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zoidtmb

zoidtmb is an implementation of the zoid package in TMB, using marginal maximum likelihood instead of Bayesian estimation. This may be particularly useful for datasets with large dimensions.

The syntax of fitting models matches zoid, and can be done with

fit <- fit_zoidTMB(formula = formula, # required formula
                   design_matrix = design_matrix, # optional covariates
                   data_matrix = data.matrix, # required data matrix
                   overdispersion = FALSE, # optional estimated overdispersion
                   overdispersion_sd = 5, # optional penalty/prior on overdispersion
                   prior_sd = NA) # optional prior/penalty on fixed effects

Parameter estimates and uncertainty can be extracted from

fit$sdreport

Derived quantities (means) are provided with fit$mu and uncertainties fit$mu_se.

For additional details, see the documentation for zoid, (https://github.com/nwfsc-cb/zoid/tree/main)

How to cite

Jensen, Alexander J., Ryan P. Kelly, Eric C. Anderson, William H. Satterthwaite, Andrew Olaf Shelton, and Eric J. Ward. 2022. “ Introducing Zoid: A Mixture Model and R Package for Modeling Proportional Data with Zeros and Ones in Ecology.” Ecology 103(11): e3804. https://doi.org/10.1002/ecy.3804

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