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sisus (version 3.9-12)

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

15

Version

3.9-12

License

GPL (>= 2)

Maintainer

Erik Erhardt

Last Published

March 11th, 2014

Functions in sisus (3.9-12)

progress.time

returns the time taken since the time started
additional.linear.constraints

Additional Linear Constraints
mcmc.diagnostics

MCMC Diagnostics
write.Ab

write A matrix and b vector
resample.dirichlet.p

Resamples weighted samples from the polytope from the Dirichlet distribution on the p vector
write.model.settings

Write model settings to the process log
s.plot.scatterplot.sample

Scatterplot matrix
assign.variables

Assign variables from input file to variable names
polytope.multiple.samples

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

driver program for SISUS
polytope.constraints

Polytope constraints (incorporates both Isotope and Additional linear constraints)
sisus-package

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

outside titles Convex Hull matrix plot
s.plot.settings.begin.end

Plot settings for all plots
dirichlet.moments

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

Write input values out to a file
model.mass.balance.equation

Mass balance equations for converting isotope values to biomass values
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
write.out

write directly to the screen
filename.clean

Clean up filenames, replacing spaces and bad characters with "_" and "-"
indy.mixture.isotope.mvn.sample

Strip out the samples associated with the current mixture
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
isotope.mvn.sampling

Samples isotope values from the Multivariate Normal Distribution
s.plot.convex.hull

Convex Hull plot
write.progress

write progress to the screen
s.plot.marginal.histogram

Plot marginal histograms
get.data

Get data from Excel spreadsheet
numerical.summaries

Numerical summaries