Quick links:
These features are not yet on CRAN. Install with
remotes::install_github("OuhscBbmc/REDCapR")
These changes could possibly break existing code –but it’s very unlikely. We feel they will (directly and indirectly) improve the package considerably.
redcap_read()
, redcap_read_oneshot()
,
redcap_dag_read()
, redcap_log_read()
, and
redcap_report()
return a tibble instead of a data.frame.
(#415)
This should affect client code only if you expect a call like
ds[, 3]
to return a vector instead of a single-column
data.frame/tibble. One solution is to upcast the tibble to a data.frame
(with something like as.data.frame()
). We recommend using
an approach that works for both data.frames and tibbles, such as
ds[[3]]
or dplyr::pull(ds, "gender")
.
For more information, read the short chapter in R for Data Science.
The *_collapsed
parameters are deprecated. When your
want to limit on records/fields/forms/events, pass the vector of
characters, not the scalar character separated by commas (which I think
everyone does already). In other words use
c("demographics", "blood_pressure")
instead of
"demographics,blood_pressure"
.
Here are the relationships between the four pairs of variables:
<- collapse_vector(records , records_collapsed)
records_collapsed <- collapse_vector(fields , fields_collapsed)
fields_collapsed <- collapse_vector(forms , forms_collapsed)
forms_collapsed <- collapse_vector(events , events_collapsed) events_collapsed
If someone is using the *_collapsed parameter, they can programmatically convert it to a vector like:
<- trimws(unlist(strsplit(field_names_collapsed, ","))) field_names
redcap_read()
will automatically include the
“plumbing” variables, even if they’re not included the list of requested
fields & forms. (#442). Specifically:
record_id
(or it’s customized name) will always be
returnedredcap_event_name
will be returned for longitudinal
projectsredcap_repeat_instrument
and
redcap_repeat_instance
will be returned for projects with
repeating instrumentsThis will help extract forms from longitudinal & repeating projects.
redcap_read()
and redcap_read_oneshot()
now return an empty dataset if no records are retrieved (such as no
records meet the filter criteria). Currently a 0x0 tibble is returned,
but that may change in the future. Until now an error was deliberately
thrown. (#452)
redcap_event_instruments()
now by default returns
mappings for all arms. The previous default was to return the mappings
for only the first arm. To recreate the previous behavior use a call
like
REDCapR::redcap_event_instruments(uri, token_2, arms = "1")
.
(Suggested by @januz,
#482)
redcap_users_export()
used to return a boolean for
user_rights
, but now it can be 0, 1, or 2. (#523)
redcap_metadata_coltypes()
function. Inspects the
fields types and validation text of each field to generate a suggested
readr::col_types
object that reflects the project’s current
data dictionary. The object then can be passed to the
col_types
parameter of redcap_read()
or
redcap_read_oneshot()
. (Suggested and discussed with @pbchase, @nutterb, @skadauke, & others,
#405 & #294)redcap_log_read()
function. Exports a project’s
log. (Thanks @joundso, #383, #320)redcap_project_info_read()
function. Exports a
project’s information, such as its language and production status.
(Suggested by @skadauke, @timothytsai, @pbchase, #236, #410)blank_for_gray_form_status
in the
functions redcap_read()
,
redcap_read_oneshot()
, and
redcap_read_oneshot_eav()
. (@greg-botwin, #386, #389)httr::handle
value is accepted by functions that
contact the server. This will accommodate some institutions with
unconventional environments. (Suggested by @brandonpotvin, #429)sanitized_token()
now accepts an alternative regex
pattern. (Suggested by @maeon & @michalkouril, #370)redcap_read_eav_oneshot()
is an UNexported function
that returns data in an EAV format (#437)redcap_metadata_read()
now correctly subsets the forms
(identified & corrected by @ezraporter, #431 & #445)redcap_event_read()
function. Exports metadata
associated with a project’s longitudinal events (@ezraporter, #457 & #460)read_read_oneshot()
’s parameter guess_max
now allows floating point values to support
readr::read_csv()
ability to accept a Inf value. (Suggested
by @eveyp, #392)redcap_download_file_oneshot()
to
redcap_file_download_oneshot()
redcap_file_upload_oneshot()
to
redcap_file_upload_oneshot()
redcap_download_instrument()
to
redcap_instrument_download()
redcap_dag_read()
has new
data_access_group_id
field (introduced maybe in 13.1.0)
(#459)redcap_users_export()
has new
mycap_participants
field (introduced maybe in 13.0.0)
(#459)has_repeating_instruments_or_events
,
missing_data_codes
, external_modules
,
bypass_branching_erase_field_prompt
(@the-mad-statter, #465, #466)redcap_meta_coltypes()
correctly determines data type
for autonumber record_id
fields. It suggests a character if
the project has DAGs, and an integer if not. (@pwildenhain, #472)redcap_log_read()
now returns a new column reflecting
the affected record id value (ref #478)redcap_read()
and redcap_read_oneshot()
now remove “pseudofields” (e.g., redcap_event_name
,
redcap_repeat_instrument
, &
redcap_repeat_instance
) from the fields
parameter. Starting with REDCap v13.4.10, an error is thrown by the
server. REDCap will return a message if a common pseudofield is
requested explicitly by the user. (#477)redcap_event_instruments()
now can return mappings for
all arms, instead of one arm per call.(Suggested by @januz, #482)validate_for_write()
contains a few more checks. (#485)
The complete list is now:
validate_data_frame_inherits()
validate_field_names()
validate_record_id_name()
validate_uniqueness()
validate_repeat_instance()
validate_no_logical()
redcap_read()
checks the event
parameter
and throws an error if a value is not recognized, or the project is not
longitudinal (#493)regex_named_captures()
is forgiving if
there’s an unnecessary leading space (@BlairCooper, #495, #501)redcap_log_read()
assumes all columns are character,
except for timestamp
(#525)redcap_file_download_oneshot()
no longer asks for the
unnecessary parameter for repeating_instrument
(that the
REDCap server ignores). (@BlairCooper, #506, #530)redcap_read()
and redcap_read_oneshot()
accommodate readr::read_csv()
’s parameter of
na
. (Suggested by @rmtrane in #529)redcap_delete()
function. It deletes a vector of
records. (Thanks @joundso, #372, #373)redcap_arm_export()
function. It retrieves a list
of REDCap project arms. (#375)redcap_read()
and redcap_read_oneshot()
accept a new locale
parameter that specifies date, time,
and number formats, like using a comma as the decimal separator. It is a
readr::locale
object. (#377, suggested by @joundso)redcap_instruments()
function exports a list of the
data collection instruments for a project. (#381, @vcastro)redcap_event_instruments()
function exports the
instrument-event mappings for a project (i.e., how the data collection
instruments are designated for certain events in a longitudinal
project). (#381, @vcastro)redcap_dag_read()
function returns the Data Access
Groups for a project (#382, @joundso)sanitize_token()
now allows lowercase characters –in
addition to uppercase characters & digits. (#347, @jmbarbone)redcap_metadata_read()
now uses json (instead of csv)
to transfer the dictionary between server & client. This
accommodates super-wide dictionaries with 35k+ variables. The user
shouldn’t notice a difference, and still will receive a data.frame.
(#335, @januz &
@datalorax)testthat::skip_on_cran()
calls to
comply with CRAN’s “fail
gracefully” policy. Similarly, skip remaining examples that depend
on external resources. (#352)retrieve_credential_local()
can now user
username
to identify the desired credential row (#364)redcap_read()
and redcap_read_oneshot()
gain the http_response_encoding
parameter that’s passed to
httr::content()
.
The default value remains “UTF-8”. (#354, @lrasmus)redcap_users_export()
(which calls REDCap’s user
export). The API dropped the data_export
variable and added
the forms_export
variable. (#396)redcap_read_oneshot_eav()
: if the project isn’t
longitudinal, a dummy value for event_id
is used internally
(#396)httr::user_agent
, following the advice of httr’s
vignette (#397)The package has been stable for years and should be reflected in the major version number.
redcap_write()
and redcap_write_oneshot()
have
a new parameter that converts R’s logical
/boolean columns
to integers. This meshes well with T/F and Y/N items that are coded as
1/0 underneath. The default will be FALSE (ie, the integers are not
converted by default), so it doesn’t break existing code. (#305)redcap_write()
and redcap_write_oneshot()
can
toggle the ability to overwrite with blank/NA cells (suggested by @auricap, #315)redcap_read_oneshot()
,
redcap_read()
, & redcap_read_oneshot_eav()
now support the parameters datetime_range_begin
and
datetime_range_end
. The are passed to the REDCap parameters
dateRangeBegin
and dateRangeEnd
, which
restricts records returned, based on their last modified date in the
server. (Thanks @pbchase, #321 & #323.)export_survey_fields
parameter in the functions redcap_read()
&
redcap_read_oneshot()
. (Thanks @isaactpetersen, #333)redcap_report()
export records that populate a REDCap report. (#326.)create_credential_local()
starts a well-formed csv file that can contain tokens. (#340, after
conversations with @higgi13425 & @kamclean.)config_option
element. (Proposed
by @BastienRance, #307)success
value returned by
redcap_read()
and redcap_write()
when the
parameter continue_on_error
is true. (Bug found by @llrs, #317)redcap_survey_link_export_oneshot()
documentation corrected & improved (@jrob95, #526)kernel_api()
defaults to “text/csv” and UTF-8 encoding. Formerly, the function would
decide on the content-type and encoding. More details are below in the
‘Stability Features’ subsection.
constant()
no longer accepts simplify
as an options. An integer vector
is always returned. (#280)
It’s now possible to specify the exact col_types
(a
readr::cols
object) that is passed to readr::read_csv()
inside redcap_read_oneshot()
.
(#258)
reader::type_convert()
is used after all the batches are stacked on top of each other.
This way, batches cannot have incompatible data types as they’re
combined. (#257; thanks @isaactpetersen #245) Consequently,
the guess_max
parameter in redcap_read()
no
longer serves a purpose, and has been soft-deprecated. (#267)
redcap_metadata_write()
writes to the project’s metadata. (#274, @felixetorres)
redcap_survey_link_export_oneshot()
retrieves the URL to a specific record’s survey (e.g.,
“https://bbmc.ouhsc.edu/redcap/surveys/?s=8KuzSLMHf6”) (#293)
convert_logical_to_integer
is a new parameter for redcap_write()
and redcap_write_oneshot()
.
If TRUE
, all [base::logical] columns in ds
are
cast to an integer before uploading to REDCap. Boolean values are
typically represented as 0/1 in REDCap radio buttons. Defaults to
FALSE
to maintain backwards compatibility. (#305)
httr::content()
(which is inside
kernel_api()
) now processes the returned value as
“text/csv”, by default. This should prevent strange characters from
tricking the process as the internal variable raw_text
is
being formed. See the
[httr::content()](https://httr.r-lib.org/reference/content.html) documentation for a list of possible values for the
content_type`
parameter. (Thanks to great debugging by @vortexing #269, @sybandrew #272, & @begavett, #290)
Similarly, kernel_api()
now has an
encoding
parameter, which defaults to “UTF-8”.
(#270)
‘checkmate’ package is now imported, not suggested (Thanks @dtenenba, #255).
Allow more than one httr::config()
parameter to be
passed (Thanks @BastienRance, #307).
redcap_next_free_record_name()
: API call for ‘Generate
Next Record Name’, which returns the next available record ID (Issue
#237)redcap_read()
and redcap_read_oneshot()
allow the user to specify if all variables should be returned with the
character
data type. The default is to allow
readr::read_csv()
to guess the data type. (#194)redcap_read_oneshot()
allows use to specify how many
rows should be considered when readr::read_csv()
guesses
the data type. (#194)redcap_read()
, redcap_read_oneshot()
, and
redcap_read_oneshot_eav()
always return Linux-style line
endings (ie \n
) instead of Windows style line endings (ie,
\r\n
) on all OSes. (#198)read_metadata()
always returns character
vectors for all variables. With readr 1.2.0, some column were returned
differently than before. (#193)redcap_users_export()
now included (#163)redcap_read()
,
redcap_read_oneshot()
, &
redcap_read_oneshot_eav()
(#206). It was already implemented
for redcap_metadata_read()
.constants()
) easily exposes
REDCap-specific constants. (#217)id_position
allows user to specify if the record_id
isn’t in the first position (#207). However, we recommend that all
REDCap projects keep this important variable first in the data
dictionary.redcap_read()
and
redcap_read_oneshot()
are more consistent with the order in
raw REDCap API. (#204)verbose
parameter is NULL, then the value from
getOption(“verbose”) is used. (#215)guess_max
parameter provided in
redcap_read()
(no longer just
redcap_read_oneshot()
). Suggested by @isaactpetersen in #245.redcap_variables()
now throws an error when passed a
bad URI (commit e542155639bbb7).kernal_api()
function, which uses the ‘httr’ and ‘curl’
packages underneath. Until now, each function called those packages
directly. (#213)readr::read_csv()
is used instead of
utils::read.csv()
(Issue #127).odbc
package to retrieve credentials from the
token server. Remove RODBC and RODBCext (#188). Thanks to @krlmlr for error checking
advice in https://stackoverflow.com/a/50419403/1082435.data.table::rbindlist()
replaced by
dplyr::bind_rows()
testit::assert()
and base:stop()
) (#190
& #208).collapse_vector()
is refactored and tested (#209)pkgload
package (#218)retrieve_token_mssql()
, because
retrieve_credential_mssql()
is more general and more
useful.redcap_variables()
.redcap_read_oneshot_eav()
,
which can be accessed with a triple colon (ie,
REDCapR::redcap_read_oneshot_eav()
).redcap_read()
and
redcap_read_oneshot()
(PR #126)retrieve_credential_mssql()
and
retrieve_credential_local()
. These transition from storing
& retrieving just the token (ie,
retrieve_token_mssql()
) to storing & retrieving more
information. retrieve_credential_local()
facilitates a
standard way of storing tokens locally, which should make it easier to
follow practices of keeping it off the repository.data.table::rbindlist()
is used. This should prevent errors
with the first batch’s data type (for a column) isn’t compatible with a
later batch. For instance, this occurs when the first batch has only
integers for record_id
, but a subsequent batch has values
like aa-test-aa
. The variable for the combined dataset
should be a character. (Issue #128 & https://stackoverflow.com/questions/39377370/bind-rows-of-different-data-types;
Thanks @arunsrinivasan)dplyr
package instead of plyr
.
This shouldn’t affect callers, because immediately before returning the
data, REDCapR::redcap_read()
coerces the
tibble::tibble
(which was formerly called
dplyr::tbl_df
) back to a vanilla data.frame
with as.data.frame()
.retrieve-token()
tests now account for the (OS X)
builds where the RODBC package isn’t available.curl
package, instead of RCurl
).requireNamespace()
instead of
require()
.readcap_read()
is being
used without ‘Full Data Set’ export privileges. The problem involves the
record IDs are hashed.id_position
in the
first stage of batching. The metadata needed to be read before that,
after the updates for REDCap Version 6.0.x.retrieve_token_mssql()
uses regexes to validate
parametersconfig_options
in the httr package are exposed to
the REDCapR user. See issues #55 & #58; thanks to @rparrish and @nutterb for their
contributions (https://github.com/OuhscBbmc/REDCapR/issues/55 & https://github.com/OuhscBbmc/REDCapR/issues/58).redcap_metadata_read()
are tested and public.testthat::skip_on_cran()
before any
call involving OUHSC’s REDCap server.redcap_write()
and redcap_write_oneshot()
are now tested and public.redcap_write()
and redcap_write_oneshot()
are now tested and public.redcap_download_file_oneshot()
function contributed by
John Aponte (@johnaponte; Pull request #35)redcap_upload_file_oneshot()
function contributed by
@johnaponte (Pull
request #34)verbose==TRUE
. Follows advice of @johnaponte, Benjamin Nutter (@nutterb), and Rollie
Parrish (@rparrish).
Closes #43.records_collapsed
default empty value is now an
empty string (i.e., ""
) instead of
NULL
. This applies when records_collapsed
is
either a parameter, or a returned value.redcap_download_file_oneshot()
documentation, thanks to Andrew Peters (@ARPeters #45).httr
package, which provides benefits
like the status code message can be captured (eg, 200-OK, 403-Forbidden,
404-NotFound). See https://cran.r-project.org/package=httr.status_message
to
outcome_message
. This is because the message associated
with http code returned is conventionally called the ‘status messages’
(eg, OK, Forbidden, Not Found).raw_text
value
(which was formerly called raw_csv
) is returned as an empty
string to save RAM. It’s not really necessary with httr’s status message
exposed.redcap_column_sanitize()
function to address
non-ASCII charactersredcap_write()
(as an internal function).redcap_project()
object reduces repeatedly passing
parameters like the server URL, the user token, and the SSL cert
location.redcap_read_batch()
to
redcap_read()
. These changes reflect our suggestion that
reads should typically be batched.redcap_read()
to
redcap_read_oneshot()
redcap_write()
to
redcap_write_oneshot()
(which is an internal
function).redcap_read()
and
redcap_read_batch()
with documentationredcap_read()
takes parameter for
raw_or_label
(Thanks Rollie Parrish #3)redcap_read()
takes parameter for
export_data_access_groups
thanks to Rollie Parrish (@rparrish #4)GitHub Commits and Releases