sisus: SISUS: Stable Isotope Sourcing using Sampling

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SISUS for source partitioning using stable isotopes. SISUS reads in a specific Excel-like workbook and performs an IsoSource-type analysis by returning a sample of feasible solutions to p in the non-over constrained linear systems, b=Ap. Edit \file{sisus_*_template.xls} and input data values and run parameters. Run \code{\link{sisus.run}(filename)}. See output in current working directory.

Author
Erik Barry Erhardt [aut, cre]
Date of publication
2014-11-22 02:13:02
Maintainer
Erik Barry Erhardt <erike@stat.unm.edu>
License
GPL (>= 2)
Version
3.9-13
URLs

View on CRAN

Man pages

additional.linear.constraints
Additional Linear Constraints
assign.variables
Assign variables from input file to variable names
diag.panel.hist
define scatterplot diagonal formatting
dirichlet.moments
Calculate the moments of the Dirichlet distribution given the...
filename.clean
Clean up filenames, replacing spaces and bad characters with...
get.data
Get data from Excel spreadsheet
indy.mixture.isotope.mvn.sample
Strip out the samples associated with the current mixture
isotope.mvn.sampling
Samples isotope values from the Multivariate Normal...
mcmc.diagnostics
MCMC Diagnostics
model.mass.balance.equation
Mass balance equations for converting isotope values to...
model.mass.balance.equation.inverse
Inverse Mass balance equations for converting biomass sampled...
numerical.summaries
Numerical summaries
polytope.constraints
Polytope constraints (incorporates both Isotope and...
polytope.multiple.samples
Defines linear constraints for each sample from the isotope...
prior.on.p
Prior on the vector of source proportions, p, is defined by...
progress.time
returns the time taken since the time started
resample.dirichlet.p
Resamples weighted samples from the polytope from the...
sample.from.polytope
CORE function to draw the samples from the polytope
sisus-package
SISUS: Stable Isotope Sourcing using Sampling
sisus.run
driver program for SISUS
s.plot.convex.hull
Convex Hull plot
s.plot.convex.hull.titles
outside titles Convex Hull matrix plot
s.plot.marginal.histogram
Plot marginal histograms
s.plot.scatterplot.sample
Scatterplot matrix
s.plot.settings.begin.end
Plot settings for all plots
write.Ab
write A matrix and b vector
write.input
Write input values out to a file
write.model.settings
Write model settings to the process log
write.out
write directly to the screen
write.progress
write progress to the screen

Files in this package

sisus
sisus/inst
sisus/inst/extdata
sisus/inst/extdata/SISUS_v0_09_template.xls
sisus/NAMESPACE
sisus/R
sisus/R/get.data.R
sisus/R/s.plot.settings.begin.end.R
sisus/R/s.plot.scatterplot.sample.R
sisus/R/s.plot.convex.hull.R
sisus/R/mcmc.diagnostics.R
sisus/R/progress.time.R
sisus/R/diag.panel.hist.R
sisus/R/s.plot.convex.hull.titles.R
sisus/R/write.progress.R
sisus/R/write.out.R
sisus/R/resample.dirichlet.p.R
sisus/R/model.mass.balance.equation.inverse.R
sisus/R/prior.on.p.R
sisus/R/polytope.multiple.samples.R
sisus/R/write.Ab.R
sisus/R/assign.variables.R
sisus/R/numerical.summaries.R
sisus/R/indy.mixture.isotope.mvn.sample.R
sisus/R/isotope.mvn.sampling.R
sisus/R/additional.linear.constraints.R
sisus/R/filename.clean.R
sisus/R/model.mass.balance.equation.R
sisus/R/sisus.run.R
sisus/R/polytope.constraints.R
sisus/R/s.plot.marginal.histogram.R
sisus/R/sample.from.polytope.R
sisus/R/write.input.R
sisus/R/write.model.settings.R
sisus/R/dirichlet.moments.R
sisus/MD5
sisus/DESCRIPTION
sisus/man
sisus/man/sisus-package.Rd
sisus/man/write.progress.Rd
sisus/man/get.data.Rd
sisus/man/model.mass.balance.equation.inverse.Rd
sisus/man/numerical.summaries.Rd
sisus/man/indy.mixture.isotope.mvn.sample.Rd
sisus/man/dirichlet.moments.Rd
sisus/man/write.model.settings.Rd
sisus/man/assign.variables.Rd
sisus/man/mcmc.diagnostics.Rd
sisus/man/isotope.mvn.sampling.Rd
sisus/man/s.plot.scatterplot.sample.Rd
sisus/man/filename.clean.Rd
sisus/man/model.mass.balance.equation.Rd
sisus/man/write.out.Rd
sisus/man/write.Ab.Rd
sisus/man/prior.on.p.Rd
sisus/man/s.plot.marginal.histogram.Rd
sisus/man/polytope.multiple.samples.Rd
sisus/man/progress.time.Rd
sisus/man/s.plot.convex.hull.Rd
sisus/man/s.plot.settings.begin.end.Rd
sisus/man/s.plot.convex.hull.titles.Rd
sisus/man/sisus.run.Rd
sisus/man/resample.dirichlet.p.Rd
sisus/man/additional.linear.constraints.Rd
sisus/man/sample.from.polytope.Rd
sisus/man/write.input.Rd
sisus/man/polytope.constraints.Rd
sisus/man/diag.panel.hist.Rd