R/surv.h.R
In jonathon-love/deathwatch: Survival Analysis
Defines functions
surv
Documented in
surv
# This file is automatically generated, you probably don't want to edit this
survOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"survOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
elapsed = NULL,
event = NULL,
eventLevel = NULL,
groups = NULL,
tests = NULL,
testspw = FALSE,
sc = TRUE,
chf = FALSE,
ci = FALSE,
cens = FALSE,
risk = FALSE,
median = FALSE,
logscale = FALSE,
units = "", ...) {
super$initialize(
package="deathwatch",
name="surv",
requiresData=TRUE,
...)
private$..elapsed <- jmvcore::OptionVariable$new(
"elapsed",
elapsed,
suggested=list(
"continuous"),
permitted=list(
"numeric"))
private$..event <- jmvcore::OptionVariable$new(
"event",
event,
suggested=list(
"continuous",
"nominal"),
permitted=list(
"factor",
"numeric"))
private$..eventLevel <- jmvcore::OptionLevel$new(
"eventLevel",
eventLevel,
variable="(event)")
private$..groups <- jmvcore::OptionVariable$new(
"groups",
groups,
suggested=list(
"nominal"),
permitted=list(
"factor"))
private$..tests <- jmvcore::OptionNMXList$new(
"tests",
tests,
options=list(
"logrank",
"gehan",
"taroneware",
"petopeto"))
private$..testspw <- jmvcore::OptionBool$new(
"testspw",
testspw,
default=FALSE)
private$..sc <- jmvcore::OptionBool$new(
"sc",
sc,
default=TRUE)
private$..chf <- jmvcore::OptionBool$new(
"chf",
chf,
default=FALSE)
private$..ci <- jmvcore::OptionBool$new(
"ci",
ci,
default=FALSE)
private$..cens <- jmvcore::OptionBool$new(
"cens",
cens,
default=FALSE)
private$..risk <- jmvcore::OptionBool$new(
"risk",
risk,
default=FALSE)
private$..median <- jmvcore::OptionBool$new(
"median",
median,
default=FALSE)
private$..logscale <- jmvcore::OptionBool$new(
"logscale",
logscale,
default=FALSE)
private$..units <- jmvcore::OptionString$new(
"units",
units,
default="")
self$.addOption(private$..elapsed)
self$.addOption(private$..event)
self$.addOption(private$..eventLevel)
self$.addOption(private$..groups)
self$.addOption(private$..tests)
self$.addOption(private$..testspw)
self$.addOption(private$..sc)
self$.addOption(private$..chf)
self$.addOption(private$..ci)
self$.addOption(private$..cens)
self$.addOption(private$..risk)
self$.addOption(private$..median)
self$.addOption(private$..logscale)
self$.addOption(private$..units)
}),
active = list(
elapsed = function() private$..elapsed$value,
event = function() private$..event$value,
eventLevel = function() private$..eventLevel$value,
groups = function() private$..groups$value,
tests = function() private$..tests$value,
testspw = function() private$..testspw$value,
sc = function() private$..sc$value,
chf = function() private$..chf$value,
ci = function() private$..ci$value,
cens = function() private$..cens$value,
risk = function() private$..risk$value,
median = function() private$..median$value,
logscale = function() private$..logscale$value,
units = function() private$..units$value),
private = list(
..elapsed = NA,
..event = NA,
..eventLevel = NA,
..groups = NA,
..tests = NA,
..testspw = NA,
..sc = NA,
..chf = NA,
..ci = NA,
..cens = NA,
..risk = NA,
..median = NA,
..logscale = NA,
..units = NA)
)
survResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"survResults",
inherit = jmvcore::Group,
active = list(
summary = function() private$.items[["summary"]],
medianestimates = function() private$.items[["medianestimates"]],
tests = function() private$.items[["tests"]],
testspw = function() private$.items[["testspw"]],
sc = function() private$.items[["sc"]],
chf = function() private$.items[["chf"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Survival Analysis")
self$add(jmvcore::Table$new(
options=options,
name="summary",
title="Events Summary",
clearWith=list(
"event",
"eventLevel",
"elapsed",
"groups"),
columns=list(
list(
`name`="group",
`title`="",
`type`="text",
`content`="($key)",
`visible`="(groups)"),
list(
`name`="n",
`title`="N",
`type`="integer"),
list(
`name`="censored",
`title`="Censored",
`type`="integer"),
list(
`name`="obs",
`title`="Observed Events",
`type`="integer"),
list(
`name`="exp",
`title`="Expected Events",
`type`="number"))))
self$add(jmvcore::Table$new(
options=options,
name="medianestimates",
title="Median Estimates",
clearWith=list(
"times",
"status"),
columns=list(
list(
`name`="group",
`title`="",
`type`="text",
`content`="($key)",
`visible`="(groups)"),
list(
`name`="median",
`title`="Median",
`type`="number"),
list(
`name`="cilb",
`title`="Lower",
`type`="number"),
list(
`name`="ciub",
`title`="Upper",
`type`="number"))))
self$add(jmvcore::Table$new(
options=options,
name="tests",
title="Analysis of the differences",
visible="(tests)",
clearWith=list(
"event",
"eventLevel",
"elapsed",
"groups"),
columns=list(
list(
`name`="stat[logrank]",
`title`="Test",
`type`="text",
`refs`=list(
"survival1",
"survival2"),
`content`="Log-rank",
`visible`="(tests:logrank)"),
list(
`name`="stat[gehan]",
`title`="Test",
`type`="text",
`refs`=list(
"coin1",
"coin2"),
`content`="Gehan",
`visible`="(tests:gehan)"),
list(
`name`="stat[taroneware]",
`title`="Test",
`type`="text",
`refs`=list(
"coin1",
"coin2"),
`content`="Tarone-Ware",
`visible`="(tests:taroneware)"),
list(
`name`="stat[petopeto]",
`title`="Test",
`type`="text",
`refs`=list(
"survival1",
"survival2"),
`content`="Peto-Peto",
`visible`="(tests:petopeto)"),
list(
`name`="chisqr[logrank]",
`title`="\u03C7\u00B2",
`type`="number",
`visible`="(tests:logrank)"),
list(
`name`="chisqr[gehan]",
`title`="\u03C7\u00B2",
`type`="number",
`visible`="(tests:gehan)"),
list(
`name`="chisqr[taroneware]",
`title`="\u03C7\u00B2",
`type`="number",
`visible`="(tests:taroneware)"),
list(
`name`="chisqr[petopeto]",
`title`="\u03C7\u00B2",
`type`="number",
`visible`="(tests:petopeto)"),
list(
`name`="df[logrank]",
`title`="df",
`type`="integer",
`visible`="(tests:logrank)"),
list(
`name`="df[gehan]",
`title`="df",
`type`="integer",
`visible`="(tests:gehan)"),
list(
`name`="df[taroneware]",
`title`="df",
`type`="integer",
`visible`="(tests:taroneware)"),
list(
`name`="df[petopeto]",
`title`="df",
`type`="integer",
`visible`="(tests:petopeto)"),
list(
`name`="pvalue[logrank]",
`title`="p",
`type`="number",
`format`="zto,pvalue",
`visible`="(tests:logrank)"),
list(
`name`="pvalue[gehan]",
`title`="p",
`type`="number",
`format`="zto,pvalue",
`visible`="(tests:gehan)"),
list(
`name`="pvalue[taroneware]",
`title`="p",
`type`="number",
`format`="zto,pvalue",
`visible`="(tests:taroneware)"),
list(
`name`="pvalue[petopeto]",
`title`="p",
`type`="number",
`format`="zto,pvalue",
`visible`="(tests:petopeto)"))))
self$add(jmvcore::Table$new(
options=options,
name="testspw",
title="Pairwise Comparisons",
visible="(testspw)",
refs=list(
"multcomp"),
clearWith=list(
"event",
"eventLevel",
"elapsed",
"groups"),
columns=list(
list(
`name`="v1",
`title`="",
`type`="text",
`content`="($key[1])"),
list(
`name`="v2",
`title`="",
`type`="text",
`content`="($key[2])"),
list(
`name`="statpw[logrank]",
`title`="Test",
`type`="text",
`content`="Log-rank",
`visible`="(tests:logrank)"),
list(
`name`="statpw[gehan]",
`title`="Test",
`type`="text",
`content`="Gehan",
`visible`="(tests:gehan)"),
list(
`name`="statpw[taroneware]",
`title`="Test",
`type`="text",
`content`="Tarone-Ware",
`visible`="(tests:taroneware)"),
list(
`name`="statpw[petopeto]",
`title`="Test",
`type`="text",
`content`="Peto-Peto",
`visible`="(tests:petopeto)"),
list(
`name`="nupw[logrank]",
`title`="\u03BD",
`visible`="(tests:logrank)"),
list(
`name`="nupw[gehan]",
`title`="\u03BD",
`visible`="(tests:gehan)"),
list(
`name`="nupw[taroneware]",
`title`="\u03BD",
`visible`="(tests:taroneware)"),
list(
`name`="nupw[petopeto]",
`title`="\u03BD",
`visible`="(tests:petopeto)"),
list(
`name`="nusepw[logrank]",
`title`="SE",
`visible`="(tests:logrank)"),
list(
`name`="nusepw[gehan]",
`title`="SE",
`visible`="(tests:gehan)"),
list(
`name`="nusepw[taroneware]",
`title`="SE",
`visible`="(tests:taroneware)"),
list(
`name`="nusepw[petopeto]",
`title`="SE",
`visible`="(tests:petopeto)"),
list(
`name`="zpw[logrank]",
`title`="z",
`format`="zto,p",
`visible`="(tests:logrank)"),
list(
`name`="zpw[gehan]",
`title`="z",
`format`="zto,p",
`visible`="(tests:gehan)"),
list(
`name`="zpw[taroneware]",
`title`="z",
`visible`="(tests:taroneware)"),
list(
`name`="zpw[petopeto]",
`title`="z",
`visible`="(tests:petopeto)"),
list(
`name`="ppw[logrank]",
`title`="p",
`type`="number",
`format`="zto,pvalue",
`visible`="(tests:logrank)"),
list(
`name`="ppw[gehan]",
`title`="p",
`type`="number",
`format`="zto,pvalue",
`visible`="(tests:gehan)"),
list(
`name`="ppw[taroneware]",
`title`="p",
`type`="number",
`format`="zto,pvalue",
`visible`="(tests:taroneware)"),
list(
`name`="ppw[petopeto]",
`title`="p",
`type`="number",
`format`="zto,pvalue",
`visible`="(tests:petopeto)"))))
self$add(jmvcore::Image$new(
options=options,
name="sc",
title="Survival Curve",
visible="(sc)",
width=600,
height=400,
renderFun=".plot",
clearWith=list(
"event",
"eventLevel",
"elapsed",
"groups",
"cens",
"ci",
"units",
"risk",
"median")))
self$add(jmvcore::Image$new(
options=options,
name="chf",
title="Cumulative Hazard Function",
visible="(chf)",
width=600,
height=400,
renderFun=".plot",
clearWith=list(
"event",
"eventLevel",
"elapsed",
"groups",
"units",
"logscale")))}))
survBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"survBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "deathwatch",
name = "surv",
version = c(1,0,0),
options = options,
results = survResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'auto')
}))
#' Survival Analysis
#'
#'
#' @param data .
#' @param elapsed .
#' @param event .
#' @param eventLevel .
#' @param groups .
#' @param tests .
#' @param testspw .
#' @param sc .
#' @param chf .
#' @param ci .
#' @param cens .
#' @param risk .
#' @param median .
#' @param logscale .
#' @param units .
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$summary} \tab \tab \tab \tab \tab a table \cr
#' \code{results$medianestimates} \tab \tab \tab \tab \tab a table \cr
#' \code{results$tests} \tab \tab \tab \tab \tab a table \cr
#' \code{results$testspw} \tab \tab \tab \tab \tab a table \cr
#' \code{results$sc} \tab \tab \tab \tab \tab an image \cr
#' \code{results$chf} \tab \tab \tab \tab \tab an image \cr
#' }
#'
#' Tables can be converted to data frames with \code{asDF} or \code{\link{as.data.frame}}. For example:
#'
#' \code{results$summary$asDF}
#'
#' \code{as.data.frame(results$summary)}
#'
#' @export
surv <- function(
data,
elapsed,
event,
eventLevel,
groups,
tests,
testspw = FALSE,
sc = TRUE,
chf = FALSE,
ci = FALSE,
cens = FALSE,
risk = FALSE,
median = FALSE,
logscale = FALSE,
units = "") {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("surv requires jmvcore to be installed (restart may be required)")
if ( ! missing(elapsed)) elapsed <- jmvcore::resolveQuo(jmvcore::enquo(elapsed))
if ( ! missing(event)) event <- jmvcore::resolveQuo(jmvcore::enquo(event))
if ( ! missing(groups)) groups <- jmvcore::resolveQuo(jmvcore::enquo(groups))
if (missing(data))
data <- jmvcore::marshalData(
parent.frame(),
`if`( ! missing(elapsed), elapsed, NULL),
`if`( ! missing(event), event, NULL),
`if`( ! missing(groups), groups, NULL))
for (v in groups) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
options <- survOptions$new(
elapsed = elapsed,
event = event,
eventLevel = eventLevel,
groups = groups,
tests = tests,
testspw = testspw,
sc = sc,
chf = chf,
ci = ci,
cens = cens,
risk = risk,
median = median,
logscale = logscale,
units = units)
analysis <- survClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
jonathon-love/deathwatch documentation built on Feb. 17, 2025, 1:56 p.m.
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Defines functions surv
Documented in surv
# This file is automatically generated, you probably don't want to edit this
survOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"survOptions",
inherit = jmvcore::Options,
public = list(
initialize = function(
elapsed = NULL,
event = NULL,
eventLevel = NULL,
groups = NULL,
tests = NULL,
testspw = FALSE,
sc = TRUE,
chf = FALSE,
ci = FALSE,
cens = FALSE,
risk = FALSE,
median = FALSE,
logscale = FALSE,
units = "", ...) {
super$initialize(
package="deathwatch",
name="surv",
requiresData=TRUE,
...)
private$..elapsed <- jmvcore::OptionVariable$new(
"elapsed",
elapsed,
suggested=list(
"continuous"),
permitted=list(
"numeric"))
private$..event <- jmvcore::OptionVariable$new(
"event",
event,
suggested=list(
"continuous",
"nominal"),
permitted=list(
"factor",
"numeric"))
private$..eventLevel <- jmvcore::OptionLevel$new(
"eventLevel",
eventLevel,
variable="(event)")
private$..groups <- jmvcore::OptionVariable$new(
"groups",
groups,
suggested=list(
"nominal"),
permitted=list(
"factor"))
private$..tests <- jmvcore::OptionNMXList$new(
"tests",
tests,
options=list(
"logrank",
"gehan",
"taroneware",
"petopeto"))
private$..testspw <- jmvcore::OptionBool$new(
"testspw",
testspw,
default=FALSE)
private$..sc <- jmvcore::OptionBool$new(
"sc",
sc,
default=TRUE)
private$..chf <- jmvcore::OptionBool$new(
"chf",
chf,
default=FALSE)
private$..ci <- jmvcore::OptionBool$new(
"ci",
ci,
default=FALSE)
private$..cens <- jmvcore::OptionBool$new(
"cens",
cens,
default=FALSE)
private$..risk <- jmvcore::OptionBool$new(
"risk",
risk,
default=FALSE)
private$..median <- jmvcore::OptionBool$new(
"median",
median,
default=FALSE)
private$..logscale <- jmvcore::OptionBool$new(
"logscale",
logscale,
default=FALSE)
private$..units <- jmvcore::OptionString$new(
"units",
units,
default="")
self$.addOption(private$..elapsed)
self$.addOption(private$..event)
self$.addOption(private$..eventLevel)
self$.addOption(private$..groups)
self$.addOption(private$..tests)
self$.addOption(private$..testspw)
self$.addOption(private$..sc)
self$.addOption(private$..chf)
self$.addOption(private$..ci)
self$.addOption(private$..cens)
self$.addOption(private$..risk)
self$.addOption(private$..median)
self$.addOption(private$..logscale)
self$.addOption(private$..units)
}),
active = list(
elapsed = function() private$..elapsed$value,
event = function() private$..event$value,
eventLevel = function() private$..eventLevel$value,
groups = function() private$..groups$value,
tests = function() private$..tests$value,
testspw = function() private$..testspw$value,
sc = function() private$..sc$value,
chf = function() private$..chf$value,
ci = function() private$..ci$value,
cens = function() private$..cens$value,
risk = function() private$..risk$value,
median = function() private$..median$value,
logscale = function() private$..logscale$value,
units = function() private$..units$value),
private = list(
..elapsed = NA,
..event = NA,
..eventLevel = NA,
..groups = NA,
..tests = NA,
..testspw = NA,
..sc = NA,
..chf = NA,
..ci = NA,
..cens = NA,
..risk = NA,
..median = NA,
..logscale = NA,
..units = NA)
)
survResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"survResults",
inherit = jmvcore::Group,
active = list(
summary = function() private$.items[["summary"]],
medianestimates = function() private$.items[["medianestimates"]],
tests = function() private$.items[["tests"]],
testspw = function() private$.items[["testspw"]],
sc = function() private$.items[["sc"]],
chf = function() private$.items[["chf"]]),
private = list(),
public=list(
initialize=function(options) {
super$initialize(
options=options,
name="",
title="Survival Analysis")
self$add(jmvcore::Table$new(
options=options,
name="summary",
title="Events Summary",
clearWith=list(
"event",
"eventLevel",
"elapsed",
"groups"),
columns=list(
list(
`name`="group",
`title`="",
`type`="text",
`content`="($key)",
`visible`="(groups)"),
list(
`name`="n",
`title`="N",
`type`="integer"),
list(
`name`="censored",
`title`="Censored",
`type`="integer"),
list(
`name`="obs",
`title`="Observed Events",
`type`="integer"),
list(
`name`="exp",
`title`="Expected Events",
`type`="number"))))
self$add(jmvcore::Table$new(
options=options,
name="medianestimates",
title="Median Estimates",
clearWith=list(
"times",
"status"),
columns=list(
list(
`name`="group",
`title`="",
`type`="text",
`content`="($key)",
`visible`="(groups)"),
list(
`name`="median",
`title`="Median",
`type`="number"),
list(
`name`="cilb",
`title`="Lower",
`type`="number"),
list(
`name`="ciub",
`title`="Upper",
`type`="number"))))
self$add(jmvcore::Table$new(
options=options,
name="tests",
title="Analysis of the differences",
visible="(tests)",
clearWith=list(
"event",
"eventLevel",
"elapsed",
"groups"),
columns=list(
list(
`name`="stat[logrank]",
`title`="Test",
`type`="text",
`refs`=list(
"survival1",
"survival2"),
`content`="Log-rank",
`visible`="(tests:logrank)"),
list(
`name`="stat[gehan]",
`title`="Test",
`type`="text",
`refs`=list(
"coin1",
"coin2"),
`content`="Gehan",
`visible`="(tests:gehan)"),
list(
`name`="stat[taroneware]",
`title`="Test",
`type`="text",
`refs`=list(
"coin1",
"coin2"),
`content`="Tarone-Ware",
`visible`="(tests:taroneware)"),
list(
`name`="stat[petopeto]",
`title`="Test",
`type`="text",
`refs`=list(
"survival1",
"survival2"),
`content`="Peto-Peto",
`visible`="(tests:petopeto)"),
list(
`name`="chisqr[logrank]",
`title`="\u03C7\u00B2",
`type`="number",
`visible`="(tests:logrank)"),
list(
`name`="chisqr[gehan]",
`title`="\u03C7\u00B2",
`type`="number",
`visible`="(tests:gehan)"),
list(
`name`="chisqr[taroneware]",
`title`="\u03C7\u00B2",
`type`="number",
`visible`="(tests:taroneware)"),
list(
`name`="chisqr[petopeto]",
`title`="\u03C7\u00B2",
`type`="number",
`visible`="(tests:petopeto)"),
list(
`name`="df[logrank]",
`title`="df",
`type`="integer",
`visible`="(tests:logrank)"),
list(
`name`="df[gehan]",
`title`="df",
`type`="integer",
`visible`="(tests:gehan)"),
list(
`name`="df[taroneware]",
`title`="df",
`type`="integer",
`visible`="(tests:taroneware)"),
list(
`name`="df[petopeto]",
`title`="df",
`type`="integer",
`visible`="(tests:petopeto)"),
list(
`name`="pvalue[logrank]",
`title`="p",
`type`="number",
`format`="zto,pvalue",
`visible`="(tests:logrank)"),
list(
`name`="pvalue[gehan]",
`title`="p",
`type`="number",
`format`="zto,pvalue",
`visible`="(tests:gehan)"),
list(
`name`="pvalue[taroneware]",
`title`="p",
`type`="number",
`format`="zto,pvalue",
`visible`="(tests:taroneware)"),
list(
`name`="pvalue[petopeto]",
`title`="p",
`type`="number",
`format`="zto,pvalue",
`visible`="(tests:petopeto)"))))
self$add(jmvcore::Table$new(
options=options,
name="testspw",
title="Pairwise Comparisons",
visible="(testspw)",
refs=list(
"multcomp"),
clearWith=list(
"event",
"eventLevel",
"elapsed",
"groups"),
columns=list(
list(
`name`="v1",
`title`="",
`type`="text",
`content`="($key[1])"),
list(
`name`="v2",
`title`="",
`type`="text",
`content`="($key[2])"),
list(
`name`="statpw[logrank]",
`title`="Test",
`type`="text",
`content`="Log-rank",
`visible`="(tests:logrank)"),
list(
`name`="statpw[gehan]",
`title`="Test",
`type`="text",
`content`="Gehan",
`visible`="(tests:gehan)"),
list(
`name`="statpw[taroneware]",
`title`="Test",
`type`="text",
`content`="Tarone-Ware",
`visible`="(tests:taroneware)"),
list(
`name`="statpw[petopeto]",
`title`="Test",
`type`="text",
`content`="Peto-Peto",
`visible`="(tests:petopeto)"),
list(
`name`="nupw[logrank]",
`title`="\u03BD",
`visible`="(tests:logrank)"),
list(
`name`="nupw[gehan]",
`title`="\u03BD",
`visible`="(tests:gehan)"),
list(
`name`="nupw[taroneware]",
`title`="\u03BD",
`visible`="(tests:taroneware)"),
list(
`name`="nupw[petopeto]",
`title`="\u03BD",
`visible`="(tests:petopeto)"),
list(
`name`="nusepw[logrank]",
`title`="SE",
`visible`="(tests:logrank)"),
list(
`name`="nusepw[gehan]",
`title`="SE",
`visible`="(tests:gehan)"),
list(
`name`="nusepw[taroneware]",
`title`="SE",
`visible`="(tests:taroneware)"),
list(
`name`="nusepw[petopeto]",
`title`="SE",
`visible`="(tests:petopeto)"),
list(
`name`="zpw[logrank]",
`title`="z",
`format`="zto,p",
`visible`="(tests:logrank)"),
list(
`name`="zpw[gehan]",
`title`="z",
`format`="zto,p",
`visible`="(tests:gehan)"),
list(
`name`="zpw[taroneware]",
`title`="z",
`visible`="(tests:taroneware)"),
list(
`name`="zpw[petopeto]",
`title`="z",
`visible`="(tests:petopeto)"),
list(
`name`="ppw[logrank]",
`title`="p",
`type`="number",
`format`="zto,pvalue",
`visible`="(tests:logrank)"),
list(
`name`="ppw[gehan]",
`title`="p",
`type`="number",
`format`="zto,pvalue",
`visible`="(tests:gehan)"),
list(
`name`="ppw[taroneware]",
`title`="p",
`type`="number",
`format`="zto,pvalue",
`visible`="(tests:taroneware)"),
list(
`name`="ppw[petopeto]",
`title`="p",
`type`="number",
`format`="zto,pvalue",
`visible`="(tests:petopeto)"))))
self$add(jmvcore::Image$new(
options=options,
name="sc",
title="Survival Curve",
visible="(sc)",
width=600,
height=400,
renderFun=".plot",
clearWith=list(
"event",
"eventLevel",
"elapsed",
"groups",
"cens",
"ci",
"units",
"risk",
"median")))
self$add(jmvcore::Image$new(
options=options,
name="chf",
title="Cumulative Hazard Function",
visible="(chf)",
width=600,
height=400,
renderFun=".plot",
clearWith=list(
"event",
"eventLevel",
"elapsed",
"groups",
"units",
"logscale")))}))
survBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
"survBase",
inherit = jmvcore::Analysis,
public = list(
initialize = function(options, data=NULL, datasetId="", analysisId="", revision=0) {
super$initialize(
package = "deathwatch",
name = "surv",
version = c(1,0,0),
options = options,
results = survResults$new(options=options),
data = data,
datasetId = datasetId,
analysisId = analysisId,
revision = revision,
pause = NULL,
completeWhenFilled = FALSE,
requiresMissings = FALSE,
weightsSupport = 'auto')
}))
#' Survival Analysis
#'
#'
#' @param data .
#' @param elapsed .
#' @param event .
#' @param eventLevel .
#' @param groups .
#' @param tests .
#' @param testspw .
#' @param sc .
#' @param chf .
#' @param ci .
#' @param cens .
#' @param risk .
#' @param median .
#' @param logscale .
#' @param units .
#' @return A results object containing:
#' \tabular{llllll}{
#' \code{results$summary} \tab \tab \tab \tab \tab a table \cr
#' \code{results$medianestimates} \tab \tab \tab \tab \tab a table \cr
#' \code{results$tests} \tab \tab \tab \tab \tab a table \cr
#' \code{results$testspw} \tab \tab \tab \tab \tab a table \cr
#' \code{results$sc} \tab \tab \tab \tab \tab an image \cr
#' \code{results$chf} \tab \tab \tab \tab \tab an image \cr
#' }
#'
#' Tables can be converted to data frames with \code{asDF} or \code{\link{as.data.frame}}. For example:
#'
#' \code{results$summary$asDF}
#'
#' \code{as.data.frame(results$summary)}
#'
#' @export
surv <- function(
data,
elapsed,
event,
eventLevel,
groups,
tests,
testspw = FALSE,
sc = TRUE,
chf = FALSE,
ci = FALSE,
cens = FALSE,
risk = FALSE,
median = FALSE,
logscale = FALSE,
units = "") {
if ( ! requireNamespace("jmvcore", quietly=TRUE))
stop("surv requires jmvcore to be installed (restart may be required)")
if ( ! missing(elapsed)) elapsed <- jmvcore::resolveQuo(jmvcore::enquo(elapsed))
if ( ! missing(event)) event <- jmvcore::resolveQuo(jmvcore::enquo(event))
if ( ! missing(groups)) groups <- jmvcore::resolveQuo(jmvcore::enquo(groups))
if (missing(data))
data <- jmvcore::marshalData(
parent.frame(),
`if`( ! missing(elapsed), elapsed, NULL),
`if`( ! missing(event), event, NULL),
`if`( ! missing(groups), groups, NULL))
for (v in groups) if (v %in% names(data)) data[[v]] <- as.factor(data[[v]])
options <- survOptions$new(
elapsed = elapsed,
event = event,
eventLevel = eventLevel,
groups = groups,
tests = tests,
testspw = testspw,
sc = sc,
chf = chf,
ci = ci,
cens = cens,
risk = risk,
median = median,
logscale = logscale,
units = units)
analysis <- survClass$new(
options = options,
data = data)
analysis$run()
analysis$results
}
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