etm: closPseudo – R documentation

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etm

closPseudo

Pseudo Value Regression for the Extra Length-of-Stay

Description

Pseudo Value Regression for the Extra Length-of-Stay

Usage

closPseudo(data, state.names, tra, cens.name, s = 0,
           formula, na.action,
           aw = FALSE, ratio = FALSE,
           ncores = 1,
           trick_ties = FALSE)

Arguments

`data`	data.frame of the form data.frame(id,from,to,time) or (id,from,to,entry,exit) id: patient id from: the state from where the transition occurs to: the state to which a transition occurs time: time when a transition occurs entry: entry time in a state exit: exit time from a state
`state.names`	A vector of characters giving the states names.
`tra`	A quadratic matrix of logical values describing the possible transitions within the multistate model.
`cens.name`	A character giving the code for censored observations in the column 'to' of `data`. If there is no censored observations in your data, put 'NULL'.
`s`	Starting value for computing the transition probabilities.
`formula`	A formula with the covariates at the right of a `~` operator. Leave the left part empty.
`na.action`	A function which indicates what should happen when the data contain 'NA's. The default is set by the 'na.action' setting of 'options', and is 'na.fail' if that is unset. The 'factory-fresh' default is 'na.omit'.
`aw`	Logical. Whether to compute the expected change of LOS using alternative weighting. Default is `FALSE`.
`ratio`	Logical. Compute the ratio of the expected length-of-stay given instermediate event status instead of a difference. Default value is `FALSE`
`ncores`	Number of cores used if doing parallel computation using the parallel package
`trick_ties`	If `TRUE`, pseudo values are computed only one per subject sharing the same entry, exit times / transition types.

Details

The function calculates the pseudo-observations for the extra length-of-stay for each individual. These pseudo-observations can then be used to fit a direct regression model using generalized estimating equation (e.g., package geepack).

Computation of the pseudo-observations can be parallelised using the mclapply function of the parallel package. See argument ncores.

Recent versions of R have changed the data.frame function, where the default for the stringsAsFactors argument from TRUE to FALSE. etm currently depends on the states being factors, so that the user should use data.frame(..., stringsAsFactors=TRUE).

Value

An object of class closPseudo with the following components:

`pseudoData`	a data.frame containing `id`, computed pseudo values (see details) and the covariates as specified in the formula
`theta`	Estimates of excess LoS in the whole sample
`aw`	like in the function call
`call`	Function call

Author(s)

Arthur Allignol arthur.allignol@gmail.com

References

Andersen, P.K, Klein, J.P, Rosthoj, S. (2003). Generalised linear models for correlated pseudo-observations, with applications to multi-state models. Biometrika, 90(1):15–27.

Examples

if(require("kmi", quietly = TRUE)) {

    ## data in kmi package
    data(icu.pneu)
    my.icu.pneu <- icu.pneu
    
    my.icu.pneu <- my.icu.pneu[order(my.icu.pneu$id, my.icu.pneu$start), ]
    masque <- diff(my.icu.pneu$id)
    
    my.icu.pneu$from <- 0
    my.icu.pneu$from[c(1, masque) == 0] <- 1
    
    my.icu.pneu$to2 <- my.icu.pneu$event
    my.icu.pneu$to2[my.icu.pneu$status == 0] <- "cens"
    my.icu.pneu$to2[c(masque, 1) == 0] <- 1
    
    
    my.icu.pneu$to <- ifelse(my.icu.pneu$to2 %in% c(2, 3), 2,
                             my.icu.pneu$to2)

    my.icu.pneu <- my.icu.pneu[, c("id", "start", "stop", "from", "to",
                                   "to2", "age", "sex")]
    names(my.icu.pneu)[c(2, 3)] <- c("entry", "exit")

    ## computation of the pseudo-observations
    ## Not run: 
        ps.icu.pneu <- closPseudo(my.icu.pneu, c("0", "1", "2"), tra_ill(), "cens",
                                  formula = ~ sex + age)
        
        ## regression model using geepack
        require(geepack)
        fit <- geeglm(ps.e.phi ~ sex + age, id = id, data = ps.icu.pneu$pseudoData,
                      family = gaussian)
        
        summary(fit)
    
## End(Not run)
} else {
    print("This example requires the kmi package")
}

etm

Empirical Transition Matrix

v1.1.1

MIT + file LICENSE

Authors

Mark Clements [aut, cre], Arthur Allignol [aut]

Initial release