Package: coevolve 1.2.1

Scott Claessens

coevolve: Fit Bayesian Generalized Dynamic Phylogenetic Models using 'Stan' or 'JAX'

Fit Bayesian generalized dynamic phylogenetic models using 'Stan' or 'JAX'. The package allows an arbitrary number of variables with different response distributions to coevolve on a phylogenetic tree via an Ornstein-Uhlenbeck evolutionary process, allowing users to assess directionality between coevolving variables. The optional JAX backend enables high-performance sampling with NumPyro and potential GPU acceleration via 'reticulate'.

Authors:Scott Claessens [aut, cre], Erik Ringen [aut], Rob Moss [rev], Krzysztof Bartoszek [rev]

coevolve_1.2.1.tar.gz
coevolve_1.2.1.zip(r-4.7-any)coevolve_1.2.1.zip(r-4.6-any)coevolve_1.2.1.zip(r-4.5-any)
coevolve_1.2.1.tgz(r-4.6-any)coevolve_1.2.1.tgz(r-4.5-any)
coevolve_1.2.1.tar.gz(r-4.7-any)coevolve_1.2.1.tar.gz(r-4.6-any)
coevolve_1.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
coevolve/json (API)

# Install 'coevolve' in R:
install.packages('coevolve', repos = c('https://ropensci-staging.r-universe.dev', 'https://cloud.r-project.org'))

Reviews:rOpenSci Software Review #()

Bug tracker:https://github.com/scottclaessens/coevolve/issues

Pkgdown/docs site:https://scottclaessens.github.io

Datasets:
  • authority - Political and religious authority in Austronesian societies
  • primates - Brain weight, body weight, diet, and sociality in primates
  • repeated - Example dataset with repeated observations

On CRAN:

Conda:

bayesian-statisticscoevolveevolutionstanstatistical-models

6.81 score 15 stars 19 scripts 18 exports 87 dependencies

Last updated from:52bdfcc1cf. Checks:7 ERROR, 3 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-develERROR789
pkgdown docsOK235
source / vignettesOK283
linux-releaseERROR831
macos-releaseERROR691
macos-oldrelERROR596
windows-develERROR732
windows-releaseERROR823
windows-oldrelERROR832
wasm-releaseOK195

Exports:coev_ancestral_statescoev_calculate_delta_thetacoev_calculate_thetacoev_fitcoev_make_stancodecoev_make_standatacoev_plot_delta_thetacoev_plot_flowfieldcoev_plot_pred_seriescoev_plot_predictive_checkcoev_plot_selection_gradientcoev_plot_trait_valuescoev_pred_seriescoev_simulate_coevolutionextract_samplessave_coevfitstancodestandata

Dependencies:abindapebackportsbayesplotbitbit64checkmateclicliprclusterGenerationcmdstanrcodacodetoolscolorspacecombinatcpp11crayondata.tableDEoptimdigestdistributionaldoParalleldplyrexpmfarverfastmatchforeachgenericsggdistggplot2ggridgesgluegridExtragtablehmsigraphisobanditeratorsjsonlitelabelinglatticelifecyclemagrittrmapsMASSMatrixmatrixStatsmnormtnlmenumDerivoptimParallelpatchworkphangornphaseRphytoolspillarpkgconfigplyrposteriorprettyunitsprocessxprogresspspurrrquadprogR6RColorBrewerRcppreadrreshape2rlangS7scalesscatterplot3dstringistringrtensorAtibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwhiskerwithr

Accelerated sampling using JAX and nutpie
Introduction | Setup | A working example
Rendered fromjax.Rmdusingknitr::rmarkdown

Last update: 2026-10-06
Started: 2026-07-22

Accounting for repeated observations
Introduction | A working example | Limitations of repeated observations models | References
Rendered fromrepeated.Rmdusingknitr::rmarkdown

Last update: 2026-10-06
Started: 2026-07-22

Algorithmic scaling
Introduction | Computation time scaling | Improving computation times | References
Rendered fromscaling.Rmdusingknitr::rmarkdown

Last update: 2026-10-06
Started: 2026-09-15

Ancestral state reconstruction
Overview | Setup | Fit the model | Ancestral states on the latent scale | Visualizing latent ancestral states on the tree | Joint latent-space scatterplot | Ancestral states on the response scale | Pie chart tree: response-scale probabilities | Working with raw posterior draws | Identifying nodes on the tree | Selecting specific nodes and variables
Rendered fromancestral_states.Rmdusingknitr::rmarkdown

Last update: 2026-10-06
Started: 2026-08-12

Averaging over samples of trees
Introduction | A working example
Rendered frommultiphylo.Rmdusingknitr::rmarkdown

Last update: 2026-10-06
Started: 2026-07-22

Controlling for spatial locations
Introduction | A working example
Rendered fromspatial.Rmdusingknitr::rmarkdown

Last update: 2026-10-06
Started: 2026-07-22

Handling missing data
Introduction | A working example | References
Rendered frommissing.Rmdusingknitr::rmarkdown

Last update: 2026-10-06
Started: 2026-07-22

Introduction to the coevolve package
Introduction | The generalized dynamic phylogenetic model | A working example | Available response distributions | Conclusion | References
Rendered fromcoevolve.Rmdusingknitr::rmarkdown

Last update: 2026-10-06
Started: 2023-12-06

Model comparison
Introduction | A working example
Rendered fromcompare.Rmdusingknitr::rmarkdown

Last update: 2026-10-06
Started: 2026-07-22

Setting manual priors
Introduction | Default priors | Limitations on setting priors
Rendered frompriors.Rmdusingknitr::rmarkdown

Last update: 2026-10-06
Started: 2026-08-19

Readme and manuals

Help Manual

Help pageTopics
Political and religious authority in Austronesian societiesauthority
Extract ancestral state estimates from a fitted coevolutionary modelcoev_ancestral_states
Calculate delta theta from a fitted 'coevfit' objectcoev_calculate_delta_theta
Calculate equilibrium trait values (theta) for a fitted 'coevfit' objectcoev_calculate_theta
Fit Bayesian dynamic coevolutionary model in Stancoev_fit
Make Stan code for dynamic coevolutionary modelcoev_make_stancode
Make Stan data for dynamic coevolutionary modelcoev_make_standata
Plot delta theta values from a fitted 'coevfit' objectcoev_plot_delta_theta
Plot flowfield of expected evolutionary change from a fitted 'coevfit' objectcoev_plot_flowfield
Plot a predicted coevolutionary time series from a fitted 'coevfit' objectcoev_plot_pred_series
Plot predictive check from a fitted 'coevfit' objectcoev_plot_predictive_check
Plot selection gradient heatmap from a fitted 'coevfit' objectcoev_plot_selection_gradient
Plot estimated trait values from a fitted 'coevfit' objectcoev_plot_trait_values
Predict a co-evolutionary time series from a fitted 'coevfit' objectcoev_pred_series
Simulate the coevolution of multiple variables in discrete time stepscoev_simulate_coevolution
Extract draws from jax_fit objectdraws.jax_fit
Extract draws from nutpie_fit objectdraws.nutpie_fit
Extract samples (draws) from a fitted 'coevfit' objectextract_samples
Extract metadata from jax_fit objectmetadata.jax_fit
Extract metadata from nutpie_fit objectmetadata.nutpie_fit
Create a matrix of output plots from a 'coevfit' objectpairs.coevfit
Trace and density plots for 'coevfit' objectsplot.coevfit
Brain weight, body weight, diet, and sociality in primatesprimates
Print a summary of a fitted model represented by a 'coevfit' objectprint.coevfit print.coevsummary
Example dataset with repeated observationsrepeated
Save a fitted 'coevfit' object to a filesave_coevfit
Expose the Stan code of a fitted model represented by a 'coevfit' objectstancode
Expose the Stan data list for a fitted model represented by a 'coevfit' objectstandata
Create a summary of a fitted model represented by a 'coevfit' objectsummary.coevfit
Summary statistics for jax_fit objectsummary.jax_fit
Compute summary statistics for nutpie_fit objectsummary.nutpie_fit