SIBER: Stable Isotope Bayesian Ellipses in R

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

Author
Andrew Jackson and Andrew Parnell
Date of publication
2016-08-04 00:57:39
Maintainer
Andrew Jackson <a.jackson@tcd.ie>
License
GPL (>= 2)
Version
2.0.3

View on CRAN

Man pages

addEllipse
Adds an ellipse around some data to an existing plot
bayesianLayman
Calculate Layman metrics on Bayesian postrior samples of a...
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...
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
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...
posteriorSEA
Calculate the SEA based on a posterior distribution of Sigma
SIBER
SIBER: A package for fitting Bayesian Ellipses to Stable...
siberConvexhull
Calculate metrics and plotting information for convex hulls
siberDensityPlot
Plot credible intervals as shaded boxplots using...
siberEllipses
Calculate the point estimates of the Layman metrics for each...
siberMVN
Fit Bayesian bivariate normal distributions to each group in...
sigmaSEA
Calculate metrics corresponding to the Standard Ellipse based...

Files in this package

SIBER
SIBER/inst
SIBER/inst/CITATION
SIBER/inst/extdata
SIBER/inst/extdata/test.community.names.csv
SIBER/inst/extdata/demo.siber.data.csv
SIBER/inst/extdata/test.group.names.csv
SIBER/inst/doc
SIBER/inst/doc/Introduction-to-SIBER.Rmd
SIBER/inst/doc/Customising-Plots-Manually.R
SIBER/inst/doc/Customising-Plots-Manually.html
SIBER/inst/doc/Introduction-to-SIBER.html
SIBER/inst/doc/Customising-Plots-Manually.Rmd
SIBER/inst/doc/Introduction-to-SIBER.R
SIBER/NAMESPACE
SIBER/NEWS.md
SIBER/data
SIBER/data/demo.siber.data.rda
SIBER/R
SIBER/R/genCircle.R
SIBER/R/generateSiberData.R
SIBER/R/bayesianLayman.R
SIBER/R/SIBER.R
SIBER/R/siberMVN.R
SIBER/R/ellipseBackTransform.R
SIBER/R/generateSiberGroup.R
SIBER/R/generateSiberCommunity.R
SIBER/R/plotSiberObject.R
SIBER/R/laymanmetrics.R
SIBER/R/groupMetricsML.R
SIBER/R/siberConvexhull.R
SIBER/R/plotGroupHulls.R
SIBER/R/fitEllipse.R
SIBER/R/addEllipse.R
SIBER/R/siberdensityplot.R
SIBER/R/datalist.R
SIBER/R/hullarea.R
SIBER/R/siberEllipses.R
SIBER/R/plotCommunityHulls.R
SIBER/R/createSiberObject.R
SIBER/R/posteriorSEA.R
SIBER/R/communityMetricsML.R
SIBER/R/extractPosteriorMeans.R
SIBER/R/plotGroupEllipses.R
SIBER/R/sigmaSEA.R
SIBER/vignettes
SIBER/vignettes/test-nonnumeric-community-labels.Rmd
SIBER/vignettes/Introduction-to-SIBER.Rmd
SIBER/vignettes/test-nonnumeric-group-labels.Rmd
SIBER/vignettes/Customising-Plots-Manually.Rmd
SIBER/MD5
SIBER/build
SIBER/build/vignette.rds
SIBER/DESCRIPTION
SIBER/man
SIBER/man/generateSiberCommunity.Rd
SIBER/man/plotGroupEllipses.Rd
SIBER/man/plotSiberObject.Rd
SIBER/man/siberEllipses.Rd
SIBER/man/posteriorSEA.Rd
SIBER/man/hullArea.Rd
SIBER/man/laymanMetrics.Rd
SIBER/man/communityMetricsML.Rd
SIBER/man/groupMetricsML.Rd
SIBER/man/extractPosteriorMeans.Rd
SIBER/man/generateSiberData.Rd
SIBER/man/sigmaSEA.Rd
SIBER/man/addEllipse.Rd
SIBER/man/fitEllipse.Rd
SIBER/man/createSiberObject.Rd
SIBER/man/siberDensityPlot.Rd
SIBER/man/siberConvexhull.Rd
SIBER/man/generateSiberGroup.Rd
SIBER/man/bayesianLayman.Rd
SIBER/man/plotCommunityHulls.Rd
SIBER/man/siberMVN.Rd
SIBER/man/SIBER.Rd
SIBER/man/genCircle.Rd
SIBER/man/plotGroupHulls.Rd
SIBER/man/demo.siber.data.Rd
SIBER/man/ellipseBackTransform.Rd