extend_env_future: Extend environmental data into the future.

In EcoGRAPH/epidemiar: epidemiar: Create EPIDEMIA Environmentally-Mediated Disease Forecasts

Description

Extend environmental data into the future.

Usage

extend_env_future(
  env_data,
  quo_groupfield,
  quo_obsfield,
  quo_valuefield,
  env_ref_data,
  env_info,
  fc_model_family,
  epi_date_type,
  valid_run,
  groupings,
  env_variables_used,
  report_dates
)

Arguments

env_data	Daily environmental data for the same groupfields and date range as the epidemiological data. It may contain extra data (other districts or date ranges). The data must be in long format (one row for each date and environmental variable combination), and must start at absolutel minimum report_settings$env_lag_length days (default 180) before epi_data for forecasting.
quo_groupfield	Quosure of the user given geographic grouping field to run_epidemia().
quo_obsfield	Quosure of user given field name of the environmental data variables.
quo_valuefield	Quosure of user given field name of the value of the environmental data variable observations.
env_ref_data	Historical averages by week of year for environmental variables. Used in extended environmental data into the future for long forecast time, to calculate anomalies in early detection period, and to display on timeseries in reports.
env_info	Lookup table for environmental data - reference creation method (e.g. sum or mean), report labels, etc.
fc_model_family	The family parameter passsed to mgcv::bam, and the extended families in family.mgcv can also be used. This sets the type of generalized additive model (GAM) to run: it specifies the distribution and link to use in model fitting. E.g. for a Poisson regression, the user would input "poisson()". If a cached model is being used, set the parameter to '"cached"'.
epi_date_type	Extract from 'report_settings$epi_date_type'
valid_run	Internal TRUE/FALSE for whether this is part of a validation run.
groupings	A unique list of the geographic groupings (from groupfield).
env_variables_used	List of environmental variables that were used in the modeling (in 'report_settings$env_var' & found in env_data and env_info)
report_dates	Internally generated set of report date information: min, max, list of dates for full report, known epidemiological data period, forecast period, and early detection period.

Value

Environmental dataset, with data extended into the future forecast period. Unknown environmental data with runs of < 2 weeks is filled in with last known data (i.e. "persistence" method, using the mean of the previous week of known data). For missing data runs more than 2 weeks, the values are filled in using a progressive blend of the the mean of the last known week and the historical means.

EcoGRAPH/epidemiar documentation built on Nov. 13, 2020, 5:31 p.m.