Nothing
"a.datums" <-
function(x, depths = NULL, skip = 0,
increasing.down = FALSE, ...){
if(!is.strat.column(x)){
stop(paste('argument to a.datums is not of class strat.column'))
}
if(is.null(x$depths) && is.null(depths)){
stop('appearance datums are meaningless if depths are not supplied; for indices, set depths = 1:ncol(x)')
}
y <- x$counts
nas <- sum(is.na(y))
if(nas > 0){
warning(paste(nas, 'NAs replaced with zeros for the purposes of calculating stratigraphic ranges; original counts have not been modified'))
y[is.na(y)] <- 0
}
if(is.null(depths)){
depths <- x$depths
}
index.pos <- function(x) {return((1:length(x))[x > 0])}
presence.index <- apply(y, 2, index.pos)
if(skip > 0){
depths[c(1:skip, (length(depths) - skip):length(depths))] <- NA
}
if(increasing.down){
fads <- depths[as.numeric(lapply(presence.index, max))]
lads <- depths[as.numeric(lapply(presence.index, min))]
}else{
lads <- depths[as.numeric(lapply(presence.index, max))]
fads <- depths[as.numeric(lapply(presence.index, min))]
}
if(is.null(x$taxa)){
names(fads) <- colnames(x$counts)
names(lads) <- colnames(x$counts)
}else{
names(fads) <- x$taxa
names(lads) <- x$taxa
}
return(data.frame(fads = fads, lads = lads))
}
"fads" <-
function(x, depths = NULL, skip = 0,
increasing.down = FALSE, ...){
a.datums <- a.datums(x, depths = depths, skip = skip,
increasing.down = increasing.down, ...)
fads <- a.datums$fads
names(fads) <- rownames(a.datums)
return(fads)
}
"lads" <-
function(x, depths = NULL, skip = 0,
increasing.down = FALSE, ...){
a.datums <- a.datums(x, depths = depths, skip = skip,
increasing.down = increasing.down, ...)
lads <- a.datums$lads
names(lads) <- rownames(a.datums)
return(lads)
}
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