errors: Calculates Jaccard and Euclidean error rates.

In BinMat: Processes Binary Data Obtained from Fragment Analysis (Such as AFLPs, ISSRs, and RFLPs)

Calculates Jaccard and Euclidean error rates.

Description

Calculates the Jaccard and Euclidean error rates for the dataset. Jaccard's error does not take shared absences of bands as being biologically meaningful. JE = (f10 + f01)/(f10 + f01 + f11) and EE = (f10 + f01)/(f10 + f01 + f11 + f00). At each locus, f01 and f10 indicates a case where a 0 was present in one replicate, and a 1 in the other. f11 indicates the shared presence of a band in both replicates, and f00 indicates a shared absence. For example, if a replicate pair comprises Rep1 = 00101 and Rep2 = 01100, JE = (1+1)/(1+1+1) = 2/3 = 0.67, EE = (1+1)/(1+1+1+2) = 2/5 = 0.4.

Usage

errors(x)

Arguments

x	Consolidated binary matrix.

Value

JE (Jaccard Error), EE (Euclidean Error), and standard deviations.

Examples

data(BinMatInput_reps)
mat = BinMatInput_reps
cons = consolidate(mat)
errors(cons)

BinMat documentation built on March 18, 2022, 7:05 p.m.