score.coa: Reciprocal scaling after a correspondence analysis

In ade4: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

Reciprocal scaling after a correspondence analysis

Description

performs the canonical graph of a correspondence analysis.

Usage

## S3 method for class 'coa'
score(x, xax = 1, dotchart = FALSE, clab.r = 1, clab.c = 1, 
    csub = 1, cpoi = 1.5, cet = 1.5, ...)
reciprocal.coa(x)

Arguments

x	an object of class coa
xax	the column number for the used axis
dotchart	if TRUE the graph gives a "dual scaling", if FALSE a "reciprocal scaling"
clab.r	a character size for row labels
clab.c	a character size for column labels
csub	a character size for the sub-titles, used with par("cex")*csub
cpoi	a character size for the points
cet	a coefficient for the size of segments in standard deviation
...	further arguments passed to or from other methods

Details

In a "reciprocal scaling", the reference score is a numeric code centred and normalized of the non zero cells of the array which both maximizes the variance of means by row and by column. The bars are drawn with half the length of this standard deviation.

Value

return a data.frame with the scores, weights and factors of correspondences (non zero cells)

Author(s)

Daniel Chessel

References

Thioulouse, J. and Chessel D. (1992) A method for reciprocal scaling of species tolerance and sample diversity. Ecology, 73, 670–680.

Examples

layout(matrix(c(1,1,2,3), 2, 2), resp = FALSE)
data(aviurba)
dd1 <- dudi.coa(aviurba$fau, scan = FALSE)
score(dd1, clab.r = 0, clab.c = 0.75)
recscal <- reciprocal.coa(dd1)
head(recscal)
abline(v = 1, lty = 2, lwd = 3)
sco.distri(dd1$l1[,1], aviurba$fau)
sco.distri(dd1$c1[,1], data.frame(t(aviurba$fau)))

# 1 reciprocal scaling correspondence score -> species amplitude + sample diversity
# 2 sample score -> averaging -> species amplitude
# 3 species score -> averaging -> sample diversity

layout(matrix(c(1,1,2,3), 2, 2), resp = FALSE)
data(rpjdl)
rpjdl1 <- dudi.coa(rpjdl$fau, scan = FALSE)
score(rpjdl1, clab.r = 0, clab.c = 0.75)
if (requireNamespace("MASS", quietly = TRUE)) {
   data(caith, package = "MASS")
   score(dudi.coa(caith, scan = FALSE), clab.r = 1.5, clab.c = 1.5, cpoi = 3)
   data(housetasks)
   score(dudi.coa(housetasks, scan = FALSE), clab.r = 1.25, clab.c = 1.25, 
        csub = 0, cpoi = 3)
}
par(mfrow = c(1,1))
score(rpjdl1, dotchart = TRUE, clab.r = 0)

ade4 documentation built on Feb. 16, 2023, 7:58 p.m.