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Read/Export records from a REDCap project –still in development

Source: R/redcap-read-oneshot-eav.R
redcap_read_oneshot_eav.Rd

This function uses REDCap's API to select and return data. This function is still in development.

Usage

redcap_read_oneshot_eav(
  redcap_uri,
  token,
  records = NULL,
  fields = NULL,
  forms = NULL,
  events = NULL,
  raw_or_label = "raw",
  raw_or_label_headers = "raw",
  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,
  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 field. 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_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 (https://stat.ethz.ch/R-manual/R-devel/library/base/html/as.POSIXlt.html) 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 (https://stat.ethz.ch/R-manual/R-devel/library/base/html/as.POSIXlt.html) 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.

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.

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.

Details

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 5.2.3: 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.

As of REDCap 6.14.3, this field is not exported in the EAV API call.

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

# \dontrun{
uri      <- "https://redcap-dev-2.ouhsc.edu/redcap/api/"
token    <- "9A068C425B1341D69E83064A2D273A70"

# Return all records and all variables.
ds <- REDCapR:::redcap_read_oneshot_eav(redcap_uri=uri, token=token)$data
#> The data dictionary describing 17 fields was read from REDCap in 0.2 seconds.  The http status code was 200.
#> 24 variable metadata records were read from REDCap in 0.2 seconds.  The http status code was 200.
#> 5 records and 20 columns were read from REDCap in 0.2 seconds.  The http status code was 200.

# Return only records with IDs of 1 and 3
desired_records_v1 <- c(1, 3)
ds_some_rows_v1    <- REDCapR:::redcap_read_oneshot_eav(
   redcap_uri = uri,
   token      = token,
   records    = desired_records_v1
)$data
#> The data dictionary describing 17 fields was read from REDCap in 0.2 seconds.  The http status code was 200.
#> 24 variable metadata records were read from REDCap in 0.2 seconds.  The http status code was 200.
#> 2 records and 20 columns were read from REDCap in 0.2 seconds.  The http status code was 200.

# 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_eav(
   redcap_uri = uri,
   token      = token,
   fields     = desired_fields_v1
)$data
#> The data dictionary describing 17 fields was read from REDCap in 0.2 seconds.  The http status code was 200.
#> 24 variable metadata records were read from REDCap in 0.2 seconds.  The http status code was 200.
#> 5 records and 4 columns were read from REDCap in 0.3 seconds.  The http status code was 200.
# }