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sisus (version 3.9-13)

SISUS: Stable Isotope Sourcing using Sampling

Description

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.

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Version

Install

install.packages('sisus')

Monthly Downloads

5

Version

3.9-13

License

GPL (>= 2)

Maintainer

Erik Barry Erhardt

Last Published

November 22nd, 2014

Functions in sisus (3.9-13)

get.data

Get data from Excel spreadsheet
sisus.run

driver program for SISUS
model.mass.balance.equation

Mass balance equations for converting isotope values to biomass values
s.plot.scatterplot.sample

Scatterplot matrix
isotope.mvn.sampling

Samples isotope values from the Multivariate Normal Distribution
sisus-package

SISUS: Stable Isotope Sourcing using Sampling
s.plot.convex.hull

Convex Hull plot
indy.mixture.isotope.mvn.sample

Strip out the samples associated with the current mixture
s.plot.settings.begin.end

Plot settings for all plots
numerical.summaries

Numerical summaries
diag.panel.hist

define scatterplot diagonal formatting
model.mass.balance.equation.inverse

Inverse Mass balance equations for converting biomass sampled values back to isotope values
dirichlet.moments

Calculate the moments of the Dirichlet distribution given the values of vector alpha
write.input

Write input values out to a file
write.out

write directly to the screen
polytope.multiple.samples

Defines linear constraints for each sample from the isotope distribution, passed to sample.from.polytope()
assign.variables

Assign variables from input file to variable names
polytope.constraints

Polytope constraints (incorporates both Isotope and Additional linear constraints)
resample.dirichlet.p

Resamples weighted samples from the polytope from the Dirichlet distribution on the p vector
filename.clean

Clean up filenames, replacing spaces and bad characters with "_" and "-"
s.plot.convex.hull.titles

outside titles Convex Hull matrix plot
progress.time

returns the time taken since the time started
write.model.settings

Write model settings to the process log
additional.linear.constraints

Additional Linear Constraints
s.plot.marginal.histogram

Plot marginal histograms
write.Ab

write A matrix and b vector
prior.on.p

Prior on the vector of source proportions, p, is defined by the given vector alpha
sample.from.polytope

CORE function to draw the samples from the polytope
mcmc.diagnostics

MCMC Diagnostics
write.progress

write progress to the screen