Input dataframe for fitting the site-level infection dynamics wastewater model
Source:R/data.R
example_df.RdA 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
- t
The time index in days
- 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
- 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.
- date
Sample collection date, formatted as YYYY-MM-DD
- lod_sewage
The log scaled limit of detection reported by the lab-site on that date
- 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
- 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.
- 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
- pop
The number of people in the "state" or whatever population contributes to the daily hospital admissions
- forecast_date
The date the forecast is made, formatted as YYYY-MM-DD
- hosp_calibration_time
The duration of time in days to calibrate the model to hospital admissions data
- 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.
- ww_pop
The population size of the site (wastewater catchment area)