Event history frame

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Description

Extract event history data and design matrix including specials from call

Usage

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EventHistory.frame(formula, data, unspecialsDesign = TRUE, specials,
  specialsFactor = TRUE, specialsDesign = FALSE, stripSpecials = NULL,
  stripArguments = NULL, stripAlias = NULL, stripUnspecials = NULL,
  dropIntercept = TRUE, check.formula = TRUE, response = TRUE)

Arguments

formula

Formula whose left hand side specifies the event history, i.e., either via Surv() or Hist().

data

Data frame in which the formula is interpreted

unspecialsDesign

Passed as is to model.design.

specials

Character vector of special function names. Usually the body of the special functions is function(x)x but e.g., strata from the survival package does treat the values

specialsFactor

Passed as is to model.design.

specialsDesign

Passed as is to model.design

stripSpecials

Passed as specials to strip.terms

stripArguments

Passed as arguments to strip.terms

stripAlias

Passed as alias.names to strip.terms

stripUnspecials

Passed as unspecials to strip.terms

dropIntercept

Passed as is to model.design

check.formula

If TRUE check if formula is a Surv or Hist thing.

response

If FALSE do not get response data (event.history).

Details

Obtain a list with the data used for event history regression analysis. This function cannot be used directly on the user level but inside a function to prepare data for survival analysis.

Value

A list which contains - the event.history (see Hist) - the design matrix (see model.design) - one entry for each special (see model.design)

Author(s)

Thomas A. Gerds <tag@biostat.ku.dk>

See Also

model.frame model.design Hist

Examples

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## Here are some data with an event time and no competing risks
## and two covariates X1 and X2.
## Suppose we want to declare that variable X1 is treated differently
## than variable X2. For example, X1 could be a cluster variable, or
## X1 should have a proportional effect on the outcome.
dsurv <- data.frame(time=1:7,
                    status=c(0,1,1,0,0,0,1),
                    X2=c(2.24,3.22,9.59,4.4,3.54,6.81,5.05),
                    X3=c(1,1,1,1,0,0,1),
                    X4=c(44.69,37.41,68.54,38.85,35.9,27.02,41.84),
                    X1=factor(c("a","b","a","c","c","a","b"),
                        levels=c("c","a","b")))
## We pass a formula and the data
e <- EventHistory.frame(Hist(time,status)~prop(X1)+X2+cluster(X3)+X4,
                        data=dsurv,
                        specials=c("prop","cluster"),
                        stripSpecials=c("prop","cluster"))
names(e)
## The first element is the event.history which is result of the left hand
## side of the formula:
e$event.history
## same as
with(dsurv,Hist(time,status))
## to see the structure do
colnames(e$event.history)
unclass(e$event.history)
## in case of competing risks there will be an additional column called event,
## see help(Hist) for more details

## The other elements are the design, i.e., model.matrix for the non-special covariates
e$design
## and a data.frame for the special covariates
e$prop
## The special covariates can be returned as a model.matrix
e2 <- EventHistory.frame(Hist(time,status)~prop(X1)+X2+cluster(X3)+X4,
                         data=dsurv,
                         specials=c("prop","cluster"),
                         stripSpecials=c("prop","cluster"),
                         specialsDesign=TRUE)
e2$prop
## and the non-special covariates can be returned as a data.frame
e3 <- EventHistory.frame(Hist(time,status)~prop(X1)+X2+cluster(X3)+X4,
                         data=dsurv,
                         specials=c("prop","cluster"),
                         stripSpecials=c("prop","cluster"),
                         specialsDesign=TRUE,
                         unspecialsDesign=FALSE)
e3$design

## the general idea is that the function is used to parse the combination of
## formula and data inside another function. Here is an example with
## competing risks
SampleRegression <- function(formula,data=parent.frame()){
    thecall <- match.call()
    ehf <- EventHistory.frame(formula=formula,
                              data=data,
                              stripSpecials=c("prop","cluster","timevar"),
                              specials=c("prop","timevar","cluster"))
    time <- ehf$event.history[,"time"]
    status <- ehf$event.history[,"status"]
    ## event as a factor
    if (attr(ehf$event.history,"model")=="competing.risks"){
        event <- ehf$event.history[,"event"]
        Event <- getEvent(ehf$event.history)
        list(response=data.frame(time,status,event,Event),X=ehf[-1])
    }
    else{ # no competing risks
        list(response=data.frame(time,status),X=ehf[-1])
    }
}
dsurv$outcome <- c("cause1","0","cause2","cause1","cause2","cause2","0")
SampleRegression(Hist(time,outcome)~prop(X1)+X2+cluster(X3)+X4,dsurv)

## let's test if the parsing works
form1 <- Hist(time,outcome!="0")~prop(X1)+X2+cluster(X3)+X4
form2 <- Hist(time,outcome)~prop(X1)+cluster(X3)+X4
ff <- list(form1,form2)
lapply(ff,function(f){SampleRegression(f,dsurv)})


## here is what the riskRegression package uses to
## distinguish between covariates with
## time-proportional effects and covariates with
## time-varying effects:
## Not run: 
library(riskRegression)
data(Melanoma)
f <- Hist(time,status)~prop(thick)+strata(sex)+age+prop(ulcer,power=1)+timevar(invasion,test=1)
## here the unspecial terms, i.e., the term age is treated as prop
## also, strata is an alias for timvar

EHF <- prodlim::EventHistory.frame(formula,
                                   Melanoma[1:10],
                                   specials=c("timevar","strata","prop","const","tp"),
                                   stripSpecials=c("timevar","prop"),
                                   stripArguments=list("prop"=list("power"=0),
                                       "timevar"=list("test"=0)),
                                   stripAlias=list("timevar"=c("strata"),
                                       "prop"=c("tp","const")),
                                   stripUnspecials="prop",
                                   specialsDesign=TRUE,
                                   dropIntercept=TRUE)
EHF$prop
EHF$timevar

## End(Not run)

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