redcaptools
redcaptools.Rmd
library(redcaptools)redcaptools assists in exporting data from REDCap via
the API, converting variable types (e.g. radio-buttons to factors),
labelling etc.
Exporting from REDCap
REDCap exports generally come in a single files, with repeating elements as new rows, lots of empty variables (e.g. because they don’t exist for a given visit). To use the data, it must often be subsetted by form or event, variables selected, etc.
redcaptools eases this by exporting the data by form
from the beginning with the redcap_export_byform
function.
token <- "my-redcap-token"
url <- "https://redcap.mydomain.com/api/"
data <- redcap_export_byform(token, url)Other export functions are redcap_export_meta (for
downloading various metadata objects - currently the data dictionary,
form-event-mapping and event tables) and redcap_export_tbl,
which can be used to use whatever parameters you like for the API (see
the REDCap documentation for details). The dataset that REDCap exports
through the website interface is accessed for instance via:
record <- redcap_export_tbl(token, url, "record")Using manual exports
REDCap also allows exporting data manually through the web interface.
While redcaptools is primarily intended to used with the
API, there much of it will also work with manually exported datasets.
Important to note is that the data dictionary must be provided manually
in this case.
For example, the redcap_toform function tries to split a
manually downloaded dataset into it’s constituent forms. As less
information is available, it’s not as robust as the API version, but it
may still be useful.
# a small manually downloaded testing dataset
data <- readRDS(system.file("extdata/test.rda", package = "redcaptools"))
# the data dictionary
dd <- read.csv(system.file("extdata/DataDictionary.csv", package = "redcaptools"))
formdata <- redcap_toform(data, dd)Processing REDCap data
To make the data more usable in R, it’s often nice to label data,
create factor, convert dates etc. redcaptools has functions
to help with that too. Each of the following functions also label
variables.
The redcap_prep function is the easiest to use. It wraps
all of the functions in the following section.
meta <- redcap_export_meta(token, url)
# could also use a data dictionary exported manually
# where all data is in a single dataframe
prepped <- redcap_prep(record, meta$metadata)
# for data split by forms, use sapply
prepped <- sapply(data, redcap_prep, metadata = meta$metadata)Create factors
REDCap has both single and multiple choice factor type variables. These need handling separately, so there are two sets of functions.
Lists of the options can be obtained with the
singlechoice_opts and multichoice_opts
functions. These are rather for your information.
singlechoice_opts(meta$metadata)
mutlichoice_opts(meta$metadata)Factors can be created easily with