ltt.network: Lineages thru time on a network
In jjustison/SiPhyNetwork: A Phylogenetic Simulator for Reticulate Evolution
ltt.network R Documentation
Lineages thru time on a network
Description
This function Computes the number of lineages thru time on a network
Usage
ltt.network(phy, node_times = NULL)
Arguments
phy
An object of class 'evonet.'
node_times
A numeric vector specifying times of each node. If left NULL then the function will use the output from node.depth.edgelength(phy)
Value
A dataframe that consists of intervals. The first column denotes the start time of the interval while the second column denotes the end time. The third column depicts the number of lineages present in that interval.
NOTE: due to computational precision, two nodes that appear to occur on the same time (as in the case of lineage neutral and generative hybridization) may be part of different intervals in the output data frame.
Examples
set.seed(17) ##smallest Quartan prime as seed
##Generate a tree with extinct leaves
net<-sim.bdh.age(1,1,5,2,1,c(1/3,1/3,1/3),hyb.inher.fxn = make.uniform.draw(),complete=TRUE)[[1]]
ltt.network(net)
jjustison/SiPhyNetwork documentation built on Sept. 14, 2024, 8:58 a.m.
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| ltt.network | R Documentation |
Lineages thru time on a network
Description
This function Computes the number of lineages thru time on a network
Usage
ltt.network(phy, node_times = NULL)
Arguments
phy |
An object of class 'evonet.' |
node_times |
A numeric vector specifying times of each node. If left NULL then the function will use the output from node.depth.edgelength(phy) |
Value
A dataframe that consists of intervals. The first column denotes the start time of the interval while the second column denotes the end time. The third column depicts the number of lineages present in that interval. NOTE: due to computational precision, two nodes that appear to occur on the same time (as in the case of lineage neutral and generative hybridization) may be part of different intervals in the output data frame.
Examples
set.seed(17) ##smallest Quartan prime as seed
##Generate a tree with extinct leaves
net<-sim.bdh.age(1,1,5,2,1,c(1/3,1/3,1/3),hyb.inher.fxn = make.uniform.draw(),complete=TRUE)[[1]]
ltt.network(net)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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