NEWS.md

In admiralophtha: ADaM in R Asset Library - Ophthalmology

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 The function derive_var_bcvacrtixfl() is now superseded.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 The function derive_var_bcvacrtixfl() is now superseded.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).

admiralophtha documentation built on April 3, 2025, 9:46 p.m.