||||
"utils",
|
||||
"vroom"
|
||||
],
|
||||
"Hash": "9de96463d2117f6ac49980577939dfb3"
|
||||
},
|
||||
"renv": {
|
||||
"Package": "renv",
|
||||
"Version": "1.0.3",
|
||||
"Version": "1.0.9",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"utils"
|
||||
],
|
||||
"Hash": "41b847654f567341725473431dd0d5ab"
|
||||
"Hash": "ef233f0e9064fc88c898b340c9add5c2"
|
||||
},
|
||||
"rlang": {
|
||||
"Package": "rlang",
|
||||
"Version": "1.1.3",
|
||||
"Version": "1.1.4",
|
||||
"Source": "Repository",
|
||||
"Repository": "RSPM",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"utils"
|
||||
],
|
||||
"Hash": "42548638fae05fd9a9b5f3f437fbbbe2"
|
||||
"Hash": "3eec01f8b1dee337674b2e34ab1f9bc1"
|
||||
},
|
||||
"rmarkdown": {
|
||||
"Package": "rmarkdown",
|
||||
"Version": "2.25",
|
||||
"Version": "2.28",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
@ -1007,20 +782,19 @@
|
||||
"jsonlite",
|
||||
"knitr",
|
||||
"methods",
|
||||
"stringr",
|
||||
"tinytex",
|
||||
"tools",
|
||||
"utils",
|
||||
"xfun",
|
||||
"yaml"
|
||||
],
|
||||
"Hash": "d65e35823c817f09f4de424fcdfa812a"
|
||||
"Hash": "062470668513dcda416927085ee9bdc7"
|
||||
},
|
||||
"sass": {
|
||||
"Package": "sass",
|
||||
"Version": "0.4.8",
|
||||
"Version": "0.4.9",
|
||||
"Source": "Repository",
|
||||
"Repository": "RSPM",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R6",
|
||||
"fs",
|
||||
@ -1028,7 +802,7 @@
|
||||
"rappdirs",
|
||||
"rlang"
|
||||
],
|
||||
"Hash": "168f9353c76d4c4b0a0bbf72e2c2d035"
|
||||
"Hash": "d53dbfddf695303ea4ad66f86e99b95d"
|
||||
},
|
||||
"scales": {
|
||||
"Package": "scales",
|
||||
@ -1052,7 +826,7 @@
|
||||
},
|
||||
"stringi": {
|
||||
"Package": "stringi",
|
||||
"Version": "1.8.3",
|
||||
"Version": "1.8.4",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
@ -1061,7 +835,7 @@
|
||||
"tools",
|
||||
"utils"
|
||||
],
|
||||
"Hash": "058aebddea264f4c99401515182e656a"
|
||||
"Hash": "39e1144fd75428983dc3f63aa53dfa91"
|
||||
},
|
||||
"stringr": {
|
||||
"Package": "stringr",
|
||||
@ -1124,7 +898,7 @@
|
||||
},
|
||||
"tidyselect": {
|
||||
"Package": "tidyselect",
|
||||
"Version": "1.2.0",
|
||||
"Version": "1.2.1",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
@ -1136,7 +910,7 @@
|
||||
"vctrs",
|
||||
"withr"
|
||||
],
|
||||
"Hash": "79540e5fcd9e0435af547d885f184fd5"
|
||||
"Hash": "829f27b9c4919c16b593794a6344d6c0"
|
||||
},
|
||||
"timechange": {
|
||||
"Package": "timechange",
|
||||
@ -1151,24 +925,13 @@
|
||||
},
|
||||
"tinytex": {
|
||||
"Package": "tinytex",
|
||||
"Version": "0.49",
|
||||
"Version": "0.53",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"xfun"
|
||||
],
|
||||
"Hash": "5ac22900ae0f386e54f1c307eca7d843"
|
||||
},
|
||||
"tzdb": {
|
||||
"Package": "tzdb",
|
||||
"Version": "0.4.0",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"cpp11"
|
||||
],
|
||||
"Hash": "f561504ec2897f4d46f0c7657e488ae1"
|
||||
"Hash": "9db859e8aabbb474293dde3097839420"
|
||||
},
|
||||
"utf8": {
|
||||
"Package": "utf8",
|
||||
@ -1204,55 +967,30 @@
|
||||
],
|
||||
"Hash": "c826c7c4241b6fc89ff55aaea3fa7491"
|
||||
},
|
||||
"vroom": {
|
||||
"Package": "vroom",
|
||||
"Version": "1.6.5",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"bit64",
|
||||
"cli",
|
||||
"cpp11",
|
||||
"crayon",
|
||||
"glue",
|
||||
"hms",
|
||||
"lifecycle",
|
||||
"methods",
|
||||
"progress",
|
||||
"rlang",
|
||||
"stats",
|
||||
"tibble",
|
||||
"tidyselect",
|
||||
"tzdb",
|
||||
"vctrs",
|
||||
"withr"
|
||||
],
|
||||
"Hash": "390f9315bc0025be03012054103d227c"
|
||||
},
|
||||
"withr": {
|
||||
"Package": "withr",
|
||||
"Version": "3.0.0",
|
||||
"Version": "3.0.1",
|
||||
"Source": "Repository",
|
||||
"Repository": "RSPM",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"grDevices",
|
||||
"graphics"
|
||||
],
|
||||
"Hash": "d31b6c62c10dcf11ec530ca6b0dd5d35"
|
||||
"Hash": "07909200e8bbe90426fbfeb73e1e27aa"
|
||||
},
|
||||
"xfun": {
|
||||
"Package": "xfun",
|
||||
"Version": "0.42",
|
||||
"Version": "0.48",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"grDevices",
|
||||
"stats",
|
||||
"tools"
|
||||
],
|
||||
"Hash": "fd1349170df31f7a10bd98b0189e85af"
|
||||
"Hash": "89e455b87c84e227eb7f60a1b4e5fe1f"
|
||||
},
|
||||
"xml2": {
|
||||
"Package": "xml2",
|
||||
@ -1269,10 +1007,10 @@
|
||||
},
|
||||
"yaml": {
|
||||
"Package": "yaml",
|
||||
"Version": "2.3.8",
|
||||
"Version": "2.3.10",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Hash": "29240487a071f535f5e5d5a323b7afbd"
|
||||
"Hash": "51dab85c6c98e50a18d7551e9d49f76c"
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
181
renv/activate.R
181
renv/activate.R
@ -2,11 +2,13 @@
|
||||
local({
|
||||
|
||||
# the requested version of renv
|
||||
version <- "1.0.3"
|
||||
version <- "1.0.9"
|
||||
attr(version, "sha") <- NULL
|
||||
|
||||
# the project directory
|
||||
project <- getwd()
|
||||
project <- Sys.getenv("RENV_PROJECT")
|
||||
if (!nzchar(project))
|
||||
project <- getwd()
|
||||
|
||||
# use start-up diagnostics if enabled
|
||||
diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE")
|
||||
@ -31,6 +33,14 @@ local({
|
||||
if (!is.null(override))
|
||||
return(override)
|
||||
|
||||
# if we're being run in a context where R_LIBS is already set,
|
||||
# don't load -- presumably we're being run as a sub-process and
|
||||
# the parent process has already set up library paths for us
|
||||
rcmd <- Sys.getenv("R_CMD", unset = NA)
|
||||
rlibs <- Sys.getenv("R_LIBS", unset = NA)
|
||||
if (!is.na(rlibs) && !is.na(rcmd))
|
||||
return(FALSE)
|
||||
|
||||
# next, check environment variables
|
||||
# TODO: prefer using the configuration one in the future
|
||||
envvars <- c(
|
||||
@ -50,9 +60,22 @@ local({
|
||||
|
||||
})
|
||||
|
||||
if (!enabled)
|
||||
# bail if we're not enabled
|
||||
if (!enabled) {
|
||||
|
||||
# if we're not enabled, we might still need to manually load
|
||||
# the user profile here
|
||||
profile <- Sys.getenv("R_PROFILE_USER", unset = "~/.Rprofile")
|
||||
if (file.exists(profile)) {
|
||||
cfg <- Sys.getenv("RENV_CONFIG_USER_PROFILE", unset = "TRUE")
|
||||
if (tolower(cfg) %in% c("true", "t", "1"))
|
||||
sys.source(profile, envir = globalenv())
|
||||
}
|
||||
|
||||
return(FALSE)
|
||||
|
||||
}
|
||||
|
||||
# avoid recursion
|
||||
if (identical(getOption("renv.autoloader.running"), TRUE)) {
|
||||
warning("ignoring recursive attempt to run renv autoloader")
|
||||
@ -75,6 +98,66 @@ local({
|
||||
unloadNamespace("renv")
|
||||
|
||||
# load bootstrap tools
|
||||
ansify <- function(text) {
|
||||
if (renv_ansify_enabled())
|
||||
renv_ansify_enhanced(text)
|
||||
else
|
||||
renv_ansify_default(text)
|
||||
}
|
||||
|
||||
renv_ansify_enabled <- function() {
|
||||
|
||||
override <- Sys.getenv("RENV_ANSIFY_ENABLED", unset = NA)
|
||||
if (!is.na(override))
|
||||
return(as.logical(override))
|
||||
|
||||
pane <- Sys.getenv("RSTUDIO_CHILD_PROCESS_PANE", unset = NA)
|
||||
if (identical(pane, "build"))
|
||||
return(FALSE)
|
||||
|
||||
testthat <- Sys.getenv("TESTTHAT", unset = "false")
|
||||
if (tolower(testthat) %in% "true")
|
||||
return(FALSE)
|
||||
|
||||
iderun <- Sys.getenv("R_CLI_HAS_HYPERLINK_IDE_RUN", unset = "false")
|
||||
if (tolower(iderun) %in% "false")
|
||||
return(FALSE)
|
||||
|
||||
TRUE
|
||||
|
||||
}
|
||||
|
||||
renv_ansify_default <- function(text) {
|
||||
text
|
||||
}
|
||||
|
||||
renv_ansify_enhanced <- function(text) {
|
||||
|
||||
# R help links
|
||||
pattern <- "`\\?(renv::(?:[^`])+)`"
|
||||
replacement <- "`\033]8;;ide:help:\\1\a?\\1\033]8;;\a`"
|
||||
text <- gsub(pattern, replacement, text, perl = TRUE)
|
||||
|
||||
# runnable code
|
||||
pattern <- "`(renv::(?:[^`])+)`"
|
||||
replacement <- "`\033]8;;ide:run:\\1\a\\1\033]8;;\a`"
|
||||
text <- gsub(pattern, replacement, text, perl = TRUE)
|
||||
|
||||
# return ansified text
|
||||
text
|
||||
|
||||
}
|
||||
|
||||
renv_ansify_init <- function() {
|
||||
|
||||
envir <- renv_envir_self()
|
||||
if (renv_ansify_enabled())
|
||||
assign("ansify", renv_ansify_enhanced, envir = envir)
|
||||
else
|
||||
assign("ansify", renv_ansify_default, envir = envir)
|
||||
|
||||
}
|
||||
|
||||
`%||%` <- function(x, y) {
|
||||
if (is.null(x)) y else x
|
||||
}
|
||||
@ -108,6 +191,24 @@ local({
|
||||
|
||||
}
|
||||
|
||||
heredoc <- function(text, leave = 0) {
|
||||
|
||||
# remove leading, trailing whitespace
|
||||
trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text)
|
||||
|
||||
# split into lines
|
||||
lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]]
|
||||
|
||||
# compute common indent
|
||||
indent <- regexpr("[^[:space:]]", lines)
|
||||
common <- min(setdiff(indent, -1L)) - leave
|
||||
text <- paste(substring(lines, common), collapse = "\n")
|
||||
|
||||
# substitute in ANSI links for executable renv code
|
||||
ansify(text)
|
||||
|
||||
}
|
||||
|
||||
startswith <- function(string, prefix) {
|
||||
substring(string, 1, nchar(prefix)) == prefix
|
||||
}
|
||||
@ -268,7 +369,11 @@ local({
|
||||
)
|
||||
|
||||
if ("headers" %in% names(formals(utils::download.file)))
|
||||
args$headers <- renv_bootstrap_download_custom_headers(url)
|
||||
{
|
||||
headers <- renv_bootstrap_download_custom_headers(url)
|
||||
if (length(headers) && is.character(headers))
|
||||
args$headers <- headers
|
||||
}
|
||||
|
||||
do.call(utils::download.file, args)
|
||||
|
||||
@ -347,10 +452,22 @@ local({
|
||||
for (type in types) {
|
||||
for (repos in renv_bootstrap_repos()) {
|
||||
|
||||
# build arguments for utils::available.packages() call
|
||||
args <- list(type = type, repos = repos)
|
||||
|
||||
# add custom headers if available -- note that
|
||||
# utils::available.packages() will pass this to download.file()
|
||||
if ("headers" %in% names(formals(utils::download.file)))
|
||||
{
|
||||
headers <- renv_bootstrap_download_custom_headers(url)
|
||||
if (length(headers) && is.character(headers))
|
||||
args$headers <- headers
|
||||
}
|
||||
|
||||
# retrieve package database
|
||||
db <- tryCatch(
|
||||
as.data.frame(
|
||||
utils::available.packages(type = type, repos = repos),
|
||||
do.call(utils::available.packages, args),
|
||||
stringsAsFactors = FALSE
|
||||
),
|
||||
error = identity
|
||||
@ -432,6 +549,14 @@ local({
|
||||
|
||||
}
|
||||
|
||||
renv_bootstrap_github_token <- function() {
|
||||
for (envvar in c("GITHUB_TOKEN", "GITHUB_PAT", "GH_TOKEN")) {
|
||||
envval <- Sys.getenv(envvar, unset = NA)
|
||||
if (!is.na(envval))
|
||||
return(envval)
|
||||
}
|
||||
}
|
||||
|
||||
renv_bootstrap_download_github <- function(version) {
|
||||
|
||||
enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE")
|
||||
@ -439,16 +564,16 @@ local({
|
||||
return(FALSE)
|
||||
|
||||
# prepare download options
|
||||
pat <- Sys.getenv("GITHUB_PAT")
|
||||
if (nzchar(Sys.which("curl")) && nzchar(pat)) {
|
||||
token <- renv_bootstrap_github_token()
|
||||
if (nzchar(Sys.which("curl")) && nzchar(token)) {
|
||||
fmt <- "--location --fail --header \"Authorization: token %s\""
|
||||
extra <- sprintf(fmt, pat)
|
||||
extra <- sprintf(fmt, token)
|
||||
saved <- options("download.file.method", "download.file.extra")
|
||||
options(download.file.method = "curl", download.file.extra = extra)
|
||||
on.exit(do.call(base::options, saved), add = TRUE)
|
||||
} else if (nzchar(Sys.which("wget")) && nzchar(pat)) {
|
||||
} else if (nzchar(Sys.which("wget")) && nzchar(token)) {
|
||||
fmt <- "--header=\"Authorization: token %s\""
|
||||
extra <- sprintf(fmt, pat)
|
||||
extra <- sprintf(fmt, token)
|
||||
saved <- options("download.file.method", "download.file.extra")
|
||||
options(download.file.method = "wget", download.file.extra = extra)
|
||||
on.exit(do.call(base::options, saved), add = TRUE)
|
||||
@ -610,6 +735,9 @@ local({
|
||||
|
||||
# if the user has requested an automatic prefix, generate it
|
||||
auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA)
|
||||
if (is.na(auto) && getRversion() >= "4.4.0")
|
||||
auto <- "TRUE"
|
||||
|
||||
if (auto %in% c("TRUE", "True", "true", "1"))
|
||||
return(renv_bootstrap_platform_prefix_auto())
|
||||
|
||||
@ -801,24 +929,23 @@ local({
|
||||
|
||||
# the loaded version of renv doesn't match the requested version;
|
||||
# give the user instructions on how to proceed
|
||||
remote <- if (!is.null(description[["RemoteSha"]])) {
|
||||
dev <- identical(description[["RemoteType"]], "github")
|
||||
remote <- if (dev)
|
||||
paste("rstudio/renv", description[["RemoteSha"]], sep = "@")
|
||||
} else {
|
||||
else
|
||||
paste("renv", description[["Version"]], sep = "@")
|
||||
}
|
||||
|
||||
# display both loaded version + sha if available
|
||||
friendly <- renv_bootstrap_version_friendly(
|
||||
version = description[["Version"]],
|
||||
sha = description[["RemoteSha"]]
|
||||
sha = if (dev) description[["RemoteSha"]]
|
||||
)
|
||||
|
||||
fmt <- paste(
|
||||
"renv %1$s was loaded from project library, but this project is configured to use renv %2$s.",
|
||||
"- Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.",
|
||||
"- Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.",
|
||||
sep = "\n"
|
||||
)
|
||||
fmt <- heredoc("
|
||||
renv %1$s was loaded from project library, but this project is configured to use renv %2$s.
|
||||
- Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.
|
||||
- Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.
|
||||
")
|
||||
catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote)
|
||||
|
||||
FALSE
|
||||
@ -1041,7 +1168,7 @@ local({
|
||||
# if jsonlite is loaded, use that instead
|
||||
if ("jsonlite" %in% loadedNamespaces()) {
|
||||
|
||||
json <- catch(renv_json_read_jsonlite(file, text))
|
||||
json <- tryCatch(renv_json_read_jsonlite(file, text), error = identity)
|
||||
if (!inherits(json, "error"))
|
||||
return(json)
|
||||
|
||||
@ -1050,7 +1177,7 @@ local({
|
||||
}
|
||||
|
||||
# otherwise, fall back to the default JSON reader
|
||||
json <- catch(renv_json_read_default(file, text))
|
||||
json <- tryCatch(renv_json_read_default(file, text), error = identity)
|
||||
if (!inherits(json, "error"))
|
||||
return(json)
|
||||
|
||||
@ -1063,14 +1190,14 @@ local({
|
||||
}
|
||||
|
||||
renv_json_read_jsonlite <- function(file = NULL, text = NULL) {
|
||||
text <- paste(text %||% read(file), collapse = "\n")
|
||||
text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
|
||||
jsonlite::fromJSON(txt = text, simplifyVector = FALSE)
|
||||
}
|
||||
|
||||
renv_json_read_default <- function(file = NULL, text = NULL) {
|
||||
|
||||
# find strings in the JSON
|
||||
text <- paste(text %||% read(file), collapse = "\n")
|
||||
text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
|
||||
pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]'
|
||||
locs <- gregexpr(pattern, text, perl = TRUE)[[1]]
|
||||
|
||||
@ -1118,14 +1245,14 @@ local({
|
||||
map <- as.list(map)
|
||||
|
||||
# remap strings in object
|
||||
remapped <- renv_json_remap(json, map)
|
||||
remapped <- renv_json_read_remap(json, map)
|
||||
|
||||
# evaluate
|
||||
eval(remapped, envir = baseenv())
|
||||
|
||||
}
|
||||
|
||||
renv_json_remap <- function(json, map) {
|
||||
renv_json_read_remap <- function(json, map) {
|
||||
|
||||
# fix names
|
||||
if (!is.null(names(json))) {
|
||||
@ -1152,7 +1279,7 @@ local({
|
||||
# recurse
|
||||
if (is.recursive(json)) {
|
||||
for (i in seq_along(json)) {
|
||||
json[i] <- list(renv_json_remap(json[[i]], map))
|
||||
json[i] <- list(renv_json_read_remap(json[[i]], map))
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@ -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
|
||||
|
||||
@ -1,3 +0,0 @@
|
||||
if(requireNamespace('spelling', quietly = TRUE))
|
||||
spelling::spell_check_test(vignettes = TRUE, error = FALSE,
|
||||
skip_on_cran = TRUE)
|
||||
Binary file not shown.
@ -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]]))
|
||||
|
||||
BIN
tests/testthat/testthat-problems.rds
Normal file
BIN
tests/testthat/testthat-problems.rds
Normal file
Binary file not shown.
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Reference in New Issue
Block a user