define_species.BipartiteEvol: Build the phylogenies for BipartiteEvol

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/sim.BipartiteEvol.R

Description

Build the phylogenies from the output of BipartiteEvol and the corresponding genealogies

Usage

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define_species.BipartiteEvol(genealogy, threshold = 1, 
      distanceH = NULL, distanceP = NULL, verbose = T)

Arguments

genealogy

The output of a run of make_gen.BipartiteEvol

threshold

The species definition ratchet (s)

distanceH

Distance (ie nb of mutations) matrix between the individual of clade H

distanceP

Distance (ie nb of mutations) matrix between the individual of clade P

verbose

Should the progression of the computation be printed?

Value

a list with

P

The species identity of each individual in guild P

H

The species identity of each individual in guild H

Pphylo

The phylogeny for guild P

Hphylo

The phylogeny for guild H

Author(s)

O. Maliet

References

Maliet, O., Loeuille, N. and Morlon, H. (2020), An individual-based model for the eco-evolutionary emergence of bipartite interaction networks. Ecol Lett. doi:10.1111/ele.13592

See Also

sim.BipartiteEvol

Examples

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# run the model
set.seed(1)
mod = sim.BipartiteEvol(nx = 8,ny = 4,NG = 800,
                        D = 3, muP = 0.1 , muH = 0.1,
                        alphaP = 0.12,alphaH = 0.12,
                        rP = 10, rH = 10,
                        verbose = 100, thin = 5)

#build the genealogies
gen = make_gen.BipartiteEvol(mod)
plot(gen$H)

#compute the phylogenies
phy1 = define_species.BipartiteEvol(gen,threshold=1)

#plot the result
plot_div.BipartiteEvol(gen,phy1, 1)

#build the network
net = build_network.BipartiteEvol(gen, phy1)

trait.id = 1
plot_net.BipartiteEvol(gen,phy1,trait.id, net,mod, nx = nx, spatial = FALSE)


## add time steps to a former run
seed=as.integer(10)
set.seed(seed)

mod = sim.BipartiteEvol(nx = 8,ny = 4,NG = 200,
                        D = 3, muP = 0.1 , muH = 0.1,
                        alphaP = 0.12,alphaH = 0.12,
                        rP = 10, rH = 10,
                        verbose = 100, thin = 5,
                        P=mod$P,H=mod$H)  # former run output

# update the genealogy
gen = make_gen.BipartiteEvol(mod,
                             treeP=gen$P, treeH=gen$H)

# update the phylogenies...
phy1 = define_species.BipartiteEvol(gen,threshold=1)

#... and the network
net = build_network.BipartiteEvol(gen, phy1)

trait.id = 1
plot_net.BipartiteEvol(gen,phy1,trait.id, net,mod, nx = 10, spatial = FALSE)

RPANDA documentation built on Nov. 10, 2021, 9:08 a.m.