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Identify Missing Events in REDCap Data

Source: R/rd_event.R
rd_event.Rd

[Stable]

Helps identify records in a REDCap longitudinal project that are missing one or more specified events. Because REDCap typically omits empty events from exports, an event that contains no data for a record will not appear. This function finds those absent events and returns a per-record query table and a summarized HTML report.

Usage

rd_event(
  project = NULL,
  data = NULL,
  dic = NULL,
  event_form = NULL,
  event,
  filter = NA,
  query_name = NA,
  addTo = NA,
  report_title = NA,
  report_zeros = FALSE,
  link = list()
)

Arguments

project

A list containing the REDCap data, dictionary, and event mapping (expected redcap_data() output). Overrides data, dic, and event_form.

data

A data.frame or tibble with the REDCap dataset.

dic

A data.frame with the REDCap dictionary.

event_form

Only applicable for longitudinal projects (presence of events). Event-to-form mapping for longitudinal projects.

event

Character vector with one or more REDCap event names to check for missing records.

filter

Optional. A single character string containing a filter expression to subset the dataset before checking for missing events. Example: "age >= 18".

query_name

Optional character vector describing each query. Defaults to a standard format: The event (event_name) is missing.

addTo

Optional data frame from a previous query report to which the new results can be appended.

report_title

Optional string specifying the title of the final report. Defaults to "Report of queries".

report_zeros

Logical, include variables with zero queries in the report. Default is FALSE.

Optional list containing project information (domain, redcap_version, proj_id, event_id) to generate clickable links for each query.

Value

A named list with two elements:

queries

A data frame listing records missing the specified events. Columns: Identifier, DAG, Event, Instrument, Field, Repetition, Description, Query, Code, and optionally Link. If no queries are found this will be an empty data frame with the expected columns.

results

An HTML table (knitr::kable styled with kableExtra) summarising the number of missing records per event. Returned as knitr::kable (HTML).

Examples

# Minimal reproducible example
data0 <- data.frame(
  record_id = c("100-1", "100-2", "200-1"),
  redcap_event_name = c("baseline_arm_1", "baseline_arm_1", "follow_up_arm_1"),
  redcap_event_name.factor = factor(c("Baseline", "Baseline", "Follow-up")),
  stringsAsFactors = FALSE
)

# Suppose we want to check that every record has the follow-up event
res <- rd_event(
  data = data0,
  dic = data.frame(),       # placeholder dictionary
  event = "follow_up_arm_1",
  report_zeros = TRUE
)

# Records missing the event:
res$queries
#>   Identifier DAG           Event Instrument Field Repetition Description
#> 1      100-1   - follow_up_arm_1          -     -          -   Follow-up
#> 2      100-2   - follow_up_arm_1          -     -          -   Follow-up
#>                               Query    Code
#> 1 The event 'Follow-up' is missing. 100-1-1
#> 2 The event 'Follow-up' is missing. 100-2-1

# HTML summary (in RMarkdown or Viewer)
res$results
#> <table class="table table-striped table-condensed" style="width: auto !important; margin-left: auto; margin-right: auto;">
#> <caption>Report of queries</caption>
#>  <thead>
#>   <tr>
#>    <th style="text-align:center;border-bottom: 1px solid grey"> Events </th>
#>    <th style="text-align:center;border-bottom: 1px solid grey"> Description </th>
#>    <th style="text-align:center;border-bottom: 1px solid grey"> Total </th>
#>   </tr>
#>  </thead>
#> <tbody>
#>   <tr>
#>    <td style="text-align:center;"> follow_up_arm_1 </td>
#>    <td style="text-align:center;"> Follow-up </td>
#>    <td style="text-align:center;"> 2 </td>
#>   </tr>
#> </tbody>
#> </table>