From 72315142504557d6a516e2485c711a85aafbb3d0 Mon Sep 17 00:00:00 2001 From: Aurelie Zaros Date: Fri, 10 Apr 2020 10:50:37 +0200 Subject: [PATCH] TP --- module3/exo3/TP.csv | 1315 ++++++++++++++++++++++++++++++++++ module3/exo3/exercice_fr.Rmd | 143 +++- 2 files changed, 1443 insertions(+), 15 deletions(-) create mode 100644 module3/exo3/TP.csv diff --git a/module3/exo3/TP.csv b/module3/exo3/TP.csv new file mode 100644 index 0000000..6c47065 --- /dev/null +++ b/module3/exo3/TP.csv @@ -0,0 +1,1315 @@ +"Smoker","Status","Age" +"Yes","Alive",21 +"Yes","Alive",19.3 +"No","Dead",57.5 +"No","Alive",47.1 +"Yes","Alive",81.4 +"No","Alive",36.8 +"No","Alive",23.8 +"Yes","Dead",57.5 +"Yes","Alive",24.8 +"Yes","Alive",49.5 +"Yes","Alive",30 +"No","Dead",66 +"Yes","Alive",49.2 +"No","Alive",58.4 +"No","Dead",60.6 +"No","Alive",25.1 +"No","Alive",43.5 +"No","Alive",27.1 +"No","Alive",58.3 +"Yes","Alive",65.7 +"No","Dead",73.2 +"Yes","Alive",38.3 +"No","Alive",33.4 +"Yes","Dead",62.3 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output: html_document --- - ```{r setup, include=FALSE} knitr::opts_chunk$set(echo = TRUE) ``` -## Quelques explications +# Préparation des données + +Le jeu de données a directement été téléchargé sur le [lien donné](https://gitlab.inria.fr/learninglab/mooc-rr/mooc-rr-ressources/blob/master/module3/Practical_session/Subject6_smoking.csv). Le fichier est sous forme CSV. + +```{r} +data_file = "TP.csv" +``` + +Voici l'explication des colonnes donnée : + +| Nom de colonne | Libellé de colonne | +|----------------+-----------------------------------------------------------------------------------------------------------------------------------| +| `Smoker` | Fumeur (YES) ou non fumeur (NO) +| `Status` | Vivant (ALIVE) ou mort (DEAD) +| `Age` | Age + +# Téléchargement du fichier +```{r} +data = read.csv(data_file) +``` + +Il ne manque aucunes données dans notre fichier : +```{r} +na_records = apply(data, 1, function (x) any(is.na(x))) +data[na_records,] +``` + +Les classes des données sont correctes : +```{r} +class(data$Smoker) +class(data$Status) +class(data$Age) +``` + + +## **Première question** + +_**a. Représentez dans un tableau le nombre total de femmes vivantes et décédées sur la période en fonction de leur habitude de tabagisme.**_ + +Afin d'avoir une répresentation dans un tableau, on émet un tableau qui nous donne le nombre de femmes dans chaque condition. + +```{r} +library(MASS) +tbl = table(data$Smoker, data$Status) +tbl +``` + +```{r} +library(gmodels) +library(ggplot2) +ggplot(data) + + aes(x = Status, fill = Smoker) + + geom_bar(position = "dodge") + + xlab("Status") + + ylab("Effectifs") + + labs(fill = "Fume") +``` + +Donc, dans notre échantillon, il y a 502 femmes non-fumeuses en vie, 443 femmes fumeuses en vie, 230 femmes non-fumeuses mortes et 139 femmes fumeuses mortes. + +**_b. Calculez dans chaque groupe (fumeuses/ non fumeuses) le taux de mortalité (le rapport entre le nombre de femmes décédées dans un groupe avec le nombre total de femmes dans ce groupe)._** -Ceci est un document R markdown que vous pouvez aisément exporter au format HTML, PDF, et MS Word. Pour plus de détails sur R Markdown consultez . +Afin de connaitre le taux de mortalité dans chaque groupe de femme (fumeuse ou non), nous faisons une analyse avec un khi² : +```{r} +SmokerStatus <- table(data$Smoker, data$Status) -Lorsque vous cliquerez sur le bouton **Knit** ce document sera compilé afin de ré-exécuter le code R et d'inclure les résultats dans un document final. Comme nous vous l'avons montré dans la vidéo, on inclue du code R de la façon suivante: +khi_SmokerStatus <- chisq.test(SmokerStatus, + correct = FALSE) + +library(gmodels) +library(ggplot2) +CrossTable(SmokerStatus, + fisher = TRUE, + chisq = TRUE, + expected = TRUE, + sresid = TRUE, + format = 'SPSS') -```{r cars} -summary(cars) ``` +Afin de connaitre le taux de mortalité dans chaque groupe de femme, nous nous basons sur le pourcentage brute (Row Percent). Nous avons donc un taux de mortalité de 31% chez les femmes non fumeuses et de 23% chez les fumeuses. Le taux de mortalité est supérieur chez les femmes non-fumeuses. + -Et on peut aussi aisément inclure des figures. Par exemple: +### **Deuxième question** -```{r pressure, echo=FALSE} -plot(pressure) + +**_Reprenez la question 1 (effectifs et taux de mortalité) en rajoutant une nouvelle catégorie liée à la classe d'âge. On considérera par exemple les classes suivantes: 18-34 ans, 34-54 ans, 55-64 ans, plus de 65 ans.En quoi ce résultat est-il surprenant ? Arrivez vous à expliquer ce paradoxe ? De même, vous pourrez proposer une représentation graphique de ces données pour étayer vos explications._** + +```{r} +data$Classe <- cut(data$Age, c(17, 34, 54 , 64 , 100)) +table(data$Classe) +ggplot(data) + + aes(x = Classe, fill = Smoker) + + geom_bar(position = "dodge") + + xlab("Classe d'âge") + + ylab("Effectifs") + + labs(fill = "Fume") ``` -Vous remarquerez le paramètre `echo = FALSE` qui indique que le code ne doit pas apparaître dans la version finale du document. Nous vous recommandons dans le cadre de ce MOOC de ne pas utiliser ce paramètre car l'objectif est que vos analyses de données soient parfaitement transparentes pour être reproductibles. +Le paradoxe de Simpson est un paradoxe statistique dans lequel un phénomène observé de plusieurs groupes semble s’inverser lorsque les groupes sont combinés. Un des raisons possibles qu’un paradoxe de Simpson s’applique à des données est la présence d’un **facteur de confusion** : il s’agit d’une *variable qui va avoir une influence à la fois sur la cause observée et l’effet observé*. + + +### **Troisème question** + -Comme les résultats ne sont pas stockés dans les fichiers Rmd, pour faciliter la relecture de vos analyses par d'autres personnes, vous aurez donc intérêt à générer un HTML ou un PDF et à le commiter. +**_Afin d'éviter un biais induis par des regroupements en tranches d'âges arbitraires et non régulières, il est envisageable d'essayer de réaliser une régression logistique. Si on introduit une variable Death valant 1 ou 0 pour indiquer si l'individu est décédé durant la période de 20 ans, on peut étudier le modèle Death~Age pour étudier la probabilité de décès en fonction de l'âge selon que l'on considère le groupe des fumeuses ou des non fumeuses. Ces régressions vous permettent de conclure ou pas sur la nocivité du tabagisme ? Vous pourrez proposer une représentation graphique de ces régressions (en n'omettant pas les régions de confiance)._** + +D'abord on recode la variable Status en Death : + +```{r} +library(forcats) +data$Death_binomiale <- fct_recode(data$Status, + "1" = "Alive", + "0" = "Dead") +table(data$Death_binomiale) +``` +Notre variable a bien été recodée. Dans notre échantillons, 945 femmes sont en vie contre 369 sont décédées. + +Ensuite, on analyse le modèle Death~Age pour étudier la probabilité de décès en fonction de l'âge selon que l'on considère le groupe des fumeuses ou des non fumeuses : + +```{r} +reg <- glm(Age ~ Death_binomiale+Smoker, + data = data) +summary(reg) +exp(coefficients(reg)) +``` + +Conclusion : + +```{r} +options(digits = 2, scipen = 999) +ggplot(data, aes(x=Status, y=Age, color=Smoker)) + + geom_boxplot() + + theme(legend.position = "right") +``` -Maintenant, à vous de jouer! Vous pouvez effacer toutes ces informations et les remplacer par votre document computationnel. +Il semble qu'il n'y ait pas d'impact du tabagisme sur la longévité. -- 2.18.1