Changelog • admiralophtha

admiralophtha 1.1.0.9005

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

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).

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):
- 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”.

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).

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).

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 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).