[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 ...

Many thanks in advance,
Best regards,



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

Adresse postale:
Bâtiment de Vidy
CH - 1015 Lausanne

Rte de Chavannes 33
1007 Lausanne

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