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R: Loglikelihood for diversity-dependent diversification models...

dd_KI_loglik

R Documentation

Loglikelihood for diversity-dependent diversification models with decoupling of a subclade from a main clade at time t = t_d

Description

This function computes loglikelihood of a diversity-dependent diversification model for a given set of branching times and parameter values where the diversity-dependent dynamics of a subclade decouple from the dynamics of the main clade at time t_d, potentially accompanied by a shift in parameters.

Usage

dd_KI_loglik(pars1, pars2, brtsM, brtsS, missnumspec, methode = 'analytical')

Arguments

`pars1`	Vector of parameters: `pars1[1]` corresponds to lambda_M (speciation rate) of the main clade `pars1[2]` corresponds to mu_M (extinction rate) of the main clade `pars1[3]` corresponds to K_M (clade-level carrying capacity) of the main clade `pars1[4]` corresponds to lambda_M (speciation rate) of the subclade `pars1[5]` corresponds to mu_S (extinction rate) of the subclade `pars1[6]` corresponds to K_S (clade-level carrying capacity) of the subclade `pars1[7]` corresponds to t_d (the time of decoupling)
`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[4]` sets the time of splitting of the branch that will decouple `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)
`brtsM`	A set of branching times of the main clade in the phylogeny, all positive
`brtsS`	A set of branching times of the subclade in the phylogeny, all positive
`missnumspec`	The number of species that are in the clade but missing in the phylogeny. One can specify the sum of the missing species in main clade and subclade or a vector c(missnumspec_M,missnumspec_S) with missing species in main clade and subclade respectively.
`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

Examples

pars1 = c(0.25,0.12,25.51,1.0,0.16,8.61,9.8)
pars2 = c(200,1,0,18.8,1,2)
missnumspec = 0
brtsM = c(25.2,24.6,24.0,22.5,21.7,20.4,19.9,19.7,18.8,17.1,15.8,11.8,9.7,8.9,5.7,5.2)
brtsS = c(9.6,8.6,7.4,4.9,2.5)
dd_KI_loglik(pars1,pars2,brtsM,brtsS,missnumspec,method = 'ode45')

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/dd_KI_loglik.Rd_%03d_medium.png", width=480, height=480)
> ### Name: dd_KI_loglik
> ### Title: Loglikelihood for diversity-dependent diversification models
> ###   with decoupling of a subclade from a main clade at time t = t_d
> ### Aliases: dd_KI_loglik
> ### Keywords: models
> 
> ### ** Examples
> 
> pars1 = c(0.25,0.12,25.51,1.0,0.16,8.61,9.8)
> pars2 = c(200,1,0,18.8,1,2)
> missnumspec = 0
> brtsM = c(25.2,24.6,24.0,22.5,21.7,20.4,19.9,19.7,18.8,17.1,15.8,11.8,9.7,8.9,5.7,5.2)
> brtsS = c(9.6,8.6,7.4,4.9,2.5)
> dd_KI_loglik(pars1,pars2,brtsM,brtsS,missnumspec,method = 'ode45')
Parameters: 0.250000 0.120000 25.510000 1.000000 0.160000 8.610000 9.800000, Loglikelihood: -77.815687
[1] -77.81569
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>