started pairwise chi square, copied from jmv

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: ClinicoPath
 Title: Analysis for Clinicopathological Research
-Version: 0.0.1.0011
-Date: 2020-05-04
+Version: 0.0.1.0012
+Date: 2020-05-08
 Authors@R: 
     person(given = "Serdar",
            family = "Balci",
@@ -52,14 +52,20 @@ Imports:
     epiR,
     magrittr,
     corrr,
-    correlation
+    correlation,
+    RVAideMemoire
 Remotes:
+    ddsjoberg/gtsummary,
     ndphillips/FFTrees,
     easystats/report,
-    spgarbet/tangram@0.3.2
+    spgarbet/tangram,
+    cran/rmngb
 Suggests:
     circlize,
-    randomForest
+    randomForest,
+    huxtable,
+    flextable,
+    Hmisc
 VignetteBuilder:
     knitr
 Encoding: UTF-8

NAMESPACE

@@ -1,56 +1,47 @@
 # Generated by roxygen2: do not edit by hand
 
-export("%>%")
 export(agreement)
 export(agreementClass)
 export(competingsurvival)
-export(competingsurvivalClass)
 export(correlation)
-export(correlationClass)
 export(crosstable)
 export(crosstableClass)
 export(decision)
-export(decisionClass)
 export(decisioncalculator)
-export(decisioncalculatorClass)
+export(gtsummary)
+export(gtsummaryClass)
 export(icccoeff)
-export(icccoeffClass)
 export(multisurvival)
-export(multisurvivalClass)
 export(oddsratio)
-export(oddsratioClass)
 export(pairchi)
-export(pairchiClass)
 export(reportcat)
-export(reportcatClass)
 export(roc)
-export(rocClass)
 export(statsplot2)
-export(statsplot2Class)
 export(summarydata)
-export(summarydataClass)
 export(survival)
-export(survivalClass)
 export(tableone)
-export(tableoneClass)
 export(tree)
-export(treeClass)
 export(vartree)
-export(vartreeClass)
+import(RVAideMemoire)
 import(caret)
 import(dplyr)
 import(finalfit)
 import(ggalluvial)
 import(ggplot2)
 import(ggstatsplot)
-import(irr)
+import(gtsummary)
 import(jmvcore)
+import(rmngb)
 import(survival)
 import(survminer)
+import(tangram)
 import(vtree)
 importFrom(R6,R6Class)
 importFrom(caret,confusionMatrix)
 importFrom(ggalluvial,StatStratum)
+importFrom(irr,agree)
+importFrom(irr,kappa2)
+importFrom(irr,kappam.fleiss)
 importFrom(jmvcore,toNumeric)
 importFrom(magrittr,"%$%")
 importFrom(magrittr,"%>%")

R/00jmv.R

@@ -255,4 +255,11 @@
         `year`=2019, 
         `title`="rpart.plot: Plot 'rpart' Models: An Enhanced Version of 'plot.rpart'", 
         `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=rpart.plot", 
-        `url`="https://CRAN.R-project.org/package=rpart.plot"))
+        `url`="https://CRAN.R-project.org/package=rpart.plot"), 
+    `gtsummary`=list(
+        `type`="software", 
+        `author`="Daniel D. Sjoberg, Margie Hannum, Karissa Whiting and Emily C. Zabor", 
+        `year`=2020, 
+        `title`="gtsummary: Presentation-Ready Data Summary and Analytic Result Tables", 
+        `publisher`="[R package]. Retrieved from https://CRAN.R-project.org/package=gtsummary", 
+        `url`="https://CRAN.R-project.org/package=gtsummary"))

R/agreement.b.R

@@ -1,126 +1,102 @@
 #' Interrater Reliability Analysis
-#'
-#' @return
+#' @return Table
 #' @export
-#'
-#'
-#'
 #' @importFrom R6 R6Class
 #' @import jmvcore
-#' @import irr
+#' @importFrom irr kappa2
+#' @importFrom irr kappam.fleiss
+#' @importFrom irr agree
 #'
-#'
-
-
-# See \url{http://www.cookbook-r.com/Statistical_analysis/Inter-rater_reliability/#ordinal-data-weighted-kappa}
-
-
-agreementClass <- if (requireNamespace('jmvcore'))
-    R6::R6Class("agreementClass",
-                inherit = agreementBase,
-                private = list(
-                    .run = function() {
-
-                        # Data definition ----
-
-
-                        exct <- self$options$exct
-                        wght <- self$options$wght
-
-                        mydata <- self$data
-
-                        formula <-
-                            jmvcore::constructFormula(terms = self$options$vars)
-
-                        myvars <- jmvcore::decomposeFormula(formula = formula)
-
-                        myvars <- unlist(myvars)
-
-                        ratings <- mydata %>%
-                            dplyr::select(myvars)
-
-
-                        if (is.null(self$options$vars) || length(self$options$vars) < 2) {
-                            # No variables ----
-
-                            # todo <- glue::glue(
-                            #     "This function "
-                            # )
-
-                            # self$results$todo$setContent(todo)
-
-                        } else {
-                            if (nrow(self$data) == 0)
-                                stop('Data contains no (complete) rows')
-
-
-                            # 2 & categorical ----
-
-                            if (length(self$options$vars) == 2) {
-                                # todo <- "Cohen"
-
-                                # self$results$todo$setContent(todo)
-
-
-                                xorder <- unlist(lapply(ratings, is.ordered))
-
-                                if ( wght %in% c("equal", "squared") && !all(xorder == TRUE) )
-stop("Use ordinal variables when using weight argument")
-
-                                if ( exct == TRUE )
-                                    stop("Use exact argument only >=3 variables")
-
-
-                                result2 <- irr::kappa2(ratings = ratings,
-                                                       weight = wght)
-
-                                # self$results$text2$setContent(result2)
-
-
-                                # >=2 & categorical ----
-
-
-                            } else if (length(self$options$vars) >= 2) {
-                                # todo <- "kappam.fleiss"
-
-                                # self$results$todo$setContent(todo)
-
-                                result2 <- irr::kappam.fleiss(ratings = ratings,
-                                                              exact = exct,
-                                                              detail = TRUE)
-
-                                # self$results$text2$setContent(result2)
-
-                            }
-
-
-
-                            result <- table(ratings)
-
-                            self$results$text$setContent(result)
-
-
-                            result1 <- irr::agree(ratings)
-
-                            # self$results$text1$setContent(result1)
-
-
-                            table2 <- self$results$irrtable
-                            table2$setRow(
-                                rowNo = 1,
-                                values = list(
-                                    method = result2[["method"]],
-                                    subjects = result1[["subjects"]],
-                                    raters = result1[["raters"]],
-                                    peragree = result1[["value"]],
-                                    kappa = result2[["value"]],
-                                    z = result2[["statistic"]],
-                                    p = result2[["p.value"]]
-                                )
-                            )
-
-                        }
 
 
-                    }
-                ))
+# See
+# \url{http://www.cookbook-r.com/Statistical_analysis/Inter-rater_reliability/#ordinal-data-weighted-kappa}
+
+
+agreementClass <- if (requireNamespace("jmvcore")) R6::R6Class("agreementClass", 
+    inherit = agreementBase, private = list(.run = function() {
+        # Data definition ----
+
+
+        exct <- self$options$exct
+        wght <- self$options$wght
+
+        mydata <- self$data
+
+        formula <- jmvcore::constructFormula(terms = self$options$vars)
+
+        myvars <- jmvcore::decomposeFormula(formula = formula)
+
+        myvars <- unlist(myvars)
+
+        ratings <- mydata %>% dplyr::select(myvars)
+
+
+        if (is.null(self$options$vars) || length(self$options$vars) < 2) {
+            # No variables ----
+
+            # todo <- glue::glue( 'This function ' )
+
+            # self$results$todo$setContent(todo)
+
+        } else {
+            if (nrow(self$data) == 0) stop("Data contains no (complete) rows")
+
+
+            # 2 & categorical ----
+
+            if (length(self$options$vars) == 2) {
+                # todo <- 'Cohen'
+
+                # self$results$todo$setContent(todo)
+
+
+                xorder <- unlist(lapply(ratings, is.ordered))
+
+                if (wght %in% c("equal", "squared") && !all(xorder == TRUE)) stop("Use ordinal variables when using weight argument")
+
+                if (exct == TRUE) stop("Use exact argument only >=3 variables")
+
+
+                result2 <- irr::kappa2(ratings = ratings, weight = wght)
+
+                # self$results$text2$setContent(result2)
+
+
+                # >=2 & categorical ----
+
+
+            } else if (length(self$options$vars) >= 2) {
+                # todo <- 'kappam.fleiss'
+
+                # self$results$todo$setContent(todo)
+
+                result2 <- irr::kappam.fleiss(ratings = ratings, exact = exct, 
+                  detail = TRUE)
+
+                # self$results$text2$setContent(result2)
+
+            }
+
+
+
+            result <- table(ratings)
+
+            self$results$text$setContent(result)
+
+
+            result1 <- irr::agree(ratings)
+
+            # self$results$text1$setContent(result1)
+
+
+            table2 <- self$results$irrtable
+            table2$setRow(rowNo = 1, values = list(method = result2[["method"]], 
+                subjects = result1[["subjects"]], raters = result1[["raters"]], 
+                peragree = result1[["value"]], kappa = result2[["value"]], 
+                z = result2[["statistic"]], p = result2[["p.value"]]))
+
+        }
+
+
+    }))

R/competingsurvival.b.R

@@ -1,7 +1,7 @@
 #' Competing Survival Analysis
 #'
-#' @return
-#' @export
+
+
 #'
 #' 
 #'

R/correlation.b.R

@@ -1,7 +1,7 @@
 #' Correlation Analysis
 #'
-#' @return
-#' @export
+
+
 #'
 #'
 #' @importFrom R6 R6Class