twintable: Community Table Ordered by Twinspan Classification

In jarioksa/twinspan: Two-Way Indicator Species Analysis

Community Table Ordered by Twinspan Classification

Description

Prints a community table of pseudospecies ordered by twinspan classification.

Usage

twintable(object, maxspp, goodspecies, subset)

Arguments

object	twinspan result object.
maxspp	Maximum number of most abundant species displayed. The abundance is estimated with pseudospecies cut levels. The default is to show all species.
goodspecies	Select “good species” for tabulation. These are either species that were used as indicator pseudospecies ("indicator"), or most abundant species in each final species group breaking ties with frequency ("leading"), or "both" (default). The abundance is estimated after pseudospecies transformation for all quadrats and cannot be used together with maxspp.
subset	Select a subset of quadrats.

Details

Function prints a compact community table of pseudospecies values. The table is ordered by clustering both species and quadrats similarly as in summary.twinspan or in plot of as.dendrogram.twinspan. The classification of each quadrat and species is shown by a sequence of 0 and 1 indicating division of each level. This string is binary presentation of the decimal class number without the leading 1.

Only one character is used for each abundance, and the table is very compact. However, large tables can be divided over several pages or screen windows. The width of the displayed table is controlled by R option width (see options). It is possible to select only a subset of the quadrats for tabulation giving narrower tables. The number of species can be reduced by setting the maximum number of most abundant species, or alternatively, by restricting tabulation only to “good species” which are the most abundant species of each species group (ties broken by species frequency), or species used as indicators, or both.

Value

Function returns invisibly the data that vegemite used. This data can also be exported or used as any other data set.

Examples

data(ahti)
tw <- twinspan(ahti)
## complete table would be large, but we show subset of group 4
twintable(tw, subset = twingroup(tw, 4), goodspecies = "both")

jarioksa/twinspan documentation built on Nov. 23, 2024, 2:49 p.m.