plot_dtt: Plot diversity through time

In hmorlon/PANDA: Phylogenetic ANalyses of DiversificAtion

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

Author(s)

H Morlon

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)

hmorlon/PANDA documentation built on Jan. 13, 2025, 5:35 a.m.