TraMineR: seqdistmc – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

seqdistmc

Multichannel distances between sequences

Description

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).

Usage

seqdistmc(channels, method, norm="none", indel=1, sm=NULL,
     with.missing=FALSE, full.matrix=TRUE, link="sum", cval=2,
     miss.cost=2, cweight=NULL)

Arguments

`channels`	A list of state sequence objects defined with the `seqdef` function, each state sequence object corresponding to a "channel".
`method`	a character string indicating the metric to be used. One of `"OM"` (Optimal Matching), `"LCS"` (Longest Common Subsequence), `"HAM"` (Hamming distance), `"DHD"` (Dynamic Hamming distance).
`norm`	String. Default: `"none"`. The normalization method to use. See `seqdist`.
`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 `seqsubm`).
`with.missing`	Must be set to `TRUE` when sequences contain non deleted gaps (missing values) or when channels are of different length. See details.
`full.matrix`	If `TRUE` (default), the full distance matrix is returned. If `FALSE`, an object of class `dist` is returned.
`link`	One of `"sum"` or `"mean"`. Method to compute the "link" between channels. Default is to sum the substitution costs.
`cval`	Substitution cost for `"CONSTANT"` matrix, see `seqsubm`.
`miss.cost`	Missing values substitution cost, see `seqsubm`.
`cweight`	A vector of channel weights. Default is 1 (same weight for each channel).

Details

The seqdistmc function returns a matrix of multichannel distances between sequences. 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.

The seqdistmc function computes a multichannel distance in two steps following the strategy proposed by Pollock (2007). First it builds a new sequence object derived from the combination of the sequences of each channel. Second, it derives the substitution cost matrix by summing (or averaging) the costs of substitution across channels. It then calls seqdist to compute the distance matrix.

Normalization may be useful when dealing with sequences that are not all of the same length. For details on the applied normalization, see seqdist.

Value

A matrix of pairwise distances between multichannel sequences is returned.

Author(s)

Matthias Studer (with Gilbert Ritschard for the help page)

References

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.

Examples

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))

TraMineR

Trajectory Miner: a Toolbox for Exploring and Rendering Sequences

v2.2-1

GPL (>= 2)

Authors

Alexis Gabadinho [aut, cph], Matthias Studer [aut, cph] (<https://orcid.org/0000-0002-6269-1412>), Nicolas M"{u}ller [aut], Reto B"{u}rgin [aut], Pierre-Alexandre Fonta [aut], Gilbert Ritschard [aut, cre, cph] (<https://orcid.org/0000-0001-7776-0903>)

Initial release

2020-10-24