Data Structure

Source: vignettes/data_structure.Rmd

Overview

RtD3 accepts data with flexible column names. Below, we describe the default data structure of each input in detail. For more information on passing data with custom column names, see the default_data_ref and summaryWidget documentation.

geoData

Geodata should be an sf object that must contain the columns:

"sovereignt", "geometry"

rtData

rtData should be a JSON-like list object. rtData can have an arbitrary number of entries, allowing for the visualization of rts from multiple data sources.

All entries in the rtData list must contain the values:

"rtData", "casesInfectionData", "casesReportData", "obsCasesData"

"rtData" - R estimates
"casesInfectionData" - Cases by date of infection estimates
"casesReportData" - Cases by date of report estimates
"obsCasesData" - Observed case data
"summaryData" - Summary data for each area

Each entry of the rtData list must contain data.frame objects

All rtData, casesInfectionData, casesReportData values in rtData must contain the columns:

"country","date","type","median","lower_XX","upper_XX" where XX specifies an arbitrary credible interval.

You can use any number of credible intervales. The default structure supports 90%, 50%, and 20%.

summaryData in rtData must contain the columns:

"region", "New confirmed cases by infection date", "Expected change in daily cases", "Effective reproduction no.", "Rate of growth", "Doubling/halving time (days)"

obsCasesData in rtData must contain the columns:

"region", "confirm"

An example of the overall structure of an rtData list from two data sources (“Cases” and “Deaths”):

rtData = list('Cases' = list('summaryData' = summaryData,
                             'rtData' = rtData, 
                             'casesInfectionData' = casesInfectionData, 
                             'casesReportData' = casesReportData, 
                             'obsCasesData' = obsCasesData),
              'Deaths' = list('summaryData' = summaryData_death,
                             'rtData' = rtData_death, 
                             'casesInfectionData' = casesInfectionData_death, 
                             'casesReportData' = casesReportData_death, 
                             'obsCasesData' = obsCasesData_death))

Custom data inputs

For more information on using custom dataset columns, legend variables, and legend colors, see the documentation for the relevant generator functions (default_data_ref, default_map_legend_ref, default_ts_color_ref, legend_qualitative, legend_sequential).