pseudo.onedim {recurrentpseudo}

Function that computes univariate pseudo-observations

Description

This function computes univariate pseudo-observations of the marginal mean function (in the presence of terminal events)

Usage

pseudo.onedim(tstart, tstop, status, covar_names, id, tk, data)

Arguments

tstart

Start time - expecting counting process notation

tstop

Stop time - expecting counting process notation

status

Status variable (0 = censoring, 1 = recurrent event, 2 = death)

covar_names

Vector containing names of covariates intended for further analysis

id

ID variable for subject

tk

Vector of time points to calculate pseudo-observations at

data

Data set which contains variables of interest

Value

An object of class pseudo.onedim.

• outdata contains the semi-wide version of the computed pseudo-observations (one row per time, tk, per id).

• outdata_long contains the long version of the computed pseudo-observations (one row per observation, several per id).

• indata contains the input data which the pseudo-observations are based on.

• ts vector with time points used for computation of pseudo-observations.

• k number of time points used for computation of pseudo-observations (length(ts)).

References

Furberg, J.K., Andersen, P.K., Korn, S. et al. Bivariate pseudo-observations for recurrent event analysis with terminal events. Lifetime Data Anal (2021). https://doi.org/10.1007/s10985-021-09533-5

Examples

# Example: Bladder cancer data from survival package
require(survival)

# Make a three level status variable
bladder1$status3 <- ifelse(bladder1$status %in% c(2, 3), 2, bladder1$status)

# Add one extra day for the two patients with start=stop=0
# subset(bladder1, stop <= start)
bladder1[bladder1$id == 1, "stop"] <- 1
bladder1[bladder1$id == 49, "stop"] <- 1

# Restrict the data to placebo and thiotepa
bladdersub <- subset(bladder1, treatment %in% c("placebo", "thiotepa"))

# Make treatment variable two-level factor
bladdersub$Z <- as.factor(ifelse(bladdersub$treatment == "placebo", 0, 1))
levels(bladdersub$Z) <- c("placebo", "thiotepa")
head(bladdersub)

# Pseudo observations
pseudo_bladder_1d <- pseudo.onedim(tstart = bladdersub$start,
                                   tstop = bladdersub$stop,
                                   status = bladdersub$status3,
                                   id = bladdersub$id,
                                   covar_names = "Z",
                                   tk = c(30),
                                   data = bladdersub)
head(pseudo_bladder_1d$outdata)

# GEE fit
fit_bladder_1d <- pseudo.geefit(pseudodata = pseudo_bladder_1d,
                                covar_names = c("Z"))
fit_bladder_1d