ausplotsR (version 2.0.5)

plot_opt: Plot a set of species accumulation curves together

Description

This function plots different species accumulation curves obtained through different optimisers in the optim_species function.

Usage

plot_opt(optim_result, choices=c("Richness", "RRR", "CWE", "Shannon", 
  "Simpson", "SimpsonBeta", "Frequent", "SimpsonBeta_randSeed", "Random"))

Value

This function will return a plot of the species cumulative curves obtained by the different optimisers in the optim_species function.

Arguments

optim_result

Object returned from the optim_species function, which is a list of species accumulation objects (see specaccum) obtained with the different optimisers.

choices

select the optimisers from which the species accumulations curves are going to be plotted. The choices can be "Richness", "RRR", "CWE", "Shannon", "Simpson", "SimpsonBeta", "Frequent", "SimpsonBeta_randSeed", "Random"

Author

Greg R. Guerin

Details

Line colours are assigned randomly on each run.

See Also

optim_species

Examples

  #example with dune database from vegan
  library(vegan)
  data(dune)
  
  example1 <- optim_species(dune, n.plt=15, frequent=FALSE, plot=FALSE)
  
  plot_opt(example1)
  plot_opt(example1, choices=c("Richness", "SimpsonBeta"))
      
  #example with auplots database from ausplotsR
  if (FALSE) {
  library(ausplotsR)
  
  ausplotsdata <- get_ausplots(veg.PI=TRUE)
  ausplotsPAdata <- species_table(ausplotsdata$veg.PI, m_kind="PA", 
  species_name="SN")
  
  example2 <- optim_species(ausplotsPAdata, n.plt=5, iterations=5, plot=FALSE)
  plot_opt(example2)
  plot_opt(example2, 
  choices=c("RRR", "SimpsonBeta", "Frequent", "SimpsonBeta_randSeed"))
  }