# Stable Isotope Bayesian Ellipses in R

## Documentation for package ‘SIBER’ version 2.1.9

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

addEllipse | Adds an ellipse around some data to an existing plot
allCentroidVectors | Plot the pairwise distances and angles describing the difference between centroids of all groups
allgroups | The entire set of Geese isotope data
bayesianLayman | Calculate Layman metrics on Bayesian posterior samples of a community
bayesianOverlap | Calculate the overlap between two ellipses based on their posterior distributions.
communityMetricsML | Calculate the point estimates of the Layman metrics for each community
concdepdemo | A set of concentration dependence values for stable isotope analysis
correctionsdemo | A set of trophic discrimination factors for brent geese feeding on their sources.
createSiberObject | Read in SIBER format data and generate the SIBER object
demo.siber.data | Simulated d13C and d15N isotope-space data
demo.siber.data.2 | Simulated d13C and d15N isotope-space data
ellipseBackTransform | Back-transform a z-score siber ellipse to original location and scale.
ellipseInOut | Test whether a set of points are inside or outside a defined circle
ellipsoidTransform | Apply a normalisation transformation to vectors of data onto ellipsoids
extractPosteriorMeans | Extract posterior means from call to 'siberMVN'
fitEllipse | Fit a multivariate normal distribution to x and y data using jags
geese1demo | A single group of the geese data
geese2demo | A single group of the geese data
genCircle | Create a sequence of points on a circle
generateSiberCommunity | A utility function to simulate a single community comprised of groups
generateSiberData | A utility function to simulate isotope data for several communities
generateSiberGroup | A utility function to simulate a single group of data
groupMetricsML | Calculate maximum likelihood based measures of dispersion of bivariate data
hullArea | Calculate the area of a convex hull given its coordinates
kapow | KAPOW!
laymanMetrics | Calculates the 6 Layman metrics on a vector of x and y data
maxLikOverlap | Calculate the overlap between two ellipses based on the maximum likelihood fitted ellipses.
mongoose | A set of isotope observations for mongooses nested within packs
plotCommunityHulls | Adds convex hulls to each community to an existing plot
plotGroupEllipses | Adds ellipses to an existing plot for each of your groups
plotGroupHulls | Plots illustrative convex hulls for each group within all communities
plotSiberObject | Creates an isotope scatterplot and provides a wrapper to ellipse and hull plotting
pointsToEllipsoid | Test whether a set of points are inside or outside a defined ellipse
posteriorSEA | Calculate the SEA based on a posterior distribution of Sigma
siberCentroids | Calculate the polar form of the vector between pairs of ellipse centroids
siberConvexhull | Calculate metrics and plotting information for convex hulls
siberDensityPlot | Plot credible intervals as shaded boxplots using 'hdr.boxplot'
siberEllipses | Calculate the Bayesian Standard Ellipse Area for all groups
siberKapow | Calculates the boundary of a union of ellipses
siberMVN | Fit Bayesian bivariate normal distributions to each group in each community
sigmaSEA | Calculate metrics corresponding to the Standard Ellipse based on a covariance matrix
sourcesdemo | A set of isotope observations on food sources of brent geese
specificCentroidVectors | Calculate the pairwise distances and angles describing the difference between centroids of paired groups