scatter.enfa {adehabitat}R Documentation

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 basille@biomserv.univ-lyon1.fr

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.
tmp <- lynxjura$locs[,4]!="D"
locs <- lynxjura$locs[tmp, c("X","Y")]

## We perform a square root transformation
## of the variable to normalize it
map[,4] <- sqrt(map[,4])

## We perform the ENFA
tmp <- data2enfa(map, locs[tmp, c("X","Y")])
(enfa1 <- enfa(dudi.pca(tmp$tab, scannf=FALSE),
               tmp$pr, scannf = FALSE))
scatter(enfa1)


[Package adehabitat version 1.8.2 Index]