NourEdinDarwish · NourEdinDarwish · May 23, 2026 · May 22, 2026 · May 22, 2026 · May 22, 2026
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: SummaryTables
 Title: Publication-Ready Summary Tables for Jamovi
-Version: 1.2.1
+Version: 1.3.0
 Authors@R: 
     person("Nour Edin", "Darwish", , "nouredindarwish@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0009-0009-5527-4539"))
@@ -32,6 +32,7 @@ Imports:
     cards (>= 0.7.1),
     cardx (>= 0.3.1),
     cli,
+    datawizard,
     dplyr,
     effectsize,
     flextable,
@@ -50,7 +51,7 @@ Remotes:
     insightsengineering/cards@v0.7.1,
     insightsengineering/cardx@v0.3.1,
     ddsjoberg/gtsummary@952b665
+Config/roxygen2/version: 8.0.0
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.3
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,10 @@
+## SummaryTables 1.3.0
+
+* Added Standardized Coefficients for Linear Regression analyses (both Univariable and Multivariable).
+* Added a rounding option for 16 decimal places across all analyses.
+* Enhanced UI labels.
+* General bug-fixes and improvements.
+
 ## SummaryTables 1.2.1
 
 * Fixed an issue that caused an error when customizing the number of decimal places in the Continuous Table.

diff --git a/R/regression.R b/R/regression.R
@@ -37,7 +37,7 @@ validateFactorPolynomials <- function(data, terms) {
 #' @param terms modelTerms list from self$options$modelTerms
 #' @return A formula object
 buildFormula <- function(y, terms) {
-  as.formula(
+  stats::as.formula(
     paste(
       y,
       "~",
@@ -128,6 +128,54 @@ buildMultiRegTable <- function(model, options, b64Map) {
 }
 
 
+# lmStd ---------------------------------------------------------------------
+
+#' Fit standard linear regression model on standardized variables
+#'
+#' @param formula Model formula
+#' @param data Data frame
+#' @param ... Extra arguments passed to lm
+#' @return An lm model object fitted on standardized complete cases
+lmStd <- function(formula, data, ...) {
+  # Goal: produce the same standardized coefficients (betas) as
+  # parameters::standardize_parameters(method = "refit").
+  #
+  # How standardize_parameters(method = "refit") works internally:
+  #   1. Extracts the model frame via insight::get_data(model, source = "mf"),
+  #      which is the data AFTER listwise deletion — rows with NA in ANY
+  #      variable used by the model (numeric OR factor) are already gone.
+
+  #   2. Standardizes that complete-case data with datawizard::standardize()
+  #      (factors are left untouched by default since force = FALSE).
+  #   3. Refits the model on the standardized complete-case data.
+  #
+  # Previously we used:
+  #   datawizard::standardize(data, select = select_vars, remove_na = "selected")
+  # This had a bug: with force = FALSE (default), datawizard internally
+  # excludes factor columns from the "selected" set, so remove_na = "selected"
+  # only checked numeric columns for NAs. Rows with NA in a factor (but not
+  # in any numeric column) were KEPT, meaning mean/SD was computed from MORE
+  # rows than lm() actually uses (lm() does its own listwise deletion).
+  # This produced different standardized coefficients than
+  # parameters::standardize_parameters(method = "refit").
+  #
+  # We also cannot use remove_na = "all" on the full data frame, because
+  # "all" checks EVERY column — including ones not in the formula. NAs in
+  # unrelated columns would incorrectly drop rows.
+  #
+  # Fix: subset to formula columns first (data[select_vars]), then use
+  # remove_na = "all". This performs listwise deletion on exactly the
+  # variables the model uses, matching what lm() and
+  # parameters::standardize_parameters(method = "refit") do.
+  select_vars <- all.vars(formula)
+  data <- datawizard::standardize(
+    data[select_vars],
+    remove_na = "all"
+  )
+  stats::lm(formula, data = data, ...)
+}
+
+
 # buildUniRegTable ----------------------------------------------------------
 
 #' Build a univariable tbl_uvregression table

diff --git a/R/survival.R b/R/survival.R
@@ -78,7 +78,7 @@ buildSurvfitList <- function(data, elapsedB64, eventB64, strataB64, confInt) {
   survLHS <- sprintf("survival::Surv(%s, %s)", elapsedB64, eventB64)
 
   # Overall
-  overallF <- reformulate("1", response = survLHS)
+  overallF <- stats::reformulate("1", response = survLHS)
   fits <- list(
     rlang::inject(survival::survfit(
       !!overallF,
@@ -89,7 +89,7 @@ buildSurvfitList <- function(data, elapsedB64, eventB64, strataB64, confInt) {
 
   # One fit per stratifying variable (each analyzed independently)
   for (s in strataB64) {
-    stratumF <- reformulate(s, response = survLHS)
+    stratumF <- stats::reformulate(s, response = survLHS)
     fits <- c(
       fits,
       list(

diff --git a/R/tblcontinuous.h.R b/R/tblcontinuous.h.R
@@ -199,7 +199,8 @@ tblContinuousOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cla
                     "2",
                     "3",
                     "4",
-                    "5"),
+                    "5",
+                    "16"),
                 default="auto")
             private$..addPvalue <- jmvcore::OptionBool$new(
                 "addPvalue",

diff --git a/R/tblcross.h.R b/R/tblcross.h.R
@@ -88,7 +88,8 @@ tblCrossOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "2",
                     "3",
                     "4",
-                    "5"),
+                    "5",
+                    "16"),
                 default="auto")
             private$..margin <- jmvcore::OptionList$new(
                 "margin",

diff --git a/R/tbllikert.h.R b/R/tbllikert.h.R
@@ -81,7 +81,8 @@ tblLikertOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "2",
                     "3",
                     "4",
-                    "5"),
+                    "5",
+                    "16"),
                 default="auto")
             private$..levelOrder <- jmvcore::OptionList$new(
                 "levelOrder",

diff --git a/R/tblregcox.h.R b/R/tblregcox.h.R
@@ -114,7 +114,8 @@ tblRegCoxOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "2",
                     "3",
                     "4",
-                    "5"),
+                    "5",
+                    "16"),
                 default="auto")
             private$..confInt <- jmvcore::OptionBool$new(
                 "confInt",

diff --git a/R/tblreglinear.b.R b/R/tblreglinear.b.R
@@ -67,14 +67,58 @@ tblRegLinearClass <- R6::R6Class(
           # Formula and model ---------------------------------------------------
           termsB64 <- lapply(terms, jmvcore::toB64)
           formula <- buildFormula(depB64, termsB64)
-          model <- runSafe(lm(formula, data = data), collector)
+
+          if (self$options$standardize) {
+            # Goal: produce the same standardized coefficients (betas) as
+            # parameters::standardize_parameters(method = "refit").
+            #
+            # How standardize_parameters(method = "refit") works internally:
+            #   1. Extracts the model frame (data AFTER listwise deletion —
+            #      rows with NA in ANY variable, numeric OR factor, are gone).
+            #   2. Standardizes that complete-case data with
+            #      datawizard::standardize() (factors untouched, force = FALSE).
+            #   3. Refits the model on the standardized complete-case data.
+            #
+            # Previously we used:
+            #   standardize(data, select = ..., remove_na = "selected")
+            # Bug: with force = FALSE (default), datawizard excludes factors
+            # from the internal "selected" set, so remove_na = "selected" only
+            # checked numeric columns for NAs. Rows with NA in a factor (but
+            # not in any numeric) were KEPT, meaning mean/SD was computed from
+            # MORE rows than lm() actually uses — producing wrong betas.
+            #
+            # We also cannot use remove_na = "all" on the full data frame,
+            # because "all" checks EVERY column — including ones not in the
+            # formula. NAs in unrelated columns would incorrectly drop rows.
+            #
+            # Fix: subset to formula columns first (data[select_vars]), then
+            # use remove_na = "all". This performs listwise deletion on exactly
+            # the variables the model uses, matching what lm() and
+            # parameters::standardize_parameters(method = "refit") do.
+            select_vars <- all.vars(formula)
+            data <- datawizard::standardize(
+              data[select_vars],
+              remove_na = "all"
+            )
+          }
+
+          model <- runSafe(stats::lm(formula, data = data), collector)
 
           # Regression table ----------------------------------------------------
           table <- runSafe(
             buildMultiRegTable(model, self$options, b64Map),
             collector
           )
 
+          # Change header -------------------------------------------------------
+          coefHeader <- if (self$options$standardize) {
+            "**Standardized Coefficient**"
+          } else {
+            "**Coefficient**"
+          }
+          table <- table |>
+            gtsummary::modify_header(estimate = coefHeader)
+
           # Pipeline ------------------------------------------------------------
           table <- pipeAddGlobalP(
             table,

diff --git a/R/tblreglinear.h.R b/R/tblreglinear.h.R
@@ -12,6 +12,7 @@ tblRegLinearOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Clas
             manualRun = FALSE,
             run = FALSE,
             modelTerms = NULL,
+            standardize = FALSE,
             digitsCoef = "auto",
             confInt = TRUE,
             confLevel = 95,
@@ -83,6 +84,10 @@ tblRegLinearOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Clas
             private$..modelTerms <- jmvcore::OptionTerms$new(
                 "modelTerms",
                 modelTerms)
+            private$..standardize <- jmvcore::OptionBool$new(
+                "standardize",
+                standardize,
+                default=FALSE)
             private$..digitsCoef <- jmvcore::OptionList$new(
                 "digitsCoef",
                 digitsCoef,
@@ -93,7 +98,8 @@ tblRegLinearOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Clas
                     "2",
                     "3",
                     "4",
-                    "5"),
+                    "5",
+                    "16"),
                 default="auto")
             private$..confInt <- jmvcore::OptionBool$new(
                 "confInt",
@@ -275,6 +281,7 @@ tblRegLinearOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Clas
             self$.addOption(private$..manualRun)
             self$.addOption(private$..run)
             self$.addOption(private$..modelTerms)
+            self$.addOption(private$..standardize)
             self$.addOption(private$..digitsCoef)
             self$.addOption(private$..confInt)
             self$.addOption(private$..confLevel)
@@ -315,6 +322,7 @@ tblRegLinearOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Clas
         manualRun = function() private$..manualRun$value,
         run = function() private$..run$value,
         modelTerms = function() private$..modelTerms$value,
+        standardize = function() private$..standardize$value,
         digitsCoef = function() private$..digitsCoef$value,
         confInt = function() private$..confInt$value,
         confLevel = function() private$..confLevel$value,
@@ -354,6 +362,7 @@ tblRegLinearOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Clas
         ..manualRun = NA,
         ..run = NA,
         ..modelTerms = NA,
+        ..standardize = NA,
         ..digitsCoef = NA,
         ..confInt = NA,
         ..confLevel = NA,
@@ -445,6 +454,7 @@ tblRegLinearBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #' @param manualRun .
 #' @param run .
 #' @param modelTerms .
+#' @param standardize .
 #' @param digitsCoef .
 #' @param confInt .
 #' @param confLevel .
@@ -498,6 +508,7 @@ tblRegLinear <- function(
     manualRun = FALSE,
     run = FALSE,
     modelTerms,
+    standardize = FALSE,
     digitsCoef = "auto",
     confInt = TRUE,
     confLevel = 95,
@@ -554,6 +565,7 @@ tblRegLinear <- function(
         manualRun = manualRun,
         run = run,
         modelTerms = modelTerms,
+        standardize = standardize,
         digitsCoef = digitsCoef,
         confInt = confInt,
         confLevel = confLevel,

diff --git a/R/tblreglogistic.h.R b/R/tblreglogistic.h.R
@@ -100,7 +100,8 @@ tblRegLogisticOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Cl
                     "2",
                     "3",
                     "4",
-                    "5"),
+                    "5",
+                    "16"),
                 default="auto")
             private$..confInt <- jmvcore::OptionBool$new(
                 "confInt",

diff --git a/R/tblsummary.h.R b/R/tblsummary.h.R
@@ -278,7 +278,8 @@ tblSummaryOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "2",
                     "3",
                     "4",
-                    "5"),
+                    "5",
+                    "16"),
                 default="auto")
             private$..statCatDefault <- jmvcore::OptionList$new(
                 "statCatDefault",
@@ -317,7 +318,8 @@ tblSummaryOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "2",
                     "3",
                     "4",
-                    "5"),
+                    "5",
+                    "16"),
                 default="auto")
             private$..percent <- jmvcore::OptionList$new(
                 "percent",
@@ -407,7 +409,8 @@ tblSummaryOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "2",
                     "3",
                     "4",
-                    "5"),
+                    "5",
+                    "16"),
                 default="auto")
             private$..diffDichotDefault <- jmvcore::OptionList$new(
                 "diffDichotDefault",
@@ -444,7 +447,8 @@ tblSummaryOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "2",
                     "3",
                     "4",
-                    "5"),
+                    "5",
+                    "16"),
                 default="auto")
             private$..diffDigitsCat <- jmvcore::OptionList$new(
                 "diffDigitsCat",
@@ -456,7 +460,8 @@ tblSummaryOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "2",
                     "3",
                     "4",
-                    "5"),
+                    "5",
+                    "16"),
                 default="auto")
             private$..addPvalue <- jmvcore::OptionBool$new(
                 "addPvalue",
@@ -623,7 +628,8 @@ tblSummaryOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "2",
                     "3",
                     "4",
-                    "5"),
+                    "5",
+                    "16"),
                 default="auto")
             private$..ciCatDefault <- jmvcore::OptionList$new(
                 "ciCatDefault",
@@ -670,7 +676,8 @@ tblSummaryOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "2",
                     "3",
                     "4",
-                    "5"),
+                    "5",
+                    "16"),
                 default="auto")
             private$..path <- jmvcore::OptionString$new(
                 "path",

diff --git a/R/tblsurvfit.h.R b/R/tblsurvfit.h.R
@@ -113,7 +113,8 @@ tblSurvfitOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "2",
                     "3",
                     "4",
-                    "5"),
+                    "5",
+                    "16"),
                 default="auto")
             private$..confLevel <- jmvcore::OptionNumber$new(
                 "confLevel",

diff --git a/R/tbluniregcox.h.R b/R/tbluniregcox.h.R
@@ -117,7 +117,8 @@ tblUniRegCoxOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Clas
                     "2",
                     "3",
                     "4",
-                    "5"),
+                    "5",
+                    "16"),
                 default="auto")
             private$..confInt <- jmvcore::OptionBool$new(
                 "confInt",
-Original file line number
+Diff line change
@@ Expand Up @@
                         "2",
                         "3",
                         "4",
-                        "5"),
+                        "5",
+                        "16"),
                     default="auto")
                 private$..addPvalue <- jmvcore::OptionBool$new(
                     "addPvalue",
@@ Expand Down @@