Simupop

- separate user's guide and reference manual
- streamline getParam, usage, help etc.
- add scripts folder for common simupop templates
- add quiet option to simuPOP to suppress initial input
- add tk support for easy inputing of variables. This is
a major enhancement for userfriendliness. A first glimpse of a GUI
- fix a bug in saving shared variables. Exam saved format. Full backward
compatibility should start from here.
- simuComplexDisease.py. It uses almost all features of simuPOP
- remove headers support for object. They are not very useful and
hard to use.

- savePopulation saves local variables as well. This is used to save special info like
disease susceptibility loci.
- Label save population with max allowed allele number.
- merge some parameters through python code. Now, parameters like rate
can be either a number or an array. Same is true for value, indRange.
- caseControlSample can takes array cases/controls parameters.
- optimized genoStructure access, fix a bug about transferring the structure
- add LoadRandFam ( not easy :-)
- add parameters loci, chrom, indRange, subPop to dumper() and Dump()
Dump() is finally useful now.
- more efficient handling of ancestral pops

- add simulator::getPopulation get a copy of population
- add simuOpt to control simuPOP behavior, hide other modules
- add pointMutator
- change the meaning of rate in recombinator, add parameter intensity
- IMPORTANT: population can contain multiple generations.
add: population.pushAndDiscard (CPPONLY), Lots of work.
parameter ancestry for population.__init__
parameter ancestry for dumper
- add SavePopulations and LoadPopulations function.
- add stat(homoFreq and expHetero)
- fix a small bug with end < 0 and step > 1
- add splitSubPop(ByProportion), mergeSubPops member functions, operators
and functions.
- make duringMating oeprators re-order automatically
- add numOffspringsFunc, mode=MATE_NumOffsprings, MATE_GeometricDistribution etc
- add affected sibpair sampling scheme
- export to linkage format (affected sibpair samples)
- export to randfam format
- test parentsTagger, successfully track pedigree info

- variables are now population associated. (pop.evaluate(...)
- add quantitative trait and penetrance support
- add dryrun parameter to apply and evolve
- dvars() function. (Automatic dictionary wrapper class)
- add more flexibility to initializers. (indRanges, subPop, atLoci etc)
- varPlotter becomes an operator.
- add D, D' and r2 measures
- add newSubPopSizeFunc option to Mating schemes
- change haploFreq to count all haplotypes.
- add multi-allele Fst, LD etc. (average)
- fixes all memory leak and reference count problems
- save/load auto format according to file extension.
- fix a small bug of unclosed files.
- finsh LoadSimulatorFromFiles (uses in pair with savePopulation operator)
- fix two bugs in AvgLD calculation and in recombinator.

- add simuPOP_la library for long alleles.
- add exposePop option to pyEval (better pure-python operator support)
- better treatment for carray. (fix a bug)
- more statistics: Fst, Rst, H_est, H_obs etc
- read/write, FSTAT format
- use simple string instead of list to store statements.
- merge alleleCounter and popStat since alleleCounter may depend on popStat
- add operator pause for presentation purpose
new operator is called 'basicStat'
- Genomic control (use R/gap package, simple subpop vs subpop version)

- bug fixes
- better distribution process and binaries.
- remove internal language and use Python expression only
- more mutation models
- some hybrid operators added
- simuPOP website