Merge branch 'main' into main

DESCRIPTION

@@ -24,7 +24,6 @@ LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Imports:
-    dplyr,
     WeightIt,
     marginaleffects,
     stats,
@@ -38,8 +37,9 @@ Imports:
     gtools,
     cobalt,
     stringr,
-    mitml,
-    psych
+    huxtable,
+    officer,
+    flextable
 Suggests: 
     testthat (>= 3.0.0)
 Config/testthat/edition: 3

NAMESPACE

@@ -17,12 +17,4 @@ export(get_reference_values)
 export(make_love_plot)
 export(perform_multiple_comparison_correction)
 export(trimWeights)
-import(ggplot2)
-import(stats)
-import(utils)
-importFrom(WeightIt,weightitMSM)
-importFrom(dplyr,"%>%")
-importFrom(dplyr,mutate)
-importFrom(dplyr,select)
-importFrom(gtools,permutations)
-importFrom(stringr,str_count)
+importFrom(survey,svyglm)

R/compareHelpers.R

@@ -17,9 +17,11 @@
 #'                           reference = "h-h-h" )
 
 get_reference_values <- function(d, reference) {
+
   ref_vals <- sapply(seq_len(length(unlist(strsplit(reference, "-")))), function(x) {
     d[x, unlist(strsplit(reference, "-"))[x]]
   })
+
   ref_vals
 }
 
@@ -41,11 +43,13 @@ get_reference_values <- function(d, reference) {
 #' r <- get_comparison_values(d = d,
 #'                          comp_histories = c("h-h-h", "h-h-l"))
 get_comparison_values <- function(d, comp_histories) {
+
   comp_vals <- sapply(comp_histories, function(comp) {
     sapply(seq_len(length(unlist(strsplit(comp, "-")))), function(x) {
       d[x, unlist(strsplit(comp, "-"))[x]]
     })
   })
+
   t(comp_vals)
 }
 
@@ -60,6 +64,7 @@ get_comparison_values <- function(d, comp_histories) {
 #' @return contrasts
 #' @export
 create_custom_contrasts <- function(d, reference, comp_histories, exposure, preds) {
+
   if (is.na(reference) | is.null(comp_histories)) {
     return(NULL)  # Invalid input, return early
   }
@@ -121,7 +126,8 @@ create_custom_comparisons <- function(preds, ref_vals, comp_vals, exposure) {
 #' @export
 
 add_histories <- function(p, d) {
-  if((is.list(p)) & length(p) == 1){
+
+  if((is.list(p)) && length(p) == 1){
     history <- matrix(data = NA, nrow = nrow(p[[1]]), ncol = 1) # Get histories from the first element
     p <- p[[1]]
   }
@@ -150,6 +156,7 @@ add_histories <- function(p, d) {
     }
     else { #comps
       for (i in seq_len(nrow(p))) {
+
         temp <- as.character(p$term[i])
         pair <- lapply(1:2, function(y) {
           a <- sapply(strsplit(temp, " - "), "[", y)
@@ -209,7 +216,7 @@ perform_multiple_comparison_correction <- function(comps, reference, comp_histor
     cat("\n")
     cat(paste0("Conducting multiple comparison correction using the ", method, " method."), "\n")
     cat("\n")
-    corr_p <-stats::p.adjust(comps$p.value, method = method)
+    corr_p <- stats::p.adjust(comps$p.value, method = method)
     comps <- cbind(comps, p.value_corr = corr_p)
   }
   else {