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)