mirror of
https://github.com/agdamsbo/stRoke.git
synced 2024-10-30 03:11:52 +01:00
66 lines
1.7 KiB
Plaintext
66 lines
1.7 KiB
Plaintext
|
---
|
||
|
|
title: "Data set to data dictionary (ds2dd)"
|
||
|
|
output: rmarkdown::html_vignette
|
||
|
|
vignette: >
|
||
|
|
%\VignetteIndexEntry{ds2dd}
|
||
|
|
%\VignetteEngine{knitr::rmarkdown}
|
||
|
|
%\VignetteEncoding{UTF-8}
|
||
|
|
---
|
||
|
|
|
||
|
|
```{r, include = FALSE}
|
||
|
|
knitr::opts_chunk$set(
|
||
|
|
collapse = TRUE,
|
||
|
|
comment = "#>"
|
||
|
|
)
|
||
|
|
```
|
||
|
|
|
||
|
|
```{r setup}
|
||
|
|
library(stRoke)
|
||
|
|
```
|
||
|
|
|
||
|
|
# Easy data set to data base workflow
|
||
|
|
|
||
|
|
This function can be used as a simple tool for creating at data base metadata file for REDCap (called a DataDictionary) based on a given data set file.
|
||
|
|
|
||
|
|
## Step 1 - Load your data set
|
||
|
|
|
||
|
|
Here we'll use the sample TALOS dataset included with the package.
|
||
|
|
|
||
|
|
```{r}
|
||
|
|
data("talos")
|
||
|
|
# As the data set lacks an ID column, one is added
|
||
|
|
talos$id <- seq_len(nrow(talos))
|
||
|
|
```
|
||
|
|
|
||
|
|
## Step 2 - Create the DataDictionary
|
||
|
|
|
||
|
|
```{r}
|
||
|
|
datadictionary <- ds2dd(talos,record.id = "id")
|
||
|
|
```
|
||
|
|
|
||
|
|
Now 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.
|
||
|
|
|
||
|
|
## Step 3 - 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).
|
||
|
|
|
||
|
|
Use one of the two approaches below:
|
||
|
|
|
||
|
|
### Manual upload
|
||
|
|
|
||
|
|
```{r eval=FALSE}
|
||
|
|
write.csv(datadictionary,"datadictionary.csv")
|
||
|
|
```
|
||
|
|
|
||
|
|
### Upload with `REDCapR`
|
||
|
|
|
||
|
|
```{r eval=FALSE}
|
||
|
|
REDCapR::redcap_metadata_write(
|
||
|
|
datadictionary,
|
||
|
|
redcap_uri = keyring::key_get("DB_URI"),
|
||
|
|
token = keyring::key_get("DB_TOKEN")
|
||
|
|
)
|
||
|
|
```
|
||
|
|
|
||
|
|
In the ["REDCap R Handbook"](https://agdamsbo.github.io/redcap-r-handbook/) more is written on interfacing with REDCap in R using the `library(keyring)`to store credentials in [chapter 1.1](https://agdamsbo.github.io/redcap-r-handbook/access.html#sec-getting-access).
|