Stable Isotope Bayesian Ellipses in R

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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