plot.betaper {betaper}R Documentation

Plot of distance decay of similarity among floristic inventories in the face of taxonomic uncertainty

Description

Plot of maximum and minimum correlation bounds between floristic and geographical or environmental distances under simulated scenarios of species identities in the face of taxonomic uncertainty

Usage

plot.betaper(x, xlab = "Distances (km)", ylab = "Sorensen's similarity index", pch = c(18, 3), ...)

Arguments

x a betaper object.
xlab x-axis label.
ylab y-axis label.
pch A vector of the form c(x1, x2) specifying a symbol or a single character to represent the points that minimize and maximize the correlation between floristic and geographical or environmental distances.
... any other graphical parameter.

Details

This plot function produces a quick, standard plot with estimated minimum and maximum correlation bounds between floristic and geographical or environmental distances.

Author(s)

Luis Cayuela luis.cayuela@uah.es and Marcelino de la Cruz marcelino.delacruz@upm.es

See Also

betaper

Examples

## Not run: 
require(vegan)
################################################
# Tree data from 16 0.1-ha plots from the Highlands of Chiapas, southern Mexico

data(HCP)
data(HCP.coords)

geodist.HCP <- dist(HCP.coords)/1000    # Geographical distances in kms

# Define a new index that includes the terms used in the HCPdataset to define undetermined taxa at genus and family levels
index.new <- c(paste("Genus", as.character(c(1:20)), sep=""), paste("Family", as.character(c(1:20)), sep=""))

beta.HCP <- betaper(HCP, geodist = geodist.HCP, index = index.new)
beta.HCP        # This results in a relatively low uncertainty range of the estimated correlation
beta.HCP$taxunc # Number of identified and unidentified species at different taxonomic levels

plot(beta.HCP)

################################################
# Tree data from nine lowland sites in Western Amazonia

data(Amazonia)
data(soils)

# Define a new index that includes the terms used in the Amazonia dataset to define undetermined taxa at different taxonomic levels
index.Amazon <- c(paste("sp.", rep(1:20), sep=""), "Indet.", "indet.")

beta.Amazonia <- betaper(Amazonia, geodist = dist(log(soils)), index = index.Amazon, nsim = 50) # This can take a few minutes
beta.Amazonia   # The uncertainty range of the estimated correlation is much larger than in the previous example
beta.Amazonia$taxunc    # Number of identified and unidentified species at different taxonomic levels

plot(beta.Amazonia)
  ## End(Not run)

[Package betaper version 1.0-0 Index]