scatter.enfa: Scatter Plot of the Results of the ENFA

Description

Performs the scatter diagrams of objects of class enfa.

Usage

# S3 method for enfa
scatter(x, xax = 1, yax = 2, pts = FALSE, nc = TRUE, 
             percent = 95, clabel = 1, side = c("top", "bottom", "none"),
             Adensity, Udensity, Aangle, Uangle, Aborder, Uborder, 
             Acol, Ucol, Alty, Ulty, Abg, Ubg, Ainch, Uinch, …)

Arguments

an object of class enfa

xax

the column number for the x-axis

yax

the column number for the y-axis

pts

logical. Whether the points should be drawn. If FALSE, minimum convex polygons are displayed

whether or not the niche center should be displayed

percent

100 minus the proportion of outliers to be excluded from the computation of the minimum convex polygons

clabel

a character size for the columns

side

if "top", the legend of the kept axis is upside, if "bottom" it is downside, if "none" no legend

Adensity

the density of shading lines, in lines per inch, for the available pixels polygon. See polygon for more details

Udensity

the density of shading lines, in lines per inch, for the used pixels polygon. See polygon for more details

Aangle

the slope of shading lines, given as an angle in degrees (counter-clockwise), for the available pixels polygon

Uangle

the slope of shading lines, given as an angle in degrees (counter-clockwise), for the used pixels polygon

Aborder

the color for drawing the border of the available pixels polygon. See polygon for more details

Uborder

the color for drawing the border of the used pixels polygon. See polygon for more details

Acol

the color for filling the available pixels polygon. if pts == FALSE, the color for the points corresponding to available pixels

Ucol

the color for filling the used pixels polygon. if pts == FALSE, the color for the points corresponding to used pixels

Alty

the line type for the available pixels polygon, as in par

Ulty

the line type for the used pixels polygon, as in par

Abg

if pts == TRUE, background color for open plot symbols of available pixels

Ubg

if pts == TRUE, background color for open plot symbols of used pixels

Ainch

if pts == TRUE, heigth in inches of the available pixels

Uinch

if pts == TRUE, heigth in inches of the largest used pixels

…

further arguments passed to or from other methods

Details

scatter.enfa displays a factorial map of pixels, as well as the projection of the vectors of the canonical basis multiplied by a constant of rescaling. The kept axes for the plot are specified in a corner.

References

Basille, M., Calenge, C., Marboutin, E., Andersen, R. & Gaillard, J.M. (2008) Assessing habitat selection using multivariate statistics: Some refinements of the ecological-niche factor analysis. Ecological Modelling, 211, 233--240.

Examples

Run this code

# NOT RUN {
data(lynxjura)

map <- lynxjura$map

## We keep only "wild" indices.
locs <- lynxjura$locs
locs <- locs[slot(locs, "data")[,2]!="D",]

hist(map, type = "l")
## The variable artif is far from symetric

## We perform a square root transformation
## of this variable
## We therefore normalize the variable 'artif'
slot(map,"data")[,4] <- sqrt(slot(map,"data")[,4])
hist(map, type = "l")

## We prepare the data for the ENFA
tab <- slot(map, "data")
pr <- slot(count.points(locs, map), "data")[,1]


## We then perform the PCA before the ENFA
pc <- dudi.pca(tab, scannf = FALSE)

## We perform the ENFA
(enfa1 <- enfa(pc, pr, scannf = FALSE))

scatter(enfa1)


# }