Suggests: covr, jsonlite (>= 1.1), testthat (>= 3.0.0), xml2

Suggests: ggplot2, knitr, microbenchmark, quarto, scales, TDA, tdaunif,
tinysnapshot, tinytest

Imports: methods, phylobase, ape, grid, stats

Depends: R (>= 4.1)
Imports: ape, cli, cowplot, dplyr, forcats, ggnewscale, ggplot2 (>=
4.0.0), ggraph, igraph, lifecycle, rlang, scales, tidygraph
Suggests: knitr, rmarkdown, testthat (>= 3.0.0)

Imports: ade4, ape (>= 3.0), Rcpp (>= 0.11.0), rncl (>= 0.6.0), grid,
methods, stats, RNeXML
LinkingTo: Rcpp
Suggests: MASS, testthat (>= 0.8.1), knitr, rmarkdown

Imports: ape (>= 4.0), phylobase, htmlwidgets, methods (>= 3.3.0)

Suggests: testthat, knitr, rmarkdown, ape

Suggests: combinat (>= 0.0.8), doParallel (>= 1.0.10), phytools (>=
0.5.38), testthat (>= 1.0.2), TreeSim (>= 2.2), knitr,
rmarkdown

Suggests: dendextend, knitr, rmarkdown, testthat

Imports: ape, loo, methods, phytools, Rcpp (>= 0.12.0), RcppParallel
(>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.4.0)

Depends: R (>= 4.1.0)
Imports: ape, phangorn, Matrix, betapart, parallel, methods,
colorspace, igraph, clustMixType, maptpx, terra, vegan,
predicts, smoothr
Suggests: tinytest, knitr, rmarkdown, mapproj, survival, rJava,
phyloseq, V8

Suggests: cowplot, ggplot2, knitr, purrr, RColorBrewer, reshape2,
rmarkdown, testthat (>= 3.0.0)

Imports: sem, ape, phylobase, phylopath, methods
Suggests: semPlot, TreeTools, Rphylopars, phylolm, fishtree, phyr,
knitr, rmarkdown, ggplot2, testthat, phylosignal, adephylo

Imports: ggnetwork (>= 0.5.1), igraph (>= 1.1.2)

Imports: Rcpp (>= 0.11.0), adephylo, igraph, ape, phylobase, boot, DBI,
graphics, grDevices, methods, stats, utils

Depends: R (>= 3.5)
Imports: ape, sf, stats, terra, utils, vegan
Suggests: canaper, furrr, future, testthat (>= 3.0.0), betapart, knitr,
rmarkdown, tmap, magrittr, hillR, picante, phytools, nullcat

Imports: igraph, methods, NHPoisson, phylobase

Suggests: knitr, rmarkdown, purrr, dplyr, testthat (>= 3.0.0)

Imports: ape, ggplot2, reshape2, Rfast, RSpectra, stats, utils

Depends: R (>= 3.1)
Imports: stats, ape, Rcpp, Matrix, methods, graphics, dplyr, lme4,
nloptr, gridExtra, mvtnorm, latticeExtra, tidyr
LinkingTo: Rcpp, RcppArmadillo
Suggests: testthat, pez, knitr, rmarkdown, covr, picante, rbenchmark,
INLA, MCMCglmm, logistf, phylolm, ggplot2, ggridges, DHARMa,
rr2, future.apply