rTraitDisc: Discrete Character Simulation

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/rTrait.R

Description

This function simulates the evolution of a discrete character along a phylogeny. If model is a character or a matrix, evolution is simulated with a Markovian model; the transition probabilities are calculated for each branch with P = e^{Qt} where Q is the rate matrix given by model and t is the branch length. The calculation is done recursively from the root. See Paradis (2006, p. 101) for a general introduction applied to evolution.

Usage

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rTraitDisc(phy, model = "ER", k = if (is.matrix(model)) ncol(model) else 2,
           rate = 0.1, states = LETTERS[1:k], freq = rep(1/k, k),
           ancestor = FALSE, root.value = 1, ...)

Arguments

phy

an object of class "phylo".

model

a character, a square numeric matrix, or a function specifying the model (see details).

k

the number of states of the character.

rate

the rate of change used if model is a character; it is not recycled if model = "ARD" of model = "SYM".

states

the labels used for the states; by default “A”, “B”, ...

freq

a numeric vector giving the equilibrium relative frequencies of each state; by default the frequencies are equal.

ancestor

a logical value specifying whether to return the values at the nodes as well (by default, only the values at the tips are returned).

root.value

an integer giving the value at the root (by default, it's the first state). To have a random value, use root.value = sample(k).

...

further arguments passed to model if it is a function.

Details

There are three possibilities to specify model:

Value

A factor with names taken from the tip labels of phy. If ancestor = TRUE, the node labels are used if present, otherwise, “Node1”, “Node2”, etc.

Author(s)

Emmanuel Paradis

References

Paradis, E. (2006) Analyses of Phylogenetics and Evolution with R. New York: Springer.

See Also

rTraitCont, rTraitMult, ace

Examples

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data(bird.orders)
### the two followings are the same:
rTraitDisc(bird.orders)
rTraitDisc(bird.orders, model = matrix(c(0, 0.1, 0.1, 0), 2))

### two-state model with irreversibility:
rTraitDisc(bird.orders, model = matrix(c(0, 0, 0.1, 0), 2))

### simple two-state model:
tr <- rcoal(n <- 40, br = runif)
x <- rTraitDisc(tr, ancestor = TRUE)
plot(tr, show.tip.label = FALSE)
nodelabels(pch = 19, col = x[-(1:n)])
tiplabels(pch = 19, col = x[1:n])

### an imaginary model with stasis 0.5 time unit after a node, then
### random evolution:
foo <- function(x, l) {
    if (l < 0.5) return(x)
    sample(2, size = 1)
}
tr <- rcoal(20, br = runif)
x <- rTraitDisc(tr, foo, ancestor = TRUE)
plot(tr, show.tip.label = FALSE)
co <- c("blue", "yellow")
cot <- c("white", "black")
Y <- x[1:20]
A <- x[-(1:20)]
nodelabels(A, bg = co[A], col = cot[A])
tiplabels(Y, bg = co[Y], col = cot[Y])

Example output

Struthioniformes     Tinamiformes      Craciformes      Galliformes 
               A                A                B                B 
    Anseriformes    Turniciformes       Piciformes    Galbuliformes 
               A                B                A                B 
  Bucerotiformes      Upupiformes    Trogoniformes    Coraciiformes 
               B                B                A                A 
     Coliiformes     Cuculiformes   Psittaciformes      Apodiformes 
               A                B                B                A 
  Trochiliformes  Musophagiformes     Strigiformes    Columbiformes 
               A                A                B                A 
      Gruiformes    Ciconiiformes    Passeriformes 
               B                A                B 
Levels: A B
Struthioniformes     Tinamiformes      Craciformes      Galliformes 
               B                B                B                B 
    Anseriformes    Turniciformes       Piciformes    Galbuliformes 
               B                B                A                A 
  Bucerotiformes      Upupiformes    Trogoniformes    Coraciiformes 
               B                A                A                A 
     Coliiformes     Cuculiformes   Psittaciformes      Apodiformes 
               B                B                B                B 
  Trochiliformes  Musophagiformes     Strigiformes    Columbiformes 
               B                A                B                B 
      Gruiformes    Ciconiiformes    Passeriformes 
               A                B                B 
Levels: A B
Struthioniformes     Tinamiformes      Craciformes      Galliformes 
               B                B                B                B 
    Anseriformes    Turniciformes       Piciformes    Galbuliformes 
               B                B                A                B 
  Bucerotiformes      Upupiformes    Trogoniformes    Coraciiformes 
               A                B                A                B 
     Coliiformes     Cuculiformes   Psittaciformes      Apodiformes 
               B                B                B                B 
  Trochiliformes  Musophagiformes     Strigiformes    Columbiformes 
               B                B                A                A 
      Gruiformes    Ciconiiformes    Passeriformes 
               B                A                A 
Levels: A B

ape documentation built on Sept. 24, 2018, 9:03 a.m.