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derive_extreme_event() was fixed such that
check_type = "none" is accepted again. (#2462)Added helper functions to derive_vars_merged()
(get_flagged_records()) and
derive_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 to
derive_var_trtemfl() to derive TRTEMFL 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 the lookup_table contains duplicates.
(#2247)
derive_vars_merged() and
derive_vars_transposed() have a relationship
argument added (the same as found in dplyr::*_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 in get_terms_fun() argument
for function create_query_data(). (#2265)
Messaging updated for derive_extreme_event() to
improve clarity around duplicates. #2405
The id_vars argument was added to
derive_vars_transposed() and derive_vars_atc()
to allow additional variables, beyond those in by_vars, to
uniquely identify records in the dataset_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 with
create_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 of
derive_extreme_event() when
keep_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 the check_type argument is
ignored (an error is issued) if order 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 in
AVALC would be redundant with AVAL.
(#2442)
The function dplyr::transmute() is superseded in
favor of dplyr::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 and ATPTN consistent.
(#2328)
ADLB template updated to make PARAM consistent for
PARAMCD values "BASO" and
"LYMPH". (#2327)
renv was the default framework
used to manage package dependencies. Now, we use devtools
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 for
R CMD CHECKS jobs, there is an associated renv.lock file
(under the deps artifact).R and test files for
date/time functions for cyclomatic complexity refactor
(#2340)(#2339)get_summary_records().
(#2304)get_imputation_target_date() (#2378)derive_param_tte() where argument
dataset populated and PARAMCD in
set_values_to argument is an expression. Previously, there
was a check early in function to see if PARAMCD defined in
set_values_to argument, already existed in the dataset
passed into dataset argument. If PARAMCD was
not an expression i.e. PARAMCD = "XYZ" then check worked.
However, if PARAMCD 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, where PARAMCD is resolved in
the dataset holding the new parameters. (#2336)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 as derive_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 to
set_admiral_options() to handle floating point issue, the
value is set to 15, and is used with the
base R function signif() when comparing 2
numeric values. This is implemented in admiral functions
derive_var_atoxgr_dir() and
derive_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 as derive_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()
and derive_vars_merged() were enhanced with the arguments
true_value and false_value to align with
preexisting functions that had similar functionality. (#2125)
restrict_derivation() now allows
{dplyr} functions like mutate() in the
derivation argument. (#2143)
derive_summary_records(),
derive_var_merged_summary(), and
get_summary_records() were enhanced such that more than one
summary variable can be derived, e.g., AVAL as the sum and
ADT 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 that
dataset_add can be set to the same value as
dataset if a different additional dataset is not required.
derive_param_exposure() was enhanced with
dataset_add as well. (#2142)
The missing_values argument was added to
derive_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 for
derive_summary_records() and
derive_param_exposure(). (#2142)
The “joined” functions (derive_vars_joined(),
derive_var_joined_exist_flag(),
filter_joined(), and event_joined()) were
unified: (#2126)
dataset_add and filter_add arguments
were added to derive_var_joined_exist_flag() and
filter_joined().filter argument was renamed to
filter_join in derive_var_joined_exist_flag()
and filter_joined().tmp_obs_nr_var, the join_type, the
first_cond_lower, and the first_cond_upper
arguments were added to derive_vars_joined().derive_var_joined_exist_flag(),
filter_joined(), and event_joined() the
first_cond argument was renamed to
first_cond_upper and the first_cond_lower
argument was added.filter_add argument is
applied to the additional dataset grouped by by_vars and
the filter_join argument is applied to the joined dataset
grouped by the observations from the input dataset. I.e., summary
functions like all() or any() can be
used.The tmp_event_nr_var argument was added to
derive_extreme_records() to allow more control of the
selection of records. It creates a temporary variable for the event
number, which can be used in order. (#2140)
signif_dig argument added to both
derive_var_atoxgr_dir() and
derive_var_anrind() functions with default value set to
general option signif_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 whenever dataset_ref
contained variables that were neither key variables, nor
APERIOD, ASPER, APHASEN, nor
mentioned in the new_vars argument. (#2231)
compute_duration(),
derive_vars_duration(), derive_vars_aage() now
accepts more terms for the in_unit, out_unit,
and age_unit arguments (#2255)
Updated the unit test for derive_var_obs_number().
The new test checked the derivation of the default and customized
new_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 of SRCVAR for
derive_vars_query() (#2264)
DAIDS grading criteria fixed for Grade = 0 for
TERM = "Absolute Lymphocyte Count, Low", criteria was
AVAL <= 0.65, now corrected to
AVAL >= 0.65 (#2284).
A bug in derive_extreme_event() was fixed. The
condition field is no longer ignored if mode
is specified for event() (#2291).
A bug in derive_vars_joined() was fixed. The
function no longer fails if renaming is used in by_vars and
new_vars is not specified (#2289).
{admiral} now only supports R >= 4.0.0
In derive_extreme_records() the
dataset_add argument is now mandatory. (#2139)
In derive_summary_records() and
get_summary_records() the arguments
analysis_var and summary_fun were deprecated
in favor of set_values_to. (#1792)
In derive_summary_records() and
derive_param_exposure() the argument filter
was renamed to filter_add (#2142)
In derive_var_merged_summary() the arguments
new_var, analysis_var, and
summary_fun were deprecated in favor of
new_vars. (#1792)
In derive_vars_merged(), the argument
match_flag was renamed to exist_flag
(#2125)
The default value for the false_value argument in
derive_extreme_records() was changed to
NA_character_ (#2125)
In consolidate_metadata(), the argument
check_keys was renamed to check_type to align
with other functions (#2184)
In filter_joined() and
derive_var_joined_exist_flag() (#2126)
first_cond argument was deprecated in favor of
first_cond_upper andfilter argument was deprecated in favor of
filter_join.In event_joined() the first_cond
argument was deprecated in favor of first_cond_upper.
(#2126)
In derive_extreme_event(), the
ignore_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 by order. Now
they are selected by order 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() and
derive_vars_query() were updated to rename variables in
query data set as follows: (#2186)
TERMNAME to TERMCHARTERMID to TERMNUMUsers 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 of derive_extreme_event().
(#2141)
The functions derive_var_dthcaus(),
derive_var_extreme_dt(), and
derive_var_extreme_dtm() have been superseded in favor of
derive_vars_extreme_event(). (#2138)
The documentation of the by_vars and
constant_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 an internal 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 the admiral 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 the order argument for all functions. (#2230,
#2257)
Website now has button/links to Slack channel and GitHub Issues. (#2127)
Added example derivations of DTHCAUS and
DTHCGR1 to the ADSL template. (#2218)
Cheat Sheet now added to website front page (#2130)
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)derive_param_computed() was modified in
anticipation of major user-facing changes to R version 4.4 (#2147)derive_extreme_records() no longer fails if
dataset_add is specified and a variable specified for
order is not in dataset. (#2113)
The type argument in compute_duration()
changed the underlying default behavior in
derive_vars_duration() without allowing the user to toggle
between "duration" and "interval" as
originally intended. This was fixed by adding the type
argument for derive_vars_duration() and a wrapper function
derive_vars_aage() such that it gets passed through
compute_duration() appropriately (#2112)
Template ad_adpp.R updated to replace
left_join() with derive_vars_merged()
(#2109).
event_joined() events were added. They can be
specified for the events argument in
derive_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 here
atoxgr_criteria_daids()
The functions derive_param_bmi() and
derive_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() and
compute_age_years() are updated to return an
NA age in the case that the age unit is missing. (#2001)
The argument unit for derive_vars_aage() is
also changed to age_unit for consistency between these
age-related functions. (#2025)
The derive_var_ontrtfl() function has been updated
to allow for the column passed in ref_end_date to contain
NA values. Previously, if the end date was NA,
the row would never be flagged. Now, an NA 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)
analysis_value and analysis_var
arguments were deprecated in favor of set_values_to. This
enables users to compute more than one variable.keep_nas argument was added. If it is set to
TRUE, observations are created even if values contributing
to the computed values are NA.The function derive_vars_dy() is updated to avoid
potential error when the input dataset with columns ending
with temp. (#2012)
Argument keep_source_vars was added to
derive_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 in
date_source() and dthcaus_source were
deprecated in favor of set_values_to. The
date_source() function creates a date_source object as
input for derive_var_extreme_dt() and
derive_var_extreme_dtm(),users can now define the
traceability variables by assigning those variables to the
set_values_toargument.Similarly, the
dthcaus_source creates a dthcaus_source Object.
(#2068)
derive_extreme_event() was enhanced (#1960):
event_joined() events can be specified for the
events 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 the dataset_name field to
event(). 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 the keep_source_vars field to
event(). It allows to select which variables should be kept
for the selected observations.
The mode and order field were added to
event(). 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 to
event(). 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 argument
meta_criteria to create ATOXGRL and
ATOXGRH 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.
(https://github.com/pharmaverse/admiral/pull/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 function
derive_param_exist_flag() and subject_keys
have been deprecated versions using the next phase of the deprecation
process. (#1950)
The argument wt in the function
compute_egfr() was deprecated in favor of
weight using the first phase of the deprecation process.
(#2020)
The filter argument in
derive_extreme_records() was deprecated in favor of the
filter_add using the next phase of the deprecation process.
(#1950)
The analysis_value and analysis_var
arguments in derive_param_computed() were deprecated in
favor of set_values_to (#1968).
The na_val argument in
derive_var_shift() has been deprecated in favor of
missing_value using the first phase of the deprecation
process. (#2014)
The dataset_expected_obs argument in
derive_expected_records() and
derive_locf_records() has been deprecated in favor of
dataset_ref. (#2037)
The span_period argument in
derive_var_ontrtfl() has been updated to only accept
TRUE or FALSE, where is previously accepted
"Y" and NULL. (#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 function derive_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 acknowledgements have been moved to README section (#1941).
derive_vars_joined() had two bugs with regards to
duplicates messaging and when new_vars was set to
NULL that have now been addressed (#1966).
compute_dtf() had a bug with regards to imputing
days to full date-time character strings. (#2042)
derive_param_tte(). (#1962)In the function derive_var_anrind(), added argument
use_a1hia1lo to turn the usage of A1HI and
A1LO 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() and
filter_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 of derive_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 affects censor_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)
missing_values argument to assign values to the new
variables for non-matching observations was added.new_vars argument accepts expressions now.derive_vars_joined() updates: (#1727)
missing_values argument to assign values to the new
variables for non-matching observations was added.new_vars and the join_vars argument
accept expressions now.The date field of date_source() accepts
expressions now. This affects derive_var_extreme_dt() and
derive_var_extreme_dtm(). (#1727)
The date and dthcaus field of
dthcaus_source() accept expressions now. This affects
derive_var_dthcaus(). (#1727)
The date field of event_source() and
censor_source() accepts expressions now. This affects
derive_param_tte(). (#1727)
The derive_param_computed() function was enhanced:
(#1873)
dataset_add argument allows to consider
parameters from a different dataset than the input dataset.analysis_var argument allows to specify the
variable to be populated, e.g., AVALC.parameters and constant_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.analysis_value argument was enhanced such that any
variable of the form <variable>.<parameter> can
be used, e.g., QSORRES.CHSF13.create_query_data() and
derive_vars_query() updated to rename variables in query
data set as follows: (#1907)
VAR_PREFIX to PREFIXQUERY_NAME to GRPNAMEQUERY_ID to GRPIDQUERY_SCOPE to SCOPEQUERY_SCOPE_NUM to SCOPENTERM_LEVEL to SRCVARTERM_NAME to TERMNAMETERM_ID to TERMIDUsers need to adjust their get_terms() function
accordingly.
The aval_fun argument of
derive_param_exist_flag() was deprecated in favor of the
set_values_to argument. (#1727)
derive_var_merged_cat() and
derive_var_merged_character() have been deprecated in favor
of derive_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
of derive_extreme_records(). (#1725)
The filter argument in
derive_extreme_records() was deprecated in favor of the
filter_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 of
derive_vars_joined(). (#1797)
derive_var_basetype() was deprecated in favor of
derive_basetype_records(). (#1796)
In the function derive_param_exist_flag() the
arguments dataset_adsl and subject_keys have
been renamed to dataset_ref and by_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 the README.md. (#1890)
vars() which was used in the admiral function calls
that expected a list of quosures has been removed. The admiral option
force_admiral_vars was removed as well. (#1694)
derive_vars_dtm() and derive_vars_dt()
had a bug pertaining to imputations associated with supplying both
min_dates and max_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 from
admiral functions. (#1842)
restrict_derivation() had a bug which led to failure
if the derivation argument was not in the global
environment. (#1765)
derive_vars_dtm() and
derive_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 to derive_locf_records(),
analysis_var allows to specify analysis variable,
keep_vars keeps variables that need carrying the last
observation forward other than analysis_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 parameter
nominal_time defaults as NULL and does not
change the normal operation of the function. If a
nominal_time is specified such as NFRLT (Nominal Relative
Time from First Dose) then the nominal time is incremented by the
interval specified in EXDOSFRQ 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 of EXDOSFRQ with units in days but expected values
less than 24 hours, such as “BID”, “TID”, and “QID”. Previously these
values of EXDOSFRQ may result in duplicate records where
the day values are incremented but the time values are not.
(#1643)
The function derive_var_confirmation_flag() and
filter_confirmation() gained the
tmp_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(), and
derive_vars_merged_lookup() were updated to allow renaming
in the argument by_vars. (#1680)
The units “min” and “sec” are added as valid values of
out_unit in compute_duration() and
derive_vars_duration(). (#1647)
The function derive_vars_query() now includes a
consistency check for QUERY_SCOPE and
QUERY_SCOPE_NUM values. (#652)
Argument new_var in
derive_param_extreme_event() is made optional.
(#1630)
derive_vars_last_dose() no longer fails if
USUBJID 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
by exprs(). For example, instead of
by_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 the vars()
function such that it returns a list of expressions. This can be
disabled by the admiral option force_admiral_vars (see
set_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 in dataset_adsl.
(#1576)
Function derive_var_disposition_status() has been
deprecated, please use derive_var_merged_cat() instead.
(#1681)
Function derive_var_worst_flag() has been
deprecated, in favor of
slice_derivation()/derive_var_extreme_flag().
(#1682)
Function derive_vars_disposition_reason() has been
deprecated, in favor of derive_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 and get_sdg_fun from the
create_query_data() functiondate_imputation, time_imputation and
preserve parameters from date_source()
functionfilter parameter from
derive_var_extreme_flag()ADLB metadata data set called
atoxgr_criteria_ctcv5 updated to remove unit check for
HYPERURICEMIA as grade criteria based on ANRHI
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() and
filter_confirmation() to
derive_var_joined_exist_flag() and
filter_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 of
restrict_derivation(), slice_derivation(), and
call_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() and
derive_vars_duration(). (#1620, #1634)
Increased the level of documentation for
derive_var_age_years() to describe the data type of the
newly created new_var column. (#970)
derive_vars_dtm() and
derive_vars_dt() had a bug pertaining to imputations
associated with NA values that has now been fixed.
(#1646)if_else() from the release of
dplyr version 1.1.0, which affects
derive_vars_dtm() and and 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 adding
AVISIT, AWLO, AWHI based on time
windows and ADY 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() and
set_admiral_options() to allow more flexibility on common
function inputs; e.g. like subject_keys to avoid several
find and replace instances of vars(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 when
AVAL is NA for particular visits/time points.
(#1316)
New function convert_na_to_blanks() to convert
character NA to blanks. (#1624)
Function derive_param_first_event() has been
replaced by a more generalized derive_param_extreme_event()
function with new argument mode allowing for the selection
of either the "first" or "last" event record
according to the conditions provided. Also the date_var
argument has been replaced with the order argument instead.
In addition, three new arguments new_var,
true_value, and false_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 to
derive_var_ontrtfl(), which controls if time is considered
for the condition if start_date is after
ref_end_date + ref_end_window days.
(#989)
derive_var_atoxgr_dir() default value of
atoxgr_criteria_ctcv4 removed for parameter
meta_criteria. Can now also choose
atoxgr_criteria_ctcv5 for parameter
meta_criteria, to implement NCI-CTCAEv5 grading
criteria.
Environment objects were consolidated into a single
admiral_environment object under
R/admiral__environment.R. (#1572)
The default value of the keep_source_vars argument
in create_single_dose_dataset() was updated such that it
takes the values of the other arguments into account and the
start_datetime and end_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 use derive_param_extreme_event() with
the order argument instead of the date_var
argument. (#1317)
Functions smq_select() and sdg_select()
have been deprecated and replaced with basket_select(). In
the create_query_data() function,
meddra_version and whodd_version argument has
been replaced by version and get_smq_fun and
get_sdg_fun argument by get_terms_fun.
(#1597)
Function derive_param_tte() had a bug that set
ADT to NA when start_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)
{lifecylce} caused
several admiral tests to break (#1500)derive_vars_duration() that surfaced
after changes in R-devel (#1486)derive_var_extreme_dt() and
derive_var_extreme_dtm() were updated such that source
observations where the date is NA 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 functions
count_vals(), min_cond(), and
max_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
grade ATOXGR from ATOXGRL and
ATOXGRH. ATOXGRL holds toxicity/severity grade
for low lab values, and ATOXGRH 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 a
package parameter and is now exported (#1212)
list_all_templates() and
use_ad_template() gain a package 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() to
derive_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 to
derive_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 the
time_imputation argument NULL is no longer a
permitted value.)
It is now possible to impute completely missing dates by
specifying highest_imputation = "Y" and the
min_dates or max_dates argument.
order parameter added to
dthcaus_source() which allows an additional character
vector to be used for sorting the dataset,
derive_vars_dthcaus() updated to process additional
parameter (#1125).
create_single_dose_dataset() Fixed bug where
ASTDTM and AENDTM were not updated when
start_date = ASTDT and end_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 (#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() and
derive_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, and
preserve in date_source()The following arguments no longer accept DTC variables:
date in date_source(),
dthcaus_source(), censor_source(), and
event_source()dose_date and analysis_date in
derive_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 the
time_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 the highest_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 in
derive_var_extreme_flag() and
derive_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 in new_vars is supplied to the
dose_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
that
AVAL is derived instead of AVALN andcreate_single_dose_dataset() Fixed bug where ASTDTM
and AENDTM were not updated when start_date=ASTDT and
end_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() and
convert_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
Variablecreate_query_data() is provided to create the queries
dataset required as input for derive_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 SourcesNew 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)
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 to
admiral_adsl. Corresponding SDTM datasets in
{admiral.test} have also been renamed, e.g.dm
to admiral_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 by derive_vars_dtm() the function failed.
This bug was fixed (#1097).
impute_dtc() - Fixed imputation bug. A user setting
date_imputation = MID and preserve = FALSE
would expect the date 2019---07 to be imputed to
2019-06-30, but the function was returning
2019-06-15. Now returns it correctly. This bug fix also
addresses the issue in the downstream functions
derive_vars_dt() and derive_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
of derive_var_extreme_dt() (#753).
derive_vars_disposition_reason() now is updated such
that the default is populating DCSREASP only when
DSDECOD 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 called combine_supp() and is available on CRAN
(#950)
The filter parameter in
derive_var_extreme_flag() and
derive_var_worst_flag() has been deprecated in favor of
restrict_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 in lstalvdt_source and
dthcaus_sourceThe 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
DayThe 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 TreatmentThe derive_var_disposition_dt() function was
deprecated in favor of derive_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 calling mutate() and
case_when().
Additional explanation added to derive_param_* and
derive_derived_param functions regarding which variables
are populated in the additional rows (#939)
Updated derive_var_worst_flag() and
derive_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() and
filter_date_sources() (#745)
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 function derive_vars_last_dose() and three
wrapper functions derive_var_last_dose_amt(),
derive_var_last_dose_date(), and
derive_var_last_dose_grp() (#385)
derive_var_ontrtfl() now has a new_var
parameter to support the derivation of ONTRxxFL and
ONTRTwFL variables (#721)
derive_vars_dtm(),
derive_var_disposition and derive_var_lstalvdt
now have preserve argument. A user can preserve partial
dates when doing date imputation, e.g. 2019---07 would
become 2019-06-07 by setting preserve to
TRUE when doing date_imputation (#592)
derive_vars_dtm() now has
ignore_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 of derive_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(), and
derive_vars_disposition_reason() respectively
(#738)
derive_var_basec() and
derive_baseline() have been deprecated in favor of the
extended derive_var_base() function (#695)
derive_params_exposure() has been deprecated and
renamed as derive_param_exposure() (#722)
The derive_last_dose() function has been deprecated
in favor of derive_var_last_dose_date() (#385)
The behavior of all functions providing the
date_imputation parameter, e.g.,
derive_vars_dtm() and derive_vars_dt(), has
changed for date_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 specify
date_imputation = "06-15". Please note the behavior has not
changed if only the day is missing. In this case the day is imputed as
15 (#592)
derive_var_ontrtfl() now has a new_var
parameter to support the derivation of ONTRxxFL and
ONTRTwFL variables (#721)
The following functions and parameters, which were deprecated in previous {admiral} versions, were removed (#513):
derive_aage(), derive_duration(),
derive_query_vars(), and
derive_suppqual_vars() functionfns and filter_rows parameters in
derive_summary_records()date_var and traceabilty_vars parameters
in dthcaus_source()flag_filter parameter in
derive_extreme_flag()flag_filter parameter in
derive_var_extreme_flag()date_var parameter in
lstalvdt_source()date parameter in
derive_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
and filter_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 with select()
Unit checks in derive_param_*() functions are no
longer case sensitive (#631)
derive_agegr_ema() and
derive_agegr_fda() gain a age_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 and max_dates parameters
of derive_vars_dt() and derive_vars_dtm() no
longer expect a list() but vars() 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 the lapply 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 the flag_imputation parameter should be either
TRUE or FALSE. 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 R NA 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()
and derive_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 the
AVAL 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 from
derive_summary_records() (#425)
The format of the date_imputation parameter of
derive_vars_dt() and derive_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 of
lstalvdt_source() has been renamed to
date
The filter_rows parameter of
derive_summary_records() has been renamed to
filter. The fns parameter has been deprecated
in favor of analysis_var and summary_fun
(#491)
The date_var and traceabilty_vars
parameters of dthcaus_source() have been renamed to
date and traceability_vars, respectively
(#493)
The flag_filter parameter of
derive_extreme_flag() has been renamed to
filter (#487)
derive_agegr_fda() used to return NA 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)
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 using derive_suppqual_vars() (#145)
In case a derivation detects duplicate records after applying a
filter, the dataset of duplicate records is made available
to users via get_duplicates_dataset() (#202)
derive_vars_dt() and derive_vars_dtm()
gain a min_dates and max_dates parameter which
can be used to ensure that the imputed date(time) is not before the
min_dates nor after the max_dates, e.g. avoid
that AENDT is after the data cut date or ASTDT
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
using list_all_templates() (#110)
EMA and FDA defined age groupings can be derived using
derive_agegr_ema() and derive_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)
DTYPE == "AVERAGE", can be derived using
derive_summary_records() (#177)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() or exprs() as inputs; instead filter
expressions can be passed “as is” and multiple variables have to be
wrapped inside vars() (#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() and initialize() have
been migrated to {admiral.roche} (#272)
The start_date and end_date parameters
of derive_var_ady(), derive_var_aendy() and
derive_var_astdy() have been renamed to
reference_date and date, respectively
(#121)
derive_var_basetype() no longer drops records which
do not match any condition defined in the basetype 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)
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.