Dear All,
I am a bit struggling with the many packages for Markov models available
in R.
Apologies for now posting a code snippet, but I am looking for some
guidance here.
Please consider a set like the one below (which you can get with
data<-read.csv('http://dl.dropboxusercontent.com/u/5685598/data_table.csv')
).
ID therapy age1 age2 EFS
7308 ormo_lunga 78 84 73
7308 ormo_medio 78 84 73
7308 ormo_lunga 78 84 73
4902 chemio_lunga 46 56 120
4902 ormo_lunga 46 56 120
4902 ormo_lunga 46 56 120
4902 ormo_breve 46 56 120
4902 chemio_lunga 46 56 120
4902 ormo_breve 46 56 120
5299 ormo_lunga 61 70 100
5299 ormo_breve 61 70 100
5299 chemio_breve 61 70 100
5299 chemio_lunga 61 70 100
5926 ormo_lunga 66 67 3
5926 ormo_lunga 66 67 3
5926 ormo_breve 66 67 3
5926 ormo_medio 66 67 3
5926 chemio_lunga 66 67 3
5926 ormo_breve 66 67 3
5374 ormo_lunga 39 59 242
5374 ormo_lunga 39 59 242
5374 ormo_lunga 39 59 242
4912 ormo_medio 40 50 124
4912 chemio_lunga 40 50 124
4912 chemio_lunga 40 50 124
4912 ormo_breve 40 50 124
4912 chemio_lunga 40 50 124
4532 ormo_breve 61 63 26
4532 ormo_breve 61 63 26
4532 chemio_lunga 61 63 26
I have a list of (short) series of states identified by the ID of the
patient who undergoes several therapies.
I then have other info about each patient (for instance its age when the
disease was first detected and so on).
The point is to calculate the transition matrix for the sequence of
therapies undergone by the patients and then possibly use the
complementary information available for the patients.
The purpose is not so much to understand whether the patient will be alive
or dead (this info is not available for all the patients after its last
therapy), but to try to guess the next therapy one is likely to undergo at
some stage using a Markovian model.
Let us assume that all patients are given the i-th therapy cycle at the
same time.
I did some experiments with the mcm package
(http://cran.r-project.org/web/packages/msm/index.html), but I am banging
a bit my head against the wall.
In general, I do not have a death state and time does not play a
particular role here (I could say that the i-th therapy is given at time
i, but this is arbitrary). Later on this may change, though, a time
sequence may be introduced for the therapies of each patient (varying from
patient to patient).
Any suggestion is appreciated.
Cheers
Lorenzo
