help dynhamming

Title

dynhamming -- Calculate inter-sequence distances using dynamic Hamming distance

Syntax

dynhamming varlist , options [option]

options

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

ref(integer) (Optional) compare all sequences to the first N sequences, instead of calculating all pairwise distances.

MAwindow(integer) (Optional) Moving average window to smooth transition rates over (defaults to (3 1 3)). See the window() option of tssmooth ma.

Description

dynhamming calculates Lesnard's dynamic Hamming distances
between all pairs of sequences in the data, where 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 maketrpr to
calculate the transition rates, smoothing over a rolling seven (3+1+3)
observations. See also trprgr which uses maketrpr to graph
the time-dependent transition structure.

States must be numbered as integers from 1 up.

Author

Brendan Halpin, brendan.halpin@ul.ie

Examples

. dynhamming mon1-mon36, pwdist(dist)

. matrix list dist