Resp: Response objects

In tramME: Transformation Models with Mixed Effects

Response objects

Description

Response objects to represent censored and truncated observations

Usage

Resp(
  cleft,
  cright,
  tleft,
  tright,
  bounds = c(-Inf, Inf),
  open_lwr_bnd = TRUE,
  tol = sqrt(.Machine$double.eps)
)

## S3 method for class 'Resp'
R(object, ...)

## S3 method for class 'Resp'
print(x, ...)

## S3 method for class 'Resp'
x[i, j, drop = FALSE]

## S3 method for class 'Resp'
is.na(x)

## S3 method for class 'Resp'
length(x)

## S3 method for class 'Resp'
format(x, ...)

Arguments

cleft	A vector of left borders of censoring intervals
cright	A vector of right borders of censoring intervals
tleft	A vector of left truncation values
tright	A vector of right truncation values
bounds	An optional numeric vector of two elements (c(a, b)) that denotes the lower and upper boundaries of the outcome.
open_lwr_bnd	Logical; if TRUE, the lower boundary of the outcome is open, and we want to enforce this.
tol	Tolerance level.
object	A Resp object
...	Optional arguments
x	A Resp object
i	Row index (typically the only index)
j	Column index (typically missing)
drop	If TRUE the result is coerced to the lowest possible dimension

Details

Resp extends the functionality of Surv class by allowing cases that cannot be defined with it. An example is an interval-censored outcome with left truncatation (see Examples).

Censored and exactly observed data can be defined similarly to type = "interval2" objects in Surv. NA values for left or right censoring borders mean left- or right-censored observations, respectively. If both borders are NA, the observation is considered NA by is.na(). Truncation times (tleft and tright arguments) can be omitted or take NA values, which means no truncation. If only the censoring intervals are provided, i.e., no trunction is present, the function returns a Surv object.

Resp also provides a limited interface between tramME and the response class (technically, inherits from it) of mlt (see R), which uses an internal representation that is not compatible with tramME.

The optional argument open_lwr_bnd can be used to enforce lower boundaries of the outcome. Left boundaries in the Resp object (cleft and tleft) that are equal to the first element of bounds will be increased with one tol value to avoid downstream numerical problems in mlt. This adjustment is recorded and reversed when we print the object.

Value

A Resp object or a Surv object

Methods (by generic)

• R(Resp): Converting Resp objects to response (from mlt) objects (see R)

• print(Resp): Print method for the Resp class

• [: Subsetting Resp objects

• is.na(Resp): Missing values

• length(Resp): Length of a Resp object

• format(Resp): format method for a Resp object

Warning

This function is experimental and currently limited to continuous outcome types. It may be subject to change.

Examples

dat <- data.frame(x1 = 1:10, x2 = c(2:10, NA), x3 = c(NA, 0:8))
dat$r <- with(dat, Resp(x1, x2, x3))

dat$r
dat[1:3, ]$r
dat$r[1:3]

is.na(dat$r)

model.frame(r ~ 1, data = dat, na.action = na.omit)

tramME documentation built on July 9, 2023, 7:10 p.m.