R: Function to simulate the macro-evolutionary succession...
dd_MS_sim
R Documentation
Function to simulate the macro-evolutionary succession process assuming diversity-dependent diversification
Description
Simulating a diversity-dependent diversification process where at a given time a new clade emerges with different inherent speciation rate and extinction rate
Usage
dd_MS_sim(pars, age, ddmodel = 1.3)
Arguments
pars
Vector of parameters:
pars[1] corresponds to lambda_M (speciation rate of the main clade) pars[2] corresponds to mu_M (extinction rate of the main clade) pars[3] corresponds to K' (maximum number of species or a proxy for it in case of exponential decline in speciation rate)
pars[4] corresponds to lambda_S (speciation rate of the novel subclade) pars[5] corresponds to mu_S (extinction rate) pars[6] tinn, the time the shift in rates occurs in the lineage leading to the subclade
age
Sets the crown age for the simulation
ddmodel
Sets the model of diversity-dependence: ddmodel == 1.3 : linear dependence in speciation rate with parameter K' (= diversity where speciation = 0); ddmodel = 1 will be interpreted as this model ddmodel == 2.1 : variant of exponential dependence in speciation rate with offset at infinity; ddmodel = 2 will be interpreted as this model ddmodel == 2.2 : 1/n dependence in speciation rate ddmodel == 2.3 : exponential dependence in speciation rate with parameter x (= exponent)
Value
out
A list with the following elements:
The first element is the tree of extant species in phylo format
The second element is the tree of all species, including extinct species, in phylo format
The third element is a matrix of all species where
- the first column is the time at which a species is born
- the second column is the label of the parent of the species; positive and negative values only indicate whether the species belongs to the left or right crown lineage
- the third column is the label of the daughter species itself; positive and negative values only indicate whether the species belongs to the left or right crown lineage
- the fourth column is the time of extinction of the species
If the fourth element equals -1, then the species is still extant.
- the fifth column indicates whether the species belong to the main clade (0) or the subclade (1)
The fourth element is the subclade tree of extant species (without stem)
The fifth element is the subclade tree of all species (without stem)
The sixth element is the same as the first, except that it has attributed 0 for the main clade and 1 for the subclade
The seventh element is the same as the Second, except that it has attributed 0 for the main clade and 1 for the subclade
The sixth and seventh element will be NULL if the subclade does not exist (because it went extinct).
Author(s)
Rampal S. Etienne
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
dd_MS_sim(c(0.2,0.1,20,0.1,0.05,4),10)
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)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> 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_MS_sim.Rd_%03d_medium.png", width=480, height=480)
> ### Name: dd_MS_sim
> ### Title: Function to simulate the macro-evolutionary succession process
> ### assuming diversity-dependent diversification
> ### Aliases: dd_MS_sim
> ### Keywords: models
>
> ### ** Examples
> dd_MS_sim(c(0.2,0.1,20,0.1,0.05,4),10)
$tes
Phylogenetic tree with 5 tips and 4 internal nodes.
Tip labels:
[1] "t1" "t6" "t4" "t5" "t3"
Rooted; includes branch lengths.
$tas
Phylogenetic tree with 7 tips and 6 internal nodes.
Tip labels:
t1, t7, t6, t4, t5, t2, ...
Rooted; includes branch lengths.
$L
[,1] [,2] [,3] [,4] [,5]
[1,] 10.000000 0 -1 -1.0000000 0
[2,] 10.000000 -1 2 8.5270740 0
[3,] 9.976752 2 3 -1.0000000 0
[4,] 6.684524 -1 -4 -1.0000000 1
[5,] 1.870183 -4 -5 -1.0000000 1
[6,] 1.547025 -1 -6 -1.0000000 0
[7,] 1.319253 -1 -7 0.6245083 0
$tesS
Phylogenetic tree with 2 tips and 1 internal nodes.
Tip labels:
[1] "t4" "t5"
Rooted; includes branch lengths.
$tasS
Phylogenetic tree with 2 tips and 1 internal nodes.
Tip labels:
[1] "t4" "t5"
Rooted; includes branch lengths.
$tes2
Phylogenetic tree with 5 tips and 4 internal nodes.
Tip labels:
[1] "t1" "t6" "t4" "t5" "t3"
The tree includes a mapped, 2-state discrete character with states:
0, 1
Rooted; includes branch lengths.
$tas2
Phylogenetic tree with 7 tips and 6 internal nodes.
Tip labels:
t1, t7, t6, t4, t5, t2, ...
The tree includes a mapped, 2-state discrete character with states:
0, 1
Rooted; includes branch lengths.
>
>
>
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> dev.off()
null device
1
>
providing 
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