Due: Thursday, February 20, 2026 (11:59 pm ET)
Topics: One-way ANOVA + Correlation (based on
Lectures/Labs 02–03)
Dataset: bmd.csv (NHANES 2017–2018 DEXA
subsample)
AI policy (Homework 1): AI tools (ChatGPT, Gemini, Claude, Copilot, etc.) are not permitted for coding assistance on HW1. You must write/debug your code independently.
This homework uses bmd.csv, a subset of NHANES 2017–2018 respondents who completed a DEXA scan.
Key variables:
| Variable | Description | Type |
|---|---|---|
DXXOFBMD |
Total femur bone mineral density | Continuous (g/cm²) |
RIDRETH1 |
Race/ethnicity | Categorical (1–5) |
RIAGENDR |
Sex | Categorical (1=Male, 2=Female) |
RIDAGEYR |
Age in years | Continuous |
BMXBMI |
Body mass index | Continuous (kg/m²) |
smoker |
Smoking status | Categorical (1=Current, 2=Past, 3=Never) |
calcium |
Dietary calcium intake | Continuous (mg/day) |
DSQTCALC |
Supplemental calcium | Continuous (mg/day) |
vitd |
Dietary vitamin D intake | Continuous (mcg/day) |
DSQTVD |
Supplemental vitamin D | Continuous (mcg/day) |
totmet |
Total physical activity (MET-min/week) | Continuous |
Load required packages and import the dataset.
# Import data (adjust path as needed)
bmd <- readr::read_csv("/Users/nataliasmall/Downloads/EPI 553/Assignments/HW01/bmd.csv", show_col_types = FALSE)
# Inspect the data
glimpse(bmd)## Rows: 2,898
## Columns: 14
## $ SEQN <dbl> 93705, 93708, 93709, 93711, 93713, 93714, 93715, 93716, 93721…
## $ RIAGENDR <dbl> 2, 2, 2, 1, 1, 2, 1, 1, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2…
## $ RIDAGEYR <dbl> 66, 66, 75, 56, 67, 54, 71, 61, 60, 60, 64, 67, 70, 53, 57, 7…
## $ RIDRETH1 <dbl> 4, 5, 4, 5, 3, 4, 5, 5, 1, 3, 3, 1, 5, 4, 2, 3, 2, 4, 4, 3, 3…
## $ BMXBMI <dbl> 31.7, 23.7, 38.9, 21.3, 23.5, 39.9, 22.5, 30.7, 35.9, 23.8, 2…
## $ smoker <dbl> 2, 3, 1, 3, 1, 2, 1, 2, 3, 3, 3, 2, 2, 3, 3, 2, 3, 1, 2, 1, 1…
## $ totmet <dbl> 240, 120, 720, 840, 360, NA, 6320, 2400, NA, NA, 1680, 240, 4…
## $ metcat <dbl> 0, 0, 1, 1, 0, NA, 2, 2, NA, NA, 2, 0, 0, 0, 1, NA, 0, NA, 1,…
## $ DXXOFBMD <dbl> 1.058, 0.801, 0.880, 0.851, 0.778, 0.994, 0.952, 1.121, NA, 0…
## $ tbmdcat <dbl> 0, 1, 0, 1, 1, 0, 0, 0, NA, 1, 0, 0, 1, 0, 0, 1, NA, NA, 0, N…
## $ calcium <dbl> 503.5, 473.5, NA, 1248.5, 660.5, 776.0, 452.0, 853.5, 929.0, …
## $ vitd <dbl> 1.85, 5.85, NA, 3.85, 2.35, 5.65, 3.75, 4.45, 6.05, 6.45, 3.3…
## $ DSQTVD <dbl> 20.557, 25.000, NA, 25.000, NA, NA, NA, 100.000, 50.000, 46.6…
## $ DSQTCALC <dbl> 211.67, 820.00, NA, 35.00, 13.33, NA, 26.67, 1066.67, 35.00, …
Create readable labels for the main categorical variables:
bmd <- bmd %>%
mutate(
sex = factor(RIAGENDR,
levels = c(1, 2),
labels = c("Male", "Female")),
ethnicity = factor(RIDRETH1,
levels = c(1, 2, 3, 4, 5),
labels = c("Mexican American",
"Other Hispanic",
"Non-Hispanic White",
"Non-Hispanic Black",
"Other")),
smoker_f = factor(smoker,
levels = c(1, 2, 3),
labels = c("Current", "Past", "Never"))
)Report the total sample size and create the analytic dataset for ANOVA by removing missing values:
# Total observations
n_total <- nrow(bmd)
# Create analytic dataset for ANOVA (complete cases for BMD and ethnicity / remove missing BMD and ethnicity)
anova_df <- bmd %>%
filter(!is.na(DXXOFBMD), !is.na(ethnicity))
# Sample size for ANOVA analysis
n_anova <- nrow(anova_df)
# Display sample sizes
n_total## [1] 2898
## [1] 2286
2–4 sentences summarizing analytic sample
The total sample contains 2898 observations and 17 variables. 612 observations were removed due to missing data, which accounts for about 21% missing before cleaning. The final analytic sample size is 2286 for the ANOVA analysis.
Research question: Do mean BMD values differ across ethnicity groups?
Statistical notation:
Plain language:
Table showing sample size, mean, and standard deviation of BMD for each ethnicity group:
anova_df %>%
group_by(ethnicity) %>%
summarise(
n = n(),
mean_bmd = mean(DXXOFBMD, na.rm = TRUE),
sd_bmd = sd(DXXOFBMD, na.rm = TRUE)
) %>%
arrange(desc(n)) %>%
kable(digits = 3)| ethnicity | n | mean_bmd | sd_bmd |
|---|---|---|---|
| Non-Hispanic White | 846 | 0.888 | 0.160 |
| Non-Hispanic Black | 532 | 0.973 | 0.161 |
| Other | 409 | 0.897 | 0.148 |
| Mexican American | 255 | 0.950 | 0.149 |
| Other Hispanic | 244 | 0.946 | 0.156 |
Visualization comparing BMD distributions across ethnicity groups:
ggplot(anova_df, aes(x = ethnicity, y = DXXOFBMD)) +
geom_boxplot(outlier.shape = NA) +
geom_jitter(width = 0.15, alpha = 0.25) +
labs(
x = "Ethnicity group",
y = "Bone mineral density (g/cm²)"
) +
theme(axis.text.x = element_text(angle = 25, hjust = 1))Interpret the plot: What patterns do you observe in BMD across ethnicity groups? “Non-Hispanic Black” individuals show the higher mean BMD compared to other ethnicity groups. The “Mexican American” and “Other Hispanic” groups follow closely behind, with “Non-Hispanic White” and “Other” groups displaying lower mean BMD values. The “Non-Hispanic Black” and “Non-Hispanic White” have the highest concentration of dots, indicating that they have greater number of people within their ethnicity groups, compared to the other ethnicity groups, like “Mexican American” and “Other Hispanic” who have lower a lower number of people in their groups.
Fit a one-way ANOVA with:
DXXOFBMD)# Fit ANOVA model
fit_aov <- aov(DXXOFBMD ~ ethnicity, data = anova_df)
# Display ANOVA table
summary(fit_aov)## Df Sum Sq Mean Sq F value Pr(>F)
## ethnicity 4 2.95 0.7371 30.18 <2e-16 ***
## Residuals 2281 55.70 0.0244
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
Report the F-statistic, degrees of freedom, and p-value in a formatted table:
| term | df | sumsq | meansq | statistic | p.value |
|---|---|---|---|---|---|
| ethnicity | 4 | 2.9482 | 0.7371 | 30.185 | 0 |
| Residuals | 2281 | 55.6973 | 0.0244 | NA | NA |
Write your interpretation here: Since p < 0.05, we reject H₀. There is statistically significant evidence that at least one mean BMD value differs across ethnicity groups.
ANOVA requires three assumptions: independence, normality of residuals, and equal variances. Check the latter two graphically and with formal tests.
If assumptions are not satisfied, say so clearly, but still proceed with the ANOVA and post-hoc tests.
Create diagnostic plots:
par(mfrow = c(1, 2))
plot(fit_aov, which = 1) # Residuals vs fitted
plot(fit_aov, which = 2) # QQ plot## Levene's Test for Homogeneity of Variance (center = median)
## Df F value Pr(>F)
## group 4 1.5728 0.1788
## 2281
Summarize what you see in 2–4 sentences:
Based on the QQ plot, points do follow the diagonal line, so normality assumption is reasonable. Based on Levene’s test, since p > 0.05, fail to reject equal variances. Equal variance assumption is met. Residuals vs Fitted show random scatter with no pattern, indicating that the independence assumption holds.
Because ethnicity has 5 groups, you must do a multiple-comparisons procedure.
Use Tukey HSD and report:
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = DXXOFBMD ~ ethnicity, data = anova_df)
##
## $ethnicity
## diff lwr upr
## Other Hispanic-Mexican American -0.004441273 -0.042644130 0.03376158
## Non-Hispanic White-Mexican American -0.062377249 -0.092852618 -0.03190188
## Non-Hispanic Black-Mexican American 0.022391619 -0.010100052 0.05488329
## Other-Mexican American -0.053319344 -0.087357253 -0.01928144
## Non-Hispanic White-Other Hispanic -0.057935976 -0.088934694 -0.02693726
## Non-Hispanic Black-Other Hispanic 0.026832892 -0.006150151 0.05981593
## Other-Other Hispanic -0.048878071 -0.083385341 -0.01437080
## Non-Hispanic Black-Non-Hispanic White 0.084768868 0.061164402 0.10837333
## Other-Non-Hispanic White 0.009057905 -0.016633367 0.03474918
## Other-Non-Hispanic Black -0.075710963 -0.103764519 -0.04765741
## p adj
## Other Hispanic-Mexican American 0.9978049
## Non-Hispanic White-Mexican American 0.0000003
## Non-Hispanic Black-Mexican American 0.3276613
## Other-Mexican American 0.0001919
## Non-Hispanic White-Other Hispanic 0.0000036
## Non-Hispanic Black-Other Hispanic 0.1722466
## Other-Other Hispanic 0.0010720
## Non-Hispanic Black-Non-Hispanic White 0.0000000
## Other-Non-Hispanic White 0.8719109
## Other-Non-Hispanic Black 0.0000000
Create and present a readable table (you can tidy the Tukey output):
# YOUR CODE HERE to create a tidy table from Tukey results
# Hint: Convert to data frame, add rownames as column, filter for significance
# Extract and format results
tukey_summary <- as.data.frame(tuk$ethnicity)
tukey_summary$Comparison <- rownames(tukey_summary)
tukey_summary <- tukey_summary[, c("Comparison", "diff", "lwr", "upr", "p adj")]
# Add interpretation columns
tukey_summary$Significant <- ifelse(tukey_summary$`p adj` < 0.05, "Yes", "No")
tukey_summary$Direction <- ifelse(
tukey_summary$Significant == "Yes",
ifelse(tukey_summary$diff > 0, "First group higher", "Second group higher"),
"No difference"
)
kable(tukey_summary, digits = 4,
caption = "Tukey HSD post-hoc comparisons with 95% confidence intervals")| Comparison | diff | lwr | upr | p adj | Significant | Direction | |
|---|---|---|---|---|---|---|---|
| Other Hispanic-Mexican American | Other Hispanic-Mexican American | -0.0044 | -0.0426 | 0.0338 | 0.9978 | No | No difference |
| Non-Hispanic White-Mexican American | Non-Hispanic White-Mexican American | -0.0624 | -0.0929 | -0.0319 | 0.0000 | Yes | Second group higher |
| Non-Hispanic Black-Mexican American | Non-Hispanic Black-Mexican American | 0.0224 | -0.0101 | 0.0549 | 0.3277 | No | No difference |
| Other-Mexican American | Other-Mexican American | -0.0533 | -0.0874 | -0.0193 | 0.0002 | Yes | Second group higher |
| Non-Hispanic White-Other Hispanic | Non-Hispanic White-Other Hispanic | -0.0579 | -0.0889 | -0.0269 | 0.0000 | Yes | Second group higher |
| Non-Hispanic Black-Other Hispanic | Non-Hispanic Black-Other Hispanic | 0.0268 | -0.0062 | 0.0598 | 0.1722 | No | No difference |
| Other-Other Hispanic | Other-Other Hispanic | -0.0489 | -0.0834 | -0.0144 | 0.0011 | Yes | Second group higher |
| Non-Hispanic Black-Non-Hispanic White | Non-Hispanic Black-Non-Hispanic White | 0.0848 | 0.0612 | 0.1084 | 0.0000 | Yes | First group higher |
| Other-Non-Hispanic White | Other-Non-Hispanic White | 0.0091 | -0.0166 | 0.0347 | 0.8719 | No | No difference |
| Other-Non-Hispanic Black | Other-Non-Hispanic Black | -0.0757 | -0.1038 | -0.0477 | 0.0000 | Yes | Second group higher |
Write a short paragraph: The groups that differed were Non-Hispanic White - Mexican American, Other - Mexican American, Non-Hispanic White - Other Hispanic, Other - Other Hispanic, Non-Hispanic Black - Non-Hispanic White, and Other - Non-Hispanic Black. Moreover, Non-Hispanic White - Mexican American, Other - Mexican American, Non-Hispanic White - Other Hispanic, Other - Other Hispanic, Non-Hispanic Black - Non-Hispanic White, and Other - Non-Hispanic Black were specific ethnicity pairs that showed statistically significant differences in mean BMD.
Compute η² and interpret it (small/moderate/large is okay as a qualitative statement).
Formula: η² = SS_between / SS_total
## # A tibble: 2 × 6
## term df sumsq meansq statistic p.value
## <chr> <dbl> <dbl> <dbl> <dbl> <dbl>
## 1 ethnicity 4 2.95 0.737 30.2 1.65e-24
## 2 Residuals 2281 55.7 0.0244 NA NA
# YOUR CODE HERE to compute eta-squared
# Hint: Extract SS for ethnicity and Residuals, then calculate proportion
ss_between<- anova_tbl$sumsq[1]
ss_residuals<- anova_tbl$sumsq [2]
ss_total <- ss_between + ss_residuals
eta_squared <- ss_between / ss_totalInterpret in 1–2 sentences:
Our calculated effect size is η² = 0.0503 which is around medium. This means ethnicity explains approximately 5.03% of the variance in BMD.
In this section you will:
Calculate total nutrient intake by adding dietary and supplemental sources:
Before calculating correlations, examine the distributions of continuous variables. Based on skewness and the presence of outliers, you may need to apply transformations.
Create histograms to assess distributions:
# YOUR CODE HERE: Create histograms for key continuous variables
# Recommended: BMXBMI, calcium_total, vitd_total, totmet
library(patchwork)
p1 <- ggplot(bmd2, aes(x = BMXBMI)) + geom_histogram(bins = 30)
p2 <- ggplot(bmd2, aes(x = calcium_total)) + geom_histogram(bins = 30)
p3 <- ggplot(bmd2, aes(x = vitd_total)) + geom_histogram(bins = 30)
p4 <- ggplot(bmd2, aes(x = totmet)) + geom_histogram(bins = 30)
(p1 | p2) / (p3 | p4)Based on your assessment, apply transformations as needed:
bmd2 <- bmd2 %>%
mutate(
# Add your transformation code here
#doing log bmi for table A further down
log_calcium_total = log(calcium_total),
sqrt_totmet = sqrt(totmet),
sqrt_vitd_total = sqrt(vitd_total),
log_bmi = log(BMXBMI)
)Document your reasoning: I applied transformations to vitd_total,calcium_total, and totmet because relationships are clearly non-linear. vitd_total and totmet appear severely right skewed, and calcium_total while not as severely affected can also be seen as rightly skewed.
For each correlation, report:
# Function to calculate Pearson correlation for a pair of variables
corr_pair <- function(data, x, y) {
# Select variables and remove missing values
d <- data %>%
select(all_of(c(x, y))) %>%
drop_na()
# Need at least 3 observations for correlation
if(nrow(d) < 3) {
return(tibble(
x = x,
y = y,
n = nrow(d),
estimate = NA_real_,
p_value = NA_real_
))
}
# Calculate Pearson correlation
ct <- cor.test(d[[x]], d[[y]], method = "pearson")
# Return tidy results
tibble(
x = x,
y = y,
n = nrow(d),
estimate = unname(ct$estimate),
p_value = ct$p.value
)
}Examine correlations between potential predictors and BMD:
Use transformed versions where appropriate.
# YOUR CODE HERE
# Use the corr_pair function to create correlations
# Use bind_rows() to combine multiple correlation results
# Format with kable()
tableA <- bind_rows(
corr_pair(bmd2, "RIDAGEYR", "DXXOFBMD"),
corr_pair(bmd2, "log_bmi", "DXXOFBMD"),
corr_pair(bmd2, "log_calcium_total", "DXXOFBMD"),
corr_pair(bmd2, "sqrt_vitd_total", "DXXOFBMD")
) %>%
mutate(
estimate = round(estimate, 3),
p_value = signif(p_value, 3)
)
tableA %>% kable()| x | y | n | estimate | p_value |
|---|---|---|---|---|
| RIDAGEYR | DXXOFBMD | 2286 | -0.232 | 0.00000 |
| log_bmi | DXXOFBMD | 2275 | 0.425 | 0.00000 |
| log_calcium_total | DXXOFBMD | 2129 | 0.012 | 0.59200 |
| sqrt_vitd_total | DXXOFBMD | 2129 | -0.062 | 0.00426 |
Interpret the results: RIDAGEYR, log_bmi, and sqrt_vitd_total show statistically significant correlations with BMD. RIDAGEYR is going in the negative direction, and has a weak correlation relationship. log_bmi is going in the positive direction, and has a moderate correlation relationship. sqrt_vitd_total is going in the negative direction, and has a weak correlation relationship.
Examine correlations between potential confounders and physical activity:
# YOUR CODE HERE
# Follow the same structure as Table A
# Use sqrt_totmet (or transformed version) as the outcome variable
tableB <- bind_rows(
corr_pair(bmd2, "RIDAGEYR", "sqrt_totmet"),
corr_pair(bmd2, "log_bmi", "sqrt_totmet"),
corr_pair(bmd2, "log_calcium_total", "sqrt_totmet"),
corr_pair(bmd2, "sqrt_vitd_total", "sqrt_totmet")
) %>%
mutate(
estimate = round(estimate, 3),
p_value = signif(p_value, 3)
)
tableB %>% kable()| x | y | n | estimate | p_value |
|---|---|---|---|---|
| RIDAGEYR | sqrt_totmet | 1934 | -0.097 | 1.96e-05 |
| log_bmi | sqrt_totmet | 1912 | 0.001 | 9.51e-01 |
| log_calcium_total | sqrt_totmet | 1777 | 0.086 | 2.82e-04 |
| sqrt_vitd_total | sqrt_totmet | 1777 | -0.002 | 9.32e-01 |
Interpret the results: RIDAGEYR, log_calcium_total, and sqrt_vitd_total are associated with physical activity levels.
Examine correlations among all predictor variables (all pairwise combinations):
# YOUR CODE HERE
# Create all pairwise combinations of predictors
# Hint: Use combn() to generate pairs, then map_dfr() with corr_pair()
preds <- c("RIDAGEYR", "log_bmi", "log_calcium_total", "sqrt_vitd_total")
pairs <- combn(preds, 2, simplify = FALSE)
tableC <- map_dfr(pairs, ~corr_pair(bmd2, .x[1], .x[2])) %>%
mutate(
estimate = round(estimate, 3),
p_value = signif(p_value, 3)
)
tableC %>% kable()| x | y | n | estimate | p_value |
|---|---|---|---|---|
| RIDAGEYR | log_bmi | 2834 | -0.098 | 2.00e-07 |
| RIDAGEYR | log_calcium_total | 2605 | 0.048 | 1.36e-02 |
| RIDAGEYR | sqrt_vitd_total | 2605 | 0.153 | 0.00e+00 |
| log_bmi | log_calcium_total | 2569 | 0.000 | 9.81e-01 |
| log_bmi | sqrt_vitd_total | 2569 | 0.007 | 7.31e-01 |
| log_calcium_total | sqrt_vitd_total | 2605 | 0.314 | 0.00e+00 |
Interpret the results:
There are no strong correlations among predictors that might indicate multicollinearity concerns in future regression analyses.
Create scatterplots to visualize key relationships:
#BMD vs BMI
ggplot(bmd2, aes(x = log_bmi, y = DXXOFBMD)) +
geom_point(alpha = 0.25) +
geom_smooth(method = "lm", se = FALSE) +
labs(
x = "log(BMI)",
y = "BMD (g/cm²)",
title = "BMD vs BMI (transformed)"
)
#BMD vs Physical Activity
ggplot(bmd2, aes(x = sqrt_totmet, y = DXXOFBMD)) +
geom_point(alpha = 0.25) +
geom_smooth(method = "lm", se = FALSE) +
labs(
x = "sqrt(totmet)",
y = "BMD (g/cm²)",
title = "BMD vs MET (transformed)"
)You would use ANOVA versus correlation in epidemiological research when one variable is categorical. ANOVA addresses the multiple comparisons problem. When comparing 3+ groups. While, correlation measures the strength and direction of the LINEAR relationship between two continuous variables. One example of a research question better suited to ANOVA is: How does respiratory hospital admission rate vary by air pollution level (low/moderate/high)? One example of a research question better suited to correlation is: Is there a correlation between age and systolic blood pressure among US adults?
In this assignment the independence assumption was most challenging to meet.I feel like the QQ plot made it clear to assume normality, Levene for variance, and although we has Residuals vs Fitted for independence, it was still tricky. Violation of assumptions can affect conclusions because they can distort results. For example: outliers can have large effects on F-test validity. The limitations of cross-sectional correlation analysis for understanding relationships between nutrition/activity and bone health is that you can’t determine causality, correlation does not equal causation.
The most difficult part of the R coding for this assignment was making sure that the right variables were going into the right places, especially when creating correlation tables. Also, the process to get eta_squared was difficult because I wanted to use the SUM function like previous in-class examples to get the total, but I was running into errors because of the order I was placing things. I ultimately determined that I could simply just use a plus sign instead.I also assumed ss_ethnicity was ss_between because there were 2 rows in the table ethnicity and residuals. And from previous examples I knew that I would have to sum the two in the table so, process of elimination. The R skill that I strengthen through completing this assignment was probably pearson correlation tables.
Before submitting, verify: