| seqdistmc {TraMineR} | R Documentation |
Compute multichannel pairwise optimal matching (OM) distances between sequences by deriving the substitution costs from the costs of the single channels. Works with OM and its following variants: distance based on longest common subsequence (LCS), Hamming distance (HAM), and Dynamic Hamming distance (DHD).
seqdistmc(channels, method, norm="none", indel=1, sm=NULL,
with.missing=FALSE, full.matrix=TRUE, link="sum", cval=2,
miss.cost=2, cweight=NULL, what="diss")
channels |
A list of state sequence objects defined
with the |
method |
a character string indicating the metric to be used.
One of |
norm |
String.
Default: |
indel |
A vector with an insertion/deletion cost for each channel (OM method). |
sm |
A list with a substitution-cost matrix for each channel (OM, HAM and DHD
method) or a list of method names for generating the substitution-costs
(see |
with.missing |
Must be set to |
full.matrix |
If |
link |
One of |
cval |
Substitution cost for |
miss.cost |
Missing values substitution cost, see |
cweight |
A vector of channel weights. Default is 1 (same weight for each channel). |
what |
Character string. What output should be returned? One of |
The seqdistmc function builds a state sequence by combining the channels, derives the multichannel indel and substitution costs from the indel and substitution costs of each channel (following the strategy proposed by Pollock, 2007), and computes the multichannel distances using the multichannel distances. The available metrics (see 'method' option) are optimal matching ("OM"), longest common subsequence ("LCS"), Hamming distance ("HAM"), and Dynamic Hamming Distance ("DHD"). See seqdist for more information about distances between sequences.
Normalization may be useful when dealing with sequences that are not all of the same length. For details on the applied normalization, see seqdist.
When what="diss", a matrix of pairwise distances between multichannel sequences.
When what="sm", the matrix of substitution costs with three attributes: indel the indel, alphabet the alphabet of the combined state sequences, and cweight the channel weight used.
When seqmc, the combined state sequence object.
Matthias Studer (with Gilbert Ritschard for the help page)
Pollock, Gary (2007) Holistic trajectories: a study of combined employment, housing and family careers by using multiple-sequence analysis. Journal of the Royal Statistical Society: Series A 170, Part 1, 167–183.
data(biofam)
## Building one channel per type of event left, children or married
bf <- as.matrix(biofam[, 10:25])
children <- bf==4 | bf==5 | bf==6
married <- bf == 2 | bf== 3 | bf==6
left <- bf==1 | bf==3 | bf==5 | bf==6
## Building sequence objects
child.seq <- seqdef(children)
marr.seq <- seqdef(married)
left.seq <- seqdef(left)
## Using transition rates to compute substitution costs on each channel
mcdist <- seqdistmc(channels=list(child.seq, marr.seq, left.seq),
method="OM", sm =list("TRATE", "TRATE", "TRATE"))
## Using a weight of 2 for children channel and specifying substitution-cost
smatrix <- list()
smatrix[[1]] <- seqsubm(child.seq, method="CONSTANT")
smatrix[[2]] <- seqsubm(marr.seq, method="CONSTANT")
smatrix[[3]] <- seqsubm(left.seq, method="TRATE")
mcdist2 <- seqdistmc(channels=list(child.seq, marr.seq, left.seq),
method="OM", sm =smatrix, cweight=c(2,1,1))