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

Functions

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

Files

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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