ade4 (version 1.7-8)

score.coa: Reciprocal scaling after a correspondence analysis

Description

performs the canonical graph of a correspondence analysis.

Usage

# S3 method for 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

Value

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

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.

References

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

Examples

# NOT RUN {
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(MASS::caith)
   score(dudi.coa(MASS::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)
# }