predict.prodlim {prodlim} | R Documentation |
Evaluation of estimated survival or event probabilities at given times and covariate constellations.
## S3 method for class 'prodlim': predict(object, times, newdata, level.chaos=1, type=c("surv","cuminc","list"), mode="list", bytime=FALSE, cause=1, ...)
object |
A fitted object of class "prodlim". |
times |
Vector of times at which to return the estimated probabilities. |
newdata |
A data frame with the same variable names as those that appear on the right hand side of the 'prodlim' formula. If there are covariates this argument is required. |
level.chaos |
Integer specifying the sorting of the output: `0' sort by time and newdata; `1' only by time; `2' no sorting at all |
type |
Choice between "surv","cuminc","list":
"surv": predict survival probabilities only survival models "cuminc": predict cumulative incidences only competing risk models "list": find the indices corresponding to times and newdata. See value. Defaults to "surv" for two-state models and to "cuminc" for competing risk models. |
mode |
Only for type=="surv" and type=="cuminc" .
Can either be "list" or "matrix". For "matrix"
the predicted probabilities will be returned in matrix form.
|
bytime |
Logical. If TRUE and mode=="matrix"
the matrix with predicted probabilities will
have a column for each time and a row for each
newdata. Only when object$covariate.type>1
and more than one time is given.
|
cause |
The cause for predicting the cause-specific cumulative incidence function in competing risk models. |
... |
Only for compatibility reasons. |
Predicted (survival) probabilities are returned that can be plotted, summarized and used for inverse of probability of censoring weighting.
type=="surv"
A list or a matrix with survival
probabilities for all times and all newdata.
type=="cuminc"
A list or a matrix with cumulative
incidences for all times and all newdata.
type=="list"
A list with the following components:
times |
The argument times carried forward |
predictors |
The relevant part of the argument newdata . |
indices |
A list with the following components
time : Where to find values corresponding to the requested times
strata : Where to find values corresponding to the
values of the variables in newdata.
Together time and strata show where to find the predicted probabilities.
|
dimensions |
a list with the following components:
time : The length of times
strata : The number of rows in newdata
names.strata : Labels for the covariate values.
|
Thomas Alexander Gerds <tag@biostat.ku.dk>
dat <- SimSurv(400) fit <- prodlim(Hist(time,status)~1,data=dat) ## predict the survival probs at selected times predict(fit,times=c(10,100,1000)) ## works also outside the usual range of the Kaplan-Meier predict(fit,times=c(-1,0,10,100,1000,10000)) ## newdata is required if there are strata ## or neighborhoods (i.e. overlapping strata) mfit <- prodlim(Hist(time,status)~X1+X2,data=dat) predict(mfit,times=c(-1,0,10,100,1000,10000),newdata=dat[18:21,]) ## this can be requested in matrix form predict(mfit,times=c(-1,0,10,100,1000,10000),newdata=dat[18:21,],mode="matrix") ## and even transposed predict(mfit,times=c(-1,0,10,100,1000,10000),newdata=dat[18:21,],mode="matrix",bytime=TRUE)