-
Notifications
You must be signed in to change notification settings - Fork 8
/
README.Rmd
85 lines (55 loc) · 5.41 KB
/
README.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# REDCapTidieR <a href="https://chop-cgtinformatics.github.io/REDCapTidieR/"><img src="man/figures/logo.png" align="right" height="138" /></a>
<!-- badges: start -->
[](https://lifecycle.r-lib.org/articles/stages.html#stable)
[](https://github.com/CHOP-CGTInformatics/REDCapTidieR/actions/workflows/R-CMD-check.yaml)
[](https://CRAN.R-project.org/package=REDCapTidieR)
[](https://cran.r-project.org/package=REDCapTidieR)
[](https://cran.r-project.org/package=REDCapTidieR)
[](https://app.codecov.io/gh/CHOP-CGTInformatics/REDCapTidieR?branch=main)
[](https://bestpractices.coreinfrastructure.org/projects/6845)
<!-- badges: end -->
The REDCapTidieR package provides an elegant way to [import](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#import) data from a [REDCap](https://projectredcap.org/) [project](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#project) into an R environment. It builds upon the [REDCapR](https://ouhscbbmc.github.io/REDCapR/) package to query the [REDCap API](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#redcap-api) and then transforms the returned data into a set of [tidy](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#tidy) [tibbles](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#tibble).
REDCapTidieR is especially useful for dealing with complex REDCap projects that are [longitudinal](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#longitudinal-project) or include [repeating](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#repeating) [instruments](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/glossary.html#instrument) or both.
## Installation
The release version can be installed from [CRAN](https://cran.r-project.org/package=REDCapTidieR).
```r
install.packages("REDCapTidieR")
```
You can install the development version of REDCapTidieR from [GitHub](https://github.com/CHOP-CGTInformatics/REDCapTidieR):
```r
devtools::install_github("CHOP-CGTInformatics/REDCapTidieR")
```
## Usage
Use `read_redcap()` together with `bind_tibbles()` to import data from all instruments into your environment.
REDCapTidieR supports labelled data using the [labelled](https://larmarange.github.io/labelled/) package, and it can generate statistical summaries using the [skimr](https://docs.ropensci.org/skimr/) package.
Read the [Getting Started vignette](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/REDCapTidieR.html) to learn more.
In addition, you can easily create collaborator-friendly Excel files using the `write_redcap_xlsx()` function:
```{r, eval=FALSE}
redcap_uri <- "https://my.institution.edu/redcap/api/"
token <- "123456789ABCDEF123456789ABCDEF04"
my_redcap_data <- read_redcap(redcap_uri, token)
write_redcap_xlsx(my_redcap_data, file = "my_redcap_data.xlsx")
```
To learn more about how to work with and customize the output, read the [Exporting to Excel vignette](https://chop-cgtinformatics.github.io/REDCapTidieR/articles/export_to_xlsx.html).
## Collaboration
We invite you to give feedback and collaborate with us! If you are familiar with GitHub and R packages, please feel free to submit a [pull request](https://github.com/CHOP-CGTInformatics/REDCapTidieR/pulls). Please do let us know if REDCapTidieR fails for whatever reason with your database and submit a bug report by creating a GitHub [issue](https://github.com/CHOP-CGTInformatics/REDCapTidieR/issues).
Please note that this project is released with a [Contributor Code of Conduct](https://github.com/CHOP-CGTInformatics/REDCapTidieR/blob/main/CONDUCT.md). By participating you agree to abide by its terms.
We'd like to thank the following folks for their advice and code contributions: [Will Beasley](https://github.com/wibeasley) and [Paul Wildenhain](https://github.com/pwildenhain).
## Funding
This package was developed by the [Children's Hospital of Philadelphia](https://www.chop.edu) Cell and Gene Therapy Informatics Team to support the needs of the [Cellular Therapy and Transplant Section](https://www.chop.edu/centers-programs/cellular-therapy-and-transplant-section). The development was funded using the following sources:
- *Stephan Kadauke Start-up funds.* Stephan Kadauke, PI, CHOP, 2018-2024
- *CHOP-based GMP cell manufacturing (MFG) for CAR T clinical trials*. Stephan Grupp, PI; Stephan Kadauke, co-PI, CHOP, 2021-2023