geo2envpca: Interactive plot to explore points in geographical and environmental space

Description

An interactive plot with options to select to explore points in the geographical or environmental space. The environmental space is defined by the values of two principal components from a principal components analysis on several environmental variables.

Usage

geo2envpca(edat, g1, group1 = "Species", group2 = "", 
world, scaling = 1, vars = c("AMT", "AP", "MTCM", "MTWM", 
"PWQ", "PCQ"), showrecord = "", ext = c(-180, 180, -60, 90))

Arguments

edat

a dataframe containing fields with the following names: ID, x, y, Species, x_original, y_original, Correction, Modified, Exclude and the values of selected environmental variables

the name of the species to select

group1

this is usually the column of species names

group2

a second grouping variable

world

a shapefile of the world, where the column containing the country names must be "NAMES"; see data(wrld_simpl)

scaling

a value of 1 or 2 for the type of scaling of the PCA space

vars

a character vector of environmental variable names that will be used to define the environmental space. Values of these variables must be present in edat.

showrecord

the ID of a selected record to be shown on the map

ext

The extent, which can be specified as c(xmin, xmax, ymin, ymax) default extent c(-180, 180, -90, 90). Alternatively if ext="p" then the extent will be calculated from the coordinates of the points in the dataset.

Value

Details

The selected records are marked with a red dot and ID numbers are shown. Records that are considered to be outliers can be excluded by selecting the record in the environmental space. A menu with various options is produced.

Examples

Run this code

## Not run: 
# plotsetup(6,6)
# ed<-geo2envpca(edat,"Species U",group1="Species",group2="",
# world,scaling=1,vars=c("bio1","bio12","bio5","bio6","bio14"),
# showrecord="1981",ext="p")## End(Not run)