siar: Stable Isotope Analysis in R
Version 4.2

This package takes data on organism isotopes and fits a Bayesian model to their dietary habits based upon a Gaussian likelihood with a mixture dirichlet-distributed prior on the mean. It also includes SiBER metrics. See siardemo() for an example. Version 4.1.2 contains bug fixes to allow more than isotope numbers other than 2. Version 4.2 fixes a bug that stopped siar working on 64-bit systems

AuthorAndrew Parnell and Andrew Jackson
Date of publication2013-04-23 16:50:07
MaintainerAndrew Parnell <Andrew.Parnell@ucd.ie>
LicenseGPL (>= 2)
Version4.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("siar")

Getting started

Package overview

Popular man pages

bayestwoNorm: Bayesian Independent Normal Distributions
overlap: Area of overlap between two estimated ellipses
popSEA: Standard Ellipse Metrics for the Population
siarhdrs: Creates hdrs and convergence diagnostics from siar output
siar-package: Stable Isotope Analysis in R.
siarsolomcmcv4: MCMC for stable isotope data with only single target...
siarsolosinglegrouprun: siar MCMC for single group data with only one organism
See all...

All man pages Function index File listing

Man pages

allgroups: The entire set of Geese isotope data
bayesMVN: Bayesian MVN
bayestwoNorm: Bayesian Independent Normal Distributions
concdepdemo: Concentration dependence values for the geese demo data
convexhull: Convex Hull
correctionsdemo: Fractionation correction values for the geese data
geese1demo: A single group of the geese data
geese2demo: A multi-group version of the geese plasma data
hullarea: Convex Hull Area
laymanmetrics: Isotope-space Niche Width Metrics
newgraphwindow: Opens a new graphics window on a variety of platforms
overlap: Area of overlap between two estimated ellipses
panelcontour: Adds contours to a matrix plot
panelcor: Adds correlations to a matrix plot
panelhist: Adds histograms to the diagonal of a matrix plot
plotSigmaEllipse: Plot an ellipse based on a correlation matrix
popSEA: Standard Ellipse Metrics for the Population
siaraddcross: Plotting tool for adding isotope bi-plot data to a figure
siardemo: Runs the siar model and some nice plots for the siar package
siardensityplot: SIAR's Custom Density Plot
siarelicit: Elicit prior parameters for the Dirichlet distribution.
siarhdrs: Creates hdrs and convergence diagnostics from siar output
siarhistograms: Produce neat siar histograms
siarloaddata: Loads in siar data
siarmatrixplot: Matrix plots of siar output
siarmcmcdirichletv4: MCMC for stable isotope data
siarmenu: A list of menu options for running the siar package
siarmultigrouprun: siar MCMC for multi-group data
siar-package: Stable Isotope Analysis in R.
siarplotdata: Produces plots of target data and sources
siarplotdatawrapper: Handles repeated plotting instructions for siarplotdata()
siarplottarget: Plots the consumers' data in isotope space
siarproportionbygroupplot: siar proportion plots by group
siarproportionbysourceplot: siar proportion plots by source
siarsaveoutput: Saves siar output to a file
siarsinglegrouprun: siar MCMC for single group data
siarsolomcmcv4: MCMC for stable isotope data with only single target...
siarsolomultigrouprun: siar MCMC for multi-group data with only one target organism...
siarsolosinglegrouprun: siar MCMC for single group data with only one organism
siber.ellipses: The SIBER method for calculating ellipse based metrics of...
siber.hull.metrics: The SIBER method for calculating Convex Hull based metrics of...
sourcesdemo: Source (in this case plant) isotope values
standard.ellipse: Standard Ellipse

Functions

allgroups Man page
bayesMVN Man page Source code
bayestwoNorm Man page Source code
concdepdemo Man page
convexhull Man page Source code
correctionsdemo Man page
geese1demo Man page
geese2demo Man page
hullarea Man page Source code
laymanmetrics Man page Source code
newgraphwindow Man page Source code
overlap Man page Source code
panelcontour Man page Source code
panelcor Man page Source code
panelhist Man page Source code
plotSigmaEllipse Man page Source code
popSEA Man page Source code
siar Man page
siar-package Man page
siaraddcross Man page Source code
siardemo Man page Source code
siardensityplot Man page Source code
siarelicit Man page Source code
siarhdrs Man page Source code
siarhistograms Man page Source code
siarloaddata Man page Source code
siarmatrixplot Man page Source code
siarmcmcdirichletv4 Man page Source code
siarmenu Man page Source code
siarmultigrouprun Man page Source code
siarplotdata Man page Source code
siarplotdatawrapper Man page Source code
siarplottarget Man page Source code
siarproportionbygroupplot Man page Source code
siarproportionbysourceplot Man page Source code
siarsaveoutput Man page Source code
siarsinglegrouprun Man page Source code
siarsolomcmcv4 Man page Source code
siarsolomultigrouprun Man page Source code
siarsolosinglegrouprun Man page Source code
siber.ellipses Man page Source code
siber.hull.metrics Man page Source code
sourcesdemo Man page
standard.ellipse Man page Source code

Files

MD5
src
src/use.h
src/use.c
src/siarsolomcmcv4.c
src/siarmcmcv4.c
man
man/standard.ellipse.rd
man/sourcesdemo.Rd
man/siber.hull.metrics.rd
man/siber.ellipses.rd
man/siarsolosinglegrouprun.Rd
man/siarsolomultigrouprun.Rd
man/siarsolomcmcv4.Rd
man/siarsinglegrouprun.Rd
man/siarsaveoutput.Rd
man/siarproportionbysourceplot.Rd
man/siarproportionbygroupplot.Rd
man/siarplottarget.Rd
man/siarplotdatawrapper.Rd
man/siarplotdata.Rd
man/siarmultigrouprun.Rd
man/siarmenu.Rd
man/siarmcmcdirichletv4.Rd
man/siarmatrixplot.Rd
man/siarloaddata.Rd
man/siarhistograms.Rd
man/siarhdrs.Rd
man/siarelicit.Rd
man/siardensityplot.rd
man/siardemo.Rd
man/siaraddcross.Rd
man/siar-package.Rd
man/popSEA.rd
man/plotSigmaEllipse.rd
man/panelhist.Rd
man/panelcor.Rd
man/panelcontour.Rd
man/overlap.rd
man/newgraphwindow.Rd
man/laymanmetrics.rd
man/hullarea.rd
man/geese2demo.Rd
man/geese1demo.Rd
man/correctionsdemo.Rd
man/convexhull.rd
man/concdepdemo.Rd
man/bayestwoNorm.rd
man/bayesMVN.rd
man/allgroups.Rd
data
data/sourcesdemo.rda
data/geese2demo.rda
data/geese1demo.rda
data/correctionsdemo.rda
data/concdepdemo.rda
data/allgroups.rda
R
R/standard.ellipse.r
R/siber.hull.metrics.R
R/siber.ellipses.R
R/siarsolosinglegrouprun.R
R/siarsolomultigrouprun.R
R/siarsolomcmcv4.R
R/siarsinglegrouprun.R
R/siarsaveoutput.R
R/siarproportionbysourceplot.R
R/siarproportionbygroupplot.R
R/siarplottarget.R
R/siarplotdatawrapper.R
R/siarplotdata.R
R/siarmultigrouprun.R
R/siarmenu.R
R/siarmcmcdirichletv4.R
R/siarmatrixplot.R
R/siarloaddata.R
R/siarhistograms.R
R/siarhdrs.R
R/siarelicit.R
R/siardensityplot.R
R/siardemo.R
R/siaraddcross.R
R/popSEA.R
R/plotSigmaEllipse.R
R/panelhist.R
R/panelcor.R
R/panelcontour.R
R/overlap.R
R/newgraphwindow.R
R/laymanmetrics.R
R/hullarea.R
R/convexhull.R
R/bayestwoNorm.R
R/bayesMVN.R
NAMESPACE
DESCRIPTION
siar documentation built on May 20, 2017, 12:18 a.m.

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

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.