| Title: | Transfer 'REDCap' Data to Database |
|---|---|
| Description: | Transfer 'REDCap' (Research Electronic Data Capture) data to a database, specifically optimized for 'DuckDB'. Processes data in chunks to handle large datasets without exceeding available memory. Features include data labeling, coded value conversion, and hearing a "quack" sound on success. |
| Authors: | Dylan Pieper [aut, cre] |
| Maintainer: | Dylan Pieper <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 0.3.0 |
| Built: | 2026-05-28 07:20:13 UTC |
| Source: | https://github.com/dylanpieper/redquack |
Closes a DuckDB connection.
close_duckdb(conn)close_duckdb(conn)
conn |
A DuckDB connection object. |
Invisible NULL.
## Not run: conn <- use_duckdb() # Use the connection... close_duckdb(conn) ## End(Not run)## Not run: conn <- use_duckdb() # Use the connection... close_duckdb(conn) ## End(Not run)
Collect data from a database table reference (tbl) and apply column and/or value labels from REDCap metadata using the labelled package. This function works in the tidy style with dplyr.
collect_labeled( data, cols = TRUE, vals = TRUE, convert = TRUE, metadata_table_name = "metadata" )collect_labeled( data, cols = TRUE, vals = TRUE, convert = TRUE, metadata_table_name = "metadata" )
data |
A tbl_sql object (database table reference) to apply labels to. The connection and table name are automatically extracted. |
cols |
Logical indicating whether to apply column (variable) labels. Default is TRUE. |
vals |
Logical indicating whether to apply value labels to coded variables. Default is TRUE. |
convert |
Logical indicating whether to convert coded values to their text labels (e.g., 0/1 becomes "No"/"Yes"). Default is TRUE. |
metadata_table_name |
Character string specifying the metadata table name. Default is "metadata". |
A data frame with labels applied according to the cols and vals parameters. If convert = TRUE, coded values are converted to text.
## Not run: library(redquack) duckdb <- DBI::dbConnect(duckdb::duckdb(), "redcap.duckdb") # Apply both column and value labels (default) labeled_data <- tbl_redcap(duckdb, "data") |> collect_labeled() # Apply only column labels col_labeled_data <- tbl_redcap(duckdb, "data") |> collect_labeled(vals = FALSE) # Apply only value labels val_labeled_data <- tbl_redcap(duckdb, "data") |> collect_labeled(cols = FALSE) # Apply labels and convert values to text labeled_data <- tbl_redcap(duckdb, "data") |> collect_labeled(convert = TRUE) # Explicit metadata table name (useful after complex filtering) labeled_data <- tbl(duckdb, "data") |> dplyr::filter(name_last == "Nutmouse") |> collect_labeled(metadata_table_name = "metadata") DBI::dbDisconnect(duckdb) ## End(Not run)## Not run: library(redquack) duckdb <- DBI::dbConnect(duckdb::duckdb(), "redcap.duckdb") # Apply both column and value labels (default) labeled_data <- tbl_redcap(duckdb, "data") |> collect_labeled() # Apply only column labels col_labeled_data <- tbl_redcap(duckdb, "data") |> collect_labeled(vals = FALSE) # Apply only value labels val_labeled_data <- tbl_redcap(duckdb, "data") |> collect_labeled(cols = FALSE) # Apply labels and convert values to text labeled_data <- tbl_redcap(duckdb, "data") |> collect_labeled(convert = TRUE) # Explicit metadata table name (useful after complex filtering) labeled_data <- tbl(duckdb, "data") |> dplyr::filter(name_last == "Nutmouse") |> collect_labeled(metadata_table_name = "metadata") DBI::dbDisconnect(duckdb) ## End(Not run)
Takes a database table reference (tbl) and collects it into a list of instruments
with column and value labels and optional coded value conversion.
This function works in the tidy style with dplyr and separates the data by REDCap instruments.
Use collect_labeled_list as an alias for the same functionality.
collect_list( data, cols = FALSE, vals = FALSE, convert = FALSE, metadata_table_name = "metadata" ) collect_labeled_list( data, cols = TRUE, vals = TRUE, convert = TRUE, metadata_table_name = "metadata" )collect_list( data, cols = FALSE, vals = FALSE, convert = FALSE, metadata_table_name = "metadata" ) collect_labeled_list( data, cols = TRUE, vals = TRUE, convert = TRUE, metadata_table_name = "metadata" )
data |
A tbl object referencing a database table (created with |
cols |
Logical indicating whether to apply column (variable) labels. Default is FALSE. |
vals |
Logical indicating whether to apply value labels to coded variables. Default is FALSE. |
convert |
Logical indicating whether to convert labeled values to their text labels (e.g., 0/1 becomes "No"/"Yes"). Default is FALSE. |
metadata_table_name |
Character string specifying the metadata table name. Default is "metadata". |
Returns a named list of data frames, one per instrument. If only one instrument is present, returns the single data frame instead of a list.
redcap_to_db for transferring data to a database
collect_labeled for collecting labeled data as a single data frame
## Not run: library(redquack) library(dplyr) conn <- use_duckdb() result <- redcap_to_db( conn, url = "https://bbmc.ouhsc.edu/redcap/api/", token = "9A81268476645C4E5F03428B8AC3AA7B" ) # Convert table to a list of instruments instruments <- tbl_redcap(conn) |> collect_list() # Control labeling behavior instruments_no_val_labels <- tbl_redcap(conn) |> collect_list(cols = FALSE) # Convert coded values to text labels instruments_with_codes <- tbl_redcap(conn) |> collect_list(convert = TRUE) # Works with filtered data filtered_instruments <- tbl_redcap(conn) |> filter(name_last == "Nutmouse") |> collect_list() remove_duckdb(conn) ## End(Not run)## Not run: library(redquack) library(dplyr) conn <- use_duckdb() result <- redcap_to_db( conn, url = "https://bbmc.ouhsc.edu/redcap/api/", token = "9A81268476645C4E5F03428B8AC3AA7B" ) # Convert table to a list of instruments instruments <- tbl_redcap(conn) |> collect_list() # Control labeling behavior instruments_no_val_labels <- tbl_redcap(conn) |> collect_list(cols = FALSE) # Convert coded values to text labels instruments_with_codes <- tbl_redcap(conn) |> collect_list(convert = TRUE) # Works with filtered data filtered_instruments <- tbl_redcap(conn) |> filter(name_last == "Nutmouse") |> collect_list() remove_duckdb(conn) ## End(Not run)
Inspects the structure of the project data table showing column information including name, type, and properties. This is a convenience wrapper around DBI::dbGetQuery() for examining table schema. Uses the data table name stored in the connection attributes if available.
inspect(conn, table_name = NULL)inspect(conn, table_name = NULL)
conn |
A DuckDB connection object. |
table_name |
Character string specifying the table name. If NULL, uses the table name stored in connection attributes. Default is NULL. |
A data frame containing table information with columns for column ID, name, type, not null status, default value, and primary key.
## Not run: table_info <- inspect(conn) ## End(Not run)## Not run: table_info <- inspect(conn) ## End(Not run)
Assign a list of instruments (data frames) to the global environment. Each element of the list becomes a separate object in the global environment.
list_to_env(instruments)list_to_env(instruments)
instruments |
A named list of data frames, typically output from tbl_to_list(). |
Invisibly returns NULL. Side effect: assigns objects to the global environment.
## Not run: tbl(conn, "data") |> tbl_to_list() |> list_to_env() ## End(Not run)## Not run: tbl(conn, "data") |> tbl_to_list() |> list_to_env() ## End(Not run)
Creates a tbl reference to the metadata table in the database and automatically collects it as a data frame. Uses the metadata table name stored in the connection attributes if available.
metadata(conn, metadata_table_name = NULL)metadata(conn, metadata_table_name = NULL)
conn |
A DuckDB connection object. |
metadata_table_name |
Character string specifying the metadata table name. If NULL, uses the table name stored in connection attributes. Default is NULL. |
A data frame containing the metadata.
## Not run: meta <- metadata(conn) ## End(Not run)## Not run: meta <- metadata(conn) ## End(Not run)
Creates a tbl reference to the REDCap logs table in the database and automatically collects it as a data frame. Uses the REDCap logs table name stored in the connection attributes if available.
redcap_log(conn, redcap_log_table_name = NULL)redcap_log(conn, redcap_log_table_name = NULL)
conn |
A DuckDB connection object. |
redcap_log_table_name |
Character string specifying the REDCap logs table name. If NULL, uses the table name stored in connection attributes. Default is NULL. |
A data frame containing the REDCap audit log data.
## Not run: redcap_log <- redcap_log(conn) ## End(Not run)## Not run: redcap_log <- redcap_log(conn) ## End(Not run)
Transfer REDCap data to a database in chunks of record IDs to minimize memory 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, ... )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, ... )
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 |
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., |
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. |
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
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
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
## Not run: 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) ## End(Not run)## Not run: 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) ## End(Not run)
Closes a DuckDB connection and removes the database file.
remove_duckdb(conn, dbname = "redcap.duckdb")remove_duckdb(conn, dbname = "redcap.duckdb")
conn |
A DuckDB connection object. |
dbname |
Character string specifying the database file name. Default is "redcap.duckdb". |
Invisible NULL.
## Not run: conn <- use_duckdb() # Use the connection... remove_duckdb(conn) ## End(Not run)## Not run: conn <- use_duckdb() # Use the connection... remove_duckdb(conn) ## End(Not run)
Saves data directly from the database to a Parquet file using DuckDB's native COPY command. This is much faster than reading into R first and creates smaller files for easy sharing. Uses the data table name stored in the connection attributes if available.
save_parquet( conn, file_path = "redcap.parquet", table_name = NULL, query = NULL )save_parquet( conn, file_path = "redcap.parquet", table_name = NULL, query = NULL )
conn |
A DuckDB connection object. |
file_path |
Character string specifying the output file path. Default is "redcap.parquet". |
table_name |
Character string specifying the source table name. If NULL, uses the table name stored in connection attributes. Default is NULL. |
query |
Character string with custom SQL query to export. If provided, table_name is ignored. |
Invisible NULL. Side effect: creates Parquet file at specified path.
## Not run: # Save entire data table save_parquet(conn, "redcap.parquet") ## End(Not run)## Not run: # Save entire data table save_parquet(conn, "redcap.parquet") ## End(Not run)
Creates a tbl reference to the main REDCap data table in the database. The original table name is stored as an attribute to preserve context through dplyr operations (limited to filter, select, arrange, and group_by). Uses the data table name stored in the connection attributes if available.
tbl_redcap(conn, table_name = NULL)tbl_redcap(conn, table_name = NULL)
conn |
A DuckDB connection object. |
table_name |
Character string specifying the table name. If NULL, uses the table name stored in connection attributes. Default is NULL. |
A tbl_sql object referencing the data table with redcap_table attribute.
## Not run: data <- tbl_redcap(conn) ## End(Not run)## Not run: data <- tbl_redcap(conn) ## End(Not run)
Creates a tbl reference to the transfer logs table in the database and automatically collects it as a data frame. Uses the transfer logs table name stored in the connection attributes if available.
transfer_log(conn, transfer_log_table_name = NULL)transfer_log(conn, transfer_log_table_name = NULL)
conn |
A DuckDB connection object. |
transfer_log_table_name |
Character string specifying the transfer logs table name. If NULL, uses the table name stored in connection attributes. Default is NULL. |
A data frame containing the transfer log data.
## Not run: transfer_log <- transfer_log(conn) ## End(Not run)## Not run: transfer_log <- transfer_log(conn) ## End(Not run)
Creates a DuckDB connection to the REDCap database file.
use_duckdb(dbname = "redcap.duckdb")use_duckdb(dbname = "redcap.duckdb")
dbname |
Character string specifying the database file name. Default is "redcap.duckdb". |
A DuckDB connection object.
## Not run: conn <- use_duckdb() # Use the connection... remove_duckdb(conn) ## End(Not run)## Not run: conn <- use_duckdb() # Use the connection... remove_duckdb(conn) ## End(Not run)