Package: simmr 0.5.1.216

Emma Govan

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 [cre, aut], Andrew Parnell [aut]

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simmr.pdf |simmr.html✨
simmr/json (API)
NEWS

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

Peer review:

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

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • jags– Just Another Gibbs Sampler for Bayesian MCMC
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:

9 exports 28 stars 3.59 score 81 dependencies 12 mentions 72 scripts 1.4k downloads

Last updated 5 months agofrom:6cbaa51e76. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 08 2024
R-4.5-win-x86_64OKSep 08 2024
R-4.5-linux-x86_64OKSep 08 2024
R-4.4-win-x86_64OKSep 08 2024
R-4.4-mac-x86_64OKSep 08 2024
R-4.4-mac-aarch64OKSep 08 2024
R-4.3-win-x86_64OKSep 08 2024
R-4.3-mac-x86_64OKSep 08 2024
R-4.3-mac-aarch64OKSep 08 2024

Exports:combine_sourcescompare_groupscompare_sourcesposterior_predictiveprior_vizsimmr_elicitsimmr_ffvbsimmr_loadsimmr_mcmc

Dependencies:abindbackportsbayesmbayesplotbitbit64bootbroombroom.helperscardscheckmateclicliprcodacolorspacecompositionscpp11crayonDEoptimRdistributionaldplyrfansifarverforcatsgenericsGGallyggplot2ggridgesggstatsgluegridExtragtablehavenhmsisobandlabelinglabelledlatticelifecyclemagrittrMASSMatrixmatrixStatsmgcvmunsellnlmenumDerivpatchworkpillarpkgconfigplyrposteriorprettyunitsprogresspurrrR2jagsR2WinBUGSR6RColorBrewerRcppRcppArmadilloRcppDistreadrreshape2rjagsrlangrobustbasescalesstringistringrtensorAtibbletidyrtidyselecttzdbutf8vctrsviridisviridisLitevroomwithr

simmr: advanced plotting guide

Andrew Parnell

Rendered fromadvanced_plotting.Rmdusingknitr::rmarkdownon Sep 08 2024.

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

simmr: quick start guide

Andrew Parnell

Rendered fromquick_start.Rmdusingknitr::rmarkdownon Sep 08 2024.

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 Sep 08 2024.

Last update: 2023-10-13
Started: 2015-08-07