This vignette covers the the basic functions exposed by the REDCapR package which allow you to interact with REDCap through its API.
The function redcap_read_oneshot uses the RCurl package to call the REDCap API.
There is some information that is specific to the REDCap project, as opposed to an individual operation. This includes the (1) uri of the server, the (2) token for the user's project, and the (3) location of the SSL certification store, which is necessary to verify the identity of the REDCap webserver.
The REDCapR package includes a recent version of the Bundle of CA Root Certificates from the official cURL site. This version is used by default, unless the cert_location parameter is given another location.
library(REDCapR) #Load the package into the current R session.
uri <- "https://bbmc.ouhsc.edu/redcap/api/"
token <- "9A81268476645C4E5F03428B8AC3AA7B"
If no information is passed about the desired records or fields, then the entire data set is returned. Only two parameters are required, redcap_uri and token. Unless the verbose parameter is set to FALSE, a message will be printed on the R console with the number of records and fields returned.
#Return all records and all variables.
ds_all_rows_all_fields <- redcap_read_oneshot(redcap_uri=uri, token=token)$data
5 records and 16 columns were read from REDCap in 3.08 seconds.
ds_all_rows_all_fields #Inspect the returned dataset
record_id first_name last_name address telephone email dob
1 1 Nutmeg Nutmouse 14 Rose Cottage St.\nKenning UK, 323232 (432) 456-4848 nutty@mouse.com 2003-08-30
2 2 Tumtum Nutmouse 14 Rose Cottage Blvd.\nKenning UK 34243 (234) 234-2343 tummy@mouse.comm 2003-03-10
3 3 Marcus Wood 243 Hill St.\nGuthrie OK 73402 (433) 435-9865 mw@mwood.net 1934-04-09
4 4 Trudy DAG 342 Elm\nDuncanville TX, 75116 (987) 654-3210 peroxide@blonde.com 1952-11-02
5 5 John Lee Walker Hotel Suite\nNew Orleans LA, 70115 (333) 333-4444 left@hippocket.com 1955-04-15
age ethnicity race sex height weight bmi
1 10 1 2 0 5 1 400.0
2 10 1 6 1 6 1 277.8
3 79 0 4 1 180 80 24.7
4 61 1 4 0 165 54 19.8
5 58 1 4 1 193 104 27.9
comments
1 Character in a book, with some guessing
2 A mouse character from a good book
3 completely made up
4 This record doesn't have a DAG assigned\n\nSo call up Trudy on the telephone\nSend her a letter in the mail
5 Had a hand for trouble and a eye for cash\nHe had a gold watch chain and a black mustache\n\nhttps://www.youtube.com/watch?v=DUESvITrvsI
demographics_complete
1 2
2 2
3 2
4 2
5 2
If only a subset of the records is desired, the two approaches are shown below. The first is to pass an array (where each element is an ID) to the records parameter. The second is to pass a single string (where the elements are separated by commas) to the records_collapsed parameter.
The first format is more natural for more R users. The second format is what is expected by the REDCap API. If a value for records is specified, but records_collapsed is missing, then redcap_read_oneshot automatically converts the array into the format needed by the API.
#Return only records with IDs of 1 and 3
desired_records_v1 <- c(1, 3)
ds_some_rows_v1 <- redcap_read_oneshot(
redcap_uri = uri,
token = token,
records = desired_records_v1
)$data
2 records and 16 columns were read from REDCap in 1.37 seconds.
#Return only records with IDs of 1 and 3 (alternate way)
desired_records_v2 <- "1, 3"
ds_some_rows_v2 <- redcap_read_oneshot(
redcap_uri = uri,
token = token,
records_collapsed = desired_records_v2
)$data
2 records and 16 columns were read from REDCap in 1.18 seconds.
ds_some_rows_v2 #Inspect the returned dataset
record_id first_name last_name address telephone email dob age
1 1 Nutmeg Nutmouse 14 Rose Cottage St.\nKenning UK, 323232 (432) 456-4848 nutty@mouse.com 2003-08-30 10
2 3 Marcus Wood 243 Hill St.\nGuthrie OK 73402 (433) 435-9865 mw@mwood.net 1934-04-09 79
ethnicity race sex height weight bmi comments demographics_complete
1 1 2 0 5 1 400.0 Character in a book, with some guessing 2
2 0 4 1 180 80 24.7 completely made up 2
If only a subset of the fields is desired, then two approaches exist. The first is to pass an array (where each element is an field) to the fields parameter. The second is to pass a single string (where the elements are separated by commas) to the fields_collapsed parameter. Like with records and records_collapsed described above, this function converts the more natural format (ie, fields) to the format required by the API (ie, fields_collapsed) if fields is specified and fields_collapsed is not.
#Return only the fields recordid, first_name, and age
desired_fields_v1 <- c("recordid", "first_name", "age")
ds_some_fields_v1 <- redcap_read_oneshot(
redcap_uri = uri,
token = token,
fields = desired_fields_v1
)$data
5 records and 3 columns were read from REDCap in 2.49 seconds.
#Return only the fields recordid, first_name, and age (alternate way)
desired_fields_v2 <- "recordid, first_name, age"
ds_some_fields_v2 <- redcap_read_oneshot(
redcap_uri = uri,
token = token,
fields_collapsed = desired_fields_v2
)$data
5 records and 3 columns were read from REDCap in 1.26 seconds.
ds_some_fields_v2 #Inspect the returned dataset
record_id first_name age
1 1 Nutmeg 10
2 2 Tumtum 10
3 3 Marcus 79
4 4 Trudy 61
5 5 John Lee 58
The examples above have shown only the resulting data.frame, by specifying $data at the end of the call. However, more is available to those wanting additional information, such as
data object has the data.frame, as in the previous examples.raw_csv returned by the REDCap API. This might display helpful error messages, in the event something went wrong.records_collapsed field passed to the API. This shows which record subsets, if any, were requested.fields_collapsed fields passed to the API. This shows which field subsets, if any, were requested.elapsed_seconds measures the duration of the call.status_message has the number of rows and columns read in a successful operation. In an unsuccessful operation, it should contain diagnostic information.success boolean value indicates if redcap_read_oneshot believes the operation completed as intended.#Return only the fields recordid, first_name, and age
all_information <- redcap_read_oneshot(
redcap_uri = uri,
token = token,
fields = desired_fields_v1
)
5 records and 3 columns were read from REDCap in 0.98 seconds.
all_information #Inspect the additional information
$data
record_id first_name age
1 1 Nutmeg 10
2 2 Tumtum 10
3 3 Marcus 79
4 4 Trudy 61
5 5 John Lee 58
$raw_csv
[1] "record_id,first_name,age\n\"1\",\"Nutmeg\",10\n\"2\",\"Tumtum\",10\n\"3\",\"Marcus\",79\n\"4\",\"Trudy\",61\n\"5\",\"John Lee\",58\n"
attr(,"Content-Type")
charset
"text/html" "utf-8"
$records_collapsed
NULL
$fields_collapsed
[1] "recordid,first_name,age"
$elapsed_seconds
[1] 0.9847
$status_message
[1] "5 records and 3 columns were read from REDCap in 0.98 seconds."
$success
[1] TRUE
For the sake of documentation and reproducibility, the current vignette was build on a system using the following software.
Report created by Will at 2014-02-13, 22:11:28 -0600
R Under development (unstable) (2014-02-10 r64961)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] REDCapR_0.2-9 stringr_0.6.2 RCurl_1.95-4.1 bitops_1.0-6 plyr_1.8.0.99 knitr_1.5 testthat_0.8
[8] roxygen2_3.1.0 devtools_1.4.1
loaded via a namespace (and not attached):
[1] brew_1.0-6 codetools_0.2-8 digest_0.6.4 evaluate_0.5.1 formatR_0.10 httr_0.2 memoise_0.1
[8] parallel_3.1.0 Rcpp_0.11.0 tools_3.1.0 whisker_0.3-2