wrda {douconca} | R Documentation |
Performs a weighted redundancy analysis
Description
wrda
is formula-based implementation of weighted redundancy analysis.
Usage
wrda(
formula,
response = NULL,
data,
weights = rep(1/nrow(data), nrow(data)),
traceonly = FALSE,
cca_object = NULL,
object4QR = NULL
)
Arguments
formula |
one or two-sided formula for the rows (samples) with row
predictors in |
response |
matrix or data frame of the abundance data (dimension
n x m). Rownames of |
data |
matrix or data frame of the row predictors, with rows
corresponding to those in |
weights |
row weights (a vector). If not specified unit weights are used. |
traceonly |
logical, default |
cca_object |
a vegan-type cca-object of transposed
|
object4QR |
a vegan-type cca-object with weighted QR's for
|
Details
The algorithm is a modified version of published R-code for weighted redundancy analysis (ter Braak, 2022).
Compared to rda
, wrda
does not have residual
axes, i.e. no SVD or PCA of the residuals is performed.
Value
All scores in the wrda
object are in scaling "sites"
(1):
the scaling with Focus on Case distances.
References
ter Braak C.J.F. and P. Ć milauer (2018). Canoco reference manual and user's guide: software for ordination (version 5.1x). Microcomputer Power, Ithaca, USA, 536 pp.
Oksanen, J., et al. (2022) vegan: Community Ecology Package. R package version 2.6-4. https://CRAN.R-project.org/package=vegan.
See Also
scores.wrda
, anova.wrda
,
print.wrda
Examples
data("dune_trait_env")
# rownames are carried forward in results
rownames(dune_trait_env$comm) <- dune_trait_env$comm$Sites
response <- dune_trait_env$comm[, -1] # must delete "Sites"
w <- rep(1, 20)
w[1:10] <- 8
w[17:20] <- 0.5
object <- wrda(formula = response ~ A1 + Moist + Mag + Use + Condition(Manure),
data = dune_trait_env$envir,
weights = w)
object # Proportions equal to those Canoco 5.15
mod_scores <- scores(object, display = "all")
scores(object, which_cor = c("A1", "X_lot"), display = "cor")
anova(object)