comboize: combine genetics, isotopes, and habitat raster with exponents...

In eriqande/gaiah: Genetic and Isotopic Assignment Accounting for Habitat Suitability

combine genetics, isotopes, and habitat raster with exponents as given

Description

This just multiplies the rasters together, each raised to the appropriate exponent, normalizes and returns the result

Usage

comboize(Mgen, Miso, Mhab, beta_gen, beta_iso, beta_hab)

Arguments

Mgen	the genetic posteriors rasterStack. Must be a rasterStack
Miso	the isotope posteriors rasterStack.
Mhab	a single layer raster with the habitat suitabiilty measure as a normalized probability surface.
beta_gen	the exponent to raise the habitat raster to
beta_iso	the exponent to raise the isotope raster to
beta_hab	the exponent to raise the genetic raster to

Examples

# first, run through the example for isotope_posterior_probs() to get
# the rasters for two migrant birds. This gives us the list "birds2"
example(isotope_posterior_probs)

# extract the posterior probs rasters from  that output into a raster stack
miso <- lapply(birds2$regular, function(x) x$posterior_probs) %>%
  raster::stack()

# see the names of the birds we are dealing with:
names(miso)

# get the genetic posteriors for those two birds
mig_gen2 <- migrant_wiwa_genetic_posteriors %>%
  dplyr::filter(ID %in% c(names(miso)))

# make genetic posterior rasters for those two birds, make sure they are
# sorted in the same order as miso, and make a raster stack of it
mgen <- genetic_posteriors2rasters(G = mig_gen2, R = genetic_regions)[names(miso)] %>%
  raster::stack()

# make a normalized prior from habitat quality that is zeros everywhere
# outside of the "known" range.
tmp <- wiwa_habitat_unclipped * wiwa_breed
mhab <- tmp / raster::cellStats(tmp, sum)

# combine genetics, isotopes and habitat with exponents of 1 on each
mcombo <- comboize(mgen, miso, mhab, 1, 1, 1)

eriqande/gaiah documentation built on April 30, 2023, 6:31 p.m.