I played with this some more, and it seems like for accessing an
element in a vector, (v idx) is a bit faster than (nth v idx).  If you
replace this line (line 52 in the gist)...

fl (nth freq-layer layer)]

with:

fl (freq-layer layer)]

...the total time needed to compute frequencies for all 92 types goes
down from 29 seconds to 21 seconds on my machine.

On Nov 8, 6:56 am, "Gijs S." <gijsstuur...@gmail.com> wrote:
> Indeed I was not using the transients correctly. Transients are not
> designed to be bashed in-place. (http://clojure.org/transients)
>
> The gist is updated with a version that first worked without the
> transients and then had the transient operations added. (https://
> gist.github.com/666228)
>
> The times and analysis still hold.
>
> -Gijs

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