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klct v0.1.0

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@ricompute ricompute released this 18 Mar 21:14
· 14 commits to main since this release
  • This is the first functional release of klct, containing the ability to
    analyze NeoScan microCT data comparing two treatment groups.
  • Sites analyzed include femoral metaphysis (trabecular and cortical), femoral
    diaphysis (cortical), and lumbar vertebra (trabecular).
  • Supports both parametric and nonparametric statistical tests via the test
    parameter ("parametric" or "nonparametric"):
    • Two-treatment comparisons (compare_groups()): Student's t-test or
      Wilcoxon rank-sum test.
    • Two-way Treatment × Sex comparisons (compare_groups_2x2()): two-way
      ANOVA or Aligned Rank Transform via ARTool::art().
  • Dynamic measure detection: detect_trabecular_measures() matches ^Tb.
    columns; detect_cortical_measures() captures all other numeric non-metadata
    columns. A shared internal helper .resolve_measures() centralizes measure
    resolution across all analysis and plotting functions.
  • The measures parameter (available in compare_groups(),
    compare_groups_2x2(), and plot_groups()) accepts NULL for sensible
    defaults, "all" for all detected columns, or a custom character vector.
    default_trabecular_measures and default_cortical_measures are exported.
  • Omnibus tables in two-way results are trimmed to Factor, P, and Sig
    columns only.
  • Pairwise comparisons are merged directly into the Group Summaries table
    (blank for the first group, p-value and significance stars for the second
    group within each sex), matching the compare_groups() convention. The table
    heading reflects the test used (t-test or Wilcoxon).
  • Includes four R Markdown templates:
    • "Compare Two Treatments" for analyzing each sex separately.
    • "Compare Two Treatments (Mayo)" — Mayo-themed version using
      mayodown::mayohtml.
    • "Compare Two Treatments and Two Sexes" for a full two-way design.
    • "Compare Two Treatments and Two Sexes (Mayo)" — Mayo-themed version
      using mayodown::mayohtml.
  • Template features:
    • Parametric and nonparametric results are displayed as separate tabs.
    • By-sex plot tabs are consolidated into a single tab (differing only in
      significance annotations).
    • Combined Sexes Plots tabs are included in all sections.
    • All templates accept a test parameter in the YAML header.
  • Mayo-themed templates use the mayodown package for consistent branding,
    including the Mayo logo, color scheme, and copyright footer.
  • The color-text.lua Pandoc filter is provided by mayodown, enabling
    colored significance annotations in all template formats.