[phylocom-user] lttr interpretation

Adam Richman arichman at montana.edu
Fri Apr 2 10:56:13 PDT 2010


Correction: The 2nd and 3rd sentences below should read:

The rank position of the observed sample is determined by counting the
total number of random samples which have <the same or> fewer lineages
for a given time interval. If none of the random samples have <more>,
then the highest ranking is returned.

On Fri, Apr 2, 2010 at 11:00 AM, Adam Richman <arichman at montana.edu> wrote:
> The phylocom function lttr compares the number of lineages through time for
> a given sample to that of a set of randomly generated samples of equal size.
> The rank position of the observed sample is determined by finding the total
> number of random samples which have fewer lineages for a given time
> interval. If none of the random samples have fewer, then the highest ranking
> is returned.
>
> However, because of the way that lttr handles ties in determining rank
> position, the interpretation of the highest ranking is ambiguous.
>
> To see this, consider the instance where, for a given time interval, the
> number of lineages in the observed sample equals the maximum possible. In
> this case, if any of the random samples also has the maximum number, then
> the highest ranking is returned.
>
> Note that in this instance, the highest ranking has two very different
> possible explanations:
>
> 1. If a large proportion of the random samples also contain the maximum
> number of lineages, this indicates that the observed sample is not
> statistically different from random samples of the larger community.
>
> 2. If only a small fraction of random samples also contain the maximum
> number of lineages, then the observed sample is apparently quite different
> from the random samples, since it tends to have relatively divergent (older)
> lineages.
>
> I suggest that when the maximum ranking is obtained, that the rank of the
> first tie which led to this maximum ranking also be reported. This further
> information can be used to distinguish the two cases.
>
> Adam Richman
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