From eae3f65a22356d271b04fa1b948900c7e8b65a10 Mon Sep 17 00:00:00 2001
From: Matthieu Haas <m.haas@laposte.net>
Date: Mon, 1 Feb 2021 18:01:57 +0100
Subject: [PATCH] Faire le comparatif de l'incidence des syndromes grippaux

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 .../exo1/analyse-syndrome-grippal_HAAS.Rmd    | 103 ++++++++++++++++++
 1 file changed, 103 insertions(+)
 create mode 100644 module3/exo1/analyse-syndrome-grippal_HAAS.Rmd

diff --git a/module3/exo1/analyse-syndrome-grippal_HAAS.Rmd b/module3/exo1/analyse-syndrome-grippal_HAAS.Rmd
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+---
+title: "Analyse de l'incidence des syndromes grippaux"
+author: "Matthieu HAAS"
+date: "27/01/2021"
+output:
+  pdf_document: default
+  html_document: default
+---
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+```
+Ce document a pour objectif d'analyser l'incidence des syndromes grippaux en France. Ces données proviennent du réseau sentinelle et courent de 1985 à aujourd'hui.  
+```{r} 
+data_url = "https://www.sentiweb.fr/datasets/incidence-PAY-3.csv"
+```
+
+```{r}
+data = read.csv(file = data_url, skip = 1)
+head(data)
+```
+
+```{r}
+```
+
+
+```{r}
+lines_na = apply(data, 1, function(x) any(is.na(x)))
+data[lines_na,]
+```
+
+```{r}
+class(data$week)
+```
+```{r}
+class(data$inc)
+```
+
+```{r}
+library(parsedate)
+```
+
+```{r}
+convert_week = function(date){
+  ws = paste(date)
+  iso =paste0(substring(ws, 1, 4), "-W", substring(ws, 5,6))
+  as.character(parse_iso_8601(iso))
+}
+```
+
+```{r}
+data$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}
+with(tail(data,200),plot(date,inc, type = "l"))
+```
+
+Ce graphique illustre bien l'effet de l'application de gestes barrières sur la prévention du syndrome grippal. 
+```{r}
+pic_annuel=function(annee){
+  debut = paste0(annee-1, "-08-01")
+  fin   = paste0(annee, "-08-01")
+  semaines = data$date > debut & data$date <= fin
+  sum(data$inc[semaines],na.rm=TRUE)
+}
+```
+```{r}
+annees = 1986 : 2020
+```
+
+```{r}
+incidence_annuelle = data.frame(annee = annees, incidence = sapply(annees, pic_annuel))
+```
+
+```{r}
+head(incidence_annuelle)
+```
+```{r}
+plot(incidence_annuelle, type = "p")
+```
+
+```{r}
+head(incidence_annuelle[order(-incidence_annuelle$incidence),])
+```
+
+```{r}
+hist(incidence_annuelle$incidence, breaks = 10)
+```
+
-- 
2.18.1