---
title: "Your title"
author: "Your name"
date: "Today's date"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## On ouvre le fichier de données

```{r}

varicelle <- read.csv(file = "C:/Users/Sarah Chabert/Documents/mooc-rr/module3/exo2/inc-7-PAY.csv", skip = 1)

head(varicelle)
tail(varicelle)


"Est-ce qu'on a des points manquants ?"

na_records = apply(varicelle, 1, function (x) any(is.na(x)))
varicelle[na_records,]

"On véirifie les classes des variables dont on a besoin"

class(varicelle$week)
class(varicelle$inc)

```

## Conversion des numéros de la semaine

```{r}

library(parsedate)

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

varicelle$date = as.Date(convert_week(varicelle$week))

class(varicelle$week)

varicelle = varicelle[order(varicelle$date),]

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

## Inspection

```{r}

plot(varicelle$date, varicelle$inc, type="l", xlab="Date", ylab="Incidence hebdomadaire")

with(tail(varicelle, 200), plot(date, inc, type="l", xlab="Date", ylab="Incidence hebdomadaire"))
```

## Incidence annuelle

```{r}

pic_annuel = function(annee) {
      debut = paste0(annee-1,"-09-01")
      fin = paste0(annee,"-09-01")
      semaines = varicelle$date > debut & varicelle$date <= fin
      sum(varicelle$inc[semaines], na.rm=TRUE)
      }


annees = 1991:2024


inc_annuelle = data.frame(annee = annees,
                          incidence = sapply(annees, pic_annuel))
head(inc_annuelle)


plot(inc_annuelle, type="p", xlab="Année", ylab="Incidence annuelle")

```

## Identification de l'épidémie la plus forte et la plus faible 

```{r}

head(inc_annuelle[order(-inc_annuelle$incidence),])
head(inc_annuelle[order(inc_annuelle$incidence),])
```