initparsoptdefault

parsfixdefault

dd_loglik1

dd_loglik2

dd_loglik_choosepar

bd_loglik_choosepar

dd_SR_loglik1

dd_SR_loglik2

dd_SR_loglik_choosepar

dd_KI_loglik1

dd_KI_loglik2

dd_KI_loglik_choosepar

dd_MS_loglik1

dd_MS_loglik2

dd_MS_loglik_choosepar

dd_loglik_rhs

dd_loglik_M

dd_loglik_M_bw

dd_loglik_M_aux

dd_loglik_M_bw_aux

dd_loglik_M2

dd_loglik_M2_aux

dd_loglik_M3

dd_loglik_M3_aux

dd_KI_loglikold

dd_loglik_bw_rhs

dd_logliknorm_rhs1

dd_logliknorm_rhs2

dd_logliknorm_rhs3

td_loglik_rhs

td_loglik_bw_rhs

td_loglik_rhs_sim

td_sim

dd_simplex

bd_simplex

dd_SR_simplex

dd_KI_simplex

dd_MS_simplex

brts2phylo

conv

flavec

lambdamu

lambdamu2

lambdamu3

expn_dd_sp

predictsp

expn_dd

lamu_dd_td

dd_lamuN

dd_MS_lamuN

dd_KI_lamuN

dd_bootstrap_sim

simplex

changepars

expfun

logH

logLL

dd_loglik_test

dd_integrate

dd_ode_FORTRAN

dd_loglik_rhs_precomp

fill1d

initmod

runmod

runmodbw

internal

DDD-internal


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.

DDD-internal: Internal DDD Functions

Description

Arguments

Details