DDD (version 0.4)

DDD-package: Diversity dependent diversification

Description

This package is a likelihood-based statistical package to estimate parameters under diversity-dependent diversification models. New in version 0.3: - Models with shifts in the parameters at a time tshift. New in version 0.4: - Bug fix of prefactor in likelihood - bug did not affect parameter estimates. - There is an option to condition or not on non-extinction of the phylogeny. - The functions dd_loglik and dd_SR_loglik now accept untransformed parameters; the transformation is done in the auxiliary functions. - Improved help pages. - Auxiliary functions no longer in help pages

Details

ll{ Package: DDD Type: Package Version: 0.4 Date: 2012-02-09 License: GPL 2.0 } dd_loglik computes the likelihood of any of 4 different models of diversity-dependent diversification, given a set of parameters and a data set of phylogenetic branching times. dd_ML finds the parameters that maximizes the likelihood computed by dd_loglik. dd_SR_loglik is the same as dd_loglik except that it allows a shift in the parameters at time tshift. dd_SR_ML finds the parameters that maximizes the likelihood computed by dd_SR_loglik.

References

Etienne et al. 2011, Proc. Roy. Soc. B, doi: 10.1098/rspb.2011.1439

See Also

laser

Examples

cat("Estimate the parameters of the diversity-dependent model")
cat("for a set of branching times:")
brts = 1:20
dd_ML(brts)

cat("Estimating the parameters of the diversity-dependent model with shiftting rates")
cat("for a set of branching times brts with the default settings:")
brts = 1:20
dd_SR_ML(brts)