- NEW: Add a global function closeOutput to close '>>' or '>>>' output files used
in the function form of an operator.
- BUG: Fix a memory leak of LoadPopulation.
- CHG: Rename function rng() to GetRNG() for consistent naming of functions.
- NEW: Merge overloaded functions of population::setIndInfo, population::indInfo,
population::individual, population::individuals, population::vars,
simulator::vars, individual::setGenotype, individual::genotype,
individual::allele, individual::setAllele, individual::alleleChar,
individual::info, individual::setInfo to one function with more complex
input type and default parameter. This change allows keyword arguments for
all these functions.
- CHG: the parameter order of function population::ancestor has been changed!
- CHG: stat(popSize=True) accepts subPops parameter. It now output 'popSize' (a number),
'subPopSize' (a list) and subPop[vsp]['popSize'] (a number). By default, it does
not calculate population size for (virtual) subpopulations.
- CHG: Introduce parameter vars to operator stator. It will be used to replace all
blah_param parameters.
- CHG: Remove numOfAllele parameter of stat() operator.
- CHG: Parameter subPops now treats [] as no subpopulation, and accept AllSubPops as
its usual default parameter.
- CHG: Rename parameter rep to reps in all operators. This parameter now treats
input [] as no replicate and use AllReps as its default input.
- CHG: Remove expHetero statistics. Remove allele-level heterozygosity variable.
Rename heterozygosity variables.
- CHG: statGenoFreq now uses tuple (instead of string) as genotype indexes.
Parameter phase has been removed.
- CHG: statHaploFreq now uses tupe (instead of string) as loci and haplotype
indexes.
- NEW: Add statInfo to calculate sum, mean, var, max and min of information fields.
- CHG: rewrite statLD and change how primary alleles are handled. Please refer to
user's guide for details.
- NEW: add relationship SpouseAndOffspring to pedigree::locateRelatives.
- NEW: add parameter pedFields to population::extract.
- NEW: Introduce new type defdict for allele, genotype and haplotype counts
and frequencies.
- CHG: Disallow the use of nested list for parameter lociPos of population().
- NEW: Allow single-form parameter for parameters of function population().
- CHG: Rename paramter Fst of operator stat to structure, change associated
variable names. This leaves room for the implementation of other
structure related statistics.
- NEW: Add Nei's 1973 Gst statistics.
- NEW: Add parameter suffix to operator stator.