Description

EpiCurve allows the user to create epidemic curves from case-based and aggregated data.

Details

The EpiCurve function creates a graph of number of cases by time of illness (for example date of onset). Each case is represented by a square. EpiCurve allows the time unit for the x-axis to have hourly, daily, weekly or monthly intervals. The hourly interval can be split into 1, 2, 3, 4, 6, 8 or 12 hour time units.

EpiCurve works on both case-based (one case per line) or aggregated data (where there is a count of cases for each date). With aggregated data, you need to specify the variable for the count of cases in the “freq” parameter.

With case-based (non-aggregated data), the date format for EpiCurve can be:

• hourly: YYYY-MM-DD HH:MM or YYYY-mm-DD HH:MM:SS
• daily: YYYY-MM-DD
• monthly: YYYY-MM

If the date format is daily or hourly, you can change and force the period for aggregation on the graph with the parameter “period” setted with “day”, “week” or “month”.

For aggregated data, the date formats can be as above, but they can also be weekly: YYYY-Wnn. Here, we need to specify how the data are aggregated in the parameter “period”. If we want to further aggregate the aggregated data for the epidemic curve (e.g. move from daily aggregated cases to weekly aggregated cases), we can specify the parameter “to.period”.

When the date format is hourly, the dataset is considered case-based, whether the “freq” parameter of the EpiCurve function is supplied or not.

The EpiCurve function

EpiCurve (

      x,  
      date = NULL,
      freq = NULL,
      cutvar = NULL,
      period = NULL,
      to.period = NULL,
      split = 1,
      cutorder = NULL,
      colors = NULL,
      title = NULL,
      xlabel = NULL,
      ylabel = NULL,
      note = NULL,
      square = TRUE
      
    )

Arguments

Depends

ggplot2, dplyr, ISOweek, scales, timeDate

Daily - non-aggregated cases

DF <- read.csv("daily_unaggregated_cases.csv", stringsAsFactors=FALSE)
kable(head(DF, 12))

EpiCurve(DF,
         date = "UTS", period = "day", colors ="#9900ef",
         xlabel=sprintf("From %s to %s", min(DF$UTS), max(DF$UTS)))

With no squares

EpiCurve(DF,
         date = "UTS",
         period = "day",
         colors ="#9900ef",
         xlabel=sprintf("From %s to %s", min(DF$UTS), max(DF$UTS)),
         square = F)

Hourly - non-aggregated cases

DF <- read.csv("hourly_unaggregated_cases.csv", stringsAsFactors=FALSE)
kable(head(DF, 12))

EpiCurve(DF,
         date = "UTS",
         period = "hour",
         split = 1,
         colors ="#339933",
         ylabel="Number of cases",
         xlabel=sprintf("From %s to %s", min(DF$UTS), max(DF$UTS)))

Hourly - non-aggregated cases with factors

DF <- read.csv("hourly_unaggregated_cases_factors.csv", stringsAsFactors=FALSE)
kable(head(DF, 12))

EpiCurve(DF,
         date = "UTS",
         period = "hour",
         split = 1,
         cutvar = "Confirmed",
         colors = c("#339933","#eebb00"),
         xlabel=sprintf("From %s to %s", min(DF$UTS), max(DF$UTS)))

With no squares

EpiCurve(DF,
         date = "UTS",
         period = "hour",
         split = 1,
         cutvar = "Confirmed",
         colors = c("#339933","#eebb00"),
         xlabel=sprintf("From %s to %s", min(DF$UTS), max(DF$UTS)),
         square = FALSE)

Daily

EpiCurve(DF,
         date = "date",
         freq = "value",
         period = "day",
         ylabel="Number of cases",
         xlabel=sprintf("From %s to %s", min(DF$date), max(DF$date)),
         title = "Epidemic Curve",
         note = "Daily epidemic curve")

EpiCurve(DF,
         date = "date",
         freq = "value",
         cutvar = "factor",
         period = "day",
         ylabel="Number of cases",
         xlabel=sprintf("From %s to %s", min(DF$date), max(DF$date)),
         title = "Epidemic Curve",
         note = "Daily epidemic curve")

Weekly

EpiCurve(DF,
         date = "date",
         freq = "value",
         period = "week",
         colors=c("#990000"),
         ylabel="Number of cases",
         xlabel=sprintf("Du %s au %s", min(DF$date), max(DF$date)),
         title = "Epidemic Curve\n")

EpiCurve(DF,
         date = "date",
         freq = "value",
         period = "week",
         cutvar = "factor",
         colors=c("Blue", "Red"),
         ylabel="Cases",
         xlabel=sprintf("From %s to %s", min(DF$date), max(DF$date)),
         title = "Epidemic Curve\n")

Monthly

EpiCurve(DF,
         date = "date",
         freq = "value",
         period = "month",
         ylabel="Number of cases",
         xlabel=sprintf("From %s to %s", min(DF$date), max(DF$date)),
         title = "Epidemic Curve\n")

EpiCurve(DF,
         date = "date",
         freq = "value",
         cutvar = "factor",
         period = "month",
         ylabel="Number of cases",
         xlabel=sprintf("From %s to %s", min(DF$date), max(DF$date)),
         title = "Epidemic Curve\n")

“day” to “week”

EpiCurve(DF,
         date = "date",
         freq = "value",
         period = "day",
         to.period = "week",
         ylabel="Number of cases",
         xlabel=sprintf("From %s to %s", min(DF$date), max(DF$date)),
         title = "Epidemic Curve",
         note = "Daily epidemic curve")

“day” to “month”

EpiCurve(DF,
         date = "date",
         freq = "value",
         period = "day",
         to.period = "month",
         ylabel="Number of cases",
         xlabel=sprintf("From %s o %s", min(DF$date), max(DF$date)),
         title = "Epidemic Curve",
         note = "Daily epidemic curve")

## Warning in as.character.POSIXt(as.POSIXlt(x), ...): as.character(td, ..) no
## longer obeys a 'format' argument; use format(td, ..) ?

“week” to “month”

EpiCurve(DF,
         date = "date",
         freq = "value",
         period = "week",
         to.period = "month",
         colors=c("#990000"),
         ylabel="Number of cases",
         xlabel=sprintf("Du %s au %s", min(DF$date), max(DF$date)),
         title = "Epidemic Curve\n")

## Warning in as.character.POSIXt(as.POSIXlt(x), ...): as.character(td, ..) no
## longer obeys a 'format' argument; use format(td, ..) ?

“week” to “month” with factors

EpiCurve(DF,
         date = "date",
         freq = "value",
         period = "week",
         to.period = "month",
         cutvar = "factor",
         colors=c("Blue", "Red"),
         ylabel="Cases",
         xlabel=sprintf("From %s to %s", min(DF$date), max(DF$date)),
         title = "Epidemic Curve\n")

## Warning in as.character.POSIXt(as.POSIXlt(x), ...): as.character(td, ..) no
## longer obeys a 'format' argument; use format(td, ..) ?