andreas/REDCapCAST
1
0
Fork 0
mirror of https://github.com/agdamsbo/REDCapCAST.git synced 2024-11-22 05:20:23 +01:00
Code Issues Packages Projects Releases Wiki Activity

cleaning up illustration in README.md

Browse Source
This commit is contained in:
pegeler 2018-06-08 23:39:12 -04:00
parent 981d75bba6
commit d20a3625f3
1 changed files with 12 additions and 10 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

22
README.md
View File

@ -24,13 +24,15 @@ way that is not useful in most analysis software.
The normalized data can be retrieved by downloading repeating instruments individually then doing a little
data munging or by writing a few custom parameters in a series of API calls (then doing more data munging),
but this is a lot of extra steps that can make reproducible research more difficult.
Therefore, I have made a programmatic solution to handle the problem in both SAS and R.
REDCapRITS is a programmatic solution to handle the problem in both SAS and R.
### Illustration
For example, consider this mocked-up data involving some information about a subset
of cars in R's built-in `mtcars` dataset (1). Contained in the data is a repeating instrument,
*sales*, which contains sales transaction data for some of those cars.
For example, consider this mocked-up data exported from a REDCap project with repeating instruments.
The data contains information on a subset of cars in R's built-in `mtcars` dataset [1].
Within the table there is also a repeating instrument, *sales*, which has sales transaction
data for some of those cars.
| car_id|redcap_repeat_instrument |redcap_repeat_instance |make |model |mpg |cyl |motor_trend_cars_complete |price |color |customer |sale_complete |
|------:|:------------------------|:----------------------|:--------|:-----------|:----|:---|:-------------------------|:--------|:-----|:--------|:-------------|
@ -59,7 +61,7 @@ of cars in R's built-in `mtcars` dataset (1). Contained in the data is a repeati
| 10|sale |3 | | | | | |6800.55 |3 |Sharon |2 |
You can see that the data from the non-repeating forms (primary table) is interlaced with the data in the repeating forms,
You can see that the data from the non-repeating form (primary table) is interlaced with the data in the repeating form,
creating a checkerboard pattern. In order to do analysis, the data must be normalized and then the tables rejoined.
Normalization would result in two tables: 1) a *primary* table and 2) a *sale* table.
The normalized tables would look like this:
@ -98,7 +100,7 @@ The normalized tables would look like this:
|10 |sale |3 |6800.55 |3 |Sharon |2 |
Suppose you would like to do some analysis such as sale price by make of car or find
the most popular color for each model. To do so, you can join the tables together using
the most popular color for each model. To do so, you can join the tables together with
relational algebra. After inner joining the *primary* table to the *sale* table on `car_id`
and selecting only the fields you are interested in,
your resulting analytic dataset might look something like this:
@ -126,7 +128,7 @@ Such a join can be accomplished numerous ways. Just to name a few:
- The [`MERGE`](http://support.sas.com/documentation/cdl/en/lrdict/64316/HTML/default/viewer.htm#a000202970.htm) statement in a `DATA` step
- R
- [`dplyr::*_join`](https://www.rdocumentation.org/packages/dplyr/versions/0.7.5/topics/join)
- [`sqldf`](https://www.rdocumentation.org/packages/sqldf/versions/0.4-11/topics/sqldf)
- [`sqldf::sqldf`](https://www.rdocumentation.org/packages/sqldf/versions/0.4-11/topics/sqldf)
- [`base::merge`](https://www.rdocumentation.org/packages/base/versions/3.5.0/topics/merge)
### Supported Platforms
@ -273,11 +275,11 @@ Suggestions and contributions are more than welcome! Please feel free to create
## About REDCap
This code was written for [REDCap electronic data capture tools](https://projectredcap.org/)(2). Code for this project was tested on the REDCap instance hosted at Spectrum Health, Grand Rapids, MI. REDCap (Research Electronic Data Capture) is a secure, web-based application designed to support data capture for research studies, providing 1) an intuitive interface for validated data entry; 2) audit trails for tracking data manipulation and export procedures; 3) automated export procedures for seamless data downloads to common statistical packages; and 4) procedures for importing data from external sources.
This code was written for [REDCap electronic data capture tools](https://projectredcap.org/) [2]. Code for this project was tested on the REDCap instance hosted at Spectrum Health, Grand Rapids, MI. REDCap (Research Electronic Data Capture) is a secure, web-based application designed to support data capture for research studies, providing 1) an intuitive interface for validated data entry; 2) audit trails for tracking data manipulation and export procedures; 3) automated export procedures for seamless data downloads to common statistical packages; and 4) procedures for importing data from external sources.
## References
(1) Henderson and Velleman (1981), Building multiple regression models interactively. *Biometrics*, **37**, 391--411.
[1] Henderson and Velleman (1981), Building multiple regression models interactively. *Biometrics*, **37**, 391--411.
**Modified with fake data for the purpose of illustration**
(2) Paul A. Harris, Robert Taylor, Robert Thielke, Jonathon Payne, Nathaniel Gonzalez, Jose G. Conde, Research electronic data capture (REDCap) – A metadata-driven methodology and workflow process for providing translational research informatics support, J Biomed Inform. 2009 Apr;42(2):377-81.
[2] Paul A. Harris, Robert Taylor, Robert Thielke, Jonathon Payne, Nathaniel Gonzalez, Jose G. Conde, Research electronic data capture (REDCap) – A metadata-driven methodology and workflow process for providing translational research informatics support, J Biomed Inform. 2009 Apr;42(2):377-81.