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Adding illustration to README.md

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@ -19,19 +19,126 @@ might expect that the non-repeating instruments may constitute one table
that would be related to Repeating Instruments tables via a one-to-many that would be related to Repeating Instruments tables via a one-to-many
relationship. In reality, the data is outputted as one table with all relationship. In reality, the data is outputted as one table with all
possible fields; this has the effect of nesting the output table in a possible fields; this has the effect of nesting the output table in a
way that is not useful in most analysis software. Therefore, I have made way that is not useful in most analysis software.
a solution to handle the problem in both SAS and R.
## Supported Platforms 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.
### Illustration
For example, consider this mocked-up data involving some information about cars in
R's built-in `mtcars` dataset as well as some sales data for some of the cars.
| car_id|redcap_repeat_instrument |redcap_repeat_instance |make |model |mpg |cyl |motor_trend_cars_complete |price |color |customer |sale_complete |
|------:|:------------------------|:----------------------|:--------|:-----------|:----|:---|:-------------------------|:--------|:-----|:--------|:-------------|
| 1| | |AMC |Javelin |15.2 |8 |1 | | | | |
| 1|sale |1 | | | | | |12000.50 |1 |Bob |0 |
| 1|sale |2 | | | | | |13750.77 |3 |Sue |2 |
| 1|sale |3 | | | | | |15004.57 |2 |Kim |0 |
| 2| | |Cadillac |Fleetwood |10.4 |8 |0 | | | | |
| 3| | |Camaro |Z28 |13.3 |8 |0 | | | | |
| 3|sale |1 | | | | | |7800.00 |2 |Janice |2 |
| 3|sale |2 | | | | | |8000.00 |3 |Tim |0 |
| 4| | |Chrysler |Imperial |14.7 |8 |0 | | | | |
| 4|sale |1 | | | | | |7500.00 |1 |Jim |2 |
| 5| | |Datsun |710 |22.8 |4 |0 | | | | |
| 6| | |Dodge |Challenger |15.5 |8 |0 | | | | |
| 7| | |Duster |360 |14.3 |8 |0 | | | | |
| 7|sale |1 | | | | | |8756.40 |4 |Sarah |1 |
| 7|sale |2 | | | | | |6800.88 |2 |Pablo |0 |
| 7|sale |3 | | | | | |8888.88 |1 |Erica |0 |
| 7|sale |4 | | | | | |970.00 |4 |Juan |0 |
| 8| | |Ferrari |Dino |19.7 |6 |0 | | | | |
| 9| | |Mazda |RX4 Wag |21 |6 |0 | | | | |
| 10| | |Merc |230 |22.8 |4 |0 | | | | |
| 10|sale |1 | | | | | |7800.98 |2 |Ted |0 |
| 10|sale |2 | | | | | |7954.00 |1 |Quentin |0 |
| 10|sale |3 | | | | | |6800.55 |3 |Sharon |2 |
*Data credit*: Henderson and Velleman (1981), Building multiple regression models interactively. *Biometrics*, **37**, 391--411.
**Modified with fake data for the purpose of illustration**
You can see that the data from the non-repeating forms (primary table) is interlaced with the data in the repeating forms,
creating a checkerboard pattern. In order to do analysis, the data must be normalized and then the tables rejoined.
The normalized tables would look like this:
**Primary table**
| car_id|make |model |mpg |cyl |motor_trend_cars_complete |
|------:|:--------|:----------|:----|:---|:-------------------------|
| 1|AMC |Javelin |15.2 |8 |1 |
| 2|Cadillac |Fleetwood |10.4 |8 |0 |
| 3|Camaro |Z28 |13.3 |8 |0 |
| 4|Chrysler |Imperial |14.7 |8 |0 |
| 5|Datsun |710 |22.8 |4 |0 |
| 6|Dodge |Challenger |15.5 |8 |0 |
| 7|Duster |360 |14.3 |8 |0 |
| 8|Ferrari |Dino |19.7 |6 |0 |
| 9|Mazda |RX4 Wag |21 |6 |0 |
| 10|Merc |230 |22.8 |4 |0 |
**Child table**
|car_id |redcap_repeat_instrument |redcap_repeat_instance |price |color |customer |sale_complete |
|:------|:------------------------|:----------------------|:--------|:-----|:--------|:-------------|
|1 |sale |1 |12000.50 |1 |Bob |0 |
|1 |sale |2 |13750.77 |3 |Sue |2 |
|1 |sale |3 |15004.57 |2 |Kim |0 |
|3 |sale |1 |7800.00 |2 |Janice |2 |
|3 |sale |2 |8000.00 |3 |Tim |0 |
|4 |sale |1 |7500.00 |1 |Jim |2 |
|7 |sale |1 |8756.40 |4 |Sarah |1 |
|7 |sale |2 |6800.88 |2 |Pablo |0 |
|7 |sale |3 |8888.88 |1 |Erica |0 |
|7 |sale |4 |970.00 |4 |Juan |0 |
|10 |sale |1 |7800.98 |2 |Ted |0 |
|10 |sale |2 |7954.00 |1 |Quentin |0 |
|10 |sale |3 |6800.55 |3 |Sharon |2 |
After inner joining the primary table to the child table on `car_id` and selecting only the fields you are interested in,
your resulting analytic dataset might look something like this:
| car_id|make |model |price |color |customer |
|------:|:--------|:--------|:--------|:-----|:--------|
| 1|AMC |Javelin |12000.50 |1 |Bob |
| 1|AMC |Javelin |13750.77 |3 |Sue |
| 1|AMC |Javelin |15004.57 |2 |Kim |
| 3|Camaro |Z28 |7800.00 |2 |Janice |
| 3|Camaro |Z28 |8000.00 |3 |Tim |
| 4|Chrysler |Imperial |7500.00 |1 |Jim |
| 7|Duster |360 |8756.40 |4 |Sarah |
| 7|Duster |360 |6800.88 |2 |Pablo |
| 7|Duster |360 |8888.88 |1 |Erica |
| 7|Duster |360 |970.00 |4 |Juan |
| 10|Merc |230 |7800.98 |2 |Ted |
| 10|Merc |230 |7954.00 |1 |Quentin |
| 10|Merc |230 |6800.55 |3 |Sharon |
### Supported Platforms
Currently, the R and SAS code is well-tested with mocked-up data.
- R - R
- SAS - SAS
### Coming Soon I have made some effort to replicate the
messiness of real-world data and have tried to include as many special cases and data types as possible.
However, this code may not account for all contingencies or changes in the native REDCap export format.
If you find a bug, please feel free to open an issue or pull request.
#### Coming Soon
Currently, we have given some consideration to expand the capabilities into the following languages.
- Python - Python
- VBA - VBA
If you have some talents in these or other languages, please feel free to open a pull request! We
welcome your contributions!
## Instructions ## Instructions
### R ### R
@ -48,7 +155,7 @@ devtools::install_github("SpectrumHealthResearch/REDCapRITS/R")
After the package is installed, follow these instructions: After the package is installed, follow these instructions:
1. Download the record dataset and metadata. This can 1. Download the record dataset and metadata (data dictionary). This can
be accomplished by several methods: be accomplished by several methods:
- Using the API. Check with your REDCap administrator for details. - Using the API. Check with your REDCap administrator for details.
- Exporting the data from the web interface by selecting *CSV / Microsoft Excel (raw data)*. - Exporting the data from the web interface by selecting *CSV / Microsoft Excel (raw data)*.