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File	Version	Author	Date	Message
Rmd	7ec169f	linmatch	2024-10-03	update sibling distribution
Rmd	27b986f	linmatch	2024-10-01	update stability cohort analysis
Rmd	57a97db	linmatch	2024-09-30	Update relative-distribution.Rmd
Rmd	52aa7f8	linmatch	2024-09-27	improving code on Part1
Rmd	c54a746	linmatch	2024-09-26	update and fix step 2
Rmd	94d00b3	linmatch	2024-09-24	fix step1
Rmd	1225480	linmatch	2024-09-23	update on step1
Rmd	83174c0	Tina Lasisi	2024-09-22	Instructions and layout for relative distribution
html	83174c0	Tina Lasisi	2024-09-22	Instructions and layout for relative distribution
Rmd	78c1621	Tina Lasisi	2024-09-21	Update relative-distribution.Rmd
Rmd	f4c2830	Tina Lasisi	2024-09-21	Update relative-distribution.Rmd
Rmd	2851385	Tina Lasisi	2024-09-21	rename old analysis
html	2851385	Tina Lasisi	2024-09-21	rename old analysis

Introduction

The relative genetic surveillance of a population is influenced by the number of genetically detectable relatives individuals have. First-degree relatives (parents, siblings, and children) are especially relevant in forensic analyses using short tandem repeat (STR) loci, where close familial searches are commonly employed. To explore potential disparities in genetic detectability between African American and European American populations, we examined U.S. Census data from four census years (1960, 1970, 1980, and 1990) focusing on the number of children born to women over the age of 40.

Data Sources

We used publicly available data from the Integrated Public Use Microdata Series (IPUMS) for the U.S. Census years 1960, 1970, 1980, and 1990. The datasets include information on:

AGE: Age of the respondent.
RACE: Self-identified race of the respondent.
chborn_num: Number of children ever born to the respondent.

Data citation: Steven Ruggles, Sarah Flood, Matthew Sobek, Daniel Backman, Annie Chen, Grace Cooper, Stephanie Richards, Renae Rogers, and Megan Schouweiler. IPUMS USA: Version 14.0 [dataset]. Minneapolis, MN: IPUMS, 2023. https://doi.org/10.18128/D010.V14.0

Data Preparation

Filtering Criteria: We selected women aged 40 and above to ensure that most had completed childbearing.

Due to the terms of agreement for using this data, we cannot share the full dataset but our repo contains the subset that was used to calculate the mean number of offspring and variance.

Race Classification: We categorized individuals into two groups:

African American: Those who identified as “Black” or “African American”.
European American: Those who identified as “White”.

Calculating Number of Siblings: For each child of these women, the number of siblings (n_sib) is one less than the number of children born to the mother:

\[ n_{sib} = chborn_{num} - 1 \]

path <- file.path(".", "data")
savepath <- file.path(".", "output")

prop_race_year <- file.path(path, "proportions_table_by_race_year.csv")
data_filter <- file.path(path, "data_filtered_recoded.csv")

children_data = read.csv(prop_race_year)
mother_data = read.csv(data_filter)

df <- mother_data %>%
  # Filter for women aged 40 and above
  filter(AGE >= 40) %>%
  mutate(
    # Create new age ranges
    AGE_RANGE = case_when(
      AGE >= 70 ~ "70+",
      AGE >= 60 ~ "60-69",
      AGE >= 50 ~ "50-59",
      AGE >= 40 ~ "40-49",
      TRUE ~ as.character(AGE_RANGE)  # This shouldn't occur due to the filter, but included for completeness
    ),
    # Convert CHBORN to ordered factor
    CHBORN = factor(case_when(
      chborn_num == 0 ~ "No children",
      chborn_num == 1 ~ "1 child",
      chborn_num == 2 ~ "2 children",
      chborn_num == 3 ~ "3 children",
      chborn_num == 4 ~ "4 children",
      chborn_num == 5 ~ "5 children",
      chborn_num == 6 ~ "6 children",
      chborn_num == 7 ~ "7 children",
      chborn_num == 8 ~ "8 children",
      chborn_num == 9 ~ "9 children",
      chborn_num == 10 ~ "10 children",
      chborn_num == 11 ~ "11 children",
      chborn_num >= 12 ~ "12+ children"
    ), levels = c("No children", "1 child", "2 children", "3 children", 
                  "4 children", "5 children", "6 children", "7 children", 
                  "8 children", "9 children", "10 children", "11 children", 
                  "12+ children"), ordered = TRUE),
    
    # Ensure RACE variable is correctly formatted and filtered
    RACE = factor(RACE, levels = c("White", "Black/African American"))
  ) %>%
  # Filter for African American and European American women
  filter(RACE %in% c("Black/African American", "White")) %>%
  # Select and reorder columns
  dplyr::select(YEAR, SEX, AGE, BIRTHYR, RACE, CHBORN, AGE_RANGE, chborn_num)

# Display the first few rows of the processed data
head(df)

  YEAR    SEX AGE BIRTHYR  RACE      CHBORN AGE_RANGE chborn_num
1 1960 Female  65    1894 White No children     60-69          0
2 1960 Female  49    1911 White  2 children     40-49          2
3 1960 Female  54    1905 White No children     50-59          0
4 1960 Female  56    1903 White     1 child     50-59          1
5 1960 Female  54    1905 White     1 child     50-59          1
6 1960 Female  50    1910 White No children     50-59          0

# Summary of the processed data
summary(df)

      YEAR          SEX                 AGE            BIRTHYR    
 Min.   :1960   Length:1917477     Min.   : 41.00   Min.   :1859  
 1st Qu.:1970   Class :character   1st Qu.: 49.00   1st Qu.:1905  
 Median :1970   Mode  :character   Median : 58.00   Median :1916  
 Mean   :1976                      Mean   : 59.24   Mean   :1916  
 3rd Qu.:1980                      3rd Qu.: 68.00   3rd Qu.:1926  
 Max.   :1990                      Max.   :100.00   Max.   :1949  
                                                                  
                     RACE                 CHBORN        AGE_RANGE        
 White                 :1740755   2 children :452594   Length:1917477    
 Black/African American: 176722   No children:343319   Class :character  
                                  3 children :335119   Mode  :character  
                                  1 child    :292001                     
                                  4 children :204983                     
                                  5 children :113593                     
                                  (Other)    :175868                     
   chborn_num   
 Min.   : 0.00  
 1st Qu.: 1.00  
 Median : 2.00  
 Mean   : 2.57  
 3rd Qu.: 4.00  
 Max.   :12.00

# Check the levels of the RACE factor
levels(df$RACE)

[1] "White"                  "Black/African American"

# Count of observations by RACE
table(df$RACE)


                 White Black/African American 
               1740755                 176722

# Count of observations by AGE_RANGE
table(df$AGE_RANGE)


 40-49  50-59  60-69    70+ 
529160 517620 436829 433868

Distribution of Number of Children Across Census Years

First we visualize the general trends in the frequency of the number of children for African American and European American mothers across the Census years by age group.

# Calculate proportions within each group, ensuring proper normalization
df_proportions <- df %>%
  group_by(YEAR, RACE, AGE_RANGE, chborn_num) %>%
  summarise(count = n(), .groups = "drop") %>%
  group_by(YEAR, RACE, AGE_RANGE) %>%
  mutate(proportion = count / sum(count)) %>%
  ungroup()

# Reshape data for the mirror plot
df_mirror <- df_proportions %>%
  mutate(proportion = if_else(RACE == "White", -proportion, proportion))

# Create color palette
my_colors <- colorRampPalette(c("#FFB000", "#F77A2E", "#DE3A8A", "#7253FF", "#5E8BFF"))(13)

# Create the plot
ggplot(df_mirror, aes(x = chborn_num, y = proportion, fill = as.factor(chborn_num))) +
  geom_col(aes(alpha = RACE)) +
  geom_hline(yintercept = 0, color = "black", size = 0.5) +
  facet_grid(AGE_RANGE ~ YEAR, scales = "free_y") +
  coord_flip() +
  scale_y_continuous(
    labels = function(x) abs(x),
    limits = function(x) c(-max(abs(x)), max(abs(x)))
  ) +
  scale_x_continuous(breaks = 0:12, labels = c(0:11, "12+")) +
  scale_fill_manual(values = my_colors) +
  scale_alpha_manual(values = c("White" = 0.7, "Black/African American" = 1)) +
  labs(
    title = "Distribution of Number of Children by Census Year, Race, and Age Range",
    x = "Number of Children",
    y = "Proportion",
    fill = "Number of Children",
    caption = "White population shown on left (negative values), Black/African American on right (positive values)\nProportions normalized within each age range, race, and census year\nFootnote: The category '12+' includes families with 12 or more children."
  ) +
  theme_minimal() +
  theme(
    plot.title = element_text(size = 14, hjust = 0.5),
    axis.text.y = element_text(size = 8),
    strip.text = element_text(size = 10),
    legend.position = "none",
    panel.grid.major.y = element_blank(),
    panel.grid.minor.y = element_blank()
  )

Version	Author	Date
83174c0	Tina Lasisi	2024-09-22
2851385	Tina Lasisi	2024-09-21

# Save the plot (optional)
# ggsave("children_distribution_mirror_plot.png", width = 20, height = 25, units = "in", dpi = 300)

# Print summary to check age ranges and normalization
print(df_proportions %>%
  group_by(YEAR, RACE, AGE_RANGE) %>%
  summarise(total_proportion = sum(proportion), .groups = "drop") %>%
  arrange(YEAR, RACE, AGE_RANGE))

# A tibble: 32 × 4
    YEAR RACE                   AGE_RANGE total_proportion
   <int> <fct>                  <chr>                <dbl>
 1  1960 White                  40-49                    1
 2  1960 White                  50-59                    1
 3  1960 White                  60-69                    1
 4  1960 White                  70+                      1
 5  1960 Black/African American 40-49                    1
 6  1960 Black/African American 50-59                    1
 7  1960 Black/African American 60-69                    1
 8  1960 Black/African American 70+                      1
 9  1970 White                  40-49                    1
10  1970 White                  50-59                    1
# ℹ 22 more rows

With this visualization of the distribution of the data, we can see that there are differences between White and Black Americans.

We will now test for differences in 1) the mean and variance, and 2) zero-inflation.

[instructions for Manqing] Model Fit Across Census Years

Question 1) What is the best model for the distribution of the data in each of these subsets of data (by race, by census year, by age range combined)?

Step 1: Fit Models Across All Subsets

For each combination of race, census year, and age range, fit your candidate models:

Poisson Model
Negative Binomial (NB) Model
Zero-Inflated Poisson (ZIP) Model
Zero-Inflated Negative Binomial (ZINB) Model

This should be done for each subset of the data (race × census year × age range).

Understanding the Data:

Data Type: Count data representing the number of children per woman.
Characteristics:
- Potential overdispersion (variance greater than the mean).
- Possible zero-inflation (excess zeros) in some subsets.
- Different distributions across races, census years, and age ranges.

Candidate Models for Count Data:

Poisson Distribution:
- Assumes mean equals variance.
- Not suitable if overdispersion is present.
Negative Binomial Distribution:
- Handles overdispersion by introducing a dispersion parameter.
- Suitable when variance exceeds the mean.
Zero-Inflated Models:
- Zero-Inflated Poisson (ZIP):
  - Combines a Poisson distribution with a point mass at zero.
  - Suitable if there’s an excess of zeros.
- Zero-Inflated Negative Binomial (ZINB):
  - Combines a negative binomial distribution with a point mass at zero.
  - Handles both overdispersion and excess zeros.
Hurdle Models: (optional)
- Similar to zero-inflated models but model zeros and positive counts separately.

Recommended Approach:

1: Exploratory Data Analysis (EDA)

Compute Mean and Variance:
- For each subset (race, census year, age range), calculate the mean and variance of the number of children.
- Check for overdispersion: If variance > mean, overdispersion is present.
Check for Zero-Inflation:
- Calculate the proportion of zeros in each subset.
- If the proportion of zeros is significantly higher than expected under a standard Poisson or negative binomial model, consider zero-inflated models.

2: Model Selection

Scenario 1: Overdispersion Without Excess Zeros

Model: Negative Binomial Distribution
Justification: Handles overdispersion effectively.

Scenario 2: Overdispersion With Excess Zeros

Model: Zero-Inflated Negative Binomial (ZINB) Distribution
Justification: Accounts for both overdispersion and excess zeros.

Scenario 3: No Overdispersion, No Excess Zeros

Model: Poisson Distribution
Justification: Appropriate if mean equals variance and no excess zeros.

3: Fit Models to Each Subset

For Each Subset:
- Fit a Poisson model.
- Fit a Negative Binomial model.
- If necessary, fit a Zero-Inflated Poisson (ZIP) and Zero-Inflated Negative Binomial (ZINB) model.
Compare Models:
- Use goodness-of-fit measures such as Akaike Information Criterion (AIC) or Bayesian Information Criterion (BIC).
- Lower AIC/BIC indicates a better-fitting model.
- Perform likelihood ratio tests where appropriate.

Step 2: Model Comparison Using AIC or BIC

Once the models are fitted, compare them using goodness-of-fit criteria like AIC or BIC for each subset. The model with the lowest AIC/BIC is the best fit for that subset.

Assess Model Fit:
- Check residuals for patterns.
- Use diagnostic plots.
Check Dispersion Parameter:
- For negative binomial models, examine the estimated dispersion parameter.
Vuong Test:
- Compare zero-inflated models to standard models to assess if zero-inflation significantly improves the fit.

## Approach 1:
combinations <- df %>%
  group_by(YEAR, RACE, AGE_RANGE) %>%
  group_split()

# Initialize the data frame for storing results
EDA_df <- data.frame(
  Race = character(),
  Census_Year = numeric(),
  Age_Range = character(),
  Overdispersion = logical(), 
  Zero_Inflation = logical(),
  stringsAsFactors = FALSE
)

# Initialize vectors for overdispersion and zero-inflation
overdispersion <- logical(length(combinations))
zero_inflation <- logical(length(combinations))

for (i in seq_along(combinations)) {
  subset_data <- combinations[[i]]
  mean_chborn <- mean(subset_data$chborn_num)
  var_chborn <- var(subset_data$chborn_num)
  
  # Check for overdispersion (variance > mean)
  overdispersion[i] <- var_chborn > mean_chborn
  
  # Check for zero-inflation
  prop_zero <- sum(subset_data$chborn_num == 0) / nrow(subset_data)
  
  # Compare prop_zero to expected under Poisson
  exp_poisson <- exp(-mean_chborn)

  # Compare prop_zero to expected under Negative Binomial
  standard_nb <- glm.nb(chborn_num ~ 1, data = subset_data)
  theta_nb <- standard_nb$theta
  exp_zero_nb <- (theta_nb / (theta_nb + mean_chborn))^theta_nb
  
  zero_inflation[i] <- prop_zero > exp_poisson | prop_zero > exp_zero_nb
  
  # Store the results in the EDA_df
  EDA_df <- rbind(
    EDA_df,
    data.frame(
      Race = unique(subset_data$RACE),
      Census_Year = unique(subset_data$YEAR),
      Age_Range = unique(subset_data$AGE_RANGE),
      Overdispersion = overdispersion[i], 
      Zero_Inflation = zero_inflation[i],
      stringsAsFactors = FALSE
    )
  )
}

EDA_df$model <- NA  # Create an empty column for the model

for(i in 1:nrow(EDA_df)) {
  if(EDA_df$Overdispersion[i] & EDA_df$Zero_Inflation[i]) {
    EDA_df$model[i] <- "Zero-Inflated Negative Binomial"
  } else if(EDA_df$Overdispersion[i] & !EDA_df$Zero_Inflation[i]) {
    EDA_df$model[i] <- "Negative Binomial"
  } else if(!EDA_df$Overdispersion[i] & !EDA_df$Zero_Inflation[i]) {
    EDA_df$model[i] <- "Poisson"
  } else if(!EDA_df$Overdispersion[i] & EDA_df$Zero_Inflation[i]){
    EDA_df$model[i] <- "Zero-Inflated Poisson"  
  }
}

# View the final EDA_df
print(EDA_df)

## Approach 2
# Initialize the data frame to store results
best_models <- data.frame(
  Race = character(),
  Census_Year = numeric(),
  Age_Range = character(),
  AIC_poisson = numeric(),
  AIC_nb = numeric(),
  AIC_zip = numeric(),
  AIC_zinb = numeric(),
  stringsAsFactors = FALSE
)

# Loop through each subset of data
for (i in seq_along(combinations)) {
  subset_data <- combinations[[i]]
  
  # Fit Poisson model
  poisson_model <- glm(chborn_num ~ 1, family = poisson, data = subset_data)
  # Fit Negative Binomial model
  nb_model <- glm.nb(chborn_num ~ 1, data = subset_data)

  # Fit Zero-Inflated Poisson model
  zip_model <- zeroinfl(chborn_num ~ 1 | 1, data = subset_data, dist = "poisson")

  # Fit Zero-Inflated Negative Binomial model
  zinb_model <- zeroinfl(chborn_num ~ 1 | 1, data = subset_data, dist = "negbin")
  
  # Append the result to the best_models data frame
  best_models <- rbind(
    best_models,
    data.frame(
      Race = unique(subset_data$RACE),
      Census_Year = unique(subset_data$YEAR),
      Age_Range = unique(subset_data$AGE_RANGE),
      AIC_poisson = AIC(poisson_model),
      AIC_nb = AIC(nb_model),
      AIC_zip = AIC(zip_model),
      AIC_zinb = AIC(zinb_model),
      stringsAsFactors = FALSE
    )
  )
}

# Add a Best_Model column to store the best model based on minimum AIC
best_models$Best_Model <- apply(best_models, 1, function(row) {
  # Get AIC values for Poisson, NB, ZIP, and ZINB models
  aic_values <- c(Poisson = as.numeric(row['AIC_poisson']),
                  Negative_Binomial = as.numeric(row['AIC_nb']),
                  Zero_Inflated_Poisson = as.numeric(row['AIC_zip']),
                  Zero_Inflated_NB= as.numeric(row['AIC_zinb']))
  
  # Find the name of the model with the minimum AIC value
  best_model <- names(which.min(aic_values))
  
  return(best_model)
})

best_models <- best_models %>% dplyr::select(Race, Census_Year, Age_Range, Best_Model)
# View the updated table with the Best_Model column
print(best_models)

Step 3: Record the Best Model for Each Subset

Create a table or data frame where you store the best model for each combination of race, census year, and age range based on AIC/BIC. For example:

Race	Census Year	Age Range	Best Model
Black/African Am.	1990	40-49	Negative Binomial
White	1990	40-49	Zero-Inflated NB
White	1980	50-59	Poisson
…	…	…	…

(but obviously do this as a dataframe so we can analyze it)

Step 4: Analyze the Effect of Race, Census Year, and Age Range

Once you’ve gathered the best model for each subset, you can analyze which factor (race, census year, or age range) is most influential in determining the best-fitting model.

Options for statistical analysis:

Chi-Square Test of Independence: You can use a chi-square test to determine whether there is a significant association between race and the best-fitting model, or census year/age group and the best-fitting model. This test will help you see if certain races or age ranges are more likely to have a particular model as the best fit.

#example
# Need large sample size, warning message "Chi-squared approximation may be incorrect," usually occurs when some of the expected counts in the contingency table are too small (typically less than 5)
## Create a contingency table
#table_model_race <- table(best_models$Race, best_models$Best_Model)

# Perform chi-square test
#chisq.test(table_model_race)

Logistic Regression: You could fit a logistic regression model where the response variable is the best-fitting model (binary or multinomial) and the predictor variables are race, census year, and age range. This will allow you to quantify the effect of each variable on the model choice.

Example in R (assuming binary outcome: Poisson vs. NB):

# Recode Best_Model to a binary variable (e.g., "Zero_Inflated_NB" vs. "Other")
best_models$Best_Model_Binary <- ifelse(best_models$Best_Model == "Zero_Inflated_NB", 1, 0)

# Fit binary logistic regression
model_logistic <- glm(Best_Model_Binary ~ Race + Census_Year + Age_Range, family = binomial(), data = best_models)

# Summary of the logistic regression model
summary(model_logistic)

Multinomial Logistic Regression (if more than two models): If you have multiple possible best-fitting models (Poisson, NB, ZIP, ZINB), you can use multinomial logistic regression to assess the impact of race, census year, and age range on model selection.

Example in R using the nnet package:

## Not appropriate since only 2 levels in best_model
# Fit multinomial logistic regression
#model_multinom <- multinom(Best_Model ~ Race + Census_Year + Age_Range, data = best_model_data)

# Summary of results
#summary(model_multinom)

Step 5: Summarize the Results

Significance of Each Variable: From the regression analysis (or chi-square tests), you can determine which variable (race, census year, or age range) has the most significant impact on the model choice.
Effect Sizes: Logistic regression will provide coefficients that describe how much each variable influences the probability of choosing a particular model.
Best Model by Race: You can summarize which model tends to fit best for each race across years and age groups. For example, you might find that the Negative Binomial model consistently fits the best for a specific race or age group, indicating more overdispersion in that subset.

Visualize the Results

Finally, visualize the distribution of the best-fitting models across races, census years, and age groups.

Bar Plots: Show the proportion of each model for different races or age groups.
Heatmap: Use a heatmap to visualize how the best model varies across race, census year, and age range.

Example of a simple bar plot in R:

# Bar plot showing the distribution of best models across races
ggplot(best_models, aes(x = Race, fill = Best_Model)) +
  geom_bar(position = "dodge") +
  labs(title = "Best-Fitting Models by Race", x = "Race", y = "Count", fill = "Best Model")

# Bar plot showing the distribution of best models across races
ggplot(best_models, aes(x = Census_Year, fill = Best_Model)) +
  geom_bar(position = "dodge") +
  labs(title = "Best-Fitting Models by Census Year", x = "Census Year", y = "Count", fill = "Best Model")

# Bar plot showing the distribution of best models across races
ggplot(best_models, aes(x = Age_Range, fill = Best_Model)) +
  geom_bar(position = "dodge") +
  labs(title = "Best-Fitting Models by Age Range", x = "Age Range", y = "Count", fill = "Best Model")

ggplot(best_models, aes(x = Census_Year, y = Age_Range, fill = Best_Model)) +
  geom_tile(color = "white", lwd = 0.5, linetype = 1) + # Create the tiles
  facet_wrap(~Race, nrow = 2) + # Facet by Race
  scale_fill_manual(values = c("Zero_Inflated_Poisson" = "#0072B2", "Zero_Inflated_NB" = "#F0E442")) + 
  labs(
    title = "Best Model by Race, Census Year, and Age Range",
    x = "Census Year",
    y = "Age Range",
    fill = "Best Model"
  ) +
  theme_minimal() +
  theme(
    axis.text.x = element_text(angle = 45, hjust = 1), # Rotate x-axis labels for readability
    plot.title = element_text(size = 14, face = "bold"),
    legend.position = "bottom"
  )

Conclusion:

Best Model Analysis: The best-fitting model can be assessed across different races, census years, and age ranges by comparing models using AIC/BIC.
Significance Testing: Use chi-square or logistic regression to assess which variable most influences the model selection.
Summarizing Across Years: After analyzing the data, you’ll be able to conclude which model fits each race best across different years, and whether race, census year, or age group is the dominant factor.

[Instructions for Manqing] Cohort Stability Analysis

For Question 2: Cohort Stability Analysis, the goal is to determine if there is a significant change in zero inflation, family size, or model fit for the same cohort across different census years, given race.

Step 1: Add a Birth-Year “Cohort” Variable

Using the existing table of model summaries, calculate the birth-year cohort based on the Census Year and Age Range. For example, if a woman is in the 40-49 age range in the 1990 Census, her birth cohort would be 1941-1950.

Formula to Calculate Cohort: For each row in the table, subtract the age range from the census year to get the cohort. For example:
- Census Year: 1990
- Age Range: 40-49
- Cohort: 1990 - (40 to 49) → Cohort: 1941-1950
Add a new column to the summary table called Cohort.

Example Table:

Race	Census Year	Age Range	Best Model	Cohort
Black/African Am.	1990	40-49	Negative Binomial	1941-1950
White	1990	40-49	Zero-Inflated NB	1941-1950
White	1980	50-59	Poisson	1921-1930
…	…	…	…	…

calculate_cohort <- function(census_year, age_range) {
  # Extract the lower and upper age limits from the Age_Range
  age_limits <- as.numeric(unlist(strsplit(age_range, "-|\\+")))
  
  # If the age range is "70+", treat the upper bound as 70+ (i.e., infinity)
  if (length(age_limits) == 1) {
    lower_age <- age_limits
    upper_age <- Inf  # For ages 70+, we assume no upper bound
  } else {
    lower_age <- age_limits[1]
    upper_age <- age_limits[2]
  }
  
  # Calculate birth cohort bounds
  lower_cohort <- census_year - upper_age
  upper_cohort <- census_year - lower_age
  
  # If it's the 70+ age range, we'll assume the lower bound goes back to a reasonable limit
  if (upper_age == Inf) {
    upper_cohort <- census_year - 70
  }
  
  # Return the birth cohort as a string (e.g., "1941-1950")
  return(paste(lower_cohort, upper_cohort, sep = "-"))
}

# Apply this function to your best_models table to create a new 'Cohort' column
best_models <- best_models %>%
  mutate(Cohort = mapply(calculate_cohort, Census_Year, Age_Range)) %>% 
  dplyr::select(Race, Census_Year, Age_Range, Best_Model, Cohort)

# View the updated table
print(best_models)

Step 2: Compute Summary Statistics for Each Subset

For each combination of Race, Cohort, and Census Year, compute additional summary statistics for family size distributions: - Mean, Variance, Mode of the number of children. - Probability of having 0, 1, 2, …, 12+ children (empirical or from the best-fitting model).

These statistics will help quantify family size changes over time.

Example Summary Table:

Race	Cohort	Census Year	Best Model	Mean	Variance	Mode	Prob(0)	Prob(1)	Prob(2)	…	Prob(12+)
Black/African Am.	1941-1950	1990	Negative Binomial	2.5	1.2	2	0.20	0.30	0.25	…	0.01
White	1941-1950	1990	Zero-Inflated NB	2.1	1.0	2	0.35	0.28	0.20	…	0.01
White	1921-1930	1980	Poisson	3.0	1.5	3	0.15	0.25	0.30	…	0.05
…	…	…	…	…	…	…	…	…	…	…	…

df_merg <- df %>%
  rename(Census_Year = YEAR, Race = RACE, Age_Range = AGE_RANGE)

# Perform a left join to merge the data frames
merged_data <- left_join(df_merg, best_models, by = c("Race", "Census_Year", "Age_Range"))

calculate_mode <- function(x) {
  ux <- unique(x)
  ux[which.max(tabulate(match(x, ux)))]
}

summary_table <- merged_data %>% group_by(Race, Cohort, Census_Year) %>%
  summarise(
    Mean = mean(chborn_num),
    Variance = var(chborn_num),
    Mode = calculate_mode(chborn_num),
    Prob_0 = mean(chborn_num == 0),
    Prob_1 = mean(chborn_num == 1),
    Prob_2 = mean(chborn_num == 2),
    Prob_3 = mean(chborn_num == 3),
    Prob_4 = mean(chborn_num == 4),
    Prob_5 = mean(chborn_num == 5),
    Prob_6 = mean(chborn_num == 6),
    Prob_7 = mean(chborn_num == 7),
    Prob_8 = mean(chborn_num == 8),
    Prob_9 = mean(chborn_num == 9),
    Prob_10 = mean(chborn_num == 10),
    Prob_11 = mean(chborn_num == 11),
    Prob_12plus = mean(chborn_num >= 12)
    #Total_Prob = Prob_0 + Prob_1 + Prob_2 + Prob_3 + Prob_4 + Prob_5 + Prob_6 + 
                # Prob_7 + Prob_8 + Prob_9 + Prob_10 + Prob_11 + Prob_12plus
  ) %>%
  ungroup() %>% as.data.frame()

# View the summary table
print(summary_table)

Step 3: Test for Significant Changes Over Time Within Each Cohort

Once the cohort information and summary statistics are available, the goal is to determine if there is a significant change in any of the following across census years for the same cohort:

Zero Inflation: Check if the proportion of women with zero children changes significantly over time for the same cohort.
Family Size: Test if the mean or variance in the number of children changes for the same cohort over time.
Model Fit: Analyze if the best-fitting model for the cohort changes over time.

a. Zero-Inflation Analysis

Use a logistic regression model to assess if the probability of having zero children changes significantly over time for the same cohort.

Example Code:

# Fit logistic regression to check if zero-inflation changes over time
zero_inflation_model <- glm(Prob_0 ~ Census_Year + Race + Cohort, 
                            family = binomial(), data = summary_table)

# Summary of the model
summary(zero_inflation_model)

Result: The p-value of “Census_Year” is greater than 0.05, suggesting no statistically significance. Therefore, the probability of having zero children does not change significantly over time for the same cohort.

b. Family Size Analysis

Use an ANOVA or linear regression to test if the mean or variance in family size changes over census years for the same cohort.

Example Code:

  # Fit linear model to check for changes in family size over time
  family_size_model <- lm(Mean ~ Census_Year + Race + Cohort, data = summary_table)
  
  # ANOVA to check for significant differences in mean
  anova(family_size_model)

Result: The p-value of “Census_Year” is greater than 0.05, suggesting no statistically significance. Therefore, the mean in family size does not change over census years for the same cohort.

c. Model Fit Analysis

If the best-fitting model changes for the same cohort over time, this suggests that the distribution of family sizes has shifted. Use multinomial logistic regression to test if the model fit differs across census years for the same cohort.

Example Code:

cohort_data <- summary_table %>%
  left_join(best_models, by = c("Race", "Census_Year", "Cohort")) %>%
    mutate(Best_Model_Binary = ifelse(Best_Model == "Zero_Inflated_NB", 1, 0))


# Fit multinomial logistic regression to test changes in best-fitting model
model_fit_analysis <- glm(Best_Model_Binary ~ Census_Year + Race + Cohort, data = cohort_data)

# Summary of the model
summary(model_fit_analysis)

Result: The p-value of “Census_Year” is greater than 0.05, suggesting no statistically significant effect on choice between best models.

Step 4: Interpret the Results

For each cohort, you will assess whether: - Zero-inflation changes significantly over time (i.e., whether the probability of having no children decreases or increases across census years). - Family size (mean, variance, mode) changes significantly over time. - The best-fitting model changes over time, indicating a shift in family size distributions.

If significant changes are detected for a cohort (e.g., the same cohort switches from a zero-inflated model to a non-zero-inflated model, or family sizes decrease), this indicates a shift in the demographic pattern for that group.

Conclusion

This analysis will allow you to evaluate cohort stability by testing whether demographic patterns (e.g., zero-inflation, family size) are consistent over time for the same cohort or if there are notable shifts. If the patterns change significantly, you will be able to identify when and how the demographic trends for each cohort begin to deviate from their earlier distribution.

[Instructions for Manqing] Question 3: Analyzing and Visualizing Significant Fertility Shifts

For Question 3: Significant Fertility shifts, the goal is to summarize the information in the top 2 questions and create a comprehensive analysis and visualization that illustrates significant fertility shifts in cohorts, compares fertility patterns of 40-49 year-olds to 50-59 year-olds in the 1990 census so we can pick the set of fertility distributions we want to use to visualize the sibling distribution and do the math on the genetic surveillance.

Objective

Create a comprehensive analysis and visualization that:

Illustrates significant fertility shifts in cohorts based on the stability analysis from Question 2.
Compares fertility patterns of 40-49 year-olds to 50-59 year-olds in the 1990 census, highlighting any significant differences.
Synthesizes the findings to discuss overall trends and their implications.

The steps below are suggestions: use critical thinking and your judgement to complete this task and answer the question

Step 1: Prepare the Data

1.1 Use Results from Stability Analysis (Question 2)

Identify Cohorts with Significant Shifts:
- Review the results from your stability analysis in Question 2.
- List the cohorts where significant shifts in fertility distributions were observed for 40-49 year-olds.
- Note the nature of these shifts for each cohort, such as changes in mean number of children, variance, or zero inflation (proportion of women with zero children).

1.2 Extract Data for Age Groups in 1990 Census

Filter Data for 1990 Census:
- Use your existing dataset to extract data specifically from the 1990 census year.
Select Age Groups:
- Focus on women in the age ranges of 40-49 and 50-59.
- Ensure the data includes necessary variables:
  - Number of children (chborn_num)
  - Age range (AGE_RANGE)
  - Race (RACE)
  - Any other relevant variables used in previous analyses

Step 2: Create Visualizations

Design visualizations that effectively communicate your findings.

2.1 Panel A: Fertility Distribution Shifts Across Cohorts

Use Existing Fertility Distribution Plots:
- Leverage the fertility distribution plots you created in Question 1.
Highlight Significant Cohorts:
- Emphasize the cohorts identified in Step 1.1 where significant shifts occurred.
  - This could be done by using distinct colors, markers, or annotations.
Annotate the Plots:
- Include text or labels that describe the nature of the significant shifts for each highlighted cohort.
  - For example, indicate if there was a decrease in mean number of children or an increase in childlessness.

2.2 Panel B: Comparison of 40-49 and 50-59 Age Groups in 1990

Create Comparative Distribution Plots:
- Generate side-by-side or overlaid histograms or density plots for the 40-49 and 50-59 age groups within each racial group.
Include Summary Statistics:
- On each plot or in accompanying tables, provide:
  - Mean number of children
  - Variance
  - Proportion of women with zero children (zero inflation)
Ensure Clarity in Visuals:
- Properly label axes, legends, and titles.
- Use consistent color schemes for easy comparison between groups.

Step 3: Perform Statistical Comparisons

Conduct statistical tests to determine if observed differences are significant.

3.1 T-Test for Difference in Means

Compare Means Between Age Groups:
- For each racial group, perform a t-test to compare the mean number of children between the 40-49 and 50-59 age groups.
Check Assumptions:
- Ensure that the data meets the assumptions of the t-test (normality, equal variances).
- If assumptions are violated, consider using a non-parametric test like the Mann-Whitney U test.

3.2 F-Test for Difference in Variances

Assess Variance Differences:
- Perform an F-test or Levene’s test to compare the variances of the number of children between the two age groups within each racial group.

3.3 Chi-Square Test for Difference in Zero Inflation

Analyze Zero Inflation:
- Create contingency tables showing the counts of women with zero children and those with one or more children for each age group.
- Perform a chi-square test to determine if the proportion of childlessness differs significantly between the age groups within each racial group.

Step 4: Summarize Findings

Write a clear and concise summary addressing the following points.

4.1 Significant Fertility Shifts Across Cohorts

Identify Timing of Shifts:
- Specify when significant fertility shifts occurred for each racial group based on your analysis in Question 2.
Describe Nature of Shifts:
- Detail the characteristics of the shifts, such as:
  - Decrease in mean number of children
  - Increase in childlessness (zero inflation)
  - Changes in variance or distribution shape
Highlight Differences Between Racial Groups:
- Compare the timing and nature of shifts between African American and European American women.
- Discuss any patterns or discrepancies observed.

4.2 Comparison of 40-49 and 50-59 Age Groups in 1990

Summarize Key Differences:
- Present the differences in fertility patterns between the two age groups for each racial group.
- Include comparisons of:
  - Distribution shapes
  - Mean number of children
  - Variance
  - Zero inflation
Report Statistical Test Results:
- Provide the results of the t-tests, F-tests, and chi-square tests.
- Interpret the significance of these results in the context of your analysis.
Discuss Implications:
- Consider what these differences suggest about fertility trends and behaviors.
- Reflect on whether the older age group represents completed fertility patterns.

4.3 Synthesis and Implications

Integrate Findings:
- Connect the insights from the cohort analysis with the age group comparison.
- Discuss how the patterns observed in the 1990 census relate to the shifts identified across cohorts.
Consider Contributing Factors:
- Explore potential social, economic, or policy factors that may have contributed to the observed fertility shifts.
  - For example, changes in access to education, employment opportunities, or family planning resources.
Reflect on Broader Implications:
- Discuss how these fertility trends might impact your broader research topic, such as genetic surveillance disparities.
- Consider the implications for future demographic research or policy development.

Additional Considerations

Visual Clarity:
- Ensure all visualizations are easy to interpret.
- Use clear labels, legends, and annotations.
Contextualize Statistical Significance:
- Explain not just whether results are statistically significant, but also what they mean in practical terms.
Acknowledge Data Limitations:
- Discuss any limitations or biases in the data that could affect your findings.
  - For instance, sample size constraints or missing data.
Ethical Considerations:
- Approach discussions of race and fertility sensitively and responsibly.
- Avoid drawing causal conclusions without robust evidence.

Integration with Previous Work

Leverage Previous Analyses:
- Use the visualizations and statistical summaries from Questions 1 and 2 as foundations for this analysis.
Create a Cohesive Narrative:
- Ensure that your findings from all questions are connected and build upon each other.
- Tell a comprehensive story about fertility trends across cohorts and racial groups.

Final Deliverables

Multi-Panel Visualization:
- Panel A: Fertility distribution shifts across cohorts with highlighted significant shifts.
- Panel B: Comparative distribution plots for 40-49 and 50-59 age groups in 1990, including summary statistics.
Written Summary:
- A concise report that addresses the points outlined in Step 4.
- Include interpretations of statistical analyses and discuss broader implications.
Statistical Analysis Documentation:
- Provide details of the statistical tests conducted, including test assumptions, results, and interpretations.
Annotated Code (if applicable):
- While not the focus, include any new code used for this analysis with appropriate comments.

Distribution of Number of Siblings Across Census Years

Having analyzed the distribution of the number of children, we now turn our attention to the distribution of the number of siblings. We will explore the trends in the frequency of the number of siblings for African American and European American mothers across the Census years by age group.

Frequency of siblings is calculated as follows.

\[ \text{freq}_{n_{\text{sib}}} = \text{freq}_{\text{mother}} \cdot \text{chborn}_{\text{num}} \]

For example, suppose 10 mothers (generation 0) have 7 children, then there will be 70 children (generation 1) in total who each have 6 siblings.

We take our original data and calculate the frequency of siblings for each mother based on the number of children they have. We then aggregate this data to get the frequency of siblings for each generation along with details on the birthyears of the relevant children to visualize the distribution of the number of siblings across generations.

[Instructions for Manqing] Plot Across Census Years for Children

Objective

Create a mirror plot for the distribution of siblings across census years, races, and birth ranges, similar to the one created for the number of children.

Step 1: Calculate Sibling Frequencies

Start with your dataframe that includes the birth_range column.

df2 <- df %>%
  mutate(birth_range = mapply(calculate_cohort, YEAR, AGE_RANGE)) %>% 
  dplyr::select(RACE, YEAR, AGE_RANGE, birth_range, chborn_num)

Create a new column for the number of siblings:

df2 <- df2 %>%
 mutate(n_siblings = chborn_num - 1)

Calculate the frequency of siblings:

df2 <- df2 %>%
mutate(sibling_freq = n_siblings * 1)  # Assuming each mother represents 1 in frequency

Step 2: Aggregate Sibling Data

Group the data and calculate sibling frequencies:

df_siblings <- df2 %>%
 group_by(YEAR, RACE, birth_range, n_siblings) %>%
 summarise(
   sibling_count = sum(sibling_freq),
   .groups = "drop"
 )

Calculate proportions within each group:

df_sibling_proportions <- df_siblings %>%
 group_by(YEAR, RACE, birth_range) %>%
 mutate(proportion = sibling_count / sum(sibling_count)) %>%
 ungroup()

Step 3: Check Normalization

Before creating the plot, verify that the proportions are correctly normalized:

normalization_check <- df_sibling_proportions %>%
  group_by(YEAR, RACE, birth_range) %>%
  summarise(total_proportion = sum(proportion), .groups = "drop") %>%
  arrange(YEAR, RACE, birth_range)

print(normalization_check)

Ensure that the total_proportion for each group is very close to 1.0. If not, revisit your calculations in Step 2.

Step 4: Prepare Data for Mirror Plot

Reshape data for the mirror plot:

df_sibling_mirror <- df_sibling_proportions %>%
  mutate(proportion = if_else(RACE == "White", -proportion, proportion))

Step 5: Create the Mirror Plot

Create the color palette:

my_colors <- colorRampPalette(c("#FFB000", "#F77A2E", "#DE3A8A", "#7253FF", "#5E8BFF"))(13)

Create the plot:

ggplot(df_sibling_mirror, aes(x = n_siblings, y = proportion, fill = as.factor(n_siblings))) +
 geom_col(aes(alpha = RACE)) +
 geom_hline(yintercept = 0, color = "black", size = 0.5) +
 facet_grid(birth_range ~ YEAR, scales = "free_y") +
 coord_flip() +
 scale_y_continuous(
   labels = function(x) abs(x),
   limits = function(x) c(-max(abs(x)), max(abs(x)))
 ) +
 scale_x_continuous(breaks = 0:12, labels = c(0:11, "12+")) +
 scale_fill_manual(values = my_colors) +
 scale_alpha_manual(values = c("White" = 0.7, "Black/African American" = 1)) +
 labs(
   title = "Distribution of Number of Siblings by Census Year, Race, and Birth Range",
   x = "Number of Siblings",
   y = "Proportion",
   fill = "Number of Siblings",
   caption = "White population shown on left (negative values), Black/African American on right (positive values)\nProportions normalized within each birth range, race, and census year\nFootnote: The category '12+' includes individuals with 12 or more siblings."
 ) +
 theme_minimal() +
 theme(
   plot.title = element_text(size = 14, hjust = 0.5),
   axis.text.y = element_text(size = 8),
   strip.text = element_text(size = 10),
   legend.position = "none",
   panel.grid.major.y = element_blank(),
   panel.grid.minor.y = element_blank()
 )

Step 6: Interpret the Plot

After creating the plot, examine it carefully:

Look for patterns in sibling distribution across different census years and birth ranges. Result: -By Census Year: We can observe a decrease in family size over time. The distribution of centered toward smaller number of siblings. By 1990, most of the distribution are more compact, with a peak around 2–4 siblings, and the tail of the distribution (larger numbers of siblings) has reduced significantly. -By birth range:For individuals born in earlier periods like pre-1900 or 1910, the distribution is skewed toward larger families, with more people having a larger number of siblings.As we move to more recent birth ranges, the distributions shift toward smaller family sizes.
Compare the distributions between White and Black/African American populations. Result: In general, the White population tends to have a more concentrated distribution around 2–4 siblings in later census years, while the Black/African American population often shows a slightly more spread-out distribution. However, the trend of decreasing family size over time is visible in both populations, though it appears more pronounced for the White population.
Note any significant changes or trends in the number of siblings over time. Result: -Decrease in Family Size: Both distribution of children and siblings indicate a clear societal trend toward smaller family sizes over time, with fewer people having a large number of siblings or children. -Cohort Effects: Individuals born earlier (pre-1900 or early 1900s) tend to come from larger families, while those born later (1930s-1950s) tend to have fewer siblings and children.
Consider how these sibling distributions might differ from the children distributions you analyzed earlier, and think about potential reasons for these differences. Result: While both distributions show a trend toward smaller families, the sibling distribution is more spread out across different sibling counts. This might be due to the calculation difference in proportion between number of children and number of siblings. For example, if a family have 12 children, then all of these 12 children have 11 siblings, leading to

[Instructions for Manqing] Model Fit Across Census Years

Objective

Repeat the model fitting process we performed for the children distribution, this time using the sibling distribution data.

Steps

Prepare the Sibling Data Use the sibling distribution data you calculated earlier (df_sibling_proportions).
Fit Models For each combination of RACE, YEAR, and birth_range, fit the following distributions:
- Poisson
- Negative Binomial
- Zero-Inflated Poisson
- Zero-Inflated Negative Binomial
Use the same R functions and packages as in the children distribution analysis.
Compare Model Fits Use AIC (Akaike Information Criterion) to compare the fits of different models for each group.
Identify Best-Fitting Models Determine which model fits best for each combination of RACE, YEAR, and birth_range.
Analyze Patterns
- Examine how the best-fitting model changes across years and birth ranges for each race.
- Compare these patterns to those observed in the children distribution analysis.
Visualize Results Create a summary plot showing the best-fitting models across years and birth ranges for each race, similar to the one created for the children distribution.
Interpret Findings
- Discuss any differences in the best-fitting models between the sibling and children distributions.
- Consider the implications of these differences for understanding family structures and fertility patterns.

[Instructions for Manqing] Cohort Stability Analysis Siblings

Objective

Analyze the stability of sibling distributions across cohorts, similar to the analysis performed for children.

Steps

Use the sibling distribution data (df_sibling_proportions).
For each combination of RACE and birth_range:
- Compare the sibling distributions across different census years.
- Use statistical tests (e.g., Kolmogorov-Smirnov test) to assess if distributions are significantly different.
Create a summary table showing:
- RACE
- birth_range
- Whether the distribution is stable across census years
- Any significant changes observed
Visualize stability:
- Create a heatmap or similar plot showing stability/changes across cohorts and races.
Interpret results:
- Identify which cohorts show stable sibling distributions.
- Compare stability patterns to those observed in the children distribution analysis.
- Discuss implications of stability or lack thereof for understanding family structure changes over time.

[Instructions for Manqing] Plot Across Census Years Siblings

Objective

Create a visualization showing how sibling distributions change across census years for different races and birth ranges.

Steps

Use the sibling distribution data (df_sibling_proportions).
Create a multi-panel plot:
- X-axis: Number of siblings (0 to 12+)
- Y-axis: Proportion
- Color: Census Year
- Facet by: RACE and birth_range
Use ggplot2 to create the plot:

ggplot(df_sibling_proportions, aes(x = n_siblings, y = proportion, color = factor(YEAR))) +
 geom_line() +
 facet_grid(RACE ~ birth_range) +
 labs(title = "Sibling Distribution Across Census Years",
      x = "Number of Siblings", y = "Proportion", color = "Census Year") +
 theme_minimal() +
 theme(axis.text.x = element_text(angle = 45, hjust = 1))

Analyze the plot:
- Identify trends in sibling distribution changes over time.
- Compare patterns between races and across birth ranges.
- Note any significant shifts or stable periods.
Compare with children distribution plot:
- Highlight similarities and differences in trends.
- Discuss what these comparisons reveal about changing family structures.

Remember to reference your findings from the children distribution analysis when discussing the results, highlighting any notable similarities or differences between the two analyses.

sessionInfo()

Estimating Differences in the Distribution of First-degree Relatives

Manqing Lin, Tina Lasisi

2024-10-04 13:31:25

Introduction

Data Sources

Data Preparation

Distribution of Number of Children Across Census Years

[instructions for Manqing] Model Fit Across Census Years

Step 1: Fit Models Across All Subsets

Step 2: Model Comparison Using AIC or BIC

Step 3: Record the Best Model for Each Subset

Step 4: Analyze the Effect of Race, Census Year, and Age Range

Step 5: Summarize the Results

Visualize the Results

Conclusion:

[Instructions for Manqing] Cohort Stability Analysis

Step 1: Add a Birth-Year “Cohort” Variable

Step 2: Compute Summary Statistics for Each Subset

Step 3: Test for Significant Changes Over Time Within Each Cohort

a. Zero-Inflation Analysis

b. Family Size Analysis

c. Model Fit Analysis

Step 4: Interpret the Results

Conclusion

[Instructions for Manqing] Question 3: Analyzing and Visualizing Significant Fertility Shifts

Objective

Step 1: Prepare the Data

1.1 Use Results from Stability Analysis (Question 2)

1.2 Extract Data for Age Groups in 1990 Census

Step 2: Create Visualizations

2.1 Panel A: Fertility Distribution Shifts Across Cohorts

2.2 Panel B: Comparison of 40-49 and 50-59 Age Groups in 1990

Step 3: Perform Statistical Comparisons

3.1 T-Test for Difference in Means

3.2 F-Test for Difference in Variances

3.3 Chi-Square Test for Difference in Zero Inflation

Step 4: Summarize Findings

4.1 Significant Fertility Shifts Across Cohorts

4.2 Comparison of 40-49 and 50-59 Age Groups in 1990

4.3 Synthesis and Implications

Additional Considerations

Integration with Previous Work

Final Deliverables

Distribution of Number of Siblings Across Census Years

[Instructions for Manqing] Plot Across Census Years for Children

Objective

Step 1: Calculate Sibling Frequencies

Step 2: Aggregate Sibling Data

Step 3: Check Normalization

Step 4: Prepare Data for Mirror Plot

Step 5: Create the Mirror Plot

Step 6: Interpret the Plot

[Instructions for Manqing] Model Fit Across Census Years

Objective

Steps

[Instructions for Manqing] Cohort Stability Analysis Siblings

Objective

Steps

[Instructions for Manqing] Plot Across Census Years Siblings

Objective

Steps