Nothing
assist.ado <- function(data, meta, is.OTU=TRUE, ranks=NULL,
data.trans=NULL, dist=NULL, meta.strata=NULL,
perm=1000, top=NULL, mode="number") {
if ( is.OTU ) {
.valid.data(data, is.OTU=is.OTU)
}
num.data <- length(data)
labels <- names(data)
matched <- match.data(data, is.OTU=is.OTU, meta=meta)
# rework with the data based on OTU or tax.abund matrix
data.new <- data.revamp(data=data, is.OTU=is.OTU, ranks=ranks,
stand.method=data.trans, top=top, mode=mode)
# filter METAdata, exclude variable with only 1 level, with
# missing data, and non numeric&&factor/charactor (NNF)
suppressWarnings(meta.new <- filter.META(meta,
exclude=meta.strata))
if ( is.null(meta.strata) ) {
strata <- NULL
} else {
strata <- meta.new[[meta.strata]]
}
# adonis
# either use distance matrix of the ecology data
# or use the ecology data with or without being standardized.
ado.list <- list()
for ( i in 1:length(data.new) ) {
dt <- data.new[[i]]
if ( is.null(dt) ) { break }
label <- names(data.new)[i]
if ( is.null(dist) ) {
ado <- vegan::adonis(dt ~ ., data=meta.new,
permutations=perm,
strata= strata)
} else {
ado <- vegan::adonis(dt ~ ., data=meta.new,
method=dist,
permutations=perm,
strata=strata)
}
#names(data.ado)[i] <- names(data.new)[i]
ado.list[[label]] <- ado
}
return(ado.list)
}
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