| Title: | Phylogenetic Estimation of Shifts in the Tempo of Origination |
| Version: | 0.1.4 |
| Description: | Implements diversification analyses using the phylogenetic birth-death-shift model. It leverages belief propagation techniques to calculate branch-specific diversification rates, see Kopperud & Hoehna (2025) <doi:10.1093/sysbio/syaf041>. |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.3 |
| Imports: | tidytree, treeio, ape |
| Config/rextendr/version: | 0.4.2 |
| SystemRequirements: | Cargo (Rust's package manager), rustc |
| Depends: | R (≥ 4.2) |
| NeedsCompilation: | yes |
| Packaged: | 2025-11-21 10:49:56 UTC; bkopper |
| Author: | Bjørn Tore Kopperud [aut, cre], Sebastian Höhna [aut] |
| Maintainer: | Bjørn Tore Kopperud <kopperud@protonmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2025-11-26 14:00:02 UTC |
RPesto: Phylogenetic Estimation of Shifts in the Tempo of Origination (in R)
Description
Implements diversification analyses using the phylogenetic birth-death-shift model. It leverages belief propagation techniques to calculate branch-specific diversification rates, see Kopperud & Hoehna (2025) doi:10.1093/sysbio/syaf041.
References
Kopperud, B. T., & Höhna, S. (2025). Phylogenetic Estimation of branch-specific Shifts in the Tempo of Origination. Systematic Biology, syaf041.
Höhna, S., Freyman, W. A., Nolen, Z., Huelsenbeck, J. P., May, M. R., & Moore, B. R. (2019). A Bayesian approach for estimating branch-specific speciation and extinction rates. BioRxiv, 555805.
Author(s)
Maintainer: Bjørn Tore Kopperud kopperud@protonmail.com
Authors:
Sebastian Höhna
Phylogeny constructor
Description
Constructs a phylogeny that lives in the "rust" part of the program
Usage
Phylogeny(newick)
Arguments
newick |
a newick string |
Format
An object of class environment of length 10.
Examples
phy <- Phylogeny$new("((A:0.5,B:0.5):0.5,C:1.0);")
phy$print()
phy$write_newick()
fits the bds model
Description
fits the bds model
Usage
fit_bds(
phy,
sampling_fraction,
lambda_hat,
mu_hat,
eta,
num_speciation_classes = 6,
num_extinction_classes = 6,
sd = 0.587,
tol = 1e-06,
condition_survival = TRUE,
condition_root_speciation = TRUE,
condition_marginal = FALSE,
extinction_approximation = FALSE,
verbose = FALSE,
numthreads = 0
)
Arguments
phy |
an object of type phylo |
sampling_fraction |
the probability that each species was sampled in the tree |
lambda_hat |
the overall scale of the log-normal base distribution for the speciation rates. If not specified, the function will estimate it using ML |
mu_hat |
the overall scale of the log-normal base distribution for the extinction rates. If not specified, the function will estimate it using ML |
eta |
the shift rate parameter. If not specified, the function will estimate it using ML |
num_speciation_classes |
the number of speciation rate class discretizations, such that rate categories is k = n_sp * n_mu |
num_extinction_classes |
the number of extinction rate class discretizations, such that rate categories is k = n_sp * n_mu |
sd |
the spread parameter for the log-normal base distribution |
tol |
the local error threshold in the numerical ODE solver (per delta_t time step) |
condition_survival |
whether or not to condition on the survival of the left and right lineages descending from the root (default TRUE) |
condition_root_speciation |
whether or not to condition on that there was a speciation event at the root node (default TRUE) |
condition_marginal |
whether or condition using the marginal or per-category approach (default FALSE, i.e., to condition per rate category) |
extinction_approximation |
whether or not to approximate the extinction probability calculations, by assuming that rate shift events are not allowed on extinct lineages (default FALSE) |
verbose |
whether or not to print more information |
numthreads |
how many threads to use in likelihood calculation. If 0, then the program uses all available cores |
Value
a list with three items: $model (the parameter estimates), $td (a tidytree object with branch-rate estimates), and $tip_rates (a data frame of the tip rates)
Examples
data("primates")
analysis <- fit_bds(primates, sampling_fraction = 0.6, numthreads = 2)
fits the constant-rate birth-death model
Description
fits the constant-rate birth-death model
Usage
fit_cbd(
phy,
sampling_fraction,
tol = 1e-06,
condition_survival = TRUE,
condition_root_speciation = TRUE,
verbose = FALSE
)
Arguments
phy |
an object of type phylo |
sampling_fraction |
the probability that each species was sampled in the tree |
tol |
the local error threshold in the numerical ODE solver (per delta_t time step) |
condition_survival |
whether or not to condition on the survival of the left and right lineages descending from the root (default TRUE) |
condition_root_speciation |
whether or not to condition on that there was a speciation event at the root node (default TRUE) |
verbose |
whether or not to print more information |
Value
a list with the maximum-likelihood parameter estimates of the speciation rate and the extinction rate
Primates phylogenetic tree
Description
This tree is from Vos & Mooers (2006)
Usage
data(primates)
Format
An object of class phylo of length 5.
Details
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.
Objects exported from other packages
Description
These objects are imported from other packages. Follow the links below to see their documentation.
- tidytree