RPANDA (version 2.3)

CreateGeoObject_BioGeoBEARS: Create biogeography object using a stochastic map from BioGeoBEARS

Description

Create biogeography object using a stochastic map created from any model in BioGeoBEARS (see documentation in BioGeoBEARS package).

Usage

CreateGeoObject_BioGeoBEARS( full.phylo, trimmed.phylo = NULL, ana.events,
clado.events, stratified=FALSE, simmap.out=FALSE)

Value

a list with the following components:

geography.object

a list of matrices specifying sympatry (1) or allopatry (0) for each species pair for each internode interval (see Details)

times

a vector containing the time since the root of the tree at which nodes or changes in biogeography occur (used internally in other functions)

spans

a vector specifying the distances between times (used internally in other functions)

Arguments

full.phylo

the object of type 'phylo' (see ape documentation) that was used to construct the stochastic map in BioGeoBEARS

trimmed.phylo

if the desired biogeography object excludes some species that were initially included in the stochastic map, this specifies a phylo object for the trimmed set of species

ana.events

the "ana.events" table produced in BioGeoBEARS that lists anagenetic events in the stochastic map

clado.events

the "clado.events" table produced in BioGeoBEARS that lists cladogenetic events in the stochastic map

stratified

logical indicating whether the stochastic map was built from a stratified analysis in BioGeoBEARS

simmap.out

logical indicating whether output should be a stochastic map (simmap) object (see note)

Author

Jonathan Drury

Details

Note: generating a stochastic map output using simmap.out=TRUE and passing to fit_t_comp for diversity dependent models with biogeography greatly speeds up model fitting compared to output generated when simmap.out=FALSE. This cannot be used for matching competition or any two-regime models with biogeography.

References

Drury, J., Clavel, J., Manceau, M., and Morlon, H. 2016. Estimating the effect of competition on trait evolution using maximum likelihood inference. Systematic Biology doi 10.1093/sysbio/syw020

Matzke, N. 2014. Model selection in historical biogeography reveals that founder-event speciation is a crucial process in island clades. Systematic Biology 63:951-970.

See Also

fit_t_comp CreateGeoObject

Examples

data(BGB.examples)

# \donttest{


##Example with a non-stratified tree

Canidae.geography.object<-CreateGeoObject_BioGeoBEARS(full.phylo=BGB.examples$Canidae.phylo,
ana.events=BGB.examples$Canidae.ana.events, clado.events=BGB.examples$Canidae.clado.events)

#on a subclade
Canidae.trimmed<-drop.tip(BGB.examples$Canidae.phylo 
							,BGB.examples$Canidae.phylo$tip.label[1:9])
							
Canidae.trimmed.geography.object<-CreateGeoObject_BioGeoBEARS(
full.phylo=BGB.examples$Canidae.phylo, trimmed.phylo=Canidae.trimmed, 
ana.events=BGB.examples$Canidae.ana.events, clado.events=BGB.examples$Canidae.clado.events)

##Example with a stratified tree

Ochotonidae.geography.object<-CreateGeoObject_BioGeoBEARS( 
full.phylo = BGB.examples$Ochotonidae.phylo, ana.events = BGB.examples$Ochotonidae.ana.events,
clado.events = BGB.examples$Ochotonidae.clado.events, stratified = TRUE)

#on a subclade
Ochotonidae.trimmed<-drop.tip(BGB.examples$Ochotonidae.phylo, 
BGB.examples$Ochotonidae.phylo$tip.label[1:9])
								
Ochotonidae.trimmed.geography.object<-CreateGeoObject_BioGeoBEARS(
full.phylo=BGB.examples$Ochotonidae.phylo, trimmed.phylo=Ochotonidae.trimmed, 
ana.events=BGB.examples$Ochotonidae.ana.events, 
clado.events=BGB.examples$Ochotonidae.clado.events, stratified=TRUE)

# }