Description Usage Arguments Value Author(s) Examples
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.
1 2 3 4 5 6 | chooseTaxa(object, ...)
## Default S3 method:
chooseTaxa(object, n.occ = 1, max.abun = 0,
type = c("AND","OR"), value = TRUE, na.rm = FALSE,
...)
|
object |
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. |
n.occ |
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 |
max.abun |
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 |
type |
character; one of |
value |
logical; should the data for the selected taxa be
returned? If |
na.rm |
logical; should missing values |
... |
arguments passed on to subsequent methods. |
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.
Gavin L. Simpson
1 2 3 4 5 6 7 | 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)
|
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-7
analogue version 0.17-5
[1] 61 27
[1] 61 27
O.univ G.cglob G.ruber G.tenel G.saccu G.rubes G.pacL G.pacR G.bullo G.falco
TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
G.calid G.aequi G.gluti G.duter G.infla G.trnL G.trnR G.crasf G.scitu G.mentu
TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
P.obliq C.nitid S.dehis G.digit Other G.quin G.hirsu
TRUE TRUE TRUE TRUE TRUE TRUE TRUE
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