R: Loglikelihood for diversity-dependent diversification models...
dd_SR_loglik
R Documentation
Loglikelihood for diversity-dependent diversification models with a shift in the parameters at time t = tshift
Description
This function computes loglikelihood of a diversity-dependent diversification model
for a given set of branching times and parameter values where the parameters are allowed to shift at time t = tshift
pars1[1] corresponds to lambda (speciation rate) before the shift pars1[2] corresponds to mu (extinction rate) before the shift pars1[3] corresponds to K (clade-level carrying capacity) before the shift pars1[4] corresponds to lambda (speciation rate) after the shift pars1[5] corresponds to mu (extinction rate) after the shift pars1[6] corresponds to K (clade-level carrying capacity) after the shift pars1[7] corresponds to tshift (the time of shift)
pars2
Vector of model settings:
pars2[1] sets the maximum number of species for which a probability must be computed.
This must be larger than 1 + missnumspec + length(brts).
pars2[2] sets the model of diversity-dependence:
- pars2[2] == 1 linear dependence in speciation rate with parameter K (= diversity where speciation = extinction)
- pars2[2] == 1.3 linear dependence in speciation rate with parameter K' (= diversity where speciation = 0)
- pars2[2] == 2 exponential dependence in speciation rate with parameter K (= diversity where speciation = extinction)
- pars2[2] == 2.1 variant of exponential dependence in speciation rate with offset at infinity
- pars2[2] == 2.2 1/n dependence in speciation rate
- pars2[2] == 2.3 exponential dependence in speciation rate with parameter x (= exponent)
- pars2[2] == 3 linear dependence in extinction rate
- pars2[2] == 4 exponential dependence in extinction rate
- pars2[2] == 4.1 variant of exponential dependence in extinction rate with offset at infinity
- pars2[2] == 4.2 1/n dependence in extinction rate
pars2[3] sets the conditioning:
- pars2[3] == 0 no conditioning
- pars2[3] == 1 conditioning on non-extinction of the phylogeny
- pars2[3] == 2 conditioning on non-extinction of the phylogeny and on the total number of extant taxa (including missing species)
pars2[4] sets whether the likelihood is for the branching times (0) or the phylogeny (1)
pars2[5] sets whether the parameters and likelihood should be shown on screen (1) or not (0)
pars2[6] 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 'analytical' which uses matrix exponentiation; alternatively numerical ODE solvers can be used, such as 'lsoda' or 'ode45'. These were used in the package before version 3.1.
Value
The loglikelihood
Author(s)
Rampal S. Etienne & Bart Haegeman
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
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/dd_SR_loglik.Rd_%03d_medium.png", width=480, height=480)
> ### Name: dd_SR_loglik
> ### Title: Loglikelihood for diversity-dependent diversification models
> ### with a shift in the parameters at time t = tshift
> ### Aliases: dd_SR_loglik
> ### Keywords: models
>
> ### ** Examples
> dd_SR_loglik(pars1 = c(0.2,0.1,50,0.2,0.1,70,5), pars2 = c(100,1,1,1,0,2),
+ brts = 1:10, missnumspec = 0)
[1] -27.37304
>
>
>
>
> dev.off()
null device
1
>