Nothing
`wa` <- function(x, ...) UseMethod("wa")
`wa.default` <-
function(x, env,
deshrink = c("inverse", "classical", "expanded", "none", "monotonic"),
tol.dw = FALSE, useN2 = TRUE,
na.tol = c("min","mean","max"),
small.tol = c("min","mean","fraction","absolute"),
min.tol = NULL, f = 0.1, ...)
{
## x = species abundances (weights), env = response vector
x <- as.matrix(x)
env <- as.numeric(env)
## drop species with no information
if(any(csum <- colSums(x) == 0L)) {
x <- x[, !csum, drop = FALSE]
warning("Some species contained no data. These have been deleted.")
}
## drop samples with no species
if(any(rsum <- rowSums(x) == 0L)) {
x <- x[!rsum, , drop = FALSE]
env <- env[!rsum]
warning("Some sites contained no data. These have been deleted.")
}
if(missing(deshrink))
deshrink <- "inverse"
deshrink <- match.arg(deshrink)
if(missing(na.tol))
na.tol <- "min"
na.tol <- match.arg(na.tol)
if(missing(small.tol))
small.tol <- "min"
small.tol <- match.arg(small.tol)
## do the WA
fit <- waFit(x = x, y = env, tol.dw = tol.dw, useN2 = useN2,
deshrink = deshrink, na.tol = na.tol,
small.tol = small.tol, min.tol = min.tol, f = f)
## site/sample names need to be reapplied
names(fit$fitted.values) <- rownames(x)
## species names need to be reapplied
names(fit$wa.optima) <- colnames(x)
## residuals
residuals <- env - fit$fitted.values
## RMSE of predicted/fitted values
rmse <- sqrt(mean(residuals^2))
## r-squared
r.squared <- cor(fit$fitted.values, env)^2
## bias statistics
avg.bias <- mean(residuals)
max.bias <- maxBias(residuals, env)
## the function call
.call <- match.call()
## need to reset due to method dispatch
.call[[1]] <- as.name("wa")
## returned object
res <- list(wa.optima = fit$wa.optima,
tolerances = fit$tolerances,
model.tol = fit$model.tol,
fitted.values = fit$fitted.values,
residuals = residuals,
coefficients = fit$coefficients,
rmse = rmse, r.squared = r.squared,
avg.bias = avg.bias, max.bias = max.bias,
n.samp = fit$n.samp,
n.spp = fit$n.spp,
deshrink = deshrink, tol.dw = tol.dw,
call = .call,
orig.x = x, orig.env = env,
options.tol =
list(useN2 = useN2,
na.tol = na.tol,
small.tol = small.tol,
min.tol = min.tol,
f = f))
class(res) <- "wa"
res
}
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