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Showing content from https://github.com/jackmurphy2351/riskdiff below:

jackmurphy2351/riskdiff: Calculate risk or prevalence differences using robust model fitting.

riskdiff

The riskdiff package provides robust methods for calculating risk differences (also known as prevalence differences in cross-sectional studies) using generalized linear models with automatic link function selection and boundary detection.

riskdiff v0.2.1 is now published on CRAN with cutting-edge boundary detection capabilities that identify when maximum likelihood estimates lie at the edge of the parameter space - a common issue with identity link models that other packages ignore.

🎯 Smart boundary detection: Automatically detects when GLMs hit parameter constraints
🔧 Robust model fitting: Tries identity, log, and logit links with graceful fallback
📊 Stratified analysis: Support for multi-level stratification
📋 Publication-ready output: Formatted tables and confidence intervals
🛡️ Missing data handling: Graceful handling of incomplete cases
⚙️ Flexible confidence intervals: Robust methods for boundary cases
📈 Multiple link functions: Automatic selection with boundary-aware switching
🔍 Transparent diagnostics: Clear reporting of model methods and boundary issues

John D. Murphy, MPH, PhD ORCID: 0000-0002-7714-9976

Install the latest stable version from CRAN:

install.packages("riskdiff")

You can install the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("jackmurphy2351/riskdiff")

library(riskdiff)

# Load example data
data(cachar_sample)

# Simple risk difference with boundary detection
result <- calc_risk_diff(
  data = cachar_sample,
  outcome = "abnormal_screen",
  exposure = "smoking"
)
#> Waiting for profiling to be done...

print(result)
#> Risk Difference Analysis Results (v0.2.0+)
#> ========================================== 
#> 
#> Confidence level: 95% 
#> Number of comparisons: 1 
#> 
#>  Exposure Risk Difference          95% CI P-value    Model Boundary CI Method
#>   smoking          10.68% (5.95%, 15.75%)  <0.001 identity               wald

🎯 Boundary Detection in Action

# Create data that challenges standard GLM methods
set.seed(123)
challenging_data <- data.frame(
  outcome = c(rep(0, 40), rep(1, 60)),  # High baseline risk
  exposure = factor(c(rep("No", 50), rep("Yes", 50))),
  age = rnorm(100, 45, 10)
)

# riskdiff handles this gracefully with boundary detection
result <- calc_risk_diff(
  data = challenging_data,
  outcome = "outcome", 
  exposure = "exposure",
  adjust_vars = "age",
  verbose = TRUE  # Shows diagnostic information
)
#> Formula: outcome ~ exposure + age
#> Sample size: 100
#> Trying identity link...
#> Using starting values: 0.2, 0.8, 0.004
#> Identity link error: cannot find valid starting values: please specify some
#> Trying log link...
#> log link error: no valid set of coefficients has been found: please supply starting values
#> Trying logit link...
#> [Huzzah!]logit link converged
#> Waiting for profiling to be done...
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm): collapsing to unique
#> 'x' values
#> Boundary case detected: separation
#> Warning: Logit model may have separation issues. Very large coefficient estimates detected.
#> Note: 1 of 1 analyses had MLE on parameter space boundary. Robust confidence intervals were used.

print(result)
#> Risk Difference Analysis Results (v0.2.0+)
#> ========================================== 
#> 
#> Confidence level: 95% 
#> Number of comparisons: 1 
#> Boundary cases detected: 1 of 1 
#> Boundary CI method: auto 
#> 
#>  Exposure Risk Difference              95% CI P-value Model          Boundary
#>  exposure          80.06% (-199.05%, 359.17%)   0.993 logit [Uh oh]separation
#>          CI Method
#>  wald_conservative
#> 
#> Boundary Case Details:
#> =====================
#> Row 1 ( exposure ):  Logit model may have separation issues. Very large coefficient estimates detected. 
#> 
#> Boundary Type Guide:
#> - upper_bound: Fitted probabilities near 1
#> - lower_bound: Fitted probabilities near 0
#> - separation: Complete/quasi-separation detected
#> - both_bounds: Probabilities near both 0 and 1
#> - [Uh oh] indicates robust confidence intervals were used
#> 
#> Note: Standard asymptotic theory may not apply for boundary cases.
#> Confidence intervals use robust methods when boundary detected.

# Check if boundary cases were detected
if (any(result$on_boundary)) {
  cat("\n🚨 Boundary case detected! Using robust inference methods.\n")
  cat("Boundary type:", unique(result$boundary_type[result$on_boundary]), "\n")
  cat("CI method:", unique(result$ci_method[result$on_boundary]), "\n")
}
#> 
#> 🚨 Boundary case detected! Using robust inference methods.
#> Boundary type: separation 
#> CI method: wald_conservative

Basic Usage with Enhanced Diagnostics

# Age-adjusted risk difference with boundary detection
rd_adjusted <- calc_risk_diff(
  data = cachar_sample,
  outcome = "abnormal_screen", 
  exposure = "smoking",
  adjust_vars = "age",
  boundary_method = "auto"  # Automatic robust method selection
)
#> Waiting for profiling to be done...

print(rd_adjusted)
#> Risk Difference Analysis Results (v0.2.0+)
#> ========================================== 
#> 
#> Confidence level: 95% 
#> Number of comparisons: 1 
#> 
#>  Exposure Risk Difference          95% CI P-value Model Boundary CI Method
#>   smoking          10.94% (7.57%, 14.32%)  <0.001 logit               wald

Stratified Analysis with Boundary Awareness

# Stratified by residence with boundary detection
rd_stratified <- calc_risk_diff(
  data = cachar_sample,
  outcome = "abnormal_screen",
  exposure = "smoking",
  adjust_vars = "age",
  strata = "residence"
)
#> Waiting for profiling to be done...
#> Waiting for profiling to be done...
#> Waiting for profiling to be done...

print(rd_stratified)
#> Risk Difference Analysis Results (v0.2.0+)
#> ========================================== 
#> 
#> Confidence level: 95% 
#> Number of comparisons: 3 
#> 
#>  Exposure Risk Difference           95% CI P-value    Model Boundary CI Method
#>   smoking          11.63%  (7.83%, 15.44%)  <0.001    logit               wald
#>   smoking           9.99% (-5.89%, 25.87%)   0.218 identity               wald
#>   smoking          -3.86%  (-9.05%, 1.32%)   0.706      log               wald

# Summary of boundary cases across strata
boundary_summary <- rd_stratified[rd_stratified$on_boundary, 
                                  c("residence", "boundary_type", "ci_method")]
if (nrow(boundary_summary) > 0) {
  cat("\nBoundary cases by stratum:\n")
  print(boundary_summary)
}

Table Creation with Boundary Indicators

# Create a simple text table with boundary information
cat(create_simple_table(rd_stratified, "Risk by Smoking Status and Residence"))
#> Risk by Smoking Status and Residence
#> ====================================================================================
#> Exposure             Risk Diff       95% CI                    P-value    Model     
#> ====================================================================================
#> smoking              11.63%          (7.83%, 15.44%)           <0.001     logit     
#> smoking              9.99%           (-5.89%, 25.87%)          0.218      identity  
#> smoking              -3.86%          (-9.05%, 1.32%)           0.706      log       
#> ====================================================================================

# Create publication-ready table (requires kableExtra)
library(kableExtra)
create_rd_table(rd_stratified, 
                caption = "Risk of Abnormal Screening Result by Smoking Status",
                include_model_type = TRUE)

🧠 Statistical Methodology GLM Approach with Boundary Detection

The package uses generalized linear models with different link functions:

Identity link (preferred): Directly estimates risk differences
Log link: Estimates relative risks, transforms to risk differences
Logit link: Estimates odds ratios, transforms to risk differences

Key Innovation: When models hit parameter space boundaries (common with identity links), the package: - 🔍 Detects boundary cases automatically - ⚠️ Warns users about potential inference issues

🛡️ Uses robust confidence intervals when appropriate - 📊 Reports methodology transparently

Upper bound: Fitted probabilities near 1 (risk saturation)
Lower bound: Fitted probabilities near 0 (risk floor)
Separation: Complete/quasi-separation in logistic models
Both bounds: Multiple boundary issues detected

# Force specific boundary handling
rd_conservative <- calc_risk_diff(
  cachar_sample,
  "abnormal_screen", 
  "smoking",
  boundary_method = "auto"  # Options: "auto", "profile", "wald"
)
#> Waiting for profiling to be done...

# Check which methods were used
table(rd_conservative$ci_method)
#> 
#> wald 
#>    1

Link Function Selection with Boundary Awareness

# Force a specific link function
rd_logit <- calc_risk_diff(
  cachar_sample, 
  "abnormal_screen", 
  "smoking",
  link = "logit"
)
#> Waiting for profiling to be done...

# Check which model was used and if boundaries detected
cat("Model used:", rd_logit$model_type, "\n")
#> Model used: logit
cat("Boundary detected:", rd_logit$on_boundary, "\n")
#> Boundary detected: FALSE

Confidence Intervals with Robust Methods

# 90% confidence intervals with boundary detection
rd_90 <- calc_risk_diff(
  cachar_sample,
  "abnormal_screen", 
  "smoking",
  alpha = 0.10  # 1 - 0.10 = 90% CI
)
#> Waiting for profiling to be done...

print(rd_90)
#> Risk Difference Analysis Results (v0.2.0+)
#> ========================================== 
#> 
#> Confidence level: 90% 
#> Number of comparisons: 1 
#> 
#>  Exposure Risk Difference          95% CI P-value    Model Boundary CI Method
#>   smoking          10.68% (6.68%, 14.91%)  <0.001 identity               wald

# The package automatically uses appropriate CI methods for boundary cases

Enhanced Result Structure

# Examine the enhanced result structure
data(cachar_sample)
result <- calc_risk_diff(cachar_sample, "abnormal_screen", "smoking")
#> Waiting for profiling to be done...
names(result)
#>  [1] "exposure_var"  "rd"            "ci_lower"      "ci_upper"      "p_value"      
#>  [6] "model_type"    "on_boundary"   "boundary_type" "ci_method"     "n_obs"

# Key columns:
# - on_boundary: Was a boundary case detected?
# - boundary_type: What type of boundary?
# - boundary_warning: Detailed diagnostic message
# - ci_method: Which CI method was used?

The package includes a realistic simulated cancer screening dataset:

data(cachar_sample)
str(cachar_sample)
#> 'data.frame':    2500 obs. of  12 variables:
#>  $ id                : int  1 2 3 4 5 6 7 8 9 10 ...
#>  $ age               : int  53 25 18 28 51 25 56 20 58 18 ...
#>  $ sex               : Factor w/ 2 levels "male","female": 2 1 2 2 1 2 1 1 1 1 ...
#>  $ residence         : Factor w/ 3 levels "rural","urban",..: 3 1 1 1 1 1 1 1 1 1 ...
#>  $ smoking           : Factor w/ 2 levels "No","Yes": 1 1 1 1 1 1 2 1 1 1 ...
#>  $ tobacco_chewing   : Factor w/ 2 levels "No","Yes": 2 1 1 2 2 1 2 1 2 2 ...
#>  $ areca_nut         : Factor w/ 2 levels "No","Yes": 2 2 2 2 1 1 2 1 2 2 ...
#>  $ alcohol           : Factor w/ 2 levels "No","Yes": 1 1 1 1 1 1 1 2 1 2 ...
#>  $ abnormal_screen   : int  0 0 0 0 0 0 1 0 1 0 ...
#>  $ head_neck_abnormal: int  0 0 0 0 0 0 0 0 0 0 ...
#>  $ age_group         : Factor w/ 3 levels "Under 40","40-60",..: 2 1 1 1 2 1 2 1 2 1 ...
#>  $ tobacco_areca_both: Factor w/ 2 levels "No","Yes": 2 1 1 2 1 1 2 1 2 2 ...

# Summary statistics showing realistic associations
table(cachar_sample$smoking, cachar_sample$abnormal_screen)
#>      
#>          0    1
#>   No  1851  317
#>   Yes  248   84

# Risk difference analysis
rd_analysis <- calc_risk_diff(cachar_sample, "abnormal_screen", "smoking")
#> Waiting for profiling to be done...
cat("Smoking increases risk of abnormal screening result by", 
    sprintf("%.1f", rd_analysis$rd * 100), "percentage points\n")
#> Smoking increases risk of abnormal screening result by 10.7 percentage points

When to Use Risk Differences

Risk differences are particularly valuable when:

Policy decisions: You need the absolute impact size
Clinical practice: Communicating real-world effect sizes
Common outcomes: When outcome prevalence > 10%
Causal inference: For intervention planning
Public health: When relative measures can mislead

Comparison with Other Measures Measure Interpretation Best When riskdiff Advantage Risk Difference Absolute change in risk Common outcomes, policy Boundary detection Risk Ratio Relative change in risk Rare outcomes Standard methods only Odds Ratio Change in odds Case-control studies Standard methods only 🔬 Statistical Foundation

This package implements methods based on:

Donoghoe & Marschner (2018) - Robust GLM fitting methods for log-binomial models
Marschner & Gillett (2012) - Boundary detection for log-binomial models
Rothman, Greenland & Lash (2008) - Modern epidemiological methods
Austin (2011) - Propensity score methods for causal inference
Hernán & Robins (2020) - Causal inference methodology

📖 Vignettes: browseVignettes("riskdiff")
🐛 Bug reports: GitHub Issues
💡 Feature requests: GitHub Issues
📧 Questions: Use GitHub Discussions
📋 CRAN page: https://CRAN.R-project.org/package=riskdiff

If you use this package in your research, please cite:

epitools: Basic epidemiological calculations (no boundary detection)
epi: Extended epidemiological functions (no boundary detection)
fmsb: Medical statistics and epidemiology (no boundary detection)
Epi: Statistical analysis in epidemiology (no boundary detection)

riskdiff uniquely provides boundary detection for robust inference!

Please note that the riskdiff project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

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