plot.dying.year.annotate: Figure - Percent Change in the Annual Probability of Dying of...

In JPSurv: Joinpoint Model for Relative and Cause-Specific Survival

Figure - Percent Change in the Annual Probability of Dying of Cancer by Diagnosis Year

Description

A function that returns a plot (or a list including the Relative Change in Hazard trend measures and the plot) for percent change in the annual probability of dying of cancer by diagnosis year using ggplot. The annotation feature is available for nJP<=3 and the number of multiple intervals selected <=3.

Usage

Plot.dying.year.annotate(plotdata, fit, nJP, yearvar, 
                         obsintvar = "Relative_Survival_Interval", 
                         predintvar = "Predicted_ProbDeath_Int", 
                         interval = "Interval", 
                         annotation = 0, topanno = 1, trend = 0,
                         title = NULL)

Arguments

plotdata	The graph data returned by function download.data with downloadtype="graph".
fit	The joinpoint object containing the model output.
nJP	The number of joinpoints in the model.
yearvar	The variable name for year of diagnosis used in argument 'year' of the function joinpoint.
obsintvar	The variable name for observed interval survival. The default is "Relative_Survival_Interval" for relative survival data. For cause-specific data, it needs to be changed accordingly.
predintvar	The variable name for predicted interval survival. The default is "Predicted_ProbDeath_Int".
interval	The variable name for year since diagnosis. The default is 'Interval'.
annotation	The indicator for the annotation feature. The default is 0 (no annotation on the plot).Two plots with and without annotations will be returned in a list when annotation=1.
topanno	The indicator for showing the top curve annotation. The default is 1 (annotation for the top curve).
trend	The indicator for returning the Relative Change in Hazard trend measures . The default is 0 (no trend tables returned).
title	The title used for the plot. If title=NULL, the default title "Annual Probability of Dying of Cancer by Diagnosis Year" will be used.

Value

The returned object is a list and depends on the values for trend and annotation. The list will contain some or all of the names plot_anno, plot_no_anno, and trends, where plot_anno is an object of class ggplot for a plot with annotations, plot_no_anno is an object of class ggplot for a plot without annotations, and trends is a list of data frames for the change in hazard trend measures with columns start.year, end.year, estimate, std.error, lowCI, upCI, and interval.

Author(s)

Fanni Zhang <[e-mail]>

See Also

download.data, Plot.surv.year.annotate, Plot.surv.int.multiyears,aapc.

Examples

data("breast.example", package="JPSurv")
data("fit1", package="JPSurv")

yearvar<-"Year_of_diagnosis_1975"
obsintvar<-"Relative_Survival_Interval"
predintvar<-"Predicted_ProbDeath_Int"
interval<-"Interval"
nJP<-3
data.graph<-download.data(breast.example,fit1,nJP,yearvar,"graph",
                          subsetStr1,interval,int.select=c(1,3,5))
out.anno<-Plot.dying.year.annotate(data.graph,fit1,nJP,yearvar,obsintvar,
                     predintvar,interval,annotation=1,topanno=1,trend=1)
out<-Plot.dying.year.annotate(data.graph,fit1,nJP,yearvar,obsintvar,
                     predintvar,interval,annotation=0,topanno=0,trend=1)
trend.rch<-out.anno$trends
plot.rch.anno<-out.anno$plot_anno
plot.rch<-out$plot_no_anno

JPSurv documentation built on June 8, 2025, 12:11 p.m.