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sbalcisbalci
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added easyalluvial. for condensation variable there is a bug self$data is selected as other variables
1 parent b92489b commit 1c226e1

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+377
-82
lines changed

‎DESCRIPTION‎

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Original file line numberDiff line numberDiff line change
@@ -25,7 +25,8 @@ Depends:
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R (>= 3.6.0)
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Imports:
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jmvcore,
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R6
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R6,
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magrittr
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Remotes:
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ddsjoberg/gtsummary,
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ndphillips/FFTrees,
@@ -56,7 +57,6 @@ Suggests:
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explore,
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rpart,
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rpart.plot,
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magrittr,
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plotROC,
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arsenal,
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easyalluvial,

‎NAMESPACE‎

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@@ -25,4 +25,5 @@ export(vartree)
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import(jmvcore)
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importFrom(R6,R6Class)
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importFrom(jmvcore,toNumeric)
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importFrom(magrittr,"%>%")
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importFrom(utils,data)

‎R/alluvial.b.R‎

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@@ -1,3 +1,10 @@
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#' @title Alluvial Plot
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#' @return Alluvial Plot
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#' @importFrom R6 R6Class
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#' @import jmvcore
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#' @importFrom magrittr %>%
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#'
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# This file is a generated template, your changes will not be overwritten
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@@ -36,15 +43,6 @@ alluvialClass <- if (requireNamespace('jmvcore')) R6::R6Class(
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# #Errors ----
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#
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# if (is.null(self$options$vars) )
@@ -106,29 +104,6 @@ alluvialClass <- if (requireNamespace('jmvcore')) R6::R6Class(
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# html$setContent(plothtml)
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}
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}
@@ -161,20 +136,20 @@ alluvialClass <- if (requireNamespace('jmvcore')) R6::R6Class(
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verbose <- FALSE
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verb <- self$options$verb
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if (isTRUE(verb)) verbose <- TRUE
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# fill_by ----
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168-
jmvcore::composeTerm(self$options$fill)
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self$options$fill
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fill <- jmvcore::composeTerm(self$options$fill)
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#bin
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bin <- self$options$bin
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if (bin = "default") bin <- 'c("LL", "ML", "M", "MH", "HH")'
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if (bin == "default") bin <- c("LL", "ML", "M", "MH", "HH")
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# Exclude NA ----
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@@ -223,5 +198,48 @@ alluvialClass <- if (requireNamespace('jmvcore')) R6::R6Class(
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print(plot)
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TRUE
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226-
})
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}
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,
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.plot2 = function(image, ...) {
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# the plot function ----
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#Errors ----
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if (is.null(self$options$condensationvar) )
212+
return()
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214+
if (nrow(self$data) == 0)
215+
stop('Data contains no (complete) rows')
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217+
# Prepare Data ----
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condvarName <- self$options$condensationvar
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condvarName <- jmvcore::composeTerm(components = condvarName)
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plot2 <- self$data %>%
226+
easyalluvial::plot_condensation(df = .,
227+
first = .data[[condvarName]])
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# Print Plot ----
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print(plot2)
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TRUE
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}
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)
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)

‎R/alluvial.h.R‎

Lines changed: 83 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -7,8 +7,12 @@ alluvialOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
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public = list(
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initialize = function(
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vars = NULL,
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condensationvar = NULL,
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excl = TRUE,
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marg = FALSE, ...) {
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marg = FALSE,
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verb = FALSE,
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fill = "first_variable",
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bin = "default", ...) {
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super$initialize(
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package='ClinicoPath',
@@ -19,6 +23,9 @@ alluvialOptions <- if (requireNamespace('jmvcore')) R6::R6Class(
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private$..vars <- jmvcore::OptionVariables$new(
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"vars",
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vars)
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private$..condensationvar <- jmvcore::OptionVariable$new(
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"condensationvar",
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condensationvar)
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private$..excl <- jmvcore::OptionBool$new(
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"excl",
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excl,
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"marg",
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marg,
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default=FALSE)
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private$..verb <- jmvcore::OptionBool$new(
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"verb",
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verb,
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default=FALSE)
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private$..fill <- jmvcore::OptionList$new(
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"fill",
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fill,
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options=list(
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"first_variable",
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"last_variable",
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"all_flows",
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"values"),
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default="first_variable")
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private$..bin <- jmvcore::OptionList$new(
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"bin",
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bin,
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options=list(
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"default",
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"mean",
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"median",
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"min_max",
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"cuts"),
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default="default")
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self$.addOption(private$..vars)
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self$.addOption(private$..condensationvar)
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self$.addOption(private$..excl)
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self$.addOption(private$..marg)
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self$.addOption(private$..verb)
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self$.addOption(private$..fill)
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self$.addOption(private$..bin)
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}),
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active = list(
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vars = function() private$..vars$value,
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condensationvar = function() private$..condensationvar$value,
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excl = function() private$..excl$value,
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marg = function() private$..marg$value),
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marg = function() private$..marg$value,
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verb = function() private$..verb$value,
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fill = function() private$..fill$value,
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bin = function() private$..bin$value),
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private = list(
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..vars = NA,
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..condensationvar = NA,
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..excl = NA,
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..marg = NA)
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..marg = NA,
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..verb = NA,
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..fill = NA,
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..bin = NA)
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)
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alluvialResults <- if (requireNamespace('jmvcore')) R6::R6Class(
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inherit = jmvcore::Group,
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active = list(
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todo = function() private$.items[["todo"]],
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plot = function() private$.items[["plot"]]),
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plot = function() private$.items[["plot"]],
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plot2 = function() private$.items[["plot2"]]),
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private = list(),
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public=list(
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initialize=function(options) {
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"vars",
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"excl",
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"marg",
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"inter")))
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"verb",
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"fill",
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"bin")))
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self$add(jmvcore::Image$new(
69114
options=options,
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title="Alluvial Diagrams",
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77122
"vars",
78123
"excl",
79124
"marg",
80-
"inter")))}))
125+
"verb",
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"fill",
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"bin")))
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self$add(jmvcore::Image$new(
129+
options=options,
130+
title="`Condensation Plot ${condensationvar}`",
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name="plot2",
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width=600,
133+
height=450,
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renderFun=".plot2",
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requiresData=TRUE,
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clearWith=list(
137+
"condensationvar"),
138+
visible="(condensationvar)"))}))
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82140
alluvialBase <- if (requireNamespace('jmvcore')) R6::R6Class(
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"alluvialBase",
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#' @param data The data as a data frame.
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#' @param vars a string naming the variables from \code{data} that contains
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#' the values used for the Alluvial Diagram.
166+
#' @param condensationvar The primary variable to be used for condensation.
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#' @param excl .
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#' @param marg .
169+
#' @param verb .
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#' @param fill A list for the argument fill for selecting the variable to be
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#' represented by color. Default is 'first_variable'.
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#' @param bin labels for the bins from low to high
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#' @return A results object containing:
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#' \tabular{llllll}{
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#' \code{results$todo} \tab \tab \tab \tab \tab a html \cr
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#' \code{results$plot} \tab \tab \tab \tab \tab an image \cr
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#' \code{results$plot2} \tab \tab \tab \tab \tab an image \cr
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#' }
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#'
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#' @export
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alluvial <- function(
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data,
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vars,
184+
condensationvar,
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excl = TRUE,
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marg = FALSE) {
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marg = FALSE,
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verb = FALSE,
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fill = "first_variable",
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bin = "default") {
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if ( ! requireNamespace('jmvcore'))
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stop('alluvial requires jmvcore to be installed (restart may be required)')
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if ( ! missing(vars)) vars <- jmvcore::resolveQuo(jmvcore::enquo(vars))
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if ( ! missing(condensationvar)) condensationvar <- jmvcore::resolveQuo(jmvcore::enquo(condensationvar))
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if (missing(data))
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data <- jmvcore::marshalData(
129198
parent.frame(),
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`if`( ! missing(vars), vars, NULL))
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`if`( ! missing(vars), vars, NULL),
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`if`( ! missing(condensationvar), condensationvar, NULL))
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options <- alluvialOptions$new(
134204
vars = vars,
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condensationvar = condensationvar,
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excl = excl,
136-
marg = marg)
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marg = marg,
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verb = verb,
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fill = fill,
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bin = bin)
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analysis <- alluvialClass$new(
139213
options = options,

‎R/crosstable.b.R‎

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@@ -104,7 +104,9 @@ crosstableClass <- if (requireNamespace('jmvcore')) R6::R6Class(
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# myvars <- unlist(myvars)
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106106
mydata %>%
107-
summary_factorlist(dependent = self$options$group,
107+
finalfit::summary_factorlist(
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.data = .,
109+
dependent = self$options$group,
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explanatory = myvars,
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# column = TRUE,
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total_col = TRUE,

‎R/multisurvival.b.R‎

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@@ -144,7 +144,7 @@ multisurvivalClass <- if (requireNamespace('jmvcore')) R6::R6Class(
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formulaR <- jmvcore::toNumeric(formulaR)
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147-
myformula <- paste("Surv(", formulaL, ",", formulaR, ")")
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myformula <- paste("survival::Surv(", formulaL, ",", formulaR, ")")
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# https://finalfit.org/reference/hr_plot.html
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formula2 <- jmvcore::constructFormula(terms = self$options$explanatory)
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207-
formula3 <- paste("Surv(", formulaL, ",", formulaR, ") ~ ", formula2)
207+
formula3 <- paste("survival::Surv(", formulaL, ",", formulaR, ") ~ ", formula2)
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209209
formula3 <- as.formula(formula3)
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‎R/reportcat.b.R‎

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#' @title Summary of Categorical Variables
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#'
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#'
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#'
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#' @return Text
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#'
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#' @importFrom R6 R6Class
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#' @import jmvcore
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#' @importFrom magrittr %>%
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#'
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reportcatClass <- if (requireNamespace('jmvcore')) R6::R6Class(

‎README.Rmd‎

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🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩
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#### Alluvial Diagrams
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🔬🔬🔬🔬 UNDER CONSTRUCTION 🛠⛔️⚠️🔩
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<img src="man/figures/jamovi-ClinicoPath-easyalluvial.gif" align="center" width = 75% />
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---
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