isotopeAssignmentModel: Isotope assignment model function

In isocat: Isotope Origin Clustering and Assignment Tools

Description

Creates isotope assignment models projections of probable origin. Results returned as a RasterStack, with layer names corresponding to individual ID.

Usage

isotopeAssignmentModel(
  ID,
  isotopeValue,
  SD_indv = 0,
  precip_raster,
  precip_SD_raster,
  additionalModels = FALSE,
  additionalModel_name = "CombinedIsotope-OtherModelAssignments",
  savePath = FALSE,
  nClusters = FALSE
)

Arguments

ID	ID value or vector of values (for naming assignment model layers). If missing, will count from 1.
isotopeValue	Isotope precipitation value or vector of values.
SD_indv	error associated with transfer function fit. Value or vector of values. If missing, will assume value of 0.
precip_raster	precipitation isoscape raster.
precip_SD_raster	precipitation isoscape standard deviation raster.
additionalModels	optional additional model raster object (e.g. an SDM, rasterized range map, or stack thereof). If specified, function will return isotope assignment rasters and the product of these additionalModels and each assignmentRaster.
additionalModel_name	optional filename for additionalModel .grd savepath
savePath	If specified, function will save results to this path as a '.grd' file.
nClusters	integer of cores to run in parallel with doParallel. Default FALSE.

Examples

myiso <- rasterFromXYZ(isoscape)
raster::plot(myiso)
myiso_sd <- rasterFromXYZ(isoscape_sd)
df <- data.frame(
         ID = paste0("Example.", 1:3),
         isotopeValue = c(-100, -80, -50),
         SD_indv = rep(5, 3)
         )
assignmentModels <- isotopeAssignmentModel(
                        ID = df$ID,
                        isotopeValue = df$isotopeValue,
                        SD_indv = df$SD_indv,
                        precip_raster = myiso,
                        precip_SD_raster = myiso_sd
                        )
raster::plot(assignmentModels)

# Add additionalModels:
range_raster <- myiso
range_raster[] <- as.numeric( 1:ncell(myiso) %% 60 >= 10)
plot(range_raster)

sdm_raster <- myiso
sdm_raster[] <- (1:ncell(sdm_raster))^2
sdm_raster <- sdm_raster / raster::cellStats(sdm_raster, "sum")
plot(sdm_raster)

extraModels <- raster::stack(range_raster, sdm_raster)
assignmentModels <- isotopeAssignmentModel(
                        ID = paste0("Combo.",df$ID),
                        isotopeValue = df$isotopeValue,
                        SD_indv = df$SD_indv,
                        precip_raster = myiso,
                        precip_SD_raster = myiso_sd,
                        additionalModels = extraModels
                        )
raster::plot(assignmentModels)

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