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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.