TransMatMaker
(Package: hisse) :
Transition Rate matrix generator
Generates and manipulates the index of the rate parameters to be optimized
● Data Source:
CranContrib
● Keywords:
● Alias: ParDrop, ParEqual, TransMatMaker
●
0 images
|
SimToPhylo
(Package: hisse) :
Convert simulated result to a tree
Converts the $results element of the return to a phylo object
● Data Source:
CranContrib
● Keywords: utility
● Alias: SimToPhylo
●
0 images
|
SimulateHisse
(Package: hisse) :
Simulate under a HiSSE model
Flexible simulation function allowing checkpointing
● Data Source:
CranContrib
● Keywords: simulation
● Alias: SimulateHisse
●
0 images
|
plot.hisse.states
(Package: hisse) :
Plotting function hisse.states objects
A plotting function for visualizing changes in states and rates over a phylogeny
● Data Source:
CranContrib
● Keywords: plotting
● Alias: plot.hisse.states
●
0 images
|
hisse.null4
(Package: hisse) :
Four state trait-independent Hidden State Speciation and Extinction
Sets up and executes a four state trait-independent HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character set.
● Data Source:
CranContrib
● Keywords: models
● Alias: hisse.null4
●
0 images
|
MarginRecon
(Package: hisse) :
Ancestral State Estimation based on Marginal Reconstruction
Estimates the likeliest states for both internal nodes and tips of a phylogeny using the marginal reconstruction algorithm.
● Data Source:
CranContrib
● Keywords: models
● Alias: MarginRecon
●
0 images
|
A simple utility function for organizing parameters from diversitree to be in the right format for marginRecon function.
● Data Source:
CranContrib
● Keywords: models
● Alias: BisseToHisse
●
0 images
|
SupportRegion
(Package: hisse) :
Adaptive Sampling of the Likelihood Surface
Adaptively samples points for each parameter to obtain an estimate of the confidence intervals.
● Data Source:
CranContrib
● Keywords: models
● Alias: SupportRegion
●
0 images
|
hisse
(Package: hisse) :
Hidden State Speciation and Extinction
Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character distribution.
● Data Source:
CranContrib
● Keywords: models
● Alias: hisse
●
0 images
|
providing 
.