admiralophtha 1.4.0

This is the 1.4 release of {admiralophtha}. The package was updated as follows:

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)

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

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

admiralophtha 1.3.0

This is the 1.3 release of {admiralophtha}. The package was updated as follows:

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.

Various

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

admiralophtha 1.2.0

This is the 1.2 release of {admiralophtha}. The package was updated as follows:

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

This is the 1.1 release of {admiralophtha}. The package was updated as follows:

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 STUYDID 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

This is the 1.0 release of {admiralophtha}, where we focused on releasing a mature and increasingly stable package for all your ophthalmology ADaM needs. The package was updated as follows:

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

This is the third release of {admiralophtha}.

admiralophtha 0.2.0

This is the second release of {admiralophtha}.

admiralophtha 0.1.0

admiralophtha 0.1.0

This is the first release of {admiralophtha}.

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).

Documentation

The {admiralophtha} package website is now up and running, complete with vignettes for popular ophthalmology datasets (ADOE, ADBCVA, ADVFQ).