Nothing
svocc <-
function (formula, data, link.sta = "cloglog", link.det = "logit", penalized = FALSE,
method = c("optim", "dc"), inits,
model = TRUE, x = FALSE, ...)
{
## parsing the formula
if (missing(data))
data <- NULL
# out <- svisitFormula(formula, data, n=sys.nframe()-1) ## parent frame
out <- svisitFormula(formula, data, n=0) ## global environment
out$call = match.call()
# out$y <- NULL
Y <- out$y
X <- out$x$sta
Z <- out$x$det
Xlevels <- out$levels
## check variables
if (length(Y) < 1)
stop("empty model")
if (all(Y > 0))
stop("invalid dependent variable, no zero value")
if (!isTRUE(all.equal(as.vector(Y), as.integer(round(Y +
0.001)))))
stop("invalid dependent variable, non-integer values")
Y <- as.integer(round(Y + 0.001))
if (any(Y < 0))
stop("invalid dependent variable, negative counts")
if (any(!(Y %in% c(0, 1))))
stop("invalid dependent variable, not in c(0, 1)")
if (setequal(colnames(Z), colnames(X)))
stop("at least one covariate should be separate for occupancy and detection parts of the formula")
if (length(Y) != NROW(X))
stop("invalid dependent variable, not a vector")
if (all(union(colnames(X), colnames(Z))[-1] %in% names(unlist(Xlevels))))
stop("model must include at least one continuous covariate")
## occ and det linkinv functions
links <- c("logit", "probit", "cloglog")
link.sta <- match.arg(link.sta, links)
link.det <- match.arg(link.det, links)
## method
method <- match.arg(method)
## fit
fit <- svocc.fit(Y, X, Z, link.sta, link.det, penalized = penalized, auc = FALSE,
method=method, inits=inits, ...)
## return value
out <- c(fit, out)
if (!model)
out$model <- NULL
if (!x)
out$x <- NULL
class(out) <- c("svocc", "svisit")
return(out)
}
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