---
title: "Incidence varicelle"
author: "Berger Audric"
date: "17/02/2022"
output: html_document
---


```read.csv("incidence-PAY-7.csv")
data_url="https://www.sentiweb.fr/datasets/incidence-PAY-7.csv"
data=read.csv(data_url, skip = 1)
head(data)

lignes_na = apply(data, 1, function(x)any(is.na(x)))
data[lignes_na, ]

class(data$week)

class(data$inc)
```

```library(parsedate)


convert_week = function(date) {
          ws = paste(date)
          iso = paste0(substring(ws,1,4), "-W", substring(ws,5,6))
          as.character(parse_iso_8601(iso))
}

data$date=as.Date(sapply(data$week, convert_week))
class(data$date)

data=data[order(data$date),]
head(data)
```

``all(diff(data$date)== 7)

pic_annuel = function(annee) {
  debut=paste0(annee-1,"-08-01")
  fin=paste0(annee,"-08-01")
  semaines=data$date > debut & data$date <= fin
  sum(data$inc[semaines], na.rm = TRUE)
}
annees=1991:2021


incidence_annuelle= data.frame(annee=annees,incidence=sapply(annees, pic_annuel))
head(incidence_annuelle)
plot(incidence_annuelle, type="p")

head(incidence_annuelle[order(-incidence_annuelle$incidence),])

tail(incidence_annuelle[order(-incidence_annuelle$incidence),])

```