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

In hmorlon/PANDA: Phylogenetic ANalyses of DiversificAtion

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

Description

Plot estimated speciation, extinction & net diversification rates as a function of the environmental data and time

Usage

plot_fit_env(fit.env, env_data, tot_time)

Arguments

fit.env	an object of class 'fit.env', output of the 'fit_env' function
env_data	environmental data, given as a data frame with two columns. The first column is time, the second column is the environmental data (temperature for instance).
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 as a function of the environmental data & time

Author(s)

H Morlon and FL Condamine

See Also

fit_env

Examples

if(require(pspline)){
data(Balaenopteridae)
tot_time<-max(node.age(Balaenopteridae)$ages)
data(InfTemp)
dof<-smooth.spline(InfTemp[,1], InfTemp[,2])$df

# Fit the pure birth model (no extinction) with exponential variation of the speciation rate
# with temperature. 
f.lamb <-function(t,x,y){y[1] * exp(y[2] * x)}
f.mu<-function(t,x,y){0}
lamb_par<-c(0.10, 0.01)
mu_par<-c()
result <- fit_env(Balaenopteridae,InfTemp,tot_time,f.lamb,f.mu,
      lamb_par,mu_par,f=1, fix.mu=TRUE, df=dof, dt=1e-3)

# plot fitted rates
plot_fit_env(result, InfTemp, tot_time)
    }
  

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