unit.distances: SOM-grid related functions In missSOM: Self-Organizing Maps with Built-in Missing Data Imputation

Description

Function `somgrid` (modified from the version in the class package) sets up a grid of units, of a specified size and topology. Distances between grid units are calculated by function `unit.distances`.

Usage

 ```1 2 3 4 5 6 7 8 9``` ```somgrid( xdim = 8, ydim = 6, topo = c("rectangular", "hexagonal"), neighbourhood.fct = c("bubble", "gaussian"), toroidal = FALSE ) unit.distances(grid, toroidal) ```

Arguments

 `xdim` dimensions of the grid. `ydim` dimensions of the grid. `topo` choose between a hexagonal or rectangular topology. `neighbourhood.fct` choose between bubble and gaussian neighbourhoods when training a SOM. `toroidal` logical, whether the grid is toroidal or not. If not provided to the `unit.distances` function, the information in the `grid` object will be used. `grid` an object of class `somgrid`.

Value

Function `somgrid` returns an object of class "somgrid", with elements `pts`, and the input arguments to the function.

Function `unit.distances` returns a (symmetrical) matrix containing distances. When `grid\$n.hood` equals "circular", Euclidean distances are used; for `grid\$n.hood` is "square" maximum distances. For toroidal maps (joined at the edges) distances are calculated for the shortest path.

Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14``` ```mygrid <- somgrid(5, 5, "hexagonal") fakesom <- list(grid = mygrid) class(fakesom) <- "missSOM" oldpar <- par(mfrow = c(2,1)) dists <- unit.distances(mygrid) plot(fakesom, type="property", property = dists[1,], main="Distances to unit 1", zlim=c(0,6), palette = rainbow, ncolors = 7) dists <- unit.distances(mygrid, toroidal=TRUE) plot(fakesom, type="property", property = dists[1,], main="Distances to unit 1 (toroidal)", zlim=c(0,6), palette = rainbow, ncolors = 7) par(oldpar) ```

missSOM documentation built on Nov. 10, 2021, 5:08 p.m.