count: Construct, coerce, and test for a count object
Description
In package untb, ecosystem data is held in one of two preferred forms:
census data and count data. Function count creates an object
of class count, and as.count() coerces to this class.
Usage
as.count(a,add="")
count(a)
is.count(a)
Arguments
a
Ecosystem data. In function as.count(), if a table,
interpret as species count data; otherwise, interpret as census
data. Special dispensation is made for single rows of a dataframe
add
In function as.count(), character argument with
default "" (empty string) meaning to leave the species
names unchanged. A non-empty string is prepended
to the species names using paste(). This is useful if the
species names are integers because the display can become confusing
Value
Returns an object of class count.
Details
A count object is a list of species together with
their abundance. It also has class table; compare
census objects.
An object of class count is a table sorted from most to least
abundant species. The singletons are thus tabulated last.
Function count() takes a vector, the elements of which are
interpreted as abundances. If any of the elements are named, the
names are interpreted as species names (unnamed elements are given the
null name). If the vector is unnamed, then the species names are
upper case letters, with the first element being named
A, the second B, and so on; this
behaviour is inherited from as.table(). Note that this means
that the species names are not necessarily in alphabetical order.
From version 1.6-9, zero elements are interpreted as zero abundance
species (ie extinct).
To access or change species names, use names() and
names<- respectively.
Function as.count() coerces its argument to count form.