optpart (version 3.0-3)

tabdev: Classification Validity Assessment by Table Deviance

Description

Table deviance is a method to assess the quality of classifications by calculating the clarity of the classification with respect to the original data, as opposed to a dissimilarity or distance matrix representation

Usage

# S3 method for default
tabdev(x,clustering,nitr=999,…)
    # S3 method for stride
tabdev(x,taxa,…)
    # S3 method for tabdev
summary(object,p=0.05,…)

Arguments

x

a matrix or data.frame of multivariate observations, with objects as rows, and attributes as columns

clustering

a vector of integer cluster assignments, or an object of class ‘clustering’ or ‘partana’

nitr

number of iterations to perform in calculating the probability of obtaining as effective a classification as observed

taxa

a data.frame with samples as rows and species as columns

object

and object of class ‘tabdev’

p

the maximum probability threshold to list species in the summary table

…

ancillary arguments to maintain compatibility with generic summary function

Value

a list with components:

spcdev

a data.frame with species, deviance, and probability as columns

totdev

the total deviance of the entire table

Details

Tabdev calculates the concentration of values within clusters. For each column, tabdev calculates the sum of values within classes and the sum within classes divided by the sum of that column to get fractional sums by class. These values are used to calculate the deviance of each row. Attributes that are widely dispersed among classes exhibit high deviance; attributes that are concentrated within a single class contribute zero deviance. An effective classification should exhibit low deviance.

Tabdev then permutes the values within columns and calculates the probability of observing as low a deviance as observed as $$ (m+1)/(niter + 1)$$ where $m$ is the number of cases with as low or lower deviance as observed.

Examples

# NOT RUN {
data(shoshveg)
dis.bc <- dsvdis(shoshveg,'bray/curtis')
opt.5 <- optpart(5,dis.bc)
tabdev(shoshveg,opt.5)
# }