R/survival.h.R
In sbalci/jsurvival: Survival Module of ClinicoPath for jamovi
Defines functions
survival
Documented in
survival
# This file is automatically generated, you probably don't want to edit this
survivalOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"survivalOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
elapsedtime = NULL,
tint = FALSE,
dxdate = NULL,
fudate = NULL,
explanatory = NULL,
outcome = NULL,
outcomeLevel = NULL,
dod = NULL,
dooc = NULL,
awd = NULL,
awod = NULL,
analysistype = "overall",
cutp = "12, 36, 60",
timetypedata = "ymd",
timetypeoutput = "months",
uselandmark = FALSE,
landmark = 3,
pw = FALSE,
padjustmethod = "holm",
ph_cox = FALSE,
sc = FALSE,
kmunicate = FALSE,
ce = FALSE,
ch = FALSE,
endplot = 60,
ybegin_plot = 0,
yend_plot = 1,
byplot = 12,
multievent = FALSE,
ci95 = FALSE,
risktable = FALSE,
censored = FALSE,
pplot = TRUE,
medianline = "none", ...) {
super$initialize(
package="jsurvival",
name="survival",
requiresData=TRUE,
...)
private$..elapsedtime <- jmvcore::OptionVariable$new(
"elapsedtime",
elapsedtime,
suggested=list(
"continuous"),
permitted=list(
"numeric"))
private$..tint <- jmvcore::OptionBool$new(
"tint",
tint,
default=FALSE)
private$..dxdate <- jmvcore::OptionVariable$new(
"dxdate",
dxdate)
private$..fudate <- jmvcore::OptionVariable$new(
"fudate",
fudate)
private$..calculatedtime <- jmvcore::OptionOutput$new(
"calculatedtime")
private$..explanatory <- jmvcore::OptionVariable$new(
"explanatory",
explanatory,
suggested=list(
"ordinal",
"nominal"),
permitted=list(
"factor"))
private$..outcome <- jmvcore::OptionVariable$new(
"outcome",
outcome,
suggested=list(
"ordinal",
"nominal",
"continuous"),
permitted=list(
"factor",
"numeric"))
private$..outcomeLevel <- jmvcore::OptionLevel$new(
"outcomeLevel",
outcomeLevel,
variable="(outcome)")
private$..dod <- jmvcore::OptionLevel$new(
"dod",
dod,
variable="(outcome)",
allowNone=TRUE)
private$..dooc <- jmvcore::OptionLevel$new(
"dooc",
dooc,
variable="(outcome)",
allowNone=TRUE)
private$..awd <- jmvcore::OptionLevel$new(
"awd",
awd,
variable="(outcome)",
allowNone=TRUE)
private$..awod <- jmvcore::OptionLevel$new(
"awod",
awod,
variable="(outcome)",
allowNone=TRUE)
private$..analysistype <- jmvcore::OptionList$new(
"analysistype",
analysistype,
options=list(
"overall",
"cause",
"compete"),
default="overall")
private$..outcomeredefined <- jmvcore::OptionOutput$new(
"outcomeredefined")
private$..cutp <- jmvcore::OptionString$new(
"cutp",
cutp,
default="12, 36, 60")
private$..timetypedata <- jmvcore::OptionList$new(
"timetypedata",
timetypedata,
options=list(
"ymdhms",
"ymd",
"ydm",
"mdy",
"myd",
"dmy",
"dym"),
default="ymd")
private$..timetypeoutput <- jmvcore::OptionList$new(
"timetypeoutput",
timetypeoutput,
options=list(
"days",
"weeks",
"months",
"years"),
default="months")
private$..uselandmark <- jmvcore::OptionBool$new(
"uselandmark",
uselandmark,
default=FALSE)
private$..landmark <- jmvcore::OptionInteger$new(
"landmark",
landmark,
default=3)
private$..pw <- jmvcore::OptionBool$new(
"pw",
pw,
default=FALSE)
private$..padjustmethod <- jmvcore::OptionList$new(
"padjustmethod",
padjustmethod,
options=list(
"holm",
"hochberg",
"hommel",
"bonferroni",
"BH",
"BY",
"fdr",
"none"),
default="holm")
private$..ph_cox <- jmvcore::OptionBool$new(
"ph_cox",
ph_cox,
default=FALSE)
private$..sc <- jmvcore::OptionBool$new(
"sc",
sc,
default=FALSE)
private$..kmunicate <- jmvcore::OptionBool$new(
"kmunicate",
kmunicate,
default=FALSE)
private$..ce <- jmvcore::OptionBool$new(
"ce",
ce,
default=FALSE)
private$..ch <- jmvcore::OptionBool$new(
"ch",
ch,
default=FALSE)
private$..endplot <- jmvcore::OptionInteger$new(
"endplot",
endplot,
default=60)
private$..ybegin_plot <- jmvcore::OptionNumber$new(
"ybegin_plot",
ybegin_plot,
default=0)
private$..yend_plot <- jmvcore::OptionNumber$new(
"yend_plot",
yend_plot,
default=1)
private$..byplot <- jmvcore::OptionInteger$new(
"byplot",
byplot,
default=12)
private$..multievent <- jmvcore::OptionBool$new(
"multievent",
multievent,
default=FALSE)
private$..ci95 <- jmvcore::OptionBool$new(
"ci95",
ci95,
default=FALSE)
private$..risktable <- jmvcore::OptionBool$new(
"risktable",
risktable,
default=FALSE)
private$..censored <- jmvcore::OptionBool$new(
"censored",
censored,
default=FALSE)
private$..pplot <- jmvcore::OptionBool$new(
"pplot",
pplot,
default=TRUE)
private$..medianline <- jmvcore::OptionList$new(
"medianline",
medianline,
options=list(
"none",
"h",
"v",
"hv"),
default="none")
self$.addOption(private$..elapsedtime)
self$.addOption(private$..tint)
self$.addOption(private$..dxdate)
self$.addOption(private$..fudate)
self$.addOption(private$..calculatedtime)
self$.addOption(private$..explanatory)
self$.addOption(private$..outcome)
self$.addOption(private$..outcomeLevel)
self$.addOption(private$..dod)
self$.addOption(private$..dooc)
self$.addOption(private$..awd)
self$.addOption(private$..awod)
self$.addOption(private$..analysistype)
self$.addOption(private$..outcomeredefined)
self$.addOption(private$..cutp)
self$.addOption(private$..timetypedata)
self$.addOption(private$..timetypeoutput)
self$.addOption(private$..uselandmark)
self$.addOption(private$..landmark)
self$.addOption(private$..pw)
self$.addOption(private$..padjustmethod)
self$.addOption(private$..ph_cox)
self$.addOption(private$..sc)
self$.addOption(private$..kmunicate)
self$.addOption(private$..ce)
self$.addOption(private$..ch)
self$.addOption(private$..endplot)
self$.addOption(private$..ybegin_plot)
self$.addOption(private$..yend_plot)
self$.addOption(private$..byplot)
self$.addOption(private$..multievent)
self$.addOption(private$..ci95)
self$.addOption(private$..risktable)
self$.addOption(private$..censored)
self$.addOption(private$..pplot)
self$.addOption(private$..medianline)
}),
active = list(
elapsedtime = function() private$..elapsedtime$value,
tint = function() private$..tint$value,
dxdate = function() private$..dxdate$value,
fudate = function() private$..fudate$value,
calculatedtime = function() private$..calculatedtime$value,
explanatory = function() private$..explanatory$value,
outcome = function() private$..outcome$value,
outcomeLevel = function() private$..outcomeLevel$value,
dod = function() private$..dod$value,
dooc = function() private$..dooc$value,
awd = function() private$..awd$value,
awod = function() private$..awod$value,
analysistype = function() private$..analysistype$value,
outcomeredefined = function() private$..outcomeredefined$value,
cutp = function() private$..cutp$value,
timetypedata = function() private$..timetypedata$value,
timetypeoutput = function() private$..timetypeoutput$value,
uselandmark = function() private$..uselandmark$value,
landmark = function() private$..landmark$value,
pw = function() private$..pw$value,
padjustmethod = function() private$..padjustmethod$value,
ph_cox = function() private$..ph_cox$value,
sc = function() private$..sc$value,
kmunicate = function() private$..kmunicate$value,
ce = function() private$..ce$value,
ch = function() private$..ch$value,
endplot = function() private$..endplot$value,
ybegin_plot = function() private$..ybegin_plot$value,
yend_plot = function() private$..yend_plot$value,
byplot = function() private$..byplot$value,
multievent = function() private$..multievent$value,
ci95 = function() private$..ci95$value,
risktable = function() private$..risktable$value,
censored = function() private$..censored$value,
pplot = function() private$..pplot$value,
medianline = function() private$..medianline$value),
private = list(
..elapsedtime = NA,
..tint = NA,
..dxdate = NA,
..fudate = NA,
..calculatedtime = NA,
..explanatory = NA,
..outcome = NA,
..outcomeLevel = NA,
..dod = NA,
..dooc = NA,
..awd = NA,
..awod = NA,
..analysistype = NA,
..outcomeredefined = NA,
..cutp = NA,
..timetypedata = NA,
..timetypeoutput = NA,
..uselandmark = NA,
..landmark = NA,
..pw = NA,
..padjustmethod = NA,
..ph_cox = NA,
..sc = NA,
..kmunicate = NA,
..ce = NA,
..ch = NA,
..endplot = NA,
..ybegin_plot = NA,
..yend_plot = NA,
..byplot = NA,
..multievent = NA,
..ci95 = NA,
..risktable = NA,
..censored = NA,
..pplot = NA,
..medianline = NA)
)
survivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"survivalResults",
inherit = jmvcore::Group,
active = list(
subtitle = function() private$.items[["subtitle"]],
todo = function() private$.items[["todo"]],
medianSummary = function() private$.items[["medianSummary"]],
medianTable = function() private$.items[["medianTable"]],
coxSummary = function() private$.items[["coxSummary"]],
coxTable = function() private$.items[["coxTable"]],
tCoxtext2 = function() private$.items[["tCoxtext2"]],
cox_ph = function() private$.items[["cox_ph"]],
plot8 = function() private$.items[["plot8"]],
survTableSummary = function() private$.items[["survTableSummary"]],
survTable = function() private$.items[["survTable"]],
pairwiseSummary = function() private$.items[["pairwiseSummary"]],
pairwiseTable = function() private$.items[["pairwiseTable"]],
plot = function() private$.items[["plot"]],
plot2 = function() private$.items[["plot2"]],
plot3 = function() private$.items[["plot3"]],
plot6 = function() private$.items[["plot6"]],
calculatedtime = function() private$.items[["calculatedtime"]],
outcomeredefined = function() private$.items[["outcomeredefined"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Survival Analysis",
refs=list(
"finalfit",
"survival",
"survminer",
"survivaltutorial",
"survivalrwnahhas",
"survivalrviews",
"appliedsurvivalanalysisR",
"ClinicoPathJamoviModule"))
self$add(jmvcore::Preformatted$new(
options=options,
name="subtitle",
title="`Survival Analysis - ${explanatory}`"))
self$add(jmvcore::Html$new(
options=options,
name="todo",
title="To Do",
clearWith=list(
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent")))
self$add(jmvcore::Preformatted$new(
options=options,
name="medianSummary",
title="`Median Survival Summary and Table - ${explanatory}`",
clearWith=list(
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent")))
self$add(jmvcore::Table$new(
options=options,
name="medianTable",
title="`Median Survival Table: Levels for ${explanatory}`",
rows=0,
columns=list(
list(
`name`="factor",
`title`="Levels",
`type`="text"),
list(
`name`="records",
`title`="Records",
`type`="integer"),
list(
`name`="events",
`title`="Events",
`type`="integer"),
list(
`name`="rmean",
`title`="rmean",
`type`="number"),
list(
`name`="se_rmean",
`title`="se_rmean",
`type`="number"),
list(
`name`="median",
`title`="Median",
`type`="number"),
list(
`name`="x0_95lcl",
`title`="Lower",
`superTitle`="95% Confidence Interval",
`type`="number"),
list(
`name`="x0_95ucl",
`title`="Upper",
`superTitle`="95% Confidence Interval",
`type`="number")),
clearWith=list(
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent")))
self$add(jmvcore::Preformatted$new(
options=options,
name="coxSummary",
title="`Cox Regression Summary and Table - ${explanatory}`",
clearWith=list(
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent")))
self$add(jmvcore::Table$new(
options=options,
name="coxTable",
title="`Cox Table- ${explanatory}`",
rows=0,
columns=list(
list(
`name`="Explanatory",
`title`="Explanatory",
`type`="text"),
list(
`name`="Levels",
`title`="Levels",
`type`="text"),
list(
`name`="all",
`title`="all",
`type`="text"),
list(
`name`="HR_univariable",
`title`="HR (Univariable)",
`type`="text")),
clearWith=list(
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent")))
self$add(jmvcore::Html$new(
options=options,
name="tCoxtext2",
title="",
refs="finalfit",
clearWith=list(
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent",
"contexpl")))
self$add(jmvcore::Preformatted$new(
options=options,
name="cox_ph",
title="Proportional Hazards Assumption",
visible="(ph_cox)",
clearWith=list(
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent",
"contexpl")))
self$add(jmvcore::Image$new(
options=options,
name="plot8",
title="`Proportional Hazards Assumption - ${explanatory}`",
width=600,
height=450,
renderFun=".plot8",
visible="(ph_cox)",
requiresData=TRUE,
clearWith=list(
"ph_cox",
"endplot",
"byplot",
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent")))
self$add(jmvcore::Preformatted$new(
options=options,
name="survTableSummary",
title="`1, 3, 5-yr Survival Summary and Table - ${explanatory}`",
clearWith=list(
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent")))
self$add(jmvcore::Table$new(
options=options,
name="survTable",
title="`1, 3, 5 year Survival - ${explanatory}`",
rows=0,
columns=list(
list(
`name`="strata",
`title`="Levels",
`type`="text"),
list(
`name`="time",
`title`="time",
`type`="integer"),
list(
`name`="n.risk",
`title`="Number at Risk",
`type`="integer"),
list(
`name`="n.event",
`title`="Number of Events",
`type`="integer"),
list(
`name`="surv",
`title`="Survival",
`type`="number",
`format`="pc"),
list(
`name`="lower",
`title`="Lower",
`superTitle`="95% Confidence Interval",
`type`="number",
`format`="pc"),
list(
`name`="upper",
`title`="Upper",
`superTitle`="95% Confidence Interval",
`type`="number",
`format`="pc")),
clearWith=list(
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent")))
self$add(jmvcore::Preformatted$new(
options=options,
name="pairwiseSummary",
title="`Pairwise Comparison Summary and Table - ${explanatory}`",
clearWith=list(
"pw",
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent"),
visible="(pw)"))
self$add(jmvcore::Table$new(
options=options,
name="pairwiseTable",
title="`Pairwise Comparison Table - ${explanatory}`",
rows=0,
columns=list(
list(
`name`="rowname",
`title`="Levels",
`type`="text"),
list(
`name`="name",
`title`="Levels",
`type`="text"),
list(
`name`="value",
`title`="p-value",
`type`="number",
`format`="zto,pvalue")),
visible="(pw)",
clearWith=list(
"pw",
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent"),
refs=list(
"padjust")))
self$add(jmvcore::Image$new(
options=options,
name="plot",
title="`Survival Plot - ${explanatory}`",
width=600,
height=450,
renderFun=".plot",
visible="(sc)",
requiresData=TRUE,
clearWith=list(
"sc",
"endplot",
"byplot",
"ybegin_plot",
"yend_plot",
"ci95",
"risktable",
"censored",
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent",
"pplot")))
self$add(jmvcore::Image$new(
options=options,
name="plot2",
title="`Cumulative Events - ${explanatory}`",
width=600,
height=450,
renderFun=".plot2",
visible="(ce)",
requiresData=TRUE,
clearWith=list(
"ce",
"endplot",
"byplot",
"ybegin_plot",
"yend_plot",
"ci95",
"risktable",
"censored",
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent")))
self$add(jmvcore::Image$new(
options=options,
name="plot3",
title="`Cumulative Hazard - ${explanatory}`",
width=600,
height=450,
renderFun=".plot3",
visible="(ch)",
requiresData=TRUE,
clearWith=list(
"ch",
"endplot",
"byplot",
"ybegin_plot",
"yend_plot",
"ci95",
"risktable",
"censored",
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent")))
self$add(jmvcore::Image$new(
options=options,
name="plot6",
title="`KMunicate-Style Plot - ${explanatory}`",
width=600,
height=450,
renderFun=".plot6",
visible="(kmunicate)",
requiresData=TRUE,
clearWith=list(
"kmunicate",
"endplot",
"byplot",
"ybegin_plot",
"yend_plot",
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent"),
refs=list(
"KMunicate",
"KMunicate2")))
self$add(jmvcore::Output$new(
options=options,
name="calculatedtime",
title="Add Calculated Time to Data",
varTitle="`Calculated Time - from ${ dxdate } to { fudate }`",
varDescription="`Calculated Time from Given Dates - from ${ dxdate } to { fudate } in Survival Analysis`",
measureType="continuous",
clearWith=list(
"tint",
"dxdate",
"fudate",
"overalltime",
"calculatedtime")))
self$add(jmvcore::Output$new(
options=options,
name="outcomeredefined",
title="Add Redefined Outcome to Data",
varTitle="`Redefined Outcome - from ${ outcome } for { analysistype } survival analysis`",
varDescription="Redefined Outcome from Outcome based on Analysis Type in Survival Analysis",
clearWith=list(
"outcome",
"analysistype",
"multievent",
"explanatory",
"outcomeLevel")))}))
survivalBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"survivalBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "jsurvival",
name = "survival",
version = c(1,0,0),
options = options,
results = survivalResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'none')
}))
#' Survival Analysis
#'
#' Function for Generating Summaries for Survival Analysis.
#'
#' @examples
#' # example will be added
#'
#' @param data The data as a data frame.
#' @param elapsedtime The time elapsed from the start of the study to the
#' event or censoring.
#' @param tint If the time is in date format, select this option to calculate
#' the survival time. The time will be calculated as the difference between
#' the event date and the diagnosis date. If the follow-up date is available,
#' the time will be calculated as the difference between the event date and
#' the follow-up date.
#' @param dxdate The date of diagnosis. If the time is in date format, the
#' time will be calculated as the difference between the event date and the
#' diagnosis date.
#' @param fudate The date of follow-up. If the time is in date format, the
#' time will be calculated as the difference between the event date and the
#' follow-up date.
#' @param explanatory The explanatory variable that will be used to compare
#' the survival times of different groups.
#' @param outcome The outcome variable that will be used to compare the
#' survival times of different groups.
#' @param outcomeLevel The level of the outcome variable that will be used as
#' the event level.
#' @param dod .
#' @param dooc .
#' @param awd .
#' @param awod .
#' @param analysistype .
#' @param cutp .
#' @param timetypedata select the time type in data
#' @param timetypeoutput select the time type in output
#' @param uselandmark .
#' @param landmark .
#' @param pw .
#' @param padjustmethod .
#' @param ph_cox .
#' @param sc .
#' @param kmunicate .
#' @param ce .
#' @param ch .
#' @param endplot .
#' @param ybegin_plot .
#' @param yend_plot .
#' @param byplot .
#' @param multievent .
#' @param ci95 .
#' @param risktable .
#' @param censored .
#' @param pplot .
#' @param medianline If true, displays a line indicating the median survival
#' time on the survival plot.
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$subtitle} \tab \tab \tab \tab \tab a preformatted \cr
#' \code{results$todo} \tab \tab \tab \tab \tab a html \cr
#' \code{results$medianSummary} \tab \tab \tab \tab \tab a preformatted \cr
#' \code{results$medianTable} \tab \tab \tab \tab \tab a table \cr
#' \code{results$coxSummary} \tab \tab \tab \tab \tab a preformatted \cr
#' \code{results$coxTable} \tab \tab \tab \tab \tab a table \cr
#' \code{results$tCoxtext2} \tab \tab \tab \tab \tab a html \cr
#' \code{results$cox_ph} \tab \tab \tab \tab \tab a preformatted \cr
#' \code{results$plot8} \tab \tab \tab \tab \tab an image \cr
#' \code{results$survTableSummary} \tab \tab \tab \tab \tab a preformatted \cr
#' \code{results$survTable} \tab \tab \tab \tab \tab a table \cr
#' \code{results$pairwiseSummary} \tab \tab \tab \tab \tab a preformatted \cr
#' \code{results$pairwiseTable} \tab \tab \tab \tab \tab a table \cr
#' \code{results$plot} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot2} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot3} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot6} \tab \tab \tab \tab \tab an image \cr
#' \code{results$calculatedtime} \tab \tab \tab \tab \tab an output \cr
#' \code{results$outcomeredefined} \tab \tab \tab \tab \tab an output \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$medianTable)}
#'
#' @export
survival <- function(
data,
elapsedtime,
tint = FALSE,
dxdate,
fudate,
explanatory,
outcome,
outcomeLevel,
dod,
dooc,
awd,
awod,
analysistype = "overall",
cutp = "12, 36, 60",
timetypedata = "ymd",
timetypeoutput = "months",
uselandmark = FALSE,
landmark = 3,
pw = FALSE,
padjustmethod = "holm",
ph_cox = FALSE,
sc = FALSE,
kmunicate = FALSE,
ce = FALSE,
ch = FALSE,
endplot = 60,
ybegin_plot = 0,
yend_plot = 1,
byplot = 12,
multievent = FALSE,
ci95 = FALSE,
risktable = FALSE,
censored = FALSE,
pplot = TRUE,
medianline = "none") {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("survival requires jmvcore to be installed (restart may be required)")
if ( ! missing(elapsedtime)) elapsedtime <- jmvcore::resolveQuo(jmvcore::enquo(elapsedtime))
if ( ! missing(dxdate)) dxdate <- jmvcore::resolveQuo(jmvcore::enquo(dxdate))
if ( ! missing(fudate)) fudate <- jmvcore::resolveQuo(jmvcore::enquo(fudate))
if ( ! missing(explanatory)) explanatory <- jmvcore::resolveQuo(jmvcore::enquo(explanatory))
if ( ! missing(outcome)) outcome <- jmvcore::resolveQuo(jmvcore::enquo(outcome))
if (missing(data))
data <- jmvcore::marshalData(
parent.frame(),
`if`( ! missing(elapsedtime), elapsedtime, NULL),
`if`( ! missing(dxdate), dxdate, NULL),
`if`( ! missing(fudate), fudate, NULL),
`if`( ! missing(explanatory), explanatory, NULL),
`if`( ! missing(outcome), outcome, NULL))
for (v in explanatory) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
options <- survivalOptions$new(
elapsedtime = elapsedtime,
tint = tint,
dxdate = dxdate,
fudate = fudate,
explanatory = explanatory,
outcome = outcome,
outcomeLevel = outcomeLevel,
dod = dod,
dooc = dooc,
awd = awd,
awod = awod,
analysistype = analysistype,
cutp = cutp,
timetypedata = timetypedata,
timetypeoutput = timetypeoutput,
uselandmark = uselandmark,
landmark = landmark,
pw = pw,
padjustmethod = padjustmethod,
ph_cox = ph_cox,
sc = sc,
kmunicate = kmunicate,
ce = ce,
ch = ch,
endplot = endplot,
ybegin_plot = ybegin_plot,
yend_plot = yend_plot,
byplot = byplot,
multievent = multievent,
ci95 = ci95,
risktable = risktable,
censored = censored,
pplot = pplot,
medianline = medianline)
analysis <- survivalClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
sbalci/jsurvival documentation built on Feb. 26, 2025, 1:20 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions survival
Documented in survival
# This file is automatically generated, you probably don't want to edit this
survivalOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"survivalOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
elapsedtime = NULL,
tint = FALSE,
dxdate = NULL,
fudate = NULL,
explanatory = NULL,
outcome = NULL,
outcomeLevel = NULL,
dod = NULL,
dooc = NULL,
awd = NULL,
awod = NULL,
analysistype = "overall",
cutp = "12, 36, 60",
timetypedata = "ymd",
timetypeoutput = "months",
uselandmark = FALSE,
landmark = 3,
pw = FALSE,
padjustmethod = "holm",
ph_cox = FALSE,
sc = FALSE,
kmunicate = FALSE,
ce = FALSE,
ch = FALSE,
endplot = 60,
ybegin_plot = 0,
yend_plot = 1,
byplot = 12,
multievent = FALSE,
ci95 = FALSE,
risktable = FALSE,
censored = FALSE,
pplot = TRUE,
medianline = "none", ...) {
super$initialize(
package="jsurvival",
name="survival",
requiresData=TRUE,
...)
private$..elapsedtime <- jmvcore::OptionVariable$new(
"elapsedtime",
elapsedtime,
suggested=list(
"continuous"),
permitted=list(
"numeric"))
private$..tint <- jmvcore::OptionBool$new(
"tint",
tint,
default=FALSE)
private$..dxdate <- jmvcore::OptionVariable$new(
"dxdate",
dxdate)
private$..fudate <- jmvcore::OptionVariable$new(
"fudate",
fudate)
private$..calculatedtime <- jmvcore::OptionOutput$new(
"calculatedtime")
private$..explanatory <- jmvcore::OptionVariable$new(
"explanatory",
explanatory,
suggested=list(
"ordinal",
"nominal"),
permitted=list(
"factor"))
private$..outcome <- jmvcore::OptionVariable$new(
"outcome",
outcome,
suggested=list(
"ordinal",
"nominal",
"continuous"),
permitted=list(
"factor",
"numeric"))
private$..outcomeLevel <- jmvcore::OptionLevel$new(
"outcomeLevel",
outcomeLevel,
variable="(outcome)")
private$..dod <- jmvcore::OptionLevel$new(
"dod",
dod,
variable="(outcome)",
allowNone=TRUE)
private$..dooc <- jmvcore::OptionLevel$new(
"dooc",
dooc,
variable="(outcome)",
allowNone=TRUE)
private$..awd <- jmvcore::OptionLevel$new(
"awd",
awd,
variable="(outcome)",
allowNone=TRUE)
private$..awod <- jmvcore::OptionLevel$new(
"awod",
awod,
variable="(outcome)",
allowNone=TRUE)
private$..analysistype <- jmvcore::OptionList$new(
"analysistype",
analysistype,
options=list(
"overall",
"cause",
"compete"),
default="overall")
private$..outcomeredefined <- jmvcore::OptionOutput$new(
"outcomeredefined")
private$..cutp <- jmvcore::OptionString$new(
"cutp",
cutp,
default="12, 36, 60")
private$..timetypedata <- jmvcore::OptionList$new(
"timetypedata",
timetypedata,
options=list(
"ymdhms",
"ymd",
"ydm",
"mdy",
"myd",
"dmy",
"dym"),
default="ymd")
private$..timetypeoutput <- jmvcore::OptionList$new(
"timetypeoutput",
timetypeoutput,
options=list(
"days",
"weeks",
"months",
"years"),
default="months")
private$..uselandmark <- jmvcore::OptionBool$new(
"uselandmark",
uselandmark,
default=FALSE)
private$..landmark <- jmvcore::OptionInteger$new(
"landmark",
landmark,
default=3)
private$..pw <- jmvcore::OptionBool$new(
"pw",
pw,
default=FALSE)
private$..padjustmethod <- jmvcore::OptionList$new(
"padjustmethod",
padjustmethod,
options=list(
"holm",
"hochberg",
"hommel",
"bonferroni",
"BH",
"BY",
"fdr",
"none"),
default="holm")
private$..ph_cox <- jmvcore::OptionBool$new(
"ph_cox",
ph_cox,
default=FALSE)
private$..sc <- jmvcore::OptionBool$new(
"sc",
sc,
default=FALSE)
private$..kmunicate <- jmvcore::OptionBool$new(
"kmunicate",
kmunicate,
default=FALSE)
private$..ce <- jmvcore::OptionBool$new(
"ce",
ce,
default=FALSE)
private$..ch <- jmvcore::OptionBool$new(
"ch",
ch,
default=FALSE)
private$..endplot <- jmvcore::OptionInteger$new(
"endplot",
endplot,
default=60)
private$..ybegin_plot <- jmvcore::OptionNumber$new(
"ybegin_plot",
ybegin_plot,
default=0)
private$..yend_plot <- jmvcore::OptionNumber$new(
"yend_plot",
yend_plot,
default=1)
private$..byplot <- jmvcore::OptionInteger$new(
"byplot",
byplot,
default=12)
private$..multievent <- jmvcore::OptionBool$new(
"multievent",
multievent,
default=FALSE)
private$..ci95 <- jmvcore::OptionBool$new(
"ci95",
ci95,
default=FALSE)
private$..risktable <- jmvcore::OptionBool$new(
"risktable",
risktable,
default=FALSE)
private$..censored <- jmvcore::OptionBool$new(
"censored",
censored,
default=FALSE)
private$..pplot <- jmvcore::OptionBool$new(
"pplot",
pplot,
default=TRUE)
private$..medianline <- jmvcore::OptionList$new(
"medianline",
medianline,
options=list(
"none",
"h",
"v",
"hv"),
default="none")
self$.addOption(private$..elapsedtime)
self$.addOption(private$..tint)
self$.addOption(private$..dxdate)
self$.addOption(private$..fudate)
self$.addOption(private$..calculatedtime)
self$.addOption(private$..explanatory)
self$.addOption(private$..outcome)
self$.addOption(private$..outcomeLevel)
self$.addOption(private$..dod)
self$.addOption(private$..dooc)
self$.addOption(private$..awd)
self$.addOption(private$..awod)
self$.addOption(private$..analysistype)
self$.addOption(private$..outcomeredefined)
self$.addOption(private$..cutp)
self$.addOption(private$..timetypedata)
self$.addOption(private$..timetypeoutput)
self$.addOption(private$..uselandmark)
self$.addOption(private$..landmark)
self$.addOption(private$..pw)
self$.addOption(private$..padjustmethod)
self$.addOption(private$..ph_cox)
self$.addOption(private$..sc)
self$.addOption(private$..kmunicate)
self$.addOption(private$..ce)
self$.addOption(private$..ch)
self$.addOption(private$..endplot)
self$.addOption(private$..ybegin_plot)
self$.addOption(private$..yend_plot)
self$.addOption(private$..byplot)
self$.addOption(private$..multievent)
self$.addOption(private$..ci95)
self$.addOption(private$..risktable)
self$.addOption(private$..censored)
self$.addOption(private$..pplot)
self$.addOption(private$..medianline)
}),
active = list(
elapsedtime = function() private$..elapsedtime$value,
tint = function() private$..tint$value,
dxdate = function() private$..dxdate$value,
fudate = function() private$..fudate$value,
calculatedtime = function() private$..calculatedtime$value,
explanatory = function() private$..explanatory$value,
outcome = function() private$..outcome$value,
outcomeLevel = function() private$..outcomeLevel$value,
dod = function() private$..dod$value,
dooc = function() private$..dooc$value,
awd = function() private$..awd$value,
awod = function() private$..awod$value,
analysistype = function() private$..analysistype$value,
outcomeredefined = function() private$..outcomeredefined$value,
cutp = function() private$..cutp$value,
timetypedata = function() private$..timetypedata$value,
timetypeoutput = function() private$..timetypeoutput$value,
uselandmark = function() private$..uselandmark$value,
landmark = function() private$..landmark$value,
pw = function() private$..pw$value,
padjustmethod = function() private$..padjustmethod$value,
ph_cox = function() private$..ph_cox$value,
sc = function() private$..sc$value,
kmunicate = function() private$..kmunicate$value,
ce = function() private$..ce$value,
ch = function() private$..ch$value,
endplot = function() private$..endplot$value,
ybegin_plot = function() private$..ybegin_plot$value,
yend_plot = function() private$..yend_plot$value,
byplot = function() private$..byplot$value,
multievent = function() private$..multievent$value,
ci95 = function() private$..ci95$value,
risktable = function() private$..risktable$value,
censored = function() private$..censored$value,
pplot = function() private$..pplot$value,
medianline = function() private$..medianline$value),
private = list(
..elapsedtime = NA,
..tint = NA,
..dxdate = NA,
..fudate = NA,
..calculatedtime = NA,
..explanatory = NA,
..outcome = NA,
..outcomeLevel = NA,
..dod = NA,
..dooc = NA,
..awd = NA,
..awod = NA,
..analysistype = NA,
..outcomeredefined = NA,
..cutp = NA,
..timetypedata = NA,
..timetypeoutput = NA,
..uselandmark = NA,
..landmark = NA,
..pw = NA,
..padjustmethod = NA,
..ph_cox = NA,
..sc = NA,
..kmunicate = NA,
..ce = NA,
..ch = NA,
..endplot = NA,
..ybegin_plot = NA,
..yend_plot = NA,
..byplot = NA,
..multievent = NA,
..ci95 = NA,
..risktable = NA,
..censored = NA,
..pplot = NA,
..medianline = NA)
)
survivalResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"survivalResults",
inherit = jmvcore::Group,
active = list(
subtitle = function() private$.items[["subtitle"]],
todo = function() private$.items[["todo"]],
medianSummary = function() private$.items[["medianSummary"]],
medianTable = function() private$.items[["medianTable"]],
coxSummary = function() private$.items[["coxSummary"]],
coxTable = function() private$.items[["coxTable"]],
tCoxtext2 = function() private$.items[["tCoxtext2"]],
cox_ph = function() private$.items[["cox_ph"]],
plot8 = function() private$.items[["plot8"]],
survTableSummary = function() private$.items[["survTableSummary"]],
survTable = function() private$.items[["survTable"]],
pairwiseSummary = function() private$.items[["pairwiseSummary"]],
pairwiseTable = function() private$.items[["pairwiseTable"]],
plot = function() private$.items[["plot"]],
plot2 = function() private$.items[["plot2"]],
plot3 = function() private$.items[["plot3"]],
plot6 = function() private$.items[["plot6"]],
calculatedtime = function() private$.items[["calculatedtime"]],
outcomeredefined = function() private$.items[["outcomeredefined"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Survival Analysis",
refs=list(
"finalfit",
"survival",
"survminer",
"survivaltutorial",
"survivalrwnahhas",
"survivalrviews",
"appliedsurvivalanalysisR",
"ClinicoPathJamoviModule"))
self$add(jmvcore::Preformatted$new(
options=options,
name="subtitle",
title="`Survival Analysis - ${explanatory}`"))
self$add(jmvcore::Html$new(
options=options,
name="todo",
title="To Do",
clearWith=list(
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent")))
self$add(jmvcore::Preformatted$new(
options=options,
name="medianSummary",
title="`Median Survival Summary and Table - ${explanatory}`",
clearWith=list(
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent")))
self$add(jmvcore::Table$new(
options=options,
name="medianTable",
title="`Median Survival Table: Levels for ${explanatory}`",
rows=0,
columns=list(
list(
`name`="factor",
`title`="Levels",
`type`="text"),
list(
`name`="records",
`title`="Records",
`type`="integer"),
list(
`name`="events",
`title`="Events",
`type`="integer"),
list(
`name`="rmean",
`title`="rmean",
`type`="number"),
list(
`name`="se_rmean",
`title`="se_rmean",
`type`="number"),
list(
`name`="median",
`title`="Median",
`type`="number"),
list(
`name`="x0_95lcl",
`title`="Lower",
`superTitle`="95% Confidence Interval",
`type`="number"),
list(
`name`="x0_95ucl",
`title`="Upper",
`superTitle`="95% Confidence Interval",
`type`="number")),
clearWith=list(
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent")))
self$add(jmvcore::Preformatted$new(
options=options,
name="coxSummary",
title="`Cox Regression Summary and Table - ${explanatory}`",
clearWith=list(
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent")))
self$add(jmvcore::Table$new(
options=options,
name="coxTable",
title="`Cox Table- ${explanatory}`",
rows=0,
columns=list(
list(
`name`="Explanatory",
`title`="Explanatory",
`type`="text"),
list(
`name`="Levels",
`title`="Levels",
`type`="text"),
list(
`name`="all",
`title`="all",
`type`="text"),
list(
`name`="HR_univariable",
`title`="HR (Univariable)",
`type`="text")),
clearWith=list(
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent")))
self$add(jmvcore::Html$new(
options=options,
name="tCoxtext2",
title="",
refs="finalfit",
clearWith=list(
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent",
"contexpl")))
self$add(jmvcore::Preformatted$new(
options=options,
name="cox_ph",
title="Proportional Hazards Assumption",
visible="(ph_cox)",
clearWith=list(
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent",
"contexpl")))
self$add(jmvcore::Image$new(
options=options,
name="plot8",
title="`Proportional Hazards Assumption - ${explanatory}`",
width=600,
height=450,
renderFun=".plot8",
visible="(ph_cox)",
requiresData=TRUE,
clearWith=list(
"ph_cox",
"endplot",
"byplot",
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent")))
self$add(jmvcore::Preformatted$new(
options=options,
name="survTableSummary",
title="`1, 3, 5-yr Survival Summary and Table - ${explanatory}`",
clearWith=list(
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent")))
self$add(jmvcore::Table$new(
options=options,
name="survTable",
title="`1, 3, 5 year Survival - ${explanatory}`",
rows=0,
columns=list(
list(
`name`="strata",
`title`="Levels",
`type`="text"),
list(
`name`="time",
`title`="time",
`type`="integer"),
list(
`name`="n.risk",
`title`="Number at Risk",
`type`="integer"),
list(
`name`="n.event",
`title`="Number of Events",
`type`="integer"),
list(
`name`="surv",
`title`="Survival",
`type`="number",
`format`="pc"),
list(
`name`="lower",
`title`="Lower",
`superTitle`="95% Confidence Interval",
`type`="number",
`format`="pc"),
list(
`name`="upper",
`title`="Upper",
`superTitle`="95% Confidence Interval",
`type`="number",
`format`="pc")),
clearWith=list(
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent")))
self$add(jmvcore::Preformatted$new(
options=options,
name="pairwiseSummary",
title="`Pairwise Comparison Summary and Table - ${explanatory}`",
clearWith=list(
"pw",
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent"),
visible="(pw)"))
self$add(jmvcore::Table$new(
options=options,
name="pairwiseTable",
title="`Pairwise Comparison Table - ${explanatory}`",
rows=0,
columns=list(
list(
`name`="rowname",
`title`="Levels",
`type`="text"),
list(
`name`="name",
`title`="Levels",
`type`="text"),
list(
`name`="value",
`title`="p-value",
`type`="number",
`format`="zto,pvalue")),
visible="(pw)",
clearWith=list(
"pw",
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent"),
refs=list(
"padjust")))
self$add(jmvcore::Image$new(
options=options,
name="plot",
title="`Survival Plot - ${explanatory}`",
width=600,
height=450,
renderFun=".plot",
visible="(sc)",
requiresData=TRUE,
clearWith=list(
"sc",
"endplot",
"byplot",
"ybegin_plot",
"yend_plot",
"ci95",
"risktable",
"censored",
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent",
"pplot")))
self$add(jmvcore::Image$new(
options=options,
name="plot2",
title="`Cumulative Events - ${explanatory}`",
width=600,
height=450,
renderFun=".plot2",
visible="(ce)",
requiresData=TRUE,
clearWith=list(
"ce",
"endplot",
"byplot",
"ybegin_plot",
"yend_plot",
"ci95",
"risktable",
"censored",
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent")))
self$add(jmvcore::Image$new(
options=options,
name="plot3",
title="`Cumulative Hazard - ${explanatory}`",
width=600,
height=450,
renderFun=".plot3",
visible="(ch)",
requiresData=TRUE,
clearWith=list(
"ch",
"endplot",
"byplot",
"ybegin_plot",
"yend_plot",
"ci95",
"risktable",
"censored",
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent")))
self$add(jmvcore::Image$new(
options=options,
name="plot6",
title="`KMunicate-Style Plot - ${explanatory}`",
width=600,
height=450,
renderFun=".plot6",
visible="(kmunicate)",
requiresData=TRUE,
clearWith=list(
"kmunicate",
"endplot",
"byplot",
"ybegin_plot",
"yend_plot",
"explanatory",
"outcome",
"outcomeLevel",
"overalltime",
"fudate",
"dxdate",
"tint",
"multievent"),
refs=list(
"KMunicate",
"KMunicate2")))
self$add(jmvcore::Output$new(
options=options,
name="calculatedtime",
title="Add Calculated Time to Data",
varTitle="`Calculated Time - from ${ dxdate } to { fudate }`",
varDescription="`Calculated Time from Given Dates - from ${ dxdate } to { fudate } in Survival Analysis`",
measureType="continuous",
clearWith=list(
"tint",
"dxdate",
"fudate",
"overalltime",
"calculatedtime")))
self$add(jmvcore::Output$new(
options=options,
name="outcomeredefined",
title="Add Redefined Outcome to Data",
varTitle="`Redefined Outcome - from ${ outcome } for { analysistype } survival analysis`",
varDescription="Redefined Outcome from Outcome based on Analysis Type in Survival Analysis",
clearWith=list(
"outcome",
"analysistype",
"multievent",
"explanatory",
"outcomeLevel")))}))
survivalBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"survivalBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "jsurvival",
name = "survival",
version = c(1,0,0),
options = options,
results = survivalResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'none')
}))
#' Survival Analysis
#'
#' Function for Generating Summaries for Survival Analysis.
#'
#' @examples
#' # example will be added
#'
#' @param data The data as a data frame.
#' @param elapsedtime The time elapsed from the start of the study to the
#' event or censoring.
#' @param tint If the time is in date format, select this option to calculate
#' the survival time. The time will be calculated as the difference between
#' the event date and the diagnosis date. If the follow-up date is available,
#' the time will be calculated as the difference between the event date and
#' the follow-up date.
#' @param dxdate The date of diagnosis. If the time is in date format, the
#' time will be calculated as the difference between the event date and the
#' diagnosis date.
#' @param fudate The date of follow-up. If the time is in date format, the
#' time will be calculated as the difference between the event date and the
#' follow-up date.
#' @param explanatory The explanatory variable that will be used to compare
#' the survival times of different groups.
#' @param outcome The outcome variable that will be used to compare the
#' survival times of different groups.
#' @param outcomeLevel The level of the outcome variable that will be used as
#' the event level.
#' @param dod .
#' @param dooc .
#' @param awd .
#' @param awod .
#' @param analysistype .
#' @param cutp .
#' @param timetypedata select the time type in data
#' @param timetypeoutput select the time type in output
#' @param uselandmark .
#' @param landmark .
#' @param pw .
#' @param padjustmethod .
#' @param ph_cox .
#' @param sc .
#' @param kmunicate .
#' @param ce .
#' @param ch .
#' @param endplot .
#' @param ybegin_plot .
#' @param yend_plot .
#' @param byplot .
#' @param multievent .
#' @param ci95 .
#' @param risktable .
#' @param censored .
#' @param pplot .
#' @param medianline If true, displays a line indicating the median survival
#' time on the survival plot.
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$subtitle} \tab \tab \tab \tab \tab a preformatted \cr
#' \code{results$todo} \tab \tab \tab \tab \tab a html \cr
#' \code{results$medianSummary} \tab \tab \tab \tab \tab a preformatted \cr
#' \code{results$medianTable} \tab \tab \tab \tab \tab a table \cr
#' \code{results$coxSummary} \tab \tab \tab \tab \tab a preformatted \cr
#' \code{results$coxTable} \tab \tab \tab \tab \tab a table \cr
#' \code{results$tCoxtext2} \tab \tab \tab \tab \tab a html \cr
#' \code{results$cox_ph} \tab \tab \tab \tab \tab a preformatted \cr
#' \code{results$plot8} \tab \tab \tab \tab \tab an image \cr
#' \code{results$survTableSummary} \tab \tab \tab \tab \tab a preformatted \cr
#' \code{results$survTable} \tab \tab \tab \tab \tab a table \cr
#' \code{results$pairwiseSummary} \tab \tab \tab \tab \tab a preformatted \cr
#' \code{results$pairwiseTable} \tab \tab \tab \tab \tab a table \cr
#' \code{results$plot} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot2} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot3} \tab \tab \tab \tab \tab an image \cr
#' \code{results$plot6} \tab \tab \tab \tab \tab an image \cr
#' \code{results$calculatedtime} \tab \tab \tab \tab \tab an output \cr
#' \code{results$outcomeredefined} \tab \tab \tab \tab \tab an output \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$medianTable)}
#'
#' @export
survival <- function(
data,
elapsedtime,
tint = FALSE,
dxdate,
fudate,
explanatory,
outcome,
outcomeLevel,
dod,
dooc,
awd,
awod,
analysistype = "overall",
cutp = "12, 36, 60",
timetypedata = "ymd",
timetypeoutput = "months",
uselandmark = FALSE,
landmark = 3,
pw = FALSE,
padjustmethod = "holm",
ph_cox = FALSE,
sc = FALSE,
kmunicate = FALSE,
ce = FALSE,
ch = FALSE,
endplot = 60,
ybegin_plot = 0,
yend_plot = 1,
byplot = 12,
multievent = FALSE,
ci95 = FALSE,
risktable = FALSE,
censored = FALSE,
pplot = TRUE,
medianline = "none") {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("survival requires jmvcore to be installed (restart may be required)")
if ( ! missing(elapsedtime)) elapsedtime <- jmvcore::resolveQuo(jmvcore::enquo(elapsedtime))
if ( ! missing(dxdate)) dxdate <- jmvcore::resolveQuo(jmvcore::enquo(dxdate))
if ( ! missing(fudate)) fudate <- jmvcore::resolveQuo(jmvcore::enquo(fudate))
if ( ! missing(explanatory)) explanatory <- jmvcore::resolveQuo(jmvcore::enquo(explanatory))
if ( ! missing(outcome)) outcome <- jmvcore::resolveQuo(jmvcore::enquo(outcome))
if (missing(data))
data <- jmvcore::marshalData(
parent.frame(),
`if`( ! missing(elapsedtime), elapsedtime, NULL),
`if`( ! missing(dxdate), dxdate, NULL),
`if`( ! missing(fudate), fudate, NULL),
`if`( ! missing(explanatory), explanatory, NULL),
`if`( ! missing(outcome), outcome, NULL))
for (v in explanatory) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
options <- survivalOptions$new(
elapsedtime = elapsedtime,
tint = tint,
dxdate = dxdate,
fudate = fudate,
explanatory = explanatory,
outcome = outcome,
outcomeLevel = outcomeLevel,
dod = dod,
dooc = dooc,
awd = awd,
awod = awod,
analysistype = analysistype,
cutp = cutp,
timetypedata = timetypedata,
timetypeoutput = timetypeoutput,
uselandmark = uselandmark,
landmark = landmark,
pw = pw,
padjustmethod = padjustmethod,
ph_cox = ph_cox,
sc = sc,
kmunicate = kmunicate,
ce = ce,
ch = ch,
endplot = endplot,
ybegin_plot = ybegin_plot,
yend_plot = yend_plot,
byplot = byplot,
multievent = multievent,
ci95 = ci95,
risktable = risktable,
censored = censored,
pplot = pplot,
medianline = medianline)
analysis <- survivalClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
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