Package: PBD 1.5

PBD: Protracted Birth-Death Model of Diversification

Conducts maximum likelihood analysis and simulation of the protracted birth-death model of diversification. See Etienne, R.S. & J. Rosindell 2012 <doi:10.1093/sysbio/syr091>; Lambert, A., H. Morlon & R.S. Etienne 2014, <doi:10.1007/s00285-014-0767-x>; Etienne, R.S., H. Morlon & A. Lambert 2014, <doi:10.1111/evo.12433>.

Authors:Rampal S. Etienne

PBD_1.5.tar.gz
PBD_1.5.zip(r-4.5)PBD_1.5.zip(r-4.4)PBD_1.5.zip(r-4.3)
PBD_1.5.tgz(r-4.5-any)PBD_1.5.tgz(r-4.4-any)PBD_1.5.tgz(r-4.3-any)
PBD_1.5.tar.gz(r-4.5-noble)PBD_1.5.tar.gz(r-4.4-noble)
PBD_1.5.tgz(r-4.4-emscripten)PBD_1.5.tgz(r-4.3-emscripten)
PBD.pdf |PBD.html✨
PBD/json (API)

# Install 'PBD' in R:
install.packages('PBD', repos = c('https://rsetienne.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rsetienne/pbd/issues

On CRAN:

Conda:

5.95 score 2 stars 49 scripts 225 downloads 9 mentions 20 exports 46 dependencies

Last updated 28 days agofrom:927c8f4811. Checks:1 OK, 7 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 11 2025
R-4.5-winNOTEFeb 11 2025
R-4.5-macNOTEFeb 11 2025
R-4.5-linuxNOTEFeb 11 2025
R-4.4-winNOTEFeb 11 2025
R-4.4-macNOTEFeb 11 2025
R-4.3-winNOTEFeb 11 2025
R-4.3-macNOTEFeb 11 2025

Exports:pbd_bootstrappbd_brts_densitypbd_durspec_cumdensitypbd_durspec_densitypbd_durspec_meanpbd_durspec_modepbd_durspec_momentpbd_durspec_quantilepbd_durspec_varpbd_loglikpbd_LRpbd_mean_durspecpbd_mean_durspecspbd_MLpbd_numspec_meanpbd_numspec_medianpbd_numspec_quantilepbd_simpbd_sim_checkedpbd_sim_cpp

Dependencies:ade4apeBHcliclusterGenerationcodacodetoolscombinatcpp11DDDDEoptimdeSolvedigestdoParallelexpmfastmatchforeachgenericsglueigraphiteratorslatticelifecyclemagrittrmapsMASSMatrixmnormtnlmenumDerivoptimParallelphangornphytoolspixmappkgconfigquadprogRcppRcppArmadilloRcppEigenrlangscatterplot3dspSparseMsubplextestitvctrs

pbd_ML demo

Richel Bilderbeek & Rampal S. Etienne

Rendered fromPBD_ML_demo.Rmdusingknitr::rmarkdownon Feb 11 2025.

Last update: 2025-02-10
Started: 2025-02-10

Readme and manuals

Help Manual

Help pageTopics
Protracted Birth-Death Model of DiversificationPBD-package PBD
Bootstrap analysis under protracted birth-death model of diversificationpbd_bootstrap
Node depth probbaility density for protracted birth-death model of diversificationpbd_brts_density
Cumulative density of duration of speciation under protracted birth-death model of diversificationpbd_durspec_cumdensity
Probability density for duration of speciation under protracted birth-death model of diversificationpbd_durspec_density
Mean duration of speciation under protracted birth-death model of diversificationpbd_durspec_mean
Actual calculation of the mean duration of speciation (equations 19 and 20 of reference article) assuming all inputs are correctpbd_durspec_mean_impl
mode of the duration of speciation under protracted birth-death model of diversificationpbd_durspec_mode
Moments of duration of speciation under protracted birth-death model of diversificationpbd_durspec_moment
Quantiles of duration of speciation under protracted birth-death model of diversificationpbd_durspec_quantile
Variance in duration of speciation under protracted birth-death model of diversificationpbd_durspec_var
Loglikelihood for protracted birth-death model of diversificationpbd_loglik
Bootstrap likelihood ratio test of protracted birth-death model of diversificationpbd_LR
Calculate the mean duration of speciation (equations 19 and 20 of reference article), non-vectorizedpbd_mean_durspec
Calculate the mean durations of speciation (equations 19 and 20 of reference article)pbd_mean_durspecs
Maximization of loglikelihood under protracted birth-death model of diversificationpbd_ML
Mean number of species under protracted birth-death model of diversificationpbd_numspec_mean
Median number of species under protracted birth-death model of diversificationpbd_numspec_median
Number of species for a given quantile under protracted birth-death model of diversificationpbd_numspec_quantile
Function to simulate the protracted speciation processpbd_sim
Checked and safer version of PBD::pbd_simpbd_sim_checked
Function to simulate the approximate protracted speciation processpbd_sim_cpp