I have a logical problem with the transition cost matrix. I am working on sequences dissimilarity using the R package Traminer.
I try to give you a simple example (very simple, but I hope useful to explain my problem):
There are three sequences and I want to be calculate the dissimilarity matrix. The alphabet is: H (in health), I (ill at home), IH (ill at hospital), D (died)
I observe the 3 subjects for 5 observations. These are the sequences:
H – H – I – D – D
H – I – I – I – D
I – I – H – IH – IH
The substitution cost matrix is a 4x4 table (state x state). It must be symmetric? This is my logical problem: while it is possible to “transit” from states H, I or IH to state Died, the contrary is illogical.
Can I use a non-symmetric substitution cost matrix in TraMineR?
If, in my database, the substitution cost (calculated with sm = "TRATE", for instance) from state “I” to “D” is lower (0.5) than the substitution cost from state 'I' to 'IH' (0.6) , the OM algorithm substitute the “I” whith “D” instead of “HI”.
it seems to me that you're looking for a custom cost matrix. It is not mandatory to use either the TRATE or CONSTANT method.
To create a custom matrix you'll just have to do something like this:
myscm <- matrix(c(0,1,2,
1,0,2,
2,2,0), nrow=3, ncol=3)
dist.om <- seqdist(my.seq, method="OM", sm=myscm)
where myscm is your custom matrix
This was taken from http://lists.r-forge.r-project.org/pipermail/traminer-users/2011-July/000075.html
I believe you have two options:
1) Create a rationale for all the transitions and a full custom matrix
2) Get the transition matrix you've already generated (using seqsubm(your.seq, method = "TRATE") ) and change just the inconsistent values. That's what I've done in my last analysis.
But keep in mind the point made by Gilbert in An "asymmetric" pairwise distance matrix