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 development version of mixtree from GitHub with:

# install.packages("pak")
pak::pak("CyGei/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