wrMisc: randIndFx – R documentation

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randIndFx

Distance of categorical data (Jaccard,Rand and adjusted Rand index)

Description

randIndFx calculates distance of categorical data (as Rand Index, Adjusted Rand Index or Jaccard Index). Note: uses/requires package flexclust Methods so far available (via flexclust): "ARI" .. adjusted Rand Index, "RI" .. Rand index, "J" .. Jaccard, "FM" .. Fowlkes-Mallows.

Usage

randIndFx(ma, method = "ARI", adjSense = TRUE, silent = FALSE, callFrom = NULL)

Arguments

`ma`	(matrix) main input for distance calulation
`method`	(character) name of distance method (eg "ARI","RI","J","FM")
`adjSense`	(logical) allows introducing correlation/anticorrelation (interprete neg distance results as anti)
`silent`	(logical) suppres messages
`callFrom`	(character) allow easier tracking of message(s) produced

Value

distance matrix

Examples

set.seed(2016); tab2 <- matrix(sample(1:2,size=42,replace=TRUE),ncol=7)
flexclust::comPart(tab2[1,],tab2[2,])
flexclust::comPart(tab2[1,],tab2[3,])
flexclust::comPart(tab2[1,],tab2[4,])
  randIndFx(tab2,adjS=FALSE)
  cor(t(tab2))
  randIndFx(tab2,adjS=TRUE)

wrMisc

Analyze Experimental High-Throughput (Omics) Data

v1.5.4

GPL-3

Authors

Wolfgang Raffelsberger [aut, cre]

Initial release