experimenting

sbalci · Jun 18, 2020 · 7687aed · 7687aed
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -156,9 +156,11 @@ jobs:
           Rscript -e "if (!requireNamespace('tableone')) install.packages('tableone', type = 'source')"
           Rscript -e "if (!requireNamespace('kableExtra')) install.packages('kableExtra', type = 'source')"
           Rscript -e "if (!requireNamespace('caret')) install.packages('caret', type = 'source')"
-          Rscript -e "if (!requireNamespace('vtree')) install.packages('vtree', type = 'source')"
           Rscript -e "if (!requireNamespace('correlation')) install.packages('correlation', type = 'source')"
           Rscript -e "if (!requireNamespace('vtree')) remotes::install_github('nbarrowman/vtree')"
+          Rscript -e "if (!requireNamespace('flextable')) remotes::install_github('davidgohel/flextable')"
+          Rscript -e "if (!requireNamespace('hrbrthemes')) remotes::install_github('hrbrmstr/hrbrthemes')"
+
 
 
       - name: "[Stage] Script"

diff --git a/NEWS.md b/NEWS.md
@@ -1,9 +1,15 @@
-# ClinicoPath 0.0.2.0004
-
-Using `spgarbet/[email protected]` until the bug is fixed.
+# ClinicoPath 0.0.2.0012
 
+- jjstatsplot is the wrapper functions for using ggstatsplot in jamovi.
+- I thought it might be a nice separate module too. I have prepared it to ask opinions.
+- Use attached `.jmo`files to install via side load in jamovi.
+- Requires latest jamovi >=1.2.22 https://www.jamovi.org/download.html
+- tangram error is fixed, but it does not reveal statistical test results.
+- arsenal's footnote is not visible in Html output
 
+# ClinicoPath 0.0.2.0004
 
+Using `spgarbet/[email protected]` until the bug is fixed.
 
 
 # ClinicoPath 0.0.2.0003

diff --git a/R/ClinicoPath-package.R b/R/ClinicoPath-package.R
@@ -7,10 +7,10 @@
 #' tests, and survival analysis with survival tables, survival plots,
 #' and natural language summaries.
 #'
-#' @details The main functions are-
-#' \itemize{
-#'   \item \code{\link[tableone]{tableone}} function to produce Table One.
-#'  }
+# @details The main functions are-
+# \itemize{
+#   \item \code{\link[tableone]{tableone}} function to produce Table One.
+#  }
 #'
 #' For more documentation, see the
 #' \href{https://sbalci.github.io/ClinicoPathJamoviModule/}{Website}.

diff --git a/R/crosstable.b.R b/R/crosstable.b.R
@@ -71,10 +71,10 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
             # tab3 <- CreateTableOne(vars = myVars, strata = "trt" , data = pbc, factorVars = catVars)
 
 
+            # Arsenal Table ----
 
             if (sty == "arsenal") {
 
-                # Arsenal Table ----
 
                 tablearsenal <- arsenal::tableby(formula = formula,
                                                  data = mydata,
@@ -83,13 +83,18 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
                                                  digits.count = 1
                 )
 
-                tablearsenal <- summary(tablearsenal, text = 'html')
+                tablearsenal <- summary(tablearsenal,
+                                        text = 'html',
+                                        pfootnote = TRUE
+                                        )
 
 
-                tablearsenal <- kableExtra::kable(tablearsenal,
-                                             format = "html",
-                                             digits = 1,
-                                             escape = FALSE)
+                tablearsenal <-
+                    kableExtra::kable(tablearsenal,
+                                      format = "html",
+                                      digits = 1,
+                                      escape = FALSE
+                                      )
 
 
                 self$results$tablestyle1$setContent(tablearsenal)
@@ -112,12 +117,14 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
                     finalfit::summary_factorlist(
                         .data = .,
                         dependent = self$options$group,
-                                       explanatory = myvars,
-                                       # column = TRUE,
-                                       total_col = TRUE,
-                                       p = TRUE,
-                                       add_dependent_label = TRUE,
-                                       na_include = FALSE
+                        explanatory = myvars,
+                        # column = TRUE,
+                        total_col = TRUE,
+                        p = TRUE,
+                        add_dependent_label = TRUE,
+                        na_include = FALSE,
+                        na_to_p = FALSE
+
                                        # catTest = catTestfisher
                 ) -> tablefinalfit
 
@@ -135,6 +142,7 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
 
 
                 # gtsummary ----
+
                 # http://www.danieldsjoberg.com/gtsummary/articles/gallery.html
 
 
@@ -174,7 +182,9 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
                             formula,
                             mydata,
                             transform=tangram::hmisc,
-                            id = "tbl3"
+                            id = "tbl3",
+                            digits = 1,
+                            include_p = TRUE
                         ),
                         fragment = TRUE,
                         style = sty,
@@ -184,8 +194,17 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
                         id = "tbl3")
 
                 self$results$tablestyle4$setContent(tabletangram)
+            }
+
+
+
+
+                # tableone ----
+                # tab3 <- CreateTableOne(vars = myVars, strata = "trt" , data = pbc, factorVars = catVars)
+
+
+
 
-}
-}
+            }
         })
 )
diff --git a/R/jjbarstats.h.R b/R/jjbarstats.h.R
@@ -13,13 +13,17 @@ jjbarstatsOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
             direction = "independent",
             excl = TRUE,
             ratio = "",
-            results.subtitle = TRUE,
             sample.size.label = TRUE,
             label = "percentage",
             perc.k = 0,
             bf.message = TRUE,
             sampling.plan = "indepMulti",
-            fixed.margin = "rows", ...) {
+            fixed.margin = "rows",
+            title = "",
+            results.subtitle = TRUE,
+            subtitle = "",
+            caption = "",
+            conf.level = 0.95, ...) {
 
             super$initialize(
                 package='ClinicoPath',
@@ -73,10 +77,6 @@ jjbarstatsOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
                 "ratio",
                 ratio,
                 default="")
-            private$..results.subtitle <- jmvcore::OptionBool$new(
-                "results.subtitle",
-                results.subtitle,
-                default=TRUE)
             private$..sample.size.label <- jmvcore::OptionBool$new(
                 "sample.size.label",
                 sample.size.label,
@@ -113,6 +113,28 @@ jjbarstatsOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
                     "rows",
                     "cols"),
                 default="rows")
+            private$..title <- jmvcore::OptionString$new(
+                "title",
+                title,
+                default="")
+            private$..results.subtitle <- jmvcore::OptionBool$new(
+                "results.subtitle",
+                results.subtitle,
+                default=TRUE)
+            private$..subtitle <- jmvcore::OptionString$new(
+                "subtitle",
+                subtitle,
+                default="")
+            private$..caption <- jmvcore::OptionString$new(
+                "caption",
+                caption,
+                default="")
+            private$..conf.level <- jmvcore::OptionNumber$new(
+                "conf.level",
+                conf.level,
+                default=0.95,
+                min=0,
+                max=1)
 
             self$.addOption(private$..dep)
             self$.addOption(private$..group)
@@ -121,13 +143,17 @@ jjbarstatsOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
             self$.addOption(private$..direction)
             self$.addOption(private$..excl)
             self$.addOption(private$..ratio)
-            self$.addOption(private$..results.subtitle)
             self$.addOption(private$..sample.size.label)
             self$.addOption(private$..label)
             self$.addOption(private$..perc.k)
             self$.addOption(private$..bf.message)
             self$.addOption(private$..sampling.plan)
             self$.addOption(private$..fixed.margin)
+            self$.addOption(private$..title)
+            self$.addOption(private$..results.subtitle)
+            self$.addOption(private$..subtitle)
+            self$.addOption(private$..caption)
+            self$.addOption(private$..conf.level)
         }),
     active = list(
         dep = function() private$..dep$value,
@@ -137,13 +163,17 @@ jjbarstatsOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
         direction = function() private$..direction$value,
         excl = function() private$..excl$value,
         ratio = function() private$..ratio$value,
-        results.subtitle = function() private$..results.subtitle$value,
         sample.size.label = function() private$..sample.size.label$value,
         label = function() private$..label$value,
         perc.k = function() private$..perc.k$value,
         bf.message = function() private$..bf.message$value,
         sampling.plan = function() private$..sampling.plan$value,
-        fixed.margin = function() private$..fixed.margin$value),
+        fixed.margin = function() private$..fixed.margin$value,
+        title = function() private$..title$value,
+        results.subtitle = function() private$..results.subtitle$value,
+        subtitle = function() private$..subtitle$value,
+        caption = function() private$..caption$value,
+        conf.level = function() private$..conf.level$value),
     private = list(
         ..dep = NA,
         ..group = NA,
@@ -152,13 +182,17 @@ jjbarstatsOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
         ..direction = NA,
         ..excl = NA,
         ..ratio = NA,
-        ..results.subtitle = NA,
         ..sample.size.label = NA,
         ..label = NA,
         ..perc.k = NA,
         ..bf.message = NA,
         ..sampling.plan = NA,
-        ..fixed.margin = NA)
+        ..fixed.margin = NA,
+        ..title = NA,
+        ..results.subtitle = NA,
+        ..subtitle = NA,
+        ..caption = NA,
+        ..conf.level = NA)
 )
 
 jjbarstatsResults <- if (requireNamespace('jmvcore')) R6::R6Class(
@@ -237,13 +271,17 @@ jjbarstatsBase <- if (requireNamespace('jmvcore')) R6::R6Class(
 #' @param direction select measurement type (repeated or independent)
 #' @param excl .
 #' @param ratio .
-#' @param results.subtitle .
 #' @param sample.size.label .
 #' @param label label
 #' @param perc.k .
 #' @param bf.message .
 #' @param sampling.plan sampling.plan
 #' @param fixed.margin fixed.margin
+#' @param title .
+#' @param results.subtitle .
+#' @param subtitle .
+#' @param caption .
+#' @param conf.level .
 #' @return A results object containing:
 #' \tabular{llllll}{
 #'   \code{results$todo} \tab \tab \tab \tab \tab a html \cr
@@ -260,13 +298,17 @@ jjbarstats <- function(
     direction = "independent",
     excl = TRUE,
     ratio = "",
-    results.subtitle = TRUE,
     sample.size.label = TRUE,
     label = "percentage",
     perc.k = 0,
     bf.message = TRUE,
     sampling.plan = "indepMulti",
-    fixed.margin = "rows") {
+    fixed.margin = "rows",
+    title = "",
+    results.subtitle = TRUE,
+    subtitle = "",
+    caption = "",
+    conf.level = 0.95) {
 
     if ( ! requireNamespace('jmvcore'))
         stop('jjbarstats requires jmvcore to be installed (restart may be required)')
@@ -295,13 +337,17 @@ jjbarstats <- function(
         direction = direction,
         excl = excl,
         ratio = ratio,
-        results.subtitle = results.subtitle,
         sample.size.label = sample.size.label,
         label = label,
         perc.k = perc.k,
         bf.message = bf.message,
         sampling.plan = sampling.plan,
-        fixed.margin = fixed.margin)
+        fixed.margin = fixed.margin,
+        title = title,
+        results.subtitle = results.subtitle,
+        subtitle = subtitle,
+        caption = caption,
+        conf.level = conf.level)
 
     analysis <- jjbarstatsClass$new(
         options = options,

diff --git a/R/tableone.b.R b/R/tableone.b.R
@@ -67,19 +67,6 @@ tableoneClass <- if (requireNamespace("jmvcore")) R6::R6Class("tableoneClass",
 
             if (sty == "t1") {
 
-
-                # tableone
-
-                # showAllLevels = TRUE
-
-                # nonnormal = TRUE
-
-
-                # tab3 <- CreateTableOne(vars = myVars, strata = "trt" , data = pbc, factorVars = catVars)
-
-
-
-
             mytable <- tableone::CreateTableOne(data = data)
 
             self$results$tablestyle1$setContent(mytable)

diff --git a/data/histopathology.omv b/data/histopathology.omv