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updates to documentation and IHR process
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,30 +1,65 @@ | ||
| #' Example input data set | ||
| #' Input dataframe for fitting the site-level infection dynamics wastewater | ||
| #' model | ||
| #' | ||
| #' SOME HIGH-LEVEL DESCRIPTION OF THE DATA. MAYBE JUST POINT READERS TO | ||
| #' THE FUNCTION THAT GENERATES IT? | ||
| #' A dataset containing the daily hospital admissons, observed wastewater | ||
| #' concentrations and other attributes needed for the model to be fit. | ||
| #' Generated via the defaults in `generate_simulated_data.R` | ||
| #' The variables are as follows: | ||
| #' | ||
| #' @format ## example_df | ||
| #' A data frame with 635 rows and 13 columns | ||
| #' \describe{ | ||
| #' \item{t}{Time} | ||
| #' \item{lab_wwtp_unique_id}{Unique identifier for each unique combination | ||
| #' of sampling site and testing lab} | ||
| #' \item{log_conc}{Genome copied per liter, log10} | ||
| #' ETC. | ||
| #' \item{t}{The time index in days} | ||
| #' \item{lab_wwtp_unique_id}{The unique identifier of the wastewater site-lab | ||
| #' combination. For this example, there are 5 unique combinations, so the | ||
| #' indices range from 1 to 5 but would vary for the number of unique | ||
| #' combinations in your input dataset if trying to construct something mirroring | ||
| #' this structure} | ||
| #' \item{log_conc}{The log scale viral genomes per mL collected from the | ||
| #' lab-site specified on day date. | ||
| #' NAs indicate days where a sample wasn't reported in that lab-site.} | ||
| #' \item{date}{Sample collection date, formatted as YYYY-MM-DD} | ||
| #' \item{lod_sewage}{The log scaled limit of detection reported by the | ||
| #' lab-site on that date} | ||
| #' \item{below_LOD}{An indicator (0,1) indicating whether the wastewater | ||
| #' observation on that date is | ||
| #' above (0) or below (1) the LOD. NAs for all days with wastewater | ||
| #' observations in that lab-site} | ||
| #' \item{daily_hosp_admits}{The number of individuals admitted to the | ||
| #' hospital on that date, | ||
| #' available as of the forecast date. Note this is repeated for each site-lab.} | ||
| #' \item{daily_hosp_admits_for_eval}{The number of individuals admitted to | ||
| #' the hospital on that date, | ||
| #' available retrospectively (so including after the forecast date). | ||
| #' Note this is repeated for each site-lab} | ||
| #' \item{pop}{The number of people in the "state" or whatever population | ||
| #' contributes to the daily hospital admissions} | ||
| #' \item{forecast_date}{The date the forecast is made, formatted as YYYY-MM-DD} | ||
| #' \item{hosp_calibration_time}{The duration of time in days to calibrate the | ||
| #' model to hospital admissions data} | ||
| #' \item{site}{The unique identifier for the site (also referred to as a | ||
| #' wastewater catchment area). There can be more than | ||
| #' one lab per site if samples are sent to different/overlapping labs.} | ||
| #' \item{ww_pop}{The population size of the site (wastewater catchment area)} | ||
| #' } | ||
| #' @source generate_simulated_data.R | ||
| "example_df" | ||
|
|
||
| #' Example input parameters | ||
| #' Input parameters used to generate `example_df` | ||
| #' | ||
| #' SOME HIGH-LEVEL DESCRIPTION OF THE DATA, INCLUDING HOW DERIVED | ||
| #' A few key parameters that were created by the default arguments in | ||
| #' `generate_simulated_data.R` | ||
| #' | ||
| #' @format ## param_df | ||
| #' A data frame with 305 rows and 4 columns | ||
| #' \describe{ | ||
| #' \item{name}{Parameter name} | ||
| #' \item{true_value}{} | ||
| #' \item{index_rows}{} | ||
| #' \item{index_cols}{} | ||
| #' \item{true_value}{ The value that was assigned to this parameter in the | ||
| #' data generation process} | ||
| #' \item{index_rows}{if this is a parameter array, the array row index for | ||
| #' this particular value; for scalar parameters it is always NA } | ||
| #' \item{index_cols}{if this is a parameter array, the array column index for | ||
| #' this particular value; for scalar parameters it is always NA) } | ||
| #' } | ||
| #' @source wwww.wherever.com | ||
| #' @source generate_simulated_data.R | ||
| "param_df" |
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