résultats exo2 orgmode R

module3/exo2/exercice_R_fr.org

@@ -82,3 +82,152 @@ faisant ~<r~ ou ~<R~ suivi de ~Tab~).
 
 Maintenant, à vous de jouer! Vous pouvez effacer toutes ces
 informations et les remplacer par votre document computationnel.
+
+* Exo
+
+
+#+begin_src R :results output :session *R* :exports both
+library(parsedate)
+options(OutDec=",")
+options(width=150)
+#+end_src
+
+#+RESULTS:
+
+#+begin_src R :results output :session *R* :exports both
+data = read.csv('C:/Users/Jade/mooc-rr/module3/exo2/inc-7-PAY.csv', skip=1)
+head(data)
+tail(data)
+#+end_src
+
+#+RESULTS:
+#+begin_example
+week indicator  inc inc_low inc_up inc100 inc100_low inc100_up geo_insee geo_name
+1 202444         7 2354     489   4219      4          1         7        FR   France
+2 202443         7 2130     625   3635      3          1         5        FR   France
+3 202442         7 2621    1246   3996      4          2         6        FR   France
+4 202441         7 2035     381   3689      3          1         5        FR   France
+5 202440         7 2125     725   3525      3          1         5        FR   France
+6 202439         7 2898    1333   4463      4          2         6        FR   France
+week indicator   inc inc_low inc_up inc100 inc100_low inc100_up geo_insee geo_name
+1765 199102         7 16277   11046  21508     29         20        38        FR   France
+1766 199101         7 15565   10271  20859     27         18        36        FR   France
+1767 199052         7 19375   13295  25455     34         23        45        FR   France
+1768 199051         7 19080   13807  24353     34         25        43        FR   France
+1769 199050         7 11079    6660  15498     20         12        28        FR   France
+1770 199049         7  1143       0   2610      2          0         5        FR   France
+#+end_example
+
+#+begin_src R :results output :session *R* :exports both
+na_records = apply(data, 1, function(x) any(is.na(x)))
+data[na_records,]
+#+end_src
+
+#+RESULTS:
+: [1] week       indicator  inc        inc_low    inc_up     inc100     inc100_low inc100_up  geo_insee  geo_name  
+: <0 lignes> (ou 'row.names' de longueur nulle)
+
+#+begin_src R :results output :session *R* :exports both
+class(data$week)
+class(data$inc)
+#+end_src
+
+#+RESULTS:
+: [1] "integer"
+: [1] "integer"
+
+#+begin_src R :results output :session *R* :exports both
+convert_week = function(w) {
+	ws = paste(w)
+	iso = paste0(substring(ws,1,4), "-W", substring(ws,5,6))
+	as.Date(parse_iso_8601(iso))
+	}
+
+data$date = as.Date(convert_week(data$week))
+class(data$date)
+data = data[order(data$date),]
+#+end_src
+
+#+RESULTS:
+: [1] "Date"
+
+#+begin_src R :results output :session *R* :exports both
+all(diff(data$date) == 7)
+#+end_src
+
+#+RESULTS:
+: [1] TRUE
+
+#+begin_src R :results file graphics :file (org-babel-temp-file "figure" ".png") :exports both :width 600 :height 400 :session *R*
+plot(data$date, data$inc, type="l", xlab="Date", ylab="Incidence hebdomadaire")
+#+end_src
+
+#+RESULTS:
+[[file:c:/Users/Jade/AppData/Local/Temp/babel-luSDal/figure7G7sme.png]]
+#+begin_src R :results file graphics :file (org-babel-temp-file "figure" ".png") :exports both :width 600 :height 400 :session *R*
+with(tail(data, 200), plot(date, inc, type="l", xlab="Date", ylab="Incidence hebdomadaire"))
+#+end_src
+
+#+RESULTS:
+[[file:c:/Users/Jade/AppData/Local/Temp/babel-luSDal/figureAF8kaK.png]]
+#+begin_src R :results output :session *R* :exports both
+pic_annuel = function(annee) {
+      debut = paste0(annee-1,"-09-01")
+      fin = paste0(annee,"-09-01")
+      semaines = data$date > debut & data$date <= fin
+      sum(data$inc[semaines], na.rm=TRUE)
+      }
+annees <- 1992:2024
+
+inc_annuelle = data.frame(annee = annees,
+                          incidence = sapply(annees, pic_annuel))
+head(inc_annuelle)
+#+end_src
+
+#+RESULTS:
+: annee incidence
+: 1  1992    834935
+: 2  1993    642921
+: 3  1994    662750
+: 4  1995    651333
+: 5  1996    564994
+: 6  1997    683577
+
+#+begin_src R :results file graphics :file (org-babel-temp-file "figure" ".png") :exports both :width 600 :height 400 :session *R*
+plot(inc_annuelle, type="p", xlab="Année", ylab="Incidence annuelle")
+#+end_src
+
+#+RESULTS:
+[[file:c:/Users/Jade/AppData/Local/Temp/babel-luSDal/figurecbYM5J.png]]
+#+begin_src R :results output :session *R* :exports both
+head(inc_annuelle[order(-inc_annuelle$incidence),])
+#+end_src
+
+#+RESULTS:
+:    annee incidence
+: 18  2009    841233
+: 1   1992    834935
+: 19  2010    834077
+: 25  2016    779816
+: 13  2004    778914
+: 12  2003    760765
+
+#+begin_src R :results file graphics :file (org-babel-temp-file "figure" ".png") :exports both :width 600 :height 400 :session *R*
+hist(inc_annuelle$incidence, breaks=10, xlab="Incidence annuelle", ylab="Nb d'observations", main="")
+#+end_src
+
+#+RESULTS:
+[[file:c:/Users/Jade/AppData/Local/Temp/babel-luSDal/figureuIwnf5.png]]
+
+#+begin_src R :results output :session *R* :exports both
+head(inc_annuelle[order(inc_annuelle$incidence),])
+#+end_src
+
+#+RESULTS:
+:    annee incidence
+: 29  2020    221183
+: 32  2023    365607
+: 30  2021    377933
+: 33  2024    479917
+: 11  2002    515343
+: 27  2018    539765