mirror of
https://github.com/agdamsbo/REDCapCAST.git
synced 2024-11-24 22:11:55 +01:00
major update with new functions and renv is out! see NEWS section
This commit is contained in:
parent
b35142f0cc
commit
4a56f4ec45
@ -6,7 +6,7 @@ options(
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)
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source("renv/activate.R")
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# source("renv/activate.R")
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if (interactive()) {
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suppressMessages(require(usethis))
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2
.github/workflows/R-CMD-check.yaml
vendored
2
.github/workflows/R-CMD-check.yaml
vendored
@ -39,7 +39,7 @@ jobs:
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http-user-agent: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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- uses: r-lib/actions/setup-renv@v2
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# - uses: r-lib/actions/setup-renv@v2
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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2
.github/workflows/pkgdown.yaml
vendored
2
.github/workflows/pkgdown.yaml
vendored
@ -30,7 +30,7 @@ jobs:
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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-renv@v2
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# - uses: r-lib/actions/setup-renv@v2
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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2
.github/workflows/test-coverage.yaml
vendored
2
.github/workflows/test-coverage.yaml
vendored
@ -21,7 +21,7 @@ jobs:
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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-renv@v2
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# - uses: r-lib/actions/setup-renv@v2
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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@ -1,6 +1,6 @@
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Package: REDCapCAST
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Title: REDCap Castellated Data Handling
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Version: 24.5.1
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Version: 24.6.1
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Authors@R: c(
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person("Andreas Gammelgaard", "Damsbo", email = "agdamsbo@clin.au.dk",
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role = c("aut", "cre"),comment = c(ORCID = "0000-0002-7559-1154")),
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25
R/doc2dd.R
25
R/doc2dd.R
@ -108,6 +108,9 @@ doc2dd <- function(data,
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)
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}
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## Defining the calculations
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if (is_missing(col.calculation)) {
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out <- out |>
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@ -115,12 +118,13 @@ doc2dd <- function(data,
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calculations = missing.default
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)
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} else {
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# With inspiration from textclean package, curly apostrophe is replaced
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out <- out |>
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dplyr::mutate(
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calculations = dplyr::pick(col.calculation) |>
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unlist() |>
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tolower() |>
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(\(.x) gsub("’", "'", .x))()
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replace_curly_quote()
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)
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}
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@ -288,3 +292,22 @@ is_missing <- function(data,nas=c("", "NA")) {
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is.na(data) | data %in% nas
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}
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}
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#' Replace curly apostrophes and quotes from word
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#'
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#' @description
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#' Copied from textclean, which has not been updated since 2018 and is not
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#' on CRAN. Github:https://github.com/trinker/textclean
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#'
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#' @param x character vector
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#'
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#' @return character vector
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replace_curly_quote <- function(x){
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replaces <- c('\x91', '\x92', '\x93', '\x94')
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Encoding(replaces) <- "latin1"
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for (i in 1:4) {
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x <- gsub(replaces[i], c("'", "'", "\"", "\"")[i], x, fixed = TRUE)
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}
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x
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}
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@ -343,10 +343,10 @@ ds2dd_detailed <- function(data,
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lapply(function(x) {
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if (is.factor(x)) {
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## Re-factors to avoid confusion with missing levels
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## Assumes alle relevant levels are represented in the data
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## Assumes all relevant levels are represented in the data
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re_fac <- factor(x)
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paste(
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paste(unique(as.numeric(re_fac)),
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paste(seq_along(levels(re_fac)),
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levels(re_fac),
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sep = ", "
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),
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@ -5,6 +5,6 @@ account: agdamsbo
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server: shinyapps.io
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hostUrl: https://api.shinyapps.io/v1
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appId: 11351429
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bundleId:
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bundleId: 8567755
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url: https://agdamsbo.shinyapps.io/redcapcast/
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version: 1
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28
app/ui.R
28
app/ui.R
@ -1,6 +1,6 @@
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ui <- shiny::shinyUI(
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shiny::fluidPage(
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theme = shinythemes::shinytheme("united"),
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theme = shinythemes::shinytheme("flatly"),
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## -----------------------------------------------------------------------------
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## Application title
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@ -11,15 +11,20 @@ ui <- shiny::shinyUI(
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# windowTitle = "REDCap database creator"
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# ),
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shiny::titlePanel(title = shiny::div(shiny::a(shiny::img(src="logo.png"),href="https://agdamsbo.github.io/REDCapCAST"),
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"Easy REDCap database creation"),
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shiny::titlePanel(
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title = shiny::div(
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shiny::a(shiny::img(src = "logo.png"), href = "https://agdamsbo.github.io/REDCapCAST"),
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"Easy REDCap database creation"
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),
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windowTitle = "REDCap database creator"
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),
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shiny::h4("This tool includes to convenient functions:",
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shiny::h4(
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"This tool includes to convenient functions:",
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shiny::br(),
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"1) creating a REDCap data dictionary based on a spreadsheet (.csv/.xls(x)/.dta) and",
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shiny::br(),
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"2) creating said database on a given REDCap server and uploading the dataset via API access."),
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"2) creating said database on a given REDCap server and uploading the dataset via API access."
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),
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## -----------------------------------------------------------------------------
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@ -60,7 +65,7 @@ ui <- shiny::shinyUI(
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label = "API key",
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value = ""
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),
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shiny::h6("An API key is an access key to the REDCap database. Please", shiny::a("see here for directions", href="https://www.iths.org/news/redcap-tip/redcap-api-101/"), " to obtain an API key for your project."),
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shiny::h6("An API key is an access key to the REDCap database. Please", shiny::a("see here for directions", href = "https://www.iths.org/news/redcap-tip/redcap-api-101/"), " to obtain an API key for your project."),
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shiny::actionButton(
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inputId = "upload.meta",
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label = "Upload datadictionary", icon = shiny::icon("book-bookmark")
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@ -112,13 +117,13 @@ ui <- shiny::shinyUI(
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shiny::tags$footer(shiny::strong("Disclaimer: "),
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"This tool is aimed at demonstrating use of REDCapCAST. No responsibility for data loss or any other problems will be taken. Please contact me for support.",
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shiny::br(),
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shiny::a("License: GPL-3+",href="https://agdamsbo.github.io/REDCapCAST/LICENSE.html"),
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shiny::a("License: GPL-3+", href = "https://agdamsbo.github.io/REDCapCAST/LICENSE.html"),
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"|",
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shiny::a("agdamsbo/REDCapCAST",href="https://agdamsbo.github.io/REDCapCAST"),
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shiny::a("agdamsbo/REDCapCAST", href = "https://agdamsbo.github.io/REDCapCAST"),
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"|",
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shiny::a("Source",href="https://github.com/agdamsbo/REDCapCAST"),
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shiny::a("Source", href = "https://github.com/agdamsbo/REDCapCAST"),
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"|",
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shiny::a("Contact",href="https://andreas.gdamsbo.dk"),
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shiny::a("Contact", href = "https://andreas.gdamsbo.dk"),
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align = "center",
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style = "
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position:fixed;
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@ -129,6 +134,7 @@ ui <- shiny::shinyUI(
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padding: 0px;
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background-color: White;
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z-index: 100;
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")
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"
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)
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)
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)
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@ -4,6 +4,7 @@ Codecov
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DOI
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DataDictionary
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GStat
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Github
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GithubActions
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JSON
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Lifecycle
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@ -14,7 +15,6 @@ README
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REDCap
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REDCapR
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REDCapRITS
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THe
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UI
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WD
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al
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@ -34,8 +34,10 @@ dplyr
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ds
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dta
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et
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github
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gues
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hms
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https
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immprovements
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io
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jbi
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@ -55,6 +57,7 @@ perl
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pos
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pre
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readr
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realising
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sel
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sep
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seperator
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@ -64,9 +67,11 @@ stRoke
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stata
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strsplit
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subheader
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textclean
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thorugh
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tibble
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tidyverse
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trinker
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ui
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uri
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wil
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18
man/replace_curly_quote.Rd
Normal file
18
man/replace_curly_quote.Rd
Normal file
@ -0,0 +1,18 @@
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% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/doc2dd.R
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\name{replace_curly_quote}
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\alias{replace_curly_quote}
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\title{Replace curly apostrophes and quotes from word}
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\usage{
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replace_curly_quote(x)
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}
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\arguments{
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\item{x}{character vector}
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}
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\value{
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character vector
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}
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\description{
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Copied from textclean, which has not been updated since 2018 and is not
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on CRAN. Github:https://github.com/trinker/textclean
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}
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52
renv.lock
52
renv.lock
@ -1,6 +1,6 @@
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{
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"R": {
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"Version": "4.3.3",
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"Version": "4.4.0",
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"Repositories": [
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{
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"Name": "CRAN",
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@ -138,14 +138,14 @@
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},
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"cachem": {
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"Package": "cachem",
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"Version": "1.0.8",
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"Version": "1.1.0",
|
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"Source": "Repository",
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"Repository": "CRAN",
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"Requirements": [
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"fastmap",
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"rlang"
|
||||
],
|
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"Hash": "c35768291560ce302c0a6589f92e837d"
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"Hash": "cd9a672193789068eb5a2aad65a0dedf"
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},
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"cellranger": {
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"Package": "cellranger",
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@ -199,16 +199,6 @@
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"Repository": "CRAN",
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"Hash": "5d8225445acb167abf7797de48b2ee3c"
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},
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"cpp11": {
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"Package": "cpp11",
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"Version": "0.4.7",
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"Source": "Repository",
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"Repository": "CRAN",
|
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"Requirements": [
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"R"
|
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],
|
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"Hash": "5a295d7d963cc5035284dcdbaf334f4e"
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},
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"crayon": {
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"Package": "crayon",
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"Version": "1.5.2",
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@ -279,10 +269,10 @@
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},
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"fastmap": {
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"Package": "fastmap",
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"Version": "1.1.1",
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"Version": "1.2.0",
|
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"Source": "Repository",
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"Repository": "CRAN",
|
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"Hash": "f7736a18de97dea803bde0a2daaafb27"
|
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"Hash": "aa5e1cd11c2d15497494c5292d7ffcc8"
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},
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"filelock": {
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"Package": "filelock",
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@ -533,13 +523,13 @@
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},
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"openssl": {
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"Package": "openssl",
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"Version": "2.1.2",
|
||||
"Version": "2.2.0",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"askpass"
|
||||
],
|
||||
"Hash": "ea2475b073243d9d338aa8f086ce973e"
|
||||
"Hash": "2bcca3848e4734eb3b16103bc9aa4b8e"
|
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},
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"openxlsx2": {
|
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"Package": "openxlsx2",
|
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@ -585,30 +575,6 @@
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],
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"Hash": "01f28d4278f15c76cddbea05899c5d6f"
|
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},
|
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"prettyunits": {
|
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"Package": "prettyunits",
|
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"Version": "1.2.0",
|
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"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R"
|
||||
],
|
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"Hash": "6b01fc98b1e86c4f705ce9dcfd2f57c7"
|
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},
|
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"progress": {
|
||||
"Package": "progress",
|
||||
"Version": "1.2.3",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
||||
"R",
|
||||
"R6",
|
||||
"crayon",
|
||||
"hms",
|
||||
"prettyunits"
|
||||
],
|
||||
"Hash": "f4625e061cb2865f111b47ff163a5ca6"
|
||||
},
|
||||
"promises": {
|
||||
"Package": "promises",
|
||||
"Version": "1.3.0",
|
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@ -785,7 +751,7 @@
|
||||
},
|
||||
"stringi": {
|
||||
"Package": "stringi",
|
||||
"Version": "1.8.3",
|
||||
"Version": "1.8.4",
|
||||
"Source": "Repository",
|
||||
"Repository": "CRAN",
|
||||
"Requirements": [
|
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@ -794,7 +760,7 @@
|
||||
"tools",
|
||||
"utils"
|
||||
],
|
||||
"Hash": "058aebddea264f4c99401515182e656a"
|
||||
"Hash": "39e1144fd75428983dc3f63aa53dfa91"
|
||||
},
|
||||
"stringr": {
|
||||
"Package": "stringr",
|
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|
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25
tests/spelling.Rout.save
Normal file
25
tests/spelling.Rout.save
Normal file
@ -0,0 +1,25 @@
|
||||
|
||||
R version 3.4.1 (2017-06-30) -- "Single Candle"
|
||||
Copyright (C) 2017 The R Foundation for Statistical Computing
|
||||
Platform: x86_64-apple-darwin15.6.0 (64-bit)
|
||||
|
||||
R is free software and comes with ABSOLUTELY NO WARRANTY.
|
||||
You are welcome to redistribute it under certain conditions.
|
||||
Type 'license()' or 'licence()' for distribution details.
|
||||
|
||||
R is a collaborative project with many contributors.
|
||||
Type 'contributors()' for more information and
|
||||
'citation()' on how to cite R or R packages in publications.
|
||||
|
||||
Type 'demo()' for some demos, 'help()' for on-line help, or
|
||||
'help.start()' for an HTML browser interface to help.
|
||||
Type 'q()' to quit R.
|
||||
|
||||
> if(requireNamespace('spelling', quietly = TRUE))
|
||||
+ spelling::spell_check_test(vignettes = TRUE, error = FALSE,
|
||||
+ skip_on_cran = TRUE)
|
||||
All Done!
|
||||
>
|
||||
> proc.time()
|
||||
user system elapsed
|
||||
0.372 0.039 0.408
|
||||
@ -18,33 +18,59 @@ knitr::opts_chunk$set(
|
||||
library(REDCapCAST)
|
||||
```
|
||||
|
||||
# Easy data set to data base workflow
|
||||
# Two different ways to create a data base
|
||||
|
||||
THe first iteration of a dataset to data dictionary function is the `ds2dd()`, which creates a very basic data dictionary with all variables stored as text. This is sufficient for just storing old datasets/spreadsheets securely in REDCap.
|
||||
`REDCapCAST` provides two approaches to creating a data dictionary aimed at helping out in two different cases:
|
||||
|
||||
```{r eval=FALSE}
|
||||
mtcars |>
|
||||
1. Easily create a REDCap data base from an existing data set.
|
||||
|
||||
2. Create a table in Word describing a variables in a data base and use this to create a data base.
|
||||
|
||||
In the following I will try to come with a few suggestions on how to use these approaches.
|
||||
|
||||
## Easy data set to data base workflow
|
||||
|
||||
The first iteration of a dataset to data dictionary function is the `ds2dd()`, which creates a very basic data dictionary with all variables stored as text. This is sufficient for just storing old datasets/spreadsheets securely in REDCap.
|
||||
|
||||
```{r eval=TRUE}
|
||||
d1 <- mtcars |>
|
||||
dplyr::mutate(record_id = seq_len(dplyr::n())) |>
|
||||
ds2dd() |>
|
||||
str()
|
||||
ds2dd()
|
||||
|
||||
d1 |>
|
||||
gt::gt()
|
||||
```
|
||||
|
||||
The more advanced `ds2dd_detailed()` is a natural development. It will try to apply the most common data classes for data validation and will assume that the first column is the id number. It outputs a list with the dataset with modified variable names to comply with REDCap naming conventions and a data dictionary.
|
||||
|
||||
The dataset should be correctly formatted for the data dictionary to preserve as much information as possible.
|
||||
|
||||
```{r eval=FALSE}
|
||||
dd_ls <- mtcars |>
|
||||
dplyr::mutate(record_id = seq_len(dplyr::n())) |>
|
||||
```{r eval=TRUE}
|
||||
d2 <- REDCapCAST::redcapcast_data |>
|
||||
dplyr::mutate(record_id = seq_len(dplyr::n()),
|
||||
region=factor(region)) |>
|
||||
dplyr::select(record_id, dplyr::everything()) |>
|
||||
ds2dd_detailed()
|
||||
dd_ls |>
|
||||
str()
|
||||
(\(.x){
|
||||
.x[!grepl("_complete$",names(.x))]
|
||||
})() |>
|
||||
(\(.x){
|
||||
.x[!grepl("^redcap",names(.x))]
|
||||
})() |>
|
||||
ds2dd_detailed() |>
|
||||
purrr::pluck("meta")
|
||||
|
||||
d2 |>
|
||||
gt::gt()
|
||||
```
|
||||
|
||||
Additional specifications to the DataDictionary can be made manually, or it can be uploaded and modified manually in the graphical user interface on the web page.
|
||||
Additional specifications to the DataDictionary can be made manually, or it can be uploaded and modified manually in the graphical user interface on the REDCap server.
|
||||
|
||||
## Step 3 - Meta data upload
|
||||
## Data base from table
|
||||
|
||||
|
||||
|
||||
|
||||
## Meta data and data upload
|
||||
|
||||
Now the DataDictionary can be exported as a spreadsheet and uploaded or it can be uploaded using the `REDCapR` package (only projects with "Development" status).
|
||||
|
||||
|
||||
@ -14,10 +14,6 @@ knitr::opts_chunk$set(
|
||||
)
|
||||
```
|
||||
|
||||
```{r setup}
|
||||
library(REDCapCAST)
|
||||
```
|
||||
|
||||
To make the easiest possible transition from spreadsheet/dataset to REDCap, I have created a small Shiny app, which adds a graphical interface to the casting of a data dictionary and data upload. Install the package and run the app as follows:
|
||||
|
||||
```{r eval=FALSE}
|
||||
|
||||
Loading…
Reference in New Issue
Block a user