redcap_read_oneshot: Read/Export records from a REDCap project

In REDCapR: Interaction Between R and REDCap

Read/Export records from a REDCap project

Description

This function uses REDCap's API to select and return data.

Usage

redcap_read_oneshot(
  redcap_uri,
  token,
  records = NULL,
  fields = NULL,
  forms = NULL,
  events = NULL,
  raw_or_label = "raw",
  raw_or_label_headers = "raw",
  export_checkbox_label = FALSE,
  export_survey_fields = FALSE,
  export_data_access_groups = FALSE,
  filter_logic = "",
  datetime_range_begin = as.POSIXct(NA),
  datetime_range_end = as.POSIXct(NA),
  blank_for_gray_form_status = FALSE,
  col_types = NULL,
  na = c("", "NA"),
  guess_type = TRUE,
  guess_max = 1000,
  http_response_encoding = "UTF-8",
  locale = readr::default_locale(),
  verbose = TRUE,
  config_options = NULL,
  handle_httr = NULL
)

Arguments

redcap_uri	The uri/url of the REDCap server typically formatted as "https://server.org/apps/redcap/api/". 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.
fields	An array, where each element corresponds to a desired project field. Optional.
forms	An array, where each element corresponds to a desired project form. Optional.
events	An array, where each element corresponds to a desired project event. Optional.
raw_or_label	A string (either 'raw' or 'label') that specifies whether to export the raw coded values or the labels for the options of multiple choice fields. Default is 'raw'.
raw_or_label_headers	A string (either 'raw' or 'label' that specifies for the CSV headers whether to export the variable/field names (raw) or the field labels (label). Default is 'raw'.
export_checkbox_label	specifies the format of checkbox field values specifically when exporting the data as labels. If raw_or_label is 'label' and export_checkbox_label is TRUE, the values will be the text displayed to the users. Otherwise, the values will be 0/1.
export_survey_fields	A boolean that specifies whether to export the survey identifier field (e.g., 'redcap_survey_identifier') or survey timestamp fields (e.g., instrument+'_timestamp'). The timestamp outputs reflect the survey's completion time (according to the time and timezone of the REDCap server.)
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.
datetime_range_begin	To return only records that have been created or modified after a given datetime, provide a POSIXct value. If not specified, REDCap will assume no begin time.
datetime_range_end	To return only records that have been created or modified before a given datetime, provide a POSIXct value. If not specified, REDCap will assume no end time.
blank_for_gray_form_status	A boolean value that specifies whether or not to export blank values for instrument complete status fields that have a gray status icon. All instrument complete status fields having a gray icon can be exported either as a blank value or as "0" (Incomplete). Blank values are recommended in a data export if the data will be re-imported into a REDCap project. Default is FALSE.
col_types	A readr::cols() object passed internally to readr::read_csv(). Optional.
na	A character vector passed internally to readr::read_csv(). Defaults to c("", "NA").
guess_type	A boolean value indicating if all columns should be returned as character. If true, readr::read_csv() guesses the intended data type for each column. Ignored if col_types is not null.
guess_max	A positive base::numeric value passed to readr::read_csv() that specifies the maximum number of records to use for guessing column types.
http_response_encoding	The encoding value passed to httr::content(). Defaults to 'UTF-8'.
locale	a readr::locale() object to specify preferences like number, date, and time formats. This object is passed to readr::read_csv(). Defaults to readr::default_locale().
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 passed to httr::POST(). See details at httr::httr_options(). Optional.
handle_httr	The value passed to the handle parameter of httr::POST(). This is useful for only unconventional authentication approaches. It should be NULL for most institutions. Optional.

Details

If you do not pass an export_data_access_groups value, it will default to FALSE. The following is from the API help page for version 10.5.1: This flag is only viable if the user whose token is being used to make the API request is not in a data access group. If the user is in a group, then this flag will revert to its default value.

The REDCap project may contain "pseudofields", depending on its structure. Pseudofields are exported for certain project structures, but are not defined by users and do not appear in the codebook. If a recognized pseudofield is passed to the fields api parameter, it is suppressed by redcap_read() and redcap_read_oneshot() so the server doesn't throw an error. Requesting a pseudofield is discouraged, so a message is returned to the user.

Pseudofields include:

• redcap_event_name: for longitudinal projects or multi-arm projects.

• redcap_repeat_instrument: for projects with repeating instruments.

• redcap_repeat_instance: for projects with repeating instruments.

• redcap_data_access_group: for projects with DAGs when the export_data_access_groups api parameter is TRUE.

• redcap_survey_identifier: for projects with surveys when the export_survey_fields api parameter is TRUE.

• instrument_name⁠_timestamp⁠: for projects with surveys. For example, an instrument called "demographics" will have a pseudofield named demographics_timestamp. REDCapR does not suppress requests for timestamps, so the server will throw an error like

  ERROR: The following values in the parameter fields are not valid: 'demographics_timestamp'
  

Value

Currently, a list is returned with the following elements:

• data: A tibble::tibble() of the desired records and columns.

• success: A boolean value indicating if the operation was apparently successful.

• status_code: The http status code of the operation.

• outcome_message: A human readable string indicating the operation's outcome.

• records_collapsed: The desired records IDs, collapsed into a single string, separated by commas.

• fields_collapsed: The desired field names, collapsed into a single string, separated by commas.

• filter_logic: The filter statement passed as an argument.

• elapsed_seconds: The duration of the function.

• raw_text: If an operation is NOT successful, the text returned by REDCap. If an operation is successful, the raw_text is returned as an empty string to save RAM.

If no records are retrieved (such as no records meet the filter criteria), a zero-row tibble is returned. Currently the empty tibble has zero columns, but that may change in the future.

Author(s)

Will Beasley

References

The official documentation can be found on the 'API Help Page' and 'API Examples' pages on the REDCap wiki (i.e., 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

## Not run: 
uri      <- "https://bbmc.ouhsc.edu/redcap/api/"
token    <- "9A81268476645C4E5F03428B8AC3AA7B"

# Return all records and all variables.
ds <- REDCapR::redcap_read_oneshot(redcap_uri=uri, token=token)$data

# Return only records with IDs of 1 and 3
desired_records_v1 <- c(1, 3)
ds_some_rows_v1 <- REDCapR::redcap_read_oneshot(
  redcap_uri = uri,
  token      = token,
  records    = desired_records_v1
)$data

# Return only the fields record_id, name_first, and age
desired_fields_v1 <- c("record_id", "name_first", "age")
ds_some_fields_v1 <- REDCapR::redcap_read_oneshot(
  redcap_uri = uri,
  token      = token,
  fields     = desired_fields_v1
)$data

# Specify the column types.
col_types <- readr::cols(
  record_id  = readr::col_integer(),
  race___1   = readr::col_logical(),
  race___2   = readr::col_logical(),
  race___3   = readr::col_logical(),
  race___4   = readr::col_logical(),
  race___5   = readr::col_logical(),
  race___6   = readr::col_logical()
)
ds_col_types <- REDCapR::redcap_read_oneshot(
  redcap_uri = uri,
  token      = token,
  col_types  = col_types
)$data

## End(Not run)

REDCapR documentation built on Sept. 11, 2024, 7:46 p.m.