R/timeinterval.h.R
# This file is automatically generated, you probably don't want to edit this
timeintervalOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"timeintervalOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
explanatory = NULL,
overalltime = NULL,
outcome = NULL,
outcomeLevel = NULL, ...) {
super$initialize(
package="ClinicoPath",
name="timeinterval",
requiresData=TRUE,
...)
private$..explanatory <- jmvcore::OptionVariables$new(
"explanatory",
explanatory,
suggested=list(
"ordinal",
"nominal"),
permitted=list(
"factor"))
private$..overalltime <- jmvcore::OptionVariable$new(
"overalltime",
overalltime,
suggested=list(
"continuous"),
permitted=list(
"numeric"))
private$..outcome <- jmvcore::OptionVariable$new(
"outcome",
outcome)
private$..outcomeLevel <- jmvcore::OptionLevel$new(
"outcomeLevel",
outcomeLevel,
variable="(outcome)")
self$.addOption(private$..explanatory)
self$.addOption(private$..overalltime)
self$.addOption(private$..outcome)
self$.addOption(private$..outcomeLevel)
}),
active = list(
explanatory = function() private$..explanatory$value,
overalltime = function() private$..overalltime$value,
outcome = function() private$..outcome$value,
outcomeLevel = function() private$..outcomeLevel$value),
private = list(
..explanatory = NA,
..overalltime = NA,
..outcome = NA,
..outcomeLevel = NA)
)
timeintervalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"timeintervalResults",
inherit = jmvcore::Group,
active = list(
text1 = function() private$.items[["text1"]],
text1table = function() private$.items[["text1table"]],
text1html = function() private$.items[["text1html"]],
text2 = function() private$.items[["text2"]],
medianTable = function() private$.items[["medianTable"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Time Interval",
refs=list(
"ClinicoPathJamoviModule"))
self$add(jmvcore::Preformatted$new(
options=options,
name="text1",
title="denemeler"))
self$add(jmvcore::Preformatted$new(
options=options,
name="text1table",
title="fit"))
self$add(jmvcore::Preformatted$new(
options=options,
name="text1html",
title="fit"))
self$add(jmvcore::Preformatted$new(
options=options,
name="text2",
title="Median Survival Summary and Table"))
self$add(jmvcore::Table$new(
options=options,
name="medianTable",
title="Median Survival Table",
rows=0,
columns=list(
list(
`name`="factor",
`title`="Levels",
`type`="text"),
list(
`name`="records",
`title`="Records",
`type`="number"),
list(
`name`="events",
`title`="Events",
`type`="integer"),
list(
`name`="rmean",
`title`="rmean",
`type`="number"),
list(
`name`="se_rmean",
`title`="se_rmean",
`type`="number"),
list(
`name`="median",
`title`="Median",
`type`="number"),
list(
`name`="x0_95lcl",
`title`="Lower",
`superTitle`="95% Confidence Interval",
`type`="number"),
list(
`name`="x0_95ucl",
`title`="Upper",
`superTitle`="95% Confidence Interval",
`type`="number"))))}))
timeintervalBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"timeintervalBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "ClinicoPath",
name = "timeinterval",
version = c(1,0,0),
options = options,
results = timeintervalResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'auto')
}))
#' Time Interval
#'
#'
#' @param data The data as a data frame.
#' @param explanatory .
#' @param overalltime .
#' @param outcome .
#' @param outcomeLevel .
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$text1} \tab \tab \tab \tab \tab a preformatted \cr
#' \code{results$text1table} \tab \tab \tab \tab \tab a preformatted \cr
#' \code{results$text1html} \tab \tab \tab \tab \tab a preformatted \cr
#' \code{results$text2} \tab \tab \tab \tab \tab a preformatted \cr
#' \code{results$medianTable} \tab \tab \tab \tab \tab a table \cr
#' }
#'
#' Tables can be converted to data frames with \code{asDF} or \code{\link{as.data.frame}}. For example:
#'
#' \code{results$medianTable$asDF}
#'
#' \code{as.data.frame(results$medianTable)}
#'
#' @export
timeinterval <- function(
data,
explanatory,
overalltime,
outcome,
outcomeLevel) {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("timeinterval requires jmvcore to be installed (restart may be required)")
if ( ! missing(explanatory)) explanatory <- jmvcore::resolveQuo(jmvcore::enquo(explanatory))
if ( ! missing(overalltime)) overalltime <- jmvcore::resolveQuo(jmvcore::enquo(overalltime))
if ( ! missing(outcome)) outcome <- jmvcore::resolveQuo(jmvcore::enquo(outcome))
if (missing(data))
data <- jmvcore::marshalData(
parent.frame(),
`if`( ! missing(explanatory), explanatory, NULL),
`if`( ! missing(overalltime), overalltime, NULL),
`if`( ! missing(outcome), outcome, NULL))
for (v in explanatory) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
options <- timeintervalOptions$new(
explanatory = explanatory,
overalltime = overalltime,
outcome = outcome,
outcomeLevel = outcomeLevel)
analysis <- timeintervalClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}