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$sdreportDerived quantities (means) are provided with fit$mu and uncertainties
fit$mu_se.
For additional details, see the documentation for zoid,
(https://github.com/nwfsc-cb/zoid/tree/main)
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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