Ellipse and convex hull fitting package to estimate niche width for stable isotope data (and potentially other relevant types of data)
MixSIAR is intended to encompass all the mixing model functionality in the SIAR package. SIAR development will stop at some point in the future (probably in 2015), and the SIBER routines will become orphaned. This is the start of a full recode of SIBER to be a standalone package. Also intended are some major improvements to model fitting, via z-scoring and back-transforming to improve fitting via MCMC in JAGS.
Comments and suggestions welcome. If anyone wants to contribute code, please let me know and we can chat about how to proceed.
This package is currently not at a stage where it can be installed as a proper package, and needs to be run as a set of scripts and functions instead. Download this repo and set your working directory to the parent folder SIBER. Then open and/or source the file "test_siber_object_creation_and_plotting.R" which will source the functions it needs, load some example data, plot it and calculate some basic maximum likelihood based summary statistics. I am working on this example to add the Bayesian fitting and subsequent analyses for both the ellipse, and hull based metrics for among group and among community comparisons respectively. More information and examples from the current version of SIBER which is part of the SIAR package is available from my website.
##Acknowledgments Some code and much input from my collaborator and co-author Andrew Parnell @aparnellstats. Thanks to Alex Bond @thelabandfield for helping identify some problems in model fitting which will be resolved by z-scoring, fitting and back-transforming. This functionality is yet to be implemented here, but is currently available in my repo SIBER-sandbox
Jackson, A.L., Parnell, A.C., Inger R., & Bearhop, S. 2011. Comparing isotopic niche widths among and within communities: SIBER – Stable Isotope Bayesian Ellipses in R. Journal of Animal Ecology, 80, 595-602. doi