PBD: Protracted Birth-Death Model of Diversification
Version 1.4

Conducts maximum likelihood analysis and simulation of the protracted birth-death model of diversification. See Etienne, R.S. & J. Rosindell 2012 ; Lambert, A., H. Morlon & R.S. Etienne 2014, ; Etienne, R.S., H. Morlon & A. Lambert 2014, .

AuthorRampal S. Etienne
Date of publication2017-05-04 16:32:06 UTC
MaintainerRampal S. Etienne <r.s.etienne@rug.nl>
LicenseGPL-2
Version1.4
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("PBD")

Getting started

Package overview
pbd_ML demo"

Popular man pages

pbd_durspec_mean: Mean duration of speciation under protracted birth-death...
pbd_durspec_mode: mode of the duration of speciation under protracted...
pbd_durspec_moment: Moments of duration of speciation under protracted...
pbd_durspec_var: Variance in duration of speciation under protracted...
pbd_loglik: Loglikelihood for protracted birth-death model of...
PBD-package: Protracted Birth-Death Model of Diversification
pbd_sim_cpp: Function to simulate the approximate protracted speciation...
See all...

All man pages Function index File listing

Man pages

pbd_bootstrap: Bootstrap analysis under protracted birth-death model of...
pbd_brts_density: Node depth probbaility density for protracted birth-death...
pbd_durspec_cumdensity: Cumulative density of duration of speciation under protracted...
pbd_durspec_density: Probability density for duration of speciation under...
pbd_durspec_mean: Mean duration of speciation under protracted birth-death...
pbd_durspec_mode: mode of the duration of speciation under protracted...
pbd_durspec_moment: Moments of duration of speciation under protracted...
pbd_durspec_quantile: Quantiles of duration of speciation under protracted...
pbd_durspec_var: Variance in duration of speciation under protracted...
pbd_loglik: Loglikelihood for protracted birth-death model of...
pbd_LR: Bootstrap likelihood ratio test of protracted birth-death...
pbd_ML: Maximization of loglikelihood under protracted birth-death...
PBD-package: Protracted Birth-Death Model of Diversification
pbd_sim: Function to simulate the protracted speciation process
pbd_sim_cpp: Function to simulate the approximate protracted speciation...

Functions

Files

inst
inst/doc
inst/doc/PBD_ML_demo.Rmd
inst/doc/PBD_ML_demo.R
inst/doc/PBD_ML_demo.html
tests
tests/testthat
tests/testthat/test-test_PBD.R
NAMESPACE
R
R/pbd_durspec_var.R
R/pbd_loglik.R
R/pbd_ML.R
R/pbd_sim.R
R/pbd_durspec_moment.R
R/pbd_utils.R
R/pbd_bootstrap_sim.R
R/pbd_durspec_mode.R
R/pbd_durspec_mean.R
R/pbd_loglik_choosepar.R
R/pbd_incipient.R
R/pbd_durspec_cumdensity.R
R/pbd_bootstrap.R
R/pbd_durspec_quantile.R
R/pbd_incipient_rhs.R
R/pbd_loglik_rhs.R
R/pbd_brts_density.R
R/pbd_LR.R
R/pbd_durspec_density.R
R/pbd_sim_cpp.R
vignettes
vignettes/PBD_ML_demo.Rmd
vignettes/PBD_ML_demo.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/pbd_LR.Rd
man/pbd_durspec_mode.Rd
man/pbd_ML.Rd
man/pbd_durspec_var.Rd
man/pbd_durspec_quantile.Rd
man/pbd_durspec_cumdensity.Rd
man/pbd_durspec_density.Rd
man/pbd_sim_cpp.Rd
man/pbd_brts_density.Rd
man/pbd_durspec_moment.Rd
man/pbd_durspec_mean.Rd
man/pbd_loglik.Rd
man/pbd_bootstrap.Rd
man/pbd_sim.Rd
man/PBD-package.Rd
PBD documentation built on May 19, 2017, 10:05 p.m.

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