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]

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cosimmr.pdf |cosimmr.html✨
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

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

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:

5.18 score 7 scripts 511 downloads 6 exports 56 dependencies

Last updated 3 months agofrom:659958322c. Checks:OK: 9. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 03 2024
R-4.5-win-x86_64	OK	Nov 03 2024
R-4.5-linux-x86_64	OK	Nov 03 2024
R-4.4-win-x86_64	OK	Nov 03 2024
R-4.4-mac-x86_64	OK	Nov 03 2024
R-4.4-mac-aarch64	OK	Nov 03 2024
R-4.3-win-x86_64	OK	Nov 03 2024
R-4.3-mac-x86_64	OK	Nov 03 2024
R-4.3-mac-aarch64	OK	Nov 03 2024

Exports:convergence_check cosimmr_ffvb cosimmr_load posterior_predictive print.cosimmr_input prior_viz

Dependencies:abind backports bayesplot boot checkmate cli coda colorspace distributional dplyr fansi farver generics ggnewscale ggplot2 ggridges glue gridExtra gtable isoband labeling lattice lifecycle magrittr MASS Matrix matrixStats mgcv munsell nlme numDeriv pillar pkgconfig plyr posterior R2jags R2WinBUGS R6 RColorBrewer Rcpp RcppArmadillo RcppDist reshape2 rjags rlang scales stringi stringr tensorA tibble 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 Nov 03 2024.

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

Quick start using cosimmr

Emma Govan and Andrew Parnell

Rendered fromcosimmr_quick_start.Rmdusingknitr::rmarkdownon Nov 03 2024.

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