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DOI License: GPL v2 r-cmd-check.yml

redcapAPI

redcapAPI is an R package to pull data from a REDCap project. Its design goes far beyond a 'thin' client which just exposes the raw REDCap API into R. One principal goal is to get data into memory using base R in a format that is analysis ready with a minimum of function calls. There are over 7,000 institutions and 3 million users of REDCap worldwide collecting data. Analysis in R for monitoring and reporting that data is a common concern for these projects.

Core concerns handled by the library:

  • API_KEY (which is equivalent of username/password to ones data!) secure handling practices are designed to be as seamless as possible via unlockREDCap. There are override methods available for production environments.
  • Retry strategy with exponential back off. When a REDCap server or a network is overloaded requests can fail. Each call to the API will retry multiple times, and it doubles the wait time between each call. This dramatically increases the odds of success for a script with multiple API calls to REDCap.
  • Automatically handles and caches meta data information needed to understand and translate a project's data.
  • A robust type casting strategy that every step of the process can be overridden by the user via inversion of control. The strategy proceeds as follows:
    • NA detection per REDCap (or user!) definition of NA.
    • Validation of data versus the target type/class. reviewInvalidRecords provides a summary report of all data that fails validation, with hot links to the record in question. This is an important step. Data that does not match the target format cannot be cast, e.g. "xyz" cannot be treated as a numeric and will become NA in the final data set.
    • Final type casting to target type.
  • Sparse block matrix splitting into forms/instruments with filtering of empty rows.
  • Additional helper functions, e.g. longitudinal wider/long conversions, guessing if a character field is actually a date, and SAS exports.
  • Importing data reuses a lot of the casting functions in reverse to ensure data integrity both directions.

Comparison to Other REDCap Packages

Feature redcapAPI REDCapR REDCapExporter tidyREDCap REDCapTidieR REDCapDM
CRAN Downloads
Export Data To R ✅ ✅ ✅ ✅ ✅ ✅
Import Data From R ✅ ✅ ❌ ❌ ❌ ❌
Sparse Block Splitting ✅ ✅ ❌ ✅ ✅ ✅
Field Labeling ✅ ❌ ❌ ✅ ❌ ✅
Attribute Processing ✅ ❌ ❌ ❌ ❌ ❌
Logical Expression Query partial ❌ ❌ ❌ ❌ ✅
Tidy/Tibble Support ❌ ❌ ❌ ❌ ✅ ❌
Data Summary ❌ ❌ ❌ ❌ ✅ ❌
Type Conversion Callbacks ✅ ❌ ❌ ❌ ❌ ❌
API Failure Auto-Retry ✅ ❌ ❌ ❌ ❌ ❌
Secure API Key Storage ✅ ❌ ✅ ❌ ❌ ❌
Validation Reporting ✅ ❌ ❌ ❌ ❌ ❌
Extensive Test Suite ✅ ✅ ❌ ❌ ✅ ❌
Logfile Processing ✅ ❌ ❌ ❌ ❌ ❌
Offline Calculated Fields ❌ ❌ ❌ ❌ ❌ ✅

Quick Start Guide

There are 2 basic functions that are key to understanding the core approach:

  • unlockREDCap
  • exportBulkRecords

Here's a typical call for these two:

library(redcapAPI)

# IMPORTANT: Put the following line in .Rprofile `usethis::edit_r_profile()`
options(keyring_backend=keyring::backend_file)

unlockREDCap(c(rcon    = '<MY PROJECT NAME>'),
             keyring     = 'API_KEYs',
             envir       = globalenv(),
             url         = 'https://<REDCAP_URL>/api/')
exportBulkRecords(list(db = rcon),
  forms = list(db = unique(rcon$metadata()$form_name)),
  envir = globalenv())

The <MY PROJECT NAME> is a reference for whatever you wish to call this REDCap project. The rcon is the variable you wish to assign it too. The keyring is a name for this key ring. If one uses 'API_KEYs' for all your projects, you'll have one big keyring for all your API_KEYs locally encrypted. The url is the standard url for the api at your institution. The envir call is where to write the connection object; if not specified the call will return a list.

The next call to exportBulkRecords, says to export by form and leave out records not filled out and columns not part of a form. The first argument is specifying a db reference to the connection opened and naming it the same thing. The second call is saying for this connection export back the all the forms/instruments present in that db, if this is left blank it defaults to all forms/instruments. The envir has it writing it back to the global environment as variables. Any parameter not recognized is passed to the exportRecordsTyped call--for every REDCap database connection. For most analysis projects the function exportBulkRecords provides the functionality required to get the data in memory, converted, type cast and sparse block matrix split into forms/instruments with blank rows filtered out.

These two calls will handle most analysis requests. To truly understand all these changes see: vignette("redcapAPI-best-practices").

Version 2.7.0+

2.7.0 introduced exportRecordsTyped which is a major move forward for the package. It replaces exportRecords with a far more stable and dependable call. It includes retries with exponential back off through the connection object. It has inversion of control over casting, and has a useful validation report attached when things fail. It is worth the time to convert calls to exportRecords to exportRecordsTyped and begin using this new routine. It is planned that in the next year exportRecords will be removed from the package.

Community Guidelines

This package exists to serve the research community and would not exist without community support. We are interested in volunteers who would like to translate the documentation into other languages.

Contribute

If you wish to contribute new features to this software, we are open to pull requests. Before doing a lot of work, it would be best to open issue for discussion about your idea.

Coding Style Guideline Note

  • Exported function names: dromedaryCase
  • Internal function names: .dromedaryCase
  • Constant data exported: UPPERCASE
  • Function parameters: snake_case
  • Function variables: snake_case
    • (exception) data.frame variable: CamelCase

Report Issues or Problems

REDCap and it's API have a large number of options and choices, with such complexity the possibility of bugs increases as well. This is a checklist for troubleshooting exports.

  1. Does Rec <- exportRecordsTyped(rcon) give you a warning about data that failed validations? If so, what kind of content are you seeing from reviewInvalidRecords(Rec)?
  2. Did you see 'choice string does not appear to be formatted for choices' as an error? If so see Issue #344
  3. What is returned by exportRecordsTyped(rcon, validation = skip_validation, cast = raw_cast)? This is a completely raw export with no processing by the library.
  4. Do you have any project level missing data codes? rcon$projectInformation()$missing_data_codes
  5. Do you have a secondary id field defined? rcon$projectInformation()$secondary_unique_field. In earlier versions REDCap will report one even if it's been disabled later, if this column doesn't exist then the library is unable to properly handle exports as the definition of the unique key doesn't exist. If one is defined and the field doesn't exist, one will have to contact their REDCap administrator to get the project fixed.
  6. Is it an empty row filtering issue? Try the option filter_empty_rows=FALSE and see if that fixes it.
  7. Search known open and closed issues to see if it's already been reported. If an issue matches your problem, then feel free to post a "me too" message with the information from the next step. Feel free to reopen a closed issue if one matches.
  8. If these steps fail to diagnose the issue, open an issue on github.com and we are happy to assist you. Please include your version of R, RStudio and packageVersion('redcapAPI').

What does "Project contains invalid characters. Mapped to '□'." mean?

This means that the data/meta-data stored in the REDCap database contains improperly encoded characters. It is a problem with the REDCap project itself. The authors of this library do not know the root cause of the encoding issue, but suspect it was an earlier version of REDCap that did not handle encoding properly. This library is respecting the reported encoding type when loading into memory. All cases seen to date have the data encoded in ISO-8859-1 (the default when the HTTP header is missing charset) and the REDCap server treats all data as UTF-8. This improper coding can result in data loss via the GUI if records are updated. It is best to discuss with your institutions REDCap administrator how to repair this problem and such repairs are outside the scope of this library. This error message is to make one aware of this issue in their project. The library does the best it can when it encounters encoding issues.

Seek Support

If you need help or assistance in understanding how to approach a project or problem using the library, please open an issue. We use these questions to refine the documentation. Thus asking questions contributes to refinement of documentation.

Documentation

Your institutions installation of REDCap contains a lot of documentation for the general usage of REDCap. For general questions outside the scope of interfacing the API to R please refer to your institutions REDCap instance documentation.

The help pages for functions is fairly extensive. Try ?exportRecordsTyped or ?fieldValidationAndCasting for good starting points into the help pages.

All Vignettes

There are several vignettes with helpful information and examples to explore. These provide higher level views than can be provided in help pages.

  • redcapAPI-casting-data
  • redcapAPI-data-validation
  • redcapAPI-getting-started-connecting
  • redcapAPI-missing-data-detection
  • redcapAPI-best-practices
  • redcapAPI-offline-connection

Back Matter

NOTE: Ownership transfer of this package to VUMC Biostatistics is complete.

The research community owes a big thanks to Benjamin Nutter for his years of service keeping this package current.

This package was originally created by Jeffrey Horner.

The current package was developed under REDCap Version 14+. Institutions can be a little behind on updating REDCap and so some features of the API may not always work.

Issue Review Process for Pull Requests

Goals:

  • Reproducibility
  • Test Driven
  • Robust checking of user inputs

Rules:

  • Hotfixes or documentation changes can skip this process.
  • The majority author on a pull request must not be the approving reviewer.
  • Each commit should include the issue number as a link.
  • The approving reviewer should check the following:
    • Visual review of code in pull request.
    • Was the NEWS updated?
    • Were tests written?
    • Were user inputs checked?
    • Does the VERSION need bumped?
    • Was documentation properly updated?
    • Was roxygen2 run on the updated documentation?
    • Does R CMD CHECK pass? (reviewer should run)
    • Does the test suite pass with no warnings? (reviewer should run)

License

redcapAPI A rich API client for interfacing REDCap to R

Copyright (C) 2012 Jeffrey Horner, Vanderbilt University Medical Center

Copyright (C) 2013-2022 Benjamin Nutter

Copyright (C) 2023-2024 Benjamin Nutter, Shawn Garbett, Vanderbilt University Medical Center

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.