Data and tools supporting geographic assignment of materials based on their isotopic chemistry. Isoscapes (environmental isotope maps) can be generated externally or downloaded using the getIsoscapes function. Data from samples of known origin are used to calibrate the relationship between isoscape and sample values, and can be provided by the user or extracted from the package database (knownOrig.rda). Database data or user-provided known-origin or unknown origin sample data can be transformed among different H and O isotope reference scales to improve comparability (refTrans). Functions (calRaster, pdRaster) support calibrating one or more isoscapes (multiple layers combined using isoStack) and inverting the assignment model to estimate the probability of origin for unknown samples across a geographic study domain. Functions (QA, plot.QA) allow quality assessment of assignment results and comparison of methods using split-sample tests and known origin data. Functions (oddsRatio, qtlRaster, jointP, unionP) support post-hoc classification of results, summarization of results from multiple samples, and comparison of support for different locations.
For current production release, see the vignette here and install from CRAN.
For examples demonstrating functions in the latest development release, see https://spatial-lab.github.io/assignR/.
install.packages("assignR")
library(assignR)
Datasets
d2h_lrNA - Low-resolution, North American crop of growing season d2H isoscape, used in examples.
sr_MI - Low-resolution crop of locally-weathered Sr isoscape, used in examples.
knownOrig - Hydrogen and oxygen isotope values of known-origin samples including human hair, insect chitin and bird feathers, with location information.
stds - Information on reference scales used to report data from different labs, useful for converting between scales
naMap - North America outline
states - 48 contiguous United States
Functions
subOrigData - Subset the known-origin stable isotope dataset included in this package
refTrans - Transform data among reference scales
getIsoscapes - Download and unpack isoscapes from waterisotopes.org
isoStack - Combine multiple isoscapes
plot.isoStack - Plot isoStack object
calRaster - Transform one or more isoscapes to reflect target sample type
pdRaster - Assign sample to calibrated isoscape(S) based on isotopic composition(s)
qtlRaster - Select most likely region of origin from posterior probability surface (by cumulative percent area probability)
jointP - Calculate joint probability for individuals of common origin (product of probabilities)
unionP - Calculate probability that at least one individual came from each map location (union of probabilities)
oddsRatio - Calculate ratio of odds for two locations or areas (points or polygons)
wDist - Summarize distance and direction of movement
c.wDist - Combine wDist statistics for multiple samples
plot.wDist - Plot results from wDist
QA - Quality analysis of geographic assignment
plot.QA - Plot results of one or more quality analyses from QA function
