Fits bi-variate ellipses to stable isotope data using Bayesian inference with the aim being to describe and compare their isotopic niche.
Plot-posterior-ellipsesthat shows how to plot multiple posterior ellipse draws on top of data using
fitEllipseso that it now correctly inherits
*.RDatafile to enable convergence diagnostics for each ellipse within
fitEllipse. This option is set in the higher level user-specified object
Test-convergenceto illustrate this new functionality of saving the raw
jagsoutput and testing using Gelman diagnostics.
spatstat.utilsas per instructions from their package maintainers 23/03/2017
allCentoidVectorsadded to allow pairwise comparison of the locations of two groups using vectors. Illustrated in an accompanying vignette.
bayesianOverlapfor now until I can push a hotfix to CRAN.
devtools::install_github("andrewljackson/SIBER", build_vingettes = TRUE)
atanin place of
asinwhich is a more elegant way of ensuring the sign of the returned angle is correct.
bayesianOverlap()that calculates the posterior overlap between ellipses fitted to two groups. Thanks to Josh Stewart for forcing my hand on this long-overdue feature.
maxLikOverlap()to ease the calculation of overlap between ellipses using the ML estimated ellipses which previously required more manually coding than was ideal. Thanks Mark Nowak and SarinaJ for spotting some bugs and helping work them out.
pointsToEllipsoidto enable testing of whether points lie inside or outside an n-dimensional ellipsoid, including the bivariate ellipse. These are useful for testing that the quantile prediction ellipses do indeed contain the expected number of data points from a sample. It might also be useful for assignment, identification of outliers, or measures of overlap of individual data points with other ellipses.