biodecrypt.plot: Plotting biodecrypt and biodecrypt.cross results.

In leondap/recluster: Ordination Methods for the Analysis of Beta-Diversity Indices

Plotting biodecrypt and biodecrypt.cross results.

Description

The function plots the results of biodecrypt and biodecrypt.cross analyses. It provides plot with circles with different colours to identify different kinds of records. Records known a priori can be distinguished in the plot from records attributed by biodecrypt as likely belonging to a given species or as NUR (or MIR and NIR in biodecrypt.cross).

Usage

biodecrypt.plot(x,minsize=0.3,pchid=1,cexid=0.1,square=0.001,col=c("red","darkgreen",
"blue","purple"), attributed=c("fade","points"), NUR="black", fading=50, ... )

Arguments

x	An object obtained by biodecrypt or biodecrypt.cross
minsize	The size of the dots to be plotted.
pchid	The pch of the points marking known cases in case when attributed="points".
cexid	The size of the points marking known cases in case when attributed="points".
square	The size of square grid to which occurrence are collapsed and organized in pies. If the value is lower than data resolution then records are not grouped in pies.
col	The colours to be attributed to species: 1...n.
attributed	The method to plot known records. Using attributed="fade" will make the attributed dots paler than known cases based on fading (see below). Using attributed="points" will plot a balck dot to distinguish known cases.
NUR	The colour for NUR records after biodecrypt.
fading	The degree of fading for the colours of records attributed by biodecrypt if attributed="fading" (100 makes the points white).
...	other parameters of the default plot

Details

The function adds dots to a previous plot (usually a map). The records with a priori known attribution (1...n in id) are marked with a point inside the dots ( attributed="points") or by fading the colour of the dots for the records that have been attributed by biodecrypt (attributed="fading"). In the results of biodecrypt.cross, MIR are represented as black dots and NIR as white dots. For biodecrypt black default colour for NUR can be changed.

Value

a plot

Author(s)

Leonardo Dapporto

References

Platania L. et al. Assigning occurrence data to cryptic taxa improves climatic niche assessments: biodecrypt, a new tool tested on European butterflies. Glocal Ecology and Biogeography (2020).

Examples

	#See examples in biodecrypt and biodecrypt.cross

leondap/recluster documentation built on Nov. 11, 2024, 7:11 a.m.