Apply automatic stylistic changes

jinseob2kim · Mar 27, 2024 · 7c6fc4f · 7c6fc4f
1 parent 40ca8c4
commit 7c6fc4f
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Showing 2 changed files with 79 additions and 77 deletions.
diff --git a/R/CreateTableOneJS.R b/R/CreateTableOneJS.R
@@ -52,32 +52,32 @@ CreateTableOne2 <- function(data, strata, vars, factorVars, includeNA = F, test
                             showAllLevels = T, printToggle = F, quote = F, smd = F, Labels = F, exact = NULL, nonnormal = NULL,
                             catDigits = 1, contDigits = 2, pDigits = 3, labeldata = NULL, minMax = F, showpm = T, addOverall = F) {
   setkey <- variable <- level <- . <- val_label <- NULL
-  
+
   if (length(strata) != 1) {
     stop("Please select only 1 strata")
   }
-  
+
   vars.ex <- names(which(sapply(vars, function(x) {
     !(class(data[[x]]) %in% c("integer", "numeric", "factor", "character"))
   })))
-  
+
   if (length(vars.ex) > 0) {
     warning("Variables other than numeric or factor types are excluded.")
     vars <- setdiff(vars, vars.ex)
   }
-  
-  
+
+
   res <- tableone::CreateTableOne(
     vars = vars, strata = strata, data = data, factorVars = factorVars, includeNA = includeNA, test = test,
     testApprox = testApprox, argsApprox = argsApprox,
     testExact = testExact, argsExact = argsExact,
     testNormal = testNormal, argsNormal = argsNormal,
     testNonNormal = testNonNormal, argsNonNormal = argsNonNormal, smd = smd, addOverall = addOverall
   )
-  
+
   # factor_vars <- vars[sapply(vars, function(x){class(data[[x]]) %in% c("factor", "character")})]
   factor_vars <- res[["MetaData"]][["varFactors"]]
-  
+
   if (Labels & !is.null(labeldata)) {
     labelled::var_label(data) <- sapply(names(data), function(v) {
       as.character(labeldata[get("variable") == v, "var_label"][1])
@@ -91,41 +91,41 @@ CreateTableOne2 <- function(data, strata, vars, factorVars, includeNA = F, test
         res0$CatTable[[i]][[j]]$level <- labeldata[.(j, lvs), val_label]
       }
     }
-    
+
     ptb1.res0 <- print(res0,
-                       showAllLevels = showAllLevels, printToggle = printToggle, quote = quote, varLabels = Labels, nonnormal = nonnormal,
-                       catDigits = catDigits, contDigits = contDigits, minMax = minMax
+      showAllLevels = showAllLevels, printToggle = printToggle, quote = quote, varLabels = Labels, nonnormal = nonnormal,
+      catDigits = catDigits, contDigits = contDigits, minMax = minMax
     )
     ptb1.rn <- rownames(ptb1.res0)
     ptb1.rn <- gsub("(mean (SD))", "", ptb1.rn, fixed = T)
   }
-  
+
   vars.fisher <- sapply(factor_vars, function(x) {
     is(tryCatch(chisq.test(table(data[[strata]], data[[x]])), error = function(e) e, warning = function(w) w), "warning")
   })
   vars.fisher <- factor_vars[unlist(vars.fisher)]
-  
+
   if (is.null(exact) & length(vars.fisher) > 0) {
     exact <- vars.fisher
   }
-  
+
   ptb1 <- print(res,
-                showAllLevels = showAllLevels, printToggle = printToggle, quote = quote, smd = smd, varLabels = Labels, nonnormal = nonnormal, exact = exact,
-                catDigits = catDigits, contDigits = contDigits, pDigits = pDigits, minMax = minMax
+    showAllLevels = showAllLevels, printToggle = printToggle, quote = quote, smd = smd, varLabels = Labels, nonnormal = nonnormal, exact = exact,
+    catDigits = catDigits, contDigits = contDigits, pDigits = pDigits, minMax = minMax
   )
   if (showpm) {
     ptb1[grepl("\\(mean \\(SD\\)\\)", rownames(ptb1)), ] <- gsub("\\(", "\u00B1 ", ptb1[grepl("\\(mean \\(SD\\)\\)", rownames(ptb1)), ])
     ptb1[grepl("\\(mean \\(SD\\)\\)", rownames(ptb1)), ] <- gsub("\\)", "", ptb1[grepl("\\(mean \\(SD\\)\\)", rownames(ptb1)), ])
   }
-  
+
   rownames(ptb1) <- gsub("(mean (SD))", "", rownames(ptb1), fixed = T)
   if (Labels & !is.null(labeldata)) {
     rownames(ptb1) <- ptb1.rn
     if (showAllLevels == T) ptb1[, 1] <- ptb1.res0[, 1]
   }
-  
+
   # cap.tb1 = paste("Table 1: Stratified by ", strata, sep="")
-  
+
   if (Labels & !is.null(labeldata)) {
     colname.group_var <- unlist(labeldata[.(strata, names(res$CatTable)), val_label])
     if (is.na(colname.group_var[1])) {
@@ -140,7 +140,7 @@ CreateTableOne2 <- function(data, strata, vars, factorVars, includeNA = F, test
     # ptb1[,1] = vals.tb1
     # cap.tb1 = paste("Table 1: Stratified by ", labeldata[variable == strata, "var_label"][1], sep="")
   }
-  
+
   sig <- ifelse(ptb1[, "p"] == "<0.001", "0", ptb1[, "p"])
   sig <- as.numeric(as.vector(sig))
   sig <- ifelse(sig <= 0.05, "**", "")
@@ -192,7 +192,7 @@ CreateTableOne2 <- function(data, strata, vars, factorVars, includeNA = F, test
 #' @importFrom data.table data.table := CJ
 #' @importFrom tableone CreateTableOne
 #' @importFrom labelled var_label var_label<-
-#' @importFrom stats chisq.test fisher.test kruskal.test oneway.test shapiro.test 
+#' @importFrom stats chisq.test fisher.test kruskal.test oneway.test shapiro.test
 #' @importFrom methods is
 #' @export
 
@@ -211,38 +211,40 @@ CreateTableOneJS <- function(vars, strata = NULL, strata2 = NULL, data, factorVa
   #  vals.tb1 = c(NA, unlist(sapply(vars, function(v){labeldata[get("variable") == v, "val_label"]})))
   # }
   data <- data
-  
+
   # 모든 변수에 대해 shapiro test 수행
-  if (normalityTest == T){
-    if (nrow(data) > 5000){
+  if (normalityTest == T) {
+    if (nrow(data) > 5000) {
       print("Warning: Shapiro test is not possible due to the large sample size.")
-    } else{
-      if (!is.null(nonnormal)){
+    } else {
+      if (!is.null(nonnormal)) {
         print("Warning: Nonnormal variables previously entered are ignored.")
       }
       nonnormal <- setdiff(names(data), factorVars)
-      nonnormal <- nonnormal[sapply(nonnormal, function(x){ifelse(class(data[[x]]) %in% c("integer", "numeric"), stats::shapiro.test(data[[x]])$p.value < 0.05, F)})]
+      nonnormal <- nonnormal[sapply(nonnormal, function(x) {
+        ifelse(class(data[[x]]) %in% c("integer", "numeric"), stats::shapiro.test(data[[x]])$p.value < 0.05, F)
+      })]
     }
   }
-  
+
   if (is.null(strata)) {
     if (Labels & !is.null(labeldata)) {
       labelled::var_label(data) <- sapply(names(data), function(v) {
         as.character(labeldata[get("variable") == v, "var_label"][1])
       }, simplify = F)
       data.table::setkey(labeldata, variable, level)
     }
-    
+
     res <- tableone::CreateTableOne(
       vars = vars, data = data, factorVars = factorVars, includeNA = includeNA, test = test,
       testApprox = testApprox, argsApprox = argsApprox,
       testExact = testExact, argsExact = argsExact,
       testNormal = testNormal, argsNormal = argsNormal,
       testNonNormal = testNonNormal, argsNonNormal = argsNonNormal, smd = smd
     )
-    
+
     factor_vars <- res[["MetaData"]][["varFactors"]]
-    
+
     if (Labels & !is.null(labeldata)) {
       for (i in seq_along(res$CatTable)) {
         for (j in factor_vars) {
@@ -252,17 +254,17 @@ CreateTableOneJS <- function(vars, strata = NULL, strata2 = NULL, data, factorVa
       }
       # vals.tb1 <- c(NA, unlist(sapply(vars, function(v){labeldata[get("variable") == v, "val_label"]})))
     }
-    
+
     ptb1 <- print(res,
-                  showAllLevels = showAllLevels, printToggle = printToggle, quote = quote, smd = smd, varLabels = Labels, nonnormal = nonnormal,
-                  catDigits = catDigits, contDigits = contDigits, pDigits = pDigits, minMax = minMax
+      showAllLevels = showAllLevels, printToggle = printToggle, quote = quote, smd = smd, varLabels = Labels, nonnormal = nonnormal,
+      catDigits = catDigits, contDigits = contDigits, pDigits = pDigits, minMax = minMax
     )
-    
+
     if (showpm) {
       ptb1[grepl("\\(mean \\(SD\\)\\)", rownames(ptb1)), ] <- gsub("\\(", "\u00B1 ", ptb1[grepl("\\(mean \\(SD\\)\\)", rownames(ptb1)), ])
       ptb1[grepl("\\(mean \\(SD\\)\\)", rownames(ptb1)), ] <- gsub("\\)", "", ptb1[grepl("\\(mean \\(SD\\)\\)", rownames(ptb1)), ])
     }
-    
+
     rownames(ptb1) <- gsub("(mean (SD))", "", rownames(ptb1), fixed = T)
     cap.tb1 <- "Total"
     # if (Labels & !is.null(labeldata)){
@@ -279,10 +281,10 @@ CreateTableOneJS <- function(vars, strata = NULL, strata2 = NULL, data, factorVa
       showAllLevels = showAllLevels, printToggle = printToggle, quote = quote, Labels = Labels, nonnormal = nonnormal, exact = exact,
       catDigits = catDigits, contDigits = contDigits, pDigits = pDigits, labeldata = labeldata, minMax = minMax, showpm = showpm, addOverall = addOverall
     )
-    
-    
+
+
     cap.tb1 <- paste("Stratified by ", strata, sep = "")
-    
+
     if (Labels & !is.null(labeldata)) {
       cap.tb1 <- paste("Stratified by ", labeldata[get("variable") == strata, "var_label"][1], sep = "")
       # ptb1[,1] = vals.tb1
@@ -292,24 +294,24 @@ CreateTableOneJS <- function(vars, strata = NULL, strata2 = NULL, data, factorVa
     # data.strata <-  lapply(levels(data[[strata]]), function(x){data[data[[strata]] == x, ]})
     data.strata <- split(data, data[[strata]])
     ptb1.list <- lapply(data.strata, CreateTableOne2,
-                        vars = vars, strata = strata2, factorVars = factorVars, includeNA = includeNA, test = test,
-                        testApprox = testApprox, argsApprox = argsApprox,
-                        testExact = testExact, argsExact = argsExact,
-                        testNormal = testNormal, argsNormal = argsNormal,
-                        testNonNormal = testNonNormal, argsNonNormal = argsNonNormal, smd = smd,
-                        showAllLevels = showAllLevels, printToggle = printToggle, quote = quote, Labels = F, nonnormal = nonnormal, exact = exact,
-                        catDigits = catDigits, contDigits = contDigits, pDigits = pDigits, minMax = minMax, showpm = T, addOverall = F
+      vars = vars, strata = strata2, factorVars = factorVars, includeNA = includeNA, test = test,
+      testApprox = testApprox, argsApprox = argsApprox,
+      testExact = testExact, argsExact = argsExact,
+      testNormal = testNormal, argsNormal = argsNormal,
+      testNonNormal = testNonNormal, argsNonNormal = argsNonNormal, smd = smd,
+      showAllLevels = showAllLevels, printToggle = printToggle, quote = quote, Labels = F, nonnormal = nonnormal, exact = exact,
+      catDigits = catDigits, contDigits = contDigits, pDigits = pDigits, minMax = minMax, showpm = T, addOverall = F
     )
-    
+
     if (showAllLevels == T) {
       ptb1.cbind <- Reduce(cbind, c(list(ptb1.list[[1]]), lapply(2:length(ptb1.list), function(x) {
         ptb1.list[[x]][, -1]
       })))
     } else {
       ptb1.cbind <- Reduce(cbind, ptb1.list)
     }
-    
-    
+
+
     # colnum.test = which(colnames(ptb1.cbind) == "test")
     # ptb1.2group = ptb1.cbind[, c(setdiff(1:ncol(ptb1.cbind), colnum.test), colnum.test[1])]
     cap.tb1 <- paste("Stratified by ", strata, "(", paste(levels(data[[strata]]), collapse = ", "), ") & ", strata2, sep = "")
@@ -319,7 +321,7 @@ CreateTableOneJS <- function(vars, strata = NULL, strata2 = NULL, data, factorVa
       }, simplify = F)
       # vals.tb1 <- c(NA, unlist(sapply(vars, function(v){labeldata[get("variable") == v, "val_label"]})))
       data.table::setkey(labeldata, variable, level)
-      
+
       res <- tableone::CreateTableOne(vars = vars, data = data.strata[[1]], factorVars = factorVars, includeNA = includeNA)
       factor_vars <- res[["MetaData"]][["varFactors"]]
       for (i in seq_along(res$CatTable)) {
@@ -328,20 +330,20 @@ CreateTableOneJS <- function(vars, strata = NULL, strata2 = NULL, data, factorVa
           res$CatTable[[i]][[j]]$level <- labeldata[.(j, lvs), val_label]
         }
       }
-      
+
       ptb1.res <- print(res,
-                        showAllLevels = showAllLevels, printToggle = printToggle, quote = quote, varLabels = Labels, nonnormal = nonnormal,
-                        catDigits = catDigits, contDigits = contDigits, minMax = minMax
+        showAllLevels = showAllLevels, printToggle = printToggle, quote = quote, varLabels = Labels, nonnormal = nonnormal,
+        catDigits = catDigits, contDigits = contDigits, minMax = minMax
       )
       ptb1.rn <- rownames(ptb1.res)
       rownames(ptb1.cbind) <- gsub("(mean (SD))", "", ptb1.rn, fixed = T)
       if (showAllLevels == T) {
         ptb1.cbind[, 1] <- ptb1.res[, 1]
       }
-      
+
       cap.tb1 <- paste("Stratified by ", labeldata[get("variable") == strata, "var_label"][1], "(", paste(unlist(labeldata[get("variable") == strata, "val_label"]), collapse = ", "), ") & ", labeldata[get("variable") == strata2, "var_label"][1], sep = "")
     }
-    
+
     return(list(table = ptb1.cbind, caption = cap.tb1))
   } else {
     res <- tableone::CreateTableOne(
@@ -351,20 +353,20 @@ CreateTableOneJS <- function(vars, strata = NULL, strata2 = NULL, data, factorVa
       testNormal = oneway.test, argsNormal = list(var.equal = F),
       testNonNormal = kruskal.test, argsNonNormal = list(NULL), addOverall = addOverall
     )
-    
+
     factor_vars <- res[["MetaData"]][["varFactors"]]
     # factor_vars <- vars[sapply(vars, function(x){class(data[[x]]) %in% c("factor", "character")})]
     var.strata <- paste(data[[strata2]], data[[strata]], sep = "_")
-    
+
     vars.fisher <- sapply(factor_vars, function(x) {
       is(tryCatch(chisq.test(table(var.strata, data[[x]])), error = function(e) e, warning = function(w) w), "warning")
     })
     vars.fisher <- factor_vars[unlist(vars.fisher)]
-    
+
     if (is.null(exact) & length(vars.fisher) > 0) {
       exact <- vars.fisher
     }
-    
+
     if (Labels & !is.null(labeldata)) {
       labelled::var_label(data) <- sapply(names(data), function(v) {
         as.character(labeldata[get("variable") == v, "var_label"][1])
@@ -377,43 +379,43 @@ CreateTableOneJS <- function(vars, strata = NULL, strata2 = NULL, data, factorVa
           res0$CatTable[[i]][[j]]$level <- labeldata[.(j, lvs), val_label]
         }
       }
-      
+
       ptb1.res0 <- print(res0,
-                         showAllLevels = showAllLevels, printToggle = printToggle, quote = quote, varLabels = Labels, nonnormal = nonnormal,
-                         catDigits = catDigits, contDigits = contDigits, minMax = minMax
+        showAllLevels = showAllLevels, printToggle = printToggle, quote = quote, varLabels = Labels, nonnormal = nonnormal,
+        catDigits = catDigits, contDigits = contDigits, minMax = minMax
       )
       ptb1.rn <- rownames(ptb1.res0)
       ptb1.rn <- gsub("(mean (SD))", "", ptb1.rn, fixed = T)
-      
+
       # vals.tb1 <- c(NA, unlist(sapply(vars, function(v){labeldata[get("variable") == v, "val_label"]})))
     }
-    
+
     ptb1 <- print(res,
-                  showAllLevels = showAllLevels,
-                  printToggle = F, quote = F, smd = smd, varLabels = Labels, exact = exact, nonnormal = nonnormal,
-                  catDigits = catDigits, contDigits = contDigits, pDigits = pDigits, minMax = minMax
+      showAllLevels = showAllLevels,
+      printToggle = F, quote = F, smd = smd, varLabels = Labels, exact = exact, nonnormal = nonnormal,
+      catDigits = catDigits, contDigits = contDigits, pDigits = pDigits, minMax = minMax
     )
-    
+
     if (showpm) {
       ptb1[grepl("\\(mean \\(SD\\)\\)", rownames(ptb1)), ] <- gsub("\\(", "\u00B1 ", ptb1[grepl("\\(mean \\(SD\\)\\)", rownames(ptb1)), ])
       ptb1[grepl("\\(mean \\(SD\\)\\)", rownames(ptb1)), ] <- gsub("\\)", "", ptb1[grepl("\\(mean \\(SD\\)\\)", rownames(ptb1)), ])
     }
-    
+
     rownames(ptb1) <- gsub("(mean (SD))", "", rownames(ptb1), fixed = T)
     if (Labels & !is.null(labeldata)) {
       rownames(ptb1) <- ptb1.rn
       if (showAllLevels == T) {
         ptb1[, 1] <- ptb1.res0[, 1]
       }
     }
-    
+
     sig <- ifelse(ptb1[, "p"] == "<0.001", "0", ptb1[, "p"])
     sig <- as.numeric(as.vector(sig))
     sig <- ifelse(sig <= 0.05, "**", "")
     ptb1 <- cbind(ptb1, sig)
     cap.tb1 <- paste("Table 1: Stratified by ", strata, " and ", strata2, sep = "")
-    
-    
+
+
     # Column name
     if (Labels & !is.null(labeldata)) {
       val_combination <- data.table::CJ(labeldata[variable == strata, val_label], labeldata[variable == strata2, val_label], sorted = F)
@@ -432,7 +434,7 @@ CreateTableOneJS <- function(vars, strata = NULL, strata2 = NULL, data, factorVa
           colnames(ptb1)[1:length(colname.group_var)] <- colname.group_var
         }
       }
-      
+
       # caption
       cap.tb1 <- paste("Stratified by ", labeldata[variable == strata, var_label][1], " and ", labeldata[variable == strata2, var_label][1], sep = "")
       # val_label
@@ -441,4 +443,4 @@ CreateTableOneJS <- function(vars, strata = NULL, strata2 = NULL, data, factorVa
     }
     return(list(table = ptb1, caption = cap.tb1))
   }
-}
+}
diff --git a/R/glmshow.R b/R/glmshow.R
@@ -122,16 +122,16 @@ glmshow.display <- function(glm.object, decimal = 2) {
     rn.list[[x]] <<- paste(xs[x], ": ", model$xlevels[[xs[x]]][2], " vs ", model$xlevels[[xs[x]]][1], sep = "")
   })
   lapply(varnum.mfac, function(x) {
-    if (grepl(":", xs[x])){
+    if (grepl(":", xs[x])) {
       a <- unlist(strsplit(xs[x], ":"))[1]
       b <- unlist(strsplit(xs[x], ":"))[2]
-      if (a %in% xs && b %in% xs ){
+      if (a %in% xs && b %in% xs) {
         ref <- paste0(a, model$xlevels[[a]][1], ":", b, model$xlevels[[b]][1])
         rn.list[[x]] <<- c(paste(xs[x], ": ref.=", ref, sep = ""), gsub(xs[x], "   ", rn.list[[x]]))
-      } else{
+      } else {
         rn.list[[x]] <<- c(paste(xs[x], ": ref.=NA", model$xlevels[[xs[x]]][1], sep = ""), gsub(xs[x], "   ", rn.list[[x]]))
       }
-    } else{
+    } else {
       rn.list[[x]] <<- c(paste(xs[x], ": ref.=", model$xlevels[[xs[x]]][1], sep = ""), gsub(xs[x], "   ", rn.list[[x]]))
     }
   })