isotope_posterior_probs: compute posterior probabilities of origin given isotope...

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

compute posterior probabilities of origin given isotope values

Description

This function automates the whole process described in the appendix of Vander Zanden et al. (2014) for computing the posterior probability of origin of an individual (or group of individuals) given its stable isotope values, and those of a set of reference individuals, and an ISOMAP prediction of isotope values across a landscape.

Usage

isotope_posterior_probs(
  isoscape,
  ref_birds,
  assign_birds = NULL,
  isoscape_pred_column = "predkrig",
  isoscape_sd_column = "stdkrig",
  self_assign = FALSE
)

Arguments

isoscape	the data frame read in from "prediction.txt" from ISOMAP. The latitude column must be named "lat" and the longitude column must be named "long". You have to choose which columns to use with the parameters isoscape_pred_column and isoscape_sd_column.
ref_birds	a data frame of reference birds. This should have (at least) columns of "ID" (for unique identifiers for each bird), "lat", "long", "Isotope.Value" and "Location". The "Location" column will be used to group samples for the Vander Zanden Rescaling.
assign_birds	A data frame of birds whose breeding origins are to be inferred. These must have at a minimum the column "ID" (for uniqe identifiers for the birds) and the column "Isotope.Value". This can be left NULL if there are no birds of unknown origin to assign (for example if you are performing cross-validation on the ref_birds).
isoscape_pred_column	the name of the column in isoscape to be used as the prediction (default is "predkrig").
isoscape_sd_column	the name of the column in isoscape to be used as the standard deviation (default is "stdkrig").
self_assign	if TRUE, then the birds in ref_birds will each have posterior surfaces computed for them using a leave one out procedure (i.e. each bird in turn is left out while rescaling the precip isomap to a tissue isomap). Should not be TRUE if assign_birds is non NULL.

Details

For details see:

Vander Zanden HB, Wunder MB, Hobson KA, Van Wilgenburg SL, Wassenaar LI, Welker JM, Bowen GJ (2014) Contrasting assignment of migratory organisms to geographic origins using long-term versus year-specific precipitation isotope maps. Methods in Ecology and Evolution, 5, 891-900.

And the re-explanation of that method in Ruegg et al. (2017).

Examples

# obtain posterior probability rasters for the first 2 birds in the migrant_wiwa_isotopes
# data set.  This takes about 15 seconds on my laptop (most of that time is preparatory---once
# that is done, each bird goes much faster). So we don't run it here.
## Not run: 
birds2 <- isotope_posterior_probs(isoscape = isomap_job54152_prediction,
                        ref_birds = breeding_wiwa_isotopes,
                        assign_birds = migrant_wiwa_isotopes[1:2,]
                        )

## End(Not run)

# However, you can load the results as a saved data object to see what they look like:
birds2 <- example_isotope_posteriors


# Since the ref_birds above were separate from the migrant birds, no leave-one-out was
# performed.  Hence birds2$loo_results is NULL, and all the results are in
# birds2$regular.

# Look at the names of the resulting output for the first bird:
names(birds2$regular[[1]])

names(birds2$regular[[1]]$assignment_parameters)



# If you want to do self-assignment for a whole bunch of reference birds, it takes much longer.
# It looks like this:
## Not run: 
self_ass <- isotope_posterior_probs(isoscape = isomap_job54152_prediction,
                                    ref_birds = breeding_wiwa_isotopes,
                                    self_assign = TRUE)

## End(Not run)

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