Index

A

add_property() (hyperiax.tree.tree.HypTree method)

B

BaseModel (class in hyperiax.models.basemodel)

C

children (hyperiax.tree.tree.TopologyNode attribute)

D

down() (hyperiax.models.lambdamodels.DownLambda method) (hyperiax.models.updownmodel.DownModel method)

DownLambda (class in hyperiax.models.lambdamodels) DownModel (class in hyperiax.models.updownmodel)

F

FastBiTree (class in hyperiax.tree.tree)

FixedParameter (class in hyperiax.mcmc.fixedparameter)

H

hyperiax module hyperiax.execution module hyperiax.execution.unorderedexecutor module hyperiax.mcmc module hyperiax.mcmc.fixedparameter module hyperiax.mcmc.metropolis_hastings module hyperiax.mcmc.parameter module hyperiax.mcmc.parameterstore module hyperiax.mcmc.varianceParameter module hyperiax.models module hyperiax.models.basemodel module

hyperiax.models.functional module hyperiax.models.functional.reducers module hyperiax.models.functional.shortup module hyperiax.models.lambdamodels module hyperiax.models.prebuilts module hyperiax.models.prebuilts.mean_estimation module hyperiax.models.updatemodel module hyperiax.models.updownmodel module hyperiax.tree module hyperiax.tree.tree module HypTree (class in hyperiax.tree.tree)

I

inverse_gamma_logpdf() (in module hyperiax.mcmc.varianceParameter) iter_topology_bfs() (hyperiax.tree.tree.HypTree method) iter_topology_dfs() (hyperiax.tree.tree.HypTree method)

iter_topology_leaves_bfs() (hyperiax.tree.tree.HypTree method) iter_topology_leaves_dfs() (hyperiax.tree.tree.HypTree method) iter_topology_levels() (hyperiax.tree.tree.HypTree method)

L

log_prior() (hyperiax.mcmc.fixedparameter.FixedParameter method) (hyperiax.mcmc.parameter.Parameter method) (hyperiax.mcmc.parameterstore.ParameterStore method) (hyperiax.mcmc.varianceParameter.VarianceParameter method)

M

metropolis_hastings() (in module hyperiax.mcmc.metropolis_hastings) module hyperiax hyperiax.execution hyperiax.execution.unorderedexecutor hyperiax.mcmc hyperiax.mcmc.fixedparameter hyperiax.mcmc.metropolis_hastings hyperiax.mcmc.parameter hyperiax.mcmc.parameterstore hyperiax.mcmc.varianceParameter hyperiax.models hyperiax.models.basemodel hyperiax.models.functional hyperiax.models.functional.reducers hyperiax.models.functional.shortup hyperiax.models.lambdamodels hyperiax.models.prebuilts hyperiax.models.prebuilts.mean_estimation hyperiax.models.updatemodel hyperiax.models.updownmodel hyperiax.tree hyperiax.tree.tree tree

N

name (hyperiax.tree.tree.TopologyNode attribute)

P

Parameter (class in hyperiax.mcmc.parameter) ParameterStore (class in hyperiax.mcmc.parameterstore) parent (hyperiax.tree.tree.TopologyNode attribute) pass_up() (in module hyperiax.models.functional.shortup)

PhyloMeanModel (class in hyperiax.models.prebuilts.mean_estimation) propose() (hyperiax.mcmc.fixedparameter.FixedParameter method) (hyperiax.mcmc.parameter.Parameter method) (hyperiax.mcmc.parameterstore.ParameterStore method) (hyperiax.mcmc.varianceParameter.VarianceParameter method)

R

ReducerModel (class in hyperiax.models.basemodel)

S

sum_fuse_children() (in module hyperiax.models.functional.reducers)

T

TopologyNode (class in hyperiax.tree.tree) transform() (hyperiax.models.lambdamodels.UpLambdaReducer method) (hyperiax.models.prebuilts.mean_estimation.PhyloMeanModel method) (hyperiax.models.updownmodel.UpReducer method)

tree module TreeField (class in hyperiax.tree.tree)

U

UnorderedExecutor (class in hyperiax.execution.unorderedexecutor) up() (hyperiax.models.lambdamodels.UpdateLambdaReducer method) (hyperiax.models.lambdamodels.UpLambda method) (hyperiax.models.lambdamodels.UpLambdaReducer method) (hyperiax.models.prebuilts.mean_estimation.PhyloMeanModel method) (hyperiax.models.updatemodel.UpdateReducer method) (hyperiax.models.updownmodel.UpModel method) (hyperiax.models.updownmodel.UpReducer method) update() (hyperiax.execution.unorderedexecutor.UnorderedExecutor method) (hyperiax.mcmc.fixedparameter.FixedParameter method) (hyperiax.mcmc.parameter.Parameter method) (hyperiax.mcmc.varianceParameter.VarianceParameter method) (hyperiax.models.lambdamodels.UpdateLambda method) (hyperiax.models.lambdamodels.UpdateLambdaReducer method) (hyperiax.models.updatemodel.UpdateModel method) (hyperiax.models.updatemodel.UpdateReducer method)

UpdateLambda (class in hyperiax.models.lambdamodels) UpdateLambdaReducer (class in hyperiax.models.lambdamodels) UpdateModel (class in hyperiax.models.updatemodel) UpdateReducer (class in hyperiax.models.updatemodel) UpLambda (class in hyperiax.models.lambdamodels) UpLambdaReducer (class in hyperiax.models.lambdamodels) UpModel (class in hyperiax.models.updownmodel) UpReducer (class in hyperiax.models.updownmodel)

V

values() (hyperiax.mcmc.parameterstore.ParameterStore method)

VarianceParameter (class in hyperiax.mcmc.varianceParameter)