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Transfer 'REDCap' Data to a Database

redcap_to_db.Rd

Transfer REDCap data to a database in chunks of record IDs to minimize memory usage.

Usage

redcap_to_db(
  conn,
  url,
  token,
  data_table_name = "data",
  metadata_table_name = "metadata",
  transfer_log_table_name = "transfer_log",
  redcap_log_table_name = "redcap_log",
  redcap_log_begin_date = Sys.Date() - 6,
  redcap_log_end_date = Sys.Date(),
  export_survey_fields = FALSE,
  export_data_access_groups = FALSE,
  blank_for_gray_form_status = FALSE,
  filter_logic = "",
  datetime_range_begin = as.POSIXct(NA),
  datetime_range_end = as.POSIXct(NA),
  fields = NULL,
  forms = NULL,
  events = NULL,
  record_id_name = "record_id",
  chunk_size = 1000,
  chunk_delay = 0.5,
  max_retries = 10,
  echo = "all",
  beep = TRUE,
  ...
)

Arguments

conn

A DBI connection object to a database.

url

Character string specifying the URI (uniform resource identifier) of the REDCap server's API.

token

Character string containing the REDCap API token specific to your project. This token is used for authentication and must have export permissions.

data_table_name

Character string specifying the name of the table to create or append data to. Default is "data". Can include schema name (e.g. "schema.table").

metadata_table_name

Character string specifying the name of the table to store REDCap metadata. Default is "metadata". Can include schema name (e.g. "schema.metadata").

transfer_log_table_name

Character string specifying the name of the table to store transfer logs. Default is "transfer_log". Can include schema name (e.g. "schema.transfer_log"). Set to NULL to disable logging.

redcap_log_table_name

Character string specifying the name of the table to store REDCap audit logs. Default is "redcap_log". Can include schema name (e.g. "schema.redcap_log"). Set to NULL to skip REDCap log retrieval.

redcap_log_begin_date

Date/POSIXct specifying the start date for REDCap log retrieval. Default is 6 days prior to today.

redcap_log_end_date

Date/POSIXct specifying the end date for REDCap log retrieval. Default is today.

export_survey_fields

Logical that specifies whether to export the survey identifier field (e.g., 'redcap_survey_identifier') or survey timestamp fields. Default is FALSE.

export_data_access_groups

Logical 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.

blank_for_gray_form_status

Logical that specifies whether or not to export blank values for instrument complete status fields that have a gray status icon. Default is FALSE.

filter_logic

String of logic text (e.g., [gender] = 'male') for filtering the data to be returned, where the API will only return records where the logic evaluates as TRUE. Default is an empty string.

datetime_range_begin

To return only records that have been created or modified after a given datetime, provide a POSIXct value. Default is NA (no begin time).

datetime_range_end

To return only records that have been created or modified before a given datetime, provide a POSIXct value. Default is NA (no end time).

fields

Character vector specifying which fields to export. Default is NULL (all fields).

forms

Character vector specifying which forms to export. Default is NULL (all forms).

events

Character vector specifying which events to export. Default is NULL (all events).

record_id_name

Character string specifying the field name that contains record identifiers used for chunking requests. Default is "record_id".

chunk_size

Integer specifying the number of record IDs per chunk. Default is 1000. Consider decreasing this for projects with many fields.

chunk_delay

Numeric value specifying the delay in seconds between chunked requests. Default is 0.5 seconds. Adjust to respect REDCap server limits.

max_retries

Integer specifying the maximum number of retry attempts for failed API connection or HTTP 504 error. Default is 10.

echo

String to show a progress bar and all status messages ("all"), only a progress bar ("progress"), or nothing ("none"). Default is "all".

beep

Logical indicating whether to play sound notifications when the process completes or encounters errors. Default is TRUE.

...

Additional arguments passed to the REDCap API call.

Value

Returns a list with the following components:

  • success: Logical if the transfer was completed with no failed processing

  • error_chunks: Vector of chunk numbers that failed processing

  • time_s: Numeric value for total seconds to transfer and optimize data

Details

This function transfers data from REDCap to any database in chunks, which helps manage memory usage when dealing with large projects. It creates up to four tables in the database:

  • data_table_name: Contains all transferred REDCap records

  • metadata_table_name: Contains REDCap metadata for field definitions and labeling

  • transfer_log_table_name: Contains timestamped logs of the transfer process

  • redcap_log_table_name: Contains REDCap audit logs (optional)

The function automatically detects existing databases and handles them in three ways:

  • If no table exists, starts a new transfer process

  • If a table exists but is incomplete, resumes from the last processed record ID

  • If a table exists and is complete, returns success without reprocessing

The function fetches record IDs, then processes records in chunks. If any error occurs during processing, the function will continue with remaining chunks but mark the transfer as incomplete.

If redcap_log_table_name is provided, the function will also retrieve REDCap audit logs and store them in a separate table. The date range for log retrieval can be controlled with redcap_log_begin_date and redcap_log_end_date parameters.

Data is first set to VARCHAR/TEXT type for consistent handling across chunks. For DuckDB, data types are automatically optimized after data is inserted:

  • INTEGER: Columns with only whole numbers

  • DOUBLE: Columns with decimal numbers

  • DATE: Columns with valid dates

  • TIMESTAMP: Columns with valid timestamps

  • VARCHAR/TEXT: All other columns remain as strings

See also

use_duckdb for establishing a local duckdb connection close_duckdb for closing a local duckdb connection remove_duckdb for closing a local duckdb connection and removing the file collect_labeled for collecting a database table into a single data frame with column and value labels (converts coded values to their text labels by default) collect_list for collecting a database table into a list of instruments collect_labeled_list for collecting a database table into a list of instruments with column and value labels (converts coded values to their text labels by default) list_to_env for assigning a list of instruments to the global environment

Examples

if (FALSE) { # \dontrun{
library(redquack)
library(dplyr)

conn <- use_duckdb()

result <- redcap_to_db(
  conn,
  url = "https://bbmc.ouhsc.edu/redcap/api/",
  token = "9A81268476645C4E5F03428B8AC3AA7B"
)

data <- tbl_redcap(conn) |>
  collect()

remove_duckdb(conn)
} # }