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major update with new functions and renv is out! see NEWS section

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Andreas Gammelgaard Damsbo 2024-06-07 10:35:16 +02:00
parent b35142f0cc
commit 4a56f4ec45
16 changed files with 158 additions and 93 deletions
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2
.Rprofile
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@ -6,7 +6,7 @@ options(
)
source("renv/activate.R")
# source("renv/activate.R")
if (interactive()) {
suppressMessages(require(usethis))

2
.github/workflows/R-CMD-check.yaml vendored
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@ -39,7 +39,7 @@ jobs:
http-user-agent: ${{ matrix.config.http-user-agent }}
use-public-rspm: true
- uses: r-lib/actions/setup-renv@v2
# - uses: r-lib/actions/setup-renv@v2
- uses: r-lib/actions/setup-r-dependencies@v2
with:

2
.github/workflows/pkgdown.yaml vendored
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@ -30,7 +30,7 @@ jobs:
with:
use-public-rspm: true
- uses: r-lib/actions/setup-renv@v2
# - uses: r-lib/actions/setup-renv@v2
- uses: r-lib/actions/setup-r-dependencies@v2
with:

2
.github/workflows/test-coverage.yaml vendored
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@ -21,7 +21,7 @@ jobs:
with:
use-public-rspm: true
- uses: r-lib/actions/setup-renv@v2
# - uses: r-lib/actions/setup-renv@v2
- uses: r-lib/actions/setup-r-dependencies@v2
with:

2
DESCRIPTION
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@ -1,6 +1,6 @@
Package: REDCapCAST
Title: REDCap Castellated Data Handling
Version: 24.5.1
Version: 24.6.1
Authors@R: c(
person("Andreas Gammelgaard", "Damsbo", email = "agdamsbo@clin.au.dk",
role = c("aut", "cre"),comment = c(ORCID = "0000-0002-7559-1154")),

2
NEWS.md
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@ -1,4 +1,4 @@
# REDCapCAST 24.5.1
# REDCapCAST 24.6.1
### Functions

25
R/doc2dd.R
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@ -108,6 +108,9 @@ doc2dd <- function(data,
)
}
## Defining the calculations
if (is_missing(col.calculation)) {
out <- out |>
@ -115,12 +118,13 @@ doc2dd <- function(data,
calculations = missing.default
)
} else {
# With inspiration from textclean package, curly apostrophe is replaced
out <- out |>
dplyr::mutate(
calculations = dplyr::pick(col.calculation) |>
unlist() |>
tolower() |>
(\(.x) gsub("’", "'", .x))()
replace_curly_quote()
)
}
@ -288,3 +292,22 @@ is_missing <- function(data,nas=c("", "NA")) {
is.na(data) | data %in% nas
}
}
#' Replace curly apostrophes and quotes from word
#'
#' @description
#' Copied from textclean, which has not been updated since 2018 and is not
#' on CRAN. Github:https://github.com/trinker/textclean
#'
#' @param x character vector
#'
#' @return character vector
replace_curly_quote <- function(x){
replaces <- c('\x91', '\x92', '\x93', '\x94')
Encoding(replaces) <- "latin1"
for (i in 1:4) {
x <- gsub(replaces[i], c("'", "'", "\"", "\"")[i], x, fixed = TRUE)
}
x
}

4
R/ds2dd_detailed.R
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@ -343,10 +343,10 @@ ds2dd_detailed <- function(data,
lapply(function(x) {
if (is.factor(x)) {
## Re-factors to avoid confusion with missing levels
## Assumes alle relevant levels are represented in the data
## Assumes all relevant levels are represented in the data
re_fac <- factor(x)
paste(
paste(unique(as.numeric(re_fac)),
paste(seq_along(levels(re_fac)),
levels(re_fac),
sep = ", "
),

2
app/rsconnect/shinyapps.io/agdamsbo/redcapcast.dcf
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@ -5,6 +5,6 @@ account: agdamsbo
server: shinyapps.io
hostUrl: https://api.shinyapps.io/v1
appId: 11351429
bundleId:
bundleId: 8567755
url: https://agdamsbo.shinyapps.io/redcapcast/
version: 1

48
app/ui.R
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@ -1,6 +1,6 @@
ui <- shiny::shinyUI(
shiny::fluidPage(
theme = shinythemes::shinytheme("united"),
theme = shinythemes::shinytheme("flatly"),
## -----------------------------------------------------------------------------
## Application title
@ -11,15 +11,20 @@ ui <- shiny::shinyUI(
# windowTitle = "REDCap database creator"
# ),
shiny::titlePanel(title = shiny::div(shiny::a(shiny::img(src="logo.png"),href="https://agdamsbo.github.io/REDCapCAST"),
"Easy REDCap database creation"),
shiny::titlePanel(
title = shiny::div(
shiny::a(shiny::img(src = "logo.png"), href = "https://agdamsbo.github.io/REDCapCAST"),
"Easy REDCap database creation"
),
windowTitle = "REDCap database creator"
),
shiny::h4("This tool includes to convenient functions:",
shiny::br(),
"1) creating a REDCap data dictionary based on a spreadsheet (.csv/.xls(x)/.dta) and",
shiny::br(),
"2) creating said database on a given REDCap server and uploading the dataset via API access."),
shiny::h4(
"This tool includes to convenient functions:",
shiny::br(),
"1) creating a REDCap data dictionary based on a spreadsheet (.csv/.xls(x)/.dta) and",
shiny::br(),
"2) creating said database on a given REDCap server and uploading the dataset via API access."
),
## -----------------------------------------------------------------------------
@ -60,7 +65,7 @@ ui <- shiny::shinyUI(
label = "API key",
value = ""
),
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."),
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."),
shiny::actionButton(
inputId = "upload.meta",
label = "Upload datadictionary", icon = shiny::icon("book-bookmark")
@ -110,17 +115,17 @@ ui <- shiny::shinyUI(
shiny::br(),
shiny::hr(),
shiny::tags$footer(shiny::strong("Disclaimer: "),
"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.",
shiny::br(),
shiny::a("License: GPL-3+",href="https://agdamsbo.github.io/REDCapCAST/LICENSE.html"),
"|",
shiny::a("agdamsbo/REDCapCAST",href="https://agdamsbo.github.io/REDCapCAST"),
"|",
shiny::a("Source",href="https://github.com/agdamsbo/REDCapCAST"),
"|",
shiny::a("Contact",href="https://andreas.gdamsbo.dk"),
align = "center",
style = "
"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.",
shiny::br(),
shiny::a("License: GPL-3+", href = "https://agdamsbo.github.io/REDCapCAST/LICENSE.html"),
"|",
shiny::a("agdamsbo/REDCapCAST", href = "https://agdamsbo.github.io/REDCapCAST"),
"|",
shiny::a("Source", href = "https://github.com/agdamsbo/REDCapCAST"),
"|",
shiny::a("Contact", href = "https://andreas.gdamsbo.dk"),
align = "center",
style = "
position:fixed;
bottom:40px;
width:100%;
@ -129,6 +134,7 @@ ui <- shiny::shinyUI(
padding: 0px;
background-color: White;
z-index: 100;
")
"
)
)
)

7
inst/WORDLIST
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@ -4,6 +4,7 @@ Codecov
DOI
DataDictionary
GStat
Github
GithubActions
JSON
Lifecycle
@ -14,7 +15,6 @@ README
REDCap
REDCapR
REDCapRITS
THe
UI
WD
al
@ -34,8 +34,10 @@ dplyr
ds
dta
et
github
gues
hms
https
immprovements
io
jbi
@ -55,6 +57,7 @@ perl
pos
pre
readr
realising
sel
sep
seperator
@ -64,9 +67,11 @@ stRoke
stata
strsplit
subheader
textclean
thorugh
tibble
tidyverse
trinker
ui
uri
wil

18
man/replace_curly_quote.Rd Normal file
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@ -0,0 +1,18 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/doc2dd.R
\name{replace_curly_quote}
\alias{replace_curly_quote}
\title{Replace curly apostrophes and quotes from word}
\usage{
replace_curly_quote(x)
}
\arguments{
\item{x}{character vector}
}
\value{
character vector
}
\description{
Copied from textclean, which has not been updated since 2018 and is not
on CRAN. Github:https://github.com/trinker/textclean
}

52
renv.lock
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@ -1,6 +1,6 @@
{
"R": {
"Version": "4.3.3",
"Version": "4.4.0",
"Repositories": [
{
"Name": "CRAN",
@ -138,14 +138,14 @@
},
"cachem": {
"Package": "cachem",
"Version": "1.0.8",
"Version": "1.1.0",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"fastmap",
"rlang"
],
"Hash": "c35768291560ce302c0a6589f92e837d"
"Hash": "cd9a672193789068eb5a2aad65a0dedf"
},
"cellranger": {
"Package": "cellranger",
@ -199,16 +199,6 @@
"Repository": "CRAN",
"Hash": "5d8225445acb167abf7797de48b2ee3c"
},
"cpp11": {
"Package": "cpp11",
"Version": "0.4.7",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"R"
],
"Hash": "5a295d7d963cc5035284dcdbaf334f4e"
},
"crayon": {
"Package": "crayon",
"Version": "1.5.2",
@ -279,10 +269,10 @@
},
"fastmap": {
"Package": "fastmap",
"Version": "1.1.1",
"Version": "1.2.0",
"Source": "Repository",
"Repository": "CRAN",
"Hash": "f7736a18de97dea803bde0a2daaafb27"
"Hash": "aa5e1cd11c2d15497494c5292d7ffcc8"
},
"filelock": {
"Package": "filelock",
@ -533,13 +523,13 @@
},
"openssl": {
"Package": "openssl",
"Version": "2.1.2",
"Version": "2.2.0",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
"askpass"
],
"Hash": "ea2475b073243d9d338aa8f086ce973e"
"Hash": "2bcca3848e4734eb3b16103bc9aa4b8e"
},
"openxlsx2": {
"Package": "openxlsx2",
@ -585,30 +575,6 @@
],
"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"
},
"promises": {
"Package": "promises",
"Version": "1.3.0",
@ -785,7 +751,7 @@
},
"stringi": {
"Package": "stringi",
"Version": "1.8.3",
"Version": "1.8.4",
"Source": "Repository",
"Repository": "CRAN",
"Requirements": [
@ -794,7 +760,7 @@
"tools",
"utils"
],
"Hash": "058aebddea264f4c99401515182e656a"
"Hash": "39e1144fd75428983dc3f63aa53dfa91"
},
"stringr": {
"Package": "stringr",

25
tests/spelling.Rout.save Normal file
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@ -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

54
vignettes/Database-creation.Rmd
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@ -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).

4
vignettes/Shiny-app.Rmd
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@ -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}