- New function
derive_vars_crit_flag()
for deriving criterion flag variables (CRITy
,CRITyFL
,CRITyFLN
). (#2468)
- The following function arguments are entering the next phase of the deprecation process: (#2487)
consolidate_metadata(check_keys)
- Removed at v1.1.1
compute_egfr(wt)
- Removed at v1.1.1
derive_expected_records(dataset_expected_obs)
- Removed at v1.1.1
derive_locf_records(dataset_expected_obs)
derive_extreme_event(ignore_event_order)
derive_vars_merged(match_flag)
derive_var_merged_summary(new_var, analysis_var, summary_fun)
- Removed at v1.1.1
derive_param_computed(analysis_value, analysis_var)
derive_param_exposure(filter, analysis_var, summary_fun)
derive_summary_records(filter)
- Removed at v1.1.1
derive_extreme_records(filter)
derive_var_joined_exist_flag(first_cond, filter)
event_joined(first_cond)
filter_joined(first_cond, filter)
Developer Notes
-
derive_extreme_event()
was fixed such thatcheck_type = "none"
is accepted again. (#2462) -
derive_locf_records()
documentation example was fixed to display LOCF records. (#2461)
-
Added helper functions to
derive_vars_merged()
(get_flagged_records()
) andderive_vars_query()
(get_vars_query()
) so that those can be called independently as per user's request.derive_vars_merged()
function call results are not impacted by the change (#2441). -
Error Messaging has been made more "user-friendly". (#2372)
-
New
country_code_lookup()
metadata added to decode countries based on ISO 3166 codes. (#2388)
-
group_var
(optional) parameter is added toderive_var_trtemfl()
to deriveTRTEMFL
for AE data if the data are collected as one episode of AE with multiple lines. (#2302) -
Templates for ADPC, ADPPK and ADPP are updated to handle urine records. (#2392)
-
create_single_dose_dataset()
has been updated to error if thelookup_table
contains duplicates. (#2247) -
derive_vars_merged()
andderive_vars_transposed()
have arelationship
argument added (the same as found indplyr::*_join()
functions) for users to specify what type of join (one-to-one, one-to-many, etc.) should take place. (#2247) -
basket_select()
function updated to add...
argument to allow other qualifiers to be passed to user-defined function specified inget_terms_fun()
argument for functioncreate_query_data()
. (#2265) -
Messaging updated for
derive_extreme_event()
to improve clarity around duplicates. #2405 -
The
id_vars
argument was added toderive_vars_transposed()
andderive_vars_atc()
to allow additional variables, beyond those inby_vars
, to uniquely identify records in thedataset_merge
argument. (#2325) -
Update PK Programming vignette and templates for ADPC and ADPPK for the nominal time formula
NFRLT
to reduce duplicate records in dose expansion withcreate_single_dose_dataset()
. (#2426) -
Template for ADSL updated so that
EOSSTT
is assigned as"ONGOING"
when no study completion rows exist yet in DS. (#2436) -
The
slice_derivation()
function was updated such that it works now when called in a function where objects from the function environment are used. (#2244)
-
The following function arguments are entering the next phase of the deprecation process: (#2299)
compute_egfr(wt)
consolidate_metadata(check_keys)
derive_expected_records(dataset_expected_obs)
derive_locf_records(dataset_expected_obs)
derive_extreme_event(ignore_event_order)
derive_vars_merged(match_flag, new_var, analysis_var, summary_fun)
derive_param_computed(analysis_value, analysis_var)
derive_param_exposure(filter, analysis_var, summary_fun)
derive_summary_records(filter)
derive_extreme_records(filter)
derive_var_joined_exist_flag(first_cond, filter)
event_joined(first_cond)
filter_joined(first_cond, filter)
-
The following function arguments have reached the end of the deprecation process and been removed: (#2299)
dthcaus_source(traceability_vars)
date_source(traceability_vars)
derive_var_ontrtfl(span_period)
derive_var_shift(na_val)
derive_vars_aage(unit)
-
Documentation for
derive_extreme_event()
has been updated to include a description for the value ofderive_extreme_event()
whenkeep_source_vars = NULL
. (#2398) -
The "Visit and Period Variables" vignette was updated and refactored to include example code to create a period reference dataset. (#2321)
-
The documentation of
derive_vars_merged()
function is updated to describe that thecheck_type
argument is ignored (an error is issued) iforder
is not specified. (#2326) -
The "User Guides" section has been reorganized. A new "Programming Concepts and Conventions" vignette was also added to provide more context and information around common
{admiral}
behaviors and ways of working. (#2395) -
The "Get Started" section has been revamped, placing greater focus on material that may help users familiarize themselves with
{admiral}
. There are now new sections showcasing the various types of{admiral}
functions and some of the more advanced topics have been moved to the new "Programming Concepts and Conventions" vignette. (#2395) -
The Examples section of
derive_param_computed()
now contains a new item showcasing how to create a derived parameter in the case that a variable contributing to the derived parameter has some/all of its values missing. (#2338)
-
Templates and vignettes do not add or populate
AVALC
for BDS-findings datasets where the information contained inAVALC
would be redundant withAVAL
. (#2442) -
The function
dplyr::transmute()
is superseded in favor ofdplyr::mutate(.keep = "none")
. Consequently, all the admiral functions that utilized the former have been updated accordingly. (#2274) -
The templates for ADPP and ADPC are updated for missing variables (#2308) and to make
ATPT
andATPTN
consistent. (#2328) -
ADLB template updated to make
PARAM
consistent forPARAMCD
values"BASO"
and"LYMPH"
. (#2327)
Developer Notes
- In the previous version,
renv
was the default framework used to manage package dependencies. Now, we usedevtools
as our main package manager (some changes also occurred for admiralci workflows). There is a possibility to get package dependency versions used for the workflows to ensure local reproducibility. For this, you need to go under the latest action summary in your current PR. You can see a deps artifact. For each version of R used forR CMD CHECKS
jobs, there is an associated renv.lock file (under the deps artifact). - Splitting out
R
andtest
files for date/time functions for cyclomatic complexity refactor (#2340)(#2339) - Created three unit tests for
get_summary_records()
. (#2304) - Created unit tests for developer internal function
get_imputation_target_date()
(#2378) - Modified date/time unit tests to use unified example (#2424)
- Fix bug in
derive_param_tte()
where argumentdataset
populated andPARAMCD
inset_values_to
argument is an expression. Previously, there was a check early in function to see ifPARAMCD
defined inset_values_to
argument, already existed in the dataset passed intodataset
argument. IfPARAMCD
was not an expression i.e.PARAMCD = "XYZ"
then check worked. However, ifPARAMCD
to be created was an expression, and wasn't resolved yet, this caused an ERROR. The check has been moved to near the end of the function, wherePARAMCD
is resolved in the dataset holding the new parameters. (#2336)
- Fix bug in
derive_vars_query()
where if AE terms were in mixed case no terms are flagged. (#2311)
-
The new function
derive_vars_extreme_event()
, which works asderive_extreme_event()
but adds variables instead of a parameter. (#2138) -
The new function
derive_var_merged_ef_msrc()
is provided to add a flag indicating if one of the conditions in one of multiple source datasets is fulfilled. (#1728) -
New global option created
signif_digits
and added toset_admiral_options()
to handle floating point issue, the value is set to15
, and is used with thebase R
functionsignif()
when comparing 2 numeric values. This is implemented inadmiral
functionsderive_var_atoxgr_dir()
andderive_var_anrind()
. (#2134)For more information, please see blog: How admiral handles floating points
-
The new function
derive_vars_computed()
is provided which has the same functionality asderive_param_computed()
but instead of adding the computed values as a new parameter, adds it as a new variable. (#2178)
-
Fixed a bug in
compute_tmf()
where the time imputation flag was being incorrectly populated when any of the existing time components (hour, minute and/or second) of the date character vector ('--DTC'
), was imputed. (#2146) -
derive_extreme_records()
,derive_var_extreme_flag()
,derive_vars_joined()
andderive_vars_merged()
were enhanced with the argumentstrue_value
andfalse_value
to align with preexisting functions that had similar functionality. (#2125) -
restrict_derivation()
now allows{dplyr}
functions likemutate()
in thederivation
argument. (#2143) -
derive_summary_records()
,derive_var_merged_summary()
, andget_summary_records()
were enhanced such that more than one summary variable can be derived, e.g.,AVAL
as the sum andADT
as the maximum of the contributing records. (#1792) -
derive_summary_records()
was enhanced with the following arguments:dataset_add
(required),dataset_ref
(optional),missing_values
(optional). These arguments respectively, generate summary variables from additional datasets, retain/add specific records from a reference dataset, and impute user-defined missing values. Note thatdataset_add
can be set to the same value asdataset
if a different additional dataset is not required.derive_param_exposure()
was enhanced withdataset_add
as well. (#2142) -
The
missing_values
argument was added toderive_var_merged_summary()
. It allows to define values for by groups, e.g., subjects which are not in the additional dataset. (#2230) -
The argument
dataset
is now optional forderive_summary_records()
andderive_param_exposure()
. (#2142) -
The "joined" functions (
derive_vars_joined()
,derive_var_joined_exist_flag()
,filter_joined()
, andevent_joined()
) were unified: (#2126)- The
dataset_add
andfilter_add
arguments were added toderive_var_joined_exist_flag()
andfilter_joined()
. - The
filter
argument was renamed tofilter_join
inderive_var_joined_exist_flag()
andfilter_joined()
. - The
tmp_obs_nr_var
, thejoin_type
, thefirst_cond_lower
, and thefirst_cond_upper
arguments were added toderive_vars_joined()
. - In
derive_var_joined_exist_flag()
,filter_joined()
, andevent_joined()
thefirst_cond
argument was renamed tofirst_cond_upper
and thefirst_cond_lower
argument was added. - In all "joined" functions the
filter_add
argument is applied to the additional dataset grouped byby_vars
and thefilter_join
argument is applied to the joined dataset grouped by the observations from the input dataset. I.e., summary functions likeall()
orany()
can be used.
- The
-
The
tmp_event_nr_var
argument was added toderive_extreme_records()
to allow more control of the selection of records. It creates a temporary variable for the event number, which can be used inorder
. (#2140) -
signif_dig
argument added to bothderive_var_atoxgr_dir()
andderive_var_anrind()
functions with default value set to general optionsignif_digits
. The new argument to these functions handles any floating point issues. (#2134) -
Fixed a bug in
derive_vars_period()
where the function was throwing an error wheneverdataset_ref
contained variables that were neither key variables, norAPERIOD
,ASPER
,APHASEN
, nor mentioned in thenew_vars
argument. (#2231) -
compute_duration()
,derive_vars_duration()
,derive_vars_aage()
now accepts more terms for thein_unit
,out_unit
, andage_unit
arguments (#2255) -
Updated the unit test for
derive_var_obs_number()
. The new test checked the derivation of the default and customizednew_var
, sorting with the the missing value and expected conditions. (#2260) -
The check for existence of
TERMNUM
/TERMCHAR
in queries dataset is now less strict depending on values ofSRCVAR
forderive_vars_query()
(#2264) -
DAIDS grading criteria fixed for
Grade = 0
forTERM = "Absolute Lymphocyte Count, Low"
, criteria wasAVAL <= 0.65
, now corrected toAVAL >= 0.65
(#2284). -
A bug in
derive_extreme_event()
was fixed. Thecondition
field is no longer ignored ifmode
is specified forevent()
(#2291). -
A bug in
derive_vars_joined()
was fixed. The function no longer fails if renaming is used inby_vars
andnew_vars
is not specified (#2289).
-
{admiral}
now only supports R >= 4.0.0 -
In
derive_extreme_records()
thedataset_add
argument is now mandatory. (#2139) -
In
derive_summary_records()
andget_summary_records()
the argumentsanalysis_var
andsummary_fun
were deprecated in favor ofset_values_to
. (#1792) -
In
derive_summary_records()
andderive_param_exposure()
the argumentfilter
was renamed tofilter_add
(#2142) -
In
derive_var_merged_summary()
the argumentsnew_var
,analysis_var
, andsummary_fun
were deprecated in favor ofnew_vars
. (#1792) -
In
derive_vars_merged()
, the argumentmatch_flag
was renamed toexist_flag
(#2125) -
The default value for the
false_value
argument inderive_extreme_records()
was changed toNA_character_
(#2125) -
In
consolidate_metadata()
, the argumentcheck_keys
was renamed tocheck_type
to align with other functions (#2184) -
In
filter_joined()
andderive_var_joined_exist_flag()
(#2126)- the
first_cond
argument was deprecated in favor offirst_cond_upper
and - the
filter
argument was deprecated in favor offilter_join
.
- the
-
In
event_joined()
thefirst_cond
argument was deprecated in favor offirst_cond_upper
. (#2126) -
In
derive_extreme_event()
, theignore_event_order
argument was deprecated and the selection of the records was changed to allow more control. Before, the records were selected first by event and then byorder
. Now they are selected byorder
only, but the event number can be added to it.To achieve the old behavior update
order = exprs(my_order_var),
ignore_event_order = FALSE,
to
tmp_event_nr_var = event_nr,
order = exprs(event_nr, my_order_var),
and
order = exprs(my_order_var),
ignore_event_order = TRUE,
to
order = exprs(my_order_var),
-
create_query_data()
andderive_vars_query()
were updated to rename variables in query data set as follows: (#2186)TERMNAME
toTERMCHAR
TERMID
toTERMNUM
Users need to adjust their
get_terms()
function accordingly. -
The following functions, which were deprecated in previous
{admiral}
versions, have been removed: (#2098)derive_param_extreme_event()
derive_vars_last_dose()
derive_var_last_dose_amt()
derive_var_last_dose_date()
derive_var_last_dose_grp()
derive_var_basetype()
derive_var_merged_cat()
derive_var_merged_character()
derive_var_confirmation_flag()
-
The following function arguments are entering the next phase of the deprecation process: (#2098)
compute_egfr(wt)
derive_extreme_records(filter)
derive_param_computed(analysis_value, analysis_var)
derive_var_shift(na_val)
derive_expected_records(dataset_expected_obs)
derive_var_ontrtfl(span_period)
-
The
derive_param_extreme_record()
function has been superseded in favor ofderive_extreme_event()
. (#2141) -
The functions
derive_var_dthcaus()
,derive_var_extreme_dt()
, andderive_var_extreme_dtm()
have been superseded in favor ofderive_vars_extreme_event()
. (#2138)
-
The documentation of the
by_vars
andconstant_by_vars
argument was improved and unified across all functions where it is used. (#2137) -
The functions
assert_db_requirements()
,assert_terms()
,assert_valid_queries()
,extend_source_datasets()
,filter_date_sources()
,validate_basket_select()
,validate_query()
are no longer exported and have had documentation removed. (#2220) -
The function
extract_duplicate_records()
has been re-classified as aninternal
function, which means that the function still appears in our help pages but not on our website. (#2220) -
The "Generic Functions" vignette (now "Generic Derivations") was rewritten. Now it provides a more complete overview of the generic derivations, describe the common concepts, and makes it easier to find the appropriate function. (#2230)
-
A way to standardize roxygen labels and descriptions for function arguments was implemented and tested. (#2034)
-
A link to published CDISC Population PK (ADPPK) implementation guide was added. (#2161)
-
Removed Deprecation section in Reference tab. Added new Superseded section in Reference tab. (#2174)
-
Added a link to the previous versions of the website to the navigation bar. (#2205)
-
The meaning of
date_imputation = "mid"
was clarified in the documentation of the imputation functions, e.g.derive_vars_dtm()
. (#2222) -
Added an example derivation of
DTHCGR1
to the ADSL vignette. (#2218) -
Moved Development Process from
{admiraldev}
to Contribution Model in theadmiral
website, updated GitHub strategy. (#2196) -
Added new drop downs in Get Started navigation bar- Getting Started, Admiral Discovery, Cheatsheet. Community removed from top. (#2217)
-
All "Example Script(s)" sections in the User Guide vignettes were updated to point the user towards using
use_ad_template("ADaM")
rather than linking to the template in the code repository. (#2239) -
Handling of
NA
values was added to the documentation of theorder
argument for all functions. (#2230, #2257)
-
Website now has button/links to Slack channel and GitHub Issues. (#2127)
-
Added example derivations of
DTHCAUS
andDTHCGR1
to the ADSL template. (#2218) -
Cheat Sheet now added to website front page (#2130)
- Fixed a bug in
derive_var_dthcaus()
where if a subject has observations in more than one of the sources, the one from the last source was selected regardless of the date. Now the function works as described in its documentation. (#2154)
- A unit test for
derive_param_computed()
was modified in anticipation of major user-facing changes to R version 4.4 (#2147)
-
derive_extreme_records()
no longer fails ifdataset_add
is specified and a variable specified fororder
is not indataset
. (#2113) -
The
type
argument incompute_duration()
changed the underlying default behavior inderive_vars_duration()
without allowing the user to toggle between"duration"
and"interval"
as originally intended. This was fixed by adding thetype
argument forderive_vars_duration()
and a wrapper functionderive_vars_aage()
such that it gets passed throughcompute_duration()
appropriately (#2112) -
Template
ad_adpp.R
updated to replaceleft_join()
withderive_vars_merged()
(#2109).
-
event_joined()
events were added. They can be specified for theevents
argument inderive_extreme_event()
. This allows to define events based on more than one observation, e.g., events which need to be confirmed by a second assessment. (#1960) -
atoxgr_criteria_daids.rda
added, which holds metadata for Division of AIDS (DAIDS) Table for Grading the Severity of Adult and Pediatric Adverse Events. You can find additional documentation hereatoxgr_criteria_daids()
-
The functions
derive_param_bmi()
andderive_param_bsa()
are updated to have the option of producing more values at visits when only weight is collected (#1228). -
The functions
derive_var_age_years()
andcompute_age_years()
are updated to return anNA
age in the case that the age unit is missing. (#2001) The argumentunit
forderive_vars_aage()
is also changed toage_unit
for consistency between these age-related functions. (#2025) -
The
derive_var_ontrtfl()
function has been updated to allow for the column passed inref_end_date
to containNA
values. Previously, if the end date wasNA
, the row would never be flagged. Now, anNA
value is interpreted as the treatment being ongoing, for example. (#1984) -
The function
derive_var_extreme_flag()
has a new function argument,flag_all
that additionally flags all records if the first or last record is not unique. (#1979) -
The function
derive_param_computed()
was enhanced: (#1968)- The
analysis_value
andanalysis_var
arguments were deprecated in favor ofset_values_to
. This enables users to compute more than one variable. - The
keep_nas
argument was added. If it is set toTRUE
, observations are created even if values contributing to the computed values areNA
.
- The
-
The function
derive_vars_dy()
is updated to avoid potential error when the inputdataset
with columns ending withtemp
. (#2012) -
Argument
keep_source_vars
was added toderive_extreme_records()
which specifies which variables in the new observations should be kept. (#1697) -
Templates, vignettes, and other uses of
{admiral.test}
SDTM data are updated to use{pharmaversesdtm}
instead. (#2040) -
The
traceability_vars
argument indate_source()
anddthcaus_source
were deprecated in favor ofset_values_to
. Thedate_source()
function creates a date_source object as input forderive_var_extreme_dt()
andderive_var_extreme_dtm()
,users can now define the traceability variables by assigning those variables to theset_values_to
argument.Similarly, thedthcaus_source
creates a dthcaus_source Object. (#2068) -
derive_extreme_event()
was enhanced (#1960):-
event_joined()
events can be specified for theevents
argument. This allows to define events based on more than one observation, e.g., events which need to be confirmed by a second assessment. -
The
source_datasets
argument was added to the function and thedataset_name
field toevent()
. It can be used to define events based on a different dataset than the input dataset. -
The
keep_source_vars
argument was added to the function and thekeep_source_vars
field toevent()
. It allows to select which variables should be kept for the selected observations. -
The
mode
andorder
field were added toevent()
. They allow to select the first or last observation per by group if there are multiple observation fulfilling the event condition. -
The
ignore_event_order
argument was added. -
The
description
field was added toevent()
. It can be used to provide a description of the event in plain language.
-
-
derive_var_atoxgr_dir()
was enhanced (#1859):-
Can now select
atoxgr_criteria_daids
in argumentmeta_criteria
to createATOXGRL
andATOXGRH
based on Division of AIDS (DAIDS) Table for Grading the Severity of Adult and Pediatric Adverse Events -
New argument
signif_dig
added to control the number of significant digits to use when comparing 2 numeric values. (#2060)
-
-
The
compute_duration(type)
argument added the"duration"
type calculation, and this is the new default (previously"interval"
differences were returned). See function help file for details on the difference between"duration"
and"interval"
calculations. (#1875) -
The following functions, which were deprecated in previous
{admiral}
versions, have been removed: (#1950)derive_var_disposition_status()
derive_vars_disposition_reason()
format_eoxxstt_default()
format_reason_default()
derive_var_worst_flag()
-
The following functions have been deprecated from previous
{admiral}
versions using the next phase of the deprecation process: (#1950)derive_param_extreme_event()
derive_vars_last_dose()
derive_var_last_dose_amt()
derive_var_last_dose_date()
derive_var_last_dose_grp()
derive_var_basetype()
derive_var_merged_cat()
derive_var_merged_character()
-
The arguments
dataset_adsl
in the functionderive_param_exist_flag()
andsubject_keys
have been deprecated versions using the next phase of the deprecation process. (#1950) -
The argument
wt
in the functioncompute_egfr()
was deprecated in favor ofweight
using the first phase of the deprecation process. (#2020) -
The
filter
argument inderive_extreme_records()
was deprecated in favor of thefilter_add
using the next phase of the deprecation process. (#1950) -
The
analysis_value
andanalysis_var
arguments inderive_param_computed()
were deprecated in favor ofset_values_to
(#1968). -
The
na_val
argument inderive_var_shift()
has been deprecated in favor ofmissing_value
using the first phase of the deprecation process. (#2014) -
The
dataset_expected_obs
argument inderive_expected_records()
andderive_locf_records()
has been deprecated in favor ofdataset_ref
. (#2037) -
The
span_period
argument inderive_var_ontrtfl()
has been updated to only acceptTRUE
orFALSE
, where is previously accepted"Y"
andNULL
. (#2033)
-
Non-exported utility and print functions were previously listed on the admiral website reference page. They have been removed. (#2049, #2050)
-
The description of the argument
reference_date
in the functionderive_vars_dy()
has been clarified to make it agnostic to start/end selection. (#2027) -
Date and Time Imputation User Guide/Vignette has section on preserving partial dates updated (#2028)
-
The list of package authors/contributors has been reformatted so that those who are actively maintaining the code base are now marked as authors, whereas those who made a significant contribution in the past are now down as contributors. All other acknowledgments have been moved to README section (#1941).
-
derive_vars_joined()
had two bugs with regards to duplicates messaging and whennew_vars
was set toNULL
that have now been addressed (#1966). -
compute_dtf()
had a bug with regards to imputing days to full date-time character strings. (#2042)
- Fix bug in
derive_param_tte()
. (#1962) - Get Started page now points to correct article. (#1969)
-
In the function
derive_var_anrind()
, added argumentuse_a1hia1lo
to turn the usage ofA1HI
andA1LO
off and on, with the default being off. (#1795) -
Added a "Report a bug" link to
{admiral}
website. (#1836) -
New function
compute_age_years()
for converting a vector of age values to years. (#1794) -
New functions
filter_exist()
andfilter_not_exist()
for selecting records from a dataset dependent on the existence of the corresponding by groups in a filtered source dataset. (#1699) -
New function
derive_param_extreme_record()
that adds parameter based on the first or last record from multiple sources. (#1822) -
New ADPPK template script available
ad_adppk.R
which creates Population PK Analysis Dataset based on forthcoming CDISC Implementation guide. (#1772) -
New function
compute_egfr()
for calculating Estimated Glomerular Filtration Rate (eGFR) and Creatinine Clearance for Kidney Function. (#1826)
-
derive_extreme_records()
was enhanced such that it includes the functionality ofderive_param_extreme_event()
. (#1725) -
For the
set_values_to
argument expressions are accepted now. For example,set_values_to = exprs(PARAMCD = str_to_upper(QSTESTCD))
. This affectscensor_source()
,derive_expected_records()
,derive_extreme_event()
,derive_extreme_records()
,derive_param_bmi()
,derive_param_bsa()
,derive_param_computed()
,derive_param_doseint()
,derive_param_exposure()
,derive_param_framingham()
,derive_param_map()
,derive_param_exist_flag()
,derive_param_extreme_event()
,derive_param_qtc()
,derive_param_rr()
,derive_param_wbc_abs()
,derive_summary_records()
,event_source()
,get_summary_records()
. (#1727) -
For the
order
argument expressions are accepted now. (#1727) -
derive_vars_merged()
updates: (#1727)- The
missing_values
argument to assign values to the new variables for non-matching observations was added. - The
new_vars
argument accepts expressions now.
- The
-
derive_vars_joined()
updates: (#1727)- The
missing_values
argument to assign values to the new variables for non-matching observations was added. - The
new_vars
and thejoin_vars
argument accept expressions now.
- The
-
The
date
field ofdate_source()
accepts expressions now. This affectsderive_var_extreme_dt()
andderive_var_extreme_dtm()
. (#1727) -
The
date
anddthcaus
field ofdthcaus_source()
accept expressions now. This affectsderive_var_dthcaus()
. (#1727) -
The
date
field ofevent_source()
andcensor_source()
accepts expressions now. This affectsderive_param_tte()
. (#1727) -
The
derive_param_computed()
function was enhanced: (#1873)- The new
dataset_add
argument allows to consider parameters from a different dataset than the input dataset. - The new
analysis_var
argument allows to specify the variable to be populated, e.g.,AVALC
. - For
parameters
andconstant_parameters
a list of expressions can be specified now. This allows to create temporary parameter codes, e.g., if SDTM data is used as input. - The
analysis_value
argument was enhanced such that any variable of the form<variable>.<parameter>
can be used, e.g.,QSORRES.CHSF13
.
- The new
-
create_query_data()
andderive_vars_query()
updated to rename variables in query data set as follows: (#1907)VAR_PREFIX
toPREFIX
QUERY_NAME
toGRPNAME
QUERY_ID
toGRPID
QUERY_SCOPE
toSCOPE
QUERY_SCOPE_NUM
toSCOPEN
TERM_LEVEL
toSRCVAR
TERM_NAME
toTERMNAME
TERM_ID
toTERMID
Users need to adjust their
get_terms()
function accordingly. -
The
aval_fun
argument ofderive_param_exist_flag()
was deprecated in favor of theset_values_to
argument. (#1727) -
derive_var_merged_cat()
andderive_var_merged_character()
have been deprecated in favor ofderive_vars_merged()
. (#1727) -
The following functions, which were deprecated in previous
{admiral}
versions, have been removed: (#1747)derive_vars_merged_dt()
derive_vars_merged_dtm()
derive_var_agegr_ema()
derive_var_agegr_fda()
derive_param_first_event()
derive_derived_param()
derive_var_confirmation_flag()
filter_confirmation()
-
The following functions have been deprecated from previous
{admiral}
versions using the next phase of the deprecation process: (#1747)derive_var_disposition_status()
derive_vars_disposition_reason()
format_eoxxstt_default()
format_reason_default()
derive_var_worst_flag()
-
derive_param_extreme_event()
was deprecated in favor ofderive_extreme_records()
. (#1725) -
The
filter
argument inderive_extreme_records()
was deprecated in favor of thefilter_add
argument. (#1725) -
derive_vars_last_dose()
,derive_var_last_dose_amt()
,derive_var_last_dose_date()
,derive_var_last_dose_grp()
, were deprecated in favor ofderive_vars_joined()
. (#1797) -
derive_var_basetype()
was deprecated in favor ofderive_basetype_records()
. (#1796) -
In the function
derive_param_exist_flag()
the argumentsdataset_adsl
andsubject_keys
have been renamed todataset_ref
andby_vars
respectively. (#1793)
-
Updated example dataset to trigger deterioration flags in the vignette "Creating Questionnaire ADaMs". (#1853, #1854)
-
Updated PK Programming vignette to include new Population PK Template
ad_adppk.R
. (#1772) -
Updated "Lab Grading" Vignette to link to grading metadata available in
{admiral}
and clarify how abnormal baseline values are assigned in NCI-CTCAEv5. (#1863) -
Updated "Visit and Period Variables" Vignette to add more detail about Study Specific Code that is required. (#1831)
-
Increased documentation for those functions which are regarded as wrapper functions. (#1726)
-
Examples in function documentation no longer rely on
library(admiral.test)
. (#1752) -
Conferences where
{admiral}
was presented were updated on theREADME.md
. (#1890)
-
vars()
which was used in the admiral function calls that expected a list of quosures has been removed. The admiral optionforce_admiral_vars
was removed as well. (#1694) -
derive_vars_dtm()
andderive_vars_dt()
had a bug pertaining to imputations associated with supplying bothmin_dates
andmax_dates
that has now been resolved. (#1843) -
Examples for
derive_var_extreme_flag()
were reworked to reduce runtime that occasionally led to failing CI check. (#1780) -
create_period_dataset()
had a bug that led to an error when both DT and DTM columns existed. (#1845) -
External functions are now consistently imported via namespace.
package::function()
calls have been removed fromadmiral
functions. (#1842) -
restrict_derivation()
had a bug which led to failure if thederivation
argument was not in the global environment. (#1765)
- Changing package maintainer from Thomas Neitmann to Ben Straub. (#1848)
- Fix checks on
derive_vars_dtm()
andderive_vars_dt()
that were too restrictive. (#1810)
-
Using
{testthat}
3rd edition for unit testing. This is stricter in that messages must be addressed and deprecated functions throw errors. (#1754) -
New function
consolidate_metadata()
for consolidating multiple meta datasets into a single one. (#1479) -
New function
compute_scale()
for computing the average of a vector and transforming the result from a source to a target range. (#1692) -
New ADPC template script available
ad_adpc.R
which creates PK Concentration Analysis Dataset (#849). This script includes formatting suitable for Non-Compartmental Analysis (ADNCA). (#851) -
New function
derive_expected_records()
for adding expected records. (#1729) -
New function
derive_extreme_event()
for adding the worst or best observation for each by group as new records. (#1755)
-
Arguments
analysis_var
,keep_vars
were added toderive_locf_records()
,
analysis_var
allows to specify analysis variable,keep_vars
keeps variables that need carrying the last observation forward other thananalysis_var
(e.g.,PARAMN
,VISITNUM
). (#1636) -
The function
create_single_dose_dataset()
adds support for expanding relative nominal time (e.g. NFRLT) used in Pharmacokinetic (PK) analyses. The new parameternominal_time
defaults asNULL
and does not change the normal operation of the function. If anominal_time
is specified such as NFRLT (Nominal Relative Time from First Dose) then the nominal time is incremented by the interval specified inEXDOSFRQ
for example for "QD" records the NFRLT is incremented by 24 hours, e.g. 0, 24, 48... (#1640) -
create_single_dose_dataset()
is also updated for values ofEXDOSFRQ
with units in days but expected values less than 24 hours, such as "BID", "TID", and "QID". Previously these values ofEXDOSFRQ
may result in duplicate records where the day values are incremented but the time values are not. (#1643) -
The function
derive_var_confirmation_flag()
andfilter_confirmation()
gained thetmp_obs_nr_var
argument. It helps flagging or selecting consecutive observations or the first or last observation in a by group. (#1724) -
The functions
derive_vars_merged()
,derive_var_merged_cat()
,derive_var_merged_character()
,derive_var_merged_exist_flag()
,derive_var_merged_summary()
, andderive_vars_merged_lookup()
were updated to allow renaming in the argumentby_vars
. (#1680) -
The units "min" and "sec" are added as valid values of
out_unit
incompute_duration()
andderive_vars_duration()
. (#1647) -
The function
derive_vars_query()
now includes a consistency check forQUERY_SCOPE
andQUERY_SCOPE_NUM
values. (#652) -
Argument
new_var
inderive_param_extreme_event()
is made optional. (#1630) -
derive_vars_last_dose()
no longer fails ifUSUBJID
is not included in the input dataset. (#1787)
-
All function arguments which expected a list of quosures created by
vars()
are now expecting a list of expressions created byexprs()
. For example, instead ofby_vars = vars(STUDYID, USUBJID)
by_vars = exprs(STUDYID, USUBJID)
must be used now.To enable running old scripts using
vars()
in the admiral function calls admiral redefines thevars()
function such that it returns a list of expressions. This can be disabled by the admiral optionforce_admiral_vars
(seeset_admiral_options()
). Please note that this is a temporary solution and will be removed in a future admiral release. (#1627) -
Function
derive_param_tte()
has been updated such that only observations are added for subjects who have both an event or censoring and an observation indataset_adsl
. (#1576) -
Function
derive_var_disposition_status()
has been deprecated, please usederive_var_merged_cat()
instead. (#1681) -
Function
derive_var_worst_flag()
has been deprecated, in favor ofslice_derivation()
/derive_var_extreme_flag()
. (#1682) -
Function
derive_vars_disposition_reason()
has been deprecated, in favor ofderive_vars_merged()
. (#1683) -
The following functions have been deprecated from previous
{admiral}
versions using the next phase of the deprecation process: (#1712)derive_derived_param()
derive_param_first_event()
derive_vars_merged_dt()
derive_vars_merged_dtm()
derive_var_agegr_ema()
derive_var_agegr_fda()
-
The following functions, which were deprecated in previous
{admiral}
versions, have been removed: (#1712)derive_var_ady()
derive_var_aendy()
derive_var_astdy()
derive_var_atirel()
derive_vars_suppqual()
smq_select()
sdg_select()
-
The following parameters, which were deprecated in previous
{admiral}
versions, have been removed: (#1712)meddra_version
,whodd_version
,get_smq_fun
andget_sdg_fun
from thecreate_query_data()
functiondate_imputation
,time_imputation
andpreserve
parameters fromdate_source()
functionfilter
parameter fromderive_var_extreme_flag()
-
ADLB
metadata data set calledatoxgr_criteria_ctcv5
updated to remove unit check forHYPERURICEMIA
as grade criteria based onANRHI
only. This metadata holds criteria for lab grading based on Common Terminology Criteria for Adverse Events (CTCAE) v5.0. (#1650) -
Renamed
derive_var_confirmation_flag()
andfilter_confirmation()
toderive_var_joined_exist_flag()
andfilter_joined()
respectively. (#1738)
-
New vignette "Creating a PK NCA ADaM (ADPC/ADNCA)". (#1639)
-
New vignette "Hy's Law Implementation". (#1637)
-
New vignette "Creating Questionnaire ADaMs". (#1715)
-
The expected value for the
derivation
argument ofrestrict_derivation()
,slice_derivation()
, andcall_derivation()
is described now. (#1698) -
Removed authors from function documentation, as we will now only be tracking an overall list of authors for admiral. (#1673)
-
Added an imputation example for
create_single_source_dataset()
in function documentation. (#1408, #1760) -
Updates to examples for
derive_var_age_years()
andderive_vars_duration()
. (#1620, #1634) -
Increased the level of documentation for
derive_var_age_years()
to describe the data type of the newly creatednew_var
column. (#970)
- Functions
derive_vars_dtm()
andderive_vars_dt()
had a bug pertaining to imputations associated withNA
values that has now been fixed. (#1646)
- Implement changes to
if_else()
from the release ofdplyr
version 1.1.0, which affectsderive_vars_dtm()
andand compute_tmf()
. (#1641)
-
The new function
derive_vars_joined()
adds variables from an additional dataset. The selection of the observations can depend on variables from both datasets. This can be used for addingAVISIT
,AWLO
,AWHI
based on time windows andADY
or deriving the lowest value (nadir) before the current observation. (#1448) -
New function
derive_var_trtemfl()
for deriving treatment emergent flags. (#989) -
The new function
chr2vars()
turns a character vector into a list of quosures. (#1448) -
New function
derive_var_relative_flag()
for flagging observations before or after a condition is fulfilled. (#1453) -
New functions
get_admiral_option()
andset_admiral_options()
to allow more flexibility on common function inputs; e.g. likesubject_keys
to avoid several find and replace instances ofvars(STUDYID, USUBJID)
. (#1338) -
The new function
create_period_dataset()
for creating a reference dataset for subperiods, periods, or phases from the ADSL dataset was added. The reference dataset can be used to create subperiod, period, and phase variables in OCCDS and BDS datasets. (#1477) -
The new function
derive_vars_period()
adds subperiod, period, or phase variables to ADSL. The values for the new variables are provided by a period reference dataset. (#1477) -
New function
derive_var_merged_summary()
adds a variable of summarized values to the input dataset. (#1564) -
A
print()
method was added for all S3 objects defined by admiral, e.g.,date_source()
,dthcaus_source()
, ... (#858) -
New metadata data set called
atoxgr_criteria_ctcv5
which holds criteria for lab grading based on Common Terminology Criteria for Adverse Events (CTCAE) v5.0. -
Removed the
{assertthat}
dependency in{admiral}
. (#1392) -
Removed R Version 3.6 check in CI/CD workflows in favor of the three most recent versions: 4.0, 4.1 and 4.2. (#1556)
-
The new function
derive_locf_records()
adds LOCF records as new observations. This can be used when the input dataset does not contain observations for missed visits/time points or whenAVAL
isNA
for particular visits/time points. (#1316) -
New function
convert_na_to_blanks()
to convert characterNA
to blanks. (#1624)
-
Function
derive_param_first_event()
has been replaced by a more generalizedderive_param_extreme_event()
function with new argumentmode
allowing for the selection of either the"first"
or"last"
event record according to the conditions provided. Also thedate_var
argument has been replaced with theorder
argument instead. In addition, three new argumentsnew_var
,true_value
, andfalse_value
have been added to allow the user to choose what variable is used to indicate whether an event happened, and the values it is given. (#1317, #1242) -
Argument
ignore_time_for_ref_end_date
was added toderive_var_ontrtfl()
, which controls if time is considered for the condition ifstart_date
is afterref_end_date
+ref_end_window
days. (#989) -
derive_var_atoxgr_dir()
default value ofatoxgr_criteria_ctcv4
removed for parametermeta_criteria
. Can now also chooseatoxgr_criteria_ctcv5
for parametermeta_criteria
, to implement NCI-CTCAEv5 grading criteria. -
Environment objects were consolidated into a single
admiral_environment
object underR/admiral__environment.R
. (#1572) -
The default value of the
keep_source_vars
argument increate_single_dose_dataset()
was updated such that it takes the values of the other arguments into account and thestart_datetime
andend_datetime
arguments are optional now. (#1598) -
Function
create_query_data()
has been updated such that the dictionary version is stored in the output dataset. (#1337)
-
Function
derive_param_first_event()
has been deprecated. Please usederive_param_extreme_event()
with theorder
argument instead of thedate_var
argument. (#1317) -
Functions
smq_select()
andsdg_select()
have been deprecated and replaced withbasket_select()
. In thecreate_query_data()
function,meddra_version
andwhodd_version
argument has been replaced byversion
andget_smq_fun
andget_sdg_fun
argument byget_terms_fun
. (#1597)
- New vignette "Generic Functions". (#734)
- New vignette "Visit and Period Variables". (#1478)
-
Function
derive_param_tte()
had a bug that setADT
toNA
whenstart_date
was missing, which has now been fixed. (#1540) -
Function
derive_vars_merged()
had an improperly formatted error message which has been corrected. (#1473) -
Templates now save datasets as
.rds
instead of.rda
. (#1501) -
Function
create_single_dose_dataset()
no longer fails if the input dataset contains observations with dose frequency"ONCE"
. (#1375)
- Fixed a bug where a recent update to
{lifecylce}
caused severaladmiral
tests to break (#1500)
- Second attempt to address issue where CRAN identified a failing test when "a strict Latin-1* locale" is used (#1469)
- Fixed a bug in
derive_vars_duration()
that surfaced after changes in R-devel (#1486)
- Fixed an issue where CRAN identified a failing test when "a strict Latin-1* locale" is used (#1469)
derive_var_extreme_dt()
andderive_var_extreme_dtm()
were updated such that source observations where the date isNA
are excluded (#1419)
-
get_summary_records()
creates summary records e.g. derive analysis value (AVAL
) from multiple records, only keeping the derived observations (#525) -
derive_param_framingham()
adds a Parameter for Framingham Heart Study Cardiovascular Disease 10-Year Risk Score (#977) -
compute_qual_imputation()
imputes values when qualifier exists in character result (#976) -
derive_vars_merged_lookup()
maps lookup tables (#940) -
filter_confirmation()
filters out confirmed observations (#1292) including supporting functionscount_vals()
,min_cond()
, andmax_cond()
. -
derive_var_confirmation_flag()
derives a flag which depends on other observations of the input dataset (#1293) -
derive_var_atoxgr()
derives lab toxicity/severity gradeATOXGR
fromATOXGRL
andATOXGRH
.ATOXGRL
holds toxicity/severity grade for low lab values, andATOXGRH
holds toxicity/severity grade for high lab values. -
derive_var_atoxgr_dir()
derives lab toxicity/severity grade for low lab values (ATOXGRL
) or for high lab values (ATOXGRH
). The grading is created from metadata. -
New metadata data set called
atoxgr_criteria_ctcv4
which holds criteria for lab grading based on Common Terminology Criteria for Adverse Events (CTCAE) v4.0
-
list_tte_source_objects()
gains apackage
parameter and is now exported (#1212) -
list_all_templates()
anduse_ad_template()
gain apackage
parameter which can be used to indicate in which package to look for templates (#1205) -
Randomization Date
RANDDT
variable added to ADSL template and vignette (#1126) -
Renamed
derive_derived_param()
toderive_param_computed()
and added a deprecation notice (#1229) -
derive_vars_duration()
updated to not display units when there is missing duration (#1207) -
value_var
parameter added toderive_vars_atc()
(#1120) -
format_eoxxstt_default()
- Updated the default value of EOSSTT for screen failure patients (#885) -
The imputation functions (
derive_vars_dtm()
,derive_vars_dt()
,convert_dtc_to_dtm()
,convert_dtc_to_dt()
) have been enhanced to address users feedback (#1300):-
Partial dates with missing components in the middle like
"2003-12-15T-:15:18"
,"2003-12-15T13:-:19"
,"2020-07--T00:00"
are handled now. -
The control of the level of imputation has been refined by adding the
highest_imputation
argument. For example,highest_imputation = "D"
requests imputation for day and time but not for year and month.(For the
date_imputation
and thetime_imputation
argumentNULL
is no longer a permitted value.) -
It is now possible to impute completely missing dates by specifying
highest_imputation = "Y"
and themin_dates
ormax_dates
argument.
-
-
order
parameter added todthcaus_source()
which allows an additional character vector to be used for sorting thedataset
,derive_vars_dthcaus()
updated to process additional parameter (#1125). -
create_single_dose_dataset()
Fixed bug whereASTDTM
andAENDTM
were not updated whenstart_date = ASTDT
andend_date = AENDT
. The function has been amended to now requirestart_datetime
andend_datetime
parameters in addition tostart_date
andend_date
.Thekeep_source_vars
has been added to specify the variables to be retained from the source dataset (#1224)
-
Moved all developer-facing functions and vignettes to
{admiraldev}
.{admiraldev}
is now a dependency of{admiral}
(#1231) -
All ADaM datasets but
admiral_adsl
have been removed from the package (#1234) -
derive_var_agegr_ema()
andderive_var_agegr_fda()
have been deprecated (#1333) -
Imputation related arguments have been deprecated for all functions except the imputation functions themselves (#1299). I.e., if a derivation like last known alive date is based on dates, DTC variables have to be converted to numeric date or datetime variables in a preprocessing step. For examples see the ADSL vignette. The following arguments were deprecated:
date_imputation
,time_imputation
, andpreserve
indate_source()
The following arguments no longer accept DTC variables:
date
indate_source()
,dthcaus_source()
,censor_source()
, andevent_source()
dose_date
andanalysis_date
inderive_vars_last_dose()
,derive_var_last_dose_amt()
,derive_var_last_dose_date()
,derive_var_last_dose_grp()
The following functions were deprecated:
derive_vars_merged_dt()
derive_vars_merged_dtm()
-
For the
date_imputation
and thetime_imputation
argument of the imputation functions (derive_vars_dtm()
,derive_vars_dt()
,convert_dtc_to_dtm()
,convert_dtc_to_dt()
)NULL
is no longer a permitted value. The level of imputation can be controlled by thehighest_imputation
argument now. -
The following functions, which were deprecated in previous {admiral} versions, have been removed:
derive_var_disposition_dt()
derive_var_lstalvdt()
lstalvdt_source()
derive_var_trtedtm()
derive_var_trtsdtm()
-
The following functions and parameters, which were deprecated in previous {admiral} versions, are now defunct and will output an ERROR if used:
derive_var_ady()
derive_var_aendy()
derive_var_astdy()
derive_var_atirel()
filter
parameter inderive_var_extreme_flag()
andderive_var_worst_flag()
-
New ADMH template script can be accessed using
admiral::use_ad_template("admh")
(#502) -
New vignette "Higher Order Functions" (#1047)
-
New vignette "Lab Grading" (#1369)
-
Fixed
derive_var_disposition_status()
argument to render correctly (#1268) -
Added link to pharmaverse YouTube channel to README
-
Restructured Reference page and updated all functions to use
family
tag in roxygen headers for finding similar functions. (#1105) -
Rename "Articles" page on website to "User Guides" and moved developer vignettes to
{admiraldev}
website (#1356)
-
derive_vars_last_dose()
no longer fails when a variable renamed innew_vars
is supplied to thedose_date
parameter (#1206) -
derive_vars_duration()
updated to not display units when there is missing duration (#1207) -
derive_param_first_event()
was updated (#1214) such thatAVAL
is derived instead ofAVALN
and- all variables from the source dataset are kept.
-
create_single_dose_dataset()
Fixed bug where ASTDTM and AENDTM were not updated whenstart_date=ASTDT
andend_date=AENDT
. The function has been amended to now require start_datetime and end_datetime parameters in addition to start_date and end_date.The keep_source_vars has been added to specify the variables to be retained from the source dataset. -
slice_derivation()
was updated such that it no longer fails if a slice is empty (#1309)
-
Updates to date/time imputation functions (#761):
-
convert_date_to_dtm()
andconvert_dtc_to_dtm()
now have time_imputation = "00:00:00" as default -
derive_vars_dt()
now has flag_imputation = "auto" as default
-
-
New functions for merging variables (#607):
derive_vars_merged()
- Merge Variables from a Dataset to the Input Datasetderive_vars_merged_dt()
- Merge a (Imputed) Date Variablederive_vars_merged_dtm()
- Merge a (Imputed) Datetime Variablederive_var_merged_cat()
- Merge a Categorization Variablederive_var_merged_exist_flag()
- Merge an Existence Flagderive_var_merged_character()
- Merge a Character Variable
-
create_query_data()
is provided to create the queries dataset required as input forderive_vars_query()
(#606) -
create_single_dose_dataset()
- Derives dataset of single dose from aggregate dose information (#660) -
New functions for deriving first or last dates from multiple source datasets (#753):
derive_var_extreme_dtm()
- Derive First or Last Datetime from Multiple Sourcesderive_var_extreme_dt()
- Derive First or Last Date from Multiple Sources
-
New function
derive_extreme_records()
for adding the first or last observation within each by group to the dataset (#1042) -
New function
derive_param_first_event()
: Add a new parameter for the first event occurring in a dataset. (#1063) -
New function
derive_param_exist_flag()
: Add a new parameter indicating that a certain event exists in a dataset. (#1064) -
New high order functions (#701):
restrict_derivation()
- Execute a derivation on a subset of the input datasetslice_derivation()
- The input dataset is split into slices (subsets) and for each slice a derivation is called separately. Some or all arguments of the derivation may vary depending on the slice.
-
filter_relative()
- Selects observations before or after the observation where a specified condition is fulfilled. For example, all observations up to first disease progression. (#1023)
-
New ADLB template script available
ad_adlb.R
, specific ADLB functions developed and BDS Finding vignette has examples enhanced with ADLB functions. (#1122) -
derive_var_shift()
- Derives a character shift variable containing concatenated shift in values based on user-defined pairing (#944) -
derive_var_analysis_ratio()
- Derives a ratio variable based on user-supplied variables from a BDS dataset, e.g. ADLB. (#943) -
derive_param_wbc_abs()
- Adds a parameter for lab differentials converted to absolute values. (#941)
- New ADPP template script available
ad_adpp.R
which creates Pharmacokinetics Parameters Analysis Dataset (#850)
-
Datasets internal to the package have been renamed with prefix
admiral_
, e.g.adsl
has been renamed toadmiral_adsl
. Corresponding SDTM datasets in{admiral.test}
have also been renamed, e.g.dm
toadmiral_dm
. These changes will impact examples, vignettes, unit tests and templates (#1108 and #1088) -
When
derive_vars_dtm_to_tm()
was called for variables created byderive_vars_dtm()
the function failed. This bug was fixed (#1097). -
impute_dtc()
- Fixed imputation bug. A user settingdate_imputation = MID
andpreserve = FALSE
would expect the date2019---07
to be imputed to2019-06-30
, but the function was returning2019-06-15
. Now returns it correctly. This bug fix also addresses the issue in the downstream functionsderive_vars_dt()
andderive_vars_dtm()
. (#1081) -
format_eoxxstt_default()
- Updated to have a more meaningful parameter name i.e. the parameter that was x is now status (#911)
-
derive_var_lstalvdt()
has been deprecated in favor ofderive_var_extreme_dt()
(#753). -
derive_vars_disposition_reason()
now is updated such that the default is populatingDCSREASP
only whenDSDECOD
is equal to'OTHER'
, which is consistent with ADaMIG_v1.3 (#886). -
derive_vars_suppqual()
has been removed from {admiral} as adding supplementary qualifiers is now done in another package called {metatools} in a function calledcombine_supp()
and is available on CRAN (#950) -
The
filter
parameter inderive_var_extreme_flag()
andderive_var_worst_flag()
has been deprecated in favor ofrestrict_derivation()
(#701). -
The following functions and parameters, which were deprecated in previous {admiral} versions, have been removed (#1056):
derive_agegr_ema()
derive_agegr_fda()
derive_disposition_dt()
derive_disposition_status()
derive_extreme_flag()
derive_worst_flag()
derive_obs_number()
derive_disposition_reason()
derive_var_basec()
derive_baseline()
derive_params_exposure()
derive_last_dose()
dataset
parameter inlstalvdt_source
anddthcaus_source
-
The following functions were deprecated in favor of
derive_vars_dy()
(#1076):derive_var_ady()
- Derive Analysis Study Dayderive_var_aendy()
- Derive Analysis End Relative Dayderive_var_astdy()
- Derive Analysis Start Relative Day
-
The following functions were deprecated in favor of
derive_vars_merged_dtm()
(#1076):derive_var_trtedtm()
- Derive Datetime of Last Exposure to Treatmentderive_var_trtsdtm()
- Derive Datetime of First Exposure to Treatment
-
The
derive_var_disposition_dt()
function was deprecated in favor ofderive_vars_merged_dt()
(#1076) -
The
derive_var_atirel()
function was deprecated, as it is deemed as too specific for admiral. Derivations like this can be implemented callingmutate()
andcase_when()
.
-
Additional explanation added to
derive_param_*
andderive_derived_param
functions regarding which variables are populated in the additional rows (#939) -
Updated
derive_var_worst_flag()
andderive_var_extreme_flag()
vignettes to clarify their purpose (#691) -
Added example of ASEQ derivation in ADCM to OCCDS vignette (#720)
-
Examples have been added for
format_reason_default()
,format_eoxxstt_default()
,extend_source_datasets()
andfilter_date_sources()
(#745)
- Naming convention of admiral.xxx packages change to admiralxxx from this point onwards (#968)
Address CRAN comments raised after submitting v0.6.2 (#946)
Address CRAN comments raised after submitting v0.6.1 (#925)
Address CRAN comments raised after submitting v0.6.0 (#918)
derive_vars_dy()
derives the analysis day from one or more--DT(M)
variables (#700)
-
The
derive_last_dose()
function has been split into a general functionderive_vars_last_dose()
and three wrapper functionsderive_var_last_dose_amt()
,derive_var_last_dose_date()
, andderive_var_last_dose_grp()
(#385) -
derive_var_ontrtfl()
now has anew_var
parameter to support the derivation ofONTRxxFL
andONTRTwFL
variables (#721) -
derive_vars_dtm()
,derive_var_disposition
andderive_var_lstalvdt
now havepreserve
argument. A user can preserve partial dates when doing date imputation, e.g.2019---07
would become2019-06-07
by settingpreserve
toTRUE
when doing date_imputation (#592) -
derive_vars_dtm()
now hasignore_seconds_flag
argument so users can suppress"S"
flag if seconds are not recorded in the data (#589)
-
derive_agegr_ema()
,derive_agegr_fda()
,derive_disposition_dt()
,derive_disposition_status()
,derive_extreme_flag()
,derive_worst_flag()
,derive_obs_number()
,derive_disposition_reason()
have been deprecated and renamed in favor ofderive_var_agegr_ema()
,derive_var_agegr_fda()
,derive_var_disposition_dt()
,derive_var_disposition_status()
,derive_var_extreme_flag()
,derive_var_worst_flag()
,derive_var_last_dose()
,derive_var_obs_number()
, andderive_vars_disposition_reason()
respectively (#738) -
derive_var_basec()
andderive_baseline()
have been deprecated in favor of the extendedderive_var_base()
function (#695) -
derive_params_exposure()
has been deprecated and renamed asderive_param_exposure()
(#722) -
The
derive_last_dose()
function has been deprecated in favor ofderive_var_last_dose_date()
(#385) -
The behavior of all functions providing the
date_imputation
parameter, e.g.,derive_vars_dtm()
andderive_vars_dt()
, has changed fordate_imputation = "mid"
. Before the date was imputed as June 15th if both month and day were missing. Now it is imputed as June 30th. For the old behavior please specifydate_imputation = "06-15"
. Please note the behavior has not changed if only the day is missing. In this case the day is imputed as15
(#592) -
derive_var_ontrtfl()
now has anew_var
parameter to support the derivation ofONTRxxFL
andONTRTwFL
variables (#721) -
The following functions and parameters, which were deprecated in previous {admiral} versions, were removed (#513):
derive_aage()
,derive_duration()
,derive_query_vars()
, andderive_suppqual_vars()
functionfns
andfilter_rows
parameters inderive_summary_records()
date_var
andtraceabilty_vars
parameters indthcaus_source()
flag_filter
parameter inderive_extreme_flag()
flag_filter
parameter inderive_var_extreme_flag()
date_var
parameter inlstalvdt_source()
date
parameter inderive_var_ontrtfl()
-
derive_var_agegr_fda()
has been updated to use ranges <18, 18-64, >=65 (#829)
-
README and site homepage has been updated with important new section around expectations of {admiral}, as well as other useful references such as links to conference talks (#868 & #802)
-
New vignette Development Process and improvements made to contribution vignettes (#765 & #758)
-
Updated Pull Request Review Guidance on using
task-list-completed
workflow (#817)
-
GitHub repo moved to pharmaverse org and associated broken site links fixed (#803 & #820)
-
Examples have been added for
format_reason_default
,format_eoxxstt_default
,extend_source_datasets
andfilter_date_sources
(#745)
-
The first truly open source release licensed under Apache 2.0 (#680)
-
New vignette Contributing to admiral (#679)
-
New vignette Unit Test Guidance (#679)
-
Broken links in README have been fixed (#564)
-
derive_vars_dtm_to_tm()
enables the easy conversion of datetime to time variables (#551) -
derive_var_age_years()
derives age in years from a variable providing the age in different units (#569)
-
derive_param_tte()
derives time-to-event-parameters (#546) -
For common time-to-event endpoints event and censoring source objects are provided (#612)
-
assert_list_element()
checks if an element of a list of lists/classes fulfills a condition -
assert_one_to_one()
checks if there is a one to one mapping between two lists of variables -
negate_vars()
negates a list of variables to remove them from a dataset withselect()
-
Unit checks in
derive_param_*()
functions are no longer case sensitive (#631) -
derive_agegr_ema()
andderive_agegr_fda()
gain aage_unit
parameter used to specify the unit of the input age (#569)
-
All SDTM datasets have been moved to the {admiral.test} package (#639)
-
The
min_dates
andmax_dates
parameters ofderive_vars_dt()
andderive_vars_dtm()
no longer expect alist()
butvars()
as input (#405)
-
derive_vars_dtm()
no longer shifts the time of the input--DTC
variable (#436) -
derive_vars_dtm()
Change the min_dates with max_dates in thelapply
statement when computing max_dates (#687)
-
New vignette Creating a BDS Time-to-Event ADaM (#549)
-
New vignette Queries Dataset Documentation (#561)
-
New vignette Writing Vignettes (#334)
-
New vignette Pull Request Review Guidance (#554)
-
A section on handling missing values when working with {admiral} has been added to the "Get Started" vignette (#577)
-
Package installation instructions have been added to the README (#558)
-
The documentation of
derive_vars_dtm()
falsely stated that theflag_imputation
parameter should be eitherTRUE
orFALSE
. It now correctly states that the possible values are"time"
,"date"
or"auto"
(#539)
-
convert_blanks_to_na()
can be used to convert SAS blanks, i.e.""
, into proper RNA
values (#482) -
call_derivation()
enables users to call the same function multiple times with some parameters being fixed across iterations and others varying (#403) -
derive_vars_dtm_to_dt()
enables the easy conversion of datetime to date variables (#376) -
derive_var_ontrtfl()
can now handle events with a start and end date rather than just a single assessment date (#395) -
derive_worst_flag()
enables the flagging of worst records (#300)
-
derive_derived_param()
can be used to derive a new parameter from existing parameters in a BDS dataset (#325) -
derive_param_bmi()
,derive_param_bsa()
andderive_param_map()
enables the derivation of the body mass index, body surface area and mean arterial pressure parameters respectively (#368) -
derive_param_qtc()
enables the derivation of corrected QT intervals according to the formula of Bazett, Fridericia or Sagie (#325) -
derive_param_rr()
enables the derivation of the RR interval (#325) -
derive_params_exposure()
enables the derivation of summary exposure parameters (#400) -
derive_param_doseint()
enables the derivation of dose intensity (#179)
-
derive_var_atirel()
enables the derivation of the "Analysis Time Relative to Reference" (#397) -
derive_vars_atc()
can be used to add ATC variables from FACM to ADCM (#396)
-
derive_var_anrind()
now checks whether theAVAL
variable is present in the input dataset (#486) -
All derivation functions check whether the input dataset is grouped and throw an error if it is (#408)
-
use_ad_template()
has been refactored to no longer make use of the {usethis} package which is no longer a dependency of {admiral} (#433) -
A performance issue in
derive_vars_dt()
has been resolved (#384)
-
The
drop_values_from
parameter has been removed fromderive_summary_records()
(#425) -
The format of the
date_imputation
parameter ofderive_vars_dt()
andderive_vars_dtm()
has been changed from "dd-mm" to "mm-dd". Thus, "01-12" now refers to January 12th rather than December 1st (#492) -
Several functions have been renamed. The old names are now deprecated. They can still be used but a warning will be issued (#507)
derive_aage()
->derive_vars_aage()
derive_duration()
->derive_vars_duration()
derive_query_vars()
->derive_vars_query()
derive_suppqual_vars()
->derive_vars_suppqual()
-
The
date_var
parameter oflstalvdt_source()
has been renamed todate
-
The
filter_rows
parameter ofderive_summary_records()
has been renamed tofilter
. Thefns
parameter has been deprecated in favor ofanalysis_var
andsummary_fun
(#491) -
The
date_var
andtraceabilty_vars
parameters ofdthcaus_source()
have been renamed todate
andtraceability_vars
, respectively (#493) -
The
flag_filter
parameter ofderive_extreme_flag()
has been renamed tofilter
(#487)
derive_agegr_fda()
used to returnNA
for ages less than or equal 18. It now returns<=18
(#441)
-
New vignette on "Date and Time Imputation" has been created (#198)
-
A "Guidance for git Usage" has been created (#266)
-
"OCCDS" has been added as a new section on the reference page on the package website (#485)
-
The Programming Strategy has been updated (#495)
-
A search feature has been added to the package website (#438)
-
New template scripts for ADEX (#181), ADCM (#268) and ADEG (#258) have been created
-
New vignette for programming ADEX has been created (#372)
-
A section on how to create query variables (e.g. SMQs in ADAE) has been added to the Occurrence datasets vignette (#370)
-
The BDS vignette has been updated to incorporate examples of ADVS and ADEG specific functions (#371)
- Fixed a critical bug in
use_ad_template()
that prevented the function from being usable at all (#326)
-
Function argument checks have been completely re-written to provide clearer error messages to users (#263, #288)
-
SDTM
SUPP--
datasets can be merged onto their parent domain usingderive_suppqual_vars()
(#145) -
In case a derivation detects duplicate records after applying a
filter
, the dataset of duplicate records is made available to users viaget_duplicates_dataset()
(#202) -
derive_vars_dt()
andderive_vars_dtm()
gain amin_dates
andmax_dates
parameter which can be used to ensure that the imputed date(time) is not before themin_dates
nor after themax_dates
, e.g. avoid thatAENDT
is after the data cut date orASTDT
is before the first treatment date (#158) -
use_ad_template()
can be used to open a template script for an ADaM dataset; all available templates can be displayed usinglist_all_templates()
(#110)
-
EMA and FDA defined age groupings can be derived using
derive_agegr_ema()
andderive_agegr_fda()
, respectively -
Disposition Status can be derived using
derive_disposition_status()
(#92) -
Disposition Reason can be derived using
derive_disposition_reason()
-
Disposition Dates can be derived using
derive_disposition_dt()
(#91) -
Date Last Known Alive can be derived using
derive_var_lstalvdt()
(#94) -
Cause of Death can be derived using
derive_var_dthcaus()
(#93)
- Summary records for BDS datasets, e.g. with
DTYPE == "AVERAGE"
, can be derived usingderive_summary_records()
(#177)
- Last Dose Date(time) can be derived using
derive_last_dose()
-
derive_merged_vars()
has been removed from {admiral} in favor of smaller special purpose functions, e.g.derive_disposition_status()
(#167) -
Function arguments no longer accept expressions created with
expr()
orexprs()
as inputs; instead filter expressions can be passed "as is" and multiple variables have to be wrapped insidevars()
(#187)Old:
derive_extreme_flag( vs, new_var = LASTFL, by_vars = exprs(USUBJID, VSTESTCD, VISIT), order = exprs(VSTPTNUM), mode = "last", flag_filter = expr(VISIT != "BASELINE") )
New:
derive_extreme_flag( vs, new_var = LASTFL, by_vars = vars(USUBJID, VSTESTCD, VISIT), order = vars(VSTPTNUM), mode = "last", flag_filter = VISIT != "BASELINE" )
-
read_dap_m3()
andinitialize()
have been migrated to {admiral.roche} (#272) -
The
start_date
andend_date
parameters ofderive_var_ady()
,derive_var_aendy()
andderive_var_astdy()
have been renamed toreference_date
anddate
, respectively (#121)
-
derive_var_basetype()
no longer drops records which do not match any condition defined in thebasetype
argument (#226) -
Join warnings like "Column
USUBJID
has different attributes on LHS and RHS of join when using left_join()" are no longer displayed (#271) -
For datetimes with time imputed to "00:00:00" the time part is now displayed (#206)