Overview

RtD3 has strict requirements for the format of input data. Below, The structure of each input dataset is described in detail.

geoData

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

"sovereignt", "geometry"

summaryData

summaryData should be a data.frame that must contain the columns:

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

rtData

rtData should be a JSON-like list object, containing either data.frame values or NULL values.

rtData can have an arbitrary number of entries, allowing for the visualization of rts from multiple data sources.

All data.frame values in rtData must contain the columns:

"country","date","type","median","lower_90","upper_90","lower_50","upper_50"

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

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

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

An example of the overall structure of an rtData list with some NULL values:

rtData = list('Cases' = list('rtData' = rtData,
                             'casesInfectionData' = NULL,
                             'casesReportData' = casesReportData,
                             'obsCasesData' = NULL))