isocat (version 0.3.0)

isotopeAssignmentModel: Isotope assignment model function

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)