R: Generate a Kohonen map for sample quality control

sits_som_map {sits} | R Documentation

## Generate a Kohonen map for sample quality control

### Description

This function uses package self-organized maps to find clusters in satellite image time series to cluster the samples. It also evaluates the quality of each sample using SOM properties.

The results is a list with three members: (1) the samples tibble, with one additional column indicating to which neuron it has been mapped; (2) the Kohonen map, used for plotting and cluster quality measures; (3) a tibble with the labelled neurons, where each class of each neuron is associated to two values: (a) the prior probability that this class belongs to a cluster based on the frequency of samples of this class allocated to the neuron; (b) the posterior probability that this class belongs to a cluster, using data for the neighbours on the SOM map.

### Usage

    sits_som_map(
      data,
      grid_xdim = 10,
      grid_ydim = 10,
      alpha = 1,
      rlen = 100,
      distance = "euclidean",
      som_radius = 2,
      mode = "online"
    )

### Arguments

`data` | A tibble with samples to be clustered.
`grid_xdim` | X dimension of the SOM grid (default = 25).
`grid_ydim` | Y dimension of the SOM grid.
`alpha` | Starting learning rate (decreases according to number of iterations).
`rlen` | Number of iterations to produce the SOM.
`distance` | The type of similarity measure (distance).
`som_radius` | Radius of SOM neighborhood
`mode` | Type of learning algorithm (default = "online")

### Value

A list of tibbles containing statistics about the samples and the neuron in each iteration.

### Author(s)

Lorena Alves, lorena.santos@inpe.br

Karine Ferreira. karine.ferreira@inpe.br

### References

'kohonen' package (https://CRAN.R-project.org/package=kohonen)

### Examples

    ## Not run:
    # Produce a cluster map
    som_cluster <- sits_som_map(samples_modis_4bands)
    # plot the som map
    plot(som_cluster)
    # Clean the samples to get better quality ones
    clean_samples <- sits_som_clean_samples(som_cluster)

    ## End(Not run)

[Package sits version 0.12.0 Index]