help sadi

Title

sadi -- Sequence analysis distance measures and utilities

Description

sadi is a package of tools for sequence analysis. It
provides a range of distance measures, including Hamming, standard OM,
Hollister's localised OM, Halpin's duration-adjusted OM, Time-Warp Edit
Distance, and a duration-weighted version of Elzinga's Number of Common
Subsequences measure. It also provides a number of utilities.

Several of the distance measures are coded using C plugins, for
speed. These are faster than Mata but less portable. On some platforms
the plugins will not work. Please let me know if you have problems in
this regard.

Some of the distance measures deal with duplicates efficiently
(i.e., by not re-estimating the distances redundantly). This facility
requires the mata function mm_expand() from Ben Jann's
moremata package. You can install this by doing
ssc install moremata.

Some of the graphics commands depend on Ben Jann's heatplot,
palettes and colrspace packages. These can be installed from SSC.

Author

Brendan Halpin, brendan.halpin@ul.ie

Also see

Distance measures:

sdhamming

Hamming distance

oma

Optimal Matching Algorithm

omav

Halpin's duration-adjusted OM

sdhollister

Hollister's "Localised OM"

dynhamming

An implementation of Lesnard's Dynamic Hamming measure

twed

Time-Warp Edit Distance

combinadd

Elzinga's number of common subsequences measure, duration-weighted

Utilities:

combinprep

Change data from wide calendar to wide spell format (needed for combinadd)

trans2subs

Generate substitution costs for OM and related distances based on observed transition rates

maketrpr

Calculate smoothed time-dependent transition rates (needed for dynhamming)

sdstripe

Generates a string representation of the sequence

metricp

Tests distance matrices for the triangle inequality

permtab

Compare two cluster solutions by permuting one to maximise the agreement

ari

Calculate the Adjusted Rand Index of agreement between two cluster solutions

corrsqm

Calculate the correlation between two distance matrices

nspells

Calculate the number of spells in a sequence

cumuldur

Calculate the cumulative duration in each state

sdentropy

Calculate the Shannon entropy of a sequence

sddiscrep

Calculate the Studer Discrepancy

Visualisation:

sdchronoplot

Graph the time-dependent state distribution

sdindexplot

Indexplots graph trajectories, maintaining individual detail.

trprgr

Graph the time-dependent structure of transitions