Marmote Core
The project aims at realizing the prototype of a software environment dedicated to modeling with Markov chains.
felsenstein81 Member List

This is the complete list of members for felsenstein81, including all inherited members.

_abstractmarkovChainprotected
_abstractNbremarkovChainprotected
_debugmarkovChainprotected
_formatmarkovChainprotected
_generatormarkovChainprotected
_initDistributionmarkovChainprotected
_isAbstractmarkovChainprotected
_modelNamemarkovChainprotected
_sizefelsenstein81protected
_stateSpacefelsenstein81protected
_stateSpaceSizemarkovChainprotected
_transDistribfelsenstein81protected
_transSpeedfelsenstein81protected
_typemarkovChainprotected
Absorbing()markovChain
absorbingStates()markovChain
abstract()markovChaininline
abstractNbre()markovChaininline
averageHittingTime(bool *hittingSet)felsenstein81
averageHittingTimeDT(bool *hitSetIndicator)markovChain
averageHittingTimeDT_iterative(bool *hitSetIndicator)markovChain
BandIMSUB(std::string modelName="modelName")markovChain
charVectorElt2State(SEXP elt, std::string function)markovChain
communicatingClasses()markovChain
copy()markovChainvirtual
embed()markovChainvirtual
felsenstein81(double p[4], double mu)felsenstein81
felsenstein81(discreteDistribution *d, double mu)felsenstein81
format()markovChaininline
generator()markovChaininline
hittingTimeDistribution(int iState, bool *hittingSet)felsenstein81
isaccessible(int stateFrom, int stateTo)markovChain
isirreducible()markovChain
makeMarkovChain()felsenstein81
markovChain(int sz, timeType t)markovChain
markovChain(transitionStructure *tr)markovChain
markovChain(string format, string param[], int nbreParam, string modelName, bool isAbstract)markovChain
modelName()markovChaininline
NCDProperty(double epsilon)markovChain
ProdFundSW(std::string modelName="modelName")markovChain
read()markovChain
recurrentClasses()markovChain
RInside typedefmarkovChainprotected
Rmotor()markovChain
RowSum(std::string modelName="modelName")markovChain
RowVincent()markovChain
setAbstract(string abstract[])markovChain
setAbstractNbre(int abstractNbre)markovChaininline
setFormat(string format)markovChaininline
setGenerator(transitionStructure *tr)markovChaininline
setInitDistribution(discreteDistribution *d)markovChaininline
setModelName(string modelName)markovChaininline
setSizeType(const string path)markovChain
SEXP typedefmarkovChainprotected
simulateChain(double tMax, bool stats, bool traj, bool withIncrements, bool trace)felsenstein81virtual
simulateChainCT(double tMax, bool stats, bool traj, bool withIncrements, bool trace)markovChainvirtual
simulateChainDT(int tMax, bool stats, bool traj, bool trace)markovChainvirtual
simulateChainR(double tMax, bool stats, bool traj, bool trace)markovChain
simulateHittingTime(int iState, bool *hittingSet, int nbSamples, int tMax)markovChain
simulatePSI(int tMax, bool stats, bool Traj, bool Print)markovChain
stateSpaceSize()markovChaininline
stationaryDistribution()felsenstein81
markovChain::stationaryDistribution(bool progress)markovChain
stationaryDistribution_iterative(string method, int tmax, double precision, string initDistribType, discreteDistribution *initDistrib, bool progress)markovChain
stationaryDistribution_power(int tMax, double epsilon, discreteDistribution *iDis, bool progress)markovChainvirtual
stationaryDistributionCT(bool progress)markovChainvirtual
stationaryDistributionCT_embedding(int tMax, double epsilon, discreteDistribution *iDis, bool progress)markovChainvirtual
stationaryDistributionGthLD()markovChain
stationaryDistributionR()markovChain
stationaryDistributionSample(int nbSamples)markovChain
stationaryDistributionSOR()markovChain
toString(std::string format)markovChain
transientDistribution(double)felsenstein81
transientDistributionDT(int fromState, int t)markovChain
transientDistributionR(int fromState, double t)markovChain
transitionProbability(int stateFrom, int stateTo)markovChain
uniformize()markovChainvirtual
Vincent()markovChain
write(FILE *out, bool withReward)markovChainvirtual
write(string format, string modelName)markovChainvirtual
write(string format)markovChaininline
~felsenstein81()felsenstein81
~markovChain()markovChainvirtual