RPANDA (version 1.2)

plot_dtt: Plot diversity through time

Description

Plot the estimated number of species through time

Usage

plot_dtt(fit.bd, tot_time, N0)

Arguments

fit.bd

an object of class 'fit.bd', output of the 'fit_bd' function

tot_time

the age of the underlying phylogeny (crown age, or stem age if known). If working with crown ages, tot_time is given by max(node.age(phylo)$ages).

N0

number of extant species. If all extant species are represented in the phylogeny, N0 is given by length(phylo$tip.label)

Value

Plot representing how the estimated number of species vary through time

References

Morlon, H., Parsons, T.L. and Plotkin, J.B. (2011) Reconciling molecular phylogenies with the fossil record Proc Nat Acad Sci 108: 16327-16332 Morlon, H. (2014) Phylogenetic approaches for studying diversification, Eco Lett 17:508-525

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,f=1,
                     expo.lamb = TRUE, fix.mu=TRUE)

# plot estimated number of species through time
# plot_dtt(result, tot_time, N0=9)