Nothing
"coca.default" <- function(y, x, method = c("predictive", "symmetric"),
reg.method = c("simpls", "eigen"),
weights = NULL,
n.axes = NULL,
symmetric = FALSE,
quiet = FALSE, ...) {
nam.dat <- list(namY = deparse(substitute(y)),
namX = deparse(substitute(x)))
y <- checkCommunityData(y)
x <- checkCommunityData(x)
dropped <- c(attr(y, "dropped"), attr(x, "dropped"))
if (!quiet) {
msgIfDroppedVars(dropped, nam.dat)
}
method <- match.arg(method)
if(method == "predictive") {
reg.method <- match.arg(reg.method)
retval <- switch(reg.method,
simpls = predcoca.simpls(y, x, R0 = weights,
n.axes = n.axes, nam.dat),
eigen = predcoca.eigen(y, x, R0 = weights,
n.axes = n.axes, nam.dat))
} else {
retval <- symcoca(y, x, n.axes = n.axes, R0 = weights,
symmetric = symmetric, nam.dat)
}
class(retval) <- c("coca", class(retval))
retval
}
`checkCommunityData` <- function(x) {
dropped <- FALSE
if(any(rowSums(x) <= 0 )) {
stop("All row sums must be > 0 in data matrix")
}
if(any((csum <- colSums(x)) <= 0 )) {
x <- x[, csum > 0, drop = FALSE]
dropped <- TRUE
}
attr(x, "dropped") <- dropped
x
}
`msgIfDroppedVars` <- function(x, objNames) {
dropped <- vector(mode = "list", length = length(x))
dropped[x] <- objNames
## print message if we dropped some species
if (any(!sapply(dropped, is.null))) {
message(paste(paste("\nRemoved some species that contained no data in:",
paste(unlist(dropped), collapse = ", ")), "\n"))
}
invisible()
}
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