Package: zoid 1.3.1

Eric J. Ward

zoid: Bayesian Zero-and-One Inflated Dirichlet Regression Modelling

Fits Dirichlet regression and zero-and-one inflated Dirichlet regression with Bayesian methods implemented in Stan. These models are sometimes referred to as trinomial mixture models; covariates and overdispersion can optionally be included.

Authors:Eric J. Ward [aut, cre], Alexander J. Jensen [aut], Ryan P. Kelly [aut], Andrew O. Shelton [aut], William H. Satterthwaite [aut], Eric C. Anderson [aut]

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NEWS

# Install 'zoid' in R:
install.packages('zoid', repos = c('https://nmfs-opensci.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/noaa-nwfsc/zoid/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • chinook - Data from Satterthwaite, W.H., Ciancio, J., Crandall, E., Palmer-Zwahlen, M.L., Grover, A.M., O’Farrell, M.R., Anson, E.C., Mohr, M.S. & Garza, J.C. (2015). Stock composition and ocean spatial distribution from California recreational chinook salmon fisheries using genetic stock identification. Fisheries Research, 170, 166–178. The data genetic data collected from port-based sampling of recreationally-landed Chinook salmon in California from 1998-2002.
  • coddiet - Data from Magnussen, E. 2011. Food and feeding habits of cod (Gadus morhua) on the Faroe Bank. – ICES Journal of Marine Science, 68: 1909–1917. The data here are Table 3 from the paper, with sample proportions (columns w) multiplied by total weight to yield total grams (g) for each sample-diet item combination. Dashes have been replaced with 0s.

On CRAN:

mixture-modelsnwfsc-cbstancpp

6.58 score 8 stars 12 scripts 151 downloads 5 exports 54 dependencies

Last updated 7 months agofrom:010fba15fa. Checks:OK: 1 NOTE: 8. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 26 2024
R-4.5-win-x86_64NOTENov 26 2024
R-4.5-linux-x86_64NOTENov 26 2024
R-4.4-win-x86_64NOTENov 26 2024
R-4.4-mac-x86_64NOTENov 26 2024
R-4.4-mac-aarch64NOTENov 26 2024
R-4.3-win-x86_64NOTENov 26 2024
R-4.3-mac-x86_64NOTENov 26 2024
R-4.3-mac-aarch64NOTENov 26 2024

Exports:broken_stickfit_priorfit_zoidget_fittedget_pars

Dependencies:abindbackportsBHcallrcheckmateclicolorspacedescdistributionalfansifarvergenericsggplot2gluegridExtragtablegtoolsinlineisobandlabelinglatticelifecycleloomagrittrMASSMatrixmatrixStatsmgcvmunsellnlmenumDerivpillarpkgbuildpkgconfigposteriorprocessxpsQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelrlangrstanrstantoolsscalesStanHeaderstensorAtibbleutf8vctrsviridisLitewithr

Fitting models with zoid

Rendered froma01_fitting.Rmdusingknitr::rmarkdownon Nov 26 2024.

Last update: 2023-11-16
Started: 2021-11-11

Prior sensitivity for overdispersion

Rendered froma04_priors.Rmdusingknitr::rmarkdownon Nov 26 2024.

Last update: 2021-11-12
Started: 2021-11-11

Priors for compositions

Rendered froma03_beta_priors.Rmdusingknitr::rmarkdownon Nov 26 2024.

Last update: 2021-11-12
Started: 2021-11-11

Simulating data

Rendered froma02_simulating.Rmdusingknitr::rmarkdownon Nov 26 2024.

Last update: 2021-11-11
Started: 2021-11-11