Science Score: 33.0%
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Low similarity (16.4%) to scientific vocabulary
Repository
A framework for Bayesian mixing models in R:
Basic Info
- Host: GitHub
- Owner: brianstock
- Language: R
- Default Branch: master
- Homepage: http://brianstock.github.io/MixSIAR/
- Size: 168 MB
Statistics
- Stars: 110
- Watchers: 29
- Forks: 76
- Open Issues: 152
- Releases: 0
Metadata Files
README.md
MixSIAR
MixSIAR is an R package that helps you create and run Bayesian mixing models to analyze biotracer data (i.e. stable isotopes, fatty acids), following the MixSIAR model framework. MixSIAR represents a collaborative coding project between the investigators behind MixSIR, SIAR, and IsoSource: Brice Semmens, Brian Stock, Eric Ward, Andrew Parnell, Donald Phillips, and Andrew Jackson.
MixSIAR incorporates several years of advances in Bayesian mixing model theory since MixSIR and SIAR, currently:
- Any number of biotracers (examples with 1 isotope, 2 isotope, 8 fatty acids, and 22 fatty acids)
- Source data fit hierarchically within the model
- Source data by categorical covariate (e.g. sources by Region)
- Categorical covariates (up to 2, choice of modeling as random or fixed effects, either nested or independent)
- Continuous covariate (up to 1)
- Error structure options with covariance (Residual * Process, Residual only)
- Concentration dependence
- Plot and include "uninformative"/generalist or informative priors
- Fit multiple models and compare relative support using LOO/WAIC weights
For details, please see the MixSIAR paper:
- Full description of equations
- Advice/explanation on 4 common issues (error structures, priors, combining sources, covariates)
- Case study highlighting new functionality (model selection with LOO/WAIC weights)
Stock BC, Jackson AL, Ward EJ, Parnell AC, Phillips DL, Semmens BX. 2018. Analyzing mixing systems using a new generation of Bayesian tracer mixing models. PeerJ 6:e5096 https://doi.org/10.7717/peerj.5096
Installation
The GUI has been removed from the CRAN version of MixSIAR (if desired, see MixSIARgui on GitHub). Running MixSIAR with scripts is easier to install and better for repeated analysis.
Download and install/update R.
Download and install JAGS.
Open R and run:
install.packages("MixSIAR", dependencies=TRUE) library(MixSIAR)
If you want the latest changes and bug fixes not yet on CRAN, you can install the GitHub version:
remotes::install_github("brianstock/MixSIAR", dependencies=T)
Tutorial
We suggest walking through the vignettes to familiarize yourself with MixSIAR.
There is also an extensive user manual included in the package install. To find the directory location on your computer:
find.package("MixSIAR")
Alternatively, you can download the manual from the GitHub site here.
Clean, runnable .R scripts for each vignette are also available in the example_scripts folder of the MixSIAR package install:
library(MixSIAR)
mixsiar.dir <- find.package("MixSIAR")
file.path(mixsiar.dir, "example_scripts")
You can then run the Wolves example script with:
setwd("choose/where/to/save/output")
source(file.path(mixsiar.dir, "example_scripts", "mixsiar_script_wolves.R"))
Feedback
This software has been improved by the questions, suggestions, and bug reports of the user community. If you have a comment, please use the Issues page.
Citing MixSIAR:
If you use MixSIAR results in publications, please cite the MixSIAR manual as (similar to how you cite R):
Stock BC and Semmens BX. 2016. MixSIAR GUI User Manual. Version 3.1. https://github.com/brianstock/MixSIAR. doi:10.5281/zenodo.1209993.
The MixSIAR model framework is described in:
Stock BC, Jackson AL, Ward EJ, Parnell AC, Phillips DL, Semmens BX. 2018. Analyzing mixing systems using a new generation of Bayesian tracer mixing models. PeerJ 6:e5096 https://doi.org/10.7717/peerj.5096
The primary citation for Bayesian mixing models (MixSIR):
Moore, J. W., & Semmens, B. X. (2008). Incorporating uncertainty and prior information into stable isotope mixing models. Ecology Letters, 11(5), 470-480.
If you are using the residual error term (SIAR):
Parnell, A. C., Inger, R., Bearhop, S., & Jackson, A. L. (2010). Source partitioning using stable isotopes: coping with too much variation. PLoS One, 5(3), e9672.
If you are using a hierarchical structure/random effects:
Semmens, B. X., Ward, E. J., Moore, J. W., & Darimont, C. T. (2009). Quantifying inter-and intra-population niche variability using hierarchical Bayesian stable isotope mixing models. PLoS One, 4(7), e6187.
If you are using continuous effects:
Francis, T. B., Schindler, D. E., Holtgrieve, G. W., Larson, E. R., Scheuerell, M. D., Semmens, B. X., & Ward, E. J. (2011). Habitat structure determines resource use by zooplankton in temperate lakes. Ecology letters, 14(4), 364-372.
If you are using source fitting:
Ward, E. J., Semmens, B. X., & Schindler, D. E. (2010). Including source uncertainty and prior information in the analysis of stable isotope mixing models. Environmental science & technology, 44(12), 4645-4650.
For a detailed description of the math underlying these models, see:
Parnell, A. C., Phillips, D. L., Bearhop, S., Semmens, B. X., Ward, E. J., Moore, J. W., Jackson, A. L., Grey, J., Kelley, D. J., & Inger, R. (2013). Bayesian stable isotope mixing models. Environmetrics, 24, 387-399.
For an explanation of the error structures ("Process only" vs. "Resid only" vs. "Process * Resid"), see:
Stock, B. C., & Semmens, B. X. (2016). Unifying error structures in commonly used biotracer mixing models. Ecology, 97(10), 2562–2569.
Owner
- Name: Brian Stock
- Login: brianstock
- Kind: user
- Location: Bergen
- Company: Institute of Marine Research (IMR)
- Website: brianstock.github.io
- Repositories: 15
- Profile: https://github.com/brianstock
GitHub Events
Total
- Issues event: 15
- Watch event: 13
- Issue comment event: 22
- Fork event: 5
Last Year
- Issues event: 15
- Watch event: 13
- Issue comment event: 22
- Fork event: 5
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| brianstock | b****9@g****m | 106 |
| Brian Stock | b****k@u****u | 38 |
| eric-ward | e****d@n****v | 18 |
| Andrew Jackson | a****n@t****e | 11 |
| Jason Venkiteswaran | j****n@g****m | 5 |
| brianstock-NOAA | b****k@n****v | 5 |
| Eric Ward | 5****a | 2 |
| Andrew Parnell | a****l@u****e | 1 |
| Andrew Jackson | j****n@t****e | 1 |
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 161
- Total pull requests: 2
- Average time to close issues: about 2 months
- Average time to close pull requests: N/A
- Total issue authors: 129
- Total pull request authors: 2
- Average comments per issue: 2.4
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 15
- Pull requests: 0
- Average time to close issues: about 13 hours
- Average time to close pull requests: N/A
- Issue authors: 14
- Pull request authors: 0
- Average comments per issue: 0.13
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- naalipalo (11)
- CWR-05 (4)
- brunakliemann (3)
- EmmiKurosawa (3)
- ncttrinh (3)
- ashleystanek (2)
- mcaputo3 (2)
- BelindaCannell (2)
- klato1 (2)
- amroco (2)
- Krystalgirl (2)
- ESSANBRI (2)
- EllenMcKee (2)
- sschooler (2)
- brianstock (2)
Pull Request Authors
- diboliu (2)
- EricBollingerResearch (2)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- cran 829 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 6
- Total maintainers: 1
cran.r-project.org: MixSIAR
Bayesian Mixing Models in R
- Homepage: https://github.com/brianstock/MixSIAR
- Documentation: http://cran.r-project.org/web/packages/MixSIAR/MixSIAR.pdf
- License: GPL-3
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Latest release: 3.1.12
published over 5 years ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.6.0 depends
- MASS >= 7.3 imports
- MCMCpack >= 1.4 imports
- R2jags >= 0.5 imports
- RColorBrewer >= 1.1 imports
- bayesplot >= 1.4.0 imports
- coda >= 0.19 imports
- ggmcmc >= 1.1 imports
- ggplot2 >= 3.3.0 imports
- lattice >= 0.20 imports
- loo >= 2.0.0 imports
- reshape >= 0.8.7 imports
- reshape2 >= 1.4.3 imports
- splancs >= 2.01 imports
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests