README.Rmd

---
output: 
  github_document
---

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-figs/",
  cache.path = "README-cache/"
)
```

## 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 

```{r eval=FALSE}
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 
```{r eval=FALSE}
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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