DDD: Diversity-Dependent Diversification
Version 3.4

Implements maximum likelihood and bootstrap methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent, under various models including various types of key innovations. See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, , Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, and Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099, . Also contains functions to simulate the diversity-dependent process.

Browse man pages Browse package API and functions Browse package files

AuthorRampal S. Etienne & Bart Haegeman
Date of publication2017-02-24 08:31:37
MaintainerRampal S. Etienne <r.s.etienne@rug.nl>
LicenseGPL-3
Version3.4
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("DDD")

Man pages

bd_loglik: Loglikelihood for diversity-independent diversification model
bd_ML: Maximization of the loglikelihood under the...
DDD-internal: Internal DDD Functions
DDD-package: Diversity Dependent Diversification
dd_KI_loglik: Loglikelihood for diversity-dependent diversification models...
dd_KI_ML: Maximization of the loglikelihood under a diversity-dependent...
dd_KI_sim: Function to simulate a key innovation in macro-evolution with...
dd_loglik: Loglikelihood for diversity-dependent diversification models
dd_LR: Bootstrap likelihood ratio test of diversity-dependent...
dd_ML: Maximization of the loglikelihood under a diversity-dependent...
dd_MS_loglik: Loglikelihood for macro-evolutionary succession under...
dd_MS_ML: Maximization of the loglikelihood under a diversity-dependent...
dd_MS_sim: Function to simulate the macro-evolutionary succession...
dd_sim: Function to simulate the diversity-dependent diversification...
dd_SR_loglik: Loglikelihood for diversity-dependent diversification models...
dd_SR_ML: Maximization of the loglikelihood under a diversity-dependent...
dd_SR_sim: Function to simulate the diversity-dependent diversification...
L2brts: Function to convert a table with speciation and extinction...
L2phylo: Function to convert a table with speciation and extinction...
optimizer: Carries out optimization (finding a minimum)
roundn: Rounds up in the usual manner
sample2: Takes samples in the usual manner

Functions

DDD Man page
DDD-package Man page
L2brts Man page Source code
L2phylo Man page Source code
bd_ML Man page Source code
bd_loglik Man page Source code
bd_loglik_choosepar Man page Source code
bd_simplex Man page
brts2phylo Man page Source code
changepars Man page Source code
conv Man page Source code
dd_KI_ML Man page Source code
dd_KI_lamuN Man page Source code
dd_KI_loglik Man page Source code
dd_KI_loglik1 Man page Source code
dd_KI_loglik2 Man page Source code
dd_KI_loglik_choosepar Man page Source code
dd_KI_loglikold Man page
dd_KI_sim Man page Source code
dd_KI_simplex Man page
dd_LR Man page Source code
dd_ML Man page Source code
dd_MS_ML Man page Source code
dd_MS_lamuN Man page Source code
dd_MS_loglik Man page Source code
dd_MS_loglik1 Man page Source code
dd_MS_loglik2 Man page Source code
dd_MS_loglik_choosepar Man page Source code
dd_MS_sim Man page Source code
dd_MS_simplex Man page
dd_SR_ML Man page Source code
dd_SR_loglik Man page Source code
dd_SR_loglik1 Man page Source code
dd_SR_loglik2 Man page Source code
dd_SR_loglik_choosepar Man page Source code
dd_SR_sim Man page Source code
dd_SR_simplex Man page
dd_bootstrap_sim Man page Source code
dd_lamuN Man page Source code
dd_loglik Man page Source code
dd_loglik1 Man page Source code
dd_loglik2 Man page Source code
dd_loglik_M Man page Source code
dd_loglik_M2 Man page Source code
dd_loglik_M2_aux Man page Source code
dd_loglik_M3 Man page Source code
dd_loglik_M3_aux Man page Source code
dd_loglik_M_aux Man page Source code
dd_loglik_M_bw Man page Source code
dd_loglik_M_bw_aux Man page Source code
dd_loglik_bw_rhs Man page Source code
dd_loglik_choosepar Man page Source code
dd_loglik_rhs Man page Source code
dd_logliknorm_rhs1 Man page Source code
dd_logliknorm_rhs2 Man page Source code
dd_logliknorm_rhs3 Man page Source code
dd_sim Man page Source code
dd_simplex Man page
expn_dd Man page Source code
expn_dd_sp Man page Source code
flavec Man page Source code
lambdamu Man page Man page Source code
lambdamu2 Man page Source code
lambdamu3 Man page Source code
lamu_dd_td Man page Source code
optimizer Man page Source code
predictsp Man page Source code
roundn Man page Source code
sample2 Man page Source code
simplex Man page Source code
td_loglik_bw_rhs Man page Source code
td_loglik_rhs Man page Source code
td_loglik_rhs_sim Man page Source code
td_sim Man page Source code

Files

NAMESPACE
R
R/bd_loglik_choosepar.R
R/dd_loglik_bw_rhs.R
R/td_loglik_rhs.R
R/dd_SR_ML.R
R/td_loglik_rhs_sim.R
R/dd_KI_loglik.R
R/dd_KI_loglik_choosepar.R
R/dd_ML.R
R/lamu_dd_td.R
R/dd_LR.R
R/dd_SR_sim.R
R/dd_loglik.R
R/dd_KI_ML.R
R/dd_MS_sim.R
R/dd_sim.R
R/td_loglik_bw_rhs.R
R/bd_ML.R
R/dd_logliknorm_rhs3.R
R/dd_SR_loglik.R
R/dd_loglik_M.R
R/dd_SR_loglik_choosepar.R
R/dd_utils.R
R/dd_loglik_rhs.R
R/dd_logliknorm_rhs1.R
R/dd_MS_loglik.R
R/bd_loglik.R
R/td_sim.R
R/dd_MS_ML.R
R/dd_loglik_choosepar.R
R/dd_logliknorm_rhs2.R
R/dd_KI_sim.R
R/dd_bootstrap_sim.R
R/dd_MS_loglik_choosepar.R
MD5
DESCRIPTION
man
man/dd_SR_loglik.Rd
man/roundn.Rd
man/optimizer.Rd
man/DDD-internal.Rd
man/bd_ML.Rd
man/DDD-package.Rd
man/L2phylo.Rd
man/sample2.Rd
man/dd_SR_ML.Rd
man/dd_KI_ML.Rd
man/bd_loglik.Rd
man/dd_MS_sim.Rd
man/dd_KI_loglik.Rd
man/dd_SR_sim.Rd
man/dd_loglik.Rd
man/dd_ML.Rd
man/dd_LR.Rd
man/dd_MS_ML.Rd
man/dd_MS_loglik.Rd
man/dd_KI_sim.Rd
man/dd_sim.Rd
man/L2brts.Rd
DDD documentation built on May 19, 2017, 4:39 p.m.