kaplan.plot | R Documentation |
Kaplan-Meier plots of (repeated) time-to-event data. Includes VPCs.
kaplan.plot( x = "TIME", y = "DV", id = "ID", data = NULL, evid = "EVID", by = NULL, xlab = "Time", ylab = "Default", object = NULL, events.to.plot = "All", sim.data = NULL, sim.zip.file = NULL, VPC = FALSE, nsim.lab = "simNumber", sim.evct.lab = "counter", probs = c(0.025, 0.975), add.baseline = T, add.last.area = T, subset = NULL, main = "Default", main.sub = "Default", main.sub.cex = 0.8, nbins = NULL, real.type = "l", real.lty = 1, real.lwd = 1, real.col = "blue", real.se = if (!is.null(sim.data)) F else T, real.se.type = "l", real.se.lty = 2, real.se.lwd = 0.5, real.se.col = "red", cens.type = "l", cens.lty = 1, cens.col = "black", cens.lwd = 1, cens.rll = 0.02, inclZeroWRES = TRUE, onlyfirst = FALSE, samp = NULL, poly.alpha = 1, poly.fill = "lightgreen", poly.line.col = "darkgreen", poly.lty = 2, censor.lines = TRUE, ylim = c(-5, 105), cov = NULL, cov.fun = "mean", ... )
x |
The independent variable. |
y |
The dependent variable. event (>0) or no event (0). |
id |
The ID variable in the dataset. |
data |
A dataset can be used instead of the data in an Xpose object.
Must have the same form as an xpose data object |
evid |
The EVID data item. If not present then all rows are considered events (can be censored or an event). Otherwise, EVID!=0 are dropped from the data set. |
by |
A vector of conditioning variables. |
xlab |
X-axis label |
ylab |
Y-axis label |
object |
An Xpose object. Needed if no |
events.to.plot |
Vector of events to be plotted. "All" means that all events are plotted. |
sim.data |
The simulated data file. Should be a table file with one
header row and have, at least, columns with headers corresponding to
|
sim.zip.file |
The |
VPC |
|
nsim.lab |
The column header for |
sim.evct.lab |
The column header for |
probs |
The probabilities (non-parametric percentiles) to use in computation of the prediction intervals for the simulated data. |
add.baseline |
Should a (x=0,y=1) baseline measurement be added to each individual in the dataset. Otherwise each plot will begin at the first event in the dataset. |
add.last.area |
Should an area be added to the VPC extending the last PI? |
subset |
The subset of the data and sim.data to use. |
main |
The title of the plot. Can also be |
main.sub |
The title of the subplots. Must be a list, the same length
as the number of subplots (actual graphs), or |
main.sub.cex |
The size of the title of the subplots. |
nbins |
The number of bins to use in the VPC. If |
real.type |
Type for the real data. |
real.lty |
Line type (lty) for the curve of the original (or real) data. |
real.lwd |
Line width (lwd) for the real data. |
real.col |
Color for the curve of the original (or real) data. |
real.se |
Should the standard errors of the real (non simulated) data
be plotted? Calculated using |
real.se.type |
Type for the standard errors. |
real.se.lty |
Line type (lty) for the standard error lines. |
real.se.lwd |
Line width (lwd) for the standard error lines. |
real.se.col |
Color for the standard error lines. |
cens.type |
Type for the censored lines. |
cens.lty |
Line type (lty) for the censored lines. |
cens.col |
Color for the censored lines. |
cens.lwd |
Line width for the censored lines. |
cens.rll |
The relative line length of the censored line compared to the limits of the y-axis. |
inclZeroWRES |
Include WRES=0 rows from the real data set in the plots? |
onlyfirst |
Include only the first measurement for the real data in the plots? |
samp |
Simulated data in the xpose data object can be used as the
"real" data. |
poly.alpha |
The transparency of the VPC shaded region. |
poly.fill |
The fill color of the VPC shaded region. |
poly.line.col |
The line colors for the VPC region. |
poly.lty |
The line type for the VPC region. |
censor.lines |
Should censored observations be marked on the plot? |
ylim |
Limits for the y-axes |
cov |
The covariate in the dataset to plot instead of the survival curve. |
cov.fun |
The summary function for the covariate in the dataset to plot instead of the survival curve. |
... |
Additional arguments passed to the function. |
returns an object of class "xpose.multiple.plot".
Andrew C. Hooker
survfit
, Surv
,
xpose.multiple.plot
.
Other specific functions:
absval.cwres.vs.cov.bw()
,
absval.cwres.vs.pred.by.cov()
,
absval.cwres.vs.pred()
,
absval.iwres.cwres.vs.ipred.pred()
,
absval.iwres.vs.cov.bw()
,
absval.iwres.vs.idv()
,
absval.iwres.vs.ipred.by.cov()
,
absval.iwres.vs.ipred()
,
absval.iwres.vs.pred()
,
absval.wres.vs.cov.bw()
,
absval.wres.vs.idv()
,
absval.wres.vs.pred.by.cov()
,
absval.wres.vs.pred()
,
absval_delta_vs_cov_model_comp
,
addit.gof()
,
autocorr.cwres()
,
autocorr.iwres()
,
autocorr.wres()
,
basic.gof()
,
basic.model.comp()
,
cat.dv.vs.idv.sb()
,
cat.pc()
,
cov.splom()
,
cwres.dist.hist()
,
cwres.dist.qq()
,
cwres.vs.cov()
,
cwres.vs.idv.bw()
,
cwres.vs.idv()
,
cwres.vs.pred.bw()
,
cwres.vs.pred()
,
cwres.wres.vs.idv()
,
cwres.wres.vs.pred()
,
dOFV.vs.cov()
,
dOFV.vs.id()
,
dOFV1.vs.dOFV2()
,
data.checkout()
,
dv.preds.vs.idv()
,
dv.vs.idv()
,
dv.vs.ipred.by.cov()
,
dv.vs.ipred.by.idv()
,
dv.vs.ipred()
,
dv.vs.pred.by.cov()
,
dv.vs.pred.by.idv()
,
dv.vs.pred.ipred()
,
dv.vs.pred()
,
gof()
,
ind.plots.cwres.hist()
,
ind.plots.cwres.qq()
,
ind.plots()
,
ipred.vs.idv()
,
iwres.dist.hist()
,
iwres.dist.qq()
,
iwres.vs.idv()
,
par_cov_hist
,
par_cov_qq
,
parm.vs.cov()
,
parm.vs.parm()
,
pred.vs.idv()
,
ranpar.vs.cov()
,
runsum()
,
wres.dist.hist()
,
wres.dist.qq()
,
wres.vs.idv.bw()
,
wres.vs.idv()
,
wres.vs.pred.bw()
,
wres.vs.pred()
,
xpose.VPC.both()
,
xpose.VPC.categorical()
,
xpose.VPC()
,
xpose4-package
## Not run: library(xpose4) ## Read in the data runno <- "57" xpdb <- xpose.data(runno) #################################### # here are the real data plots #################################### kaplan.plot(x="TIME",y="DV",object=xpdb) kaplan.plot(x="TIME",y="DV",object=xpdb, events.to.plot=c(1,2), by=c("DOSE==0","DOSE!=0")) kaplan.plot(x="TIME",y="DV",object=xpdb, events.to.plot=c(1,2), by=c("DOSE==0","DOSE==10", "DOSE==50","DOSE==200")) ## make a PDF of the plots pdf(file=paste("run",runno,"_kaplan.pdf",sep="")) kaplan.plot(x="TIME",y="DV",object=xpdb, by=c("DOSE==0","DOSE==10", "DOSE==50","DOSE==200")) dev.off() #################################### ## VPC plots #################################### kaplan.plot(x="TIME",y="DV",object=xpdb,VPC=T,events.to.plot=c(1)) kaplan.plot(x="TIME",y="DV",object=xpdb,VPC=T, events.to.plot=c(1,2,3), by=c("DOSE==0","DOSE!=0")) kaplan.plot(x="TIME",y="DV",object=xpdb,VPC=T, events.to.plot=c(1), by=c("DOSE==0","DOSE==10","DOSE==50","DOSE==200")) ## make a PDF of all plots pdf(file=paste("run",runno,"_kaplan.pdf",sep="")) kaplan.plot(x="TIME",y="DV",object=xpdb,VPC=T, by=c("DOSE==0","DOSE==10","DOSE==50","DOSE==200")) dev.off() ## End(Not run)
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