# sim2dis: Converts a Similarity Matrix into a Dissimilarity Matrix In optiSel: Optimum Contribution Selection and Population Genetics

## Description

Converts a similarity matrix (e.g. a kinship matrix) into a dissimilarity matrix.

## Usage

 `1` ```sim2dis(f, a=4.0, baseF=0.03, method=1) ```

## Arguments

 `f` Similarity matrix. `a` Exponent `baseF` Old inbreeding not measured by `f` `method` Either `1` or `2`

## Details

This function converts a similarity matrix `f` with values between 0 and 1 (e.g. a kinship matrix) into a dissimilarity matrix. At first, the similarity is adjusted as

`f <- baseF + (1-baseF)*f`.

Then, for Method 1, the dissimilarity between individuals `i` and `j` is computed as

`Dij = (-log(fij))^a`,

whereas for Method 2, the dissimilarity is computed as

`Dij = sqrt((fii+fjj)/2-fij)^a`.

Although Method 2 may provide lower stress values in some cases, Method 1 has the advantage that the area reflects the diversity of a population more reasonable.

## Value

Dissimilarity matrix D.

Robin Wellmann

## Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17``` ```data(map) dir <- system.file("extdata", package = "optiSel") files <- file.path(dir, paste("Chr", unique(map\$Chr), ".phased", sep="")) f <- segIBD(files, map, minSNP=15, minL=1.0) D <- sim2dis(f, 4) ## Multidimensional scaling of animals: ## Not run: data(Cattle) library("smacof") color <- c(Angler="red", Rotbunt="green", Fleckvieh="blue", Holstein="black") col <- color[as.character(Cattle\$Breed)] Res <- smacofSym(D, itmax = 5000, eps = 1e-08) plot(Res\$conf, pch=18, col=col, main="Multidimensional Scaling", cex=0.5) mtext(paste("segIBD Stress1 = ", round(Res\$stress,3))) ## End(Not run) ```

optiSel documentation built on Jan. 16, 2021, 5:30 p.m.