Simupop

- NEW: Supports SWIG 1.3.39.
- BUG: Fix a bug when using simuRPy for R version <= 0.9.0 under windows.
- CHG: Do not set default loci name to "locX-Y". Empty string will be returned
if lociNames are not set. This also changes the behavior of functions
locusByName and lociByNames.
- CHG: Do not set default subpopulation name to "Unnamed". Empty string will be
returned if lociNames are not set. population::subPopName() is changed
accordingly.
- NEW: Add matrixMutator and an early form of actgMutator.
- NEW: Add mapIn and mapOut feature to all mutators.
- NEW: Add parameter name to population::mergeSubPops and operator mergeSubPops
- NEW: Add parameter names to population::splitSubPop and operator splitSubPops.
- NEW: Allow parameter infoFields to take single form values. Remove
population::addInfoField() because addInfoFields() now accepts single input.
- BUG: Fix a bug with persistent dirty signature.
- CHG: Replace parameter maxAllele in operator kamMutator with k (= maxAllele + 1),
and rename parameter rate to rates.
- CHG: Merge operator gsmMutator to smmMutator and pyMutator.
- CHG: Rename parameter rate to rates for operator recombinator.
- NEW: Mutators now supports virtual subpopulations (parameter VSP).
- NEW: ifElse operator now accepts lists of ifOps and elseOps.
- NEW: Allow single form input for operator lists.
- CHG: Operators are now copied to simulator::evolve. This makes counting functions
such as recombinator::recCount useless so they are removed.
- NEW: Add a hierarchical island migration model to simuUtil.py.
- NEW: Add a mixedMutator to simulated mixed mutation models.
- NEW: Move trajectory simulation functions out of the simuPOP core and
reimplement them in simuUtil.
- NEW: Add a context-dependent mutator contextMutator and context support for
pyMutator.
- NEW: Allow mitochondrialGenoTransmitter to be used in haploid populations.
- NEW: Add links to download examples to the online user's guide.

- BUG: Fix the handling of proportions in splitSubPops.
- BUG: Fix randomParentChooser when there is subpopulation structure.
- BUG: Fix a bug that concerns mutation at invalid (unused) locations.
- NEW: Allow Python parent choosers to return individual(s) directly.
- CHG: Remove image plottype from varPlotter, with simplified code and enhanced
functions.
- NEW: Add scatterPlotter that plots information fields.
- NEW: Add infoPlotter and two special cases histPlotter and qqPlotter.
- NEW: Add boxPlotter to plot boxplots of information fields.
- NEW: Introducing derivedArgs with expression values.

- BUG: Fix a bug with population::removeLoci when given keep loci are not in order.
- NEW: Prevent the use of greater than one probabilities in Bernulli trails.
- NEW: Add a Tkinter implementation for simuProgress.
- BUG: Fix a bug where subpopulation names of merged population are not properly merged.
- NEW: Allow specifying non-string values in 'chooseFrom' and 'chooseOneOf' in simuOpt
parameter specification.
- NEW: Allow operators to output to a Python function.
- NEW: Allow the use of double-click to open a browse dialog for file and directory
input in simuOpt.
- BUG: Fix a memory leak bug related to infoEval and infoExec. Optimize infoExec
for some simple statements.
- CHG: change parameter formOffGenotype of pyOperator to isTransmitter as a result of
merging concepts 'primary during mating operator' and 'genotype transmitter'.
- CHG: Move all scripts under the scripts directory to online cookbook.
- CHG: Change relatedness calculations in operator stat.
- NEW: Add calculation of HWE p-value to the stat operator.
- NEW: Test individual index in population::removeIndividuals
- BUG: Fix a bug when no subpopulation is given in splitSubPops.
- CHG: Merge stat(association) to stat(LD), in preparation for case-control association
tests.
- NEW: (experimental) Add case/control association chisq test to stat.
- NEW: (experimental) Add Tajima's pi statistics (mean pairwise difference) to
the stat() operator.

- NEW: Allow populations in a simulator to have different genotype structure.
- CHG: A simulator can no longer access genotypic structure information.
- NEW: Add simulator::add to add new populations to a simulator.
- CHG: Remove simulator::addInfoField and other functions because they can be
applied to individual populations.
- NEW: Allow the use of single form parameter in population::removeSubPops,
removeIndividuals, addLoci, removeLoci and resize.
- BUG: Fix a bug in adding locus to a population without any locus.
- NEW: Alow the use of single form parameter in controlledOffspringGenerator.
Handle single return value of allele frequency trajectory function.
- NEW: Rename parameter fromSubPop to subPops and toSubPop to toSubPops for migrator, for
naming consistency.
- NEW: Add mode = ByIndInfo to migrator so that users can explicitly set
migrate_to informatin field and migrate.
- NEW: Remove pyMigrator from the core. The varying migration rate migrator can
be easily implemented in a Python operator. The indFunc mode is not at all
useful because it can be done by a Python operator plus mode=ByIndInfo.
- NEW: Allow unordered lociPos specification in population(), lociNames will be
rearranged accordingly.
- NEW: Allow single parameter to parameters loci, ploidy in initByValue and initByFreq.
- NEW: Remove parameter chrom from dumper(), allow single parameter input for
parameter loci in this operator.
- NEW: Add pause operator to accept specified keys.
- CHG: Remove rarely used parameters preStmts and postStmts from operators pyEval and
pyExec.
- CHG: Polish operator infoEval and infoExec (they now supports virtual subpopulations).
Document them in detail in user's guide and reference manual.
- CHG: Remove hapMapUtil from the core. These functions belong more to the simuPOP
cookbook than the core.
- CHG: More scripts/loadHapMap to simuPOP online cookbook.
- CHG: Polish and document simuOpt. getParam function now belongs to the simuOpt
class.
- CHG: Remove jump and jumpIfFalse from parameter specification.
- CHG: Replace --noDialog with --gui=False (and allow for values such as Tkinter).
- CHG: Polish operator splitSubPop, replace which to subPops, and add the feature
to split subpopulations by information field. Rename this operator to
splitSubPops.
- CHG: population::splitSubPop can no longer split by proportion. Please use operator
splitSubPops and its function form SplitSubPops instead.

- NEW: Improve allele iterator so that stat(alleleFreq) can handle chromosome x and y.
- CHG: Raise an error when there is no male or female in a diploid parents chooser.
- CHG: Remove parameter newSubPopSizeExpr and rename newSubPopSize to subPopSize,
and newSubPopSizeFunc to subPopSizeFunc.
- CHG: Merge parameters subPopSize and subPopSizeFunc. This parameter can now
take both a list and a function.
- BUG: Fix population load/save under windows, add simulator equality test (__cmp__).
- CHG: Merge parameters numOffspringFunc, numOffspringParam and mode to numOffspring
in offspringGenerator.
- CHG: Merge parameter sexParam to sexMode in offspringGenerator.
- CHG: Rename mating scheme binomialSelection to randomSelection.
- CHG: Merge parameters convProb, convMode and convParam to convMode in
recombinator.
- BUG: Fix option shuffleOffspring in heteroMating().
- CHG: Change the default output of parentsTagger when only one parent is passed.
- CHG: Remove parameter numParents from offspringGenerator and parent choosers.
- CHG: Rename pyMating to homoMating. Remove unused parameters subPop and weight
from heteroMating.
- NEW: Allow a demographic function to return a number if there is only one
subpopulation.
- NEW: Allow pedigreeMating to set sex, affection status and some information
fields from the pedigree object.
- NEW: Allow random parent(s) choosers to set name of information field fitness.
- CHG: Change interface for pedigree::locateRelatives. Rename setIndexOfRelatives
to traceRelatives.
- NEW: Allow replicate numbers in a simulator to refer to the last several
_active_ populations.
- CHG: Merge parameter output and outputExpr and use '!expr' for the expression
case.
- NEW: Allow parameter baseOperator::at to take a single number in addition to a list.
- NEW: Disallow parameter alias locus to parameter loci in penetrance,
selection and quantitative trait operators. Allow loci to accept a number.
- NEW: Support other device types in varPlotter::saveAs.
- NEW: dumper now supports virtual subpopulations.

- CHG: add population::setSubPopByIndInfo to allow flexible migration.
- CHG: migrator now uses an information field "migrate_to".
- CHG: Add function population::extract.
- CHG: Remove parameter ancGen from population::clone().
- NEW: Dump() also display information fields.
- NEW: Expose population::pushAndDiscard(pop) as population::push().
- NEW: Add parameter subPops to all operators.
- CHG: Move operators pySubset(), randomSample(), caseControlSample()
and affectedSibpairSample from simuPOP core to simuUtil.py.
Remove src/sampler.*.
- CHG: Remove infoTagger, sexTagger and affectionTagger and will
replace them by pedigreeTagger.
- CHG: Remove population::removeEmptySubPops().
- NEW: Add support for subpopulation names.
- CHG: Remove intializer, spread and pyInit operators.
- CHG: Add parameter initSex to initByFreq and initByValue.
- NEW: Initializers now support virtual subpopulations.
- CHG: Recombiantor no longer supports recombination by sex,
and haplodiploid chromosomes.
- CHG: Recombinator now supports different types of chromosomes.
- NEW: Add ops parameter to mating schemes.
- NEW: add mitochondrialGenoTransmitter.
- NEW: add population::updateInfoFieldsFrom.
- NEW: Add two examples in doc/cookbook, demonstrating the use of customized
genotype transmitters and mitochondrialGenoTransmitter.