DDD: Diversity-Dependent Diversification

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.

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

View on CRAN

Functions

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.