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.

AuthorAndrew Jackson and Andrew Parnell
Date of publication2017-03-16 03:19:20
MaintainerAndrew Jackson <a.jackson@tcd.ie>
LicenseGPL (>= 2)
Version2.1.2

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...

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...

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...

Functions

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

Files

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/Points-Inside-Outside-Ellipse.Rmd
SIBER/inst/doc/Introduction-to-SIBER.Rmd
SIBER/inst/doc/Customising-Plots-Manually.R
SIBER/inst/doc/Points-Inside-Outside-Ellipse.R
SIBER/inst/doc/Ellipse-Overlap.Rmd
SIBER/inst/doc/Customising-Plots-Manually.html
SIBER/inst/doc/Introduction-to-SIBER.html
SIBER/inst/doc/Points-Inside-Outside-Ellipse.html
SIBER/inst/doc/Ellipse-Overlap.html
SIBER/inst/doc/Customising-Plots-Manually.Rmd
SIBER/inst/doc/Ellipse-Overlap.R
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/maxLikOverlap.R SIBER/R/bayesianLayman.R SIBER/R/SIBER.R SIBER/R/siberMVN.R SIBER/R/ellipseBackTransform.R SIBER/R/ellipsoidTranform.R SIBER/R/generateSiberGroup.R SIBER/R/generateSiberCommunity.R SIBER/R/hullArea.R SIBER/R/laymanMetrics.R SIBER/R/plotSiberObject.R SIBER/R/bayesianOverlap.R SIBER/R/groupMetricsML.R SIBER/R/siberConvexhull.R SIBER/R/plotGroupHulls.R SIBER/R/pointsToEllipsoid.R SIBER/R/fitEllipse.R SIBER/R/addEllipse.R SIBER/R/ellipseInOut.R SIBER/R/siberdensityplot.R SIBER/R/datalist.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/Points-Inside-Outside-Ellipse.Rmd
SIBER/vignettes/test-nonnumeric-community-labels.Rmd
SIBER/vignettes/Introduction-to-SIBER.Rmd
SIBER/vignettes/Ellipse-Overlap.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/pointsToEllipsoid.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/ellipseInOut.Rd SIBER/man/sigmaSEA.Rd SIBER/man/ellipsoidTransform.Rd SIBER/man/bayesianOverlap.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/maxLikOverlap.Rd SIBER/man/plotGroupHulls.Rd SIBER/man/demo.siber.data.Rd SIBER/man/ellipseBackTransform.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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