# [Traminer-users] Using transition rates as substitution costs

Jacques-Antoine Gauthier Jacques-Antoine.Gauthier at unil.ch
Tue Jan 11 15:15:41 CET 2011

```Dear TraMineR,

I have a small question regrading the use of transitions rates as
substitution cost.

In the TraMineR 1.4 user's guide, p. 70 you state that:"
Notice that the matrix is not symmetrical. The transition rate between
states A and B is 0.005
(0.5%), while the transition rate from B to A is 0.01 (1%). As claimed
above, the sum of the
transition rates from one state to all other states (including the
transition rate between the state
and itself) should equal 1. But we don’t trust anybody and we want to
check it. We therefore
apply the rowSums() function, which returns the sum of the rows, to the
tr object containing the
transition rates".

Now, if I want to compute the distance between two sequences x = {AAA}
and y={BBB} using the transition rates cost matrix given in the example
in a regular OM analysis:

- Does it mean that aligning x against y OR aligning y against x will
produce different distance? This should be the case given that the cost
for substituing A for B is different from that of substituing B for A.

- If it is the case the order of the sequences in the dataset may
influence the final distance matrice (e.g. if seq x comes before or
after seq y).

- If it is not the case, how does TraMineR "choose" between
substCost(A,B) vs substCost(B,A) when it come to substitute A and B.

- Of course, I may also confuse myself ...

Best regards,

Jacques-Antoine

--

Jacques-Antoine Gauthier
Maître d'enseignement et de recherche

Université de Lausanne
Faculté des Sciences sociales et politiques
Centre de recherche Méthodologie, inégalités et changement social (MISC)
&  Centre lémanique d'étude des parcours et modes de vie (PAVIE)

Tél.: ++41 +21 / 692 38 43
Jacques-Antoine.Gauthier at unil.ch
URL: http://www.unil.ch/misc