DDD: Diversity-Dependent Diversification

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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, <DOI:10.1098/rspb.2011.1439>, Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, <DOI:10.1086/667574> and Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099, <DOI:10.1111/2041-210X.12565>. Also contains functions to simulate the diversity-dependent process.

Author
Rampal S. Etienne & Bart Haegeman
Date of publication
2016-11-07 21:07:26
Maintainer
Rampal S. Etienne <r.s.etienne@rug.nl>
License
GPL-3
Version
3.3

View on CRAN

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...
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

Files in this package

DDD
DDD/NAMESPACE
DDD/R
DDD/R/bd_loglik_choosepar.R
DDD/R/dd_loglik_bw_rhs.R
DDD/R/td_loglik_rhs.R
DDD/R/dd_SR_ML.R
DDD/R/td_loglik_rhs_sim.R
DDD/R/dd_KI_loglik.R
DDD/R/dd_KI_loglik_choosepar.R
DDD/R/dd_ML.R
DDD/R/lamu_dd_td.R
DDD/R/dd_LR.R
DDD/R/dd_SR_sim.R
DDD/R/dd_loglik.R
DDD/R/dd_KI_ML.R
DDD/R/dd_MS_sim.R
DDD/R/dd_sim.R
DDD/R/td_loglik_bw_rhs.R
DDD/R/bd_ML.R
DDD/R/dd_logliknorm_rhs3.R
DDD/R/dd_SR_loglik.R
DDD/R/dd_loglik_M.R
DDD/R/dd_SR_loglik_choosepar.R
DDD/R/dd_utils.R
DDD/R/dd_loglik_rhs.R
DDD/R/dd_logliknorm_rhs1.R
DDD/R/dd_MS_loglik.R
DDD/R/bd_loglik.R
DDD/R/td_sim.R
DDD/R/dd_MS_ML.R
DDD/R/dd_loglik_choosepar.R
DDD/R/dd_logliknorm_rhs2.R
DDD/R/dd_KI_sim.R
DDD/R/dd_bootstrap_sim.R
DDD/R/dd_MS_loglik_choosepar.R
DDD/MD5
DDD/DESCRIPTION
DDD/man
DDD/man/dd_SR_loglik.Rd
DDD/man/roundn.Rd
DDD/man/optimizer.Rd
DDD/man/DDD-internal.Rd
DDD/man/bd_ML.Rd
DDD/man/DDD-package.Rd
DDD/man/L2phylo.Rd
DDD/man/sample2.Rd
DDD/man/dd_SR_ML.Rd
DDD/man/dd_KI_ML.Rd
DDD/man/bd_loglik.Rd
DDD/man/dd_MS_sim.Rd
DDD/man/dd_KI_loglik.Rd
DDD/man/dd_SR_sim.Rd
DDD/man/dd_loglik.Rd
DDD/man/dd_ML.Rd
DDD/man/dd_LR.Rd
DDD/man/dd_MS_ML.Rd
DDD/man/dd_MS_loglik.Rd
DDD/man/dd_KI_sim.Rd
DDD/man/dd_sim.Rd