Construct, coerce, and test for a count object

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

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.

Value

Returns an object of class “count”.

Author

Robin K. S. Hankin

See also

census

Examples

count(c(
   slugs = 9, pigs = 1, dogs = 1, hogs = 2, bats = 3,
   cats = 1, frogs = 1, pugs = 2, ants = 1,
   yaks = 2, rats = 4))
#> slugs  rats  bats  hogs  pugs  yaks  pigs  dogs  cats frogs  ants 
#>     9     4     3     2     2     2     1     1     1     1     1 


a <- c(rep("oak",5) ,rep("ash",2),rep("elm",3),rep("xx",4))
as.count(a)
#> oak  xx elm ash 
#>   5   4   3   2 




data(saunders)
as.count(saunders[1,-(1:150)])
#>            Exogoninae             Nematodes              Syllinae 
#>                    27                    24                    20 
#>            Nereididae            Eusyllinae            Nemerteans 
#>                     6                     5                     5 
#>          Protoaricia.            Sabellidae Spionidae...Boccardia 
#>                     4                     4                     3 

jj <- sample(1:5,5,replace=TRUE)
as.count(jj)
#> 4 5 
#> 3 2 
as.count(jj,add="spp.")
#> spp.4 spp.5 
#>     3     2