redcap_read: Read records from a REDCap project in subsets, and stacks...

Description Usage Arguments Details Value Author(s) References Examples

View source: R/redcap-read.R

Description

From an external perspective, this function is similar to redcap_read_oneshot(). The internals differ in that redcap_read retrieves subsets of the data, and then combines them before returning (among other objects) a single base::data.frame(). This function can be more appropriate than redcap_read_oneshot() when returning large datasets that could tie up the server.

Usage

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redcap_read(batch_size = 100L, interbatch_delay = 0.5,
  continue_on_error = FALSE, redcap_uri, token, records = NULL,
  records_collapsed = "", fields = NULL, fields_collapsed = "",
  events = NULL, events_collapsed = "", export_data_access_groups = FALSE,
  filter_logic = "", raw_or_label = "raw", verbose = TRUE,
  config_options = NULL, id_position = 1L)

Arguments

batch_size

The maximum number of subject records a single batch should contain. The default is 100.

interbatch_delay

The number of seconds the function will wait before requesting a new subset from REDCap. The default is 0.5 seconds.

continue_on_error

If an error occurs while reading, should records in subsequent batches be attempted. The default is FALSE, which prevents subsequent batches from running. Required.

redcap_uri

The URI (uniform resource identifier) of the REDCap project. Required.

token

The user-specific string that serves as the password for a project. Required.

records

An array, where each element corresponds to the ID of a desired record. Optional.

records_collapsed

A single string, where the desired ID values are separated by commas. Optional.

fields

An array, where each element corresponds a desired project field. Optional.

fields_collapsed

A single string, where the desired field names are separated by commas. Optional.

events

An array, where each element corresponds a desired project event Optional.

events_collapsed

A single string, where the desired event names are separated by commas. Optional.

export_data_access_groups

A boolean value that specifies whether or not to export the redcap_data_access_group field when data access groups are utilized in the project. Default is FALSE. See the details below.

filter_logic

String of logic text (e.g., [gender] = 'male') for filtering the data to be returned by this API method, in which the API will only return the records (or record-events, if a longitudinal project) where the logic evaluates as TRUE. An blank/empty string returns all records.

raw_or_label

A string (either 'rawor 'label' that specifies whether to export the raw coded values or the labels for the options of multiple choice fields. Default is'raw''.

verbose

A boolean value indicating if messages should be printed to the R console during the operation. The verbose output might contain sensitive information (e.g. PHI), so turn this off if the output might be visible somewhere public. Optional.

config_options

A list of options to pass to POST method in the httr package. See the details in redcap_read_oneshot() Optional.

id_position

The column position of the variable that unique identifies the subject. This defaults to the first variable in the dataset.

Details

Specifically, it internally uses multiple calls to redcap_read_oneshot() to select and return data. Initially, only primary key is queried through the REDCap API. The long list is then subsetted into partitions, whose sizes are determined by the batch_size parameter. REDCap is then queried for all variables of the subset's subjects. This is repeated for each subset, before returning a unified base::data.frame().

The function allows a delay between calls, which allows the server to attend to other users' requests.

For redcap_read() to function properly, the user must have Export permissions for the 'Full Data Set'. Users with only 'De-Identified' export privileges can still use redcap_read_oneshot. To grant the appropriate permissions:

Value

Currently, a list is returned with the following elements,

Author(s)

Will Beasley

References

The official documentation can be found on the 'API Help Page' and 'API Examples' pages on the REDCap wiki (ie, https://community.projectredcap.org/articles/456/api-documentation.html and https://community.projectredcap.org/articles/462/api-examples.html). If you do not have an account for the wiki, please ask your campus REDCap administrator to send you the static material.

Examples

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## Not run: 
library(REDCapR) #Load the package into the current R session.
uri     <- "https://bbmc.ouhsc.edu/redcap/api/"
token   <- "9A81268476645C4E5F03428B8AC3AA7B"
redcap_read(batch_size=2, redcap_uri=uri, token=token)

## End(Not run)

REDCapR documentation built on May 29, 2017, 9:24 a.m.