RPesto

RPesto is an alternative implementation of the Pesto software in R. It can estimate branch-specific diversification rates for large trees. The julia implementation of Pesto is described in Kopperud & Höhna (2025).

Installation

The probability calculations in RPesto are implemented in the rust programming language. Therefore you need to have rust and cargo installed. Please follow the instructions on https://rustup.rs/.

Next, we will use the R-package remotes to install the necessary R package dependencies

install.packages("remotes")

library(remotes)

install_github("YuLab-SMU/treeio")
install_github("YuLab-SMU/tidytree")

Next we install RPesto

install_github("kopperud/RPesto")

Fitting the model

Now you can load RPesto and fit the model to your tree, and we need to specify what the probability of sampling the taxa are. This is usually set by calculating the number of the tips that are sampled in the tree, and dividing by the number of accepted species for the group.

library(RPesto)

data("primates")

sampling_fraction <- 0.635

analysis <- fit_bds(primates, sampling_fraction)
mymodel <- analysis$model
tree <- analysis$td

This will give you a tidytree object which contains the average net-diversification rates for each branch

'treedata' S4 object'.

...@ phylo:

Phylogenetic tree with 233 tips and 232 internal nodes.

Tip labels:
  Galago_matschiei, Euoticus_pallidus, Euoticus_elegantulus,
Galagoides_zanzibaricus, Galagoides_demidoff, Galago_alleni, ...

Rooted; includes branch length(s).

with the following features available:
  'mean_netdiv'.

# The associated data tibble abstraction: 465 × 4
# The 'node', 'label' and 'isTip' are from the phylo tree.
    node label                   isTip mean_netdiv
   <int> <chr>                   <lgl>  <dbl>
 1     1 Galago_matschiei        TRUE  0.0869
 2     2 Euoticus_pallidus       TRUE  0.0874
 3     3 Euoticus_elegantulus    TRUE  0.0874
 4     4 Galagoides_zanzibaricus TRUE  0.0864
 5     5 Galagoides_demidoff     TRUE  0.0864
 6     6 Galago_alleni           TRUE  0.0870
 7     7 Galago_senegalensis     TRUE  0.0883
 8     8 Galago_moholi           TRUE  0.0883
 9     9 Galago_gallarum         TRUE  0.0881
10    10 Otolemur_garnettii      TRUE  0.0866
# ℹ 455 more rows
# ℹ Use `print(n = ...)` to see more rows

Plotting the results

We can also use ggtree to plot the results

library(ggtree)

ggtree(tree, aes(color = mean_netdiv))

References

• Kopperud, B. T., & Höhna, S. (2025). Phylogenetic Estimation of branch-specific Shifts in the Tempo of Origination. Systematic Biology, syaf041.
• Vos, R. and A. Mooers. 2006. A new dated supertree of the primates. in Inferring large phylogenies: the big tree problem (R Vos, Phd thesis). Simon Fraser University, Burnaby, British Columbia.