# Specifying data source and fitted variables

## inference settings

iterations_per_slot

do_inference

gt_data_path

With inference model runs, the number of simulations `nsimulations`

refers to the number of final model simulations that will be produced. The `filtering$simulations_per_slot`

setting refers to the number of iterative simulations that will be run in order to produce a single final simulation (i.e., number of simulations in a single MCMC chain).

Item | Required? | Type/Format | Description |
---|---|---|---|

iterations_per_slot | required | Integer $\geq$ 1 | Number of iterations in a single MCMC inference chain |

do_inference | required | TRUE/FALSE | TRUE if inference should be performed. If FALSE, just runs a single run per slot, without perturbing parameters |

gt_data_path | required | file path | Path to files containing "ground truth" data to which model output will be compared |

statistics | required | config subsection | Specifies details of how each model output variable will be compared to data during fitting. See inference::statistics section. |

hierarchical_stats_geo | optional | config subsection | Specifies whether a hierarchical structure should be applied the likelihood function for any of the fitted parameters. See |

priors | optional | config subsection | Specifies prior distributions on fitted parameters. See |

`f`

`f`

## inference::statistics options

### required options

name

aggregator

period

sim_var

data_var

likelihood

The statistics specified here are used to calibrate the model to empirical data. If multiple statistics are specified, this inference is performed jointly and they are weighted in the likelihood according to the number of data points and the variance of the proposal distribution.

Item | Required? | Type/Format | Description |
---|---|---|---|

name | required | string | name of statistic, user defined |

period | required |
| Duration of time over which data and model output should be aggregated before being used in the likelihood. If |

aggregator | required | string, name of any R function | Function used to aggregate data over the |

sim_var | required | string | Name of the outcome variable - as defined in |

data_var | required | string | Name of the data variable that will be compared to the model output variable when calculating the likelihood. This should be the name of a column in the file specified in |

remove_na | required | logical | if TRUE if FALSE |

add_one | required | logical | if TRUE if FALSE Will be overwritten to TRUE if the likelihood distribution is chosen to be log |

likelihood::dist | required | Distribution of the likelihood | |

likelihood::param | required | parameter value(s) for the likelihood distribution. These differ by distribution so check the code in |

`f`

`f`

### optional options ?

remove_na

add_one

gt_start_date

gt_end_date

Optional sections

`inference::hierarchical_stats_geo`

`inference::hierarchical_stats_geo`

The hierarchical settings specified here are used to group the inference of certain parameters together (similar to inference in "hierarchical" or "fixed/group effects" models). For example, users may desire to group all counties in a given state because they are geograhically proximate and impacted by the same statewide policies. The effect should be to make these inferred parameters follow a normal distribution and to observe shrinkage among the variance in these grouped estimates.

Item | Required? | Type/Format |
---|---|---|

scenario name | required | name of hierarchical scenario, user defined |

name | required | name of the estimated parameter that will be grouped (e.g., the NPI scenario name or a standardized, combined health outcome name like |

module | required | name of the module where this parameter is estimated (important for finding the appropriate files) |

geo_group_col | required | geodata column name that should be used to group parameter estimation |

transform | required | type of transform that should be applied to the likelihood: "none" or "logit" |

`inference::priors`

`inference::priors`

It is now possible to specify prior values for inferred parameters. This will have the effect of speeding up model convergence.

Item | Required? | Type/Format |
---|---|---|

scenario name | required | name of prior scenario, user defined |

name | required | name of NPI scenario or parameter that will have the prior |

module | required | name of the module where this parameter is estimated |

likelihood | required | specifies the distribution of the prior |

## Ground truth data

name

module

geo_group_col

transform

inference:::priors

inference::

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