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simmr (version 0.5.1.215)

A Stable Isotope Mixing Model

Description

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 , and Parnell et al 2013 .

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install.packages('simmr')

Monthly Downloads

475

Version

0.5.1.215

License

GPL (>= 2)

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Maintainer

Emma Govan

Last Published

October 13th, 2023

Functions in simmr (0.5.1.215)

simmr

simmr: A package for fitting stable isotope mixing models via JAGS and FFVB in R
prior_viz

Plot the prior distribution for a simmr run
print.simmr_input

Print simmr input object
simmr_data_2

A 3-isotope fake stable isotope mixing data set
simmr_data_1

A simple fake stable isotope mixing data set
print.simmr_output

Print simmr output object
plot.simmr_input

Plot the simmr_input data created from simmr_load
geese_data_day1

A smaller version of the Geese stable isotope mixing data set
combine_sources

Combine the dietary proportions from two food sources after running simmr
summary.simmr_output

Summarises the output created with simmr_mcmc or simmr_ffvb
square_data

An artificial data set used to indicate effect of priors
compare_groups

Compare dietary proportions for a single source across different groups
simmr_mcmc

Run a simmr_input object through the main simmr Markov chain Monte Carlo (MCMC) function
plot.simmr_output

Plot different features of an object created from simmr_mcmc or simmr_ffvb.
compare_sources

Compare dietary proportions between multiple sources
simmr_load

Function to load in simmr data and check for errors
simmr_ffvb

Run a simmr_input object through the Fixed Form Variational Bayes(FFVB) function
simmr_elicit

Function to allow informative prior distribution to be included in simmr
posterior_predictive

Plot the posterior predictive distribution for a simmr run
geese_data

Geese stable isotope mixing data set