Changelog

Source: NEWS.md

admiralophtha (development version)

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

Developer Notes

• Updated lintr configurations to use central configurations from admiraldev. (#280)

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 The function derive_var_bcvacrtixfl() is now superseded.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).