Uses of Interface
pal.misc.Units
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Packages that use Units Package Description pal.coalescent Classes to model population genetic processes using the coalescent.pal.mep Classes for the analysis of "measurably evolving populations" (mep).pal.misc Classes that don't fit elsewhere ;^)pal.supgma pal.tree Classes for providing the data structure of trees, for constructing and modifying trees, and for parameterizing trees (e.g., clock constraint). -
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Uses of Units in pal.coalescent
Classes in pal.coalescent that implement Units Modifier and Type Class Description classCoalescentIntervalsA series of coalescent intervals representing the time order information contained in a (serial) clock-constrained tree.classConstantPopulationThis class models coalescent intervals for a constant population (parameter: N0=present-day population size).classConstExpConstThis class models a population that grows exponentially from an initial population size alpha N0 at time y to a size N0 at time x until the present-day.classConstExpGrowthThis class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.classDemographicClockTreeProvides parameter interface to a clock-like genealogy which is assumed to have some demographic pattern of theta (diversity) as well as branch parameters (the minimal node height differences at each internal node).classDemographicModelThis abstract class contains methods that are of general use for modelling coalescent intervals given a demographic model.classExpandingPopulationThis class models a population that grows exponentially from an inital population size alpha N0 to a present-day size N0.classExponentialGrowthThis class models an exponentially growing (or shrinking) population (Parameters: N0=present-day population size; r=growth rate).classIntervalsExtractorA series of coalescent intervals representing the time order information contained in a (serial) clock-constrained tree.classSkylinePlotSkyline plot derived from a strictly bifurcating tree or a coalescent interval. -
Uses of Units in pal.mep
Classes in pal.mep that implement Units Modifier and Type Class Description classConstantMutationRateThis class models a constant mutation rate (parameter: mu = mutation rate).classMutationRateModelThis abstract class contains methods that are of general use for modelling mutation rate changes over time.classSteppedMutationRateThis class models a step-wise mutation rate.classWindowedMutationRateThis class models a windowed mutation rate (parameter: mu = mutation rate). -
Uses of Units in pal.misc
Subinterfaces of Units in pal.misc Modifier and Type Interface Description interfaceUnitsProviderinterface for classes that can provide the related Units used, (asClasses in pal.misc that implement Units Modifier and Type Class Description classTimeOrderCharacterDataCharacter data that expresses an order through time. -
Uses of Units in pal.supgma
Classes in pal.supgma that implement Units Modifier and Type Class Description classSUPGMATreeconstructs an SUPGMA tree from pairwise distances. -
Uses of Units in pal.tree
Subinterfaces of Units in pal.tree Modifier and Type Interface Description interfaceParameterizedTreeabstract base class for a tree with an Parameterized interfaceinterfaceTreeInterface for a phylogenetic or genealogical tree.Classes in pal.tree that implement Units Modifier and Type Class Description classClockTreeprovides parameter interface to a clock tree (parameters are the minimal node height differences at each internal node)classClusterTreeclassLogParameterizedTreeThis class logarithmically transforms tree parameters.classMutationRateModelTreeProvides parameter interface to any clock-like tree with serially sampled tips (parameters are the minimal node height differences at each internal node).classNeighborJoiningTreeconstructs a neighbor-joining tree from pairwise distances
Saitou, N., and Nei, M., (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees.static classParameterizedTree.ParameterizedTreeBaseFor parameterisations that work by adjusting a base tree (that is, they aren't really tree's themselves...)classReadTreeconstructs a tree reading in a New Hampshire treefile, taking care for internal labels and branch lengths and binary/nonbinary and rooted/unrooted treesclassSimpleTreedata structure for a binary/non-binary rooted/unrooted treesstatic classTree.TreeBaseclassUnconstrainedTreeprovides parameter interface to an unconstrained tree (parameters are all available branch lengths)classUPGMATreeDeprecated.Use ClusterTree
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