- Generated on Sun Jul 21 2024 08:40:35 for bpp-popgen3 by
1.9.1
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bpp-popgen3
3.0.0
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This is the complete list of members for bpp::SequenceStatistics, including all inherited members.
| dvh(const PolymorphismSequenceContainer &psc, bool gapflag=true) | bpp::SequenceStatistics | static |
| dvk(const PolymorphismSequenceContainer &psc, bool gapflag=true) | bpp::SequenceStatistics | static |
| fayWu2000(const PolymorphismSequenceContainer &psc, const Sequence &ancestralSites) | bpp::SequenceStatistics | static |
| fixedDifferences(const PolymorphismSequenceContainer &pscin, const PolymorphismSequenceContainer &pscout, PolymorphismSequenceContainer &psccons, const GeneticCode &gc) | bpp::SequenceStatistics | static |
| frequencyOfPolymorphicSites(const PolymorphismSequenceContainer &psc, bool gapflag=true, bool ignoreUnknown=true) | bpp::SequenceStatistics | static |
| fstHudson92(const PolymorphismSequenceContainer &psc, size_t id1, size_t id2) | bpp::SequenceStatistics | static |
| fuLiD(const PolymorphismSequenceContainer &ingroup, const PolymorphismSequenceContainer &outgroup, bool useNbSingletons=true, bool useNbSegregatingSites=false) | bpp::SequenceStatistics | static |
| fuLiDStar(const PolymorphismSequenceContainer &group, bool useNbSegregatingSites=false) | bpp::SequenceStatistics | static |
| fuLiF(const PolymorphismSequenceContainer &ingroup, const PolymorphismSequenceContainer &outgroup, bool useNbSingletons=true, bool useNbSegregatingSites=false) | bpp::SequenceStatistics | static |
| fuLiFStar(const PolymorphismSequenceContainer &group, bool useNbSegregatingSites) | bpp::SequenceStatistics | static |
| gcContent(const PolymorphismSequenceContainer &psc) | bpp::SequenceStatistics | static |
| gcPolymorphism(const PolymorphismSequenceContainer &psc, bool gapflag=true) | bpp::SequenceStatistics | static |
| generateLdContainer(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.) | bpp::SequenceStatistics | static |
| getNumberOfDerivedSingletons_(const Site &site_in, const Site &site_out) | bpp::SequenceStatistics | privatestatic |
| getNumberOfMutations_(const Site &site) | bpp::SequenceStatistics | privatestatic |
| getNumberOfSingletons_(const Site &site) | bpp::SequenceStatistics | privatestatic |
| getUD_(double a1, double vD) | bpp::SequenceStatistics | privatestatic |
| getUDstar_(size_t n, double a1, double vDs) | bpp::SequenceStatistics | privatestatic |
| getUsefulValues_(size_t n) | bpp::SequenceStatistics | privatestatic |
| getVD_(size_t n, double a1, double a2, double cn) | bpp::SequenceStatistics | privatestatic |
| getVDstar_(size_t n, double a1, double a2, double dn) | bpp::SequenceStatistics | privatestatic |
| heterozygosity(const PolymorphismSequenceContainer &psc, bool gapflag=true) | bpp::SequenceStatistics | static |
| hudson87(const PolymorphismSequenceContainer &psc, double precision=0.000001, double cinf=0.001, double csup=10000.) | bpp::SequenceStatistics | static |
| inverseRegressionR2(const PolymorphismSequenceContainer &psc, bool distance1=false, bool keepsingleton=true, double freqmin=0.) | bpp::SequenceStatistics | static |
| leftHandHudson_(const PolymorphismSequenceContainer &psc) | bpp::SequenceStatistics | privatestatic |
| linearRegressionD(const PolymorphismSequenceContainer &psc, bool distance1=false, bool keepsingleton=true, double freqmin=0.) | bpp::SequenceStatistics | static |
| linearRegressionDprime(const PolymorphismSequenceContainer &psc, bool distance1=false, bool keepsingleton=true, double freqmin=0.) | bpp::SequenceStatistics | static |
| linearRegressionR2(const PolymorphismSequenceContainer &psc, bool distance1=false, bool keepsingleton=true, double freqmin=0.) | bpp::SequenceStatistics | static |
| meanD(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.) | bpp::SequenceStatistics | static |
| meanDistance1(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.) | bpp::SequenceStatistics | static |
| meanDistance2(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.) | bpp::SequenceStatistics | static |
| meanDprime(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.) | bpp::SequenceStatistics | static |
| meanNumberOfNonSynonymousSites(const PolymorphismSequenceContainer &psc, const GeneticCode &gc, double ratio=1.) | bpp::SequenceStatistics | static |
| meanNumberOfSynonymousSites(const PolymorphismSequenceContainer &psc, const GeneticCode &gc, double ratio=1.) | bpp::SequenceStatistics | static |
| meanR2(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.) | bpp::SequenceStatistics | static |
| mkTable(const PolymorphismSequenceContainer &ingroup, const PolymorphismSequenceContainer &outgroup, const GeneticCode &gc, double freqmin=0.) | bpp::SequenceStatistics | static |
| neutralityIndex(const PolymorphismSequenceContainer &ingroup, const PolymorphismSequenceContainer &outgroup, const GeneticCode &gc, double freqmin=0.) | bpp::SequenceStatistics | static |
| numberOfMonoSitePolymorphicCodons(const PolymorphismSequenceContainer &psc, bool stopflag=true, bool gapflag=true) | bpp::SequenceStatistics | static |
| numberOfNonSynonymousSubstitutions(const PolymorphismSequenceContainer &psc, const GeneticCode &gc, double freqmin=0.) | bpp::SequenceStatistics | static |
| numberOfParsimonyInformativeSites(const PolymorphismSequenceContainer &psc, bool gapflag=true) | bpp::SequenceStatistics | static |
| numberOfPolymorphicSites(const PolymorphismSequenceContainer &psc, bool gapflag=true, bool ignoreUnknown=true) | bpp::SequenceStatistics | static |
| numberOfSingletons(const PolymorphismSequenceContainer &psc, bool gapflag=true) | bpp::SequenceStatistics | static |
| numberOfSitesWithStopCodon(const PolymorphismSequenceContainer &psc, const GeneticCode &gCode, bool gapflag=true) | bpp::SequenceStatistics | static |
| numberOfSynonymousPolymorphicCodons(const PolymorphismSequenceContainer &psc, const GeneticCode &gc) | bpp::SequenceStatistics | static |
| numberOfSynonymousSubstitutions(const PolymorphismSequenceContainer &psc, const GeneticCode &gc, double freqmin=0.) | bpp::SequenceStatistics | static |
| numberOfTransitions(const PolymorphismSequenceContainer &psc) | bpp::SequenceStatistics | static |
| numberOfTransversions(const PolymorphismSequenceContainer &psc) | bpp::SequenceStatistics | static |
| numberOfTriplets(const PolymorphismSequenceContainer &psc, bool gapflag=true) | bpp::SequenceStatistics | static |
| originRegressionD(const PolymorphismSequenceContainer &psc, bool distance1=false, bool keepsingleton=true, double freqmin=0.) | bpp::SequenceStatistics | static |
| originRegressionDprime(const PolymorphismSequenceContainer &psc, bool distance1=false, bool keepsingleton=true, double freqmin=0.) | bpp::SequenceStatistics | static |
| originRegressionR2(const PolymorphismSequenceContainer &psc, bool distance1=false, bool keepsingleton=true, double freqmin=0.) | bpp::SequenceStatistics | static |
| pairwiseD(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.) | bpp::SequenceStatistics | static |
| pairwiseDistances1(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.) | bpp::SequenceStatistics | static |
| pairwiseDistances2(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.) | bpp::SequenceStatistics | static |
| pairwiseDprime(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.) | bpp::SequenceStatistics | static |
| pairwiseR2(const PolymorphismSequenceContainer &psc, bool keepsingleton=true, double freqmin=0.) | bpp::SequenceStatistics | static |
| piNonSynonymous(const PolymorphismSequenceContainer &psc, const GeneticCode &gc, bool minchange=false) | bpp::SequenceStatistics | static |
| piSynonymous(const PolymorphismSequenceContainer &psc, const GeneticCode &gc, bool minchange=false) | bpp::SequenceStatistics | static |
| ratioOfTransitionsTransversions(const PolymorphismSequenceContainer &psc) | bpp::SequenceStatistics | static |
| rightHandHudson_(double c, size_t n) | bpp::SequenceStatistics | privatestatic |
| squaredHeterozygosity(const PolymorphismSequenceContainer &psc, bool gapflag=true) | bpp::SequenceStatistics | static |
| tajima83(const PolymorphismSequenceContainer &psc, bool gapflag=true, bool ignoreUnknown=true, bool scaled=false) | bpp::SequenceStatistics | static |
| tajimaDss(const PolymorphismSequenceContainer &psc, bool gapflag=true, bool ignoreUnknown=true) | bpp::SequenceStatistics | static |
| tajimaDtnm(const PolymorphismSequenceContainer &psc, bool gapflag=true, bool ignoreUnknown=true) | bpp::SequenceStatistics | static |
| testUsefulValues(std::ostream &s, size_t n) | bpp::SequenceStatistics | static |
| totalNumberOfMutations(const PolymorphismSequenceContainer &psc, bool gapflag=true) | bpp::SequenceStatistics | static |
| totalNumberOfMutationsOnExternalBranches(const PolymorphismSequenceContainer &ing, const PolymorphismSequenceContainer &outg) | bpp::SequenceStatistics | static |
| watterson75(const PolymorphismSequenceContainer &psc, bool gapflag=true, bool ignoreUnknown=true, bool scaled=false) | bpp::SequenceStatistics | static |
| watterson75NonSynonymous(const PolymorphismSequenceContainer &psc, const GeneticCode &gc) | bpp::SequenceStatistics | static |
| watterson75Synonymous(const PolymorphismSequenceContainer &psc, const GeneticCode &gc) | bpp::SequenceStatistics | static |
1.9.1