View source: R/runSTADEMmodel.R

runSTADEMmodel | R Documentation |

Run the JAGS model

```
runSTADEMmodel(
file_name = NULL,
mcmc_chainLength = 100,
mcmc_burn = 10,
mcmc_thin = 2,
mcmc_chains = 1,
jags_data = NULL,
weekly_params = FALSE,
seed = NULL,
verbose = FALSE,
parallel = TRUE,
DIC = FALSE,
win_model = c("neg_bin", "neg_bin2", "pois", "quasi_pois", "log_space"),
trap_est = TRUE
)
```

`file_name` |
name (with file path) to save the model as |

`mcmc_burn` |
number of burn-in samples in each MCMC chain |

`mcmc_thin` |
thinning interval for MCMC samples to save |

`mcmc_chains` |
number of MCMC chains |

`jags_data` |
list of data being passed to |

`weekly_params` |
should weekly estimates be saved? Default is |

`seed` |
starting seed value for RNG, to make results reproducible |

`verbose` |
passed to the |

`parallel` |
passed to the |

`DIC` |
passed to the |

`win_model` |
what type of distribution should be used when modeling the window counts. |

`trap_est` |
should an estimate of escapement based on the adult fish trap rate be used as a second observation of true total escapement, together with the window counts? Default is |

`mcmc_chainlength` |
number of total samples in each MCMC chain |

Kevin See

```
#runSTADEMmodel()
```

KevinSee/STADEM documentation built on Sept. 30, 2023, 8:38 a.m.

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