# diffDist: Distance Matrix Computation In RFLPtools: Tools to Analyse RFLP Data

## Description

This function computes and returns the distance matrix computed by using the specified distance measure to compute the distances between the rows of a data matrix. Instead of the row values as in the case of `dist`, the successive differences of the row values are used.

## Usage

 `1` ```diffDist(x, method = "euclidean", diag = FALSE, upper = FALSE, p = 2) ```

## Arguments

 `x` a numeric matrix, data frame or `"dist"` object. `method` the distance measure to be used. This must be one of `"euclidean"`, `"maximum"`, `"manhattan"`, `"canberra"`, `"binary"` or `"minkowski"`. Any unambiguous substring can be given. `diag` logical value indicating whether the diagonal of the distance matrix should be printed by `print.dist`. `upper` logical value indicating whether the upper triangle of the distance matrix should be printed by `print.dist`. `p` The power of the Minkowski distance.

## Details

This function computes and returns the distance matrix computed by using the specified distance measure to compute the distances between the rows of a data matrix. Instead of the row values as in the case of `dist`, the successive differences of the row values are used.

It's a simple wrapper function arround `dist`. For more details about the distances we refer to `dist`.

The function may be helpful, if there is a shift w.r.t.\ the measured bands; e.g.\ `c(550, 500, 300, 250)` vs.\ `c(510, 460, 260, 210)`.

## Value

`diffDist` returns an object of class `"dist"`; cf. `dist`.

## Author(s)

Matthias Kohl Matthias.Kohl@stamats.de

## References

Flessa, F., Kehl, A., Kohl, M. Analysing diversity and community structures using PCR-RFLP: a new software application. Molecular Ecology Resources 2013 Jul; 13(4):726-33.

## Examples

 ```1 2 3 4 5``` ```## assume a shift in the measured bands M <- rbind(c(550, 500, 300, 250), c(510, 460, 260, 210), c(550, 500, 300, 200)) dist(M) diffDist(M) ```

### Example output

```Loading required package: RColorBrewer
1  2
2 80
3 50 70
1  2
2  0
3 50 50
```

RFLPtools documentation built on May 4, 2021, 1:06 a.m.