ade4 (version 1.2-2)

rlq: 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, RV = TRUE, ...)

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"

RV

a logical value indicating whether the test is based on RV or inertia

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.

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)