siar: Stable Isotope Analysis in R

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

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

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

Functions

allgroups Man page
concdepdemo Man page
correctionsdemo Man page
geese1demo Man page
geese2demo Man page
newgraphwindow Man page
panelcontour Man page
panelcor Man page
panelhist Man page
siar Man page
siaraddcross Man page
siardemo Man page
siarelicit Man page
siarhdrs Man page
siarhistograms Man page
siarloaddata Man page
siarmatrixplot Man page
siarmcmcdirichletv4 Man page
siarmenu Man page
siarmultigrouprun Man page
siar-package Man page
siarplotdata Man page
siarplotdatawrapper Man page
siarplottarget Man page
siarproportionbygroupplot Man page
siarproportionbysourceplot Man page
siarsaveoutput Man page
siarsinglegrouprun Man page
siarsolomcmcv4 Man page
siarsolomultigrouprun Man page
siarsolosinglegrouprun Man page
sourcesdemo Man page

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

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

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

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