TraMineR refseq










1















I use the function seqdist from package TraMineR.



First I calculate on 2 trajectories in seq.all :



seqdist(seq.all[1:2,], method="OM", indel=1.1, sm=couts)


[,1] [,2]
[1,] 0.00000 46.91843
[2,] 46.91843 0.00000


So the distance between this trajectories seems to be 46.91843.



But when I use the argument refseq :



seqdist(seq.all[1,], method="OM", indel=1.1, sm=couts,refseq = seq.all[2,])

[1] 60.32636


Now the distance between this trajectories seems to be 60.32636.



What is the trick ?










share|improve this question






















  • Please provide the matrix couts and the two sequences.

    – Gilbert
    Nov 13 '18 at 13:28















1















I use the function seqdist from package TraMineR.



First I calculate on 2 trajectories in seq.all :



seqdist(seq.all[1:2,], method="OM", indel=1.1, sm=couts)


[,1] [,2]
[1,] 0.00000 46.91843
[2,] 46.91843 0.00000


So the distance between this trajectories seems to be 46.91843.



But when I use the argument refseq :



seqdist(seq.all[1,], method="OM", indel=1.1, sm=couts,refseq = seq.all[2,])

[1] 60.32636


Now the distance between this trajectories seems to be 60.32636.



What is the trick ?










share|improve this question






















  • Please provide the matrix couts and the two sequences.

    – Gilbert
    Nov 13 '18 at 13:28













1












1








1








I use the function seqdist from package TraMineR.



First I calculate on 2 trajectories in seq.all :



seqdist(seq.all[1:2,], method="OM", indel=1.1, sm=couts)


[,1] [,2]
[1,] 0.00000 46.91843
[2,] 46.91843 0.00000


So the distance between this trajectories seems to be 46.91843.



But when I use the argument refseq :



seqdist(seq.all[1,], method="OM", indel=1.1, sm=couts,refseq = seq.all[2,])

[1] 60.32636


Now the distance between this trajectories seems to be 60.32636.



What is the trick ?










share|improve this question














I use the function seqdist from package TraMineR.



First I calculate on 2 trajectories in seq.all :



seqdist(seq.all[1:2,], method="OM", indel=1.1, sm=couts)


[,1] [,2]
[1,] 0.00000 46.91843
[2,] 46.91843 0.00000


So the distance between this trajectories seems to be 46.91843.



But when I use the argument refseq :



seqdist(seq.all[1,], method="OM", indel=1.1, sm=couts,refseq = seq.all[2,])

[1] 60.32636


Now the distance between this trajectories seems to be 60.32636.



What is the trick ?







r traminer






share|improve this question













share|improve this question











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asked Nov 12 '18 at 11:51









CharbCharb

62




62












  • Please provide the matrix couts and the two sequences.

    – Gilbert
    Nov 13 '18 at 13:28

















  • Please provide the matrix couts and the two sequences.

    – Gilbert
    Nov 13 '18 at 13:28
















Please provide the matrix couts and the two sequences.

– Gilbert
Nov 13 '18 at 13:28





Please provide the matrix couts and the two sequences.

– Gilbert
Nov 13 '18 at 13:28












1 Answer
1






active

oldest

votes


















1














You get the distances from all sequences to one of the sequence of the considered sequence object by passing the index of the sequence as refseq argument. So, you could get the distance between your two sequences with



seqdist(seq.all, method="OM", sm=couts, indel=1.1, refseq=2)[1]


Nevertheless, your code should work too and should provide the same value.



This is a bug that may occur when the refseq sequence is passed as a sequence object. We will fix it and make the new version available in the next days on R-Forge.






share|improve this answer

























  • Thank you Gilbert !

    – Charb
    Nov 13 '18 at 20:16










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1 Answer
1






active

oldest

votes








1 Answer
1






active

oldest

votes









active

oldest

votes






active

oldest

votes









1














You get the distances from all sequences to one of the sequence of the considered sequence object by passing the index of the sequence as refseq argument. So, you could get the distance between your two sequences with



seqdist(seq.all, method="OM", sm=couts, indel=1.1, refseq=2)[1]


Nevertheless, your code should work too and should provide the same value.



This is a bug that may occur when the refseq sequence is passed as a sequence object. We will fix it and make the new version available in the next days on R-Forge.






share|improve this answer

























  • Thank you Gilbert !

    – Charb
    Nov 13 '18 at 20:16















1














You get the distances from all sequences to one of the sequence of the considered sequence object by passing the index of the sequence as refseq argument. So, you could get the distance between your two sequences with



seqdist(seq.all, method="OM", sm=couts, indel=1.1, refseq=2)[1]


Nevertheless, your code should work too and should provide the same value.



This is a bug that may occur when the refseq sequence is passed as a sequence object. We will fix it and make the new version available in the next days on R-Forge.






share|improve this answer

























  • Thank you Gilbert !

    – Charb
    Nov 13 '18 at 20:16













1












1








1







You get the distances from all sequences to one of the sequence of the considered sequence object by passing the index of the sequence as refseq argument. So, you could get the distance between your two sequences with



seqdist(seq.all, method="OM", sm=couts, indel=1.1, refseq=2)[1]


Nevertheless, your code should work too and should provide the same value.



This is a bug that may occur when the refseq sequence is passed as a sequence object. We will fix it and make the new version available in the next days on R-Forge.






share|improve this answer















You get the distances from all sequences to one of the sequence of the considered sequence object by passing the index of the sequence as refseq argument. So, you could get the distance between your two sequences with



seqdist(seq.all, method="OM", sm=couts, indel=1.1, refseq=2)[1]


Nevertheless, your code should work too and should provide the same value.



This is a bug that may occur when the refseq sequence is passed as a sequence object. We will fix it and make the new version available in the next days on R-Forge.







share|improve this answer














share|improve this answer



share|improve this answer








edited Nov 13 '18 at 16:18

























answered Nov 12 '18 at 17:00









GilbertGilbert

2,5981022




2,5981022












  • Thank you Gilbert !

    – Charb
    Nov 13 '18 at 20:16

















  • Thank you Gilbert !

    – Charb
    Nov 13 '18 at 20:16
















Thank you Gilbert !

– Charb
Nov 13 '18 at 20:16





Thank you Gilbert !

– Charb
Nov 13 '18 at 20:16

















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