# ClinicoPath 0.0.2.0015

- Added tangram statistical results - Added options to finalfit crosstables fixes: #24 fixes: jamovi/jamovi#901 fixes: ewenharrison/finalfit#52 - Added experimental biblometrics functions - includes experimental changes
sbalci · Jun 28, 2020 · 6b80edd · 6b80edd
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: ClinicoPath
 Title: Analysis for Clinicopathological Research
-Version: 0.0.2.0013
-Date: 2020-06-12
+Version: 0.0.2.0015
+Date: 2020-06-28
 Authors@R: 
     person(given = "Serdar",
            family = "Balci",
@@ -51,7 +51,6 @@ Suggests:
     rpart,
     rpart.plot,
     plotROC,
-    arsenal,
     easyalluvial,
     corrr,
     correlation,
@@ -70,13 +69,17 @@ Suggests:
     pkgnet,
     hrbrthemes,
     gtsummary,
-    vctrs
+    vctrs,
+    retractcheck,
+    RefManageR,
+    rcrossref
 Remotes:
     ndphillips/FFTrees,
     easystats/report,
     spgarbet/tangram,
     cran/rmngb,
-    mixOmicsTeam/mixOmics
+    mixOmicsTeam/mixOmics,
+    mayoverse/arsenal
 VignetteBuilder:
     knitr
 Encoding: UTF-8

diff --git a/NAMESPACE b/NAMESPACE
@@ -23,6 +23,7 @@ export(multisurvival)
 export(oddsratio)
 export(pairchi2)
 export(reportcat)
+export(retracted)
 export(roc)
 export(statsplot2)
 export(summarydata)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,22 @@
+# ClinicoPath 0.0.2.0015
+
+- Added tangram statistical results
+- Added options to finalfit crosstables
+fixes: https://github.com/sbalci/ClinicoPathJamoviModule/issues/24
+fixes: https://github.com/jamovi/jamovi/issues/901
+fixes: https://github.com/ewenharrison/finalfit/issues/52
+
+- Added experimental biblometrics functions
+- includes experimental changes
+
+
+
+# ClinicoPath 0.0.2.0014
+
+- Added footnote to arsenal crosstable
+
+
+
 # ClinicoPath 0.0.2.0012
 
 - jjstatsplot is the wrapper functions for using ggstatsplot in jamovi.

diff --git a/R/00jmv.R b/R/00jmv.R
@@ -311,4 +311,25 @@
         `year`=2020, 
         `title`="hrbrthemes: Additional Themes, Theme Components and Utilities for 'ggplot2'.", 
         `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=hrbrthemes", 
-        `url`="https://CRAN.R-project.org/package=hrbrthemes"))
+        `url`="https://CRAN.R-project.org/package=hrbrthemes"), 
+    `retractcheck`=list(
+        `type`="software", 
+        `author`=NULL, 
+        `year`=NULL, 
+        `title`="", 
+        `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=", 
+        `url`="https://CRAN.R-project.org/package="), 
+    `RefManageR`=list(
+        `type`="software", 
+        `author`=NULL, 
+        `year`=NULL, 
+        `title`="", 
+        `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=", 
+        `url`="https://CRAN.R-project.org/package="), 
+    `rcrossref`=list(
+        `type`="software", 
+        `author`=NULL, 
+        `year`=NULL, 
+        `title`="", 
+        `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=", 
+        `url`="https://CRAN.R-project.org/package="))
diff --git a/R/crosstable.b.R b/R/crosstable.b.R
@@ -13,13 +13,20 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
         .run = function() {
 
 
+
+            # Select Style ----
+
+            sty <- self$options$sty
+
+
+
+
             if (is.null(self$options$vars) || is.null(self$options$group)) {
 
                 # ToDo Message ----
 
                 todo <- glue::glue("
                 <br>
-                21:02
                 <br>Welcome to ClinicoPath.<br>
                 This tool will help you form a Cross Table.<br>
                 The functions select hypothesis tests automatically. You may see different results with different tables. Please verify your data distribution and appropriateness of the test accordingly. You may find Statkat module useful.<br>
@@ -35,6 +42,23 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
                 html <- self$results$todo
                 html$setContent(todo)
 
+
+                if (sty == "finalfit") {
+
+
+                    todo <- 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)
+
+                }
+
                 # Error Message ----
 
                 if (nrow(self$data) == 0) stop("Data contains no (complete) rows")
@@ -63,10 +87,6 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
             if (excl) {mydata <- jmvcore::naOmit(mydata)}
 
 
-            # Select Style ----
-
-            sty <- self$options$sty
-
 
             # tab3 <- CreateTableOne(vars = myVars, strata = "trt" , data = pbc, factorVars = catVars)
 
@@ -85,25 +105,32 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
 
                 tablearsenal <- summary(tablearsenal,
                                         text = 'html',
-                                        pfootnote = TRUE
+                                        pfootnote = 'html'
                                         )
 
+                # tablearsenal_output <- capture.output(tablearsenal)
 
-                tablearsenal <-
-                    kableExtra::kable(tablearsenal,
-                                      format = "html",
-                                      digits = 1,
-                                      escape = FALSE
-                                      )
+                # self$results$tablearsenal_output$setContent(tablearsenal_output)
 
 
+                # tablearsenal <-
+                #     kableExtra::kable(tablearsenal,
+                #                       format = "html",
+                #                       digits = 1,
+                #                       escape = FALSE
+                #                       )
+
+
+                tablearsenal <- capture.output(tablearsenal)
+
                 self$results$tablestyle1$setContent(tablearsenal)
 
 
             } else if (sty == "finalfit") {
 
                 # FinalFit ----
                 # https://finalfit.org/articles/tables_gallery.html#cross-tables
+                # https://finalfit.org/reference/summary_factorlist.html
 
 
                 myvars <- jmvcore::composeTerm(components = self$options$vars)
@@ -118,17 +145,57 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
                         .data = .,
                         dependent = self$options$group,
                         explanatory = myvars,
-                        # column = TRUE,
                         total_col = TRUE,
                         p = TRUE,
                         add_dependent_label = TRUE,
                         na_include = FALSE,
-                        na_to_p = FALSE
+                        na_to_p = FALSE,
+                        cont = self$options$cont,
+                        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),
+                        na_include_dependent = FALSE,
+                        na_complete_cases = FALSE,
+                        fit_id = FALSE,
+                        add_col_totals = FALSE,
+                        include_col_totals_percent = TRUE,
+                        col_totals_rowname = NULL,
+                        col_totals_prefix = "",
+                        add_row_totals = FALSE,
+                        include_row_missing_col = TRUE
 
-                                       # catTest = catTestfisher
                 ) -> tablefinalfit
 
 
+
+
+
+
+
+
                 tablefinalfit <- kableExtra::kable(tablefinalfit,
                                                   format = "html",
                                                   digits = 1,
@@ -183,6 +250,7 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
                             mydata,
                             transform=tangram::hmisc,
                             id = "tbl3",
+                            test = TRUE,
                             digits = 1,
                             include_p = TRUE
                         ),
@@ -195,16 +263,9 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
 
                 self$results$tablestyle4$setContent(tabletangram)
             }
-
-
-
-
                 # tableone ----
                 # tab3 <- CreateTableOne(vars = myVars, strata = "trt" , data = pbc, factorVars = catVars)
 
-
-
-
             }
         })
 )
diff --git a/R/crosstable.h.R b/R/crosstable.h.R
@@ -9,7 +9,9 @@ crosstableOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
             vars = NULL,
             group = NULL,
             sty = "nejm",
-            excl = TRUE, ...) {
+            excl = TRUE,
+            cont = "mean",
+            pcat = "chisq", ...) {
 
             super$initialize(
                 package='ClinicoPath',
@@ -43,22 +45,42 @@ crosstableOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
                 "excl",
                 excl,
                 default=TRUE)
+            private$..cont <- jmvcore::OptionList$new(
+                "cont",
+                cont,
+                options=list(
+                    "mean",
+                    "median"),
+                default="mean")
+            private$..pcat <- jmvcore::OptionList$new(
+                "pcat",
+                pcat,
+                options=list(
+                    "chisq",
+                    "fisher"),
+                default="chisq")
 
             self$.addOption(private$..vars)
             self$.addOption(private$..group)
             self$.addOption(private$..sty)
             self$.addOption(private$..excl)
+            self$.addOption(private$..cont)
+            self$.addOption(private$..pcat)
         }),
     active = list(
         vars = function() private$..vars$value,
         group = function() private$..group$value,
         sty = function() private$..sty$value,
-        excl = function() private$..excl$value),
+        excl = function() private$..excl$value,
+        cont = function() private$..cont$value,
+        pcat = function() private$..pcat$value),
     private = list(
         ..vars = NA,
         ..group = NA,
         ..sty = NA,
-        ..excl = NA)
+        ..excl = NA,
+        ..cont = NA,
+        ..pcat = NA)
 )
 
 crosstableResults <- if (requireNamespace('jmvcore')) R6::R6Class(
@@ -82,7 +104,9 @@ crosstableResults <- if (requireNamespace('jmvcore')) R6::R6Class(
                 title="To Do",
                 clearWith=list(
                     "vars",
-                    "group")))
+                    "group",
+                    "cont",
+                    "pcat")))
             self$add(jmvcore::Html$new(
                 options=options,
                 name="tablestyle1",
@@ -98,7 +122,9 @@ crosstableResults <- if (requireNamespace('jmvcore')) R6::R6Class(
                 title="`Cross Table - ${group}`",
                 clearWith=list(
                     "vars",
-                    "group"),
+                    "group",
+                    "cont",
+                    "pcat"),
                 visible="(sty:finalfit)",
                 refs="finalfit"))
             self$add(jmvcore::Html$new(
@@ -153,6 +179,8 @@ crosstableBase <- if (requireNamespace('jmvcore')) R6::R6Class(
 #' @param group variable in the column
 #' @param sty .
 #' @param excl .
+#' @param cont .
+#' @param pcat .
 #' @return A results object containing:
 #' \tabular{llllll}{
 #'   \code{results$todo} \tab \tab \tab \tab \tab a html \cr
@@ -168,7 +196,9 @@ crosstable <- function(
     vars,
     group,
     sty = "nejm",
-    excl = TRUE) {
+    excl = TRUE,
+    cont = "mean",
+    pcat = "chisq") {
 
     if ( ! requireNamespace('jmvcore'))
         stop('crosstable requires jmvcore to be installed (restart may be required)')
@@ -187,7 +217,9 @@ crosstable <- function(
         vars = vars,
         group = group,
         sty = sty,
-        excl = excl)
+        excl = excl,
+        cont = cont,
+        pcat = pcat)
 
     analysis <- crosstableClass$new(
         options = options,

diff --git a/R/multisurvival.b.R b/R/multisurvival.b.R
@@ -118,7 +118,7 @@ multisurvivalClass <- if (requireNamespace('jmvcore')) R6::R6Class(
             finalfit::finalfit(.data = mydata,
                                dependent = myformula,
                                explanatory = formula2,
-                               # ,
+
                                # metrics = TRUE
                                ) -> tMultivariate