Access data, meta data, and files from REDCap using the API

Description

REDCap is a database development tool built on MySQL. Visit https://projectredcap.org for more information. REDCap provides an API through which data, the data dictionary, files, and project information can be accessed. The redcapAPI package facilitates the use of these functions and simplifies the work needed to prepare data for analysis.

Details

The user should also refer to their institution's REDCap API documentation as a primary resource of what is available. Different versions of REDCap support different features–the user's REDCap API documentation will address the features specific to their version of REDCap.

Author(s)

Maintainer: Shawn Garbett shawn.garbett@vumc.org (ORCID) [contributor]

Authors:

• Benjamin Nutter benjamin.nutter@gmail.com [contributor]

• Jeffrey Horner

Other contributors:

• Savannah Obregon [contributor]

• Thomas Obadia [contributor]

• Marcus Lehr marcus.j.lehr@gmail.com [contributor]

• Brian High [contributor]

• Stephen Lane [contributor]

• Will Beasley [contributor]

• Will Gray [contributor]

• Nick Kennedy [contributor]

• Tan Hsi-Nien [contributor]

• Jeremy Stephens [contributor]

• Cole Beck [contributor]

• Bradley Johnson [contributor]

• Philip Chase [contributor]

• Paddy Tobias [contributor]

• Michael Chirico [contributor]

• William Sharp [contributor]

See Also

Useful links:

• https://github.com/vubiostat/redcapAPI

• Report bugs at https://github.com/vubiostat/redcapAPI/issues

Extraction and Assignment for redcapFactors

Description

Extract elements and make assignments to redcapFactors

Usage

## S3 method for class 'redcapFactor'
x[..., drop = FALSE]
## S3 method for class 'redcapFactor'
print(x, ...)

Arguments

Generate Allocation Tables for the Randomization Module

Description

These methods enable the user to generate allocation tables for the REDCap randomization module. Randomization may be stratified by other (categorical) variables in the data set as well as by Data Access Group. Additionally, randomization may be blocked to ensure balanced groups throughout the allocation

Usage

allocationTable(
 rcon,
 random,
 strata = NULL,
 group = NULL,
 dag.id = NULL,
 replicates,
 block.size,
 block.size.shift = 0,
 seed.dev = NULL,
 seed.prod = NULL,
 weights = NULL,
 ...
)
## S3 method for class 'redcapApiConnection'
allocationTable(
 rcon,
 random,
 strata = NULL,
 group = NULL,
 dag.id = NULL,
 replicates,
 block.size,
 block.size.shift = 0,
 seed.dev = NULL,
 seed.prod = NULL,
 weights = c(1, 1),
 ...
)
allocationTable_offline(
 meta_data,
 random,
 strata = NULL,
 group = NULL,
 dag.id = NULL,
 replicates,
 block.size,
 block.size.shift = 0,
 seed.dev = NULL,
 seed.prod = NULL,
 weights = c(1, 1),
 ...
)

Arguments

Details

Each element in block.size must be a multiple of the number of groups in the randomized variable.

The 'offline' version of the function operates on the data dictionary file downloaded from REDCap. This is made available for instances where the API cannot be accessed for some reason (such as waiting for API approval from the REDCap administrator).

The value of replicates controls how many allocations are generated. It is possible to get slightly more replicates than requested if your blocking design cannot exactly match replicates. For example, if the users asks for 30 replicates in blocks of 8, a warning will be printed and 32 replicates will be returned in the randomization table.

Value

Returns a list with the elements

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"),
 url = "your_redcap_url",
 keyring = "API_KEYs",
 envir = globalenv())
allocationTable(rcon,
 random = "treatment_assignment",
 strata = c("demographic_group", "hospital_group"),
 replicates = 12,
 block.size = 4,
 seed.dev = 12345,
 seed.prod = 54321)
## End(Not run)

Export, Import, and Delete Arms from a Project

Description

These methods enable the user to export the current arms from a project, import new arms, and modify or delete existing arms.

Usage

exportArms(rcon, ...)
importArms(rcon, data, override = FALSE, ...)
deleteArms(rcon, arms, ...)
## S3 method for class 'redcapApiConnection'
exportArms(rcon, arms = character(0), ...)
## S3 method for class 'redcapApiConnection'
importArms(rcon, data, override = FALSE, ...)
## S3 method for class 'redcapApiConnection'
deleteArms(rcon, arms, ...)

Arguments

Details

Exporting arms is not supported for classical REDCap projects. If the user attempts to export arms for a classical project, a data frame will be returned with zero rows.

When importing, arms are added when the value of arm_num does not already exist in the project.

Arm names may be modified by altering the name value associated with an existing arm_num value.

Deleting arms–whether by deleteArms or importArms with override = TRUE–is a destructive act that also deletes events and records associated with the arm. This is irreversible data loss. REDCap will only permit these actions to occur in projects in Development status.

Value

exportArms returns a data.frame with columns:

importArms invisibly returns the number of arms imported.

deleteArms invisibly returns the number of arms deleted.

Functions

• exportArms(): Export the arms defined in a project.

• importArms(): Import and modify the arms definitions in a project.

• deleteArms(): Delete arms from a project.

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
# Export all of the Arms
exportArms(rcon)
# Export only a subset of arms
exportArms(rcon, 
 arms = c(1, 3))
# Import a new arms
# Assume arms 1, 2, and 3 exist in the project already
NewData <- data.frame(arm_num = 4, 
 name = "Arm Four Name")
importArms(rcon, 
 data = NewData)
 
# Change the name of an existing arm
NewData <- data.frame(arm_num = 1, 
 name = "New Arm Name")
importArms(rcon, 
 data = NewData)
 
# Delete all arms and replace with a new specification
NewData <- data.frame(arm_num = c(1, 2), 
 name = c("Treatment Arm", "Control Arm"))
importArms(rcon, 
 data = NewData, 
 override = TRUE)
 
# Delete an existing arm
deleteArms(rcon, 
 arms = 4)
 
# Delete multiple existing arm
deleteArms(rcon, 
 arms = c(2, 3))
## End(Not run)

S3 method to turn curl response into character

Description

Converts a raw curl response into a character string.

Usage

## S3 method for class 'response'
as.character(x, ...)

Arguments

Assemble Codebook From the Data Dictionary

Description

This method enables the user to construct a code book similar in style to the REDCap project codebook. The codebook is similar in nature to the data dictionary, but multiple choice fields are represented with one line per coding.

Usage

assembleCodebook(
 rcon,
 fields = NULL,
 forms = NULL,
 drop_fields = NULL,
 field_types = NULL,
 include_form_complete = TRUE,
 expand_check = FALSE,
 ...
)
## S3 method for class 'redcapConnection'
assembleCodebook(
 rcon,
 fields = NULL,
 forms = NULL,
 drop_fields = NULL,
 field_types = NULL,
 include_form_complete = TRUE,
 expand_check = FALSE,
 ...
)
## S3 method for class 'redcapCodebook'
as.list(x, ...)

Arguments

Value

Returns a redcapCodebook object. This inherits the data.frame class and has the columns

• field_name - The name of the field.

• form - The name of the form on which the field is located.

• field_type - The field type.

• code - For multiple choice fields, the coding for the option.

• label - For multiple choice fields, the label for the option.

• min - For date and numeric fields, the minimum value in the validation, if any.

• max - For date and numeric fields, the maximum value in the validation, if any.

• branching_logic - For fields with branching logic, the string denoting the logic applied.

• field_order - The numeric order of the field in the data dictionary.

• form_order - The numeric order of the form in the data dictionary.

See Also

exportMetaData()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
 
# codebook for the entire project
assembleCodebook(rcon)
# codebook for multiple choice fields
assembleCodebook(rcon, 
 field_types = c("dropdown", "radio", "checkbox", 
 "yesno", "truefalse"))
## End(Not run)

returns a list of record IDs changed (adds, updates, deletes)

Description

This is a convenience function that scans logs and returns record IDs of changed records.

Usage

changedRecords(rcon, ...)

Arguments

Details

Makes a call to exportLogging with passed arguments. Returns filtered list or records IDs with update, delete or create events.

Value

Returns a list with the elements

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
# Changes in last 24 hours 
changedRecords(rcon, beginTime=as.POSIXct(Sys.time()-86400))
## End(Not run)

Checkbox Suffixes

Description

Checkbox variables return one vector of data for each option defined in the variable. The variables are returned with the suffix ⁠___[option]⁠. exportRecords needs these suffixes in order to retrieve all of the variables and to apply the correct labels.

Usage

checkbox_suffixes(fields, meta_data)

Arguments

Connect to REDCap and verify connection

Description

A function that given an API_KEY and a url will create a redcapConnection object and verify that it is working with a version call. If the API key is invalid it will return NULL. If the URL is invalid or there are multiple redirects it will call stop.

Usage

connectAndCheck(key, url, ...)

Arguments

Value

redcapConnection established or NULL if key is invalid.

See Also

redcapConnection()

Examples

## Not run: 
connectAndCheck("<AN API KEY HERE>", "<REDCAP URL HERE>")
## End(Not run)

Construct a Link to a REDCap Form

Description

Uses information from the project and a record to link to the form on which a data element is recorded. This is intended to be used within the report of invalid results when exporting or importing records. It should be noted that when importing records, the records may not yet exist and the links may not work.

Usage

constructLinkToRedcapForm(rcon, form_name, record_id, event_id = NULL, ...)
## S3 method for class 'redcapApiConnection'
constructLinkToRedcapForm(rcon, form_name, record_id, event_id = NULL, ...)
## S3 method for class 'redcapOfflineConnection'
constructLinkToRedcapForm(rcon, form_name, record_id, event_id = NULL, ...)

Arguments

Details

Constructing a link to a REDCap form requires knowledge of the following:

• The REDCap instance url (usually 'redcap.institution.domain').

• The REDCap instance version number.

• The REDCap project ID number

• The record ID

• The form name

• The event ID number (if the project is longitudinal).

If any of these items in unknown, a missing value will be returned. For redcapOfflineConnections, the user will need to provide the version number, the project information, and the events (if the project is longitudinal) as part of the call to offlineConnection. Note that the REDCap User Interface does not include the event ID number with the file download for events.

Value

Returns a character vector the same length of form_name.

Create a Folder in the File Repository

Description

This method enables the user to create a folder in the file repository. The folder created may also be a subfolder of an existing folder.

Usage

createFileRepositoryFolder(
 rcon,
 name,
 folder_id = numeric(0),
 dag_id = numeric(0),
 role_id = numeric(0),
 ...
)
## S3 method for class 'redcapApiConnection'
createFileRepositoryFolder(
 rcon,
 name,
 folder_id = numeric(0),
 dag_id = numeric(0),
 role_id = numeric(0),
 ...
)

Arguments

Value

Returns a data frame with the columns

See Also

exportFromFileRepository() ,
importToFileRepository() ,
deleteFromFileRepository() ,
exportFileRepository() ,
importFileRepository() ,
deleteFileRepository() ,
exportFileRepositoryListing()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"),
 url = "your_redcap_url",
 keyring = "API_KEYs",
 envir = globalenv())
# Create a folder in the top-level directory
createFileRepositoryFolder(rcon,
 name = "New Folder Name")
# Create a folder in a subfolder
createFileRepositoryFolder(rcon,
 name = "New Folder Name",
 folder_id = 12345)
# Create a folder assigned to a Data Access Group
createFileRepositoryFolder(rcon,
 name = "New Folder Name",
 dag_id = 678)
## End(Not run)

Create REDCap Project

Description

These methods enable a user with a 64-character Super API token to create a new REDCap project.

Usage

createRedcapProject(
 rcon,
 project_title,
 purpose = REDCAP_PROJECT_PURPOSE,
 purpose_other = NULL,
 is_longitudinal = FALSE,
 surveys_enabled = FALSE,
 record_autonumbering_enabled = FALSE,
 xml = NULL,
 ...
)
## S3 method for class 'redcapApiConnection'
createRedcapProject(
 rcon,
 project_title,
 purpose = REDCAP_PROJECT_PURPOSE,
 purpose_other = NULL,
 is_longitudinal = FALSE,
 surveys_enabled = FALSE,
 record_autonumbering_enabled = FALSE,
 xml = NULL,
 ...
)

Arguments

Details

The user creating the project will automatically be added to the project as a user with full user privileges and a project-level API token, which could then be used for subsequent project-level API requests.

When the project is created, it will automatically be given all the project-level defaults just as if it had been created via the web user interface, such as automatically creating a single data collection instrument seeded with a single Record ID field and Form Status field, as well as (for longitudinal projects) one arm with one event.

If the user intends to populate the project with arms and events immediately after creating the project, it is recommended that override = TRUE be used in importArms and importEvents so that the default arm and event are removed.

The xml argument must be in CDISC ODM XML format. It may come from a REDCap Project XML export file from REDCap itself (see exportProjectXml() ), or may come from another system that is capable of exporting projects and data in CDISC ODM format. If the xml argument is used in the API request, it will use the XML to import its contents into the newly created project. This will not only create the project with the API request, but also to import all fields, forms, and project attributes (and events and arms, if longitudinal) as well as record data all at the same time.

Only users with a 64-character Super API Tokens can utilize this method (the standard API token is 32 characters). Users can only be granted a super token by a REDCap administrator (using the API Tokens page in the REDCap Control Center). Please be advised that users with a Super API Token can create new REDCap projects via the API without any approval needed by a REDCap administrator.

Value

Returns a character(1) the 32-character, project level API token assigned to the user that created the project. This token is intended to be used for further project configuration using the API.

See Also

exportProjectXml()

Examples

## Not run: 
# The token must be a 64-character token
super_token <- redcapConnection(url = "your_redcap_url", 
 token = "[64-character-super-api-token]")
 
# Create a new project 
createRedcapProject(super_token, 
 project_title = "New Project Name", 
 purpose = "Quality Improvement", 
 is_longitudinal = FALSE, 
 surveys_enabled = TRUE)
 
 
 
# Copy an existing project into a new project
unlockREDCap(connections = c(rcon = "token_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
 
xml_file <- tempfile(file.ext = ".xml")
exportProjectXml(rcon, 
 file = xml_file)
 
xml_text <- paste0(readLines(xml_file), collapse = " ")
createRedcapProject(super_token, 
 xml = xml_text)
## End(Not run)

Export and Import Users Assigned to Data Access Groups

Description

These methods enable the user to export existing assignments of users to Data Access Groups, or import new or updated assignments to the project.

Usage

exportUserDagAssignments(rcon, ...)
importUserDagAssignments(rcon, data, ...)
## S3 method for class 'redcapApiConnection'
exportUserDagAssignments(rcon, ...)
## S3 method for class 'redcapApiConnection'
importUserDagAssignments(rcon, data, ...)

Arguments

Details

When modifying existing assignments using the import method, the user must provide the unique user name and the group name. If the redcap_data_access_group column is not provided, the REDCap user will not be assigned to any group.

Value

exportUserDagAssignments method returns a data frame with two columns:

importUserDagAssignments invisibly returns the number of assignments imported.

Functions

• exportUserDagAssignments(): Export current User-DAG Assignments

• importUserDagAssignments(): Import new or modified User-DAG Assignments.

See Also

exportDags() ,
importDags() ,
deleteDags() ,
switchDag()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
# Export the current assignments
exportUserDagAssignments(rcon)
# Assign a user to a Data Access Group
ForImport <- data.frame(username = "user1", 
 redcap_data_access_group = "facility_one")
importUserDagAssigments(rcon, 
 data = ForImport)
 
# Assign a multiple users to a Data Access Group
ForImport <- data.frame(username = c("user1", "user2", "user3"), 
 redcap_data_access_group = c("facility_one", 
 "facility_one", 
 "facility_two"))
importUserDagAssigments(rcon, 
 data = ForImport)
 
# Remove a user from all Data Access Groups
ForImport <- data.frame(username = "user1", 
 redcap_data_access_group = NA_character_)
importUserDagAssigments(rcon, 
 data = ForImport)
## End(Not run)

Export, Import, Delete Data Access Groups from a Project

Description

These methods enable the user to export existing Data Access Groups, import new Data Access Groups, or delete Data Access Groups from a project.

Usage

exportDags(rcon, ...)
importDags(rcon, data, ...)
deleteDags(rcon, dags, ...)
## S3 method for class 'redcapApiConnection'
exportDags(rcon, ...)
## S3 method for class 'redcapApiConnection'
importDags(rcon, data, ...)
## S3 method for class 'redcapApiConnection'
deleteDags(rcon, dags, ...)

Arguments

Details

To import new data access groups, the user must provide a value for data_access_group_name with no value (NA) for unique_group_name.

To modify a group name, provide a new value for data_access_group_name with the associated unique_group_name. If unique_group_name is provided, it must match a value currently in the project.

Value

exportDags with the columns

importDags invisibly returns the number of Data Access Groups imported.

deleteDags invisibly returns the number of Data Access Groups deleted.

Functions

• exportDags(): Export Data Access Groups from a REDCap Project

• importDags(): Import Data Access Groups to a project.

• deleteDags(): Delete Data Access Groups from a project.

See Also

switchDag() ,
exportUserDagAssignments() ,
importUserDagAssignments()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
exportDags(rcon)
# Import a new Data Access Group
NewData <- data.frame(data_access_group_name = "New DAG Name", 
 unique_group_name = NA_character_)
importDags(rcon, 
 data = NewData)
 
# Modify an existing Data Access Group Name
# The user will need to match the unique_group_name to the existing DAGs
ChangeData <- data.frame(data_access_group_name = "Altered DAG Name", 
 unique_group_name = "new_dag_name")
importDags(rcon, 
 data = ChangeData)
 
# Delete a Data Access Group
deleteDags(rcon, 
 dags = c("new_dag_name"))
## End(Not run)

Delete Records from a Project

Description

These methods enable the user to delete records from a project.

Usage

deleteRecords(
 rcon,
 records,
 arm = NULL,
 instrument = NULL,
 event = NULL,
 repeat_instance = NULL,
 delete_logging = FALSE,
 ...
)
## S3 method for class 'redcapApiConnection'
deleteRecords(
 rcon,
 records,
 arm = NULL,
 instrument = NULL,
 event = NULL,
 repeat_instance = NULL,
 delete_logging = FALSE,
 ...
)

Arguments

Value

deleteRecords invisibly returns a character value giving the number of records deleted.

See Also

exportRecords() ,
importRecords() ,
exportRecordsTyped()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
 
# Delete records
deleteRecords(rcon, 
 records = c("1", "2"))
## End(Not run)

Drop Row Where Repeat Instrument Is NA

Description

Drops rows where the repeat instrument is NA. Returns a data frame of records where repeat instruments have a value.

Usage

dropRepeatingNA(Records, rcon, quiet = FALSE)

Arguments

See Also

exportRecordsTyped() ,
exportReportsTyped()

Export, Import, and Delete Event Settings

Description

These methods enable the user to export event settings, import new events, update settings for existing events, or delete events.

Usage

exportEvents(rcon, ...)
importEvents(rcon, data, override = FALSE, ...)
deleteEvents(rcon, events = NULL, ...)
## S3 method for class 'redcapApiConnection'
exportEvents(rcon, arms = NULL, ...)
## S3 method for class 'redcapApiConnection'
importEvents(rcon, data, override = FALSE, ...)
## S3 method for class 'redcapApiConnection'
deleteEvents(rcon, events = NULL, ...)

Arguments

Details

Exporting events is not supported for classical REDCap projects. If the user attempts to export arms for a classical project, a data frame will be returned with zero rows.

Additionally, in order for events to be exported, the project must be longitudinal, have at least one arm, and at least one event defined. When these conditions are not satifisfied, exportEvents will return a data frame with zero rows.

To import new events, the user must provide data with the unique_event_name set to NA (REDCap assigns the unique event name automatically from the user provided event_name).

To modify existing events, the user must provide the unique_event_name. The other fields in the data provided will overwrite the current values for the matching event.

Deleting events–whether by deleteEvents or importEvents with override = TRUE–is a destructive act that also deletes arms and records associated with the event. This is irreversible data loss. REDCap will only permit these actions to occur in projects in Development status.

Value

exportEvents returns a data frame with the columns:

importEvents invisibly returns the number of events added or modified.

deleteEvents invisibly returns the number of events deleted.

Functions

• exportEvents(): Export events from a REDCap project.

• importEvents(): Add events to a project or modify existing events.

• deleteEvents(): Delete events from a project.

See Also

exportMappings() ,
importMappings()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
# Export all events
exportEvents(rcon)
# Export events for a subset of arms
exportEvents(rcon, 
 arms = c(1, 3))
 
# Import new events
NewEvents <- data.frame(event_name = c("Event 1", 
 "Event 2"), 
 arm_num = c(1, 1))
importEvents(rcon, 
 data = NewEvents)
 
# Modify existing events
UpdateEvents <- data.frame(event_name = "Event 2 New Name", 
 arm_num = 1, 
 unique_event_name = "event_2_arm_1", 
 custom_event_label = "The second visit")
importEvents(rcon, 
 data = UpdateEvents)
 
# Replace all events with a new set
NewEvents <- data.frame(event_name = c("Event 1", 
 "Event 2", 
 "Event 1"), 
 arm_num = c(1, 1, 2))
importEvents(rcon, 
 data = NewEvents, 
 override = TRUE)
 
# Delete events
deleteEvents(rcon, 
 events = c("event_1_arm_1", "event_1_arm_2"))
## End(Not run)

A helper function to export multiple records and forms using a single call.

Description

Exports records from multiple REDCap Databases using multiple calls to exportRecordsTyped()

Usage

exportBulkRecords(
 lcon,
 forms = NULL,
 envir = NULL,
 sep = "_",
 post = NULL,
 ...
)

Arguments

Value

Will return a named list of the resulting records if envir is NULL. Otherwise will assign them to the specified envir.

See Also

Other records exporting functions

exportRecordsTyped() ,
exportRecords() ,
exportReports()

Field validations and casting

fieldValidationAndCasting() ,
reviewInvalidRecords()

Post-processing functionality

recastRecords() ,
guessCast() ,
guessDate() ,
castForImport() ,
mChoiceCast() ,
splitForms() ,
widerRepeated()

Vignettes

vignette("redcapAPI-offline-connection")
vignette("redcapAPI-casting-data")
vignette("redcapAPI-missing-data-detection")
⁠vignette("redcapAPI-data-validation)⁠
⁠vignette("redcapAPI-faq)⁠

Examples

## Not run: 
unlockREDCap(c(test_conn = 'TestRedcapAPI',
 sandbox_conn = 'SandboxAPI'),
 keyring = 'MyKeyring',
 envir = globalenv(),
 url = 'https://<REDCAP_URL>/api/')
# After user interaction to unlock the local encrypted keyring
# the global environment will contain the REDCap connections
# `test_conn` and `sandbox_conn`
#
# Next the user wants to bulk specify importing all the forms
# of interest and post process
exportBulkRecords(
 rcon = list(test = test_conn,
 sand = sandbox_conn),
 forms = list(test = c('form1', 'form2'),
 envir = globalenv(),
 post = function(Records, rcon)
 {
 Records |>
 mChoiceCast(rcon) |>
 guessDat(rcon) |>
 widerRepeating(rcon)
 }
 )
# The environment now contains the data.frames: `test.form1`, `test.form2`, `sand`.
# Each of these were retrieved, possibly using the forms argument and all were
# post processed in the same manner as specified by `post`.
## End(Not run)

A helper function to export data queries from the Data Quality REDCap module.

Description

Exports Data Quality queries by record. The Data Quality module must be enabled on the Control Center of REDCap to use this function. Additionally, this module must be enabled on each project before it can be used.

Usage

exportDataQuality(rcon, prefix, ...)

Arguments

Export Codebook Mappings for Fields with External Dependencies

Description

These methods enable redcapAPI to obtain a mapping of codes and associated labels for fields that have external dependencies. The fields include SQL fields (dependent on another project) or fields that utilize the BioPortal Ontology modules.

Usage

exportExternalCoding(rcon, fields, ...)
## S3 method for class 'redcapApiConnection'
exportExternalCoding(rcon, fields = NULL, ..., batch_size = 1000)

Arguments

Details

These methods operate by executing two API calls to export first the coded values and then the labeled values of fields with external dependencies. The two exports are then used to generate the code-label mappings for use in casting data.

Fields of type sql are dropdown fields that are populated by a SQL query to another project.

Fields of type bioportal are text fields that have the BioPortal Ontology module enabled as the validation method.

Value

Returns a named list of named character vectors.

Each element is in the list is named for the field it maps.

The character vectors are name-value pairs where the name is the labeled data and the value is the coded data.

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
 
exportExternalCoding(rcon)
## End(Not run)
 

Export the Complete Field Names for a REDCap Project

Description

This method enables the user to access the complete field names utilized during export and import methods. These are expecially relevant when working with checkbox fields.

Usage

exportFieldNames(rcon, ...)
## S3 method for class 'redcapApiConnection'
exportFieldNames(rcon, fields = character(0), ...)

Arguments

Details

exportFieldNames returns a data frame of the field names the user may use when performing export and import functions. This is most useful when working with checkbox fields, which have a different field name than the one used in the Meta Data. The exported/imported field names for checkbox fields have the pattern ⁠[field_name]___[coded_checkbox_value]⁠ (there are exactly three underscores separating the field name and the coded value).

Fields of types "calc", "file", and "descriptive" are not included in the export. (Signature fields also have the "file" type and are not included)

Value

exportFieldNames returns a data frame with the columns:

See Also

exportMetaData() ,
importMetaData() ,
exportInstruments() ,
exportMappings() ,
importMappings() ,
exportPdf()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
# Export all of the field names
exportFieldNames(rcon)
# Export MetaData for a specific field
exportFieldNames(rcon, 
 fields = "checkbox_test")
## End(Not run)

Export a Listing of Folders and Files in the File Repository

Description

This method enables the user to export a list of folders and files saved to the File Repository. The listing may optionally include contents of subfolders.

Usage

exportFileRepositoryListing(
 rcon,
 folder_id = numeric(0),
 recursive = FALSE,
 ...
)
## S3 method for class 'redcapApiConnection'
exportFileRepositoryListing(
 rcon,
 folder_id = numeric(0),
 recursive = FALSE,
 ...
)

Arguments

Value

Returns a data frame with the columns

See Also

exportFromFileRepository() ,
importToFileRepository() ,
deleteFromFileRepository() ,
exportFileRepository() ,
importFileRepository() ,
deleteFileRepository() ,
createFileRepositoryFolder()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
 
# Export the top-level listing of the File Repository
exportFileRepositoryListing(rcon)
# Export the complete listing of the File Repository
exportFileRepositoryListing(rcon, 
 recursive = TRUE)
 
# Export the listing of a subfolder in the File Repository
exportFileRepositoryListing(rcon, 
 folder_id = 12345)
## End(Not run)

Export Multiple Files From a Project

Description

This method enables the user to export multiple files from a REDCap project with a single call. The REDCap API only allows for one file to be exported per call, and the exportFiles() methods are written to mirror that limitation. This extension allows the user to pass vectors of arguments for records, fields, events, or repeat instances. Files that can be matched to any combination of these values will be exported.

Usage

exportFilesMultiple(
 rcon,
 record,
 field,
 event = NULL,
 dir,
 file_prefix = TRUE,
 ...
)
## S3 method for class 'redcapApiConnection'
exportFilesMultiple(
 rcon,
 record,
 field,
 event = NULL,
 dir,
 file_prefix = TRUE,
 repeat_instance = NULL,
 ...,
 quiet = TRUE
)

Arguments

Details

exportFilesMultiple will construct all combinations of the record, field, event, and repeat_instance arguments and attempt to export the file associated with each combination. Should any of these combinations produce an error (for example, if a record does not have a third repeat instance), the error is captured and returned with the output.

Value

Invisibly returns a data.frame with the following columns:

See Also

exportFiles()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"),
 url = "your_redcap_url",
 keyring = "API_KEYs",
 envir = globalenv())
save_to_dir <- tempdir()
# Export files for multiple records
# Results are returned invisibly - saving to an object is
# helpful to be able to view the results
Export <-
 exportFilesMultiple(rcon,
 record = 1:4,
 field = "file_upload_field",
 event = "event_1_arm_1",
 dir = save_to_dir)
Export
# Export files for multiple instances
Export <-
 exportFilesMultiple(rcon,
 record = 1,
 field = "file_upload_field",
 event = "event_1_arm_1",
 repeat_instance = 1:4,
 dir = save_to_dir)
Export
# Export files for multiple records, fields, events, and instances
Export <-
 exportFilesMultiple(rcon,
 record = 1:10,
 field = c("registration", "waiver"),
 events = c("event_1_arm_1", "event_2_arm_1"),
 repeat_instance = 1:3,
 dir = save_to_dir)
Export
## End(Not run)

Export Instruments Defined in a Project

Description

These methods enable the user to view the instruments defined in the project.

Usage

exportInstruments(rcon, ...)
## S3 method for class 'redcapApiConnection'
exportInstruments(rcon, ...)

Arguments

Value

Returns a data frame with the columns:

See Also

exportMetaData() ,
importMetaData() ,
exportInstruments() ,
exportMappings() ,
importMappings() ,
exportPdf()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
 
exportInstruments(rcon)
## End(Not run)

Export Logging Records

Description

These methods enable to user to export the logging (audit trail) of all changes made to a project, including data exports, data changes, project metadata changes, modification of user rights, etc.

Usage

exportLogging(
 rcon,
 logtype = character(0),
 user = character(0),
 record = character(0),
 dag = character(0),
 beginTime = as.POSIXct(character(0)),
 endTime = as.POSIXct(character(0)),
 batchInterval = NULL,
 ...
)
## S3 method for class 'redcapApiConnection'
exportLogging(
 rcon,
 logtype = character(0),
 user = character(0),
 record = character(0),
 dag = character(0),
 beginTime = as.POSIXct(character(0)),
 endTime = as.POSIXct(character(0)),
 batchInterval = NULL,
 ...
)

Arguments

Value

Returns a data frame with columns

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
 
# Export all of the logging events 
exportLogging(rcon)
 
# Export all of the events for record '2'
exportLogging(rcon, 
 record = "2")
 
# Export all of the events where a record was deleted
exportLoging(rcon, 
 logtype = "record_delete")
## End(Not run)

Export PDF file of Data Collection Instruments

Description

These methods allow the user to download PDF files of data collection instruments. The download may be with or without collected data; and may return a single record, multiple records, or all records.

Usage

exportPdf(
 rcon,
 dir,
 filename = "redcap_forms_download",
 record = NULL,
 events = NULL,
 instruments = NULL,
 all_records = FALSE,
 ...
)
## S3 method for class 'redcapApiConnection'
exportPdf(
 rcon,
 dir,
 filename = "redcap_forms_download",
 record = NULL,
 events = NULL,
 instruments = NULL,
 all_records = FALSE,
 ...
)

Arguments

Details

These methods mimics the behavior of "Download PDF of Instruments" button on the REDCap user interface. They permit the user to export a PDF file for:

1. A single collection instrument (blank)c

2. All instruments (blank)

3. A single instrument (with data from a single record)c

4. All instruments (with data from a single record)

5. All instruments (with data from all records)

Value

exportPdf invisibly returns the location on the local system to whihc the files is saved.

See Also

exportMetaData() ,
importMetaData() ,
exportFieldNames() ,
exportInstruments() ,
exportMappings() ,
importMappings()

Export Entire Project as REDCap XML File

Description

These methods enable the user to export a project's settings as an XML file in CDISC ODM format. This file may be used to transfer the project to another project, REDCap instance, or any other CDISC ODM compliant database.

Usage

exportProjectXml(
 rcon,
 file,
 return_metadata_only = TRUE,
 records = NULL,
 fields = NULL,
 events = NULL,
 survey = FALSE,
 dag = FALSE,
 export_files = FALSE,
 ...
)
## S3 method for class 'redcapApiConnection'
exportProjectXml(
 rcon,
 file,
 return_metadata_only = TRUE,
 records = NULL,
 fields = NULL,
 events = NULL,
 survey = FALSE,
 dag = FALSE,
 export_files = FALSE,
 ...
)

Arguments

Details

The entire project (all records, events, arms, instruments, fields, and project attributes) can be downloaded as a single XML file, which is in CDISC ODM format (ODM version 1.3.1). This XML file can be used to create a clone of the project (including its data, optionally) on this REDCap server or on another REDCap server (it can be uploaded on the Create New Project page). Because it is in CDISC ODM format, it can also be used to import the project into another ODM-compatible system.

When the return_metadata_only parameter is set to FALSE, the Data Export user rights will be applied to any data returned. For example, if the user has 'De-Identified' or 'Remove All Identifier Fields' data export rights, then some data fields might be removed and filtered out of the data set. To make sure that no data is unnecessarily filtered out of the API request, the user should have 'Full Data Set' export rights in the project.

See Also

createRedcapProject()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "token_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
 
xml_file <- tempfile(file.ext = ".xml")
exportProjectXml(rcon, 
 file = xml_file)
## End(Not run)
 
 

Export the REDCap data as a SAS importable set of files.

Description

This creates a csv for each form and a SAS script that will load all the data into SAS.

Usage

exportSAS(rcon, directory = NULL, ...)

Arguments

Details

This function is experimental and needs feedback/suggestions to flesh it out fully. If this feature is important to you, please consider opening an issue on github to suggest improvements.

This function relies on exportBulkRecords to do the bulk of the export before formatting for SAS. ... are supplied to exportBulkRecords so full user inversion of control still applies.

Value

A vector of exported data set names.

See Also

exportBulkRecords()

Examples

## Not run: 
exportSAS(rcon)
## End(Not run)

Export the REDCap Version Number

Description

These methods enable the user to export the REDCap instance version number.

Usage

exportVersion(rcon, ...)
## S3 method for class 'redcapApiConnection'
exportVersion(rcon, ...)

Arguments

Value

Returns a character value giving the version number.

IF this function is used in a version of REDCap that does not support the method (prior to version 6.0.0), the value "5.12.2" will be returned. This is done solely for the convenience of always returning a value that can be compared against other versions.

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
 
# Export the version number
exportVersion(rcon)
## End(Not run)

Functions for Casting Fields After Export (Post Processing)

Description

The functions provided here allow for recasting fields after records have been exported. They generally have a similar interface to the casting strategy of exportRecordsTyped() , though they may not each offer all the same options.

Usage

recastRecords(
 data,
 rcon,
 fields,
 cast = list(),
 suffix = "",
 warn_zero_coded = TRUE
)
castForImport(
 data,
 rcon,
 fields = NULL,
 na = list(),
 validation = list(),
 cast = list(),
 warn_zero_coded = TRUE
)
guessCast(
 data,
 rcon,
 na = isNAorBlank,
 validation,
 cast,
 quiet = FALSE,
 threshold = 0.8
)
guessDate(
 data,
 rcon,
 na = isNAorBlank,
 validation = valRx("^[0-9]{1,4}-(0?[1-9]|1[012])-(0?[1-9]|[12][0-9]|3[01])$"),
 cast = function(x, ...) as.POSIXct(x, format = "%Y-%m-%d"),
 quiet = FALSE,
 threshold = 0.8
)
mChoiceCast(data, rcon, style = "labelled", drop_fields = TRUE)

Arguments

Details

recastRecords is a post-processing function motivated initially by the need to switch between codes and labels in multiple choice fields. Field types for which no casting function is specified will be returned with no changes. It will not attempt to validate the content of fields; fields that cannot be successfully cast will be quietly returned as missing values.

castForImport is written with defaults that will return data in a format ready to be imported to a project via importRecords. All fields are returned as character vectors. If any values fail to validation check, are report is returned as an attribute named invalid. This attribute may be retrieved using reviewInvalidRecords() . These are then set to NA, which will be imported as blanks through the API.

guessCast is a helper function to make a guess at casting uncast columns. It will do a type cast if a validation is met above a threshold ratio of non-NA records. It modifies the existing invalid attribute to reflect the cast. This attribute may be retrieved using reviewInvalidRecords() . guessDate is a special cast of guessCast that has defaults set for casting a date field.

mChoiceCast is a helper function that adds the Hmisc::mChoice multiple choice class. It adds a column for a multiple choice checkbox that is cast to the Hmisc::mChoice class. Requires Hmisc to be loaded.

Zero-Coded Check Fields

A zero-coded check field is a field of the REDCap type checkbox that has a coding definition of ⁠0, [label]⁠. When exported, the field names for these fields is ⁠[field_name]___0⁠. As in other checkbox fields, the raw data output returns binary values where 0 represent an unchecked box and 1 represents a checked box. For zero-coded checkboxes, then, a value of 1 indicates that 0 was selected.

This coding rarely presents a problem when casting from raw values (as is done in exportRecordsTyped). However, casting from coded or labeled values can be problematic. In this case, it becomes indeterminate from context if the intent of 0 is 'false' or the coded value '0' ('true') ...

The situations in which casting may fail to produce the desired results are

Because of the potential for miscast data, casting functions will issue a warning anytime a zero-coded check field is encountered. A separate warning is issued when a field is cast from coded or labeled values.

When casting from coded or labeled values, it is strongly recommended that the function castCheckForImport() be used. This function permits the user to state explicitly which values should be recognized as checked, avoiding the ambiguity resulting from the coding.

See Also

Exporting records

exportRecordsTyped() ,
exportReportsTyped() ,
fieldValidationAndCasting() ,
reviewInvalidRecords()

Other Post Processing Functions

splitForms() ,
widerRepeated()

Vignettes

vignette("redcapAPI-offline-connection", package = "redcapAPI")
vignette("redcapAPI-casting-data")
vignette("redcapAPI-missing-data-detection")
⁠vignette("redcapAPI-data-validation)⁠

Examples

## Not run: 
# Using recastRecords after export
Recs <-
 exportRecordsTyped(rcon) |>
 recastRecords(rcon,
 fields = "dropdown_test",
 cast = list(dropdown = castCode))
# Using castForImport
castForImport(Records,
 rcon)
# Using castForImport to recast zero-coded checkbox values
castForImport(Records,
 rcon,
 cast = list(checkbox = castCheckForImport(c("0", "Unchecked"))))
# Using guessCast
exportRecordsTyped(rcon,
 validation=skip_validation,
 cast = raw_cast) |>
 guessCast(rcon,
 validation=valRx("^[0-9]{1,4}-(0?[1-9]|1[012])-(0?[1-9]|[12][0-9]|3[01])$"),
 cast=as.Date,
 threshold=0.6)
# Using mChoiceCast
exportRecordsTyped(rcon) |>
 mChoiceCast(rcon)
## End(Not run)

Split a Field Choice Mapping Into a Two Column Matrix

Description

Uses the string from the select_choices_or_calculations for the meta data to create a matrix of codes and their mapped labels.

Usage

fieldChoiceMapping(object, field_name, ...)
## S3 method for class 'character'
fieldChoiceMapping(object, field_name, ...)
## S3 method for class 'redcapApiConnection'
fieldChoiceMapping(object, field_name, ...)

Arguments

Value

Returns a matrix with two columns, choice_value and choice_label

Convert a REDCap Data Field to an R Vector

Description

Converts a field exported from REDCap into a valid R vector

Usage

fieldToVar(
 records,
 meta_data,
 factors = TRUE,
 dates = TRUE,
 checkboxLabels = FALSE,
 labels = TRUE,
 handlers = list(),
 mChoice = NULL,
 ...
)

Arguments

Details

This function is called internally by exportRecords and exportReports. it is not available to the user.

Helper functions for exportRecordsTyped Validation and Casting

Description

This set of functions assists in validating that the content of fields coming from REDCap match the MetaData, allowing for a validation report to provided. The cast helpers allow for transforming the REDCap data into R data types and allowing the user to customize the end product.

Usage

isNAorBlank(x, ...)
valRx(rx)
valChoice(x, field_name, coding)
valPhone(x, field_name, coding)
valSkip(x, field_name, coding)
na_values(FUN)
castLabel(x, field_name, coding)
castLabelCharacter(x, field_name, coding)
castCode(x, field_name, coding)
castCodeCharacter(x, field_name, coding)
castRaw(x, field_name, coding)
castChecked(x, field_name, coding)
castCheckedCharacter(x, field_name, coding)
castCheckLabel(x, field_name, coding)
castCheckLabelCharacter(x, field_name, coding)
castCheckCode(x, field_name, coding)
castCheckCodeCharacter(x, field_name, coding)
castCheckForImport(checked = c("Checked", "1"))
castDpNumeric(dec_symbol = ",")
castDpCharacter(n_dec, dec_symbol = ",")
castTimeHHMM(x, field_name, coding)
castTimeMMSS(x, field_name, coding)
castLogical(x, field_name, coding)
raw_cast
default_cast_no_factor
default_cast_character
skip_validation

Arguments

Format

An object of class list of length 21.

An object of class list of length 25.

An object of class list of length 25.

An object of class list of length 21.

Details

Functions passed to the na, validation, and cast parameter of exportRecordsTyped() all take the form of ⁠function(x, coding, field_name)⁠. na and validation functions are expected to return a logical vector of the same length as the column processed. Helper routines are provided here for common cases to construct these functions.

Missing Data Detection

na_values is a helper function to create a list of functions to test for NA based on field type. Useful for bulk override of NA detection for a project. The output can be directly passed to the na parameter of exportRecordsTyped() .

Missing data detection is performed ahead of validation. Data that are found to be missing are excluded from validation reports.

REDCap users may define project-level missing value codes. If such codes are defined, they can be seen in Project Setup > Additional Customizations > Missing Data Codes. They will also be displayed in the project's Codebook. Project-level missing data codes cannot be accessed via the API, meaning redcapAPI is unable to assist in determining if a project has any. The most likely symptom of project-level codes is a high frequency of values failing validation (See vignette("redcapAPI-missing-data-detection")).

Validation Functions

isNAorBlank returns TRUE/FALSE if field is NA or blank. Helper function for constructing na overrides in exportRecordsTyped() .

valRx constructs a validation function from a regular expression pattern. The function returns a TRUE/FALSE if the value matches the pattern.

valChoice constructs a validation function from a set of choices defined in the MetaData. The functions returns a TRUE/FALSE if the value matches one of the choices.

valPhone constructs a validation function for (North American) phone numbers. It removes punctuation and spaces prior to validating with the regular expression.

valSkip is a function that supports skipping the validation for a field type. It returns a TRUE value for each record, regardless of its value. Validation skipping has occasional utility when importing certain field types (such as bioportal or sql) where not all of the eventual choices are available in the project yet.

skip_validation is a list of functions that just returns TRUE for all data passed in.

Casting Functions

castLabel constructs a casting function for multiple choice variables. The field will be cast to return the choice label (generally more human readable). castLabelCharacter is an equivalent casting function that returns a character vector instead of a factor.

castCode constructs a casting function for multiple choice variables. Similar to castLabel, but the choice value is returned instead. The values are typically more compact and their meaning may not be obvious. castCodeCharacter is an equivalent casting function that retuns a character vector instead of a factor.

castRaw constructs a casting function that returns the content from REDCap as it was received. It is functionally equivalent to identity. For multiple choice variables, the result will be coerced to numeric, if possible; otherwise, the result is character vector.

castChecked constructs a casting function for checkbox fields. It returns values in the form of Unchecked/Checked. castCheckedCharacter is an equivalent casting function that returns a character vector instead of a factor.

castCheckLabel and castCheckCode also construct casting functions for checkbox fields. For both, unchecked variables are cast to an empty string (""). Checked variables are cast to the option label and option code, respectively. castCheckLabelCharacter and castCheckCodeCharacter are equivalent casting functions that returns a character vector instead of a factor.

castCheckForImport is a special case function to allow the user to specify exactly which values are to be considered "Checked". Values that match are returned as 1 and all other values are returned as 0. This is motivated by the special case where the coding on a checkbox includes "0, Option". In the resulting field checkbox___0, a coded value of 0 actually implies the choice was selected. In order to perform an import on such data, it is necessary to cast it using castCheckForImport(c("0")).

castDpNumeric is a casting function for fields that use the number_ndp_comma field type (where n is the number of decimal places). This function will convert the values to numeric values for use in analysis. This is a function that returns the appropriate casting function, thus the appropriate usage when using the defaults is cast = list(number_1dp_comma = castDpNumeric()) (using the parentheses).

castDpCharacter is a casting function to return fields that use number_ndp_comma field types to character strings for import. This is a function that returns the appropriate casting function, thus the appropriate usage when casting for one decimal place is cast = list(number_1dp_comma = castDpCharacter(1)).

castTimeHHMM and castTimeMMSS are casting functions to facilitate importing data. They convert time data into a character format that will pass the API requirements.

castLogical is a casting function that returns a logical vector for common, binary-type responses. It is well suited to changing true/false, yes/no, and checkbox fields into logical vectors, as it returns TRUE if the value is one of c("1", "true", "yes") and returns FALSE otherwise.

Casting Lists

raw_cast overrides all casting if passed as the cast parameter. It is important the the validation specified matches the chosen cast. For fully raw it should be skip_validation.

default_cast_no_factor is a list of casting functions that matches all of the default casts but with the exception that any fields that would have been cast to factors will instead be cast to characters. It is provided for the user that prefers to work absent factors. The list default_cast_character is equivalent and is provided for those that prefer to describe their casting in terms of what the result is (and not what it is not).

Value

Validation and casting functions return the objects indicated in the following table:

See Also

fieldCastingFunctions() ,
exportRecordsTyped() ,
exportReportsTyped()

Vignettes

vignette("redcapAPI-casting-data")
vignette("redcapAPI-missing-data-detection")
⁠vignette("redcapAPI-data-validation)⁠
⁠vignette("redcapAPI-faq)⁠

Examples

## Not run: 
# Make a custom function to give special treatment to a field.
# In this function, the field "field_name_to_skip" will 
# be cast using `castRaw`. All other fields will be cast 
# using `castCode`
customCastCode <- function(x, field_name, coding){
 if (field_name == "field_name_to_skip"){
 castRaw(x, field_name, coding)
 } else {
 castCode(x, field_name, coding)
 }
}
## End(Not run)

Export, Import, or Delete Files to a Field in a REDCap Project

Description

These methods enable to the user to export a file stored in a project field, import a file, or delete an existing file.

Usage

exportFiles(
 rcon,
 record,
 field,
 event = NULL,
 dir = getwd(),
 file_prefix = TRUE,
 ...
)
importFiles(
 rcon,
 file,
 record,
 field,
 event,
 overwrite = TRUE,
 repeat_instance = NULL,
 ...
)
deleteFiles(rcon, record, field, event, ...)
## S3 method for class 'redcapApiConnection'
exportFiles(
 rcon,
 record,
 field,
 event = NULL,
 dir = getwd(),
 file_prefix = TRUE,
 repeat_instance = NULL,
 ...
)
## S3 method for class 'redcapApiConnection'
importFiles(
 rcon,
 file,
 record,
 field,
 event = NULL,
 overwrite = TRUE,
 repeat_instance = NULL,
 ...
)
## S3 method for class 'redcapApiConnection'
deleteFiles(
 rcon,
 record = NULL,
 field = NULL,
 event = NULL,
 repeat_instance = NULL,
 ...
)

Arguments

Details

These functions only export, import, or delete a single file.

When exporting, the file name cannot be changed; whatever name exists in REDCap is the name that will be used. The record ID and event name may be appended as a prefix.

Value

exportFiles invisibly returns the file path to which the exported file was saved.

importFiles invisibly returns TRUE when successful, or throws an error if the import failed.

deleteFiles invisible returns TRUE when successful, or throws an error if the deletion failed.

Functions

• exportFiles(): Export a file from a REDCap project.

• importFiles(): Import a file to a REDCap project.

• deleteFiles(): Delete a file from a REDCap project.

See Also

exportFilesMultiple() ,
importFileToRecord() (can create a record to receive the file if it does yet exist)

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
save_to_dir <- tempdir() 
# Export a file
exportFiles(rcon, 
 record = 1, 
 field = "file_upload_test", 
 dir = save_to_dir)
 
# Export a file for a specific event
exportFiles(rcon, 
 record = 1, 
 field = "file_upload_test",
 event = "event_1_arm_1", 
 dir = save_to_dir)
# Import a file 
importFiles(rcon,
 file = "file_to_upload.txt" 
 record = 1, 
 field = "file_upload_test")
 
# Delete a file
deleteFiles(rcon, 
 record = 1, 
 field = "file_upload_test")
## End(Not run)

Export, Import, or Delete Multiple Files from the File Repository

Description

These methods enable the user to export, import, or delete entire folders of files from the file repository. These actions may be done recursively to include subfolders as well.

Usage

exportFileRepository(
 rcon,
 folder_id,
 dir = getwd(),
 dir_create = FALSE,
 recursive = FALSE,
 ...
)
importFileRepository(rcon, dir, folder_id = numeric(0), ...)
deleteFileRepository(rcon, folder_id, recursive = FALSE, ...)
## S3 method for class 'redcapApiConnection'
exportFileRepository(
 rcon,
 folder_id = numeric(0),
 dir = getwd(),
 dir_create = FALSE,
 recursive = FALSE,
 ...
)
## S3 method for class 'redcapApiConnection'
importFileRepository(
 rcon,
 dir,
 folder_id = numeric(0),
 dag_id = numeric(0),
 role_id = numeric(0),
 recursive = FALSE,
 ...
)
## S3 method for class 'redcapApiConnection'
deleteFileRepository(
 rcon,
 folder_id,
 recursive = FALSE,
 ...,
 confirm = c("ask", "no", "yes")
)

Arguments

Details

deleteFileRepository will only delete files and cannot delete folders.

Deleted files will remain in the recycling bin for up to 30 days.

Value

exportFileRepository returns a data frame with the locations to which the files were saved on the local system. It has the columns:

importFileRepository returns a data frame with the locations to which the files were saved on the local system. It has the columns:

deleteFileRepository returns a data frame listing the files that were deleted from the file repository. It has the columns:

Functions

• exportFileRepository(): Export multiple files from the File Repository.

• importFileRepository(): Import multiple files to the File Repository.

• deleteFileRepository(): Delete multiple files from the File Repository.

See Also

exportFromFileRepository() ,
importToFileRepository() ,
deleteFromFileRepository() ,
exportFileRepositoryListing() ,
createFileRepositoryFolder()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
 
save_location <- tempdir()
# Export the top-level file repository folder
exportFileRepository(rcon, 
 folder_id = numeric(0), 
 dir = save_location)
 
# Export the entire repository 
exportFileRepository(rcon, 
 folder_id = numeric(0), 
 dir = save_location, 
 recursive = TRUE)
 
# Export a file repository folder below the top-level
exportFileRepository(rcon, 
 folder_id = 12345, 
 dir = save_location)
 
# Import the files from a folder to the top-level file repository
importFileRepository(rcon, 
 dir = "path/to/folder")
 
# Import the files from a folder to sub folder of the file repository
importFileRepository(rcon, 
 dir = "path/to/folder", 
 folder_id = 12345) 
 
# Import the files from a folder and assign to a specific 
# Data Access Group
importFileRepository(rcon, 
 dir = "path/to/folder", 
 dag_id = 789) 
 
# Delete files from the top-level folder of the file repository
deleteFileRepository(rcon, 
 folder_id = numeric(0))
 
# Delete all the file sfrom the file repository
deleteFileRepository(rcon, 
 folder_id = numeric(0), 
 recursive = TRUE) 
## End(Not run)

Reconstruct the file repository path

Description

Reconstruct the file repository path

Usage

fileRepositoryPath(doc_id = numeric(0), folder_id = numeric(0), fileRepo)

Arguments

Remove Rows Containing Only Missing Values

Description

Evaluates each row of a data frame for missingness. If all fields (excluding the identifying fields) are missing, the row is removed from the data. For the purpose of this function, redcap_data_access_group is considered an identifying field.

Usage

filterEmptyRow(data, rcon)

Arguments

See Also

exportRecordsTyped() ,
exportReportsTyped()

Export, Import, and Delete Individual Files from the File Repository

Description

These methods enable the user to export, import, or delete individual files from a REDCap project's file repository.

Usage

exportFromFileRepository(rcon, doc_id, dir = getwd(), dir_create = FALSE, ...)
importToFileRepository(rcon, file, folder_id = numeric(0), ...)
deleteFromFileRepository(rcon, doc_id, ...)
## S3 method for class 'redcapApiConnection'
exportFromFileRepository(rcon, doc_id, dir = getwd(), dir_create = FALSE, ...)
## S3 method for class 'redcapApiConnection'
importToFileRepository(rcon, file, folder_id = numeric(0), ...)
## S3 method for class 'redcapApiConnection'
deleteFromFileRepository(rcon, doc_id, ...)

Arguments

Details

When a file is deleted, the file will remain in the Recycle Bin folder for up to 30 days.

Value

exportFromFileRepository, importToFileRepository, and deleteFromFileRepository each return a data frame with the columns:

Functions

• exportFromFileRepository(): Export a file from the file repository.

• importToFileRepository(): Import a file to the file repository.

• deleteFromFileRepository(): Delete a file from the file repository.

See Also

exportFileRepository() ,
importFileRepository() ,
deleteFileRepository() ,
exportFileRepositoryListing() ,
createFileRepositoryFolder()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
 
 
write_to_path <- tempdir() 
 
# Export a file from the repository
exportFromFileRepository(rcon, 
 doc_id = 12345, 
 dir = write_to_path)
 
# Export a file and create the target directory if it does not exist
exportFromFileRepository(rcon, 
 doc_id = 12345, 
 dir = write_to_path, 
 dir_create = TRUE)
 
# Import a file to the top-level directory of the file repository
importFileToRepository(rcon, 
 file = "file_to_import.txt")
 
# Import a file to a specific directory of the file repository
importFileToRepository(rcon, 
 file = "file_to_import.txt", 
 folder_id = 678)
 
# Delete a file from the file repository
deleteFileFromRepository(rcon, 
 doc_id = 12345)
## End(Not run)
 

Return a vector of the Project ID Fields

Description

Returns a character vector listing the project ID fields. This will be at most a vector of length two. The first element will be the first field in the meta data. The second, if provided, will be the name of the secondary unique field specified in the project.

Usage

getProjectIdFields(rcon)

Arguments

Value

Returns a character vector with the field names that uniquely identify an experimental unit.

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"),
 url = "your_redcap_url",
 keyring = "API_KEYs",
 envir = globalenv())
getProjectIdFields(rcon)
## End(Not run)

Import a File With Option to Create A Record to Receive the File

Description

There are times when the user may desire to create a record and import a file as part of a single action. For example, a study consent form may have been collected and needs to be stored with the data of the new study participant. importFileToRecord extends importFiles to allow the concurrent creation of the record in which the file will be stored.

Usage

importFileToRecord(
 rcon,
 file,
 record = NULL,
 field,
 event,
 overwrite = TRUE,
 repeat_instance = NULL,
 ...
)

Arguments

Details

The behavior of importFileToRecord depends on

1. whether record auto numbering has been enabled in the project,

2. if the record is specified by the user

3. if the record specified by the user exists.

The following table details the actions taken based on these conditions. (force_auto_number is an argument to importRecords() ).

See Also

importFiles() ,
importRecords()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
importFileToRecord(rcon,
 file = "file_to_upload.txt" 
 record = NULL, 
 field = "file_upload_test")
## End(Not run)
 

Import Records to a Project

Description

These methods enable the user to import new records or update existing records to a project.

Usage

importRecords(
 rcon,
 data,
 overwriteBehavior = c("normal", "overwrite"),
 returnContent = c("count", "ids", "nothing", "auto_ids"),
 returnData = FALSE,
 logfile = "",
 ...
)
## S3 method for class 'redcapApiConnection'
importRecords(
 rcon,
 data,
 overwriteBehavior = c("normal", "overwrite"),
 returnContent = c("count", "ids", "nothing", "auto_ids"),
 returnData = FALSE,
 logfile = "",
 force_auto_number = FALSE,
 ...,
 batch.size = -1
)

Arguments

Details

importRecords prevents the most common import errors by testing the data before attempting the import. Namely

1. Check that all variables in data exist in the REDCap data dictionary.

2. Check that the record id variable exists

3. Force the record id variable to the first position in the data frame (with a warning)

4. Remove calculated fields (with a warning)

5. Verify that REDCap date fields are represented in the data frame as either character, POSIXct, or Date class objects.

6. Determine if values are within their specified validation limits.

See the documentation for validateImport() for detailed explanations of the validation.

A 'batched' import is one where the export is performed over a series of API calls rather than one large call. For large projects on small servers, this may prevent a single user from tying up the server and forcing others to wait on a larger job.

BioPortal Fields

Text fields that are validation enabled using the BioPortal Ontology service may be imported by providing the coded value. Importing the coded value does not, however, guarantee that the labeled value will be immediately available. Labels for BioPortal values are cached on the REDCap server in a process that occurs when viewing data in the user interface. Thus, if the label has not be previously cached on the server, the code will be used to represent both the code and the label.

Value

importRecords, when returnData = FALSE, returns the content from the API response designated by the returnContent argument.

importRecords, when returnData = TRUE, returns the data frame that was internally prepared for import. This data frame has values transformed from R objects to character values the API will accept.

See Also

exportRecords() ,
deleteRecords() ,
exportRecordsTyped()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"),
 url = "your_redcap_url",
 keyring = "API_KEYs",
 envir = globalenv())
# Import records
NewData <- data.frame(record_id = c(1, 2, 3),
 age = c(27, 43, 32),
 date_of_visit = rep(Sys.Date(), 3))
importRecords(rcon,
 data = NewData)
# Import records and save validation info to a file
NewData <- data.frame(record_id = c(1, 2, 3),
 age = c(27, 43, 32),
 date_of_visit = rep(Sys.Date(), 3))
importRecords(rcon,
 data = NewData,
 logfile = "import-validation-notes.txt")
## End(Not run)

Helper functions for formatting validation failure report

Description

exportRecordsTyped() may have an invalid attribute if validations fail. This data has some routines which help locate the failing records.

Usage

## S3 method for class 'invalid'
format(x, ...)
## S3 method for class 'invalid'
print(x, ...)
## S3 method for class 'invalid'
summary(object, ...)

Arguments

Examples

## Not run: 
rcon <- redcapConnection(url=[YOUR_REDCAP_URL], token=[API_TOKEN])
rec <- exportRecordsTyped(rcon)
attr(rec, "invalid")
## End(Not run)

Identify Check Fields with a Zero Coded Option

Description

Check fields that have 0 as a coding option can confuse certain data processing steps because it can be difficult to differentiate if a 0 value represents an unchecked or checked option. Identifying these fields is important to handling them correctly.

Usage

isZeroCodedCheckField(field_name)
warnOfZeroCodedCheckCasting(field_name, x)
warnZeroCodedFieldPresent(field_names, warn_zero_coded)

Arguments

Value

isZeroCodedCheckField returns a logical(1)

warnOfZeroCodedCheckCasting has no return and issues a warning if the field name appears to be zero-coded.

warnZeroCodedFieldPresent has no return and issues a warning if any of the fields passed appear to be zero-coded.

Zero-Coded Check Fields

A zero-coded check field is a field of the REDCap type checkbox that has a coding definition of ⁠0, [label]⁠. When exported, the field names for these fields is ⁠[field_name]___0⁠. As in other checkbox fields, the raw data output returns binary values where 0 represent an unchecked box and 1 represents a checked box. For zero-coded checkboxes, then, a value of 1 indicates that 0 was selected.

This coding rarely presents a problem when casting from raw values (as is done in exportRecordsTyped). However, casting from coded or labeled values can be problematic. In this case, it becomes indeterminate from context if the intent of 0 is 'false' or the coded value '0' ('true') ...

The situations in which casting may fail to produce the desired results are

Because of the potential for miscast data, casting functions will issue a warning anytime a zero-coded check field is encountered. A separate warning is issued when a field is cast from coded or labeled values.

When casting from coded or labeled values, it is strongly recommended that the function castCheckForImport() be used. This function permits the user to state explicitly which values should be recognized as checked, avoiding the ambiguity resulting from the coding.

Examples

## Not run: 
isZeroCodedCheckField("check_field___x")
isZeroCodedCheckField("check_field___0")
x <- factor(c(1, 0, 1, 0, 0),
 levels = 0:1)
warnOfZeroCodedCheckCasting(field_name = "check_field___0",
 x = x)
warnZeroCodedFieldPresent(c("check_field___x", "check_field___0"), TRUE)
## End(Not run)

Log event

Description

This is one of the more complex integration of services into the 'redcapAPI“ package. It's purpose is to provide the ability for a system administrator (or user) to integrate logging into a report or application. The ability to inject a logging framework without a developer's code being altered.

Usage

logEvent(severity, ...)
createSplunkFUN(
 token = Sys.getenv("SPLUNK_TOKEN"),
 url = Sys.getenv("SPLUNK_URL"),
 project = Sys.getenv("SPLUNK_PROJECT"),
 allowDebug = FALSE
)
logWarning(...)
logStop(...)
logMessage(...)

Arguments

Details

To do this the callback function is pulled from the option redcapAPI_logger which defaults to doing nothing.

When the package starts up, it checks to see if SPLUNK_TOKEN and SPLUNK_URL ENV variables are set and if so, it automatically redirects the redcapAPI_logger to point at Splunk. It will also use SPLUNK_PROJECT if defined, otherwise the project will be the directory name that the code is executing from.

There are also two helper functions logWarning and logStop which will call logging if enabled first, then warn or stop as requested.

The function createSplunkFUN will create a SPLUNK logger callback function. It will pull 'SPLUNK_TOKEN', 'SPLUNK_URL' and 'SPLUNK_PROJECT' from ENV if the corresponding arguments are not specified.

Examples

## Not run: 
 options(redcapAPI_logger=function(severity, ...) {cat(severity, ' ', dput(list(...)), '\n')})
 logEvent("INFO", "This is a logged event")
## End(Not run)

Make REDCap API Calls

Description

Constructs and executes API calls to the REDCap API. These are left deliberately abstract in order to be flexible enough to support the redcapAPI functions, but also allow users to execute calls for new REDCap features that are not yet implemented.

Usage

makeApiCall(
 rcon,
 body = list(),
 url = NULL,
 success_status_codes = 200L,
 redirect = TRUE,
 ...
)

Arguments

Details

The intent of this function is to provide an approach to execute calls to the REDCap API that is both consistent and flexible. Importantly, this provides a framework for making calls to the API using features that the R package does not yet support (redcapAPI will always lag behind when REDCap adds new features).

The API call consists of two components: the "body" and the "config." The body of the call contains all of the arguments being passed to the API. When building body components, be sure to review the documentation. options to the API that require an array need to be built using vectorToApiBodyList; options that are not an array can be entered directly (see examples).

The config list is a list of parameter overrides that reflect the curl request object. The most commonly used elements of this list is options or maybe headers.

Using the settings stored in the redcapConnection object, a response code of 408 (Request Timeout), 500 (Internal Server Error), 502 (Bad Gateway), 503 (Service Unavailable), or 504 (Gateway Timeout) will prompt reattempts at calling the API. See redcapConnection() for details. If the API reaches its attempt limit without resolving to any other code, the last response is returned. If any other response code is returned at any point in the retry loop, the loop breaks and returns that response.

Examples

## Not run: 
 unlockREDCap(c(rcon="My Project Name"), "http://apiurlhere", "mykeyringname")
 MetaData <-
 makeApiCall(rcon = rcon,
 body = list(content = "metadata",
 format = "csv",
 returnFormat = "csv"))
 MetaData <- utils::read.csv(text = as.character(MetaData),
 stringsAsFactors = FALSE,
 na.strings = "")
 # Call to export Meta Data (Data Dictionary) for specific fields
 fields <- vectorToApiBodyList(vector = c("row_purpose",
 "prereq_radio"),
 parameter_name = "fields")
 MetaData <-
 makeApiCall(rcon = rcon,
 body = c(list(content = "metadata",
 format = "csv",
 returnFormat = "csv"),
 fields))
 MetaData <- read.csv(text = as.character(MetaData),
 stringsAsFactors = FALSE,
 na.strings = "")
 # Basic call to export records
 Records <- makeApiCall(rcon = rcon,
 body = list(content = "record",
 format = "csv",
 returnFormat = "csv",
 type = "flat"))
 Records <- read.csv(text = as.character(Records),
 stringsAsFactors = FALSE,
 na.strings = "")
 # Call to export records for a single form.
 # Note that even though we are interested in a single form, the
 # API requires an array, so we use vectorToApiBodyList
 export_form <- vectorToApiBodyList("branching_logic",
 parameter_name = "forms")
 Records <- makeApiCall(rcon = rcon,
 body = c(list(content = "record",
 format = "csv",
 returnFormat = "csv",
 type = "flat"),
 export_form))
 Records <- read.csv(text = as.character(Records),
 stringsAsFactors = FALSE,
 na.strings = "")
 # Call to export records with a pipe delimiter.
 Records <- makeApiCall(rcon = rcon,
 body = list(content = "record",
 format = "csv",
 returnFormat = "csv",
 type = "flat",
 csvDelimiter = "|"))
 Records <- read.csv(text = as.character(Records),
 stringsAsFactors = FALSE,
 na.strings = "",
 sep = "|")
 # Call to export records created/modified after 25 Dec 2022 14:00.
 Records <- makeApiCall(rcon = rcon,
 body = list(content = "record",
 format = "csv",
 returnFormat = "csv",
 type = "flat",
 dateRangeBegin = "2022-12-25 14:00:00"))
 Records <- read.csv(text = as.character(Records),
 stringsAsFactors = FALSE,
 na.strings = "")
## End(Not run)

Export and Import Instrument-Event Mappings

Description

These methods enable the user to export and add/modify the mappings between instruments and events. The information provided with the methods corresponds to what is provided in the 'Designate Instruments for My Events' page in the user interface.

Usage

exportMappings(rcon, arms, ...)
importMappings(rcon, data, ...)
## S3 method for class 'redcapApiConnection'
exportMappings(rcon, arms = NULL, ...)
## S3 method for class 'redcapApiConnection'
importMappings(rcon, data, ...)

Arguments

Details

These methods are only applicable to longitudinal projects. If the project information reports that the project is not longitudinal, a data frame with 0 rows is returned without calling the API.

Value

exportMappings returns a data frame with the columns:

importMappings invisible returns the number of mappings added or edited.

Functions

• exportMappings(): Export instrument-event mappings.

• importMappings(): Import instrument-event mappings to the project.

See Also

exportFieldNames() ,
exportInstruments() ,
exportMetaData() ,
importMetaData() ,
exportPdf()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
# Export all mappings
exportMappings(rcon)
# Export mappings for a specific arm
exportMappings(rcon, 
 arms = 1)
 
# Import mappings
NewMapping <- 
 data.frame(arm_num = c(1, 1, 2), 
 unique_event_name = c("event_1_arm_1", 
 "event_2_arm_1", 
 "event_1_arm_2"), 
 form = c("registration", 
 "follow_up", 
 "registration"))
importMapping(rcon, 
 data = NewMapping)
## End(Not run)

Export and Import the Project Meta Data (Data Dictionary)

Description

These methods provide the user access to a REDCap project's data dictionary. The data dictionary may be exported or altered via the import.

Usage

exportMetaData(rcon, ...)
importMetaData(rcon, data, ...)
## S3 method for class 'redcapApiConnection'
exportMetaData(rcon, fields = character(0), forms = character(0), ...)
## S3 method for class 'redcapApiConnection'
importMetaData(
 rcon,
 data,
 ...,
 field_types = REDCAP_METADATA_FIELDTYPE,
 validation_types = REDCAP_METADATA_VALIDATION_TYPE
)

Arguments

Details

When importing meta data, the following conditions apply:

Field names may start with a letter, have any number of letters, numbers, or underscores, and end in either a letter or a number. All letters must be lowercase (the function will coerce them to lower before checking for duplicate field names).

Form names may start with a letter, have any number of letters, numbers, or underscores, and end in either a letter or a number. All letters must be lowercase (the function will coerce them to lower before checking for duplicate field names).

Field types may be one of REDCAP_METADATA_FIELDTYPE. In the event that a new field type is added to REDCap and redcapAPI is not yet updated, the user may add additional values via c(REDCAP_METADATA_FIELDTYPE, "new_type").

Validation types may be one of REDCAP_METADATA_VALIDATION_TYPE or NA. As with field types, additional values can be appended if necessary. Only fields that have a field type of "text" or "slider" should have a validation type. "slider" fields should be either NA (do not display the selected number) or "number".

For multiple choice fields, the selection choices take the format of "code1, label1 | ... | coden, labeln". For slider fields, the format is "left_value | mid_value | right_value". Any of those values may be an empty character, but the two pipes are required, nonetheless.

For calculated fields, the values in "select_choices_or_calculations" are currently unvalidated.

All of the values between brackets in the branching logic must be either a field name or an existing unique event name (such as "event_1_arm_1")

Value

exportMetaData returns a data frame. Not all 18 (or more) columns are documented here, but the most commonly used within redcapAPI are (these may appear in a different order in the data frame):

importMetaData invisibly returns the number of fields that were imported.

Functions

• exportMetaData(): Export the Meta Data (Data Dictionary) of a REDCap Project

• importMetaData(): Import New Meta Data (Data Dictionary) Definitions

See Also

exportFieldNames() ,
exportInstruments() ,
exportMappings() ,
importMappings() ,
exportPdf()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
# Export the MetaData from REDCap
exportMetaData(rcon)
# Export MetaData for select fields only (returns two rows)
exportMetaData(rcon, 
 fields = c("dropdown_test", "radio_test"))
# Export MetaData for select forms
exportMetaData(rcon, 
 forms = c("first_form", "second_form"))
 
# MetaData my be exported for a combination of fields and forms
exportMetaData(rcon, 
 fields = c("dropdown_test", "radio_test"), 
 forms = c("first_form", "second_form"))
 
# Alter and import new MetaData (change the record ID label)
Meta <- exportMetaData(rcon)
Meta$field_label[1] <- "A better description of the Record ID"
importMetaData(rcon, 
 data = Meta)
## End(Not run)

Report of Missing Values

Description

Returns a data frame of subject events with missing values.

Usage

missingSummary(rcon, excludeMissingForms = TRUE, ...)
## S3 method for class 'redcapApiConnection'
missingSummary(rcon, excludeMissingForms = TRUE, ...)
missingSummary_offline(records, meta_data, excludeMissingForms = TRUE)

Arguments

Details

The intention of this function is to generate a list of subject events that are missing and could potentially be values that should have been entered.

The branching logic from the data dictionary is parsed and translated into and R expression. When a field with branching logic passes the logical statement, it is evaluated with is.na, otherwise, it is set to FALSE (non-missing, because there was never an opportunity to provide a value). The utility of this function is limited to simple logic where all of the data exist within the same row. Any complex statements using events will result in a failure.

Optionally, forms that are entirely missing can be determined to be non-missing. This is applicable when, for instance, a patient did not have an adverse event. In this case, a form dedicated to adverse events would contain meaningless missing values and could be excluded from the report.

See Also

vignette("redcapAPI-offline-connection", package = "redcapAPI")

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
 
# Generate a summary of missing values for the entire project
missingSummary(rcon)
# Generate a summary of missing values for a single form
missingSummary(rcon, 
 exportRecordsArgs = list(forms = "target_form"))
## End(Not run)

Parse Branching Logic

Description

Branching logic from the REDCap Data Dictionary is parsed into R Code and returned as expressions. These can be evaluated if desired and allow the user to determine if missing values are truly missing or not required because the branching logic prevented the variable from being presented.

Usage

parseBranchingLogic(l)

Arguments

Details

For a study, I was asked to identify which subjects had missing values so that remaining data could be collected. The initial pass of is.na produced a lot of subjects missing values where there was no need to collect data because they did not qualify for some variables in the branching logic. Parsing the logic allowed me to determine which values we expected to be missing and narrow the search to just those subjects with legitimately missing values.

The utility of this function is limited to simple logic where all of the data exist within the same row. Any complex statements using events will result in a failure.

Value

Returns a list of unevaluated expressions.

See Also

missingSummary()

Examples

## Not run: 
parseBranchingLogic("[age] > 30")
parseBranchingLogic("[dropdown_test] = 'd'")
parseBranchingLogic(c("[age] > 30", 
 "[dropdown_test] = 'd'"))
## End(Not run)

Prepare User Data for Import

Description

Prepares a data frame for import via the API. Allows for data to be passed in either the raw format or the labeled data received from exportUsers.

Usage

prepUserImportData(data, rcon, consolidate = TRUE, user_role = FALSE)

Arguments

Value

Returns a data.frame with user settings that will be accepted by the API for import.

See Also

importUsers() ,
importUserRoles()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
# Prep user data
NewData <- data.frame(username = "target_user", 
 design = 1, 
 api_export = "Access", 
 api_import = "No Access", 
 surveys_enabled = 0)
prepUserImportData(data = NewData, 
 rcon = rcon)
 
# Prep user role data
NewData <- data.frame(unique_role_name = "target_user", 
 design = 1, 
 api_export = "Access", 
 api_import = "No Access", 
 surveys_enabled = 0)
prepUserImportData(data = NewData, 
 rcon = rcon)
## End(Not run)

Preserve Project Data Locally

Description

The methods enable the user to export a project data and meta data into local memory. For convenience, options are provided to save the objects to files on the local machine. Files may be saved as either .Rdata files or .csv files.

Usage

preserveProject(rcon, ..., save_as = NULL, dir, dir_create = TRUE)
## S3 method for class 'redcapApiConnection'
preserveProject(rcon, ..., save_as = NULL, dir, dir_create = TRUE)
readPreservedProject(x, ...)
## S3 method for class 'list'
readPreservedProject(x, ..., version = NULL, url = NULL)
## S3 method for class 'character'
readPreservedProject(x, ..., version = NULL, url = NULL)

Arguments

Details

The options to save files to local files provide the user a convenient tool set for providing other users with the ability to work with data offline. See the examples for suggestions on how to read data into an offlineConnection.

When saving to an .Rdata file, the data are saved in a list named RedcapList. The list has the same elements in the list returned when save_as = NULL and is suitable for creating an offlineConnection. The file name it is saved to follows the pattern "project-[project_id]-RedcapList.Rdata".

When saving to a .csv file, each element of the data is saved to a file with the pattern "project-[project_id]-[data type].csv".

readPreservedProject is a function of convenience for users who need to work using offline connections. If given a list, it must be in the format returned by preserveProject. If given a character, it must be the directory in which the CSV files were saved by preserveProject. If any of the file names have been changed, readPreservedProject will fail to execute. Refer to vignette("redcapAPI-offline-connection", package = "redcapAPI") for more details.

Value

'preserveProject

Whensave_as = NULL', returns a list is returned with the elements

• project_information

• arms

• events

• meta_data

• mappings

• repeating_instruments

• users

• user_roles

• user_role_assignments

• dags

• dag_assignments

• records

When save_as is not NULL, the logical TRUE is invisibly returned to provide an indication that the save operation(s) are complete.

readPreservedProject

Returns a redcapOfflineConnection object.

See Also

vignette("redcapAPI-offline-connection", package = "redcapAPI"),
offlineConnection()

purgeProject() ,
restoreProject()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
 
# Save a project to the current session
projectData <- preserveProject(rcon)
# Save a project to an Rdata file
save_to_dir <- tempdir()
preserveProject(rcon, 
 save_as = "Rdata", 
 dir = save_to_dir)
# Create an offline connection from the Rdata file
load(file.path(save_to_dir, 
 "project-[project_id]-RedcapList.Rdata"))
off_conn <- readPreservedProject(RedcapList, 
 version = "[redcap_api_version]", 
 url = "[redcap_api_url]")
 
 
# Save a project to CSV files
save_to_dir <- tempdir()
preserveProject(rcon, 
 save_as = "csv", 
 dir = save_to_dir)
 
# Create an offline connection from the CSV files
off_con <- 
 readPreservedProject(save_to_dir, 
 version = "[redcap_api_version]", 
 url = "[redcap_api_url]")
## End(Not run)
 

Export and Import Project Settings

Description

These methods enable the user to export or update project level settings, such as the project title, if it is longitudinal, if surveys are enabled, etc.

Usage

exportProjectInformation(rcon, ...)
importProjectInformation(rcon, data, ...)
## S3 method for class 'redcapApiConnection'
exportProjectInformation(rcon, ...)
## S3 method for class 'redcapApiConnection'
importProjectInformation(rcon, data, ...)

Arguments

Details

When importing, fields that are not editable will be quietly removed prior to import. This allows the user to use the result of exportProjectInformation as a template for the import.

For any values that are boolean, they should be represented as either a '0' (no/false) or '1' (yes/true).

It is not required for data to have all of the fields, but only the fields the user wishes to update (see examples).

The following project attributes can be updated:

• project_title

• project_language

• purpose

• purpose_other

• project_notes

• custom_record_label

• secondary_unique_field

• is_longitudinal

• surveys_enabled

• scheduling_enabled

• record_autonumbering_enabled

• randomization_enabled

• project_irb_number

• project_grant_number

• project_pi_firstname

• project_pi_lastname

• display_today_now_button

• bypass_branching_erase_field_prompt

Value

exportProjectInformation returns a data frame with the columns

importProjectInformation invisibly returns the number of fields updated.

Functions

• exportProjectInformation(): Export project settings.

• importProjectInformation(): Import project settings.

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
# Export Project Information
exportProjectInformation(rcon)
# Import a new project title
NewData <- data.frame(project_title = "New Title Name")
importProjectInformation(rcon, 
 data = NewData)
 
# Enable surveys in the project
NewData <- data.frame(surveys_enabled = 1)
importProjectInformation(rcon, 
 data = NewData)
 
# Change multiple fields in the project settings
NewData <- data.frame(project_irb_number = "IRB-12345", 
 display_today_now_button = 0, 
 scheduling_enabled = 1)
importProjectInformation(rcon, 
 data = NewData)
## End(Not run)

Purge and Restore Project Data

Description

These functions are primarily intended to assist with testing features of redcapAPI. Purging and restoring project data permits us to perform tests on different project structures without having to manage multiple projects or API tokens.

When purging project data, many of these actions may only be performed with a project in development status, as they are potentially destructive and may result in data loss. It is a good practice to back up your data and project structure before purging a project.

Usage

purgeProject(rcon, ...)
## S3 method for class 'redcapApiConnection'
purgeProject(
 rcon,
 arms = FALSE,
 events = FALSE,
 users = FALSE,
 user_roles = FALSE,
 dags = FALSE,
 records = FALSE,
 purge_all = FALSE,
 flush = TRUE,
 ...
)
restoreProject(object, ...)
## S3 method for class 'redcapApiConnection'
restoreProject(
 object,
 project_information = NULL,
 arms = NULL,
 events = NULL,
 meta_data = NULL,
 mappings = NULL,
 repeating_instruments = NULL,
 users = NULL,
 user_roles = NULL,
 user_role_assignments = NULL,
 dags = NULL,
 dag_assignments = NULL,
 records = NULL,
 flush = TRUE,
 ...
)
## S3 method for class 'list'
restoreProject(object, ..., rcon)

Arguments

Details

When restoring a project, all arguments are optional. Any argument that is NULL will result in no import being made. The order of reconstructing the project is (purging data occurs in the reverse order):

1. Update project information

2. Import Arms Data

3. Import Events Data

4. Import Meta Data

5. Import Mappings

6. Import Repeating Instruments

7. Import Users

8. Import User Roles

9. Import User-Role Assignments

10. Import Data Access Groups

11. Import Data Access Group Assignments

12. Import Records

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
 
# Preserve a project
preserveProject(rcon)
# Purge a project
purgeProject(rcon, 
 purge_all = TRUE)
 
# Restore a project
restoreProject(rcon)
## End(Not run)

Change labeling of checkbox variables

Description

Rewrites the labeling of checkbox variables from Checked/Unchecked to Yes/No (or some other user specified labeling).

Usage

recodeCheck(
 df,
 vars,
 old = c("Unchecked", "Checked"),
 new = c("No", "Yes"),
 reverse = FALSE
)

Arguments

Details

checkbox variables are not identified using the metadata from the REDCap database. Instead, variables are scanned, and those variables in which every value is in levels are assumed to be checkbox variables.

Realistically, this could be used to relabel any set of factors with identical labels, regardless of the data source. The number of labels is not limited, but levels and labels should have the same length.

The actual code to perform this is not particularly difficult (df[checkbox] <- lapply(df[checkbox], factor, levels=levels, labels=labels)), but checkbox variables are common enough in REDCap (and the Checked/Unchecked scheme so unpalatable) that a quick way to replace the labels was highly desirable

Save a File to a Local Directory from a Response

Description

Converts the file from a response object and saves it to the local file directory.

Usage

reconstituteFileFromExport(
 response,
 dir,
 dir_create = FALSE,
 file_prefix = "",
 filename = character(0)
)

Arguments

See Also

exportFiles() ,
exportFromFileRepository() ,
exportFileRepository() ,
exportPdf()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
 
response <- makeApiCall(rcon, 
 body = list(content = 'file', 
 action = 'export', 
 record = '1', 
 field = 'file_upload_test', 
 event = 'event_1_arm_1'))
reconstituteFileFromExport(response, 
 dir = tempdir())
## End(Not run) 
 

Export Next Record Name or Rename a Record

Description

These methods enable the user to get the next record name (when auto numbering is enabled) or rename and existing record.

Usage

exportNextRecordName(rcon, ...)
renameRecord(rcon, record_name, new_record_name, arm = NULL, ...)
## S3 method for class 'redcapApiConnection'
exportNextRecordName(rcon, ...)
## S3 method for class 'redcapApiConnection'
renameRecord(rcon, record_name, new_record_name, arm = NULL, ...)

Arguments

Value

exportNextRecordName returns an integerish value. The value is determined by looking up the highest record ID number in the project and incrementing it by 1.

renameRecord invisibly returns a logical vector that indicates if the operation was successful. Otherwise, an error is thrown.

Functions

• exportNextRecordName(): Get the ID number for the next record to be created.

• renameRecord(): Rename an existing record.

See Also

exportRecords() ,
exportReports() ,
importRecords() ,
deleteRecords() ,
exportRecordsTyped() ,
exportReportsTyped()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
 
# Get the next record name
exportNextRecordName(rcon)
# Rename an existing record
renameRecord(rcon, 
 record_name = "1", 
 new_record_name = "42")
## End(Not run)

Export Records and Reports

Description

These methods enable the user to export records and reports from a project.

Usage

exportRecords(
 rcon,
 factors = TRUE,
 fields = NULL,
 forms = NULL,
 records = NULL,
 events = NULL,
 labels = TRUE,
 dates = TRUE,
 drop = NULL,
 survey = TRUE,
 dag = TRUE,
 checkboxLabels = FALSE,
 colClasses = character(0),
 ...
)
exportRecords_offline(
 dataFile,
 metaDataFile,
 factors = TRUE,
 fields = NULL,
 forms = NULL,
 labels = TRUE,
 dates = TRUE,
 checkboxLabels = FALSE,
 colClasses = NA,
 ...,
 meta_data
)
exportReports(
 rcon,
 report_id,
 factors = TRUE,
 labels = TRUE,
 dates = TRUE,
 drop = NULL,
 checkboxLabels = FALSE,
 ...
)
## S3 method for class 'redcapApiConnection'
exportRecords(
 rcon,
 factors = TRUE,
 fields = NULL,
 forms = NULL,
 records = NULL,
 events = NULL,
 labels = TRUE,
 dates = TRUE,
 drop = NULL,
 survey = TRUE,
 dag = TRUE,
 checkboxLabels = FALSE,
 colClasses = character(0),
 ...,
 batch.size = -1,
 form_complete_auto = TRUE
)
## S3 method for class 'redcapApiConnection'
exportReports(
 rcon,
 report_id,
 factors = TRUE,
 labels = TRUE,
 dates = TRUE,
 drop = NULL,
 checkboxLabels = FALSE,
 ...
)

Arguments

Details

It is unnecessary to include '"redcap_event_name"“ in the fields argument. This field is automatically exported for any longitudinal database. If the user does include it in the fields argument, it is removed quietly in the parameter checks.

There are four ways the data from checkbox variables may be represented depending on the values of factors and checkboxLabels. The most common are the first and third rows of the table below. When checkboxLabels = TRUE, either the coded value or the labeled value is returned if the box is checked, or an empty string if it is not.

The 'offline' version of exportReports operates on the raw (unlabeled) data file downloaded from REDCap along with the data dictionary. This is made available for instances where the API cannot be accessed for some reason (such as waiting for API approval from the REDCap administrator).

A 'batched' export (or import) is one where the export is performed over a series of API calls rather than one large call. For large projects on small servers, this may prevent a single user from tying up the server and forcing others to wait on a larger job. The batched export is performed by first calling the API to export the record identifier field (the first field in the meta data). The unique ID's are then assigned a batch number with no more than batch.size ID's in any single batch. The batches are exported from the API and stacked together.

In longitudinal projects, batch.size may not necessarily be the number of records exported in each batch. If batch.size is ten and there are four records per patient, each batch will consist of 40 records. Thus, if the user is concerned about tying up the server with a large, longitudinal project, it would be prudent to use a smaller batch size.

Value

exportRecords returns a data frame with the project data. The data will be formatted consistent with the meta data and the arguments provided by the user.

exportReports returns a data frame with the data from the requested report. The data will be formatted consisted with the meta data and the arguments provided by the user.

Functions

• exportRecords(): Export records from a project.

• exportRecords_offline(): Format records from REDCap data file exports.

• exportReports(): Export data via a report.

See Also

exportRecordsTyped() ,
exportReportsTyped() ,
importRecords() ,
deleteRecords() ,
exportNextRecordName() ,
renameRecord()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
 
# Export records
exportRecords(rcon)
# Export records in batches of one hundred IDs
exportRecords(rcon, 
 batch.size = 100)
 
# Export records without factors
exportRecords(rcon, 
 factors = FALSE)
 
# Export a report
exportReports(rcon, 
 report_id = 12345)
 
# Export raw data
exportRecordsTyped(rcon, 
 validation = skip_validation,
 cast = raw_cast)
## End(Not run)

Export Records or Reports From a Project

Description

These methods enable the user to export records from a database or from a report. These methods have more control for casting fields to R objects than exportRecords.

Usage

exportRecordsTyped(
 rcon,
 fields = NULL,
 drop_fields = NULL,
 forms = NULL,
 records = NULL,
 events = NULL,
 ...
)
exportReportsTyped(rcon, report_id, ...)
## S3 method for class 'redcapApiConnection'
exportRecordsTyped(
 rcon,
 fields = NULL,
 drop_fields = NULL,
 forms = NULL,
 records = NULL,
 events = NULL,
 survey = TRUE,
 dag = FALSE,
 date_begin = NULL,
 date_end = NULL,
 na = list(),
 validation = list(),
 cast = list(),
 assignment = list(label = stripHTMLandUnicode, units = unitsFieldAnnotation),
 filter_empty_rows = TRUE,
 warn_zero_coded = TRUE,
 ...,
 csv_delimiter = ",",
 batch_size = NULL
)
## S3 method for class 'redcapOfflineConnection'
exportRecordsTyped(
 rcon,
 fields = NULL,
 drop_fields = NULL,
 forms = NULL,
 records = NULL,
 events = NULL,
 na = list(),
 validation = list(),
 cast = list(),
 assignment = list(label = stripHTMLandUnicode, units = unitsFieldAnnotation),
 warn_zero_coded = TRUE,
 ...
)
## S3 method for class 'redcapApiConnection'
exportReportsTyped(
 rcon,
 report_id,
 drop_fields = NULL,
 na = list(),
 validation = list(),
 cast = list(),
 assignment = list(label = stripHTMLandUnicode, units = unitsFieldAnnotation),
 warn_zero_coded = TRUE,
 ...,
 csv_delimiter = ","
)

Arguments

Details

The 'offline' method operates on the raw (unlabeled) data file downloaded from REDCap along with the data dictionary. This is made available for instances where the API cannot be accessed for some reason (such as waiting for API approval from the REDCap administrator).

When validating data for offlineRedcapConnection objects, links to invalid data forms will not work if the user does not provide the url, version, project_info, and events arguments (if the project is longitudinal). For the project_info, the values project_id and is_longitudinal are required. The user may be able to provide as little as ⁠project_info = data.frame(project_id = [id], is_longitudinal = [0/1])⁠. The user should be aware that the REDCap User Interface download for events does not include the event ID. To include the event ID, the user must construct a data frame to pass to offlineConnection.

Record Identifier (System) Fields

In all calls, the project's ID fields will be included–there is no option provided to prevent this. Additionally, if the project has a secondary unique field specified, it will also be included. Inclusion of these fields is necessary to support some post-processing functions.

By default, the system fields redcap_event_name, redcap_repeat_instrument, and redcap_repeat_instance are exported (when they are appropriate to the project). These are automatically included by the API. However, if the user omits any of these in fields or designates one in drop_fields, the final result will honor those conditions. Excluding any of these identifiers may cause problems with some post-processing functions that operate on repeating instrument data.

The combination of the project ID field, secondary unique field, and the system fields are what uniquely identify an experimental unit. In nearly all cases, it is desirable to have them all included.

System fields are cast to labelled values by default. They may be cast to their coded values using the override cast = list(system = castRaw). The fields affected by the system override are redcap_event_name, redcap_repeat_instrument, and redcap_data_access_group.

BioPortal Fields

Text fields that are validation enabled using the BioPortal Ontology service may be cast to labeled values so long as the labels have been cached on the REDCap server. Caching is performed when the field is viewed in a form on the web interface. However, labels are not cached when data are imported via the API. In cases where labels are not cached, the coded value is treated as both the code and the label.

Record Batching

A 'batched' export is one where the export is performed over a series of API calls rather than one large call. For large projects on small servers, this may prevent a single user from tying up the server and forcing others to wait on a larger job. The batched export is performed by first calling the API to export the subject identifier field (the first field in the meta data). The unique ID's are then assigned a batch number with no more than batch_size ID's in any single batch. The batches are exported from the API and stacked together.

In longitudinal projects, batch_size may not necessarily be the number of records exported in each batch. If batch_size is ten and there are four records per patient, each batch will consist of 40 records. Thus, if the user is concerned about tying up the server with a large, longitudinal project, it would be prudent to use a smaller batch size.

Inversion of Control

The final product of calling this is a data.frame with columns that have been type cast to most commonly used analysis class (e.g. factor). This version allows the user to override any step of this process by specifying a different function for each of the stages of the type casting. The algorithm is as follows:

1. Detect NAs in returned data (na argument).

2. Run validate functions for the field_types.

3. On the fields that are not NA and pass validate do the specified cast.

It is expected that the na and validate overrides should rarely be used. Their exposure via the function parameters is to future proof against possible bugs in the defaults, and allows for things that higher versions of REDCap add as possible field types. I.e., the overrides are for use to continue using the library when errors or changes to REDCap occur.

The cast override is one where users can specify things that were controlled by an ever increasing set of flags before. E.g., dates=as.Date was an addition to allow dates in the previous version to be overridden if the user wanted to use the Date class. In this version, it would appear called as ⁠cast=list(_date=as.Date))⁠. See fieldValidationAndCasting() for a full listing of package provided cast functions.

Value

exportRecordsTyped returns a data frame with the formatted data.

exportReportsTyped returns a data frame with the formatted data.

Functions

• exportRecordsTyped(): Export records with type casting.

• exportReportsTyped(): Export reports with type casting.

• exportRecordsTyped(redcapOfflineConnection): Export records without API access.

Zero-Coded Check Fields

A zero-coded check field is a field of the REDCap type checkbox that has a coding definition of ⁠0, [label]⁠. When exported, the field names for these fields is ⁠[field_name]___0⁠. As in other checkbox fields, the raw data output returns binary values where 0 represent an unchecked box and 1 represents a checked box. For zero-coded checkboxes, then, a value of 1 indicates that 0 was selected.

This coding rarely presents a problem when casting from raw values (as is done in exportRecordsTyped). However, casting from coded or labeled values can be problematic. In this case, it becomes indeterminate from context if the intent of 0 is 'false' or the coded value '0' ('true') ...

The situations in which casting may fail to produce the desired results are

Because of the potential for miscast data, casting functions will issue a warning anytime a zero-coded check field is encountered. A separate warning is issued when a field is cast from coded or labeled values.

When casting from coded or labeled values, it is strongly recommended that the function castCheckForImport() be used. This function permits the user to state explicitly which values should be recognized as checked, avoiding the ambiguity resulting from the coding.

See Also

Other records exporting functions

exportRecords() ,
exportReports() ,
exportBulkRecords()

Field validations and casting

fieldValidationAndCasting() ,
reviewInvalidRecords()

Post-processing functionality

recastRecords() ,
guessCast() ,
guessDate() ,
castForImport() ,
mChoiceCast() ,
splitForms() ,
widerRepeated()

Vignettes

vignette("redcapAPI-offline-connection")
vignette("redcapAPI-casting-data")
vignette("redcapAPI-missing-data-detection")
⁠vignette("redcapAPI-data-validation)⁠
⁠vignette("redcapAPI-faq)⁠

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
 
# Export records with default settings
exportRecordsTyped(rcon)
# Export records with no factors
exportRecordsTyped(rcon, 
 cast = default_cast_character)
 
# Export records for specific records
exportRecordsTyped(rcon, 
 records = 1:3)
 
# Export records for specific instruments
exportRecordsTyped(rcon, 
 forms = c("registration", "visit_1", "medications"))
 
# Export records using filterLogic, an API parameter not provided
# in the exportRecordsTyped function signature
exportRecordsTyped(
 rcon, 
 records = 1:3, 
 api_param = list(filterLogic = "[age_at_enrollment] > 25")
)
 
 
 
# Export a report 
exportReports(rcon, 
 report_id = 12345)
 
 
# Export records using files downloaded from the user interface
rcon_off <- 
 offlineConnection(
 meta_data = 
 system.file(file.path("extdata/offlineConnectionFiles", 
 "TestRedcapAPI_DataDictionary.csv"), 
 package = "redcapAPI"), 
 records = 
 system.file(file.path("extdata/offlineConnectionFiles",
 "TestRedcapAPI_Records.csv"), 
 package = "redcapAPI"))
exportRecordsTyped(rcon_off)
## End(Not run)

Connect to a REDCap Database

Description

These methods enable the user to create a connection object used to access the database.

Usage

redcapConnection(
 url = getOption("redcap_api_url"),
 token,
 config = NULL,
 retries = 5,
 retry_interval = 2^(seq_len(retries)),
 retry_quietly = TRUE,
 ...
)
## S3 method for class 'redcapApiConnection'
print(x, ...)
offlineConnection(
 meta_data = NULL,
 arms = NULL,
 events = NULL,
 instruments = NULL,
 field_names = NULL,
 mapping = NULL,
 repeat_instrument = NULL,
 users = NULL,
 user_roles = NULL,
 user_role_assignment = NULL,
 dags = NULL,
 dag_assignment = NULL,
 project_info = NULL,
 version = "14.4.0",
 file_repo = NULL,
 records = NULL,
 url = NULL,
 external_coding = list()
)
## S3 method for class 'redcapOfflineConnection'
print(x, ...)

Arguments

Details

redcapConnection objects will retrieve and cache various forms of project information. This can make metadata, arms, events, etc. available directly from the redcapConnection object. The retrieval of these objects uses the default values of the respective export functions (excepting the file repository, which uses recursive = TRUE).

For each of these objects, there are four methods that can be called from the redcapConnection object:

Information is cached for

• metadata

• arms

• events

• instruments

• fieldnames

• mapping (field-event mappings)

• repeatInstrumentEvent

• users

• user_roles

• user_role_assignment

• dags

• dag_assignment

• projectInformation

• version

• fileRepository

• externalCoding

There is also a flush_all and refresh_all method that will purge the entire cache and refresh the entire cache, respectively.

The externalCoding elements relate to the code-label mappings of text fields with the external validation types (such as sql fields or text fields with BioPortal Ontology modules enabled).

Specific to API Connections

The redcapApiConnection object also stores the user preferences for handling repeated attempts to call the API. In the event of a timeout error or server unavailability, these settings allow a system pause before attempting another API call. In the event all of the retries fail, the error message of the last attempt will be returned. These settings may be altered at any time using the methods rcon$set_retries(r), rcon$set_retry_interval(ri), and rcon$set_retry_quietly(rq). The argument to these functions have the same requirements as the corresponding arguments to redcapConnection.

Tokens are specific to a project, and a token must be created for each project for which the user wishes to use the API.

Additional Curl option can be set in the config argument. See the documentation for curl::handle_setopt for more curl options.

Specific to Offline Connections

"Offline connections" are a tool designed to provide the users without API privileges with at least a subset of the functionality available to API users. The offline connections are typically constructed from the comma separated value (CSV) files downloaded from the REDCap user interface. Alternatively, data frames may be provided with the necessary data.

Not all of the components of an offline connection are needed for most operations. Rather, the object was built to accept the same components available to the redcapApiConnection in order to provide a consistent interface and simplify future development.

The meta data will be required for nearly all operations. For validating and casting data, the records data must be provided, and works best if the data are the raw, unlabeled data downloaded from the REDCap user interface.

Other components that may prove useful when casting records are the url, version, events (if the project is longitudinal), and a subset of the project information. The user is encouraged to review the vignette for working with offline connections for more details.

With offline connections, the refresh methods have an important difference. The user may pass the refresh method a file path or data frame which will be used to replace the existing component. See examples.

See Also

For establishing connections using secure token storage.
unlockREDCap()
vignette("redcapAPI-getting-started-connecting", package = "redcapAPI")

For working with offline connections. vignette("redcapAPI-offline-connection", package = "redcapAPI")

To prepare data for an offline user, see preserveProject() and readPreservedProject() .

Examples

## Not run: 
rcon <- redcapConnection(url = [YOUR_REDCAP_URL],
 token = [API_TOKEN])
exportRecords(rcon)
# Get the complete metadata for the project
rcon$metadata()
# Get the fieldnames for a project
rcon$fieldnames()
# remove a cached value for fieldnames
rcon$flush_fieldnames()
rcon$has_fieldnames()
# Using offline connections
meta_data_file <- "path/to/meta_data_file.csv"
records_file <- "path/to/records_file.csv"
events_file <- "path/to/events_file.csv"
ProjectInfo <- data.frame(project_id = 12345,
 is_longitudinal = 1)
off_conn <- offlineConnection(meta_data = meta_data_file,
 records = records_file,
 project_info = ProjectInfo,
 version = [YOUR_REDCAP_VERSION_NUMBER],
 url = [YOUR_REDCAP_URL])
off_conn$metadata()
off_conn$records()
off_conn$projectInformation()
off_conn$version()
# Add or replace the data in the events component.
off_conn$refresh_events(events_file)
off_conn$events()
## End(Not run)

REDCap Data Structures

Description

Utilities for recognizing and validating data structures for use with the REDCap API

Usage

validateRedcapData(data, redcap_data)
REDCAP_SYSTEM_FIELDS
REDCAP_PROJECT_PURPOSE
REDCAP_METADATA_FIELDTYPE
REDCAP_METADATA_VALIDATION_TYPE
REDCAP_REPEAT_INSTRUMENT_STRUCTURE

Arguments

Format

An object of class character of length 5.

An object of class character of length 5.

An object of class character of length 11.

An object of class character of length 25.

An object of class data.frame with 0 rows and 3 columns.

Convert REDCap factors between labeled and coded

Description

Factors exported from REDCap can be toggled between the coded and labeled values with the use of the attributes assigned to the factors during export.

Usage

redcapFactorFlip(v)

Arguments

Details

Each factor type variable in REDCap is given the attributes redcapLabels and redcapLevels. With these attached to the vector, switching between the coded and labeled values can be done with ease. This may be helpful when the coded value has importance, such as 0/1 for death, or if a yes is worth six points (instead of one).

Export or Import Repeating Instrument and Events Settings

Description

These methods enable the user to export the existing repeating instrument and event settings, or import new settings to the project.

Usage

exportRepeatingInstrumentsEvents(rcon, ...)
importRepeatingInstrumentsEvents(rcon, data, ...)
## S3 method for class 'redcapApiConnection'
exportRepeatingInstrumentsEvents(rcon, ...)
## S3 method for class 'redcapApiConnection'
importRepeatingInstrumentsEvents(rcon, data, ...)

Arguments

Details

Repeating events (as opposed to repeating instruments) are provided as a row of data where the form_name column is NA.

It is not possible to update the has_repeating_instruments_or_events property of the project through importProjectInformation. Enabling of repeating instruments and events must be done through the GUI.

Although the API does not provide a delete method, it is possible to remove settings by doing an import that excludes the settings that are to be deleted. All settings can be cleared by executing importRepeatingInstrumentsEvents(rcon, REDCAP_REPEAT_INSTRUMENT_STRUCTURE).

Value

exportRepeatingInstrumentsEvents returns a data frame with the columns:

importRepeatingInstrumentsEvents invisibly returns the number of rows imported.

Functions

• exportRepeatingInstrumentsEvents(): Export repeating instruments and events.

• importRepeatingInstrumentsEvents(): Import repeating instruments and events.

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
 
# Export repeating instruments and events
exportRepeatingInstrumentsEvents(rcon)
# Import repeating instruments and events
NewData <- data.frame(event_name = c("event_1_arm_1", 
 "event_2_arm_1"), 
 form_name = c("field_observation", 
 "self_assessment"), 
 custom_form_label = c("Instructor led field observation", 
 "Trainee self assessment"))
 
importRepeatingInstrumentsEvents(rcon, 
 data = NewData)
## End(Not run)

Review Invalid Records Following Field Validation

Description

This function retrieves a summary of data elements that failed validation during field validation and casting.

Usage

reviewInvalidRecords(data, quiet = TRUE)

Arguments

Details

When discussing field validation and invalid data, it is helpful to establish the following terminology:

A Records data frame is a data frame returned by a function where the fields (columns) in the data frame have been cast for subsequent analysis.

Some casting function also perform field validation and return an Invalid data frame, which is a listing of data elements that have failed validation. The Invalid data frame is attached as an attribute to the Records data frame. If no data elements fail the validation, the Invalid data frame will have zero rows. If at least one data element fails validation, a warning is printed to notify the user so that the user may review the Invalid data frame and mitigate the failed validations.

The Invalid data frame has an additional class (c("invalid", "data.frame")) and comes with a print method. The print.invalid method displays the content of the Invalid data frame neatly in both the console and within reports utilizing markdown.

Value

If data has the "invalid" attribute, an object with class c("invalid", "data.frame") is returned. (NULL will be returned if data does not have the attribute).

The colums in the Invalid data frame are

The Invalid data frame has additional attributes

• time - The date/time at which the validation was performed.

• version - The REDCap version number (as retrieved by exportVersion).

• project - The title of the REDCap project (as retrieved by exportProjectInformation).

See Also

exportRecordsTyped() ,
exportReportsTyped() ,
castForImport() ,
guessCast()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"),
 url = "your_redcap_url",
 keyring = "API_KEYs",
 envir = globalenv())
# Review the Invalid data frame after export
Records <- exportRecordsTyped(rcon)
reviewInvalidRecords(Records)
# Review Invalid data frame before import
Records <- castForImport(rcon)
reviewInvalidRecords(Records)
# Access the Invalid data frame the attributes
Records <- exportRecordsTyped(rcon)
attr(Records, "invalid")
attributes(Records)$invalid
## End(Not run)

Split a Data Frame into its Forms

Description

Separates a data frame from REDCap into a list of data frames where each form constitutes an element in the list.

Usage

splitForms(Records, rcon, envir = NULL, base = NULL, post = NULL)

Arguments

See Also

Other post-processing functions

recastRecords() ,
guessCast() ,
guessDate() ,
castForImport() ,
mChoiceCast() ,
widerRepeated()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
 
Records <- exportRecordsTyped(rcon)
splitForms(Records, rcon)
## End(Not run)
 
 

Remove Undesired Characters From Strings

Description

These functions are utilities to clear undesired characters from REDCap output.

Usage

stripHTMLTags(
 x,
 tags = c("p", "br", "div", "span", "b", "font", "sup", "sub"),
 ignore.case = TRUE
)
stripUnicode(x)

Arguments

Value

stripHTMLTags returns a character vector.

stripUnicode returns a character vector.

Examples

stripHTMLTags("<p>Text in a paragraph <b>tag</b> with bold formatting </p>")
stripUnicode("\U00B5 = 0")

Helper Functions for exportRecordsType Attributes

Description

These functions assist in setting attributes for columns of the resulting type cast data.frame.

Usage

stripHTMLandUnicode(field_name, field_label, field_annotation)
unitsFieldAnnotation(field_name, field_label, field_annotation)

Arguments

Details

Functions passed into the assignment argument list of exportRecordsTyped() construct attributes on a column. They are expected to have a signature of ⁠function(field_name, field_label, field_annotation)⁠ and return the attribute to assign or NA. They must be vectorized.

Useful utilities are provided in stringCleanup()

stripHTMLandUnicode strips both HTML and UNICODE from the field_label.

unitsFieldAnnotation pulls a units string from the field_annotation. An example of the form searched for is ⁠units=\{"meters"\}⁠

Value

stripHTMLandUnicode returns a character vector.

unitsFieldAnnotation returns a character vector.

See Also

exportRecordsTyped() ,
exportReportsTyped() ,
stripHTMLTags() ,
stripUnicode()

Examples

## Not run: 
stripHTMLandUnicode("field_name", "<b>Field label</b>", "field annotation")
unitsFieldAnnotation("field", "label", "units={\"meters\"}")
## End(Not run)

Export Survey Participant Information

Description

These methods enable the user to export information relating to survey participants.

Usage

exportSurveyParticipants(rcon, instrument, event, ...)
exportSurveyLink(rcon, record, instrument, event, repeat_instance = 1, ...)
exportSurveyQueueLink(rcon, record, ...)
exportSurveyReturnCode(
 rcon,
 record,
 instrument,
 event,
 repeat_instance = 1,
 ...
)
## S3 method for class 'redcapApiConnection'
exportSurveyParticipants(rcon, instrument = NULL, event = NULL, ...)
## S3 method for class 'redcapApiConnection'
exportSurveyLink(
 rcon,
 record,
 instrument,
 event = NULL,
 repeat_instance = 1,
 ...
)
## S3 method for class 'redcapApiConnection'
exportSurveyQueueLink(rcon, record, ...)
## S3 method for class 'redcapApiConnection'
exportSurveyReturnCode(
 rcon,
 record,
 instrument,
 event = NULL,
 repeat_instance = 1,
 ...
)

Arguments

Value

exportSurveyParticipants returns a data frame with the columns:

exportSurveyLink returns a character(1) giving the link for the user to access the survey form.

exportSurveyQueueLink returns a character(1) giving the survey queue link for the user.

exportSurveyReturnCode returns a character(1) giving the survey return code for the user.

Functions

• exportSurveyParticipants(): Export survey participants for a survey instrument.

• exportSurveyLink(): Export a survey participant's survey instrument link.

• exportSurveyQueueLink(): Export a survey participant's survey queue link.

• exportSurveyReturnCode(): Export a survey participant's instrument return code.

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
 
# Export survey participants
exportSurveyParticipants(rcon, 
 instrument = "survey_form")
 
# Export survey participants for an event
exportSurveyParticipants(rcon, 
 instrument = "survey_form", 
 event = "event_1_arm_1")
 
# Export survey link
exportSurveyLink(rcon, 
 record = 1, 
 instrument = "survey_form")
 
# Export survey queue link
exportSurveyQueueLink(rcon, 
 record = 1)
 
# Export survey return code
exportSurveyReturnCode(rcon, 
 user = 1, 
 instrument = "survey_form")
## End(Not run)

Switch Data Access Group Assignment for the Current User

Description

This method enables the current API user to switch (assign/reassign/unassign) their current Data Access Group assignment if they have been assigned to multiple DAGs via the DAG Switcher page in the project.

Usage

switchDag(rcon, dag, ...)
## S3 method for class 'redcapApiConnection'
switchDag(rcon, dag, ...)

Arguments

Value

Invisibly returns TRUE when the call is completed successfully. Otherwise an error is thrown.

See Also

exportDags() ,
importDags() ,
deleteDags() ,
exportUserDagAssignments() ,
importUserDagAssignments()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"),
 url = "your_redcap_url",
 keyring = "API_KEYs",
 envir = globalenv())
# Switch the current user to the DAG "Facility Two"
switchDag(rcon,
 dag = "facility_two")
## End(Not run)

Synchronize coding of checkbox variables between meta data and records field names.

Description

Due to a bug in the REDCap export module, underscores in checkbox codings are not retained in the suffixes of the field names in the exported records. For example, if variable chk is a checkbox with a coding 'a_b, A and B', the field name in the data export becomes chk___ab. The loss of the underscore causes fieldToVar to fail as it cannot match variable names to the meta data. syncUnderscoreCodings rectifies this problem by searching the suffixes and meta data for underscores. If a discrepancy is found, the underscores are removed from the metadata codings, restoring harmony to the universe. This bug was fixed in REDCap version 5.5.21 and this function does not apply to that and later versions.

Usage

syncUnderscoreCodings(records, meta_data, export = TRUE)

Arguments

Details

syncUnderscoreCodings performs a series of evaluations. First, it determines if any underscores are found in the checkbox codings. If none are found, the function terminates without changing anything.

If the checkbox codings have underscores, the next evaluation is to determine if the variable names suffixes have matching underscores. If they do, then the function terminates with no changes to the meta data.

For data exports, if the prior two checks find underscores in the meta data and no underscores in the suffixes, the underscores are removed from the meta data and the new meta data returned.

For data imports, the meta data are not altered and the checkbox_field_name_map attribute is used to synchronize field names to the meta data and the expectations of REDCap (for import, REDCap expects the underscore codings to be used.

Backward Compatibility

In retrospect, we realize that the way syncUnderscoreCodings is written is backward. We should have altered the field names in the records data frame. Any scripts that make use of syncUnderscoreCodings and were written prior to version 5.5.21 will fail because the underscores in the codings will now be present where they were not before.

For backward compatibility of redcapAPI, we continue to alter the codings in the meta data. We do not anticipate many problems, as most people do not use underscores in the checkbox codings

If your scripts were written under REDCap 5.5.21 or higher, there will be no backward compatibility problems related to this issue.

Open REDCap connections using cryptolocker for storage of API_KEYs.

Description

Opens a set of connections to REDcap from API_KEYs stored in an encrypted keyring. If the keyring does not exist, it will ask for password to this keyring to use on later requests. Next it will ask for the API_KEYs specified in connections. If an API_KEY does not work, it will request again. On later executions it will use an open keyring to retrieve all API_KEYs or for a password if the keyring is currently locked.

Usage

unlockREDCap(connections, url, keyring, envir = NULL, ...)

Arguments

Details

If one forgets the password to this keyring, or wishes to start over: shelter::keyring_delete("<NAME_OF_KEY_RING_HERE>")

For production servers where the password must be stored in a readable plain text file, it will search for ⁠../<basename>.yml⁠. DO NOT USE this unless one is a sysadmin, as this defeats the security and purpose of a local encrypted file. The expected structure of this yaml file is as follows:

other-config-stuff1: blah blah
redcapAPI:
 keys:
 intake: THIS_IS_THE_INTAKE_DATABASE_APIKEY
 details: THIS_IS_THE_DETAILS_DATABASE_APIKEY
other-config-stuff2: blah blah
other-config-stuff3: blah blah

For production servers the use of ENV variables is also supported. The connection string is converted to upper case for the search of ENV. If a YAML and ENV variable both exist, the YAML will take precedence.

IMPORTANT: Make sure that R is set to NEVER save workspace to .RData as this is writing the API_KEY to a local file in clear text because connection objects contain the unlocked key in memory. Tips are provided in vignette("redcapAPI-best-practices").

To debug an entire session via what is called / returned from the server, add the argument config=list(options=list(verbose=TRUE)) to the call.

Value

If envir is NULL returns a list of opened connections. Otherwise connections are assigned into the specified envir.

See Also

redcapConnection()

Vignettes

vignette("redcapAPI-best-practices"),
vignette("redcapAPI-getting-started-connecting")

Examples

## Not run: 
unlockREDCap(c(test_conn = 'TestRedcapAPI',
 sandbox_conn = 'SandboxAPI'),
 keyring = '<NAME_OF_KEY_RING_HERE>',
 envir = globalenv(),
 url = 'https://<INSTITUTIONS_REDCAP_DOMAIN>/api/')
## End(Not run)

Export, Import, or Delete Users and User Permissisons

Description

These methods enable the user to add and remove users from a project. They also enable the user to modify the permissions granted to each user within the project.

Usage

exportUsers(rcon, ...)
importUsers(rcon, data, ...)
deleteUsers(rcon, users, ...)
## S3 method for class 'redcapApiConnection'
exportUsers(rcon, dates = TRUE, labels = TRUE, form_rights = TRUE, ...)
## S3 method for class 'redcapApiConnection'
importUsers(rcon, data, consolidate = TRUE, ...)
## S3 method for class 'redcapApiConnection'
deleteUsers(rcon, users, ...)

Arguments

Details

User project access fields (those not related to forms or exports) are mapped between coded and labeled values as:

Form access fields are mapped as:

Form export permission fields are mapped as:

Importing Users/User Roles

It is not required that the user provide a data frame with all of the fields available for modification. Only fields that are provided will be modified. The only required field for imports is the username field.

When setting permissions for a user project access fields, form access, and form export permissions, the user may provided any of the coded or labeled values above. The user data is passed through prepUserImportData() before sending it to the API; text values will be converted to the numeric value.

It is also permissible to use a column for each form individually, as can be exported via exportUsers() . With consolidate = TRUE, these settings will be consolidated into the text string expected by the API.

The REDCap API does not natively allow for modifying the rights of a user that is part of a User Role. When an attempt to modify the rights of a user in a User Role is made with this package, the user will be removed from the User Role, the rights modified, and then the User Role restored. This is done silently: be aware that modifications to a user's rights may not have an impact while the User Role is assigned.

Limitations

When importing via CSV, (as redcapAPI does by default) it appears that the form access rights are imported but may not always be reflected in the exported values. The form export rights do not appear to be imported when using the CSV format. We may be able to resolve this in the future using a JSON format.

Value

exportUsers returns a data frame with the columns:

When form_rights = TRUE, additional columns are created that give the form access and form export rights in an individual column for each form. Form access rights columns have the naming pattern ⁠[form_name]_access⁠ and the form export rights columns have the naming pattern ⁠[form_name]_export_access⁠.

importUsers invisibly returns the number of users that were added or modified.

deleteUsers invisibly returns the number of users that were deleted.

Functions

• exportUsers(): Export users affiliated with a project.

• importUsers(): Add users or modify user permissions in a project.

• deleteUsers(): Remove users from a project.

See Also

exportUserRoles() ,
importUserRoles() ,
deleteUserRoles() ,
exportUserRoleAssignments() ,
importUserRoleAssignments()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
 
# Export users
exportUsers(rcon)
# Export users without additional form access variables
exportUsers(rcon, 
 form_rights = FALSE)
 
# Export users as raw data
exportUsers(rcon, 
 labels = FALSE)
 
 
# Import new permissions
NewData <- data.frame(username = "target_user", 
 design = 0, 
 api_export = 1, 
 api_import = "No Access")
importUsers(rcon, 
 data = NewData)
 
# Remove a user from a project
deleteUsers(rcon, 
 users = "target_user")
## End(Not run)

Export or Import User-Role Assignments

Description

These methods enable the user to export the user-role assignments, add assignments, or modify existing assignments.

Usage

exportUserRoleAssignments(rcon, ...)
importUserRoleAssignments(rcon, data, ...)
## S3 method for class 'redcapApiConnection'
exportUserRoleAssignments(rcon, ...)
## S3 method for class 'redcapApiConnection'
importUserRoleAssignments(rcon, data, ...)

Arguments

Value

exportUserRoleAssignments returns a data frame with the columns:

importUserRoleAssignments invisibly returns the number of user roles assignments added or modified.

Functions

• exportUserRoleAssignments(): Export user-role assignments from a project.

• importUserRoleAssignments(): Import user-role assignments to a project.

See Also

exportUsers() ,
importUsers() ,
deleteUsers() ,
exportUserRoles() ,
importUserRoles() ,
deleteUserRoles()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
 
# Export user-role assignments
exportUserRoleAssignments(rcon)
# Import/modify a user-role assignment
NewData <- data.frame(username = "desired_user_name", 
 unique_role_name = "KN3430U")
importUserRolesAssignments(rcon, 
 data = NewData)
## End(Not run)

Export, Import, or Delete User Roles in a Project

Description

These methods enable the user to export user roles, add user roles, or remove user roles from a project. They also enable the user to modify the permissions granted to a user.

Usage

exportUserRoles(rcon, ...)
importUserRoles(rcon, data, ...)
deleteUserRoles(rcon, user_roles, ...)
## S3 method for class 'redcapApiConnection'
exportUserRoles(rcon, labels = TRUE, form_rights = TRUE, ...)
## S3 method for class 'redcapApiConnection'
importUserRoles(rcon, data, consolidate = TRUE, ...)
## S3 method for class 'redcapApiConnection'
deleteUserRoles(rcon, user_roles, ...)

Arguments

Details

User project access fields (those not related to forms or exports) are mapped between coded and labeled values as:

Form access fields are mapped as:

Form export permission fields are mapped as:

Importing Users/User Roles

It is not required that the user provide a data frame with all of the fields available for modification. Only fields that are provided will be modified. The only required field for imports is the username field.

When setting permissions for a user project access fields, form access, and form export permissions, the user may provided any of the coded or labeled values above. The user data is passed through prepUserImportData() before sending it to the API; text values will be converted to the numeric value.

It is also permissible to use a column for each form individually, as can be exported via exportUsers() . With consolidate = TRUE, these settings will be consolidated into the text string expected by the API.

The REDCap API does not natively allow for modifying the rights of a user that is part of a User Role. When an attempt to modify the rights of a user in a User Role is made with this package, the user will be removed from the User Role, the rights modified, and then the User Role restored. This is done silently: be aware that modifications to a user's rights may not have an impact while the User Role is assigned.

Limitations

When importing via CSV, (as redcapAPI does by default) it appears that the form access rights are imported but may not always be reflected in the exported values. The form export rights do not appear to be imported when using the CSV format. We may be able to resolve this in the future using a JSON format.

Value

exportUserRoles returns a data frame with the columns:

When form_rights = TRUE, additional columns are created that give the form access and form export rights in an individual column for each form. Form access rights columns have the naming pattern ⁠[form_name]_access⁠ and the form export rights columns have the naming pattern ⁠[form_name]_export_access⁠.

importUserRoles invisibly returns the number of user roles that were added or modified.

deleteUserRoles invisibly returns the number of user roles that were deleted.

Functions

• exportUserRoles(): Export user roles from a project.

• importUserRoles(): Import user roles to a project.

• deleteUserRoles(): Delete user roles from a project.

See Also

exportUsers() ,
importUsers() ,
deleteUsers() ,
exportUserRoleAssignments() ,
importUserRoleAssignments()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"), 
 url = "your_redcap_url", 
 keyring = "API_KEYs", 
 envir = globalenv())
 
# Export users-roles
exportUserRoles(rcon)
# Export user-roles without additional form access variables
exportUsersRoles(rcon, 
 form_rights = FALSE)
 
# Export users as raw data
exportUserRoles(rcon, 
 labels = FALSE)
 
 
# Import new permissions
NewData <- data.frame(unique_role_name = "KN439U", 
 design = 0, 
 api_export = 1, 
 api_import = "No Access")
importUserRoles(rcon, 
 data = NewData)
 
# Remove a user from a project
deleteUserRoles(rcon, 
 user_roles = "KN439U")
## End(Not run) 

Validate Data Frames for Import

Description

Validates the variables in a data frame prior to attempting an import to REDCap

Usage

validateImport(data, meta_data, logfile = "")

Arguments

Details

validateImport is called internally by importRecords and is not available to the user.

Each variable is validated by matching they type of variable with the type listed in the REDCap database.

Although the log messages will indicate a preference for dates to be in mm/dd/yyyy format, the function will accept mm/dd/yy, yyyy-mm-dd, yyyy/mm/dd, and yyyymmdd formats as well. When possible, pass dates as Date objects or POSIXct objects to avoid confusion. Dates are also compared to minimum and maximum values listed in the data dictionary. Records where a date is found out of range are allowed to import and a message is printed in the log.

For continuous/numeric variables, the values are checked against the minimum and maximum allowed in the data dictionary. Records where a value is found out of range are allowed to import and a message is printed in the log.

ZIP codes are tested to see if they fit either the five digit or five digit + four format. When these conditions are not met, the data point is deleted and a message printed in the log.

YesNo fields permit any of the values 'yes', 'no', '0', '1' to be imported to REDCap with 0=No, and 1=Yes. The values are converted to lower case for validation, so any combination of lower and upper case values will pass (ie, the data frame is not case-sensitive).

TrueFalse fields will accept 'TRUE', 'FALSE', 0, 1, and logical values and are also not case-sensitive.

Radio and dropdown fields may have either the coding in the data dictionary or the labels in the data dictionary. The validation will use the meta data to convert any matching values to the appropriate coding before importing to REDCap. Values that cannot be reconciled are deleted with a message printed in the log. These variables are not case-sensitive.

Checkbox fields require a value of "Checked", "Unchecked", "0", or "1". These are currently case-sensitive. Values that do not match these are deleted with a warning printed in the log.

Phone numbers are required to be ten digit numbers. The phone number is broken into three parts: 1) a three digit area code, 2) a three digit exchange code, and 3) a four digit station code. The exchange code must start with a number from 2-9, followed by 0-8, and then any third digit. The exchange code starts with a number from 2-9, followed by any two digits. The station code is four digits with no restrictions.

E-mail addresses are considered valid when they have three parts. The first part comes before the @ symbol, and may be number of characters from a-z, A-Z, a period, underscore, percent, plus, or minus. The second part comes after the @, but before the period, and may consist of any number of letters, numbers, periods, or dashes. Finally, the string ends with a period then anywhere from two to six letters.

Convert R Vector To List for the API Call Body

Description

Converts an R vector to a list that will be suitable for makeApiCall.

Usage

vectorToApiBodyList(vector, parameter_name)

Arguments

Examples

## Not run: 
vectorToApiBodyList(1:3, "records")
## End(Not run)

Transform Data Into Wide Format

Description

Converts a dataframe into wide format given a single REDCap form. This function assumes that the Records argument is the result of exportRecordsTyped, and that all empty values have been previously dropped. This will only widen data frames that have a unique identification variable (e.g. 'record_id'), "redcap_event_name" and "redcap_repeat_instrument" in the fields. Otherwise, the data passed in will be returned unchanged.

Usage

widerRepeated(Records, rcon)

Arguments

See Also

Other post-processing functions

recastRecords() ,
guessCast() ,
guessDate() ,
castForImport() ,
mChoiceCast() ,
splitForms()

Examples

## Not run: 
unlockREDCap(connections = c(rcon = "project_alias"),
 url = "your_redcap_url",
 keyring = "API_KEYs",
 envir = globalenv())
Records <- exportRecordsTyped(rcon)
widerRepeated(Records, rcon)
## End(Not run)

Prepare a Data Frame for Import Through the API

Description

Converts a dataframe into a character value in the format of a CSV for import through the API.

Usage

writeDataForImport(data)

Arguments