rlq {ade4} | R Documentation |
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).
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, ...)
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 |
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) |
IMPORTANT : row weights for dudiR
and dudiQ
must be taken from dudiL
.
as.coinertia
transforms a rlq
object into a coinertia
object but user must specify which dudi
is fixed and not modified.
Stephane Dray dray@biomserv.univ-lyon1.fr
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.
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)