update crosstable functions

sbalci · Jul 2, 2023 · 3e54797 · 3e54797
1 parent 87af7e8
commit 3e54797
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Showing 16 changed files with 115 additions and 60 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: ClinicoPathDescriptives
 Title: Descriptives Functions for Clinicopathological Research
-Version: 0.0.2.06
-Date: 2023-06-01
+Version: 0.0.2.07
+Date: 2023-07-02
 Authors@R: 
     person(given = "Serdar",
            family = "Balci",
@@ -47,10 +47,10 @@ Imports:
     DiagrammeR,
     DiagrammeRsvg,
     rsvg,
-    shiny
+    shiny,
+    gtsummary
 Remotes:
-    nbarrowman/vtree@ffa53d4ea5050fa9b26918f4bb30595e91a0f489,
-    ddsjoberg/gtsummary@f43332fde6264ff95d092da644284dac739c4e17
+    nbarrowman/vtree@ffa53d4ea5050fa9b26918f4bb30595e91a0f489
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)

diff --git a/R/alluvial.h.R b/R/alluvial.h.R
@@ -8,7 +8,7 @@ alluvialOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
         initialize = function(
             vars = NULL,
             condensationvar = NULL,
-            excl = TRUE,
+            excl = FALSE,
             marg = FALSE,
             fill = "first_variable",
             bin = "default",
@@ -31,7 +31,7 @@ alluvialOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
             private$..excl <- jmvcore::OptionBool$new(
                 "excl",
                 excl,
-                default=TRUE)
+                default=FALSE)
             private$..marg <- jmvcore::OptionBool$new(
                 "marg",
                 marg,
@@ -205,7 +205,7 @@ alluvial <- function(
     data,
     vars,
     condensationvar,
-    excl = TRUE,
+    excl = FALSE,
     marg = FALSE,
     fill = "first_variable",
     bin = "default",

diff --git a/R/crosstable.b.R b/R/crosstable.b.R
@@ -17,8 +17,6 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
             sty <- self$options$sty
 
 
-
-
             if (is.null(self$options$vars) || is.null(self$options$group)) {
 
                 # ToDo Message ----
@@ -39,27 +37,32 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
                 todo <- ""
                 html <- self$results$todo
                 html$setContent(todo)
+            }
 
 
                 if (sty == "finalfit") {
 
-
-                    todo <- glue::glue("
+                    todo2 <- glue::glue("
                     <br>
                     <b>finalfit</b> uses
                     <em>aov (analysis of variance) or t.test for Welch two sample t-test. Note continuous non-parametric test is always Kruskal Wallis (kruskal.test) which in two-group setting is equivalent to Mann-Whitney U /Wilcoxon rank sum test</em>. See full documentation <a href= 'https://finalfit.org/reference/summary_factorlist.html'>here</a>.
                     "
                     )
 
+                }
 
-                    html <- self$results$todo
-                    html$setContent(todo)
 
+            if (sty != "finalfit") {
+
+                    todo2 <- glue::glue("")
                 }
 
+                    html <- self$results$todo2
+                    html$setContent(todo2)
+
                 # Error Message ----
 
-                if (nrow(self$data) == 0) stop("Data contains no (complete) rows")
+            if (nrow(self$data) == 0) stop("Data contains no (complete) rows")
 
                 # Prepare Data ----
 
@@ -149,41 +152,48 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
                         na_include = FALSE,
                         na_to_p = FALSE,
                         cont = self$options$cont,
+                        cont_nonpara = NULL,
+                        cont_cut = 5,
                         cont_range = TRUE,
 
-
                         p_cont_para = "aov",
                         p_cat = self$options$pcat,
 
-
-
-
-
-
-
-
-                        cont_nonpara = NULL,
-                        cont_cut = 5,
                         dependent_label_prefix = "Dependent: ",
                         dependent_label_suffix = "",
                         row_totals_colname = "Total N",
                         row_missing_colname = "Missing N",
 
 
-
-
                         column = TRUE,
+
                         orderbytotal = FALSE,
-                        digits = c(1, 1, 3, 1),
+                        digits = c(1, 1, 3, 1, 0),
+
+
                         na_include_dependent = FALSE,
                         na_complete_cases = FALSE,
                         fit_id = FALSE,
-                        add_col_totals = FALSE,
+
+                        na_to_prop = TRUE,
+
+
+                        add_col_totals = TRUE,
                         include_col_totals_percent = TRUE,
                         col_totals_rowname = NULL,
                         col_totals_prefix = "",
                         add_row_totals = FALSE,
-                        include_row_missing_col = TRUE
+                        include_row_totals_percent = TRUE,
+                        include_row_missing_col = TRUE,
+
+                        catTest = NULL,
+                        weights = NULL
+
+
+
+
+
+
 
                 ) -> tablefinalfit
 
@@ -213,10 +223,22 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
 
                 tablegtsummary <-
                     gtsummary::tbl_summary(data = mydata,
-                                           by = self$options$group) %>%
-                    gtsummary::modify_header(stat_by =
-                                                 gt::md("**{level}** N =  {n} ({style_percent(p)}%)")) %>%
+                                           by = self$options$group,
+                                           statistic = list(
+                                               gtsummary::all_continuous() ~ "{mean} ({sd})",
+                                               gtsummary::all_categorical() ~ "{n} / {N} ({p}%)"
+                                           ),
+                                           digits = gtsummary::all_continuous() ~ 2,
+                                           missing_text = "(Missing)"
+
+                                           ) %>%
+                    gtsummary::modify_header(
+                        update = gtsummary::all_stat_cols() ~ structure("**{level}** N =  {n} ({style_percent(p)}%)", class = "from_markdown")
+                        # stat_by =
+                        #                          gt::md("**{level}** N =  {n} ({style_percent(p)}%)")
+                                                  ) %>%
                     gtsummary::add_n(x = .) %>%
+                    gtsummary::add_overall() %>%
                     gtsummary::bold_labels(x = .) %>%
                     gtsummary::add_p(x = .,
                                      pvalue_fun =
@@ -225,6 +247,11 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
                                              digits = 2)
                                      ) %>%
                     gtsummary::add_q()
+                # %>%
+                #     gtsummary::bold_labels() %>%
+                #     gtsummary::bold_levels() %>%
+                #     gtsummary::bold_p()
+
 
                 tablegtsummary <-
                     gtsummary::as_kable_extra(tablegtsummary)
@@ -284,5 +311,5 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
                 # tab3 <- CreateTableOne(vars = myVars, strata = "trt" , data = pbc, factorVars = catVars)
 
             }
-        })
+        )
 )
diff --git a/R/crosstable.h.R b/R/crosstable.h.R
@@ -9,7 +9,7 @@ crosstableOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
             vars = NULL,
             group = NULL,
             sty = "nejm",
-            excl = TRUE,
+            excl = FALSE,
             cont = "mean",
             pcat = "chisq", ...) {
 
@@ -44,7 +44,7 @@ crosstableOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
             private$..excl <- jmvcore::OptionBool$new(
                 "excl",
                 excl,
-                default=TRUE)
+                default=FALSE)
             private$..cont <- jmvcore::OptionList$new(
                 "cont",
                 cont,
@@ -88,6 +88,7 @@ crosstableResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
     inherit = jmvcore::Group,
     active = list(
         todo = function() private$.items[["todo"]],
+        todo2 = function() private$.items[["todo2"]],
         tablestyle1 = function() private$.items[["tablestyle1"]],
         tablestyle2 = function() private$.items[["tablestyle2"]],
         tablestyle3 = function() private$.items[["tablestyle3"]],
@@ -109,14 +110,26 @@ crosstableResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "vars",
                     "group",
                     "cont",
-                    "pcat")))
+                    "pcat",
+                    "sty")))
+            self$add(jmvcore::Html$new(
+                options=options,
+                name="todo2",
+                title="To Do",
+                clearWith=list(
+                    "vars",
+                    "group",
+                    "cont",
+                    "pcat",
+                    "sty")))
             self$add(jmvcore::Html$new(
                 options=options,
                 name="tablestyle1",
                 title="`Cross Table - ${group}`",
                 clearWith=list(
                     "vars",
-                    "group"),
+                    "group",
+                    "sty"),
                 visible="(sty:arsenal)",
                 refs="arsenal"))
             self$add(jmvcore::Html$new(
@@ -127,7 +140,8 @@ crosstableResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "vars",
                     "group",
                     "cont",
-                    "pcat"),
+                    "pcat",
+                    "sty"),
                 visible="(sty:finalfit)",
                 refs="finalfit"))
             self$add(jmvcore::Html$new(
@@ -136,7 +150,8 @@ crosstableResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                 title="`Cross Table - ${group}`",
                 clearWith=list(
                     "vars",
-                    "group"),
+                    "group",
+                    "sty"),
                 visible="(sty:gtsummary)",
                 refs="gtsummary"))
             self$add(jmvcore::Html$new(
@@ -145,7 +160,8 @@ crosstableResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                 title="`Cross Table - ${group}`",
                 clearWith=list(
                     "vars",
-                    "group"),
+                    "group",
+                    "sty"),
                 visible="(sty:nejm || sty:lancet || sty:hmisc)",
                 refs="tangram"))}))
 
@@ -188,6 +204,7 @@ crosstableBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #' @return A results object containing:
 #' \tabular{llllll}{
 #'   \code{results$todo} \tab \tab \tab \tab \tab a html \cr
+#'   \code{results$todo2} \tab \tab \tab \tab \tab a html \cr
 #'   \code{results$tablestyle1} \tab \tab \tab \tab \tab a html \cr
 #'   \code{results$tablestyle2} \tab \tab \tab \tab \tab a html \cr
 #'   \code{results$tablestyle3} \tab \tab \tab \tab \tab a html \cr
@@ -200,7 +217,7 @@ crosstable <- function(
     vars,
     group,
     sty = "nejm",
-    excl = TRUE,
+    excl = FALSE,
     cont = "mean",
     pcat = "chisq") {
 

diff --git a/R/tableone.h.R b/R/tableone.h.R
@@ -8,7 +8,7 @@ tableoneOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
         initialize = function(
             vars = NULL,
             sty = "t1",
-            excl = TRUE, ...) {
+            excl = FALSE, ...) {
 
             super$initialize(
                 package="ClinicoPathDescriptives",
@@ -31,7 +31,7 @@ tableoneOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
             private$..excl <- jmvcore::OptionBool$new(
                 "excl",
                 excl,
-                default=TRUE)
+                default=FALSE)
 
             self$.addOption(private$..vars)
             self$.addOption(private$..sty)
@@ -160,7 +160,7 @@ tableone <- function(
     data,
     vars,
     sty = "t1",
-    excl = TRUE) {
+    excl = FALSE) {
 
     if ( ! requireNamespace("jmvcore", quietly=TRUE))
         stop("tableone requires jmvcore to be installed (restart may be required)")

diff --git a/R/vartree.h.R b/R/vartree.h.R
@@ -16,7 +16,7 @@ vartreeOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
             follow = NULL,
             followLevel1 = NULL,
             followLevel2 = NULL,
-            excl = TRUE,
+            excl = FALSE,
             vp = TRUE,
             horizontal = FALSE,
             sline = TRUE,
@@ -105,7 +105,7 @@ vartreeOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
             private$..excl <- jmvcore::OptionBool$new(
                 "excl",
                 excl,
-                default=TRUE)
+                default=FALSE)
             private$..vp <- jmvcore::OptionBool$new(
                 "vp",
                 vp,
@@ -360,7 +360,7 @@ vartree <- function(
     follow,
     followLevel1,
     followLevel2,
-    excl = TRUE,
+    excl = FALSE,
     vp = TRUE,
     horizontal = FALSE,
     sline = TRUE,

diff --git a/jamovi/0000.yaml b/jamovi/0000.yaml
@@ -1,12 +1,12 @@
 ---
 title: Descriptives Functions for Clinicopathological Research
 name: ClinicoPathDescriptives
-version: 0.0.2.06
+version: 0.0.2.07
 jms: '1.0'
 authors:
   - Serdar Balci
 maintainer: Serdar Balci <[email protected]>
-date: '2023-06-01'
+date: '2023-07-02'
 type: R
 description: >-
   Descriptives Functions for Clinicopathological Research Descriptive functions

diff --git a/jamovi/alluvial.a.yaml b/jamovi/alluvial.a.yaml
@@ -30,7 +30,7 @@ options:
     - name: excl
       title: Exclude missing (NA)
       type: Bool
-      default: true
+      default: false
 
     - name: marg
       title: Marginal plots

diff --git a/jamovi/crosstable.a.yaml b/jamovi/crosstable.a.yaml
@@ -59,7 +59,7 @@ options:
     - name: excl
       title: Exclude Missing (NA)
       type: Bool
-      default: true
+      default: false
 
 
     - name: cont