plot_opt: Plot a set of species accumulation curves together

In ausplotsR: TERN AusPlots Australian Ecosystem Monitoring Data

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"))

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"

Details

Line colours are assigned randomly on each run.

Value

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

Author(s)

Greg R. Guerin

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
  ## Not run: 
  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"))
  
## End(Not run)

ausplotsR documentation built on Nov. 17, 2023, 9:06 a.m.