diff --git a/DESCRIPTION b/DESCRIPTION
index ef4713ac..ca536d8d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -25,7 +25,8 @@ Depends:
R (>= 3.6.0)
Imports:
jmvcore,
- R6
+ R6,
+ magrittr
Remotes:
ddsjoberg/gtsummary,
ndphillips/FFTrees,
@@ -56,7 +57,6 @@ Suggests:
explore,
rpart,
rpart.plot,
- magrittr,
plotROC,
arsenal,
easyalluvial,
diff --git a/NAMESPACE b/NAMESPACE
index de435809..6ac5189d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -25,4 +25,5 @@ export(vartree)
import(jmvcore)
importFrom(R6,R6Class)
importFrom(jmvcore,toNumeric)
+importFrom(magrittr,"%>%")
importFrom(utils,data)
diff --git a/R/alluvial.b.R b/R/alluvial.b.R
index 184ca8a0..18d088c5 100644
--- a/R/alluvial.b.R
+++ b/R/alluvial.b.R
@@ -1,3 +1,10 @@
+#' @title Alluvial Plot
+#' @return Alluvial Plot
+#' @importFrom R6 R6Class
+#' @import jmvcore
+#' @importFrom magrittr %>%
+#'
+
# This file is a generated template, your changes will not be overwritten
@@ -36,15 +43,6 @@ alluvialClass <- if (requireNamespace('jmvcore')) R6::R6Class(
-
-
-
-
-
-
-
-
-
# #Errors ----
#
# if (is.null(self$options$vars) )
@@ -106,29 +104,6 @@ alluvialClass <- if (requireNamespace('jmvcore')) R6::R6Class(
# html$setContent(plothtml)
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
}
}
@@ -161,20 +136,20 @@ alluvialClass <- if (requireNamespace('jmvcore')) R6::R6Class(
verbose <- FALSE
+ verb <- self$options$verb
+
if (isTRUE(verb)) verbose <- TRUE
# fill_by ----
- jmvcore::composeTerm(self$options$fill)
-
- self$options$fill
+ fill <- jmvcore::composeTerm(self$options$fill)
#bin
bin <- self$options$bin
- if (bin = "default") bin <- 'c("LL", "ML", "M", "MH", "HH")'
+ if (bin == "default") bin <- c("LL", "ML", "M", "MH", "HH")
# Exclude NA ----
@@ -223,5 +198,48 @@ alluvialClass <- if (requireNamespace('jmvcore')) R6::R6Class(
print(plot)
TRUE
- })
+ }
+
+
+ ,
+
+ .plot2 = function(image, ...) {
+ # the plot function ----
+
+ #Errors ----
+
+ if (is.null(self$options$condensationvar) )
+ return()
+
+ if (nrow(self$data) == 0)
+ stop('Data contains no (complete) rows')
+
+ # Prepare Data ----
+
+ condvarName <- self$options$condensationvar
+
+ condvarName <- jmvcore::composeTerm(components = condvarName)
+
+
+
+ plot2 <- self$data %>%
+ easyalluvial::plot_condensation(df = .,
+ first = .data[[condvarName]])
+
+
+ # Print Plot ----
+
+ print(plot2)
+ TRUE
+
+
+
+
+ }
+
+
+
+
+
+ )
)
diff --git a/R/alluvial.h.R b/R/alluvial.h.R
index c0a14931..7bac5a84 100644
--- a/R/alluvial.h.R
+++ b/R/alluvial.h.R
@@ -7,8 +7,12 @@ alluvialOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
public = list(
initialize = function(
vars = NULL,
+ condensationvar = NULL,
excl = TRUE,
- marg = FALSE, ...) {
+ marg = FALSE,
+ verb = FALSE,
+ fill = "first_variable",
+ bin = "default", ...) {
super$initialize(
package='ClinicoPath',
@@ -19,6 +23,9 @@ alluvialOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
private$..vars <- jmvcore::OptionVariables$new(
"vars",
vars)
+ private$..condensationvar <- jmvcore::OptionVariable$new(
+ "condensationvar",
+ condensationvar)
private$..excl <- jmvcore::OptionBool$new(
"excl",
excl,
@@ -27,26 +34,62 @@ alluvialOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
"marg",
marg,
default=FALSE)
+ private$..verb <- jmvcore::OptionBool$new(
+ "verb",
+ verb,
+ default=FALSE)
+ private$..fill <- jmvcore::OptionList$new(
+ "fill",
+ fill,
+ options=list(
+ "first_variable",
+ "last_variable",
+ "all_flows",
+ "values"),
+ default="first_variable")
+ private$..bin <- jmvcore::OptionList$new(
+ "bin",
+ bin,
+ options=list(
+ "default",
+ "mean",
+ "median",
+ "min_max",
+ "cuts"),
+ default="default")
self$.addOption(private$..vars)
+ self$.addOption(private$..condensationvar)
self$.addOption(private$..excl)
self$.addOption(private$..marg)
+ self$.addOption(private$..verb)
+ self$.addOption(private$..fill)
+ self$.addOption(private$..bin)
}),
active = list(
vars = function() private$..vars$value,
+ condensationvar = function() private$..condensationvar$value,
excl = function() private$..excl$value,
- marg = function() private$..marg$value),
+ marg = function() private$..marg$value,
+ verb = function() private$..verb$value,
+ fill = function() private$..fill$value,
+ bin = function() private$..bin$value),
private = list(
..vars = NA,
+ ..condensationvar = NA,
..excl = NA,
- ..marg = NA)
+ ..marg = NA,
+ ..verb = NA,
+ ..fill = NA,
+ ..bin = NA)
)
alluvialResults <- if (requireNamespace('jmvcore')) R6::R6Class(
inherit = jmvcore::Group,
active = list(
todo = function() private$.items[["todo"]],
- plot = function() private$.items[["plot"]]),
+ plot = function() private$.items[["plot"]],
+ plot2 = function() private$.items[["plot2"]]),
private = list(),
public=list(
initialize=function(options) {
@@ -64,7 +107,9 @@ alluvialResults <- if (requireNamespace('jmvcore')) R6::R6Class(
"vars",
"excl",
"marg",
- "inter")))
+ "verb",
+ "fill",
+ "bin")))
self$add(jmvcore::Image$new(
options=options,
title="Alluvial Diagrams",
@@ -77,7 +122,20 @@ alluvialResults <- if (requireNamespace('jmvcore')) R6::R6Class(
"vars",
"excl",
"marg",
- "inter")))}))
+ "verb",
+ "fill",
+ "bin")))
+ self$add(jmvcore::Image$new(
+ options=options,
+ title="`Condensation Plot ${condensationvar}`",
+ name="plot2",
+ width=600,
+ height=450,
+ renderFun=".plot2",
+ requiresData=TRUE,
+ clearWith=list(
+ "condensationvar"),
+ visible="(condensationvar)"))}))
alluvialBase <- if (requireNamespace('jmvcore')) R6::R6Class(
"alluvialBase",
@@ -105,35 +163,51 @@ alluvialBase <- if (requireNamespace('jmvcore')) R6::R6Class(
#' @param data The data as a data frame.
#' @param vars a string naming the variables from \code{data} that contains
#' the values used for the Alluvial Diagram.
+#' @param condensationvar The primary variable to be used for condensation.
#' @param excl .
#' @param marg .
+#' @param verb .
+#' @param fill A list for the argument fill for selecting the variable to be
+#' represented by color. Default is 'first_variable'.
+#' @param bin labels for the bins from low to high
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$todo} \tab \tab \tab \tab \tab a html \cr
#' \code{results$plot} \tab \tab \tab \tab \tab an image \cr
+#' \code{results$plot2} \tab \tab \tab \tab \tab an image \cr
#' }
#'
#' @export
alluvial <- function(
data,
vars,
+ condensationvar,
excl = TRUE,
- marg = FALSE) {
+ marg = FALSE,
+ verb = FALSE,
+ fill = "first_variable",
+ bin = "default") {
if ( ! requireNamespace('jmvcore'))
stop('alluvial requires jmvcore to be installed (restart may be required)')
if ( ! missing(vars)) vars <- jmvcore::resolveQuo(jmvcore::enquo(vars))
+ if ( ! missing(condensationvar)) condensationvar <- jmvcore::resolveQuo(jmvcore::enquo(condensationvar))
if (missing(data))
data <- jmvcore::marshalData(
parent.frame(),
- `if`( ! missing(vars), vars, NULL))
+ `if`( ! missing(vars), vars, NULL),
+ `if`( ! missing(condensationvar), condensationvar, NULL))
options <- alluvialOptions$new(
vars = vars,
+ condensationvar = condensationvar,
excl = excl,
- marg = marg)
+ marg = marg,
+ verb = verb,
+ fill = fill,
+ bin = bin)
analysis <- alluvialClass$new(
options = options,
diff --git a/R/crosstable.b.R b/R/crosstable.b.R
index 773944ca..14040a5b 100644
--- a/R/crosstable.b.R
+++ b/R/crosstable.b.R
@@ -104,7 +104,9 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
# myvars <- unlist(myvars)
mydata %>%
- summary_factorlist(dependent = self$options$group,
+ finalfit::summary_factorlist(
+ .data = .,
+ dependent = self$options$group,
explanatory = myvars,
# column = TRUE,
total_col = TRUE,
diff --git a/R/multisurvival.b.R b/R/multisurvival.b.R
index 5702bcc0..2046893f 100644
--- a/R/multisurvival.b.R
+++ b/R/multisurvival.b.R
@@ -144,7 +144,7 @@ multisurvivalClass <- if (requireNamespace('jmvcore')) R6::R6Class(
formulaR <- jmvcore::toNumeric(formulaR)
- myformula <- paste("Surv(", formulaL, ",", formulaR, ")")
+ myformula <- paste("survival::Surv(", formulaL, ",", formulaR, ")")
# https://finalfit.org/reference/hr_plot.html
@@ -204,7 +204,7 @@ multisurvivalClass <- if (requireNamespace('jmvcore')) R6::R6Class(
formula2 <- jmvcore::constructFormula(terms = self$options$explanatory)
- formula3 <- paste("Surv(", formulaL, ",", formulaR, ") ~ ", formula2)
+ formula3 <- paste("survival::Surv(", formulaL, ",", formulaR, ") ~ ", formula2)
formula3 <- as.formula(formula3)
diff --git a/R/reportcat.b.R b/R/reportcat.b.R
index 30b7cc16..2c28bfd5 100644
--- a/R/reportcat.b.R
+++ b/R/reportcat.b.R
@@ -1,10 +1,9 @@
#' @title Summary of Categorical Variables
-#'
-#'
-#'
+#' @return Text
#'
#' @importFrom R6 R6Class
#' @import jmvcore
+#' @importFrom magrittr %>%
#'
reportcatClass <- if (requireNamespace('jmvcore')) R6::R6Class(
diff --git a/README.Rmd b/README.Rmd
index 85a85b85..f01d6cbf 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -131,6 +131,18 @@ https://osf.io/9szud/
🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩
+
+
+#### Alluvial Diagrams
+
+🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩
+
+
+
+
+
+
+
---
### Comparisons
diff --git a/README.md b/README.md
index 1bf1feed..5855601f 100644
--- a/README.md
+++ b/README.md
@@ -94,6 +94,12 @@ DOI 10.17605/OSF.IO/9SZUD
🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩
+#### Alluvial Diagrams
+
+🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩
+
+
+
-----
### Comparisons
@@ -310,7 +316,7 @@ Badge](https://depshield.sonatype.org/badges/sbalci/ClinicoPathJamoviModule/deps
version](https://img.shields.io/badge/GitHub-0.0.1.1000-orange.svg?style=flat-square)](https://github.com/sbalci/clinicopathjamovimodule/)
[](https://github.com/sbalci/clinicopathjamovimodule/commits/master)
-[](https://github.com/sbalci/clinicopathjamovimodule/commits/master)
+[](https://github.com/sbalci/clinicopathjamovimodule/commits/master)
](https://github.com/sbalci/clinicopathjamovimodule/)
[](https://github.com/sbalci/clinicopathjamovimodule/commits/master)
-[](https://github.com/sbalci/clinicopathjamovimodule/commits/master)
+[](https://github.com/sbalci/clinicopathjamovimodule/commits/master)
![GitHub last
diff --git a/codemeta.json b/codemeta.json
index 97486e9d..23e69340 100644
--- a/codemeta.json
+++ b/codemeta.json
@@ -308,18 +308,6 @@
},
"sameAs": "https://CRAN.R-project.org/package=rpart.plot"
},
- {
- "@type": "SoftwareApplication",
- "identifier": "magrittr",
- "name": "magrittr",
- "provider": {
- "@id": "https://cran.r-project.org",
- "@type": "Organization",
- "name": "Comprehensive R Archive Network (CRAN)",
- "url": "https://cran.r-project.org"
- },
- "sameAs": "https://CRAN.R-project.org/package=magrittr"
- },
{
"@type": "SoftwareApplication",
"identifier": "plotROC",
@@ -567,6 +555,18 @@
"url": "https://cran.r-project.org"
},
"sameAs": "https://CRAN.R-project.org/package=R6"
+ },
+ {
+ "@type": "SoftwareApplication",
+ "identifier": "magrittr",
+ "name": "magrittr",
+ "provider": {
+ "@id": "https://cran.r-project.org",
+ "@type": "Organization",
+ "name": "Comprehensive R Archive Network (CRAN)",
+ "url": "https://cran.r-project.org"
+ },
+ "sameAs": "https://CRAN.R-project.org/package=magrittr"
}
],
"releaseNotes": "https://github.com/sbalci/ClinicoPathJamoviModule/blob/master/NEWS.md",
@@ -597,6 +597,6 @@
"survival-analysis",
"natural-language-summaries"
],
- "fileSize": "185.424KB",
+ "fileSize": "186.46KB",
"readme": "https://github.com/sbalci/ClinicoPathJamoviModule/blob/master/README.md"
}
diff --git a/data/histopathologyanalysis.omv b/data/histopathologyanalysis.omv
index 947e8da6..a01921e9 100644
Binary files a/data/histopathologyanalysis.omv and b/data/histopathologyanalysis.omv differ
diff --git a/jamovi/0000.yaml b/jamovi/0000.yaml
index 5dd4ef8f..d212df14 100644
--- a/jamovi/0000.yaml
+++ b/jamovi/0000.yaml
@@ -211,6 +211,6 @@ datasets:
tags:
- Classification
usesNative: true
-minApp: 1.3.0
+minApp: 1.2.19
...
diff --git a/jamovi/alluvial.a.yaml b/jamovi/alluvial.a.yaml
index 4c1ac58d..8148119e 100644
--- a/jamovi/alluvial.a.yaml
+++ b/jamovi/alluvial.a.yaml
@@ -20,6 +20,18 @@ options:
a string naming the variables from `data` that contains the
values used for the Alluvial Diagram.
+
+
+ - name: condensationvar
+ title: Condensation Variable
+ type: Variable
+ description:
+ R: >
+ The primary variable to be used for condensation.
+
+
+
+
- name: excl
title: Exclude Missing (NA)
type: Bool
@@ -66,7 +78,7 @@ options:
- title: Median
name: median
- title: Min-Max
- name: min-max
+ name: min_max
- title: Cuts
name: cuts
default: default
diff --git a/jamovi/alluvial.r.yaml b/jamovi/alluvial.r.yaml
index d356a88b..dd7e4dde 100644
--- a/jamovi/alluvial.r.yaml
+++ b/jamovi/alluvial.r.yaml
@@ -12,7 +12,10 @@ items:
- vars
- excl
- marg
- - inter
+ - verb
+ - fill
+ - bin
+
# - name: plothtml
@@ -24,7 +27,16 @@ items:
# - marg
# - inter
-
+ - title: '`Condensation Plot ${condensationvar}`'
+ name: plot2
+ type: Image
+ width: 600
+ height: 450
+ renderFun: .plot2
+ requiresData: true
+ clearWith:
+ - condensationvar
+ visible: (condensationvar)
- title: Alluvial Diagrams
@@ -38,7 +50,15 @@ items:
- vars
- excl
- marg
- - inter
+ - verb
+ - fill
+ - bin
+
+
+
+
+
+
diff --git a/jamovi/alluvial.u.yaml b/jamovi/alluvial.u.yaml
index 06aa1dbd..86ffd018 100644
--- a/jamovi/alluvial.u.yaml
+++ b/jamovi/alluvial.u.yaml
@@ -15,10 +15,61 @@ children:
name: vars
isTarget: true
maxItemCount: 6
- - type: LayoutBox
- margin: large
+ - type: CollapseBox
+ label: Options
+ stretchFactor: 1
+ collapsed: true
children:
- - type: CheckBox
- name: excl
- - type: CheckBox
- name: marg
+ - type: LayoutBox
+ margin: large
+ stretchFactor: 1
+ children:
+ - type: LayoutBox
+ cell:
+ column: 0
+ row: 0
+ stretchFactor: 1
+ children:
+ - type: Label
+ label: ''
+ fitToGrid: true
+ children:
+ - type: CheckBox
+ name: excl
+ - type: CheckBox
+ name: marg
+ - type: CheckBox
+ name: verb
+ - type: LayoutBox
+ cell:
+ column: 1
+ row: 0
+ stretchFactor: 1
+ children:
+ - type: Label
+ label: ''
+ fitToGrid: true
+ cell:
+ column: 1
+ row: 0
+ children:
+ - type: ComboBox
+ name: fill
+ - type: ComboBox
+ name: bin
+ - type: CollapseBox
+ label: Condensation Variable
+ stretchFactor: 1
+ collapsed: true
+ children:
+ - type: VariableSupplier
+ persistentItems: false
+ stretchFactor: 1
+ children:
+ - type: TargetLayoutBox
+ label: Condensation Variable
+ children:
+ - type: VariablesListBox
+ name: condensationvar
+ maxItemCount: 1
+ isTarget: true
diff --git a/man/alluvial.Rd b/man/alluvial.Rd
index bf96cc9d..07cea153 100644
--- a/man/alluvial.Rd
+++ b/man/alluvial.Rd
@@ -4,7 +4,16 @@
\alias{alluvial}
\title{Alluvial Diagrams}
\usage{
-alluvial(data, vars, excl = TRUE, marg = FALSE)
+alluvial(
+ data,
+ vars,
+ condensationvar,
+ excl = TRUE,
+ marg = FALSE,
+ verb = FALSE,
+ fill = "first_variable",
+ bin = "default"
+)
}
\arguments{
\item{data}{The data as a data frame.}
@@ -12,15 +21,25 @@ alluvial(data, vars, excl = TRUE, marg = FALSE)
\item{vars}{a string naming the variables from \code{data} that contains
the values used for the Alluvial Diagram.}
+\item{condensationvar}{The primary variable to be used for condensation.}
+
\item{excl}{.}
\item{marg}{.}
+
+\item{verb}{.}
+
+\item{fill}{A list for the argument fill for selecting the variable to be
+represented by color. Default is 'first_variable'.}
+
+\item{bin}{labels for the bins from low to high}
}
\value{
A results object containing:
\tabular{llllll}{
\code{results$todo} \tab \tab \tab \tab \tab a html \cr
\code{results$plot} \tab \tab \tab \tab \tab an image \cr
+\code{results$plot2} \tab \tab \tab \tab \tab an image \cr
}
}
\description{
diff --git a/man/alluvialClass.Rd b/man/alluvialClass.Rd
new file mode 100644
index 00000000..2634cbf1
--- /dev/null
+++ b/man/alluvialClass.Rd
@@ -0,0 +1,73 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/alluvial.b.R
+\name{alluvialClass}
+\alias{alluvialClass}
+\title{Alluvial Plot}
+\value{
+Alluvial Plot
+}
+\description{
+Alluvial Plot
+
+Alluvial Plot
+}
+\section{Super classes}{
+\code{\link[jmvcore:Analysis]{jmvcore::Analysis}} -> \code{\link[ClinicoPath:alluvialBase]{ClinicoPath::alluvialBase}} -> \code{alluvialClass}
+}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-clone}{\code{alluvialClass$clone()}}
+}
+}
+\if{html}{
+\out{Inherited methods
}
+\itemize{
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-.createImage}{\code{jmvcore::Analysis$.createImage()}}\out{}
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-.createImages}{\code{jmvcore::Analysis$.createImages()}}\out{}
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-.createPlotObject}{\code{jmvcore::Analysis$.createPlotObject()}}\out{}
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-.load}{\code{jmvcore::Analysis$.load()}}\out{}
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-.render}{\code{jmvcore::Analysis$.render()}}\out{}
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-.save}{\code{jmvcore::Analysis$.save()}}\out{}
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-.savePart}{\code{jmvcore::Analysis$.savePart()}}\out{}
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-.setCheckpoint}{\code{jmvcore::Analysis$.setCheckpoint()}}\out{}
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-.setParent}{\code{jmvcore::Analysis$.setParent()}}\out{}
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-.setReadDatasetHeaderSource}{\code{jmvcore::Analysis$.setReadDatasetHeaderSource()}}\out{}
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-.setReadDatasetSource}{\code{jmvcore::Analysis$.setReadDatasetSource()}}\out{}
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-.setResourcesPathSource}{\code{jmvcore::Analysis$.setResourcesPathSource()}}\out{}
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-.setStatePathSource}{\code{jmvcore::Analysis$.setStatePathSource()}}\out{}
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-addAddon}{\code{jmvcore::Analysis$addAddon()}}\out{}
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-asProtoBuf}{\code{jmvcore::Analysis$asProtoBuf()}}\out{}
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-asSource}{\code{jmvcore::Analysis$asSource()}}\out{}
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-check}{\code{jmvcore::Analysis$check()}}\out{}
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-init}{\code{jmvcore::Analysis$init()}}\out{}
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-optionsChangedHandler}{\code{jmvcore::Analysis$optionsChangedHandler()}}\out{}
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-postInit}{\code{jmvcore::Analysis$postInit()}}\out{}
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-print}{\code{jmvcore::Analysis$print()}}\out{}
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-readDataset}{\code{jmvcore::Analysis$readDataset()}}\out{}
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-run}{\code{jmvcore::Analysis$run()}}\out{}
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-serialize}{\code{jmvcore::Analysis$serialize()}}\out{}
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-setError}{\code{jmvcore::Analysis$setError()}}\out{}
+\item \out{}\href{../../jmvcore/html/Analysis.html#method-setStatus}{\code{jmvcore::Analysis$setStatus()}}\out{}
+\item \out{}\href{../../ClinicoPath/html/alluvialBase.html#method-initialize}{\code{ClinicoPath::alluvialBase$initialize()}}\out{}
+}
+\out{
}}
+\if{html}{\out{}}
+\if{latex}{\out{\hypertarget{method-clone}{}}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{}}\preformatted{alluvialClass$clone(deep = FALSE)}\if{html}{\out{
}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{}}
+\describe{
+\item{\code{deep}}{Whether to make a deep clone.}
+}
+\if{html}{\out{
}}
+}
+}
+}
diff --git a/man/figures/jamovi-ClinicoPath-easyalluvial.gif b/man/figures/jamovi-ClinicoPath-easyalluvial.gif
new file mode 100644
index 00000000..19e97287
Binary files /dev/null and b/man/figures/jamovi-ClinicoPath-easyalluvial.gif differ
diff --git a/man/reportcatClass.Rd b/man/reportcatClass.Rd
index 6d83ef67..3ca935fa 100644
--- a/man/reportcatClass.Rd
+++ b/man/reportcatClass.Rd
@@ -3,6 +3,9 @@
\name{reportcatClass}
\alias{reportcatClass}
\title{Summary of Categorical Variables}
+\value{
+Text
+}
\description{
Summary of Categorical Variables
diff --git a/tododata/todo.Rmd b/tododata/todo.Rmd
index 414d5899..18aadd8c 100644
--- a/tododata/todo.Rmd
+++ b/tododata/todo.Rmd
@@ -2665,10 +2665,15 @@ mydata <- jmvcore::select(df = mydata, columnNames = c(var1, var2))
mydata <- jmvcore::naOmit(mydata)
+plot <-
easyalluvial::alluvial_wide( data = mydata
, max_variables = 5
- , fill_by = 'first_variable' )
+ , fill_by = 'first_variable'
+ , verbose = TRUE
+ )
+plot %>%
+ easyalluvial::add_marginal_histograms(mydata)