diff --git a/module3/exo3/exercice_fr.Rmd b/module3/exo3/exercice_fr.Rmd index 0d509f6f4e470fef69eb8afd25d2c58a504ad54d..90c63820c03598717b8ad68ebe606964756ab5e1 100644 --- a/module3/exo3/exercice_fr.Rmd +++ b/module3/exo3/exercice_fr.Rmd @@ -54,7 +54,8 @@ vivantes_nonfum <- sum(data$Status[data$Smoker=="No"]=="Alive") decedees_fum <- sum(data$Status[data$Smoker=="Yes"]=="Dead") decedees_nonfum <- sum(data$Status[data$Smoker=="No"]=="Dead") -tab_1 <- data.frame(Vivantes = c(vivantes_fum,vivantes_nonfum), Decedees = c(decedees_fum,decedees_nonfum), row.names = c("Fumeuses","Non fumeuses")) +tab_1 <- data.frame(Vivantes = c(vivantes_fum,vivantes_nonfum), + Decedees = c(decedees_fum,decedees_nonfum), row.names = c("Fumeuses","Non fumeuses")) kable(tab_1,align = 'l') ``` @@ -73,7 +74,10 @@ nb_viv <- sum(data$Status=="Alive") nb_deces <-sum(data$Status=="Dead") tot <- sum(data$Status=="Alive"|data$Status=="Dead") -tab_2 <- data.frame(cbind(rbind(mort_fum, vivant_fum, nb_fum)), rbind(mort_nonfum,vivant_nonfum, nb_nonfum),rbind(nb_deces,nb_viv,tot)) +tab_2 <- data.frame(cbind(rbind(mort_fum, vivant_fum, nb_fum)), + rbind(mort_nonfum,vivant_nonfum, nb_nonfum), + rbind(nb_deces,nb_viv,tot)) + row.names(tab_2) <- c("Decedees", "Vivantes","Total") names(tab_2) <- c("Fumeuses", "Non Fumeuses", "Total") @@ -83,8 +87,10 @@ kable(tab_2,align = "c") # Representation graphique Ceci passe par la création d'un tableau avec les pourcentages de mortalité ```{r representation graphique taux de mortalite} -tab_3 <- data.frame(cbind(rbind((sum(data$Status[data$Smoker=="Yes"]=="Dead")/sum(data$Smoker=="Yes"))*100,(sum(data$Status[data$Smoker=="Yes"]=="Alive")/sum(data$Smoker=="Yes"))*100)), - rbind((sum(data$Status[data$Smoker=="No"]=="Dead")/sum(data$Smoker=="No"))*100,(sum(data$Status[data$Smoker=="No"]=="Alive")/sum(data$Smoker=="No"))*100)) +tab_3 <- data.frame(cbind(rbind((sum(data$Status[data$Smoker=="Yes"]=="Dead")/sum(data$Smoker=="Yes"))*100, + (sum(data$Status[data$Smoker=="Yes"]=="Alive")/sum(data$Smoker=="Yes"))*100)), + rbind((sum(data$Status[data$Smoker=="No"]=="Dead")/sum(data$Smoker=="No"))*100, + (sum(data$Status[data$Smoker=="No"]=="Alive")/sum(data$Smoker=="No"))*100)) names(tab_3) <- c("Fumeuses", "Non fumeuses") row.names(tab_3) <- c("Decedees", "Vivantes") @@ -156,10 +162,12 @@ tab_5 <- ftable(data[,c(1,2,4)]) tab_5 <- round(prop.table(tab_5,2)*100,1) tab_5 <- rbind(tab_5, tab1(data$cl_age)$output.table[,1]) tab_5 <- as.table(tab_5) -row.names(tab_5) <- c("Non fumeuses vivantes ", "Non fumeuses decedees", "Fumeuses vivantes", "Fumeuses decedees" ,"Effectifs") +row.names(tab_5) <- c("Non fumeuses vivantes ", "Non fumeuses decedees", + "Fumeuses vivantes", "Fumeuses decedees" ,"Effectifs") colnames(tab_5) <- c("[18;34]", "[35;54]", "[55;64]", "[65;[") -kable(tab_5,"latex", align = "c") %>% kable_styling(latex_options = "striped", stripe_index = c(1,2)) +kable(tab_5,"latex", align = "c") %>% kable_styling(latex_options = "striped", + stripe_index = c(1,2)) ``` ## Et maintenant on trace les barplots @@ -170,14 +178,18 @@ Et autre [lien](https://sites.google.com/site/rgraphiques/realiser-des-graphique ```{r deuxieme barplot} par(mar = c(5,5,5,13)) -barplot(tab_5[c(1:4),], col = c("gray","black","gray","black"), density = c(30,30,40,100),angle = c(70,70,0,0)) +barplot(tab_5[c(1:4),], col = c("gray","black","gray","black"), density = c(30,30,40,100), + angle = c(70,70,0,0)) xmin <- par("usr")[1] xmax <- par("usr")[2] ymin <- par("usr")[3] ymax <- par("usr")[4] par(xpd=TRUE) lambda <- 0.025 -legend(((1 + lambda) * par("usr")[2] - lambda * par("usr")[1]),50, legend = c("Non fumeuses vivantes", "Non fumeuses decedees", "Fumeuses vivantes", "Fumeuses decedees"), fill = c("gray","black","gray","black"),density = c(30,30,40,100),angle = (c(70,70,0,0))) +legend(((1 + lambda) * par("usr")[2] - lambda * par("usr")[1]),50, + legend = c("Non fumeuses vivantes", "Non fumeuses decedees", + "Fumeuses vivantes", "Fumeuses decedees"), + fill = c("gray","black","gray","black"),density = c(30,30,40,100),angle = (c(70,70,0,0))) ``` @@ -199,8 +211,8 @@ On récupère les valeurs min et max du plot précédent ## Et maintenant on peut obtenir les intervalles de confiance - -```{r IC premier groupe dage non fum, include=FALSE} +#Pour le premier groupe d'age non fumeuses decedees +```{r IC premier groupe dage non fum} x <- tab_5[2,1] n <- tab_5[5,1] @@ -209,8 +221,8 @@ IC1<- round(IC(x),1) IC1 <- paste(c(IC1[1],"[",IC1[2],"-",IC1[3],"]"),collapse = "") ``` - -```{r IC premier groupe dage fum, include=FALSE} +# Pour le premier groupe d'age fumeuses decedees +```{r IC premier groupe dage fum} x <- tab_5[4,1] n <- tab_5[5,1] @@ -219,8 +231,8 @@ IC2 <- round(IC(x),1) IC2 <- paste(c(IC2[1],"[",IC2[2],"-",IC2[3],"]"), collapse = "") ``` - -```{r IC deuxieme groupe dage non fum, include=FALSE} +# Pour le deuxième groupe d'age non fum +```{r IC deuxieme groupe dage non fum} x <- tab_5[2,2] n <- tab_5[5,2] @@ -229,8 +241,8 @@ IC3 <- round(IC(x),1) IC3 <- paste(c(IC3[1],"[",IC3[2],"-",IC3[3],"]"),collapse = "") ``` - -```{r IC deuxieme groupe dage fum, include=FALSE} +# Pour le deuxième groupe d'age fum +```{r IC deuxieme groupe dage fum} x <- tab_5[4,2] n <- tab_5[5,2] @@ -239,8 +251,8 @@ IC4 <- round(IC(x),1) IC4 <- paste(c(IC4[1],"[",IC4[2],"-",IC4[3],"]"),collapse = "") ``` - -```{r IC troisieme groupe dage non fum, include=FALSE} +# Pour le troisieme groupe d'age non fum +```{r IC troisieme groupe dage non fum} x <- tab_5[2,3] n <- tab_5[5,3] @@ -249,8 +261,8 @@ IC5 <- round(IC(x),1) IC5 <- paste(c(IC5[1],"[",IC5[2],"-",IC5[3],"]"),collapse = "") ``` - -```{r IC troisieme groupe dage fum, include=FALSE} +# Pour le troisieme groupe d'age fum +```{r IC troisieme groupe dage fum} x <- tab_5[4,3] n <- tab_5[5,3] @@ -258,8 +270,8 @@ n <- tab_5[5,3] IC6 <- round(IC(x),1) IC6 <- paste(c(IC6[1],"[",IC6[2],"-",IC6[3],"]"),collapse = "") ``` - -```{r IC quatrieme groupe dage non fum, include=FALSE} +# Pour le quatrieme groupe d'age non fum +```{r IC quatrieme groupe dage non fum} x <- tab_5[2,4] n <- tab_5[5,4] @@ -269,8 +281,8 @@ IC7 <- paste(c(IC7[1],"[",IC7[2],"-",IC7[3],"]"),collapse = "") ``` - -```{r IC quatrieme groupe dage fum, include=FALSE} +Pour le quatrieme groupe d'age fum +```{r IC quatrieme groupe dage fum} x <- tab_5[4,4] n <- tab_5[5,4] @@ -334,7 +346,8 @@ Pour cela on introduit un polynome fractionnaire dans le modèle de régression. library(mfp) -reguniage2 <- mfp(deces~fp(Age, df =4, select = 1, scale = T), family = binomial, data = data) +reguniage2 <- mfp(deces~fp(Age, df =4, select = 1, scale = T), +family = binomial, data = data) summary(reguniage2) ``` @@ -351,4 +364,8 @@ logistic.display(regtot) ``` -Et là on constate une inversion de l'odds ratio associé au tabac lorsque l'on ajuste sur l'âge... \ No newline at end of file +Et là on constate une inversion de l'odds ratio associé au tabac lorsque l'on ajuste sur l'âge... +Soit l'âge est un facteur confondant sur la relation entre le fait d'être fumeur et le risque de décés, soit il s'agit d'un modificateur de l'effet. + +Dans tous les cas l'interprétation brute du de la relation entre le fait de fumer et l'âge n'est pas juste. + diff --git a/module3/exo3/exercice_fr.log b/module3/exo3/exercice_fr.log index 2f3524e57c2d644c42ad1ed15e6b959eb9252578..bbc0e2da593478d3a2e1717ca64461ee61c8d18a 100644 --- a/module3/exo3/exercice_fr.log +++ b/module3/exo3/exercice_fr.log @@ -1,4 +1,4 @@ -This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019) (preloaded format=pdflatex 2020.3.21) 5 APR 2020 17:46 +This is pdfTeX, Version 3.14159265-2.6-1.40.20 (TeX Live 2019) (preloaded format=pdflatex 2020.3.21) 5 APR 2020 18:30 entering extended mode restricted \write18 enabled. %&-line parsing enabled. @@ -841,192 +841,214 @@ File: ts1lmtt.fd 2009/10/30 v1.6 Font defs for Latin Modern Package xcolor Warning: Incompatible color definition on input line 183. -Package xcolor Warning: Incompatible color definition on input line 193. +Package xcolor Warning: Incompatible color definition on input line 194. -Package xcolor Warning: Incompatible color definition on input line 193. +Package xcolor Warning: Incompatible color definition on input line 194. 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