Introduction:

In this homework, you will apply logistic regression to a real-world dataset: the Pima Indians Diabetes Database. This dataset contains medical records from 768 women of Pima Indian heritage, aged 21 or older, and is used to predict the onset of diabetes (binary outcome: 0 = no diabetes, 1 = diabetes) based on physiological measurements.

The data is publicly available from the UCI Machine Learning Repository and can be imported directly.

Dataset URL: https://raw.githubusercontent.com/jbrownlee/Datasets/master/pima-indians-diabetes.data.csv

Columns (no header in the CSV, so we need to assign them manually):

  1. Pregnancies: Number of times pregnant
  2. Glucose: Plasma glucose concentration (2-hour test)
  3. BloodPressure: Diastolic blood pressure (mm Hg)
  4. SkinThickness: Triceps skin fold thickness (mm)
  5. Insulin: 2-hour serum insulin (mu U/ml)
  6. BMI: Body mass index (weight in kg/(height in m)^2)
  7. DiabetesPedigreeFunction: Diabetes pedigree function (a function scoring genetic risk)
  8. Age: Age in years
  9. Outcome: Class variable (0 = no diabetes, 1 = diabetes)

Task Overview: You will load the data, build a logistic regression model to predict diabetes onset using a subset of predictors (Glucose, BMI, Age), interpret the model, evaluate it with a confusion matrix and metrics, and analyze the ROC curve and AUC.

Cleaning the dataset Don’t change the following code

library(tidyverse)
## ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
## ✔ dplyr     1.2.0     ✔ readr     2.1.6
## ✔ forcats   1.0.1     ✔ stringr   1.6.0
## ✔ ggplot2   4.0.2     ✔ tibble    3.3.1
## ✔ lubridate 1.9.5     ✔ tidyr     1.3.2
## ✔ purrr     1.2.1     
## ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
## ✖ dplyr::filter() masks stats::filter()
## ✖ dplyr::lag()    masks stats::lag()
## ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
url <- "https://raw.githubusercontent.com/jbrownlee/Datasets/master/pima-indians-diabetes.data.csv"

data <- read.csv(url, header = FALSE)

colnames(data) <- c("Pregnancies", "Glucose", "BloodPressure", "SkinThickness", "Insulin", "BMI", "DiabetesPedigreeFunction", "Age", "Outcome")

data$Outcome <- as.factor(data$Outcome)

# Handle missing values (replace 0s with NA because 0 makes no sense here)
data$Glucose[data$Glucose == 0] <- NA
data$BloodPressure[data$BloodPressure == 0] <- NA
data$BMI[data$BMI == 0] <- NA


colSums(is.na(data))
##              Pregnancies                  Glucose            BloodPressure 
##                        0                        5                       35 
##            SkinThickness                  Insulin                      BMI 
##                        0                        0                       11 
## DiabetesPedigreeFunction                      Age                  Outcome 
##                        0                        0                        0

Question 1: Create and Interpret a Logistic Regression Model - Fit a logistic regression model to predict Outcome using Glucose, BMI, and Age. - Provide the model summary.

logistic <- glm(Outcome ~ Glucose + BMI + Age , data = data, family = "binomial") 
summary(logistic)
## 
## Call:
## glm(formula = Outcome ~ Glucose + BMI + Age, family = "binomial", 
##     data = data)
## 
## Coefficients:
##              Estimate Std. Error z value Pr(>|z|)    
## (Intercept) -9.032377   0.711037 -12.703  < 2e-16 ***
## Glucose      0.035548   0.003481  10.212  < 2e-16 ***
## BMI          0.089753   0.014377   6.243  4.3e-10 ***
## Age          0.028699   0.007809   3.675 0.000238 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## (Dispersion parameter for binomial family taken to be 1)
## 
##     Null deviance: 974.75  on 751  degrees of freedom
## Residual deviance: 724.96  on 748  degrees of freedom
##   (16 observations deleted due to missingness)
## AIC: 732.96
## 
## Number of Fisher Scoring iterations: 4
## Enter your code here
r_square <- 1 - (logistic$deviance/logistic$null.deviance)

r_square
## [1] 0.25626

What does the intercept represent (log-odds of diabetes when predictors are zero)?

The interception represents when all predictors are 0, which those predictors are the glucose, BMI, and age.

For each predictor (Glucose, BMI, Age), does a one-unit increase raise or lower the odds of diabetes? Are they significant (p-value < 0.05)?

All predictors are all significant and a one-unit increase would raise the odds of diabetes.

Question 2: Confusion Matrix and Important Metric

predicted.probabilities <- logistic$fitted.values
predicted.classes <- ifelse(predicted.probabilities > 0.5, 1, 0)

data_subset <- data[complete.cases(data[, c("Glucose", "BMI", "Age")]), ]

data_subset$Outcome_num <- ifelse(data_subset$Outcome == "1", 1, 0)
confusion <- table(
  Predicted = factor(predicted.classes, levels = c(0, 1)),
  Actual = factor(data_subset$Outcome_num, levels = c(0, 1)))
confusion
##          Actual
## Predicted   0   1
##         0 429 114
##         1  59 150

Calculate and report the metrics:

Accuracy: (TP + TN) / Total Sensitivity (Recall): TP / (TP + FN) Specificity: TN / (TN + FP) Precision: TP / (TP + FP)

Use the following starter code

# Keep only rows with no missing values in Glucose, BMI, or Age
data_subset <- data[complete.cases(data[, c("Glucose", "BMI", "Age")]), ]

#Create a numeric version of the outcome (0 = no diabetes, 1 = diabetes).This is required for calculating confusion matrices.
data_subset$Outcome_num <- ifelse(data_subset$Outcome == "1", 1, 0)
# Extract Values:
TN <- 429
FP <- 59
FN <- 114
TP <- 150

# Metrics    
accuracy <- (TP + TN) / (TP + TN + FP + FN)
sensitivity <- TP / (TP + FN)
specificity <- TN / (TN + FP)
precision <- TP / (TP + FP)

f1_score <- 2 * (precision * sensitivity) / (precision + sensitivity)  

cat("Accuracy:", round(accuracy, 3), "\nSensitivity:", round(sensitivity, 3), "\nSpecificity:", round(specificity, 3), "\nPrecision:", round(precision, 3))
## Accuracy: 0.77 
## Sensitivity: 0.568 
## Specificity: 0.879 
## Precision: 0.718

Interpret: How well does the model perform? Is it better at detecting diabetes (sensitivity) or non-diabetes (specificity)? Why might this matter for medical diagnosis?

Non-diabetes (specificity) are detected at around 88% while diabetes (sensitivity) are detected at around 57%. So this model performs better when it’s detecting non-diabetes.

While experts would bring up that living a healthy lifestyle can prevent diabetes and make providing treatment easier, it would be more beneficial if the model is able to provide better results at detecting diabetes to help them get the treatment they need.

Question 3: ROC Curve, AUC, and Interpretation

#Enter your code here
library(pROC)
## Type 'citation("pROC")' for a citation.
## 
## Attaching package: 'pROC'
## The following objects are masked from 'package:stats':
## 
##     cov, smooth, var
# ROC curve & AUC on full data
roc_obj <- roc(response = data_subset$Outcome,
               predictor = logistic$fitted.values,
               levels = c("0", "1"),
               direction = "<")  # smaller prob = Healthy
# Print AUC value
auc_val <- auc(roc_obj); auc_val
## Area under the curve: 0.828
# Plot ROC with AUC displayed
plot.roc(roc_obj, print.auc = TRUE, legacy.axes = TRUE,
         xlab = "False Positive Rate (1 - Specificity)",
         ylab = "True Positive Rate (Sensitivity)")

What does AUC indicate (0.5 = random, 1.0 = perfect)?

Since the AUC was determined as 0.828, it’s greater than 0.5 making this scale of the model pretty good.

For diabetes diagnosis, prioritize sensitivity (catching cases) or specificity (avoiding false positives)? Suggest a threshold and explain.

We should prioritize our sensitivity of catching cases so that the risks of people with diabetes going untreated. With how severe the consequences of not treating people with diabetes can be, a high threshold should be necessary like 0.95 to ensure that actions are still being taken to treat diabetes prevention, and should be priority. As avoiding false positives, they only help with finding potential issues with treatments which for the nature of this topic, time really matters for when diabetes need to be treated.