```{r}
setwd('/Users/arthurdanjou/Workspace/studies/M1/General Linear Models/TP4')

set.seed(0911)
library(ggplot2)
library(gridExtra)
library(cowplot)
library(plotly) # interactif plot
library(ggfortify) # diagnostic plot
library(forestmodel) # plot odd ratio
library(arm) # binnedplot diagnostic plot in GLM

library(knitr)
library(dplyr)
library(tidyverse)
library(tidymodels)
library(broom) # funtion augment to add columns to the original data that was modeled
library(effects) # plot effect of covariate/factor
library(questionr) # odd ratio

library(lmtest) # LRtest
library(survey) # Wald test
library(vcdExtra) # deviance test

library(rsample)   # for data splitting
library(glmnet)
library(nnet) # multinom, glm
library(caret)
library(ROCR)
#library(PRROC) autre package pour courbe roc et courbe pr
library(ISLR) # dataset for statistical learning

ggplot2::theme_set(ggplot2::theme_light())# Set the graphical theme
```
```{r}
car <- read.table('car_income.txt', header = TRUE, sep = ';')
car %>% rmarkdown::paged_table()
summary(car)
```

```{r}
model_purchase <- glm(purchase ~ ., data = car, family = "binomial")
summary(model_purchase)
```

```{r}
p1 <- car %>%
  ggplot(aes(y = purchase, x = income + age)) +
  geom_point(alpha = .15) +
  geom_smooth(method = "lm") +
  ggtitle("Linear regression model fit") +
  xlab("Income") +
  ylab("Probability of Purchase")


p2 <- car %>%
  ggplot(aes(y = purchase, x = income + age)) +
  geom_point(alpha = .15) +
  geom_smooth(method = "glm", method.args = list(family = "binomial")) +
  ggtitle("Logistic regression model fit") +
  xlab("Income") +
  ylab("Probability of Purchase")

ggplotly(p1)
ggplotly(p2)
```

```{r}
car <- car %>%
  mutate(old = ifelse(car$age > 3, 1, 0))
car <- car %>%
  mutate(rich = ifelse(car$income > 40, 1, 0))
model_old <- glm(purchase ~ age + income + rich + old, data = car, family = "binomial")
summary(model_old)
```

# Diabetes in Pima Indians
```{r}
library(MASS)
pima.tr <- Pima.tr
pima.te <- Pima.te

model_train_pima <- glm(type ~ npreg + glu + bp + skin + bmi + ped + age, data = pima.tr, family = "binomial")
summary(model_train_pima)
```
```{r}
pima.te$pred <- predict(model_train_pima, newdata = pima.te, type = "response")
pima.te$pred <- ifelse(pima.te$pred > 0.55, "Yes", "No")
pima.te$pred <- as.factor(pima.te$pred)
pima.te$type <- as.factor(pima.te$type)

# Confusion matrix
confusionMatrix(data = pima.te$type, reference = pima.te$pred, positive = 'Yes')
```