Bayesian inference methods are increasingly used to reconstruct trees (e.g. phylogenetic or transmission trees) producing collections of trees, or “forests”.

mixtree provides a statistical framework to compare sets of trees and test whether they originate from the same or different generative processes.

Installation

You can install the package on CRAN with:

install.packages("mixtree")

Quick start

library(mixtree)

# Simulate two chains of transmission trees
chainA <- lapply(1:100, function(i) {
  make_tree(20, R = 2, stochastic = TRUE) |>
    igraph::as_long_data_frame()
})
chainB <- lapply(1:100, function(i) {
  make_tree(20, R = 4, stochastic = TRUE) |>
    igraph::as_long_data_frame()
})

# Compare the two chains
result <- tree_test(chainA, chainB)
print(result)
#> Permutation test for adonis under reduced model
#> Permutation: free
#> Number of permutations: 999
#> 
#> (function (formula, data, permutations = 999, method = "bray", sqrt.dist = FALSE, add = FALSE, by = NULL, parallel = getOption("mc.cores"), na.action = na.fail, strata = NULL, ...) 
#>           Df SumOfSqs      R2      F Pr(>F)    
#> Model      1     5490 0.10518 23.274  0.001 ***
#> Residual 198    46710 0.89482                  
#> Total    199    52201 1.00000                  
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1