misclassified: Report Misclassified Quadrats
In jarioksa/twinspan: Two-Way Indicator Species Analysis

misclassified

R Documentation

Report Misclassified Quadrats

Description

twinspan bases its quadrat classification primarily on ordination axis. In some cases this is in conflict with the classification derived from indicator pseudospecies. This function identifies these cases.

Usage

misclassified(x, level, verbose = TRUE, binname = FALSE)

Arguments

`x`	`twinspan` result object.
`level`	Only consider misclassification down to this level.
`verbose`	If `FALSE`, returns only the index of misclassified quadrats.
`binname`	Use binary labels instead of decimal numbers for classes and divergent division in verbose object.

Details

The function compares the final twinspan classification (from cut.twinspan) and the classification predicted from indicator pseudospecies (from predict.twinspan). If these two differ, the quadrat is “misclassified”. With verbose=FALSE, the function returns a logical vector that is TRUE for misclassified quadrats. In default, it also returns the names, twinspan classes and predicted classes of misclassified quadrats, and the division where the misclassification occurred and classifications diverged. The divisions and their numbers can be seen in summary.twinspan and plot.twinspan.

Value

If verbose=TRUE, the function returns an object of class "misclassified" with following elements.

index: Index of misclassified quadrats.
labels: Labels (names) of quadrats.
class: Final classification from twinspan.
predicted: Final classification from predict.twinspan.
division: The division where the misclassification occurred.

With verbose=FALSE, the function returns a logical vector that is TRUE for misclassified quadrats.

Examples


data(ahti)
tw <- twinspan(ahti)
misclassified(tw)
## see the ID numbers of divisions
plot(tw)
## only look at misclassifications at first two levels
misclassified(tw, level = 2)

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