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multiple updates and additions. see 'NEWS.md'

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Andreas Gammelgaard Damsbo 2024-10-10 14:13:16 +02:00
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10
DESCRIPTION
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@ -1,6 +1,6 @@
Package: stRoke Package: stRoke
Title: Clinical Stroke Research Title: Clinical Stroke Research
Version: 24.2.1 Version: 24.10.1
Authors@R: Authors@R:
person("Andreas Gammelgaard", "Damsbo", , "agdamsbo@clin.au.dk", role = c("aut", "cre"), person("Andreas Gammelgaard", "Damsbo", , "agdamsbo@clin.au.dk", role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-7559-1154")) comment = c(ORCID = "0000-0002-7559-1154"))
@ -17,7 +17,7 @@ BugReports: https://github.com/agdamsbo/stRoke/issues
License: GPL-3 License: GPL-3
Encoding: UTF-8 Encoding: UTF-8
Roxygen: list(markdown = TRUE) Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1 RoxygenNote: 7.3.2
LazyData: true LazyData: true
Suggests: Suggests:
knitr, knitr,
@ -25,7 +25,11 @@ Suggests:
testthat, testthat,
git2r, git2r,
here, here,
spelling spelling,
usethis,
pak,
roxygen2,
devtools
Config/testthat/edition: 3 Config/testthat/edition: 3
Imports: Imports:
calendar, calendar,

6
NEWS.md
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@ -1,4 +1,4 @@
# stRoke 24.2.1 # stRoke 24.10.1
### Functions: ### Functions:
@ -8,8 +8,12 @@
* UPDATE: `add_padding()` updated to include option to add leading and/or tailing string with `lead` or `tail`. * 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. * 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 # stRoke 23.9.1
### Functions: ### Functions:

4
R/ci_plot.R
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@ -42,8 +42,8 @@ ci_plot <-
title = NULL, title = NULL,
method = "auto") { 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 (method == "auto") {
if (!is.factor(ds[, y])) if (!is.factor(ds[, y]))

1
R/ds2ical.R
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@ -1,3 +1,4 @@
utils::globalVariables(c("DTSTART"))
#' Convert data set to ical file #' Convert data set to ical file
#' #'
#' @param data data set #' @param data data set

4
R/generic_stroke.R
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@ -36,13 +36,13 @@ generic_stroke <-
gtsummary::add_overall() gtsummary::add_overall()
x <- table(df[, c(group, score, strata)]) x <- table(df[, c(group, score, strata)])
f1 <- rankinPlot::grottaBar( f1 <- suppressWarnings(rankinPlot::grottaBar(
x = x, x = x,
groupName = group, groupName = group,
scoreName = score, scoreName = score,
strataName = strata, strataName = strata,
colourScheme = "custom" colourScheme = "custom"
) ))
df[, score] <- factor(df[, score], ordered = TRUE) df[, score] <- factor(df[, score], ordered = TRUE)

3
R/mfi_calc.R
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@ -1,4 +1,5 @@
#' Title utils::globalVariables(c("ndx"))
#' Reverses relevant MFI subscores
#' #'
#' @param d data frame or tibble #' @param d data frame or tibble
#' @param var numeric vector of indices of columns to reverse #' @param var numeric vector of indices of columns to reverse

2
R/str_extract.R
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@ -1,5 +1,7 @@
#' Extract string based on regex pattern #' Extract string based on regex pattern
#' #'
#' DEPRECATION: moved to `agdamsbo/project.aid`
#'
#' Use base::strsplit to #' Use base::strsplit to
#' @param d vector of character strings #' @param d vector of character strings
#' @param pattern regex pattern to match #' @param pattern regex pattern to match

2
data-raw/cprs.R
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@ -5,4 +5,4 @@ usethis::use_data(cprs, overwrite = TRUE)
cprs <- data.frame(cpr=sample(c("2310450637", "010115-4000", "0101896000", cprs <- data.frame(cpr=sample(c("2310450637", "010115-4000", "0101896000",
"010189-3000","300450-1030","010150-4021", "010189-3000","300450-1030","010150-4021",
"011085-AKE3","0101EJ-ATW3"),200,TRUE)) "011085-AKE3","0101EJ-ATW3"),200,TRUE))
save(cprs,file="cprs.rda") save(cprs,file="data/cprs.rda")

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

3
man/str_extract.Rd
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@ -15,6 +15,9 @@ str_extract(d, pattern)
vector of character strings vector of character strings
} }
\description{ \description{
DEPRECATION: moved to \code{agdamsbo/project.aid}
}
\details{
Use base::strsplit to Use base::strsplit to
} }
\examples{ \examples{

498
renv.lock
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@ -1,6 +1,6 @@
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@ -341,27 +250,15 @@
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"Requirements": [ "Requirements": [
"R", "R",
"xfun" "xfun"
], ],
"Hash": "06230136b2d2b9ba5805e1963fa6e890" "Hash": "d65ba49117ca223614f71b60d85b8ab7"
},
"hms": {
"Package": "hms",
"Version": "1.1.3",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"lifecycle",
"methods",
"pkgconfig",
"rlang",
"vctrs"
],
"Hash": "b59377caa7ed00fa41808342002138f9"
}, },
"htmltools": { "htmltools": {
"Package": "htmltools", "Package": "htmltools",
"Version": "0.5.7", "Version": "0.5.8.1",
"Source": "Repository", "Source": "Repository",
"Repository": "RSPM", "Repository": "CRAN",
"Requirements": [ "Requirements": [
"R", "R",
"base64enc", "base64enc",
"digest", "digest",
"ellipsis",
"fastmap", "fastmap",
"grDevices", "grDevices",
"rlang", "rlang",
"utils" "utils"
], ],
"Hash": "2d7b3857980e0e0d0a1fd6f11928ab0f" "Hash": "81d371a9cc60640e74e4ab6ac46dcedc"
}, },
"htmlwidgets": { "htmlwidgets": {
"Package": "htmlwidgets", "Package": "htmlwidgets",
@ -627,7 +466,7 @@
"Package": "isoband", "Package": "isoband",
"Version": "0.2.7", "Version": "0.2.7",
"Source": "Repository", "Source": "Repository",
"Repository": "RSPM", "Repository": "CRAN",
"Requirements": [ "Requirements": [
"grid", "grid",
"utils" "utils"
@ -646,13 +485,13 @@
}, },
"jsonlite": { "jsonlite": {
"Package": "jsonlite", "Package": "jsonlite",
"Version": "1.8.8", "Version": "1.8.9",
"Source": "Repository", "Source": "Repository",
"Repository": "RSPM", "Repository": "CRAN",
"Requirements": [ "Requirements": [
"methods" "methods"
], ],
"Hash": "e1b9c55281c5adc4dd113652d9e26768" "Hash": "4e993b65c2c3ffbffce7bb3e2c6f832b"
}, },
"juicyjuice": { "juicyjuice": {
"Package": "juicyjuice", "Package": "juicyjuice",
@ -666,7 +505,7 @@
}, },
"knitr": { "knitr": {
"Package": "knitr", "Package": "knitr",
"Version": "1.45", "Version": "1.48",
"Source": "Repository", "Source": "Repository",
"Repository": "CRAN", "Repository": "CRAN",
"Requirements": [ "Requirements": [
@ -678,7 +517,7 @@
"xfun", "xfun",
"yaml" "yaml"
], ],
"Hash": "1ec462871063897135c1bcbe0fc8f07d" "Hash": "acf380f300c721da9fde7df115a5f86f"
}, },
"labeling": { "labeling": {
"Package": "labeling", "Package": "labeling",
@ -691,26 +530,9 @@
], ],
"Hash": "b64ec208ac5bc1852b285f665d6368b3" "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": { "lattice": {
"Package": "lattice", "Package": "lattice",
"Version": "0.22-5", "Version": "0.22-6",
"Source": "Repository", "Source": "Repository",
"Repository": "CRAN", "Repository": "CRAN",
"Requirements": [ "Requirements": [
@ -721,13 +543,13 @@
"stats", "stats",
"utils" "utils"
], ],
"Hash": "7c5e89f04e72d6611c77451f6331a091" "Hash": "cc5ac1ba4c238c7ca9fa6a87ca11a7e2"
}, },
"lifecycle": { "lifecycle": {
"Package": "lifecycle", "Package": "lifecycle",
"Version": "1.0.4", "Version": "1.0.4",
"Source": "Repository", "Source": "Repository",
"Repository": "RSPM", "Repository": "CRAN",
"Requirements": [ "Requirements": [
"R", "R",
"cli", "cli",
@ -761,7 +583,7 @@
}, },
"markdown": { "markdown": {
"Package": "markdown", "Package": "markdown",
"Version": "1.12", "Version": "1.13",
"Source": "Repository", "Source": "Repository",
"Repository": "CRAN", "Repository": "CRAN",
"Requirements": [ "Requirements": [
@ -770,7 +592,7 @@
"utils", "utils",
"xfun" "xfun"
], ],
"Hash": "765cf53992401b3b6c297b69e1edb8bd" "Hash": "074efab766a9d6360865ad39512f2a7e"
}, },
"memoise": { "memoise": {
"Package": "memoise", "Package": "memoise",
@ -812,18 +634,18 @@
}, },
"munsell": { "munsell": {
"Package": "munsell", "Package": "munsell",
"Version": "0.5.0", "Version": "0.5.1",
"Source": "Repository", "Source": "Repository",
"Repository": "CRAN", "Repository": "CRAN",
"Requirements": [ "Requirements": [
"colorspace", "colorspace",
"methods" "methods"
], ],
"Hash": "6dfe8bf774944bd5595785e3229d8771" "Hash": "4fd8900853b746af55b81fda99da7695"
}, },
"nlme": { "nlme": {
"Package": "nlme", "Package": "nlme",
"Version": "3.1-164", "Version": "3.1-166",
"Source": "Repository", "Source": "Repository",
"Repository": "CRAN", "Repository": "CRAN",
"Requirements": [ "Requirements": [
@ -833,7 +655,7 @@
"stats", "stats",
"utils" "utils"
], ],
"Hash": "a623a2239e642806158bc4dc3f51565d" "Hash": "ccbb8846be320b627e6aa2b4616a2ded"
}, },
"pillar": { "pillar": {
"Package": "pillar", "Package": "pillar",
@ -862,30 +684,6 @@
], ],
"Hash": "01f28d4278f15c76cddbea05899c5d6f" "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": { "purrr": {
"Package": "purrr", "Package": "purrr",
"Version": "1.0.2", "Version": "1.0.2",
@ -925,13 +723,13 @@
}, },
"reactR": { "reactR": {
"Package": "reactR", "Package": "reactR",
"Version": "0.5.0", "Version": "0.6.1",
"Source": "Repository", "Source": "Repository",
"Repository": "CRAN", "Repository": "CRAN",
"Requirements": [ "Requirements": [
"htmltools" "htmltools"
], ],
"Hash": "c9014fd1a435b2d790dd506589cb24e5" "Hash": "b8e3d93f508045812f47136c7c44c251"
}, },
"reactable": { "reactable": {
"Package": "reactable", "Package": "reactable",
@ -948,53 +746,30 @@
], ],
"Hash": "6069eb2a6597963eae0605c1875ff14c" "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": { "renv": {
"Package": "renv", "Package": "renv",
"Version": "1.0.3", "Version": "1.0.9",
"Source": "Repository", "Source": "Repository",
"Repository": "CRAN", "Repository": "CRAN",
"Requirements": [ "Requirements": [
"utils" "utils"
], ],
"Hash": "41b847654f567341725473431dd0d5ab" "Hash": "ef233f0e9064fc88c898b340c9add5c2"
}, },
"rlang": { "rlang": {
"Package": "rlang", "Package": "rlang",
"Version": "1.1.3", "Version": "1.1.4",
"Source": "Repository", "Source": "Repository",
"Repository": "RSPM", "Repository": "CRAN",
"Requirements": [ "Requirements": [
"R", "R",
"utils" "utils"
], ],
"Hash": "42548638fae05fd9a9b5f3f437fbbbe2" "Hash": "3eec01f8b1dee337674b2e34ab1f9bc1"
}, },
"rmarkdown": { "rmarkdown": {
"Package": "rmarkdown", "Package": "rmarkdown",
"Version": "2.25", "Version": "2.28",
"Source": "Repository", "Source": "Repository",
"Repository": "CRAN", "Repository": "CRAN",
"Requirements": [ "Requirements": [
@ -1007,20 +782,19 @@
"jsonlite", "jsonlite",
"knitr", "knitr",
"methods", "methods",
"stringr",
"tinytex", "tinytex",
"tools", "tools",
"utils", "utils",
"xfun", "xfun",
"yaml" "yaml"
], ],
"Hash": "d65e35823c817f09f4de424fcdfa812a" "Hash": "062470668513dcda416927085ee9bdc7"
}, },
"sass": { "sass": {
"Package": "sass", "Package": "sass",
"Version": "0.4.8", "Version": "0.4.9",
"Source": "Repository", "Source": "Repository",
"Repository": "RSPM", "Repository": "CRAN",
"Requirements": [ "Requirements": [
"R6", "R6",
"fs", "fs",
@ -1028,7 +802,7 @@
"rappdirs", "rappdirs",
"rlang" "rlang"
], ],
"Hash": "168f9353c76d4c4b0a0bbf72e2c2d035" "Hash": "d53dbfddf695303ea4ad66f86e99b95d"
}, },
"scales": { "scales": {
"Package": "scales", "Package": "scales",
@ -1052,7 +826,7 @@
}, },
"stringi": { "stringi": {
"Package": "stringi", "Package": "stringi",
"Version": "1.8.3", "Version": "1.8.4",
"Source": "Repository", "Source": "Repository",
"Repository": "CRAN", "Repository": "CRAN",
"Requirements": [ "Requirements": [
@ -1061,7 +835,7 @@
"tools", "tools",
"utils" "utils"
], ],
"Hash": "058aebddea264f4c99401515182e656a" "Hash": "39e1144fd75428983dc3f63aa53dfa91"
}, },
"stringr": { "stringr": {
"Package": "stringr", "Package": "stringr",
@ -1124,7 +898,7 @@
}, },
"tidyselect": { "tidyselect": {
"Package": "tidyselect", "Package": "tidyselect",
"Version": "1.2.0", "Version": "1.2.1",
"Source": "Repository", "Source": "Repository",
"Repository": "CRAN", "Repository": "CRAN",
"Requirements": [ "Requirements": [
@ -1136,7 +910,7 @@
"vctrs", "vctrs",
"withr" "withr"
], ],
"Hash": "79540e5fcd9e0435af547d885f184fd5" "Hash": "829f27b9c4919c16b593794a6344d6c0"
}, },
"timechange": { "timechange": {
"Package": "timechange", "Package": "timechange",
@ -1151,24 +925,13 @@
}, },
"tinytex": { "tinytex": {
"Package": "tinytex", "Package": "tinytex",
"Version": "0.49", "Version": "0.53",
"Source": "Repository", "Source": "Repository",
"Repository": "CRAN", "Repository": "CRAN",
"Requirements": [ "Requirements": [
"xfun" "xfun"
], ],
"Hash": "5ac22900ae0f386e54f1c307eca7d843" "Hash": "9db859e8aabbb474293dde3097839420"
},
"tzdb": {
"Package": "tzdb",
"Version": "0.4.0",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"R",
"cpp11"
],
"Hash": "f561504ec2897f4d46f0c7657e488ae1"
}, },
"utf8": { "utf8": {
"Package": "utf8", "Package": "utf8",
@ -1204,55 +967,30 @@
], ],
"Hash": "c826c7c4241b6fc89ff55aaea3fa7491" "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": { "withr": {
"Package": "withr", "Package": "withr",
"Version": "3.0.0", "Version": "3.0.1",
"Source": "Repository", "Source": "Repository",
"Repository": "RSPM", "Repository": "CRAN",
"Requirements": [ "Requirements": [
"R", "R",
"grDevices", "grDevices",
"graphics" "graphics"
], ],
"Hash": "d31b6c62c10dcf11ec530ca6b0dd5d35" "Hash": "07909200e8bbe90426fbfeb73e1e27aa"
}, },
"xfun": { "xfun": {
"Package": "xfun", "Package": "xfun",
"Version": "0.42", "Version": "0.48",
"Source": "Repository", "Source": "Repository",
"Repository": "CRAN", "Repository": "CRAN",
"Requirements": [ "Requirements": [
"R",
"grDevices", "grDevices",
"stats", "stats",
"tools" "tools"
], ],
"Hash": "fd1349170df31f7a10bd98b0189e85af" "Hash": "89e455b87c84e227eb7f60a1b4e5fe1f"
}, },
"xml2": { "xml2": {
"Package": "xml2", "Package": "xml2",
@ -1269,10 +1007,10 @@
}, },
"yaml": { "yaml": {
"Package": "yaml", "Package": "yaml",
"Version": "2.3.8", "Version": "2.3.10",
"Source": "Repository", "Source": "Repository",
"Repository": "CRAN", "Repository": "CRAN",
"Hash": "29240487a071f535f5e5d5a323b7afbd" "Hash": "51dab85c6c98e50a18d7551e9d49f76c"
} }
} }
} }

179
renv/activate.R
View File

@ -2,10 +2,12 @@
local({ local({
# the requested version of renv # the requested version of renv
version <- "1.0.3" version <- "1.0.9"
attr(version, "sha") <- NULL attr(version, "sha") <- NULL
# the project directory # the project directory
project <- Sys.getenv("RENV_PROJECT")
if (!nzchar(project))
project <- getwd() project <- getwd()
# use start-up diagnostics if enabled # use start-up diagnostics if enabled
@ -31,6 +33,14 @@ local({
if (!is.null(override)) if (!is.null(override))
return(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 # next, check environment variables
# TODO: prefer using the configuration one in the future # TODO: prefer using the configuration one in the future
envvars <- c( 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) return(FALSE)
}
# avoid recursion # avoid recursion
if (identical(getOption("renv.autoloader.running"), TRUE)) { if (identical(getOption("renv.autoloader.running"), TRUE)) {
warning("ignoring recursive attempt to run renv autoloader") warning("ignoring recursive attempt to run renv autoloader")
@ -75,6 +98,66 @@ local({
unloadNamespace("renv") unloadNamespace("renv")
# load bootstrap tools # 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) { `%||%` <- function(x, y) {
if (is.null(x)) y else x 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*$", "", text)
# split into lines
lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]]
# compute common indent
indent <- regexpr("[^[:space:]]", lines)
common <- min(setdiff(indent, -1L)) - leave
text <- paste(substring(lines, common), collapse = "\n")
# substitute in ANSI links for executable renv code
ansify(text)
}
startswith <- function(string, prefix) { startswith <- function(string, prefix) {
substring(string, 1, nchar(prefix)) == prefix substring(string, 1, nchar(prefix)) == prefix
} }
@ -268,7 +369,11 @@ local({
) )
if ("headers" %in% names(formals(utils::download.file))) if ("headers" %in% names(formals(utils::download.file)))
args$headers <- renv_bootstrap_download_custom_headers(url) {
headers <- renv_bootstrap_download_custom_headers(url)
if (length(headers) && is.character(headers))
args$headers <- headers
}
do.call(utils::download.file, args) do.call(utils::download.file, args)
@ -347,10 +452,22 @@ local({
for (type in types) { for (type in types) {
for (repos in renv_bootstrap_repos()) { for (repos in renv_bootstrap_repos()) {
# build arguments for utils::available.packages() call
args <- list(type = type, repos = repos)
# add custom headers if available -- note that
# utils::available.packages() will pass this to download.file()
if ("headers" %in% names(formals(utils::download.file)))
{
headers <- renv_bootstrap_download_custom_headers(url)
if (length(headers) && is.character(headers))
args$headers <- headers
}
# retrieve package database # retrieve package database
db <- tryCatch( db <- tryCatch(
as.data.frame( as.data.frame(
utils::available.packages(type = type, repos = repos), do.call(utils::available.packages, args),
stringsAsFactors = FALSE stringsAsFactors = FALSE
), ),
error = identity 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) { renv_bootstrap_download_github <- function(version) {
enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE") enabled <- Sys.getenv("RENV_BOOTSTRAP_FROM_GITHUB", unset = "TRUE")
@ -439,16 +564,16 @@ local({
return(FALSE) return(FALSE)
# prepare download options # prepare download options
pat <- Sys.getenv("GITHUB_PAT") token <- renv_bootstrap_github_token()
if (nzchar(Sys.which("curl")) && nzchar(pat)) { if (nzchar(Sys.which("curl")) && nzchar(token)) {
fmt <- "--location --fail --header \"Authorization: token %s\"" fmt <- "--location --fail --header \"Authorization: token %s\""
extra <- sprintf(fmt, pat) extra <- sprintf(fmt, token)
saved <- options("download.file.method", "download.file.extra") saved <- options("download.file.method", "download.file.extra")
options(download.file.method = "curl", download.file.extra = extra) options(download.file.method = "curl", download.file.extra = extra)
on.exit(do.call(base::options, saved), add = TRUE) 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\"" fmt <- "--header=\"Authorization: token %s\""
extra <- sprintf(fmt, pat) extra <- sprintf(fmt, token)
saved <- options("download.file.method", "download.file.extra") saved <- options("download.file.method", "download.file.extra")
options(download.file.method = "wget", download.file.extra = extra) options(download.file.method = "wget", download.file.extra = extra)
on.exit(do.call(base::options, saved), add = TRUE) on.exit(do.call(base::options, saved), add = TRUE)
@ -610,6 +735,9 @@ local({
# if the user has requested an automatic prefix, generate it # if the user has requested an automatic prefix, generate it
auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA) 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")) if (auto %in% c("TRUE", "True", "true", "1"))
return(renv_bootstrap_platform_prefix_auto()) return(renv_bootstrap_platform_prefix_auto())
@ -801,24 +929,23 @@ local({
# the loaded version of renv doesn't match the requested version; # the loaded version of renv doesn't match the requested version;
# give the user instructions on how to proceed # 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 = "@") paste("rstudio/renv", description[["RemoteSha"]], sep = "@")
} else { else
paste("renv", description[["Version"]], sep = "@") paste("renv", description[["Version"]], sep = "@")
}
# display both loaded version + sha if available # display both loaded version + sha if available
friendly <- renv_bootstrap_version_friendly( friendly <- renv_bootstrap_version_friendly(
version = description[["Version"]], version = description[["Version"]],
sha = description[["RemoteSha"]] sha = if (dev) description[["RemoteSha"]]
) )
fmt <- paste( fmt <- heredoc("
"renv %1$s was loaded from project library, but this project is configured to use renv %2$s.", 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::record(\"%3$s\")` to record renv %1$s in the lockfile.
"- Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.", - Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.
sep = "\n" ")
)
catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote) catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote)
FALSE FALSE
@ -1041,7 +1168,7 @@ local({
# if jsonlite is loaded, use that instead # if jsonlite is loaded, use that instead
if ("jsonlite" %in% loadedNamespaces()) { 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")) if (!inherits(json, "error"))
return(json) return(json)
@ -1050,7 +1177,7 @@ local({
} }
# otherwise, fall back to the default JSON reader # 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")) if (!inherits(json, "error"))
return(json) return(json)
@ -1063,14 +1190,14 @@ local({
} }
renv_json_read_jsonlite <- function(file = NULL, text = NULL) { 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) jsonlite::fromJSON(txt = text, simplifyVector = FALSE)
} }
renv_json_read_default <- function(file = NULL, text = NULL) { renv_json_read_default <- function(file = NULL, text = NULL) {
# find strings in the JSON # find strings in the JSON
text <- paste(text %||% read(file), collapse = "\n") text <- paste(text %||% readLines(file, warn = FALSE), collapse = "\n")
pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]' pattern <- '["](?:(?:\\\\.)|(?:[^"\\\\]))*?["]'
locs <- gregexpr(pattern, text, perl = TRUE)[[1]] locs <- gregexpr(pattern, text, perl = TRUE)[[1]]
@ -1118,14 +1245,14 @@ local({
map <- as.list(map) map <- as.list(map)
# remap strings in object # remap strings in object
remapped <- renv_json_remap(json, map) remapped <- renv_json_read_remap(json, map)
# evaluate # evaluate
eval(remapped, envir = baseenv()) eval(remapped, envir = baseenv())
} }
renv_json_remap <- function(json, map) { renv_json_read_remap <- function(json, map) {
# fix names # fix names
if (!is.null(names(json))) { if (!is.null(names(json))) {
@ -1152,7 +1279,7 @@ local({
# recurse # recurse
if (is.recursive(json)) { if (is.recursive(json)) {
for (i in seq_along(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))
} }
} }

2
stRoke.Rproj
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@ -15,4 +15,4 @@ LaTeX: pdfLaTeX
BuildType: Package BuildType: Package
PackageUseDevtools: Yes PackageUseDevtools: Yes
PackageInstallArgs: --no-multiarch --with-keep.source PackageInstallArgs: --no-multiarch --with-keep.source
PackageRoxygenize: rd,collate,namespace PackageRoxygenize: rd,collate,namespace,vignette

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

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tests/testthat/Rplots.pdf
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4
tests/testthat/test-generic_stroke.R
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@ -2,12 +2,12 @@ test_that("generic_stroke() runs!", {
iris$ord <- iris$ord <-
factor(sample(1:3, size = nrow(iris), replace = TRUE), ordered = TRUE) factor(sample(1:3, size = nrow(iris), replace = TRUE), ordered = TRUE)
result <- result <-
generic_stroke( suppressMessages(generic_stroke(
df = iris, df = iris,
group = "Species", group = "Species",
score = "ord", score = "ord",
variables = colnames(iris)[1:3] variables = colnames(iris)[1:3]
) ))
expect_equal(length(result), 3) expect_equal(length(result), 3)
expect_equal(class(result), "list") expect_equal(class(result), "list")
expect_true("tbl_summary" %in% class(result[[1]])) expect_true("tbl_summary" %in% class(result[[1]]))

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tests/testthat/testthat-problems.rds Normal file
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