date_source() was copied to
{admiralonco} to provide a deprecation message
rather than a deprecation warning. For this to have an effect
the {admiralonco} package must be loaded after the
{admiral} package. (#319)The following functions/arguments are entering the next phase of the deprecation process:
Phase 1 (message)
derive_param_bor() is deprecated in favor of
admiral::derive_extreme_event(). (#320)derive_param_clinbenefit() is deprecated in favor of
admiral::derive_extreme_event(). (#320)derive_param_confirmed_bor() is deprecated in favor of
admiral::derive_extreme_event(). (#320)derive_param_confirmed_resp() is deprecated in favor of
admiral::derive_extreme_event(). (#320)derive_param_response() is deprecated in favor of
admiral::derive_extreme_event(). (#320)filter_pd() is deprecated in favor of
admiral::filter_relative(). (#320)Phase 2 (warning)
No functions or arguments in this phase
Phase 3 (error)
aval_fun argument in
derive_param_bor(),
derive_param_clinbenefit(),
derive_param_confirmed_bor(),
derive_param_confirmed_resp(), and
derive_param_response() is deprecated in favor of the
set_values_to argument.Phase 4 (removed)
No functions or arguments in this phase
PSA response endpoints were added to the “Creating ADRS with Prostate Cancer Working Group 3 (PCWG3) Criteria” vignette. (#317)
The response values in the “Creating ADRS with Prostate Cancer
Working Group 3 (PCWG3) Criteria” vignette were aligned to the standard
terminology and the data issue in the RS domain was fixed.
(#313)
The wording in the “Bone Response Categories Based on PCWG3 Guidelines” section of the “Creating ADRS with Prostate Cancer Working Group 3 (PCWG3) Criteria” vignette was improved. (#314)
The “Ask AI” widget was added to the bottom right of each page.
It enables users to ask questions about {admiralonco} and
receive answers from an LLM. It is trained on the documentation of the
admiral packages and provided by kapa.ai.
(#326)
A link to the {admiral} ecosystem page was added to the home page sidebar and main text. (#318)
New vignette “Creating ADRS with Prostate Cancer Working Group 3 (PCWG3) Criteria”. (#304)
Display ANL01FL in the NADIR derivation
in the ADTR vignette. (#305)
New vignette “Creating ADRS with GCIG Criteria”. (#294)
The vignettes “Creating a Basic ADRS” and “Creating ADRS
(Including Non-standard Endpoints)” were updated to describe how the
case CR followed by PR is handled.
(#276)
The documentation of the time-to-event source objects was fixed. (#293)
exprs(USUBJID, STUDYID) and
exprs(USUBJID) with
get_admiral_option("subject_keys") so the argument is
flexible and can be changed from the default by the user. (#281)bor_ne event object was updated such that
CR and PR are additionally considered as
event. This ensures that the confirmed best overall response for a
patient with a single CR or PR assessment is
derived as "NE" instead of "MISSING".
(#253)New vignette “Creating ADRS with iRECIST endpoints”. (#233)
All vignettes and templates were updated to be in line with the
changes in {admiral} (see Breaking
Changes for details)(#256).
The derive_*() functions were superseded in favor of
derive_extreme_event(). Any superseded functions can
continue to be used as demonstrated via the “Basic ADRS” vignette, as
they will remain supported and won’t be deprecated in the near future.
(#256)
The filter_pd() function was superseded in favor of
filter_relative(). (#256)
The function call_aval_fun(), which was deprecated
in admiralonco 0.4.0, has been removed. (#256)
admiral::derive_extreme_event().
(#234)The ADRS vignette and template were split into two
(#234):
{admiralonco} functions
to cover standard RECIST 1.1.admiral::derive_extreme_event(). This should be used if
non-standard ADRS parameters should be implemented or
non-standard response values should be considered. This version can also
be used as a starting point for implementing other response criteria
than RECIST 1.1, e.g., iRECIST or International Myeloma Working Group
(IMWG) criteria for the diagnosis of multiple myeloma.The ADRS vignette and template were updated such
that test data from {pharmaversesdtm} instead of
{admiral.test} is used. (#226)
The “Create ADTR” vignette and the ADTR
template were updated such that test data from
{pharmaversesdtm} instead of {admiral.test} is
used. (#247)
The confirmed response derivation was fixed in the basic
ADRS vignette and template. When calling
derive_param_confirmed_resp() the
filter_source argument has to be set to
PARAMCD == "OVR" & ANL01FL == "Y" instead of
PARAMCD == "OVR" & AVALC %in% c("CR", "PR") & ANL01FL == "Y".
Otherwise, responses like CR, NE,
NE, CR are considered as confirmed response.
(#245)
ADRS” and “Create ADTTE” vignette
has been updated to include a link to “Creating and Using New
Anti-Cancer Start Date” vignetteAdded a “Report a bug” link to {admiralonco} website
(#211)
Added a section regarding dependencies to the
{admiralonco} website (#223)
Vignettes and templates were updated due to changes in admiral and admiralonco: (#216)
AVAL variable is now populated via the
set_values_to argument as the aval_fun
argument was deprecated.admiral::derive_param_extreme_event() calls were
replaced by admiral::derive_extreme_records() calls due to
deprecation of admiral::derive_param_extreme_event().admiral::derive_param_exist_flag() calls were updated
as the dataset_adsl argument was renamed to
dataset_ref.Function derive_param_lasta(), which was deprecated
in admiralonco 0.2.0, has been removed. (#216)
The aval_fun argument of
derive_param_bor(),
derive_param_clinbenefit(),
derive_param_confirmed_bor(),
derive_param_confirmed_resp(),
derive_param_response() was deprecated in favor of the
set_values_to argument. (#216)
The call_aval_fun() function was deprecated in favor
or admiraldev::process_set_values_to(). (#216)
vars() are now expecting a list of expressions created by
exprs(). For example, instead of
by_vars = vars(STUDYID, USUBJID)
by_vars = exprs(STUDYID, USUBJID) must be used now.
(#197)ADTR” (#16)admiral::derive_param_tte() enhancement (#203)subject_keys as a function argument
now default to get_admiral_option("subject_keys")instead of
vars(STUDYID, USUBJID) to allow users to change the
variables that uniquely identify a subject once using
set_admiral_options() to avoid several instances of find +
replace in a script. (#175)derive_param_lasta() has been deprecated.
Please use admiral::derive_param_extreme_event() instead
(#89).ADRS vignette for
filtering out assessments after progressive disease compared to
source_pd argument (#168)
Need a high-speed mirror for your open-source project?
Contact our mirror admin team at info@clientvps.com.
This archive is provided as a free public service to the community.
Proudly supported by infrastructure from VPSPulse , RxServers , BuyNumber , UnitVPS , OffshoreName and secure payment technology by ArionPay.