rlq {ade4}R Documentation

RLQ analysis

Description

RLQ analysis performs a double inertia analysis of two arrays (R and Q) with a link expressed by a contingency table (L). The rows of L correspond to the rows of R and the columns of Q correspond to the rows of Q. RLQ analysis is an extension of coinertia analysis (see as.coinertia function).

Usage

rlq(dudiR, dudiL, dudiQ, scannf = TRUE, nf = 2)
print.rlq(x, ...)
plot.rlq(x, xax = 1, yax = 2, ...)
summary.rlq(object, ...)
as.coinertia (dudiRLQ, fixed="R")
randtest.rlq(xtest,nrepet = 999, ...)

Arguments

dudiR a duality diagram providing from one of the functions dudi.hillsmith, dudi.pca, ...
dudiL a duality diagram of the function dudi.coa
dudiQ a duality diagram providing from one of the functions dudi.hillsmith, dudi.pca, ...
scannf a logical value indicating whether the eigenvalues bar plot should be displayed
nf if scannf FALSE, an integer indicating the number of kept axes
x an rlq object
xax the column number for the x-axis
yax the column number for the y-axis
dudiRLQ an rlq object
object an rlq object
fixed "R" indicates that dudiR is not modified, otherwise "Q"
xtest an rlq object
nrepet the number of permutations
... further arguments passed to or from other methods

Value

Returns a list of class 'dudi', sub-class 'rlq' containing:

call call
rank rank
nf a numeric value indicating the number of kept axes
RV a numeric value, the RV coefficient
eig a numeric vector with all the eigenvalues
lw a numeric vector with the rows weigths (crossed array)
cw a numeric vector with the columns weigths (crossed array)
tab a crossed array (CA)
li R col = CA row: coordinates
l1 R col = CA row: normed scores
co Q col = CA column: coordinates
c1 Q col = CA column: normed scores
lR the row coordinates (R)
mR the normed row scores (R)
lQ the row coordinates (Q)
mQ the normed row scores (Q)
aR the axis onto co-inertia axis (R)
aQ the axis onto co-inertia axis (Q)

WARNING

IMPORTANT : row weights for dudiR and dudiQ must be taken from dudiL.

Note

as.coinertia transforms a rlq object into a coinertia object but user must specify which dudi is fixed and not modified.

Author(s)

Stephane Dray dray@biomserv.univ-lyon1.fr

References

Doledec, S., Chessel, D., ter Braak, C.J.F. and Champely, S. (1996) Matching species traits to environmental variables: a new three-table ordination method. Environmental and Ecological Statistics, 3, 143–166.

Dray, S., Pettorelli, N., Chessel, D. (2002) Matching data sets from two different spatial samplings. Journal of Vegetation Science, 13, 867–874.

See Also

coinertia

Examples

data(aviurba)
   coa1 <- dudi.coa(aviurba$fau, scannf = FALSE, nf = 2)
   dudimil <- dudi.hillsmith(aviurba$mil, scannf = FALSE, nf = 2, row.w = coa1$lw)
   duditrait <- dudi.hillsmith(aviurba$traits, scannf = FALSE, nf = 2, row.w = coa1$cw)
   rlq1 <- rlq(dudimil, coa1, duditrait, scannf = FALSE, nf = 2)
   plot(rlq1)
   summary(rlq1)
   randtest.rlq(rlq1)

[Package ade4 version 1.3-3 Index]