sisus: SISUS: Stable Isotope Sourcing using Sampling

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.

AuthorErik Barry Erhardt [aut, cre]
Date of publication2014-11-22 02:13:02
MaintainerErik Barry Erhardt <erike@stat.unm.edu>
LicenseGPL (>= 2)
Version3.9-13
http://StatAcumen.com/sisus

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

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