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ng a maximum likelihood approach with Metropolis-Hastings Monte Carlo Markov chain importanc
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<TITLE>LAMARC Documentation: Using Tracer</title>
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<H2>Using Tracer with LAMARC</H2>
<P>LAMARC can produce output readable by the utility program Tracer,
written by Andrew Rambaut and Alexei Drummond. We do not distribute
Tracer. It can be found at:
</P>
<A HREF="http://tree.bio.ed.ac.uk/software/tracer/">
http://tree.bio.ed.ac.uk/software/tracer/</A>
<P>We thank the authors for producing this useful program. It is
written in Java and runs on most systems as long as a Java runtime
environment is available. Tracer is mainly intended for Bayesian
runs. For each parameter being estimated, it can display summary
statistics (mean, standard deviation, etc) and a graph of the
change in that parameter as the run progresses. It can also
show the correlation between pairs of parameters. Finally, it
produces a statistic, the Effective Sample Size (ESS), meant to
indicate the size of a set of independent data points with the
same information as our correlated data points. A low ESS means
that even though we may have sampled many data points, due to strong
correlation between them we have not obtained much real information.
This can happen if our search is rejecting most of its proposals,
or if the proposals it accepts are all very close together so that
it is not moving freely across the surface.</P>
<P>The files that LAMARC outputs for Tracer (as of version 2.1.2) show all
values ever sampled by the program, including any
chains used prior to the last final chain.
This means that the subset of the data used for parameter estimation will be
only the final swath of data, and will not include anything before that. We
include it in the Tracer output so you can visualize the entire LAMARC run
to better see the parameters as they move from their starting values to
their final values, and then (hopefully) level off. If you use Tracer to
give you estimates, be sure to tell it to not use the initial section, as it
will bias your estimates towards the starting values. Other than that, the
estimates Tracer produces should be very similar to the estimates LAMARC
produces--the two programs use different curve-smoothing algorithms
(LAMARC's is described <A HREF="curve-smoothing.html">in this article</a>),
but should be drawn from the same underlying data.
</P>
<P>In both the Bayesian and Likelihood runs of LAMARC, one of the output
parameters will be not the estimated parameters, but the data likelihood
values for the trees (in the Likelihood run, this is the sole output value,
as it does not sample among other parameter values). These data likelihoods
are the log of the probability that the data would be produced on the given
tree, and will increase from the start of the run and should eventually
level off, just like all other parameters.</P>
<P>Tracer is
very useful in diagnosing too-short runs. If the trace
graph shows a rising line, rather than a line which plateaus and
varies around a particular value, the run is too short. Be aware,
however, that while a bad-looking trace nearly guarantees a bad
run, a good-looking trace cannot guarantee a good run. If there
is a favorable region of parameter space which was never found, no
examination of the regions which were found can reveal this.</P>
<P> Here is an example of a Bayesian run whose results for the
parameter shown (Theta for the first population) are not satisfactory.
Note the systematic upward trend through most of the run length.
Even though the trace dips back down at the end, the run has
clearly not reached a stable state yet, and should be redone with
many more steps.</P>
<p><IMG SRC="images/tracer_trend.png" ALT="upward trending trace"/></P>
<P> The authors of Tracer red-flag an Effective Sample Size (ESS)
statistic under 100 as indicating a run which is definitely too
short, but in some of their discussion express doubt about runs
with ESS < 200. We distrust runs with ESS < 200 for any
parameter. Unfortunately higher ESS is not a guarantee of good
results; note that the ESS of the displayed example is 245.</P>
You should check both trace shape and ESS for each parameter,
and doubt a run in which either one is unsatisfactory.<P>
<P>Do note that the values reported from within a LAMARC run labelled
"Number of unique sampled values for each parameter" are <b>not</b> ESS
values, but rather exactly what that title would suggest. In a sense, they
could be termed the 'actual sample size', but in addition to this not being
a useful statistical measure, nobody wants to make an acronym out of it.</P>
<P> Tracer cannot be used to track parameter estimates in a likelihood
run of LAMARC, as likelihood runs don't make running estimates of
their parameters (it would be too expensive). The only
use of Tracer in a likelihood run is to monitor the fit of the data
to the genealogy (the "data likelihood").
Again, a rising line which does not plateau definitely indicates
a too-short run, whereas a nice plateau suggests but does
not guarantee a good run.</P>
<P>LAMARC automatically writes a file suitable for Tracer for
each chromosomal region it analyzes. The files are called
"tracefile_regionname_replicate.txt". So the file containing
information on the mtDNA region, first replicate, would be
named "tracefile_mtDNA_1.txt". This file can be provided to
Tracer as-is using the "Import" option in Tracer's menu.</P>
<P>We welcome any input on how to make Tracer more useful with
LAMARC, and visa versa.</P>
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