fido (formerly stray)

Multinomial Logistic-Normal Models (really fast)
its a little tar-ball of joy

Citation

Silverman, JD, Roche, K, Holmes, ZC, David, LA, and Mukherjee, S. Journal of Machine Learning Research. 23(7), 2022:1−42.

License

All source code freely availale under GPL-3 License.

Installation

install.packages("fido")

Or to download the development version from GitHub:

devtools::install_github("jsilve24/fido", ref="develop")

A few notes:

• As of version 1.0.0, fido is now on CRAN.
• There are a few installation options that can greatly speed fido up (often by as much as 10-50 fold). For a more detailed description of installation, take a look at the installation page.
• Vignettes are prebuilt on the fido webpage. If you want vignettes to build locally during package installation you must also pass the build=TRUE and build_opts = c("--no-resave-data", "--no-manual") options to install_github.

Vignettes

• Introduction to fido::Pibble
• Non-linear models with fido::basset
• Joint Modeling (e.g., Multinomics) with fido::Orthus
• Tips for Specifying Priors
• Mitigating PCR bias

Research Using fido

• Silverman et al., Bayesian Multinomial Logistic Normal Models through Marginally Latent Matrix-T Processes
• Silverman et al., Measuring and Mitigating PCR Bias in Microbiome Data
• Holmes et al., Short-Chain Fatty Acid Production by Gut Microbiota from Children with Obesity Differs According to Prebiotic Choice and Bacterial Community Composition
• Silverman et al., Using Influenza surveillance ntworks to estimate state-specific prevalance of SARS-CoV-2 in the United States

Bugs/Feature requests

Have you checked out our FAQ?

I appreciate bug reports and feature requests. Please post to the github issue tracker here.