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Add ancestral state reconstruction (coev_ancestral_states) #110

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Add ancestral state reconstruction (coev_ancestral_states) #110

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6e66c6d
Add coev_ancestral_states() with tests (single-tree, latent scale)
claude Apr 12, 2026
408ce9f
Add response-scale transforms and multi-tree tests
claude Apr 12, 2026
032a66b
Add coev_plot_node_labels() and ASR vignette
ErikRingen Apr 27, 2026
376aefa
Convert ASR vignette from qmd to static Rmd
ErikRingen Apr 27, 2026
c3cb9c4
Fix lint issues, test failures, and multiPhylo coercion bug
ErikRingen Apr 27, 2026
4c3f112
Cover remaining ASR branches to bring patch coverage to 100%
ErikRingen Apr 29, 2026
9b34e57
Address PR #110 review feedback
ErikRingen Apr 30, 2026
0ee4a8f
Fix R CMD check WARNING: dispatch identify() via S3 generic
ErikRingen Apr 30, 2026
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: coevolve
Title: Fit Bayesian Generalized Dynamic Phylogenetic Models using 'Stan'
Version: 1.0.0.9000
Version: 1.0.0.9001
Authors@R:
c(person("Scott", "Claessens", , "scott.claessens@gmail.com",
role = c("aut", "cre"), comment = c(ORCID = "0000-0002-3562-6981")),
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3 changes: 3 additions & 0 deletions NAMESPACE
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Expand Up @@ -10,13 +10,16 @@ S3method(stancode,coevfit)
S3method(standata,coevfit)
S3method(summary,coevfit)
S3method(summary,nutpie_fit)
export(coev_ancestral_states)
export(coev_calculate_delta_theta)
export(coev_calculate_theta)
export(coev_fit)
export(coev_identify_nodes)
export(coev_make_stancode)
export(coev_make_standata)
export(coev_plot_delta_theta)
export(coev_plot_flowfield)
export(coev_plot_node_labels)
export(coev_plot_pred_series)
export(coev_plot_predictive_check)
export(coev_plot_selection_gradient)
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8 changes: 8 additions & 0 deletions NEWS.md
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Expand Up @@ -2,6 +2,14 @@

### New Features

* Added `coev_ancestral_states()` for extracting posterior estimates of
ancestral trait values at internal phylogenetic nodes, on either the
latent or response scale (#86)
* Added `coev_plot_node_labels()` for plotting the tree with internal
node IDs displayed
* Added `coev_identify_nodes()` for interactive multi-click node selection,
wrapping `ape::identify.phylo()` in a loop
* Added vignette "Ancestral State Reconstruction with coevolve"
* Allow for single traits (#107)

# coevolve 1.0.0
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