SHELF (version 1.12.0)

survivalExtrapolatePlot: Plot survival data and elicited extrapolated intervals

Description

Show Kaplan-Meier plot of available data, and credible interval for extrapolated survivor function value S(T)

Usage

survivalExtrapolatePlot(
  survDf,
  myfit1,
  myfit2 = NULL,
  fqDist1 = "best",
  fqDist2 = NULL,
  tTruncate = max(survDf$time),
  tTarget,
  alpha = 0.95,
  useWeights = FALSE,
  groups = levels(survDf$treatment),
  xl = "Time (t)",
  fontsize = 12,
  breakTime = NULL,
  showPlot = TRUE,
  returnPlot = FALSE
)

Value

a ggplot object, if returnPlot is TRUE

Arguments

survDf

data frame with individual patient data. Needs three columns with names "time", "event" and "treatment" (in that order). For weighted observations (e.g. using propensity scores), include a fourth column "weights". Values in the "event" column should be 0 for a censored observation, and 1 otherwise. The "treatment" column should be included even if there is only one treatment group, and defined as a factor variable.

myfit1

object of class elicitation, obtained from fitdist function with elicited judgements for the first treatment group.

myfit2

object of class elicitation, obtained from fitdist function with elicited judgements for the second treatment group, if there is on.

fqDist1

fitted distribution family for first treatment group. Options are "normal", "t", "skewnormal", "gamma", "lognormal", "logt","beta", "mirrorgamma", "mirrorlognormal", "mirrorlogt" "hist" (for a histogram fit), and "best" (for best fitting)

fqDist2

fitted distribution family for second treatment group if there is one. Options are "normal", "t", "skewnormal", "gamma", "lognormal", "logt","beta", "mirrorgamma", "mirrorlognormal", "mirrorlogt" "hist" (for a histogram fit), and "best" (for best fitting)

tTruncate

Optional argument to censor all observations at this time point.

tTarget

Target time for extrapolation: judgements are elicited at S(t = tTarget)

alpha

Size of probability interval to plot (100*alpha% interval).

useWeights

set to TRUE if survDf includes column of weights, as described in specification of survDf. This column is passed on to survival::survfit() as the case weights.

groups

Vector of strings for the group labels. Will be extracted from factor levels of treatment column in survDf.

xl

x-axis label in plot

fontsize

font size in plot

breakTime

Optional argument to specify tick mark spacing on x-axis

showPlot

set to TRUE to display the plot

returnPlot

set to TRUE to return the plot as a ggplot object.

Examples

if (FALSE) {
sdf <- survival::veteran[, c("time", "status", "trt")]
colnames(sdf) <- c("time", "event", "treatment")
sdf$treatment <- factor(sdf$treatment, labels = c("standard", "test"))

sdf <- survival::veteran[, c("time", "status", "trt")]
colnames(sdf) <- c("time", "event", "treatment")
sdf$treatment <- factor(sdf$treatment, labels = c("standard", "test"))
groupStandardElicitation <- fitdist(vals = c(0.15, 0.2, 0.25),
                                    probs = c(0.25, 0.5, 0.75),
                                    lower = 0,
                                    upper = 1)

groupTestElicitation <- fitdist(vals = c(0.1, 0.15, 0.2),
                                probs = c(0.25, 0.5, 0.75),
                                lower = 0,
                                upper = 1)

survivalExtrapolatePlot(sdf,
                        myfit1 = groupStandardElicitation,
                        myfit2 = groupTestElicitation,
                        fqDist1 = "beta",
                        fqDist2 = "beta",
                        tTruncate = 150,
                        tTarget=200,
                        alpha = 0.95)
}