Read records from a REDCap project in subsets, and stacks them together before returning a dataset

Source: R/redcap-read.R

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 tibble::tibble(). This function can be more appropriate than redcap_read_oneshot() when returning large datasets that could tie up the server.

redcap_read(
  batch_size = 100L,
  interbatch_delay = 0.5,
  continue_on_error = FALSE,
  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,
  guess_type = TRUE,
  guess_max = NULL,
  http_response_encoding = "UTF-8",
  locale = readr::default_locale(),
  verbose = TRUE,
  config_options = NULL,
  handle_httr = 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/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.

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

Deprecated.

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.

id_position

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

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_codes: A collection of http status codes, separated by semicolons. There is one code for each batch attempted.

  • outcome_messages: A collection of human readable strings indicating the operations' semicolons. There is one code for each batch attempted. In an unsuccessful operation, it should contain diagnostic information.

  • 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.

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.

Batching subsets of data

redcap_read() internally uses multiple calls to redcap_read_oneshot() to select and return data. Initially, only the primary key is queried through the REDCap API. The long list is then subsetted into batches, 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 tibble::tibble().

The function allows a delay between calls, which allows the server to attend to other users' requests (such as the users entering data in a browser). In other words, a delay between batches does not bog down the webserver when exporting/importing a large dataset.

A second benefit is less RAM is required on the webserver. Because each batch is smaller than the entire dataset, the webserver tackles more manageably sized objects in memory. Consider batching if you encounter the error:

ERROR: REDCap ran out of server memory. The request cannot be processed.
Please try importing/exporting a smaller amount of data.

A third benefit (compared to redcap_read()) is that important fields are included, even if not explicitly requested. As a result:

  1. record_id (or it's customized name) will always be returned

  2. redcap_event_name will be returned for longitudinal projects

  3. redcap_repeat_instrument and redcap_repeat_instance will be returned for projects with repeating instruments

Export permissions

For redcap_read_oneshot() 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:

  • go to 'User Rights' in the REDCap project site,

  • select the desired user, and then select 'Edit User Privileges',

  • in the 'Data Exports' radio buttons, select 'Full Data Set'.

Pseudofields

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'

Events

The event argument is a vector of characters passed to the server. It is the "event-name", not the "event-label". The event-label is the value presented to the users, which contains uppercase letters and spaces, while the event-name can contain only lowercase letters, digits, and underscores.

If event is nonnull and the project is not longitudinal, redcap_read() will throw an error. Similarly, if a value in the event vector is not a current event-name, redcap_read() will throw an error.

The simpler redcap_read_oneshot() function does not check for invalid event values, and will not throw errors.

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://bbmc.ouhsc.edu/redcap/api/"
token   <- "9A81268476645C4E5F03428B8AC3AA7B"

# Return the entire dataset
REDCapR::redcap_read(batch_size=2, redcap_uri=uri, token=token)$data
#> 24 variable metadata records were read from REDCap in 0.2 seconds.  The http status code was 200.
#> The data dictionary describing 17 fields was read from REDCap in 0.2 seconds.  The http status code was 200.
#> 3 instrument metadata records were read from REDCap in 0.2 seconds.  The http status code was 200.
#> 1 rows were read from REDCap in 0.2 seconds.  The http status code was 200.
#> 2 data access groups were read from REDCap in 0.2 seconds.  The http status code was 200.
#> 5 records and 1 columns were read from REDCap in 0.2 seconds.  The http status code was 200.
#> Starting to read 5 records  at 2023-09-05 00:38:26.228375.
#> Reading batch 1 of 3, with subjects 1 through 2 (ie, 2 unique subject records).
#> 2 records and 25 columns were read from REDCap in 0.2 seconds.  The http status code was 200.
#> Reading batch 2 of 3, with subjects 3 through 4 (ie, 2 unique subject records).
#> 2 records and 25 columns were read from REDCap in 0.2 seconds.  The http status code was 200.
#> Reading batch 3 of 3, with subjects 5 through 5 (ie, 1 unique subject records).
#> 1 records and 25 columns were read from REDCap in 0.2 seconds.  The http status code was 200.
#> # A tibble: 5 × 25
#>   record_id name_first name_last address  telephone email dob          age   sex
#>       <dbl> <chr>      <chr>     <chr>    <chr>     <chr> <date>     <dbl> <dbl>
#> 1         1 Nutmeg     Nutmouse  "14 Ros… (405) 32… nutt… 2003-08-30    11     0
#> 2         2 Tumtum     Nutmouse  "14 Ros… (405) 32… tumm… 2003-03-10    11     1
#> 3         3 Marcus     Wood      "243 Hi… (405) 32… mw@m… 1934-04-09    80     1
#> 4         4 Trudy      DAG       "342 El… (405) 32… pero… 1952-11-02    61     0
#> 5         5 John Lee   Walker    "Hotel … (405) 32… left… 1955-04-15    59     1
#> # ℹ 16 more variables: demographics_complete <dbl>, height <dbl>, weight <dbl>,
#> #   bmi <dbl>, comments <chr>, mugshot <chr>, health_complete <dbl>,
#> #   race___1 <dbl>, race___2 <dbl>, race___3 <dbl>, race___4 <dbl>,
#> #   race___5 <dbl>, race___6 <dbl>, ethnicity <dbl>, interpreter_needed <dbl>,
#> #   race_and_ethnicity_complete <dbl>

# Return a subset of columns while also specifying 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()
)
REDCapR::redcap_read(
  redcap_uri = uri,
  token      = token,
  col_types  = col_types,
  batch_size = 2
)$data
#> 24 variable metadata records were read from REDCap in 0.2 seconds.  The http status code was 200.
#> The data dictionary describing 17 fields was read from REDCap in 0.2 seconds.  The http status code was 200.
#> 3 instrument metadata records were read from REDCap in 0.2 seconds.  The http status code was 200.
#> 1 rows were read from REDCap in 0.2 seconds.  The http status code was 200.
#> 2 data access groups were read from REDCap in 0.2 seconds.  The http status code was 200.
#> 5 records and 1 columns were read from REDCap in 0.2 seconds.  The http status code was 200.
#> Starting to read 5 records  at 2023-09-05 00:38:29.785751.
#> Reading batch 1 of 3, with subjects 1 through 2 (ie, 2 unique subject records).
#> 2 records and 25 columns were read from REDCap in 0.2 seconds.  The http status code was 200.
#> Reading batch 2 of 3, with subjects 3 through 4 (ie, 2 unique subject records).
#> 2 records and 25 columns were read from REDCap in 0.2 seconds.  The http status code was 200.
#> Reading batch 3 of 3, with subjects 5 through 5 (ie, 1 unique subject records).
#> 1 records and 25 columns were read from REDCap in 0.2 seconds.  The http status code was 200.
#> # A tibble: 5 × 25
#>   record_id name_first name_last address  telephone email dob          age   sex
#>       <int> <chr>      <chr>     <chr>    <chr>     <chr> <date>     <dbl> <dbl>
#> 1         1 Nutmeg     Nutmouse  "14 Ros… (405) 32… nutt… 2003-08-30    11     0
#> 2         2 Tumtum     Nutmouse  "14 Ros… (405) 32… tumm… 2003-03-10    11     1
#> 3         3 Marcus     Wood      "243 Hi… (405) 32… mw@m… 1934-04-09    80     1
#> 4         4 Trudy      DAG       "342 El… (405) 32… pero… 1952-11-02    61     0
#> 5         5 John Lee   Walker    "Hotel … (405) 32… left… 1955-04-15    59     1
#> # ℹ 16 more variables: demographics_complete <dbl>, height <dbl>, weight <dbl>,
#> #   bmi <dbl>, comments <chr>, mugshot <chr>, health_complete <dbl>,
#> #   race___1 <lgl>, race___2 <lgl>, race___3 <lgl>, race___4 <lgl>,
#> #   race___5 <lgl>, race___6 <lgl>, ethnicity <dbl>, interpreter_needed <dbl>,
#> #   race_and_ethnicity_complete <dbl>
# }