help sdhollister

Title

sdhollister -- Calculate inter-sequence distances using Hollister's Localized OM

Syntax

sdhollister varlist , options [option]

options

Cost structure
subsmat(matname) use matname as the substitution cost matrix

TIMEcost(#) use # as the time cost

LOCalcost(#) use # as the local cost

Sequence length length(var) sequence
length, a variable or a constant if sequence length is fixed

Distances pwdist(matname) store the
pairwise distances in matname, as a symmetric matrix. Will be
created or overwritten.

Work-space workspace (Optional) Causes the internal
workspace matrices to be shown for each sequence comparison.

Normalisation STAndard (Optional) If "longer",
normalise by the length of the longer sequence, if "none" do no normalisation. Defaults to "longer".

Description

sdhollister calculates localised Optimal Matching distances
between all pairs of sequences in the data, where varlist is a
consecutive set of variables describing the elements of the sequence. It
uses a Stata plugin implementation of Mattissa Hollister's adaptation of
the Needleman--Wunsch algorithm. Thanks to Mattissa for help in figuring
out to code it, but if I have introduced any errors they are my own.

Hollister's measure differs from conventional OM by taking account
of the neighbours of tokens involved in OM's elementary operations.
While this is attractive from a sociological point of view, it means the
dissimilarity measure is not guaranteed to be metric. This is also true
of omav.

States must be numbered as consecutive integers from 1 up, and the
substitution cost matrix must be square, with dimension equal to the
number of states. States must not be missing.

References

Halpin, Brendan. (2014). Three narratives of sequence
analysis, Bühlmann et al (eds), Advances in Sequence Analysis.
Beyond the Core Program, Springer

Hollister, M. (2009).
Is optimal matching suboptimal?
Sociological Methods and Research, 38(2):235--264.

Author

Brendan Halpin, brendan.halpin@ul.ie

Examples

. matrix scost = (0,1,2,3\1,0,1,2\2,1,0,1\3,2,1,0)

. sdhollister mon1-mon36, subsmat(scost) time(0.5) local(0.5) pwdist(dist) len(36)

. matrix list dist

. sdhollister mon1-mon36, subsmat(scost) time(0.5) local(0.5) pwdist(dist) len(dur)

. matrix list dist