The following functions are entering the next phase of the deprecation process:
Phase 1 (message)
Phase 2 (warning)
Phase 3 (error)
Phase 4 (removed)
.github/common.yml to add new PR website workflow, accessible by placing the keyword "[create website]" in PR titles. (#295)The following functions are entering the next phase of the deprecation process:
Phase 1 (message)
derive_var_bcvacritxfl() and its internal utility function derive_var_bcvacritxfl_util(). Users are invited to use
admiral::derive_vars_crit_flag() - please see the criterion flag section of the ADBCVA vignette
for more details. Each deprecation phase for this function will only last six months (i.e. one release cycle). (#282)Phase 2 (warning)
Phase 3 (error)
Phase 4 (removed)
ADVFQ template was reviewed and modernized to be more in line with VFQ guidance. (#261)The "Ask AI" widget was added to the bottom right of each page. It enables users to ask questions about {admiralophtha} and the
rest of the {admiral} ecosystem and receive answers from an LLM. It is trained on the documentation of all {admiral} packages
and provided by kapa.ai. (#2887)
The ADVFQ vignette was reviewed and modernized to be more in line with VFQ guidance. (#261)
Started using custom {admiral} roclet, resulting in cleared "Permitted" and "Default" values in function documentation. (#277)
Removed erroneous deprecation badges for dataset and loc_vals arguments of derive_var_afeye(). (#278)
{lintr} configurations to use central configurations from {admiraldev}. (#280)ADBCVA template by showcasing use of restrict_derivation() in combination with call-derivation(). (#267)Improved model derivation of criterion flag/variable pairs in ADBCVA vignette by showcasing use of restrict_derivation() in combination with call-derivation(). (#267)
Updated ADOE template to showcase the mapping of IOP parameters, as well as the derivation of parameters for the difference between pre and post-dose IOP. (#260)
Added a citation for the source of the Visual Functioning Questionnaire (VFQ) to the ADVFQ template, vignette and test dataset documentation. (#243)
{cli} from package imports. (#264)Replaced the function derive_var_bcvacrtixfl() with the new function admiral::derive_vars_crit_flag() for the derivation of SBCVA and FBCVA criterion flags in ADBCVA template. The function derive_var_bcvacrtixfl() is now superseded. (#247)
Within the ADBCVA template, updated AVALCA1N and AVALCAT1 derivations to use new function admiral::derive_vars_cat(). (#244)
Replaced the function derive_var_bcvacrtixfl() with the new function admiral::derive_vars_crit_flag() for the derivation of SBCVA and FBCVA criterion flags in ADBCVA vignette. The function derive_var_bcvacrtixfl() is now superseded. (#247)
Within the ADBCVA vignette, updated AVALCA1N and AVALCAT1 derivations to use new function admiral::derive_vars_cat(). (#244)
The following function arguments of derive_var_afeye() are removed following the end of their deprecation cycle (#237):
dataset_occlat_valsThe following function arguments of derive_var_afeye() are entering the next (and final) phase of the deprecation process (#223):
dataset_occlat_vals{admiralophtha} have been updated to use the {admiral} subject keys option rather than
explicitly quoting key variables such as STUDYID and USUBJID. For instance, a line such as by_vars = exprs(STUDYID, USUBJID)
would be replaced by by_vars = get_admiral_option("subject_keys") (#226).Removed analysis_value argument in the calls to derive_param_computed() in ADBCVA template in line with the deprecation of this argument in the new version of {admiral}. Variable values for parameters of interest are now all populated through the set_values_to argument (#207).
Modified calls to derive_summary_records() in ADVFQ template in line with the updates to this function in the new version of the {admiral} package. The filter argument is now renamed to filter_add, the argument dataset_add is now always specified and the variable values are now all populated through the set_values_to argument (#204).
Added release date for {admiralophtha} 1.0 to the front page (#203).
Removed analysis_value argument in the calls to derive_param_computed() in ADBCVA vignette in line with the deprecation of this argument in the new version of {admiral}. Variable values for parameters of interest are now all populated through the set_values_to argument (#207).
Modified calls to derive_summary_records() in ADVFQ vignette in line with the updates to this function in the new version of the {admiral} package. The filter argument is now renamed to filter_add, the argument dataset_add is now always specified and the variable values are now all populated through the set_values_to argument (#204).
derive_var_afeye() was updated (#214):
xxLOC values were present in the input dataset.dataset_occ was deprecated in favor of dataset, in line with {admiral} conventions.lat_vals was deprecated. Laterality values are now just expected to be "LEFT", "RIGHT" or "BILATERAL".Website now has button/links to Slack channel and GitHub Issues (#206).
Test coverage is now improved to 100% (#217).
Added a new parameter crit_var to derive_var_bcvacritxfl() so that criterion flags can be derived with respect to any variable. Also removed arguments paramcds and basetype as their function can be achieved using restrict_derivation() from {admiral}. This also required renaming of argument dataset_adbcva to dataset (#119).
Added AFEYE derivation and description to ADOE Vignette (#165).
Updated ADBCVA template's calls to use restrict_derivation() in calls to derive_var_bcvacritxfl() and also to showcase use of crit_var argument of derive_var_bcvacritxfl() (#119).
Switched out all references to admiral.test for references to pharmaversesdtm in ADOE and ADBCVA templates, and updated code to refer to oe_ophtha accordingly (#184).
Switched out derive_var_merged_cat() for derive_vars_merged() in the function derive_var_studyeye() due to deprecation of the former in favor of the latter in {admiral}(#119).
OECAT and OESCAT have been added to the lookup tables in the ADOE and ADBCVA templates (#189).
Added a reference for the ETDRS to LogMAR conversion done by convert_etdrs_to_logmar() and convert_logmar_to_etdrs() (#136).
OECAT and OESCAT have been added to the lookup tables in the ADOE and ADBCVA vignettes (#189).
All function and variable names on the website are in backquotes (#173).
admiralophtha_ex and admiralophtha_qs from the package, as they now reside in pharmaversesdtm, where they are now names ex_ophtha and qs_ophtha respectively (#184).Added new parameter loc_vals to function derive_var_afeye() to allow users to specify values of xxLOC for which AFEYE is derived (issue #163).
Updated function derive_var_afeye() to resolve bug when STUDYEYE is 'Bilateral' (issue #134).
Added new parameter lat_vals to function derive_var_afeye() to allow users to specify values of xxLAT for which AFEYE is derived, as well as issuing warnings when unexpected values are found (issue #174).
Updated ADOE to refer to OESTRESU for AVALU creation (issue #139).
Updated ADOE and ADBCVA PARAM mapping to include units where applicable (issue #139).
Updated ADOE, ADVFQ and ADBCVA for the unique intermediate dataset name to avoid overwriting, corrected the link for Visit and Period variables Vignette in ADVFQ (issue #128).
Corrected values of DTYPE, VISIT, VISITNUM, OEDY, OEDTC for derived parameters in ADBCVA template (issue #137).
Updated ADBCVA and ADOE templates to include AFEYE (issue #133).
Added a "Report a bug" link to {admiralophtha} website (issue #127).
Fixed bug where the search bar didn't work for some searches (issue #141).
Added a function to derive the variable STUDYEYE in ADSL (issue #9).
Added a function to derive the variable AFEYE in Occurrence datasets (issue #10).
Added a function to derive the criterion flags in ADBCVA (issue #49).
Added a function to convert LogMAR scores to ETDRS scores (issue #50).
Added a function to convert ETDRS scores to LogMAR scores (issue #50).
Created ophthalmology-specific test data for the EX SDTM domain, stored in {admiralophtha} package and accessible by calling data(admiralophtha_ex) (issue #36).
Created ophthalmology-specific test data for the SC and OE SDTM domains, stored in {admiral} package and accessible by calling data(admiral_sc) or data(admiral_oe) (issues #11 and #13).
Updated AE and QS test datasets in {admiral} to include ophthalmology-specific variables and records, such as laterality variables in AE and VFQ records in QS (issues #12 and #52).