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 inference::hierarchical_stats_geo for details.
priors	optional	config subsection	Specifies prior distributions on fitted parameters. See inference::priors for details

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	days, weeks, or months	Duration of time over which data and model output should be aggregated before being used in the likelihood. If weeks, epiweeks are used
aggregator	required	string, name of any R function	Function used to aggregate data over theperiod, usually sum or mean
sim_var	required	string	Name of the outcome variable - as defined inoutcomes section of the config - that will be compared to data when calculating the likelihood. This will also be the column name of this variable in the hosp files in the model_output directory
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 inference::gt_data_path config option
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 inference/R/functions.R/logLikStat function.

f

optional options ?

remove_na

add_one

gt_start_date

gt_end_date

Optional sections

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 probability_incidI_incidC)
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

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::