sits_mixture_model {sits}

Multiple endmember spectral mixture analysis

Description

Create a multiple endmember spectral mixture analyses fractions images. We use the non-negative least squares (NNLS) solver to calculate the fractions of each endmember. The NNLS was implemented by Jakob Schwalb-Willmann in RStoolbox package (licensed as GPL>=3).

Usage

sits_mixture_model(
  data,
  endmembers,
  ...,
  rmse_band = TRUE,
  multicores = 2,
  progress = TRUE
)

## S3 method for class 'sits'
sits_mixture_model(
  data,
  endmembers,
  ...,
  rmse_band = TRUE,
  multicores = 2,
  progress = TRUE
)

## S3 method for class 'raster_cube'
sits_mixture_model(
  data,
  endmembers,
  ...,
  rmse_band = TRUE,
  memsize = 4,
  multicores = 2,
  output_dir,
  progress = TRUE
)

## S3 method for class 'derived_cube'
sits_mixture_model(data, endmembers, ...)

## S3 method for class 'tbl_df'
sits_mixture_model(data, endmembers, ...)

## Default S3 method:
sits_mixture_model(data, endmembers, ...)

Arguments

data

A sits data cube or a sits tibble.

endmembers

Reference spectral endmembers. (see details below).

...

Parameters for specific functions.

rmse_band

A boolean indicating whether the error associated with the linear model should be generated. If true, a new band with errors for each pixel is generated using the root mean square measure (RMSE). Default is TRUE.

multicores

Number of cores to be used for generate the mixture model.

progress

Show progress bar? Default is TRUE.

memsize

Memory available for the mixture model (in GB).

output_dir

Directory for output images.

Details

The endmembers parameter should be a tibble, csv or a shapefile. endmembers parameter must have the following columns: type, which defines the endmembers that will be created and the columns corresponding to the bands that will be used in the mixture model. The band values must follow the product scale. For example, in the case of sentinel-2 images the bands should be in the range 0 to 1. See the example in this documentation for more details.

Value

In case of a cube, a sits cube with the fractions of each endmember will be returned. The sum of all fractions is restricted to 1 (scaled from 0 to 10000), corresponding to the abundance of the endmembers in the pixels. In case of a tibble sits, the time series will be returned with the values corresponding to each fraction.

Author(s)

Felipe Carvalho, [e-mail]

Felipe Carlos, [e-mail]

Rolf Simoes, [e-mail]

Gilberto Camara, [e-mail]

Alber Sanchez, [e-mail]

References

RStoolbox package (https://github.com/bleutner/RStoolbox/)

Examples

if (sits_run_examples()) {
    # Create a sentinel-2 cube
    s2_cube <- sits_cube(
        source = "AWS",
        collection = "SENTINEL-2-L2A",
        tiles = "20LKP",
        bands = c("B02", "B03", "B04", "B8A", "B11", "B12", "CLOUD"),
        start_date = "2019-06-13",
        end_date = "2019-06-30"
    )
    # create a directory to store the regularized file
    reg_dir <- paste0(tempdir(), "/mix_model")
    dir.create(reg_dir)
    # Cube regularization for 16 days and 160 meters
    reg_cube <- sits_regularize(
        cube = s2_cube,
        period = "P16D",
        res = 160,
        roi = c(
            lon_min = -65.54870165,
            lat_min = -10.63479162,
            lon_max = -65.07629670,
            lat_max = -10.36046639
        ),
        multicores = 2,
        output_dir = reg_dir
    )

    # Create the endmembers tibble
    em <- tibble::tribble(
        ~class, ~B02, ~B03, ~B04, ~B8A, ~B11, ~B12,
        "forest", 0.02, 0.0352, 0.0189, 0.28, 0.134, 0.0546,
        "land", 0.04, 0.065, 0.07, 0.36, 0.35, 0.18,
        "water", 0.07, 0.11, 0.14, 0.085, 0.004, 0.0026
    )

    # Generate the mixture model
    mm <- sits_mixture_model(
        data = reg_cube,
        endmembers = em,
        memsize = 4,
        multicores = 2,
        output_dir = tempdir()
    )
}