Epiconcept is made up of a team of doctors, epidemiologists, data scientists and digital specialists. For more than 20 years, Epiconcept has contributed to the improvement of public health by writing software, carrying out epidemiological studies, research, evaluation and training to better detect, monitor and prevent disease and to improve treatment.
Epiconcept provides software, services and studies in the following areas:
To achieve such goals Epiconcept :
Epiconcept relies on :
Its current customers and partners include some of the greatest names in the world such as: Santé Publique France (and many public health organizations around the world), WHO, ECDC, AFD, MSF, World Bank, etc.
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EpiCurve allows the user to create epidemic curves from case-based and aggregated data.
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:
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.
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 )
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Parameter | Description
--------- | ---------------------------------------------------------------------------------
x | data.frame with at least one column with dates
date | character, name of date column
freq | character, name of a column with a value to display
cutvar | character, name of a column with factors
period | character, c("hour", "day","week", "month")
to.period | character, Convert date period to another period only for aggregated data. If period is "day", to.period can be "week" or "month". If period is "week", to.period can be "month".
split | integer, c(1,2,3,4,6,8,12) value for hourly split
cutorder | character vector of factors
colors | character, vector of colors
title | character, title of the plot
xlabel | character, label for x axis
ylabel | character, label for y axis
note | character, add a note under the graph
ggplot2, dplyr, ISOweek, scales, timeDate
library(timeDate) library(EpiCurve) library(scales) library(knitr)
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DF <- read.csv("daily_unaggregated_cases.csv", stringsAsFactors=FALSE) kable(head(DF, 12))
EpiCurve(DF, date = "UTS", period = "day", color ="#9900ef", xlabel=sprintf("From %s to %s", min(DF$UTS), max(DF$UTS)))
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DF <- read.csv("hourly_unaggregated_cases.csv", stringsAsFactors=FALSE) kable(head(DF, 12))
EpiCurve(DF, date = "UTS", period = "hour", split = 1, color ="#339933", ylabel="Number of cases", xlabel=sprintf("From %s to %s", min(DF$UTS), max(DF$UTS)))
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DF <- read.csv("hourly_unaggregated_cases_factors.csv", stringsAsFactors=FALSE) kable(head(DF, 12))
EpiCurve(DF, date = "UTS", period = "hour", split = 1, cutvar = "Confirmed", color = c("#339933","#eebb00"), xlabel=sprintf("From %s to %s", min(DF$UTS), max(DF$UTS)))
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library(timeDate) library(ggplot2) library(EpiCurve) library(scales) library(knitr)
DF <- read.csv("daily_aggregated_cases.csv", stringsAsFactors=FALSE) # DF$date <- as.Date(DF$date) kable(DF)
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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")
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DF <- read.csv("daily_aggregated_cases_factors.csv", stringsAsFactors=FALSE) # DF$date <- as.Date(DF$date) kable(DF)
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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")
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DF <- read.csv("weekly_aggregated_cases.csv", stringsAsFactors=FALSE) kable(DF)
EpiCurve(DF, date = "date", freq = "value", period = "week", color=c("#990000"), ylabel="Number of cases", xlabel=sprintf("Du %s au %s", min(DF$date), max(DF$date)), title = "Epidemic Curve\n")
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DF <- read.csv2("weekly_aggregated_cases_factors.csv", stringsAsFactors=FALSE) kable(DF)
EpiCurve(DF, date = "date", freq = "value", period = "week", cutvar = "factor", color=c("Blue", "Red"), ylabel="Cases", xlabel=sprintf("From %s to %s", min(DF$date), max(DF$date)), title = "Epidemic Curve\n")
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DF <- read.csv2("monthly_aggregated_cases.csv", stringsAsFactors=FALSE) kable(DF)
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")
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DF <- read.csv2("monthly_aggregated_cases_factors.csv", stringsAsFactors=FALSE) kable(DF)
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")
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DF <- read.csv("daily_aggregated_cases.csv", stringsAsFactors=FALSE) # DF$date <- as.Date(DF$date) kable(DF)
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")
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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")
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DF <- read.csv("weekly_aggregated_cases.csv", stringsAsFactors=FALSE) kable(DF)
EpiCurve(DF, date = "date", freq = "value", period = "week", to.period = "month", color=c("#990000"), ylabel="Number of cases", xlabel=sprintf("Du %s au %s", min(DF$date), max(DF$date)), title = "Epidemic Curve\n")
DF <- read.csv2("weekly_aggregated_cases_factors.csv", stringsAsFactors=FALSE) kable(DF)
EpiCurve(DF, date = "date", freq = "value", period = "week", to.period = "month", cutvar = "factor", color=c("Blue", "Red"), ylabel="Cases", xlabel=sprintf("From %s to %s", min(DF$date), max(DF$date)), title = "Epidemic Curve\n")
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