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

In adehabitatHS: Analysis of Habitat Selection by Animals

Scatter Plot of the Results of the ENFA

Description

Performs the scatter diagrams of objects of class enfa.

Usage

## S3 method for class '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

x	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
nc	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.

Author(s)

Mathieu Basille [e-mail]

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.

See Also

enfa, scatter

Examples

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)

adehabitatHS documentation built on Sept. 11, 2024, 7:38 p.m.