Merge pull request #157 from jakeberv/codex/release-0.1.4-prep

Prepare 0.1.4 release metadata

Author: jakeberv

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: bifrost
 Title: Branch-Level Inference Framework for Recognizing Optimal Shifts in Traits
-Version: 0.1.3
+Version: 0.1.4
 Authors@R: c(
     person(given = c("Jacob", "S."), family = "Berv", email = "jacob.berv@gmail.com", role = c("aut", "cre", "cph", "fnd"), comment = c(ORCID = "0000-0002-5962-0621")),
     person(given = "Nathan", family = "Fox", role = "aut", comment = c(ORCID = "0000-0002-2816-9751")),

NEWS.md

@@ -1,3 +1,20 @@
+# bifrost 0.1.4
+
+* Documentation / vignettes:
+  - Added a new "Quick Start with bifrost" vignette with a minimal end-to-end simulated example.
+  - Clarified `searchOptimalConfiguration()` documentation around acceptable tree inputs, recommended `mvgls()` methods (`"H&L"` vs `"LL"`), 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 on whole-tree PCA / model-selection issues.
+
+* Citation / metadata:
+  - Updated package authorship metadata to reflect the current author list.
+  - Updated `citation("bifrost")` for the live bioRxiv preprint and the in-press application paper.
+  - Added the foundational `mvMORPH` citations to the package citation metadata.
+  - Added a formatted citation section and dynamic bioRxiv badge to the README.
+
+* Maintenance:
+  - Disabled a deprecated vignette-preview step in GitHub Actions CI.
+
 # bifrost 0.1.3
 
 * Addressed CRAN reviewer feedback following review of 0.1.2:

README.md

@@ -99,7 +99,7 @@ citation("bifrost")
    Berv JS, Fox N, Thorstensen MJ, Lloyd-Laney H, Troyer EM, Rivero-Vega RA, Smith SA, Friedman M, Fouhey DF, Weeks BC (2026). *bifrost: an R package for scalable inference of phylogenetic shifts in multivariate evolutionary dynamics*. *bioRxiv*. [https://doi.org/10.64898/2026.04.12.718036](https://doi.org/10.64898/2026.04.12.718036)
 
 3. `bifrost` software citation  
-   Berv JS, Fox N, Thorstensen MJ, Lloyd-Laney H, Troyer EM, Rivero-Vega RA, Smith SA, Friedman M, Fouhey DF, Weeks BC (2026). *Branch-Level Inference Framework for Recognizing Optimal Shifts in Traits*. R package version 0.1.3. [https://CRAN.R-project.org/package=bifrost](https://CRAN.R-project.org/package=bifrost)
+   Berv JS, Fox N, Thorstensen MJ, Lloyd-Laney H, Troyer EM, Rivero-Vega RA, Smith SA, Friedman M, Fouhey DF, Weeks BC (2026). *Branch-Level Inference Framework for Recognizing Optimal Shifts in Traits*. R package version 0.1.4. [https://CRAN.R-project.org/package=bifrost](https://CRAN.R-project.org/package=bifrost)
 
 4. `mvMORPH` package paper  
    Clavel J, Escarguel G, Merceron G (2015). *mvmorph: an R package for fitting multivariate evolutionary models to morphometric data*. *Methods in Ecology and Evolution*, 6(11), 1311-1319. [https://doi.org/10.1111/2041-210X.12420](https://doi.org/10.1111/2041-210X.12420)
@@ -119,7 +119,7 @@ This project is released under the GPL (>= 2) License. See the `LICENSE` file fo
 
 `bifrost` builds on substantial work from `mvMORPH`, `phytools`, `ape`, `future`, and `future.apply`. The greedy search algorithm is adapted from [Mitov et al. 2019](https://www.pnas.org/doi/10.1073/pnas.1813823116) and [Smith et al. 2023](https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.19099). See the `DESCRIPTION` file for complete dependency and version information.
 
-The name of our R package is inspired by the Bifrost, the rainbow bridge of Norse mythology that connects Earth (Midgard) and Asgard within the cosmic structure of Yggdrasil, the Tree of Life, echoing how this framework links observable data to hidden evolutionary shifts across the history of life.
+The name of our R package is inspired by the Bifröst, the rainbow bridge of Norse mythology that connects Earth (Midgard) and Asgard within the cosmic structure of Yggdrasil, the Tree of Life, echoing how this framework links observable data to hidden evolutionary shifts across the history of life.
 
 Development of the `bifrost` R package was supported by the [Oxford Research Software Engineering Group](https://www.rse.ox.ac.uk/schmidt-ai-science), with support from [Schmidt Sciences, LLC.](https://www.schmidtsciences.org/ai-in-science/) and the [Michigan Institute for Data Science and AI in Society](https://midas.umich.edu/).
 

cran-comments.md

@@ -1,35 +1,25 @@
 ## Resubmission
 
-This is a resubmission following CRAN feedback on **bifrost 0.1.2**. The previous submission was **bifrost 0.1.2**. The current submission is **bifrost 0.1.3**.
+This is a new submission of **bifrost 0.1.4**. The current CRAN version is **bifrost 0.1.3**.
 
-### Changes made in response to CRAN comments
+### Changes since 0.1.3
 
-- Added explicit return-value documentation (`@return` / `\value{}`) for the exported
-  `print.bifrost_search()` method, documenting that the function returns the input object
-  invisibly and is called for its printing side effects.
-
-### Other updates since 0.1.2 (unrelated to the CRAN note)
-
-- `plot_ic_acceptance_matrix()` gained an optional `baseline_ic` argument to use the true
-  no-shift baseline IC for the baseline annotation and for computing the rate-of-improvement
-  series (`diff(IC)`), which is useful when `matrix_data` begins at the first evaluated shift model.
-- Jaw-shape vignette: added additional static figures (evolutionary correlation heatmap, IC
-  trajectory plot, and branch-rate visualization) and updated plotting/legend annotations for
-  clarity. Vignette continues to build under `--as-cran`.
-- Expanded unit tests to cover the new `baseline_ic` behavior and input validation.
+- 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.
 
 ## Test environments
 
 - macOS Sequoia 15.x, R 4.4.2 (local, aarch64)
-- GitHub Actions CI: macOS-latest, ubuntu-latest, windows-latest
-- R-hub (run via GitHub)
 
 ## R CMD check results
 
 0 errors | 0 warnings | 0 notes
 
-Checked locally with `R CMD check --as-cran` / `devtools::check(args = "--as-cran")`.
-GitHub Actions CI checks also pass on macOS, Linux, and Windows.
+Checked locally with `R CMD build .` and `R CMD check --as-cran bifrost_0.1.4.tar.gz`.
 
 ## Downstream dependencies
 

inst/CITATION

@@ -64,7 +64,7 @@ bibentry(
     person(c("Brian","C."),   "Weeks")
   ),
   year    = "2026",
-  note    = "R package version 0.1.3",
+  note    = "R package version 0.1.4",
   url     = "https://CRAN.R-project.org/package=bifrost"
 )
 

inst/WORDLIST

@@ -1,65 +1,195 @@
 Acknowledgements
+Allometry
+Ané
+Aristide
+Asimomitis
 BMM
+Bartoszek
 Bifröst
+Bioinformatics
 Boyko
 CMD
+CPC
+CRC
+Caetano
+Carvajal
+Cheng
+Claramunt
 Clavel
 Codecov
+Cov
+DF
 Dipnoi
+EB
+Escarguel
+Felsenstein
+Flury
 GIC
 GLS
+Gittleman
 Hoffbeck
+Houle
 IC
 ICs
+Interspecific
+Iteratively
+JS
+Jolliffe
+Kozak
 LLC
 LOOCV
+Lande
 Landgrebe
+Laney
 Lifecycle
+Ligges
+Losos
+MIPoD
+MJ
+Mariadassou
+McPeek
+Merceron
+Microevolutionary
 Midgard
 Mitov
+Mooers
+Morlon
 Morphometric
+Mächler
+Ntip
+OU
+OpenAI
 OpenMP
 Ornstein
+Paradis
 Parallelization
+PeerJ
+Pennell
+Phylogenies
+Probst
+Purvis
+README
 RStudio
-Reproducibility
+Rabosky
+Revell
+Ricklefs
 RidgeArch
+Rivero
+Roark
 Rtools
 SIMMAP
+Schliep
+Schloerke
+Schluter
+Schulte
+Scincid
+Seehausen
+Shipley
+Sidlauskas
+Sievert
+Stadler
+Stepanova
+Steppan
 Uhlenbeck
+Uyeda
 VCV
 VCVs
 Viridis
 XQuartz
+Xie
+abline
+adjustcolor
 adp
 al
+bg
+bioRxiv
+bmatrix
+bty
+byrow
+cdots
+cex
 clade
 clades
 cladogenic
 coelacanths
+cov
+covariation
+covs
+dX
+ddots
+de
+disp
 doi
+edf
+eigenstructure
+eigensystem
 env
 et
+getDescendants
+getMRCA
+grDevices
 grey
+htmltools
+idx
+ij
+intersp
 intra
+intraspecific
 iteratively
+len
+lty
+ltys
+lwd
+lwds
 macroevolutionary
+mathbf
+mathrm
+mgp
 morphometric
+mtext
 mvMORPH
 mvPGLS
 mvgls
+mvmorph
+nodelabels
 nph
+nrow
+oma
+otimes
 oversubscription
 pGLS
 parallelization
+passerine
+pch
+phylo
+phylogenetically
 phylogenies
+phytools
+pkgdown
+plotly
+pmax
+pmin
+pos
+preprint
+pty
+readonly
 reproducibility
-scalability
+rescales
+scalable
 sciadv
+scincid
 searchOptimalConfiguration
+seg
 sysbio
 syy
+tiplabels
+topleft
 ultrametric
-untransformed
+ultrametricity
+vdots
 viridis
-ΔIC
+xlab
+xlim
+yaxt
+ylab
+ylim