spatial-lab/assignr

R package for geographic assignment

assignR

Basic

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 and load latest CRAN release

install.packages("assignR")
library(assignR)

Package contents

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