Mtabs {dave}R Documentation

Structuring vegetation data tables

Description

Mimics traditional manual ordering of vegetation data table by (i) clustering rows and columns (hclust), (ii) rearranging the resulting groups according to the first AOC axis (aocc), (iii) rearranging rows and columns inside groups based on CA (cca), (iv) Putting high resolving species on top of the table (aoc). Also offers variants for ordering.

Usage

Mtabs(veg, method = "raw", y.r, y.s, k.r, k.s, ndiffs, ...)
mtab(veg, method = "raw", y.r, y.s, k.r, k.s, ndiffs)
plottab(veg,rorder=NULL,sorder=NULL,grr=NULL,grs=NULL,y=0.5)
plottabl(veg,rorder=NULL,sorder=NULL,grr=NULL,grs=NULL,y=0.5)
setgroupsize(vec)

## Default S3 method:
Mtabs(veg, method, y.r, y.s, k.r, k.s, ndiffs, ...)
## S3 method for class 'Mtabs'
plot(x,...,method="normal")
## S3 method for class 'Mtabs'
summary(object,...,range=NULL)

Arguments

veg

This is a vegetation data frame, releves are rows, species columns

method

The method used for ordering: "raw", "sort", "ca", "clust", "aoc" or "mulva"

y.r

Transformation of species scores when clustering releves (rows): x'= x exp(y.r)

y.s

Transformation of species scores when clustering species (columns): x'= x exp(y.s)

k.r

The number of releve groups

k.s

The number of species groups

ndiffs

The number of (high resolving) species used for top portion of the table

...

Use method="normal" for conventional display, "compressed" for very large tables

rorder

The order of releves (rows) for printing

sorder

The order of species (columns) for printing

grr

The group labels of releves (rows) for printing

grs

The group labels of species (columns) for printing

x

An object of class "Mtabs"

object

An object of class "Mtabs"

range

A subset of species to be displayed in summary table, e.g., c(1,10) for the first 10.

vec

A vector of group labels, analyzed similar to function table(), but without sorting

y

Transformation of species scores: x'= x exp(y)

Details

Function plottab() and plottabl() are for internal use only

Value

An object of class "Mtabs" with at least the following items:

method

The method used for ordering

transf.r

Argument y.r

transf.s

Argument y.s

order.rel

The resulting order of rows

order.sp

The resulting order of columns

order.relgr

The resulting order of releve groups

order.spgr

The resulting order of species groups

MSCC

Mean square contingency coefficient

CAeig.rel

Eigenvalues of correspondence analysis

AOCeig.rel

Eigenvalues of analysis of concentration

veg

The input vegetation data frame

centroids

The matrix of groups centroids (see summary.Mtabs

Note

This extremely complex procedure accords with conventions used in vegetation ecology. It assumes that the vegetation data frame has many zero entries (plots in which species are not found). The summary method displays a frequency table (relative frequency of all species within the releve groups, centroid).

Author(s)

Otto Wildi

References

Wildi, O. 1989. A new numerical solution to traditional phytosociological tabular classification. Vegetatio 81: 95–106.

Wildi, O. 2017. Data Analysis in Vegetation Ecology. 3rd ed. CABI, Oxfordshire, Boston.

Examples

y.r<- 0.5 ; y.s<- 0.2                 # defining transformations used
k.r <- 3 ; k.s <- 4                   # row- and column numbers
ndiffs <- 18                          # no. of columns used to show pattern
o.Mt<-Mtabs(nveg,"mulva" ,y.r,y.s,k.r,k.s,ndiffs)
plot(o.Mt,method="normal")
# to see the original order simply replace "mulva" by "raw"

[Package dave version 2.0 Index]