help sdlongdyad

Title

sdlongdyad -- Estimate sequence distance between dyads, data in long format

Syntax

sdlongdyad varlist(max=2 min=2) [if] [in] [using/], DYADid(varname) SUBSmat(string) DIST(string)
[MTYPE(string) INDELcost(real -1) LAMbda(real -1) NU(real -1) KLip(integer 0) WORkspace STAndard(string)]

options

Required
dyadid(varname) Variable identifying the dyad

subsmat(string) Substitution cost matrix

dist(string) Name of matrix to store the resulting distances

Optional
mtype(string) OMA or TWED for optimal matching or time-warp edit distance

indelcost(real) Indelcost for OMA

lambda(real) Lambda parameter for TWED

nu(real) Nu parameter for TWED

klip(integer) Maximum alignment limit (speed gain for very long sequences)

standard(string) Standardise by sequence length

Description

This command calculates OMA or TWED sequence distance for dyads,
with the data in long format. The state for each member of the dyad is
stored in one of the two variables given in the varlist. The dyad
identifier must be given in the dyadid option. The mtype
option is a choice between OMA and TWED. Both OMA and TWED require a
substitution cost matrix; OMA requires an indelcost and TWED both
lambda and nu parameters. The distance is returned in a
matrix defined by the dist option, containing one row per dyad and
three columns: the dyad id, the length of the sequence pair and the
distance.

At present, both members of the dyad are assumed to present
sequences of equal length. This is not universally applicable, and if
there is sufficient interest the command can be adapted for
unequal-length dyadic sequences.

Author

Brendan Halpin, brendan.halpin@ul.ie

Examples

. sdlongdyad ego alter, dyadid(pairid) subsmat(sm1) dist(do) mtype(oma) indel(0.5)

. sdlongdyad ego alter, dyadid(pairid) subsmat(sm1) dist(dt) mtype(twed) lambda(0.1) nu(0.33)

See Also

sadi

oma

twed