etm: etmprep – R documentation

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etmprep

Data transformation function for using etm

Description

The function transforms a data set in the wide format (i.e., one raw per subject) into the long format (i.e., one raw per transition, and possibly several raws per subjects) in a suitable way for using the etm function

Usage

etmprep(time, status, data, tra, state.names, cens.name = NULL,
start = NULL, id = NULL, keep)

Arguments

`time`	A character vector giving the name of the columns containing the transition times or last follow-up times. The length of `time` have to be equal to the number of states, some elements may be NA. See Details.
`status`	A character vector giving the name of the columns indicating whether a state has been visited (0 if not, 1 otherwise).
`data`	A data frame in which to look for the columns specified in `time` and `status`.
`tra`	A quadratic matrix of logical values describing the possible transitions within the multistate model. The (i, j)th element of `tra` is TRUE if a transition from state i to state j is possible, FALSE otherwise. The diagonal must be set to FALSE.
`state.names`	A vector of characters giving the states names. If missing, state names are set to be 0:(number of states).
`cens.name`	A character string specifying how censored observations will be indicated in the new data set. Default is NULL, i.e., no censored observation.
`start`	A list containing two elements, `state` and `time`, giving the starting states and times for all individuals. Default is NULL, in which case all individuals are considered to start in the initial state at time 0.
`id`	A character string specifying in which column of `data` the user ids are. Default is NULL, and the ids will be `1:n`.
`keep`	A character vector indicating the column names of the covariate one might want to keep in the new data.frame.

Details

This function only works for irreversible acyclic Markov processes. Therefore, the multistate model will have initial states, into which no transition are possible. For these, NAs are allowed in time and status.

Value

The function returns a data.frame suitable for using the etm function. The data frame contains the following components:

`id`	Individual id number
`entry`	Entry time into a state
`exit`	Exit time from a state
`from`	State from which a transition occurs
`to`	State into which a transition occurs
`...`	Further columns specified in `keep`

Author(s)

Arthur Allignol, arthur.allignol@gmail.com

Examples

### creation of fake data in the wild format, following an illness-death model
## transition times
tdisease <- c(3, 4, 3, 6, 8, 9)
tdeath <- c(6, 9, 8, 6, 8, 9)

## transition status
stat.disease <- c(1, 1, 1, 0, 0, 0)
stat.death <- c(1, 1, 1, 1, 1, 0)

## a covariate that we want to keep in the new data
cova <- rbinom(6, 1, 0.5)

dat <- data.frame(tdisease, tdeath,
                  stat.disease, stat.death,
                  cova, stringsAsFactors = TRUE)

## Possible transitions
tra <- matrix(FALSE, 3, 3)
tra[1, 2:3] <- TRUE
tra[2, 3] <- TRUE

## data preparation
newdat <- etmprep(c(NA, "tdisease", "tdeath"),
                  c(NA, "stat.disease", "stat.death"),
                  data = dat, tra = tra, cens.name = "cens")

etm

Empirical Transition Matrix

v1.1.1

MIT + file LICENSE

Authors

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

Initial release