View source: R/ContinuousProximities.R

ContinuousProximities | R Documentation |

Calculates proximities among rows of a continuous data matrix or among the rows of two continuous matrices.

```
ContinuousProximities(x, y = NULL, ysup = FALSE,
transpose = FALSE, coef = "Pythagorean", r = 1)
```

`x` |
Main data matrix. Distances among rows are calculated if y=NULL. |

`y` |
Supplementary data matrix. If not NULL the distances among the rows of x and y are calculated |

`ysup` |
Supplementary Y data |

`transpose` |
Transpose rows and columns |

`coef` |
Distance coefficient. Use the name or the number(see details) |

`r` |
Exponent for the Minkowsky |

The following coefficients are calculated

1.- Pythagorean = sqrt(sum((y[i, ] - x[j, ])^2)/p)

2.- Taxonomic = sqrt(sum(((y[i,]-x[j,])^2)/r^2)/p)

3.- City = sum(abs(y[i,]-x[j,])/r)/p

4.- Minkowski = (sum((abs(y[i,]-x[j,])/r)^t)/p)^(1/t)

5.- Divergence = sqrt(sum((y[i,]-x[j,])^2/(y[i,]+x[j,])^2)/p)

6.- dif_sum = sum(abs(y[i,]-x[j,])/abs(y[i,]+x[j,]))/p

7.- Camberra = sum(abs(y[i,]-x[j,])/(abs(y[i,])+abs(x[j,])))

8.- Bray_Curtis = sum(abs(y[i,]-x[j,]))/sum(y[i,]+x[j,])

9.- Soergel = sum(abs(y[i,]-x[j,]))/sum(apply(rbind(y[i,],x[j,]),2,max))

10.- Ware_hedges = sum(abs(y[i,]-x[j,]))/sum(apply(rbind(y[i,],x[j,]),2,max))

`Data` |
A matrix with the initial data (x matrix). |

`SupData` |
A matrix with the supplementary data (y matrix). |

`D` |
The matrix of distances |

`Coefficient` |
The coefficient used. |

Jose Luis Vicente-Villardon

Gower, J. C. (2006) Similarity dissimilarity and Distance, measures of. Encyclopedia of Statistical Sciences. 2nd. ed. Volume 12. Wiley

```
data(wine)
dis=ContinuousProximities(wine[,4:21])
```

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