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 publication2016-08-04 00:57:39
MaintainerAndrew Jackson <a.jackson@tcd.ie>
LicenseGPL (>= 2)
Version2.0.3

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

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

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