{smcl} {* Copyright 2012 Brendan Halpin brendan.halpin@ul.ie } {* Distribution is permitted under the terms of the GNU General Public Licence } {* 20Apr2012}{...} {cmd:help dynhamming} {hline} {title:Title} {p2colset 5 17 23 2}{...} {p2col:{hi:dynhamming} {hline 2}}Calculate inter-sequence distances using dynamic Hamming distance{p_end} {p2colreset}{...} {title:Syntax} {p 8 17 2} {cmd:dynhamming} {it: varlist} {cmd:,} {it:options} [option] {synoptset 22 tabbed}{...} {synopthdr:options} {synoptline} {syntab:Distances} {synopt :{opt pwd:ist(matname)}} store the pairwise distances in {it:matname}, as a symmetric matrix. Will be created or overwritten. {p_end} {synoptline} {p2colreset}{...} {title:Description} {pstd}{cmd:dynhamming} calculates Lesnard's dynamic Hamming distances between all pairs of sequences in the data, where {it:varlist} is a consecutive set of variables describing the elements of the sequence. Dynamic Hamming distances compare sequences element by element such that the inter-sequence distance is the sum of the element-wise distances. The element-wise distances are dynamic, based on the time-dependent structure of transition rates. The procedure uses {help maketrpr} to calculate the transition rates, smoothing over a rolling seven (3+1+3) observations. See also {help trprgr} which uses {cmd:maketrpr} to graph the time-dependent transition structure. {pstd}States must be numbered as integers from 1 up. {pstd} {title:Author} {pstd}Brendan Halpin, brendan.halpin@ul.ie{p_end} {title:Examples} {phang}{cmd:. dynhamming mon1-mon36, pwdist(dist)}{p_end} {phang}{cmd:. matrix list dist}{p_end}