How does one interpret the output of the tracecomp function of PhyloBayes, e.g.:
$ tracecomp -x 100 2 chain1 chain2 initialising random seed was : 896505 setting upper limit to : 2129 name effsize rel_diff loglik 9 0.524245 length 35 0.183442 alpha 119 0.253582 nocc 25 0.340367 stat 19 0.25722 statalpha 1426 0.185346 kappa 50 0.250689 allocent 6 0.433294
The manual states:
tracecomp -x 100 2 rnapol1 rnapol2
will produce an output summarizing the discrepancies and the effective sizes estimated for each column of the trace file. The discrepancy is defined as D=2|m1 - m2| / (s1 + s2), where mi is the mean and si the standard deviation associated with a particular column, and i runs over the chains. The effective size is evaluated using the method of Geyer (1992). The guidelines are:
- maximum discrepancy < 0.1 and minimum effective size > 100 : good run,
- maximum discrepancy < 0.3 and minimum effective size > 50 : acceptable run.