Modified data export

Added Neiman's t_f to data export, fixed a bug with config_entropy in population census data, and ensured that population and tasampled output the same variables for comparison.

Corrected Moran mutation rate

Calibrated the infinite alleles mutation rate (for all locus neutral copying) against Ewens 2004. Single locus copying yields more alleles than expected for the Moran process in the population, since copying events are necessary to weed out variants to the expected level. This model is suitable for single-locus copying model comparisons, which is sufficient for the current experiment. Needs a "all locus" interpretation of frequency-dependent biased copying, but there are difficulties in interpreting this (see lab notebook).

production release with global UUIDs for processing jobs

Added UUIDs to each batch of simulation runs to ensure large model batches had globally unique job scripts

Production version for CTMixture experiment

Debugging statements turned off in main simulation script, removed matplotlib as it was unused and was causing a random error on some (but not all) StarCluster nodes.

ctmixture experiment - minor setup fixes

2.0 codebase, but with fixed setup.py

ctmixtures

Version 2.0 includes time averaging, sampling, and Kandler survival analysis, along with neutral and conformist rules that can be mixed in a population. The simulation run builder takes an experiment configuration with prior distributions for key simulation parameters (and point estimates for parameters that do not vary) and creates simulation run files which are suitable for parallel simulation runs. Random seeds and full command line invocations are saved to the database for replicability.