Update influenza-like-illness-analysis.Rmd

module3/exo1/influenza-like-illness-analysis.Rmd

 ---
 title: "Incidence of influenza-like illness in France"
-author: "Konrad Hinsen"
+author: "Eleni Gkiouzepi"
 output:
-  pdf_document:
-    toc: true
   html_document:
     toc: true
     theme: journal
+  pdf_document:
+    toc: true
 documentclass: article
 classoption: a4paper
 header-includes:
-- \usepackage[french]{babel}
+- \usepackage[english]{babel}
 - \usepackage[upright]{fourier}
 - \hypersetup{colorlinks=true,pagebackref=true}
 ---
@@ -41,11 +41,25 @@ This is the documentation of the data from [the download site](https://ns.sentiw
 | `geo_insee`  | Identifier of the geographic area, from INSEE https://www.insee.fr                                                        |
 | `geo_name`   | Geographic label of the area, corresponding to INSEE code. This label is not an id and is only provided for human reading |
 
-### Download
+### If the local file does not exist, download the data and put them into the local file
+
+```{r}
+destfile = "incidence-PAY-3.csv"
+
+if(!file.exists(destfile)){
+  res <- tryCatch(download.file(data_url,
+                              destfile,
+                              method="auto"),
+                error=function(e) 1)
+}
+```
+ 
+### Read the local CSV file.
 
 The first line of the CSV file is a comment, which we ignore with `skip=1`.
+
 ```{r}
-data = read.csv(data_url, skip=1)
+data = read.csv(destfile, skip=1)
 ```
 
 Let's have a look at what we got:
@@ -72,7 +86,8 @@ Integers, fine!
 Date handling is always a delicate subject. There are many conventions that are easily confused. Our dataset uses the [ISO-8601](https://en.wikipedia.org/wiki/ISO_8601) week number format, which is popular in Europe but less so in North America. In `R`, it is handled by the library [parsedate](https://cran.r-project.org/package=parsedate):
 
 ```{r}
-library(parsedate)
+if(!require(parsedate)) install.packages("parsedate")
+    require(parsedate)
 ```
 
 In order to facilitate the subsequent treatment, we replace the ISO week numbers by the dates of each week's Monday. This function does it for one value:
@@ -161,5 +176,6 @@ head(annnual_inc[order(-annnual_inc$incidence),])
 
 Finally, a histogram clearly shows the few very strong epidemics, which affect about 10% of the French population, but are rare: there were three of them in the course of 35 years. The typical epidemic affects only half as many people.
 ```{r}
-hist(annnual_inc$incidence, breaks=10, xlab="Annual incidence", ylab="Number of observations", main="")
+hist(annnual_inc$incidence, breaks=10, xlab="Annual incidence",
+     ylab="Number of observations", main="")
 ```