simmatrixMaker: Generates similarity matrix for RasterStack

In isocat: Isotope Origin Clustering and Assignment Tools

Description

Applies pairwise comparisons of Schoener's D-metric between each RasterLayer in a RasterStack to populate a similarity matrix.

Usage

simmatrixMaker(assignmentRasters, nClusters = FALSE, csvSavePath = FALSE)

Arguments

assignmentRasters	Input RasterStack
nClusters	Clusters to create run in parallel using 'doParallel'. Defaults to FALSE.
csvSavePath	Optional savepath to write similarity matrix to csv file. Defaults to FALSE, will not create csv.

Examples

# Create probability-of-origin maps to compare.
myiso <- rasterFromXYZ(isoscape)
raster::plot(myiso)
myiso_sd <- rasterFromXYZ(isoscape_sd)
n <- 5
set.seed(42)
df <- data.frame(
         ID = LETTERS[1:n],
         isotopeValue = sample(-120:-40, n),
         SD_indv = rep(5, n)
         )
assignmentModels <- isotopeAssignmentModel(
                        ID = df$ID,
                        isotopeValue = df$isotopeValue,
                        SD_indv = df$SD_indv,
                        precip_raster = myiso,
                        precip_SD_raster = myiso_sd,
                        nClusters = FALSE
                        )
raster::plot(assignmentModels)
# Compare maps with simmatrixMaker.
simmatrixMaker(assignmentModels, nClusters = FALSE, csvSavePath = FALSE)

isocat documentation built on July 8, 2020, 5:15 p.m.