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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.ObjectDeme
A place with potentially interbreeding, constant population. Currently there is no dispersal, and fitness() is determined entirely by number of deleterious alleles, i.e. there is no requirement to match any particular local environmental conditions.
- generation
- completed bouts of viability selection, (assortative)mating, recombination, forward and backward mutation
- LD
- linkage disequilibrium between first and second fitness loci
- correlAB
- correlation between alleles at first and second fitness loci
- avgRec
- the average frequency of the recombination modifier
- avgFit
- the average fitness of all k individuals in the local population
- corr
- the realized correlation in fitness between all mums and dads
- qav
- the average frequency of deleterious alleles across all fitness loci
- totmut
- total number of forward mutation events this generation
- totben
- total number of* backward mutation events this generation
- totrec
- total number of recombination events this generation
- maxDel
- the maximum number of deleterious alleles found in any individual this generation. Of interest with respect to epistasis in the fitness function.
- myLD
- of all of the left/right chromosome pairings that matter with respect to recombination between the first and second fitness loci, this is the proportion that is repulsion pairings (Ab/aB). This is calculated from just the parents, and makes better sense to me than an LD at the haploid/chromosomal level.
- numSelf
- individuals are not allowed to mate with themselves. This is the number of selfings that were avoided.
Field Summary | |
double |
assort
the correlation in fitness between parents |
private double |
avgFit
|
private double |
avgRec
|
double |
benMutRate
per locus back mutation rate |
Bion |
bion
|
(package private) double |
correlAB
|
private int |
coupling
|
double[][] |
cumDist
|
private double[] |
cumFit
|
private Bion |
dad
|
private Bion[] |
dads
|
double |
delMutRate
per locus mutation rate |
int |
demeGen
|
private int |
drop
|
double |
epistasis
|
double |
initq
initial average frequency of deleterious alleles across fitness loci |
boolean[] |
isHit
|
private double[] |
juvCumFit
|
private Bion[] |
juveniles
pre-reproductives |
private double |
juvSumFit
|
private int |
k
the constant population size |
private Bion[] |
locals
les habitants |
private double |
localSumFit
|
private int |
maxDel
|
double |
minRecRate
per meiosis probability of recombination between any two adjacent loci, without modifiers |
double |
modRecRate
the increment in rec rate for homozygote for modifier |
private Bion |
mum
|
private Bion[] |
mums
|
int |
nAttribs
the number of loci in play, including recombination modifier |
double[] |
np
pre-computed binomial means |
private int |
numDel
|
private int |
numJuveniles
|
private int |
numLocals
|
private int |
numRec
|
private int |
numSelf
|
(package private) double |
pA
|
(package private) double |
pAB
|
(package private) double |
pB
|
double[] |
prob
|
MersenneTwisterFast |
rand
|
private double |
recRate
|
private int |
repulsion
|
double |
selRate
selection coefficient, exact meaning depends on function used in fitness() |
double[] |
sqrnpq
pre-computed binomial std dev |
(package private) int |
tab
|
(package private) int |
taB
|
(package private) int |
tAb
|
(package private) int |
tAB
|
(package private) int |
totben
|
static int[] |
totm
|
(package private) int |
totmut
|
static int[] |
totr
|
(package private) int |
totrec
|
Constructor Summary | |
Deme(MersenneTwisterFast rand,
int k,
int nAttribs,
double delMutRate,
double benMutRate,
double minRecRate,
double modRecRate,
double selRate,
double epistasis,
double assort,
double initq)
|
Method Summary | |
void |
fitness(Bion bion)
Whatever fitness function is desired is plugged in here. |
void |
flip()
juveniles become potentially-reproducing adults |
private void |
heapsort(Bion[] ra,
int n)
Heapsort kludged from Numerical Recipes in C. Used to sort mums and dads by fitness to generate assortativeness. |
void |
init()
Generate pre-computed values, and populate deme with Bions. |
void |
nextGeneration()
does viability selection, mating, and stats printout |
private Bion |
pickParent()
The fitter are more likely to be chosen as parents. |
int |
searchCDF(double[] cumArray,
int topIndex,
double target)
Binary search to find Cumulative Density Function array element >= target used for picking parents according to fitness, and for exact evaluation of the Binomial distribution |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
public final int nAttribs
private final int k
public final double selRate
public final double epistasis
public final double assort
public final double initq
public final double delMutRate
public final double benMutRate
public final double minRecRate
public final double modRecRate
public final double[] sqrnpq
public final double[] np
public final double[][] cumDist
public final double[] prob
public int demeGen
private int numDel
private int maxDel
public Bion bion
private int numLocals
private int numJuveniles
private int numRec
private Bion[] locals
private Bion[] juveniles
private Bion[] mums
private Bion[] dads
private Bion mum
private Bion dad
private int drop
private double[] cumFit
private double[] juvCumFit
private double localSumFit
private double juvSumFit
private double avgFit
private double avgRec
public MersenneTwisterFast rand
public static int[] totr
public static int[] totm
int tAB
int tAb
int taB
int tab
int totmut
int totben
int totrec
double correlAB
double pAB
double pA
double pB
private double recRate
private int coupling
private int repulsion
private int numSelf
public boolean[] isHit
Constructor Detail |
public Deme(MersenneTwisterFast rand, int k, int nAttribs, double delMutRate, double benMutRate, double minRecRate, double modRecRate, double selRate, double epistasis, double assort, double initq)
Method Detail |
public void init()
public void fitness(Bion bion)
public int searchCDF(double[] cumArray, int topIndex, double target)
private Bion pickParent()
private void heapsort(Bion[] ra, int n)
public void nextGeneration()
public void flip()
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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |