This vignette covers the the basic functions exposed by the httr and curl
packages which allow you to interact with REDCap through its API.
The function redcap_read_oneshot uses the httr
package to call the REDCap API.
## Loading required namespace: kableExtraThere is some information that is specific to the REDCap project, as opposed to an individual operation. This includes the (1) uri of the server, and the (2) token for the user’s project.
library(REDCapR) # Load the package into the current R session.
uri <- "https://bbmc.ouhsc.edu/redcap/api/"
token <- "9A81268476645C4E5F03428B8AC3AA7B" # `UnitTestPhiFree` user and simple project (pid 153)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(redcap_uri = uri, token = token)$dataThe data dictionary describing 17 fields was read from REDCap in 0.3 seconds. The http status code was 200.5 records and 1 columns were read from REDCap in 0.1 seconds. The http status code was 200.Starting to read 5 records at 2022-08-10 09:24:47.Reading batch 1 of 1, with subjects 1 through 5 (ie, 5 unique subject records).5 records and 25 columns were read from REDCap in 0.1 seconds. The http status code was 200.
── Column specification ────────────────────────────────────────────────────────
cols(
.default = col_double(),
name_first = col_character(),
name_last = col_character(),
address = col_character(),
telephone = col_character(),
email = col_character(),
dob = col_date(format = ""),
comments = col_character(),
mugshot = col_character()
)
ℹ Use `spec()` for the full column specifications.ds_all_rows_all_fields # Inspect the returned dataset record_id name_first name_last address
1 1 Nutmeg Nutmouse 14 Rose Cottage St.\nKenning UK, 323232
2 2 Tumtum Nutmouse 14 Rose Cottage Blvd.\nKenning UK 34243
3 3 Marcus Wood 243 Hill St.\nGuthrie OK 73402
4 4 Trudy DAG 342 Elm\nDuncanville TX, 75116
5 5 John Lee Walker Hotel Suite\nNew Orleans LA, 70115
telephone email dob age sex demographics_complete
1 (405) 321-1111 nutty@mouse.com 2003-08-30 11 0 2
2 (405) 321-2222 tummy@mouse.comm 2003-03-10 11 1 2
3 (405) 321-3333 mw@mwood.net 1934-04-09 80 1 2
4 (405) 321-4444 peroxide@blonde.com 1952-11-02 61 0 2
5 (405) 321-5555 left@hippocket.com 1955-04-15 59 1 2
height weight bmi
1 7.00 1 204.1
2 6.00 1 277.8
3 180.00 80 24.7
4 165.00 54 19.8
5 193.04 104 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\n\nHe had a gold watch chain and a black mustache
mugshot health_complete race___1 race___2 race___3 race___4 race___5
1 mugshot-1.jpg 1 0 0 0 0 1
2 mugshot-2.jpg 0 0 0 1 0 1
3 mugshot-3.jpg 2 0 0 0 1 1
4 mugshot-4.jpg 2 0 1 0 0 1
5 mugshot-5.jpg 0 1 0 0 0 0
race___6 ethnicity interpreter_needed race_and_ethnicity_complete
1 0 1 0 2
2 0 1 0 0
3 0 0 1 2
4 0 1 NA 2
5 1 2 0 2If 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
not specified, 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(
redcap_uri = uri,
token = token,
records = desired_records_v1
)$dataThe data dictionary describing 17 fields was read from REDCap in 0.2 seconds. The http status code was 200.2 records and 1 columns were read from REDCap in 0.2 seconds. The http status code was 200.Starting to read 2 records at 2022-08-10 09:24:48.Reading batch 1 of 1, with subjects 1 through 3 (ie, 2 unique subject records).2 records and 25 columns were read from REDCap in 0.1 seconds. The http status code was 200.
── Column specification ────────────────────────────────────────────────────────
cols(
.default = col_double(),
name_first = col_character(),
name_last = col_character(),
address = col_character(),
telephone = col_character(),
email = col_character(),
dob = col_date(format = ""),
comments = col_character(),
mugshot = col_character()
)
ℹ Use `spec()` for the full column specifications.# Return only records with IDs of 1 and 3 (alternate way)
desired_records_v2 <- "1, 3"
ds_some_rows_v2 <- redcap_read(
redcap_uri = uri,
token = token,
records_collapsed = desired_records_v2
)$dataThe data dictionary describing 17 fields was read from REDCap in 0.1 seconds. The http status code was 200.2 records and 1 columns were read from REDCap in 0.1 seconds. The http status code was 200.Starting to read 2 records at 2022-08-10 09:24:50.Reading batch 1 of 1, with subjects 1 through 3 (ie, 2 unique subject records).2 records and 25 columns were read from REDCap in 0.1 seconds. The http status code was 200.
── Column specification ────────────────────────────────────────────────────────
cols(
.default = col_double(),
name_first = col_character(),
name_last = col_character(),
address = col_character(),
telephone = col_character(),
email = col_character(),
dob = col_date(format = ""),
comments = col_character(),
mugshot = col_character()
)
ℹ Use `spec()` for the full column specifications.ds_some_rows_v2 # Inspect the returned dataset record_id name_first name_last address
1 1 Nutmeg Nutmouse 14 Rose Cottage St.\nKenning UK, 323232
2 3 Marcus Wood 243 Hill St.\nGuthrie OK 73402
telephone email dob age sex demographics_complete
1 (405) 321-1111 nutty@mouse.com 2003-08-30 11 0 2
2 (405) 321-3333 mw@mwood.net 1934-04-09 80 1 2
height weight bmi comments mugshot
1 7 1 204.1 Character in a book, with some guessing mugshot-1.jpg
2 180 80 24.7 completely made up mugshot-3.jpg
health_complete race___1 race___2 race___3 race___4 race___5 race___6
1 1 0 0 0 0 1 0
2 2 0 0 0 1 1 0
ethnicity interpreter_needed race_and_ethnicity_complete
1 1 0 2
2 0 1 2If 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 (i.e., fields) to
the format required by the API (ie,
fields_collapsed) if fields is specified and
fields_collapsed is not.
#Return only the fields record_id, name_first, and age
desired_fields_v1 <- c("record_id", "name_first", "age")
ds_some_fields_v1 <- redcap_read(
redcap_uri = uri,
token = token,
fields = desired_fields_v1
)$dataThe data dictionary describing 17 fields was read from REDCap in 0.1 seconds. The http status code was 200.5 records and 1 columns were read from REDCap in 0.1 seconds. The http status code was 200.Starting to read 5 records at 2022-08-10 09:24:51.Reading batch 1 of 1, with subjects 1 through 5 (ie, 5 unique subject records).5 records and 3 columns were read from REDCap in 0.1 seconds. The http status code was 200.
── Column specification ────────────────────────────────────────────────────────
cols(
record_id = col_double(),
name_first = col_character(),
age = col_double()
)#Return only the fields record_id, name_first, and age (alternate way)
desired_fields_v2 <- "record_id, name_first, age"
ds_some_fields_v2 <- redcap_read(
redcap_uri = uri,
token = token,
fields_collapsed = desired_fields_v2
)$dataThe data dictionary describing 17 fields was read from REDCap in 0.1 seconds. The http status code was 200.5 records and 1 columns were read from REDCap in 0.1 seconds. The http status code was 200.Starting to read 5 records at 2022-08-10 09:24:52.Reading batch 1 of 1, with subjects 1 through 5 (ie, 5 unique subject records).5 records and 3 columns were read from REDCap in 0.1 seconds. The http status code was 200.
── Column specification ────────────────────────────────────────────────────────
cols(
record_id = col_double(),
name_first = col_character(),
age = col_double()
)ds_some_fields_v2 #Inspect the returned dataset record_id name_first age
1 1 Nutmeg 11
2 2 Tumtum 11
3 3 Marcus 80
4 4 Trudy 61
5 5 John Lee 59The two techniques above can be combined when your datasets are large
and you don’t want to pull records with certain values. Suppose you want
to select subjects from the previous dataset if the were born
before 1960 and their weight was over 70kg. Two calls to the server are
required. The first call to REDCap pulls all the
records, but for only three columns: record_id,
dob, and weight. From this subset, identify
the records that you want to pull all the data for; in this case, the
desired record_id values are 3 &
5. The second call to REDCap pulls all the
columns, but only for the identified records.
######
## Step 1: First call to REDCap
desired_fields_v3 <- c("record_id", "dob", "weight")
ds_some_fields_v3 <- redcap_read(
redcap_uri = uri,
token = token,
fields = desired_fields_v3
)$dataThe data dictionary describing 17 fields was read from REDCap in 0.2 seconds. The http status code was 200.5 records and 1 columns were read from REDCap in 0.1 seconds. The http status code was 200.Starting to read 5 records at 2022-08-10 09:24:53.Reading batch 1 of 1, with subjects 1 through 5 (ie, 5 unique subject records).5 records and 3 columns were read from REDCap in 0.1 seconds. The http status code was 200.
── Column specification ────────────────────────────────────────────────────────
cols(
record_id = col_double(),
dob = col_date(format = ""),
weight = col_double()
)ds_some_fields_v3 #Examine the these three variables. record_id dob weight
1 1 2003-08-30 1
2 2 2003-03-10 1
3 3 1934-04-09 80
4 4 1952-11-02 54
5 5 1955-04-15 104######
## Step 2: identify desired records, based on age & weight
before_1960 <- (ds_some_fields_v3$dob <= as.Date("1960-01-01"))
heavier_than_70_kg <- (ds_some_fields_v3$weight > 70)
desired_records_v3 <- ds_some_fields_v3[before_1960 & heavier_than_70_kg, ]$record_id
desired_records_v3 #Peek at IDs of the identified records[1] 3 5######
## Step 3: second call to REDCap
#Return only records that met the age & weight criteria.
ds_some_rows_v3 <- redcap_read(
redcap_uri = uri,
token = token,
records = desired_records_v3
)$dataThe data dictionary describing 17 fields was read from REDCap in 0.1 seconds. The http status code was 200.2 records and 1 columns were read from REDCap in 0.1 seconds. The http status code was 200.Starting to read 2 records at 2022-08-10 09:24:54.Reading batch 1 of 1, with subjects 3 through 5 (ie, 2 unique subject records).2 records and 25 columns were read from REDCap in 0.1 seconds. The http status code was 200.
── Column specification ────────────────────────────────────────────────────────
cols(
.default = col_double(),
name_first = col_character(),
name_last = col_character(),
address = col_character(),
telephone = col_character(),
email = col_character(),
dob = col_date(format = ""),
comments = col_character(),
mugshot = col_character()
)
ℹ Use `spec()` for the full column specifications.ds_some_rows_v3 #Examine the results. record_id name_first name_last address
1 3 Marcus Wood 243 Hill St.\nGuthrie OK 73402
2 5 John Lee Walker Hotel Suite\nNew Orleans LA, 70115
telephone email dob age sex demographics_complete
1 (405) 321-3333 mw@mwood.net 1934-04-09 80 1 2
2 (405) 321-5555 left@hippocket.com 1955-04-15 59 1 2
height weight bmi
1 180.00 80 24.7
2 193.04 104 27.9
comments
1 completely made up
2 Had a hand for trouble and a eye for cash\n\nHe had a gold watch chain and a black mustache
mugshot health_complete race___1 race___2 race___3 race___4 race___5
1 mugshot-3.jpg 2 0 0 0 1 1
2 mugshot-5.jpg 0 1 0 0 0 0
race___6 ethnicity interpreter_needed race_and_ethnicity_complete
1 0 0 1 2
2 1 2 0 2The examples above have shown only the resulting
data.frame, by specifying $data at the end of
the call. However, more is available to those wanting additional
information, such as:
data object has the data.frame, as in
the previous examples.success boolean value indicates if
redcap_read_oneshot believes the operation completed as
intended.status_codes is a collection of http
status codes, separated by semicolons. There is one code for each
batch attempted.outcome_messages: A collection of human readable
strings indicating the operations’ semicolons. There is one code for
each batch attempted. In an unsuccessful operation, it should contain
diagnostic information.records_collapsed field passed to the API. This
shows which record subsets, if any, were requested.fields_collapsed fields passed to the API. This
shows which field subsets, if any, were requested.elapsed_seconds measures the duration of the
call.#Return only the fields record_id, name_first, and age
all_information <- redcap_read(
redcap_uri = uri,
token = token,
fields = desired_fields_v1
)The data dictionary describing 17 fields was read from REDCap in 0.2 seconds. The http status code was 200.5 records and 1 columns were read from REDCap in 0.1 seconds. The http status code was 200.Starting to read 5 records at 2022-08-10 09:24:55.Reading batch 1 of 1, with subjects 1 through 5 (ie, 5 unique subject records).5 records and 3 columns were read from REDCap in 0.2 seconds. The http status code was 200.
── Column specification ────────────────────────────────────────────────────────
cols(
record_id = col_double(),
name_first = col_character(),
age = col_double()
)all_information #Inspect the additional information$data
record_id name_first age
1 1 Nutmeg 11
2 2 Tumtum 11
3 3 Marcus 80
4 4 Trudy 61
5 5 John Lee 59
$success
[1] TRUE
$status_codes
[1] "200"
$outcome_messages
[1] "5 records and 3 columns were read from REDCap in 0.2 seconds. The http status code was 200."
$records_collapsed
[1] ""
$fields_collapsed
[1] "record_id,name_first,age"
$forms_collapsed
[1] ""
$events_collapsed
[1] ""
$filter_logic
[1] ""
$datetime_range_begin
[1] NA
$datetime_range_end
[1] NA
$elapsed_seconds
[1] 1.145227For the sake of documentation and reproducibility, the current report was rendered in the following environment. Click the line below to expand.
─ Session info ───────────────────────────────────────────────────────────────
setting value
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language (EN)
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pandoc 2.18 @ /usr/lib/rstudio/bin/quarto/bin/tools/ (via rmarkdown)
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──────────────────────────────────────────────────────────────────────────────Report rendered by wibeasley at 2022-08-10, 09:24 -0500 in 13 seconds.