strip.terms: Strip special functions from terms

In prodlim: Product-Limit Estimation for Censored Event History Analysis

Strip special functions from terms

Description

Reformulate a terms object such that some specials are stripped off

Usage

strip.terms(
  terms,
  specials,
  alias.names = NULL,
  unspecials = NULL,
  arguments,
  keep.response = TRUE
)

Arguments

terms	Terms object
specials	Character vector of specials which should be stripped off
alias.names	Optional. A named list with alias names for the specials.
unspecials	Optional. A special name for treating all the unspecial terms.
arguments	A named list of arguments, one for each element of specials. Elements are passed to parseSpecialNames.
keep.response	Keep the response in the resulting object?

Details

This function is used to remove special specials, i.e., those which cannot or should not be evaluated. IMPORTANT: the unstripped terms need to know about all specials including the aliases. See examples.

Value

Reformulated terms object with an additional attribute which contains the stripped.specials.

Author(s)

Thomas A. Gerds <[e-mail]>

See Also

parseSpecialNames reformulate drop.terms

Examples

## parse a survival formula and identify terms which
## should be treated as proportional or timevarying:
f <- Surv(time,status)~age+prop(factor(edema))+timevar(sex,test=0)+prop(bili,power=1)
tt <- terms(f,specials=c("prop","timevar"))
attr(tt,"specials")
st <- strip.terms(tt,specials=c("prop","timevar"),arguments=NULL)
formula(st)
attr(st,"specials")
attr(st,"stripped.specials")

## provide a default value for argument power of proportional treatment
## and argument test of timevarying treatment: 
st2 <- strip.terms(tt,
                   specials=c("prop","timevar"),
                   arguments=list("prop"=list("power"=0),"timevar"=list("test"=0)))
formula(st2)
attr(st2,"stripped.specials")
attr(st2,"stripped.arguments")

## treat all unspecial terms as proportional
st3 <- strip.terms(tt,
                   unspecials="prop",
                   specials=c("prop","timevar"),
                   arguments=list("prop"=list("power"=0),"timevar"=list("test"=0)))
formula(st3)
attr(st3,"stripped.specials")
attr(st3,"stripped.arguments")

## allow alias names: strata for timevar and tp, const for prop.
## IMPORTANT: the unstripped terms need to know about
## all specials including the aliases
f <- Surv(time,status)~age+const(factor(edema))+strata(sex,test=0)+prop(bili,power=1)+tp(albumin)
tt2 <- terms(f,specials=c("prop","timevar","strata","tp","const"))
st4 <- strip.terms(tt2,
                   specials=c("prop","timevar"),
                   unspecials="prop",
                   alias.names=list("timevar"="strata","prop"=c("const","tp")),
                   arguments=list("prop"=list("power"=0),"timevar"=list("test"=0)))
formula(st4)
attr(st4,"stripped.specials")
attr(st4,"stripped.arguments")

## test if alias works also without unspecial argument
st5 <- strip.terms(tt2,
                   specials=c("prop","timevar"),
                   alias.names=list("timevar"="strata","prop"=c("const","tp")),
                   arguments=list("prop"=list("power"=0),"timevar"=list("test"=0)))
formula(st5)
attr(st5,"stripped.specials")
attr(st5,"stripped.arguments")

library(survival)
data(pbc)
model.design(st4,data=pbc[1:3,],specialsDesign=TRUE)
model.design(st5,data=pbc[1:3,],specialsDesign=TRUE)

prodlim documentation built on Aug. 28, 2023, 5:07 p.m.