markovMSM (version 0.1.3)

prepMSM: Function to prepare data set for multi-state modeling in long format from data set in wide format.

Description

This function converts a data set which is in wide format (one subject per line, multiple columns indicating time and status for different states) into a data set in long format (one line for each transition for which a subject is at risk). Selected covariates are replicated per subjects.

Usage

prepMSM(data, trans, timesNames, status)

Value

An object of class "msdata", which is a data frame in long (counting process) format containing the subject id, the covariates (replicated per subject), and from the starting state to the receiving state trans the transition number Tstart the starting time of the transition Tstop the stopping time of the transition status status variable, with 1 indicating an event (transition), 0 a censoring

Arguments

data

Data frame in wide format in which to interpret time, status, id or keep, if appropriate.

trans

Transition matrix describing the states and transitions in the multi-state model. If S is the number of states in the multi-state model, trans should be an S x S matrix, with (i,j)-element a positive integer if a transition from i to j is possible in the multi-state model, NA otherwise. In particular, all diagonal elements should be NA. The integers indicating the possible transitions in the multi-state model should be sequentially numbered, 1,...,K, with K the number of transitions

timesNames

Either 1) a matrix or data frame of dimension n x S (n being the number of individuals and S the number of states in the multi-state model), containing the times at which the states are visited or last follow-up time, or 2) a character vector of length S containing the column names indicating these times. In the latter cases, some elements of time may be NA, see Details

status

Either 1) a matrix or data frame of dimension n x S, containing, for each of the states, event indicators taking the value 1 if the state is visited or 0 if it is not (censored), or 2) a character vector of length S containing the column names indicating these status variables. In the latter cases, some elements of status may be NA, see Details.

Author

Gustavo Soutinho and Luis Meira-Machado.

Examples

data("ebmt4")
db_wide <- ebmt4
positions<-list(c(2, 3, 5, 6), c(4, 5, 6), c(4, 5, 6), c(5, 6), c(6), c())
namesStates = c("Tx", "Rec", "AE", "Rec+AE", "Rel", "Death")
trans<-transMatMSM(positions, namesStates)
timesNames = c(NA, "rec", "ae","recae", "rel", "srv")
status=c(NA, "rec.s", "ae.s", "recae.s", "rel.s", "srv.s")
prepMSM(data=db_wide, trans, timesNames, status)