1v

Author: ehsanx

.Rhistory

@@ -1,71 +1,3 @@
-unweighted_pcts_strata[lvl, s_lvl])
-}
-row_data[[s_lvl]] <- val
-}
-results_list[[length(results_list) + 1]] <- row_data
-}
-} else if (is.numeric(df[[var]])) {
-unweighted_mean_overall <- mean(df[[var]], na.rm = TRUE)
-unweighted_sd_overall <- stats::sd(df[[var]], na.rm = TRUE)
-unweighted_mean_strata <- tapply(df[[var]], df[[strata_var]], mean, na.rm = TRUE)
-unweighted_sd_strata <- tapply(df[[var]], df[[strata_var]], stats::sd, na.rm = TRUE)
-if (mode %in% c("weighted", "mixed")) {
-weighted_mean_overall <- svymean(var_formula, design, na.rm = TRUE)
-weighted_var_overall <- svyvar(var_formula, design, na.rm = TRUE)
-weighted_stats_strata <- svyby(var_formula, strata_formula, design, svymean, na.rm = TRUE)
-weighted_var_strata <- svyby(var_formula, strata_formula, design, svyvar, na.rm = TRUE)
-}
-row_data <- data.frame(Variable = "", Level = "Mean (SD)", stringsAsFactors = FALSE)
-if (mode %in% c("mixed", "weighted")) {
-val <- sprintf("%.2f (%.2f)", weighted_mean_overall, sqrt(weighted_var_overall))
-} else {
-val <- sprintf("%.2f (%.2f)", unweighted_mean_overall, unweighted_sd_overall)
-}
-row_data$Overall <- val
-for (i in seq_along(strata_levels)) {
-s_lvl <- strata_levels[i]
-if (mode %in% c("mixed", "weighted")) {
-mean_val <- weighted_stats_strata[i, var]
-sd_val <- sqrt(weighted_var_strata[i, var])
-val <- sprintf("%.2f (%.2f)", mean_val, sd_val)
-} else {
-val <- sprintf("%.2f (%.2f)", unweighted_mean_strata[s_lvl], unweighted_sd_strata[s_lvl])
-}
-row_data[[s_lvl]] <- val
-}
-results_list[[length(results_list) + 1]] <- row_data
-}
-}
-final_table <- do.call(rbind, results_list)
-return(final_table)
-}
-# --- 3. Running Example: Flegal (2016) NHANES Data ---
-# --- Data Preparation ---
-# Load the dataset from a working URL.
-load(url("https://raw.githubusercontent.com/epiverse-trace/datasets/raw/main/RData/Flegal2016.RData"))
-load("E:/GitHub/EpiMethods/Data/surveydata/Flegal2016.RData")
-# --- 1. Load Required Libraries ---
-# This script requires the 'survey' and 'dplyr' packages.
-# If you don't have them, run: install.packages(c("survey", "dplyr"))
-library(survey)
-library(dplyr)
-# --- 2. The Final, Self-Contained svytable1 Function ---
-# This function is robust and handles survey complexities internally.
-svytable1 <- function(design, strata_var, table_vars,
-mode = "mixed", commas = TRUE) {
-# --- Lonely PSU Handling ---
-old_option <- getOption("survey.lonely.psu")
-options(survey.lonely.psu = "adjust")
-on.exit(options(survey.lonely.psu = old_option))
-# --- Input Validation ---
-df <- design$variables
-all_vars <- c(strata_var, table_vars)
-missing_vars <- all_vars[!all_vars %in% names(df)]
-if (length(missing_vars) > 0) {
-stop(paste("The following variables were not found in the data:",
-paste(missing_vars, collapse = ", ")))
-}
-# --- Helper function for formatting ---
 format_num <- function(n, is_weighted) {
 if (is_weighted) n <- round(n)
 if (commas) return(format(n, big.mark = ","))
@@ -510,3 +442,71 @@ devtools::check()  # Full check with vignettes
 devtools::check()  # Full check with vignettes
 # 8. IF VIGNETTES ARE IMPORTANT:
 devtools::build_vignettes()
+# 1. SETUP (do this first, once per session)
+library(devtools)
+library(roxygen2)
+# 3. UPDATE DOCUMENTATION
+devtools::document()  # This runs roxygen2::roxygenise()
+# 4. REMOVE OLD VERSION (if testing locally)
+remove.packages("svyTable1")
+# 5. TEST YOUR CHANGES
+devtools::test()  # Run unit tests
+# 6. INSTALL LOCALLY TO TEST
+devtools::install()  # Install and load to test interactively
+# 6. INSTALL LOCALLY TO TEST
+devtools::install()  # Install and load to test interactively
+# 7. COMPREHENSIVE PACKAGE CHECK
+devtools::check()  # Full check with vignettes
+# 1. SETUP (do this first, once per session)
+library(devtools)
+library(roxygen2)
+# 2. MAKE YOUR CODE CHANGES first (edit R/ files)
+# ... edit your functions, add features, fix bugs ...
+# 3. UPDATE DOCUMENTATION
+devtools::document()  # This runs roxygen2::roxygenise()
+# 4. REMOVE OLD VERSION (if testing locally)
+remove.packages("svyTable1")
+# 5. TEST YOUR CHANGES
+devtools::test()  # Run unit tests
+# 6. INSTALL LOCALLY TO TEST
+devtools::install()  # Install and load to test interactively
+# 7. COMPREHENSIVE PACKAGE CHECK
+devtools::check()  # Full check with vignettes
+# 1. SETUP (do this first, once per session)
+library(devtools)
+library(roxygen2)
+# 3. UPDATE DOCUMENTATION
+devtools::document()  # This runs roxygen2::roxygenise()
+# 4. REMOVE OLD VERSION (if testing locally)
+remove.packages("svyTable1")
+# 5. TEST YOUR CHANGES
+devtools::test()  # Run unit tests
+# 6. INSTALL LOCALLY TO TEST
+devtools::install()  # Install and load to test interactively
+devtools::check(build_args = "--no-build-vignettes")
+devtools::document()
+devtools::check(build_args = "--no-build-vignettes")
+devtools::document()
+devtools::check(build_args = "--no-build-vignettes")
+# 1. SETUP (do this first, once per session)
+library(devtools)
+library(roxygen2)
+# 2. MAKE YOUR CODE CHANGES first (edit R/ files)
+# ... edit your functions, add features, fix bugs ...
+# 3. UPDATE DOCUMENTATION
+devtools::document()  # This runs roxygen2::roxygenise()
+# 4. REMOVE OLD VERSION (if testing locally)
+remove.packages("svyTable1")
+# 5. TEST YOUR CHANGES
+devtools::test()  # Run unit tests
+# 6. INSTALL LOCALLY TO TEST
+devtools::install()
+devtools::check(build_args = "--no-build-vignettes")
+devtools::document()
+devtools::check(build_args = "--no-build-vignettes")
+# 8. IF VIGNETTES ARE IMPORTANT:
+devtools::build_vignettes()
+# 3. UPDATE DOCUMENTATION
+devtools::document()  # This runs roxygen2::roxygenise()
+# 8. IF VIGNETTES ARE IMPORTANT:
+devtools::build_vignettes()

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: svyTable1
 Title: Create Survey-Weighted Descriptive Statistics and Diagnostic Tables
-Version: 0.10.1
+Version: 0.12.0
 Authors@R: c(person("Ehsan", "Karim",
                  email = "[email protected]",
                  role = c("aut", "cre")),
@@ -12,16 +12,20 @@ Description: A tool to create publication-ready tables from complex
     interaction reports. It also provides a suite of functions to 
     evaluate survey-weighted regression models and survey-weighted 
     survival plots, including coefficient diagnostics, 
-    goodness-of-fit tests, and design-correct AUC calculations.
+    goodness-of-fit tests, design-correct AUC calculations,
+    proportional hazards assumption testing, and visualization 
+    of interaction effects.
 License: MIT + file LICENSE
 Encoding: UTF-8
 RoxygenNote: 7.3.3
 Imports: 
     dplyr,
+    emmeans,
     ggplot2,
     kableExtra,
     knitr,
     magrittr,
+    mice,
     msm,
     patchwork,
     Publish,
@@ -40,8 +44,8 @@ Imports:
     WeightedROC,
     broom
 Suggests: 
-    mice,
     NHANES,
+    mitools,
     testthat (>= 3.0.0)
 VignetteBuilder: knitr
 Config/testthat/edition: 3

NAMESPACE

@@ -5,13 +5,18 @@ export(addint)
 export(addintlist)
 export(inteffects)
 export(jointeffects)
+export(plotint)
 export(reportint)
 export(svyAUC)
+export(svycoxph_CE)
+export(svycoxph_CE_mi)
 export(svydiag)
 export(svygof)
 export(svykmplot)
 export(svypooled)
 export(svytable1)
+import(emmeans)
+import(ggplot2)
 import(stats)
 importFrom(Publish,publish)
 importFrom(WeightedROC,WeightedAUC)
@@ -26,9 +31,11 @@ importFrom(dplyr,group_by)
 importFrom(dplyr,if_else)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
+importFrom(dplyr,n)
 importFrom(dplyr,relocate)
 importFrom(dplyr,rename)
 importFrom(dplyr,select)
+importFrom(dplyr,setdiff)
 importFrom(dplyr,sym)
 importFrom(dplyr,tibble)
 importFrom(dplyr,ungroup)
@@ -57,6 +64,7 @@ importFrom(kableExtra,kable_styling)
 importFrom(kableExtra,pack_rows)
 importFrom(knitr,kable)
 importFrom(magrittr,"%>%")
+importFrom(mice,pool)
 importFrom(msm,deltamethod)
 importFrom(patchwork,plot_layout)
 importFrom(purrr,map_dfr)
@@ -89,6 +97,7 @@ importFrom(survey,degf)
 importFrom(survey,regTermTest)
 importFrom(survey,svyby)
 importFrom(survey,svyciprop)
+importFrom(survey,svycoxph)
 importFrom(survey,svydesign)
 importFrom(survey,svyglm)
 importFrom(survey,svykm)
@@ -98,6 +107,7 @@ importFrom(survey,svytable)
 importFrom(survey,svyvar)
 importFrom(survey,withReplicates)
 importFrom(survival,Surv)
+importFrom(survival,survSplit)
 importFrom(tibble,as_tibble)
 importFrom(tibble,tibble)
 importFrom(tidyr,pivot_longer)