plot_fit_bd: Plot speciation, extinction & net diversification rate...

In RPANDA: Phylogenetic ANalyses of DiversificAtion

Plot speciation, extinction & net diversification rate functions of a fitted model

Description

Plot estimated speciation, extinction & net diversification rates through time

Usage

plot_fit_bd(fit.bd, tot_time)

Arguments

fit.bd	an object of class 'fit.bd', output of the 'fit_bd' function
tot_time	the age of the phylogeny (crown age, or stem age if known). If working with crown ages, tot_time is given by max(node.age(phylo)$ages).

Value

Plots representing how the estimated speciation, extinction & net diversification rate functions vary through time

Author(s)

H Morlon

See Also

fit_bd

Examples

data(Balaenopteridae)
tot_time<-max(node.age(Balaenopteridae)$ages)

# Fit the pure birth model (no extinction) with exponential variation of the speciation rate
# with time
f.lamb <-function(t,y){y[1] * exp(y[2] * t)}
f.mu<-function(t,y){0}
lamb_par<-c(0.08, 0.01)
mu_par<-c()
result <- fit_bd(Balaenopteridae,tot_time,f.lamb,f.mu,lamb_par,mu_par,
                     expo.lamb = TRUE, fix.mu=TRUE)
# plot fitted rates
#plot_fit_bd(result, tot_time)

RPANDA documentation built on Oct. 24, 2022, 5:06 p.m.