siar: Stable Isotope Analysis in R

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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

Author
Andrew Parnell and Andrew Jackson
Date of publication
2013-04-23 16:50:07
Maintainer
Andrew Parnell <Andrew.Parnell@ucd.ie>
License
GPL (>= 2)
Version
4.2

View on CRAN

Man pages

allgroups
The entire set of Geese isotope data
concdepdemo
Concentration dependence values for the geese demo data
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
newgraphwindow
Opens a new graphics window on a variety of platforms
panelcontour
Adds contours to a matrix plot
panelcor
Adds correlations to a matrix plot
panelhist
Adds histograms to the diagonal of a matrix plot
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
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
sourcesdemo
Source (in this case plant) isotope values

Files in this package

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