get_tree_beta: Beta parameter as a function of the proportion of remaining...

In apTreeshape: Analyses of Phylogenetic Treeshape

Description

Computes the maximum likelihood estimate of the parameter beta in trees simulated by the model, as a function of the proportion of conserved species

Usage

get_tree_beta(epsilon, beta, alpha, N, sampl.frac, ntree, equal.ab = TRUE, eta = 1)

Arguments

epsilon	Minimum size of unsampled splits (see appendix 1)
beta	Imbalance index
alpha	Clade age-richness index
N	Initial tip number
sampl.frac	Vector of tips fractions for which we want to compute the beta statistic
ntree	Number of simulated trees
equal.ab	If set to TRUE, all species have the same probability to go extinct first (default to TRUE)
eta	Clade abundance-richness index (if equal.ab == FALSE)

Value

A table of size length(sample.fract)*ntree. The element in ligne i and column j is the Maximum Likelihood Estimate for the beta statistic of the j^th tree in wich a fraction sample.frac[i] has been sampled.

Author(s)

Odile Maliet, Fanny Gascuel & Amaury Lambert

References

Maliet O., Gascuel F., Lambert A. (2018) Ranked tree shapes, non-random extinctions and the loss of phylogenetic diversity, bioRxiv 224295, doi: https://doi.org/10.1101/224295

Examples

# With the field of bullets hypothesis

set.seed(813)
sampl.frac=seq(0.2,1,0.2)
Beta=get_tree_beta(epsilon=0.01, beta=-1, alpha=-1, N=20, sampl.frac=sampl.frac, ntree=3)

Beta_quantiles=sapply(1:nrow(Beta),function(x){quantile(Beta[x,],c(0.05,0.5,0.95))})

plot(1, type="n", xlab="Fraction of extinct species, p", ylab="Beta statistic", 
      ylim=c(-2,10), xlim=c(0,1))
polygon(c(1-sampl.frac, rev(1-sampl.frac)), c(Beta_quantiles[1,(1:length(sampl.frac))],
        rev(Beta_quantiles[3,(1:length(sampl.frac))])), border=NA, col=grey(0.7))
points(1-sampl.frac, Beta_quantiles[2,(1:length(sampl.frac))],t="l")


# With nonrandom extinctions

## Not run: 
set.seed(813)
sampl.frac=seq(0.2,1,0.2)
Beta=get_tree_beta(epsilon=0.01, beta=5, alpha=2, eta=2, N=20, 
                    sampl.frac=sampl.frac, ntree=3)

Beta_quantiles=sapply(1:nrow(Beta),function(x){quantile(Beta[x,],c(0.05,0.5,0.95))})

plot(1, type="n", xlab="Fraction of extinct species, p", 
      ylab="Beta statistic", ylim=c(-2,10), xlim=c(0,1))
polygon(c(1-sampl.frac, rev(1-sampl.frac)), 
      c(Beta_quantiles[1,(1:length(sampl.frac))], 
      rev(Beta_quantiles[3,(1:length(sampl.frac))])), border=NA, col=grey(0.7))
points(1-sampl.frac, Beta_quantiles[2,(1:length(sampl.frac))],t="l")

## End(Not run)

apTreeshape documentation built on Jan. 8, 2021, 2:07 a.m.