# library(methods) library(timeDate) #library(timeSeries) #library(fBasics) #library(plyr) #library(jsonlite) library(ggplot2) #library(gridExtra) library(EpiCurve) library(dplyr) library(scales) library(knitr)
DF <- read.csv("cas_date_osea_jours.csv", stringsAsFactors=FALSE) # DF <- DF[1, ] # DF[1, 2] <- 1 #DF$date <- as.Date(DF$date) # DF_V <- DF[DF[,"factor"] == "Validé", 1:2] # DF_I <- DF[DF[,"factor"] == "Invalidé", 1:2] DF2 <- DF %>% dplyr::group_by(date) %>% dplyr::summarise(value = sum(value)) %>% as.data.frame()
Tracé de la courbe épidémiologique
EpiCurve(DF2, date = "date", freq = "value", cutvar = "factor", period = "day", cutorder = c("Invalidé", "Validé"), color=c("#009900", "#000099"), ylabel="Nombre de cas", xlabel=sprintf("From %s To %s", min(DF$date), max(DF$date)), title = "Epidemic Curve", note = "Dayly epidemic curve of deseases")
DF <- read.csv2("cas_date_osea_semaines_02.csv", stringsAsFactors=FALSE, fileEncoding="latin1") #DF <- DF[1:2, ] kable(DF)
Tracé de la courbe épidémiologique
EpiCurve(DF, date = "date", freq = "value", cutvar = "factor", period = "week", cutorder = c( "Valid","Invalid"), color=c( "#990000","#009900"), ylabel="Nombre de cas", xlabel=sprintf("Du %s au %s", min(DF$date), max(DF$date)), title = "Courbe épidémique hebdomadaire\n")
DF <- read.csv2("cas_date_osea_semaines_02.csv", stringsAsFactors=FALSE) %>% select(-factor) %>% as.data.frame() kable(DF) #DF$date <- as.Date(DF$date) DF <- DF[,-3]
Tracé de la courbe épidémiologique
EpiCurve(DF, date = "date", freq = "value", period = "week", color=c("#990000"), ylabel="Nombre de cas", xlabel=sprintf("Du %s au %s", min(DF$date), max(DF$date)), title = "Courbe épidémique\n")
DF <- read.csv2("cas_date_osea_mois_sansFactor.csv", stringsAsFactors=FALSE) #DF <- DF[1, ] kable(DF) DF$date <- as.Date(paste(DF$date,"-01",sep="")) # DF <-DF[-3,]
Tracé de la courbe épidémique
EpiCurve(DF, date = "date", freq = "value", period = "month", color=c("#990066"), ylabel="Nombre de cas", xlabel=sprintf("Du %s au %s", min(DF$date), max(DF$date)), title = "Courbe épidémique mensuelle\n")
DF <- read.csv2("cas_date_osea_mois.csv", stringsAsFactors=FALSE) #DF$date <- as.Date(paste(DF$date,"-01",sep="")) #DF <- DF[1:2, ] kable(DF)
Tracé de la courbe épidémique
EpiCurve(DF, date = "date", freq = "value", period = "month", cutvar = "factor", cutorder = c( "Validé","Invalidé"), colors=c("#990000", "#009900"), ylabel="Nombre de cas", xlabel=sprintf("Du %s au %s", min(DF$date), max(DF$date)), title = "Courbe épidémique mensuelle avec factors\n")
date <- seq(as.timeDate("2017-05-10 21:35:22"), as.timeDate("2017-05-12 06:15:12"), by="12 min") val <- rep(1, length(date)) tri <- rep(c("Alive", "Died","Unknown"), length.out=length(date)) DF <- data.frame(date, val, tri) names(DF) <- c("date","value", "tri") EpiCurve(DF, date = "date", freq = "value", period = "hour", split = 4, cutvar = "tri", ylabel="Number of cases", xlabel=sprintf("Du %s au %s", min(as.Date(DF$date)), as.Date(max(DF$date))), title = "Epidemic Curve")
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