TraMineR refseq
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
asked Nov 12 '18 at 11:51
CharbCharb
62
add a comment |
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
asked Nov 12 '18 at 11:51
CharbCharb
62
Please provide the matrixcoutsand the two sequences.
– Gilbert
Nov 13 '18 at 13:28
add a comment |
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
asked Nov 12 '18 at 11:51
CharbCharb
62
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
r traminer
asked Nov 12 '18 at 11:51
CharbCharb
62
asked Nov 12 '18 at 11:51
CharbCharb
62
asked Nov 12 '18 at 11:51
CharbCharb
62
asked Nov 12 '18 at 11:51
CharbCharb
62
asked Nov 12 '18 at 11:51
CharbCharb
62
62
Please provide the matrixcoutsand the two sequences.
– Gilbert
Nov 13 '18 at 13:28
add a comment |
Please provide the matrixcoutsand 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
add a comment |
1 Answer
1
active
oldest
votes
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.
answered Nov 12 '18 at 17:00
GilbertGilbert
2,5981022
Thank you Gilbert !
– Charb
Nov 13 '18 at 20:16
add a comment |
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1 Answer
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active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
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.
answered Nov 12 '18 at 17:00
GilbertGilbert
2,5981022
Thank you Gilbert !
– Charb
Nov 13 '18 at 20:16
add a comment |
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.
answered Nov 12 '18 at 17:00
GilbertGilbert
2,5981022
Thank you Gilbert !
– Charb
Nov 13 '18 at 20:16
add a comment |
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.
answered Nov 12 '18 at 17:00
GilbertGilbert
2,5981022
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.
answered Nov 12 '18 at 17:00
GilbertGilbert
2,5981022
edited Nov 13 '18 at 16:18
answered Nov 12 '18 at 17:00
GilbertGilbert
2,5981022
answered Nov 12 '18 at 17:00
GilbertGilbert
2,5981022
answered Nov 12 '18 at 17:00
GilbertGilbert
2,5981022
2,5981022
Thank you Gilbert !
– Charb
Nov 13 '18 at 20:16
add a comment |
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
add a comment |
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Please provide the matrix
coutsand the two sequences.– Gilbert
Nov 13 '18 at 13:28