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R: Loglikelihood for diversity-independent diversification model

bd_loglik

R Documentation

Loglikelihood for diversity-independent diversification model

Description

This function computes loglikelihood of a diversity-independent diversification model for a given set of branching times and parameter values.

Usage

bd_loglik(pars1, pars2, brts, missnumspec, methode = 'lsoda')

Arguments

`pars1`	Vector of parameters: `pars1[1]` corresponds to lambda0 (speciation rate) `pars1[2]` corresponds to mu0 (extinction rate) `pars1[3]` corresponds to lambda1 (decline parameter in speciation rate) or K in diversity-dependence-like models `pars1[4]` corresponds to mu1 (decline parameter in extinction rate)
`pars2`	Vector of model settings: `pars2[1]` sets the model of time-dependence: - `pars2[1] == 0` no time dependence - `pars2[1] == 1` speciation and/or extinction rate is exponentially declining with time - `pars2[1] == 2` stepwise decline in speciation rate as in diversity-dependence without extinction - `pars2[1] == 3` decline in speciation rate following deterministic logistic equation for ddmodel = 1 - `pars2[1] == 4` decline in speciation rate such that the expected number of species matches with that of ddmodel = 1 with the same mu `pars2[2]` sets the conditioning: - `pars[2] == 0` conditioning on stem or crown age - `pars[2] == 1` conditioning on stem or crown age and non-extinction of the phylogeny - `pars[2] == 2` conditioning on stem or crown age and on the total number of extant taxa (including missing species) - `pars[2] == 3` conditioning on the total number of extant taxa (including missing species) `pars2[3]` sets whether the likelihood is for the branching times (0) or the phylogeny (1) `pars2[4]` sets whether the parameters and likelihood should be shown on screen (1) or not (0) `pars2[5]` sets whether the first data point is stem age (1) or crown age (2)
`brts`	A set of branching times of a phylogeny, all positive
`missnumspec`	The number of species that are in the clade but missing in the phylogeny
`methode`	The method used to solve the master equation, default is 'lsoda'.

Value

The loglikelihood

Author(s)

Rampal S. Etienne, Bart Haegeman & Cesar Martinez

References

- Etienne, R.S. et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, doi: 10.1098/rspb.2011.1439
- Etienne, R.S. & B. Haegeman 2012. Am. Nat. 180: E75-E89, doi: 10.1086/667574

Examples

bd_loglik(pars1 = c(0.5,0.1), pars2 = c(0,1,1,0,2), brts = 1:10, missnumspec = 0)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(DDD)
Loading required package: deSolve

Attaching package: 'deSolve'

The following object is masked from 'package:graphics':

    matplot

Loading required package: ape
Loading required package: ade4
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/DDD/bd_loglik.Rd_%03d_medium.png", width=480, height=480)
> ### Name: bd_loglik
> ### Title: Loglikelihood for diversity-independent diversification model
> ### Aliases: bd_loglik
> ### Keywords: models
> 
> ### ** Examples
> bd_loglik(pars1 = c(0.5,0.1), pars2 = c(0,1,1,0,2), brts = 1:10, missnumspec = 0) 
[1] -35.86764
> 
> 
> 
> 
> dev.off()
null device 
          1 
>