---
title: "Analyse de l'incidence du syndrôme grippal"
author: "John"
date: "2023-05-24"
output: html_document
---

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

```{r}
url_data="https://www.sentiweb.fr/datasets/incidence-PAY-3.csv"
data=read.csv(url_data,skip=1)
head(data)
```
On va retirer les datas post-2020 pour éviter la perturbation covid

```{r}
data<-data[data$week<202001,]
head(data)
```

On enlève la/les lignes vides
```{r}
lignes_na<-apply(data,1,function(x) any(is.na(x)))
data_na<-data[lignes_na,]
data_nona<-data[-lignes_na,]
nrow(data_nona)
nrow(data)

```
On check le format des colonnes
```{r}
head(data_nona)
```
Loading parsedate, configuring function
```{r}
library(parsedate)
date=199501
ws=as.character(date)
iso= paste0(substring(ws,1,4),"-W",substring(ws,5,6))
parse_iso_8601(iso)

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

```{r}
data$date=convert_week(data$week)
head(data)
class(data$date)

```
triage des données dans l'ordere chrono

```{r}
data<-data[order(data$date),]
head(data)
```
test pour la chronologie
```{r}
all(diff(data$date)==7)
```
représentation visuelle

```{r}
with(data,plot(date,inc,type="l"))
```
```{r}
with(tail(data,250),plot(date,inc,type="l"))
```

```{r}
annee=1990
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)
```
généralisation

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

rvm 1985

```{r}
annees=1986:2017
icd_annuelle = data.frame(annee=annees,icd=sapply(annees,pic_annuel))
head(icd_annuelle)
```
représentation graphique
```{r}
plot(icd_annuelle,type="p")
```
max

```{r}
head(icd_annuelle[order(-icd_annuelle$icd),])
```

représentation graphique
```{r}
hist(icd_annuelle$icd,breaks=10)
```