Package: simmr 0.5.2

simmr: A Stable Isotope Mixing Model

Fits Stable Isotope Mixing Models (SIMMs) and is meant as a longer term replacement to the previous widely-used package SIAR. SIMMs are used to infer dietary proportions of organisms consuming various food sources from observations on the stable isotope values taken from the organisms' tissue samples. However SIMMs can also be used in other scenarios, such as in sediment mixing or the composition of fatty acids. The main functions are simmr_load() and simmr_mcmc(). The two vignettes contain a quick start and a full listing of all the features. The methods used are detailed in the papers Parnell et al 2010 <doi:10.1371/journal.pone.0009672>, and Parnell et al 2013 <doi:10.1002/env.2221>.

Authors:Emma Govan [aut], Andrew Parnell [cre, aut]

simmr_0.5.2.tar.gz
simmr_0.5.2.zip(r-4.7)simmr_0.5.2.zip(r-4.6)simmr_0.5.2.zip(r-4.5)
simmr_0.5.2.tgz(r-4.6-x86_64)simmr_0.5.2.tgz(r-4.6-arm64)simmr_0.5.2.tgz(r-4.5-x86_64)simmr_0.5.2.tgz(r-4.5-arm64)
simmr_0.5.2.tar.gz(r-4.7-arm64)simmr_0.5.2.tar.gz(r-4.6-arm64)simmr_0.5.2.tar.gz(r-4.7-x86_64)simmr_0.5.2.tar.gz(r-4.6-x86_64)
simmr_0.5.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
simmr/json (API)
NEWS

# Install 'simmr' in R:
install.packages('simmr', repos = c('https://andrewcparnell.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/andrewcparnell/simmr/issues

Pkgdown/docs site:https://andrewcparnell.github.io

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • jags– Just Another Gibbs Sampler for Bayesian MCMC - binary JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS. JAGS was written with three aims in mind: * To have an engine for the BUGS language that runs on Unix * To be extensible, allowing users to write their own functions, distributions and samplers. * To be a plaftorm for experimentation with ideas in Bayesian modelling This package contains the 'jags' binary as well as the associated shared library modules loaded by the binary.
Datasets:
  • geese_data - Geese stable isotope mixing data set
  • geese_data_day1 - A smaller version of the Geese stable isotope mixing data set
  • simmr_data_1 - A simple fake stable isotope mixing data set
  • simmr_data_2 - A 3-isotope fake stable isotope mixing data set
  • square_data - An artificial data set used to indicate effect of priors

On CRAN:

Conda:

openblascppjags

7.72 score 36 stars 97 scripts 976 downloads 12 mentions 9 exports 65 dependencies

Last updated from:f27bb42742. Checks:11 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK253
source / vignettesOK411
linux-release-x86_64OK252
macos-release-arm64OK222
macos-release-x86_64OK345
macos-oldrel-arm64OK178
macos-oldrel-x86_64OK508
windows-develOK264
windows-releaseOK231
windows-oldrelOK198
wasm-releaseOK134

Exports:combine_sourcescompare_groupscompare_sourcesposterior_predictiveprior_vizsimmr_elicitsimmr_ffvbsimmr_loadsimmr_mcmc

Dependencies:abindbackportsbayesmbayesplotbootcheckmateclicodacompositionscpp11crayonDEoptimRdistributionaldplyrfarverforcatsgenericsGGallyggplot2ggridgesggstatsgluegridExtragtablehmsisobandlabelinglatticelifecyclemagrittrMASSmatrixStatsnumDerivpatchworkpillarpkgconfigplyrposteriorprettyunitsprogresspurrrR2jagsR2WinBUGSR6RColorBrewerRcppRcppArmadilloRcppDistreshape2rjagsrlangrobustbaseS7scalesstringistringrtensorAtibbletidyrtidyselectutf8vctrsviridisviridisLitewithr

simmr: advanced plotting guide

Andrew Parnell

Rendered fromadvanced_plotting.Rmdusingknitr::rmarkdownon Jun 01 2026.

Last update: 2023-10-13
Started: 2021-09-16

simmr: quick start guide

Andrew Parnell

Rendered fromquick_start.Rmdusingknitr::rmarkdownon Jun 01 2026.

Last update: 2023-10-02
Started: 2017-08-27

Stable Isotope Mixing Models in R with simmr

Andrew Parnell and Richard Inger

Rendered fromsimmr.Rmdusingknitr::rmarkdownon Jun 01 2026.

Last update: 2026-04-30
Started: 2015-08-07