SIBER: Stable Isotope Bayesian Ellipses in R
Version 2.1.3

Fits bi-variate ellipses to stable isotope data using Bayesian inference with the aim being to describe and compare their isotopic niche.

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AuthorAndrew Jackson and Andrew Parnell
Date of publication2017-04-28 22:22:58 UTC
MaintainerAndrew Jackson <a.jackson@tcd.ie>
LicenseGPL (>= 2)
Version2.1.3
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("SIBER")

Man pages

addEllipse: Adds an ellipse around some data to an existing plot
allCentroidVectors: Plot the pairwise distances and angles describing the...
bayesianLayman: Calculate Layman metrics on Bayesian postrior samples of a...
bayesianOverlap: Calculate the overlap between two ellipses based on their...
communityMetricsML: Calculate the point estimates of the Layman metrics for each...
createSiberObject: Read in SIBER format data and generate the SIBER object
demo.siber.data: Simulated d13C and d15N isotope-space data
ellipseBackTransform: Back-transform a z-score siber ellipse to original location...
ellipseInOut: Test whether a set of points are inside or outside a defined...
ellipsoidTransform: Apply a normalisation transformation to vectors of data onto...
extractPosteriorMeans: Extract posterior means from call to 'siberMVN'
fitEllipse: Fit a multivariate normal distribution to x and y data using...
genCircle: Create a sequence of points on a circle
generateSiberCommunity: A utility function to simulate a single community comprised...
generateSiberData: A utility function to simulate isotope data for several...
generateSiberGroup: A utility function to simulate a single group of data
groupMetricsML: Calculate maximum likelihood based measures of dispersion of...
hullArea: Calculate the area of a convex hull given its coordinates
laymanMetrics: Calculates the 6 Layman metrics on a vector of x and y data
maxLikOverlap: Calculate the overlap between two ellipses based on the...
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...
plotSiberObject: Creates an isotope biplot and provides a wrapper to ellipse...
pointsToEllipsoid: Test whether a set of points are inside or outside a defined...
posteriorSEA: Calculate the SEA based on a posterior distribution of Sigma
SIBER: SIBER: A package for fitting Bayesian Ellipses to Stable...
siberCentroids: Calculate the polar form of the vector between pairs of...
siberConvexhull: Calculate metrics and plotting information for convex hulls
siberDensityPlot: Plot credible intervals as shaded boxplots using...
siberEllipses: Calculate the bayesian Standard Ellipse Area for all groups
siberMVN: Fit Bayesian bivariate normal distributions to each group in...
sigmaSEA: Calculate metrics corresponding to the Standard Ellipse based...
specificCentroidVectors: Calculate the pairwise distances and angles describing the...

Functions

SIBER Man page
SIBER-package Man page
addEllipse Man page Source code
allCentroidVectors Man page Source code
bayesianLayman Man page Source code
bayesianOverlap Man page Source code
communityMetricsML Man page Source code
createSiberObject Man page Source code
demo.siber.data Man page
ellipseBackTransform Man page Source code
ellipseInOut Man page Source code
ellipsoidTransform Man page Source code
extractPosteriorMeans Man page Source code
fitEllipse Man page Source code
genCircle Man page Source code
generateSiberCommunity Man page Source code
generateSiberData Man page Source code
generateSiberGroup Man page Source code
groupMetricsML Man page Source code
hullArea Man page Source code
laymanMetrics Man page Source code
maxLikOverlap Man page Source code
plotCommunityHulls Man page Source code
plotGroupEllipses Man page Source code
plotGroupHulls Man page Source code
plotSiberObject Man page Source code
pointsToEllipsoid Man page Source code
posteriorSEA Man page Source code
siberCentroids Man page Source code
siberConvexhull Man page Source code
siberDensityPlot Man page Source code
siberEllipses Man page Source code
siberMVN Man page Source code
sigmaSEA Man page Source code
specificCentroidVectors Man page Source code

Files

inst
inst/CITATION
inst/extdata
inst/extdata/test.community.names.csv
inst/extdata/demo.siber.data.csv
inst/extdata/test.group.names.csv
inst/doc
inst/doc/Points-Inside-Outside-Ellipse.Rmd
inst/doc/Introduction-to-SIBER.Rmd
inst/doc/Customising-Plots-Manually.R
inst/doc/Points-Inside-Outside-Ellipse.R
inst/doc/Ellipse-Overlap.Rmd
inst/doc/Customising-Plots-Manually.html
inst/doc/Introduction-to-SIBER.html
inst/doc/Points-Inside-Outside-Ellipse.html
inst/doc/Centroid-Vectors.R
inst/doc/Centroid-Vectors.html
inst/doc/Ellipse-Overlap.html
inst/doc/Customising-Plots-Manually.Rmd
inst/doc/Centroid-Vectors.Rmd
inst/doc/Ellipse-Overlap.R
inst/doc/Introduction-to-SIBER.R
NAMESPACE
NEWS.md
data
data/demo.siber.data.rda
R
R/genCircle.R
R/generateSiberData.R
R/maxLikOverlap.R
R/bayesianLayman.R
R/SIBER.R
R/siberMVN.R
R/ellipseBackTransform.R
R/ellipsoidTranform.R
R/generateSiberGroup.R
R/generateSiberCommunity.R
R/hullArea.R
R/laymanMetrics.R
R/plotSiberObject.R
R/bayesianOverlap.R
R/groupMetricsML.R
R/siberConvexhull.R
R/specificCentroidVectors.R
R/allCentroidVectors.R
R/plotGroupHulls.R
R/pointsToEllipsoid.R
R/fitEllipse.R
R/siberCentroids.R
R/addEllipse.R
R/ellipseInOut.R
R/siberdensityplot.R
R/datalist.R
R/siberEllipses.R
R/plotCommunityHulls.R
R/createSiberObject.R
R/posteriorSEA.R
R/communityMetricsML.R
R/extractPosteriorMeans.R
R/plotGroupEllipses.R
R/sigmaSEA.R
vignettes
vignettes/Points-Inside-Outside-Ellipse.Rmd
vignettes/Introduction-to-SIBER.Rmd
vignettes/Ellipse-Overlap.Rmd
vignettes/Customising-Plots-Manually.Rmd
vignettes/Centroid-Vectors.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/generateSiberCommunity.Rd
man/plotGroupEllipses.Rd
man/plotSiberObject.Rd
man/pointsToEllipsoid.Rd
man/siberEllipses.Rd
man/posteriorSEA.Rd
man/hullArea.Rd
man/laymanMetrics.Rd
man/communityMetricsML.Rd
man/specificCentroidVectors.Rd
man/groupMetricsML.Rd
man/extractPosteriorMeans.Rd
man/generateSiberData.Rd
man/ellipseInOut.Rd
man/allCentroidVectors.Rd
man/sigmaSEA.Rd
man/ellipsoidTransform.Rd
man/bayesianOverlap.Rd
man/addEllipse.Rd
man/fitEllipse.Rd
man/siberCentroids.Rd
man/createSiberObject.Rd
man/siberDensityPlot.Rd
man/siberConvexhull.Rd
man/generateSiberGroup.Rd
man/bayesianLayman.Rd
man/plotCommunityHulls.Rd
man/siberMVN.Rd
man/SIBER.Rd
man/genCircle.Rd
man/maxLikOverlap.Rd
man/plotGroupHulls.Rd
man/demo.siber.data.Rd
man/ellipseBackTransform.Rd
SIBER documentation built on May 20, 2017, 12:01 a.m.