Read/Export records from a REDCap project

Source: R/redcap-read-oneshot.R

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

redcap_read_oneshot(
  redcap_uri,
  token,
  records = NULL,
  records_collapsed = "",
  fields = NULL,
  fields_collapsed = "",
  forms = NULL,
  forms_collapsed = "",
  events = NULL,
  events_collapsed = "",
  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),
  col_types = NULL,
  guess_type = TRUE,
  guess_max = 1000L,
  http_response_encoding = "UTF-8",
  locale = readr::default_locale(),
  verbose = TRUE,
  config_options = NULL
)

Arguments

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 to a desired project field. Optional.

fields_collapsed

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

forms

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

forms_collapsed

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

events

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

events_collapsed

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

col_types

A readr::cols() object passed internally to readr::read_csv(). Optional.

guess_type

A boolean value indicating if all columns should be returned as character. If false, readr::read_csv() guesses the intended data type for each column. Ignored if col_types is not null.

guess_max

A positive integer 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 to pass to POST method in the httr package. See the details below. Optional.

Value

Currently, a list is returned with the following elements:

  • data: An R base::data.frame() 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.

Details

The full list of configuration options accepted by the httr package is viewable by executing httr::httr_options(). The httr package and documentation is available at https://cran.r-project.org/package=httr.

If you do not pass in this 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.

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.

Author

Will Beasley

Examples

if (FALSE) {
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

}