read.los.data {changeLOS}R Documentation

Read the data for clos

Description

Read data fom a textfile, which contains one row per individual and one time variable per possible transition.

Usage

read.los.data(file, sep = ";", header = TRUE, row.names=NULL,
pos.id=1, pos.columns) 

Arguments

file name of the file to be read. If it does not contain an absolute path, the file name is relative to the current working directory, getwd().
sep the field separator character
header a logical value indicating whether the file contains the names of the variables as its first line
row.names a vector of row names. This can be a vector giving the actual row names, or a single number giving the column of the table which contains the row names, or character string giving the name of the table column containing the row names.
If there is a header and the first row contains one fewer field than the number of columns, the first column in the input is used for the row names. Otherwise if 'row.names' is missing, the rows are numbered.
Using 'row.names = NULL' forces row numbering.
pos.id the position of the unique id (patient id, admision id)
pos.columns the positions of the columns which are holding the observed times:
pos.columns[1]:
transition from initial state to intermediate state
pos.columns[2]:
transition from initial state to absorbing state (discharge)
pos.columns[3]:
transition from initial state to competing absorbing state (death)
pos.columns[4]:
transition from intermediate state to absorbing state
pos.columns[5]:
transition from intermediate state to competing absorbing state
pos.columns[6]:
censoring time (either in initial or intermediate state)

Details

The data textfile to be read must contain one time variable per possible transition and one row per individual. An additional variable contains censoring times. If a transition was not observed for an individual, the respective row of the textfile has entry Inf (`infinite') for that variable.

This data structure is well suited for bootstrapping with respect to the number of individuals. It is still concise for the four-state-model for change in LOS; note that this model does not allow for backward transitions. However, for a larger number of possible transitions, this data structure will be less desirable.

Value

a data frame of the form data.frame(id,j.01,j.02,j.03,j.12,j.13,cens)

id id (patient id, admision id)
j.01 observed time for jump from 0 (initial state) to 1 (intermediate state)
j.02 observed time for jump from 0 to 2 (discharge)
j.03 observed time for jump from 0 to 3 (death)
j.12 observed time for jump from 1 to 2
j.13 observed time for jump from 1 to 3
cens censoring time (either in initial or intermediate state)

Author(s)

Matthias Wangler mw@imbi.uni-freiburg.de

See Also

clos, prepare.los.data

Examples

## Locate data file "los.data.csv" in sub-directory of package "changeLOS"
filename <- paste(searchpaths()[seq(along=search())[search()==
                  "package:changeLOS"]], "/data/los.data.csv", sep="")

los.data <- read.los.data(filename,pos.id=1,pos.columns=c(2,3,4,5,6,7))

## Results in the same data frame as: data(los.data)

[Package changeLOS version 2.0.9-2 Index]