Changelog • fxtas

fxtas (development version)

Added a scheduled Clean up PR Previews workflow that prunes closed-PR gh-pages previews and compacts gh-pages history, so deleted render snapshots stop bloating the repo (closes #155).

Moved manuscript to analyses/ (#69)
Tons of polishing (#63, #64, #65)
Added gtsummary::bold_labels() to gtsummary tables
Added keywords
Reduced title to under 100 characters, including spaces
Removed numbers from headings.
Incorporated coauthors’ feedback up to 2024/11/18 draft
Added additional line-graph comparison subfigures for latent subtype clustering analysis
Added more interpretation of subtype analysis results
Removed repeated measures analysis
Added description of findings to graphical abstract

removed individual parkinsonian features from OS model (#106)
added info about displayed statistics to rows for compute_prob_correct() (#56)

added red reference line at 3 obs per stage in stage_barplot() (#91)
added grayscale legend to PVDs (#83)
added test for pvd_lineplot() (#68)
added biomarker_order argument to compact_pvd_data_prep() (default behavior should be unchanged)
added shared_flextable_settings() function to apply font, font size, and line spacing to all tables

added tools for finding journals to submit to (#66)
renamed FXTAS Stage (0-5)* to FXTAS Stage
added columns to pre-processed data:
- Male
- CGG 100-199
- CGG 55-99
substituted ≤ instead of <= in dichotomized CANTAB variable value labels
renamed SCID composite vars without capitalization (on Dr. Bourgeois’s recommendation)
added “label” attribute to FX3*
added “Disorder” suffix to SCID composite variables, on Dr. Bourgeois’s recommendation.
fixed create_any_tremor() to handle NAs before or after fix_factors().
renamed “Any Autoimmune” to “any autoimmune disorder” and make it “Yes”/“No”
decapitalized “MMSE Total Score” to “MMSE total score”
decapitalized “Parkinsonian features” to “parkinsonian features”
removed “Parkinsonian features:” prefix from:
- “Masked faces”,
- “Increased tone”,
- “pill-rolling tremor exam”,
- “Stiff gait”
Renamed “CGG (backfilled)” to CGG
Renamed “ApoE (backfilled)” to ApoE
Now using most recent ApoE value

moved analyses/ into inst (#120)
removed veccompare and pryr from Suggests; both were archived from CRAN and unused in the package, which broke dependency resolution on all CI jobs (#157)
dropped the devtag roclet (no @dev tags were in use; internal functions already use @keywords internal) and regenerated man/ with roxygen2 8.0.0, fixing the Documentation check job (#159)
updated test-coverage.yaml workflow
updated readme to specify new location of manuscript source code in analyses/
updated WORDLIST