---
title: "Analyse de l'incidence de la varicelle"
author: "Matthieu Haas"
date: "1 février 2021"
output:
  pdf_document: default
  html_document: default
---
Le présent document a pour vocation d'analyser l'incidence de la varicelle en France depuis 1991. Ce jeu de données est disponible en ligne via le réseau Sentinelle. 
```{r}
data_url= "https://www.sentiweb.fr/datasets/incidence-PAY-7.csv"
```

```{r}
data = read.csv(file = data_url, skip = 1)
head(data)
```

```{r}
lines_na = apply(data, 1, function(x) any(is.na(x)))
data[lines_na,]
```
```{r}
library(parsedate)
```

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

```{r}
data$date = as.Date(sapply(data$week, convert_week))
```

```{r}
class(data$date)
```

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

```{r}
all(diff(data$date)==7)
```
```{r}
with(data,plot(date,inc, type = "l"))
```
```{r}
pic_annuel=function(annee){
  debut = paste0(annee-1, "-09-01")
  fin   = paste0(annee, "-09-01")
  semaines = data$date > debut & data$date <= fin
  sum(data$inc[semaines],na.rm=TRUE)
}
```
```{r}
annees = 1991 : 2020
```

```{r}
incidence_annuelle = data.frame(annee = annees, incidence = sapply(annees, pic_annuel))
```

```{r}
head(incidence_annuelle)
```
```{r}
plot(incidence_annuelle, type = "p")
```

```{r}
head(incidence_annuelle[order(-incidence_annuelle$incidence),])
```