plot.betaper {betaper} | R Documentation |
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
plot.betaper(x, xlab = "Distances (km)", ylab = "Sorensen's similarity index", pch = c(18, 3), ...)
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. |
This plot function produces a quick, standard plot with estimated minimum and maximum correlation bounds between floristic and geographical or environmental distances.
Luis Cayuela luis.cayuela@uah.es and Marcelino de la Cruz marcelino.delacruz@upm.es
## 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)