recovered

Author: sbalci

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: ClinicoPath
 Title: Analysis for Clinicopathological Research
-Version: 0.0.2.0005
-Date: 2020-05-20
+Version: 0.0.2.0006
+Date: 2020-05-22
 Authors@R: 
     person(given = "Serdar",
            family = "Balci",
@@ -24,17 +24,25 @@ BugReports:
 Depends:
     R (>= 3.6.0)
 Imports: 
+    jmvcore,
+    R6
+Remotes:
+    ddsjoberg/gtsummary,
+    ndphillips/FFTrees,
+    easystats/report,
+    spgarbet/tangram@0.3.2,
+    cran/rmngb,
+    mixOmicsTeam/mixOmics
+Suggests:
     dplyr,
     finalfit,
     ggalluvial,
     ggplot2,
     ggstatsplot,
     glue,
     janitor,
-    jmvcore,
     knitr,
     purrr,
-    R6,
     scales,
     survival,
     survminer,
@@ -52,15 +60,7 @@ Imports:
     plotROC,
     arsenal,
     easyalluvial,
-    parcats
-Remotes:
-    ddsjoberg/gtsummary,
-    ndphillips/FFTrees,
-    easystats/report,
-    spgarbet/tangram@0.3.2,
-    cran/rmngb,
-    mixOmicsTeam/mixOmics
-Suggests:
+    parcats,
     corrr,
     correlation,
     RVAideMemoire,

NAMESPACE

@@ -9,6 +9,8 @@ export(decision)
 export(decisioncalculator)
 export(gtsummary)
 export(icccoeff)
+export(jjbetweenstats)
+export(jjviolin)
 export(multisurvival)
 export(oddsratio)
 export(pairchi2)
@@ -20,21 +22,7 @@ export(survival)
 export(tableone)
 export(tree)
 export(vartree)
-import(finalfit)
-import(ggalluvial)
-import(ggplot2)
-import(ggstatsplot)
 import(jmvcore)
-import(plotROC)
-import(survival)
-import(survminer)
 importFrom(R6,R6Class)
-importFrom(caret,confusionMatrix)
-importFrom(ggalluvial,StatStratum)
-importFrom(irr,agree)
-importFrom(irr,kappa2)
-importFrom(irr,kappam.fleiss)
 importFrom(jmvcore,toNumeric)
-importFrom(purrr,map)
-importFrom(tableone,CreateTableOne)
 importFrom(utils,data)

R/agreement.b.R

@@ -1,10 +1,7 @@
-#' Interrater Reliability Analysis
+#' @title Interrater Reliability Analysis
 #' @return Table
 #' @importFrom R6 R6Class
 #' @import jmvcore
-#' @importFrom irr kappa2
-#' @importFrom irr kappam.fleiss
-#' @importFrom irr agree
 #'
 
 

R/alluvial.b.R

@@ -153,8 +153,29 @@ alluvialClass <- if (requireNamespace('jmvcore')) R6::R6Class(
 
             mydata <- jmvcore::select(self$data, c(varsName))
 
+            fill <- jmvcore::composeTerm(self$options$fill)
 
 
+
+            # verbose ----
+
+            verbose <- FALSE
+
+            if (isTRUE(verb)) verbose <- TRUE
+
+            # fill_by ----
+
+            jmvcore::composeTerm(self$options$fill)
+
+            self$options$fill
+
+
+            #bin
+
+            bin <- self$options$bin
+
+            if (bin = "default") bin <- 'c("LL", "ML", "M", "MH", "HH")'
+
             # Exclude NA ----
 
             excl <- self$options$excl
@@ -168,7 +189,9 @@ alluvialClass <- if (requireNamespace('jmvcore')) R6::R6Class(
             plot <-
                 easyalluvial::alluvial_wide( data = mydata,
                                              max_variables = 6,
-                                             fill_by = 'first_variable'
+                                             fill_by = fill,
+                                             verbose = verbose,
+                                             bin_labels = bin
                 )
 
 
@@ -183,15 +206,15 @@ alluvialClass <- if (requireNamespace('jmvcore')) R6::R6Class(
 
 
 
-            # Interactive ----
-
-            inter <- self$options$inter
-
-            if (inter) {
-                plot <-
-                    parcats::parcats(plot,
-                                     data_input = mydata)
-            }
+            # # Interactive ----
+            #
+            # inter <- self$options$inter
+            #
+            # if (inter) {
+            #     plot <-
+            #         parcats::parcats(plot,
+            #                          data_input = mydata)
+            # }
 
 
 

R/alluvial.h.R

@@ -8,8 +8,7 @@ alluvialOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
         initialize = function(
             vars = NULL,
             excl = TRUE,
-            marg = FALSE,
-            inter = FALSE, ...) {
+            marg = FALSE, ...) {
 
             super$initialize(
                 package='ClinicoPath',
@@ -28,26 +27,19 @@ alluvialOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
                 "marg",
                 marg,
                 default=FALSE)
-            private$..inter <- jmvcore::OptionBool$new(
-                "inter",
-                inter,
-                default=FALSE)
 
             self$.addOption(private$..vars)
             self$.addOption(private$..excl)
             self$.addOption(private$..marg)
-            self$.addOption(private$..inter)
         }),
     active = list(
         vars = function() private$..vars$value,
         excl = function() private$..excl$value,
-        marg = function() private$..marg$value,
-        inter = function() private$..inter$value),
+        marg = function() private$..marg$value),
     private = list(
         ..vars = NA,
         ..excl = NA,
-        ..marg = NA,
-        ..inter = NA)
+        ..marg = NA)
 )
 
 alluvialResults <- if (requireNamespace('jmvcore')) R6::R6Class(
@@ -63,8 +55,7 @@ alluvialResults <- if (requireNamespace('jmvcore')) R6::R6Class(
                 name="",
                 title="Alluvial Diagrams",
                 refs=list(
-                    "easyalluvial",
-                    "parcats"))
+                    "easyalluvial"))
             self$add(jmvcore::Html$new(
                 options=options,
                 name="todo",
@@ -116,7 +107,6 @@ alluvialBase <- if (requireNamespace('jmvcore')) R6::R6Class(
 #'   the values used for the Alluvial Diagram.
 #' @param excl .
 #' @param marg .
-#' @param inter .
 #' @return A results object containing:
 #' \tabular{llllll}{
 #'   \code{results$todo} \tab \tab \tab \tab \tab a html \cr
@@ -128,8 +118,7 @@ alluvial <- function(
     data,
     vars,
     excl = TRUE,
-    marg = FALSE,
-    inter = FALSE) {
+    marg = FALSE) {
 
     if ( ! requireNamespace('jmvcore'))
         stop('alluvial requires jmvcore to be installed (restart may be required)')
@@ -144,8 +133,7 @@ alluvial <- function(
     options <- alluvialOptions$new(
         vars = vars,
         excl = excl,
-        marg = marg,
-        inter = inter)
+        marg = marg)
 
     analysis <- alluvialClass$new(
         options = options,

R/competingsurvival.b.R

@@ -1,4 +1,4 @@
-#' Competing Survival Analysis
+#' @title Competing Survival Analysis
 #'
 #'
 #'

R/correlation.b.R

@@ -1,4 +1,4 @@
-#' Correlation Analysis
+#' @title Correlation Analysis
 #'
 #'
 #'

R/crosstable.b.R

@@ -1,4 +1,4 @@
-#' Cross Table
+#' @title Cross Table
 #'
 #'
 #' @importFrom R6 R6Class

R/decision.b.R

@@ -1,4 +1,4 @@
-#' Medical Decision Making
+#' @title Medical Decision Making
 #'
 #'
 #'