Select taxa (variables) from an object on the basis of one or both of maximum abundance and number of occurrences greater than user-specified values. This is a simple utility function to encapsulate this common task in filtering palaeoecological data sets.
chooseTaxa(object, ...)# S3 method for default
chooseTaxa(object, n.occ = 1, max.abun = 0,
type = c("AND","OR"), value = TRUE, na.rm = FALSE,
...)
If value = TRUE
, returns the supplied data frame or matrix
with a subset of columns (taxa) that meet the criteria chosen. If
value = FALSE
, a logical vector is returned.
an R object for which a suitable method exists. The default method assumes a matrix-like object such as a data frame or a numeric matrix.
numeric; number of occurrences representing the lower
limit for selection. A taxon is included in the returned subset if
it is present a total of n.occ
times or more. See argument
type
for a modifier which might exclude the taxon even if it
would be included on the basis of n.occ
.
numeric; maximum abundance representing the lower
limit for selection. A taxon is included in the returned subset if
it attains abundance equal to or greater than max.abun
in one
or more sample. See argument type
for a modifier which might
exclude the taxon even if it would be included on the basis
of max.abun
.
character; one of "AND"
or "OR"
, controlling
how the criteria n.occ
and max.abun
are combined to
generate a subset of the variables in object
.
logical; should the data for the selected taxa be
returned? If TRUE
, the default, the data for the chosen taxa
are returned. If FALSE
, a logical vector is returned,
indicating which taxa met the selection criteria.
logical; should missing values NA
s be excluded
from the calculation of abundances and occurrence?
arguments passed on to subsequent methods.
Gavin L. Simpson
data(ImbrieKipp)
IK2 <- chooseTaxa(ImbrieKipp, n.occ = 5)
dim(ImbrieKipp)
dim(IK2)
## return a logical vector to select species/columns
chooseTaxa(ImbrieKipp, n.occ = 5, value = FALSE)
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