Merge pull request #158 from jakeberv/codex/cran-resubmission-vignette-links

Fix quick-start vignette links for CRAN resubmission

Author: jakeberv

cran-comments.md

@@ -1,15 +1,10 @@
 ## Resubmission
 
-This is a new submission of **bifrost 0.1.4**. The current CRAN version is **bifrost 0.1.3**.
+This is a resubmission of **bifrost 0.1.4** following CRAN feedback.
 
-### Changes since 0.1.3
+### Changes made in response to CRAN comments
 
-- Added a new package vignette, **"Quick Start with bifrost"**, with a minimal end-to-end simulated example.
-- Clarified `searchOptimalConfiguration()` documentation around tree input requirements, recommended `mvgls()` methods, and the role of `error = TRUE`.
-- Reworked the README to foreground installation, documentation, and citation guidance.
-- Added two pkgdown-only background articles on multivariate Brownian motion / shifts and whole-tree PCA / model-selection issues. These articles are excluded from the CRAN tarball via `.Rbuildignore`.
-- Updated package authorship metadata and refreshed `citation("bifrost")` for the live bioRxiv preprint, the in-press application paper, and the foundational `mvMORPH` references.
-- Disabled a deprecated vignette-preview step in GitHub Actions CI. This does not affect package runtime or CRAN checks.
+- In the installed quick-start vignette, replaced relative links to pkgdown-only background articles with full website URLs. This removes invalid local file URIs from `inst/doc/quick-start-vignette.html`.
 
 ## Test environments
 

vignettes/quick-start-vignette.Rmd

@@ -190,4 +190,4 @@ When moving from this smoke test to a real dataset:
 - archive the tree, trait matrix, formula, thresholds, and random seed used for final fits,
 - repeat searches under nearby settings before treating individual inferred shifts as robust.
 
-Once this smoke test runs cleanly, the next step is usually to move to a real dataset and inspect the returned shifts, IC support values, and regime-specific VCVs in more detail. For a full empirical workflow, continue to the [jaw-shape vignette](jaw-shape-vignette.html); for broader conceptual background, see [Brownian Motion and Multivariate Shifts](theoretical-background-vignette.html) and [Whole-Tree Models, PCA, and bifrost](pca-model-selection-and-bifrost-vignette.html).
+Once this smoke test runs cleanly, the next step is usually to move to a real dataset and inspect the returned shifts, IC support values, and regime-specific VCVs in more detail. For a full empirical workflow, continue to the [jaw-shape vignette](jaw-shape-vignette.html); for broader conceptual background on the package website, see [Brownian Motion and Multivariate Shifts](https://jakeberv.com/bifrost/articles/theoretical-background-vignette.html) and [Whole-Tree Models, PCA, and bifrost](https://jakeberv.com/bifrost/articles/pca-model-selection-and-bifrost-vignette.html).