admiralophtha 1.4.0

Breaking Changes

• 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)

Updates to Templates

• The ADVFQ template was reviewed and modernized to be more in line with VFQ guidance. (#261)

Updates to Documentation

• 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)

Various

admiralophtha 1.3.0

Updates to Templates

• Improved model derivation of criterion flag/variable pairs in ADBCVA template by showcasing use of restrict_derivation() in combination with call-derivation(). (#267)

Updates to Documentation

• 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)

Various

• Removed {cli} from package imports. (#264)

admiralophtha 1.2.0

Updates to Templates

• 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 The function derive_var_bcvacrtixfl() is now superseded.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) ## Updates to Documentation

• 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)

Updates to Functions

• The following function arguments of derive_var_afeye() are removed following the end of their deprecation cycle (#237):

  • The argument dataset_occ
  • The argument lat_vals

admiralophtha 1.1.0.

Updates to Functions

• The following function arguments of derive_var_afeye() are entering the next (and final) phase of the deprecation process (#223):

  • The argument dataset_occ
  • The argument lat_vals

Various

• All vignettes and templates in {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).

admiralophtha 1.0.0

Updates to Templates

• 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).

Updates to Documentation

• 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).

Updates to Functions

• derive_var_afeye() was updated (#214):

  • A bug was removed where the function issued warnings when missing xxLOC values were present in the input dataset.
  • The argument dataset_occ was deprecated in favor of dataset, in line with {admiral} conventions.
  • The argument lat_vals was deprecated. Laterality values are now just expected to be “LEFT”, “RIGHT” or “BILATERAL”.

Various

• Website now has button/links to Slack channel and GitHub Issues (#206).

• Test coverage is now improved to 100% (#217).

admiralophtha 0.3.0

Updates to Functions

• 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).

Updates to Templates

• 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).

Updates to Documentation

• 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).

Updates to Data

• Removed 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).

admiralophtha 0.2.0

Updates to Functions

• 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).

Updates to Templates

• 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).

Updates to Site

• 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).

admiralophtha 0.1.0

New Features

• 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).