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Comprehensive Wrapper for Cox Spline Analysis with AHR and CDE Plotting

Source: R/cox_ahr_cde_wrapper.R
cox_ahr_cde_analysis.Rd

This wrapper function combines Cox spline fitting with comprehensive visualization of Average Hazard Ratios (AHRs) and Controlled Direct Effects (CDEs) as described in the MRCT subgroups analysis documentation.

Usage

cox_ahr_cde_analysis(
  df,
  tte_name = "os_time",
  event_name = "os_event",
  treat_name = "treat",
  z_name = "biomarker",
  loghr_po_name = "loghr_po",
  theta1_name = "theta_1",
  theta0_name = "theta_0",
  spline_df = 3,
  alpha = 0.2,
  hr_threshold = 0.7,
  plot_style = c("combined", "separate", "grid"),
  save_plots = FALSE,
  output_dir = "plots",
  verbose = TRUE
)

Arguments

df

Data frame containing survival data with potential outcomes

tte_name

Character string specifying time-to-event variable name. Default: "os_time"

event_name

Character string specifying event indicator variable name. Default: "os_event"

treat_name

Character string specifying treatment variable name. Default: "treat"

z_name

Character string specifying continuous covariate/biomarker name. Default: "biomarker"

loghr_po_name

Character string specifying potential outcome log HR variable. Default: "loghr_po"

theta1_name

Optional: variable name for theta_1 (treated potential outcome). Default: "theta_1"

theta0_name

Optional: variable name for theta_0 (control potential outcome). Default: "theta_0"

spline_df

Integer degrees of freedom for spline fitting. Default: 3

alpha

Numeric significance level for confidence intervals. Default: 0.20

hr_threshold

Numeric hazard ratio threshold for subgroup identification. Default: 0.7

plot_style

Character: "combined", "separate", or "grid" for plot layout. Default: "combined"

save_plots

Logical whether to save plots to file. Default: FALSE

output_dir

Character directory for saving plots. Default: "plots"

verbose

Logical for diagnostic output. Default: TRUE

Value

List containing:

cox_fit

Results from cox_cs_fit function

ahr_results

AHR calculations for different subgroup definitions

cde_results

CDE calculations if theta variables available

optimal_cutpoint

Optimal biomarker cutpoint for subgroup

subgroup_stats

Statistics for recommended and questionable subgroups

plots

List of generated plot objects (if using ggplot2)

Examples

if (FALSE) { # \dontrun{
# Load your ForestSearch output data
results <- cox_ahr_cde_analysis(
  df = df_nonAP,
  z_name = "biomarker",
  hr_threshold = 0.7,
  plot_style = "grid"
)

# Access specific results
print(results$subgroup_stats)
print(results$optimal_cutpoint)
} # }