Make a ‘Choose All’ Table

library(tidyREDCap)
library(dplyr)

The Problem

REDCap exports a “choose all that apply” question into a series of similarly-named, binary indicator variables (i.e., the variables are equal to either “checked” or “unchecked”). For example, the following data represents a sample of responses to the Nacho Craving Index.

redcap <- readRDS(file = "./redcap.rds")
redcap %>% 
  select(starts_with("ingredients___")) %>% 
  head()
#>   ingredients___1 ingredients___2 ingredients___3 ingredients___4
#> 1         Checked         Checked         Checked         Checked
#> 2         Checked         Checked       Unchecked         Checked
#> 3       Unchecked       Unchecked       Unchecked       Unchecked
#> 4       Unchecked       Unchecked       Unchecked       Unchecked
#> 5       Unchecked       Unchecked       Unchecked       Unchecked
#> 6       Unchecked       Unchecked       Unchecked       Unchecked
#>   ingredients___5 ingredients___6 ingredients___7 ingredients___8
#> 1         Checked         Checked       Unchecked         Checked
#> 2         Checked       Unchecked         Checked         Checked
#> 3       Unchecked       Unchecked       Unchecked       Unchecked
#> 4       Unchecked       Unchecked       Unchecked       Unchecked
#> 5       Unchecked       Unchecked       Unchecked       Unchecked
#> 6       Unchecked       Unchecked       Unchecked       Unchecked

It is desirable to have a concise table showing how often each option was chosen.

Aside: Loading REDCap Data into R

See the Import All Instruments from a REDCap Project and Importing from REDCap vignettes for details/information.

The Solution

Data Loaded with import_instruments()

If you pass the make_choose_all_table() function, the name of a REDCap export, and the name of the choose all that apply question question in REDCap, it will produce a concise frequency count table.

make_choose_all_table(redcap, "ingredients") 
#> # A tibble: 8 × 2
#>   What          Count
#>   <chr>         <dbl>
#> 1 Chips             9
#> 2 Yellow cheese     7
#> 3 Orange cheese     3
#> 4 White cheese      4
#> 5 Meat              5
#> 6 Beans             7
#> 7 Tomatoes          6
#> 8 Peppers           8

Similar to the make_choose_one_table() function, we can use this function inside an analysis pipeline. We can add the kable() call to make the table publication quality.

redcap %>% 
  make_choose_all_table("ingredients") %>% 
  knitr::kable()

What	Count
Chips	9
Yellow cheese	7
Orange cheese	3
White cheese	4
Meat	5
Beans	7
Tomatoes	6
Peppers	8

Data Exported with “Data Exports, Reports and Stats” in REDCap

If you export data using the point-and-click tools built into REDCap you end up with two files, one contains R code the other data. When you run the code you end up with a dataset called data which contains two copies of some of the information. For example, if you download the Nacho Craving Index you will see the ingredients variables, showing what ingredients people are craving, and a second copy of the variables that have .factor tagged to the end of the names. The factor versions do not have the variable labels. So you will need to subset the data to drop them. The example below shows the process. Note we have copied the data data frame to have a more meaningful name.

# This is the data produced by exporting using point-and-click REDCap export.
manual_export <- data

manual_export |>   
  select(starts_with("ingredient")) |> # get all the ingredient variables
  select(-ends_with(".factor")) |>     # drop the factor version of the ingredient variables
  make_choose_all_table("ingredient")  # make the table