Package: cosimmr 1.1.01

cosimmr: Fast Fitting of Stable Isotope Mixing Models with Covariates

Fast fitting of Stable Isotope Mixing Models in R. Allows for the inclusion of covariates. Also has built-in summary functions and plot functions which allow for the creation of isospace plots. Variational Bayes is used to fit these models, methods as described in: Tran et al., (2021) <doi:10.48550/arXiv.2103.01327>.

Authors:Emma Govan [cre, aut], Andrew Parnell [aut], Ahmed Shalaby [ctb], Alan Inglis [ctb]

cosimmr_1.1.01.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
cosimmr/json (API)
NEWS

# Install 'cosimmr' in R:

install.packages('cosimmr', repos = c('https://emmagovan.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/emmagovan/cosimmr/issues

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

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library
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:

alligator_data - Alligator Data
cladocera_data - Cladocera data from Galloway et al 2015.
geese_data - Geese stable isotope mixing data set
geese_data_day1 - A smaller version of the Geese stable isotope mixing data set
iso_data - Isopod Data
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:

openblas cpp openmp jags

4.00 score 1 stars 8 scripts 660 downloads 6 exports 53 dependencies

Last updated from:659958322c. Checks:13 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	184
linux-devel-x86_64	OK	198
source / vignettes	OK	250
linux-release-arm64	OK	227
linux-release-x86_64	OK	196
macos-release-arm64	OK	189
macos-release-x86_64	OK	280
macos-oldrel-arm64	OK	168
macos-oldrel-x86_64	OK	376
windows-devel	OK	205
windows-release	OK	202
windows-oldrel	OK	208
wasm-release	OK	138

Exports:convergence_check cosimmr_ffvb cosimmr_load posterior_predictive print.cosimmr_input prior_viz

Dependencies:abind backports bayesplot boot checkmate cli coda cpp11 distributional dplyr farver generics ggnewscale ggplot2 ggridges glue gridExtra gtable isoband labeling lattice lifecycle magrittr matrixStats numDeriv pillar pkgconfig plyr posterior purrr R2jags R2WinBUGS R6 RColorBrewer Rcpp RcppArmadillo RcppDist reshape2 rjags rlang S7 scales stringi stringr tensorA tibble tidyr tidyselect utf8 vctrs viridis viridisLite withr

Stable Isotope Mixing Models with Covariates in R using cosimmr

Emma Govan and Andrew Parnell

Rendered fromcosimmr.Rmdusingknitr::rmarkdownon May 23 2026.

Last update: 2024-08-30
Started: 2023-09-13

Quick start using cosimmr

Emma Govan and Andrew Parnell

Rendered fromcosimmr_quick_start.Rmdusingknitr::rmarkdownon May 23 2026.

Last update: 2024-05-31
Started: 2024-05-30

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Alligator Data	alligator_data
Cladocera data from Galloway et al 2015.	cladocera_data
Creates a plot of mean lower bound to check the FFVB model has finished. Uses 'cosimmr_ffvb' output.	convergence_check
cosimmr: An R package for Stable Isotope Mixing Models	cosimmr-package cosimmr
Run a 'cosimmr_input' object through the Fixed Form Variational Bayes(FFVB) function	cosimmr_ffvb
Function to load in cosimmr data and check for errors	cosimmr_load
Geese stable isotope mixing data set	geese_data
A smaller version of the Geese stable isotope mixing data set	geese_data_day1
Isopod Data	iso_data
Plot the 'cosimmr_input' data created from 'cosimmr_load'	plot.cosimmr_input
Plot different features of an object created from 'cosimmr_ffvb'.	plot.cosimmr_output
Plot different features of an object created from 'cosimmr_ffvb'.	plot.cosimmr_pred_out
Plot the posterior predictive distribution for a cosimmr run	posterior_predictive
Predicts proportion of each source in a mixture, based on values provided for covariates	predict.cosimmr_output
Print simmr input object	print.cosimmr_input
Print a simmr output object	print.cosimmr_output
Plot the prior distribution for a cosimmr run	prior_viz
A simple fake stable isotope mixing data set	simmr_data_1
A 3-isotope fake stable isotope mixing data set	simmr_data_2
An artificial data set used to indicate effect of priors	square_data
Summarises the output created with 'cosimmr_ffvb'	summary.cosimmr_output
Summarises the output created with 'cosimmr_ffvb'	summary.cosimmr_pred_out