Nothing
# private class not exposed to the user
# used to allow slot 'decostand' to contain NULL
#setClassUnion("InstantSoup", c("Vegsoup", "Species", "Sites", "Taxonomy"))
#showClass("InstantSoup")
#setClass("SpeciesTaxonomyVirtual",
# representation = representation("VIRTUAL")
#)
instantsoup <- function (folder, sep = ";", dec = ",", coverscale) {
if (missing(coverscale)) {
coverscale = "braun.blanquet"
}
#folder <- "~/Documents/vegsoup-data/hohewand dta"
files <- list.files(folder)
paths <- list.files(folder, full.names = TRUE)
x.file <- grep("species", files)
y.file <- grep("sites", files)
z.file <- grep("taxonomy", files)
z <- "~/Documents/vegsoup-standards/austrian standard list 2008/austrian standard list 2008.csv"
if (!c(length(x.file) == 1 & length(y.file) == 1)) {
stop("need both files for species and sites", call. = FALSE)
}
if (length(grep("wide", files[x.file])) > 0) {
x <- stackSpecies(file = paths[x.file])
} else {
x <- species(paths[x.file], sep = sep, dec = dec)[,1:4]
}
if (length(grep("wide", files[y.file])) > 0) {
y <- stackSites(file = paths[y.file])
} else {
y <- sites(paths[y.file], sep = sep, dec = dec)
}
if (length(z.file) == 0) {
xz <- SpeciesTaxonomy(x = x,
file.y = z)
} else {
z <- taxonomy(z,sep = sep, dec = dec)
xz <- SpeciesTaxonomy(x, z)
}
res <- Vegsoup(xz, y, coverscale = coverscale)
return(res)
}
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