sim_traits_nets_par: Simulate networks, with interactions propoprtional to trait...

In sckott/treeshape: treeshape fxns

Description

Simulate networks, with interactions propoprtional to trait matching

Usage

  sim_traits_nets_par(listoftraitvecs, type = NULL,
    traitm = NULL, matdir = "~",
    method = c("complementarity", "barrier", "twomethods"),
    includetraitvar = FALSE, value = NULL,
    output = "matrix")

Arguments

listoftraitvecs	Nested list of trait vectors.
type	Balanced ("bal") or unbalanced ("unbal").
traitm	Evolutionary model, used to create file name, one of "bm", "ou", or "eb".
matdir	directory to put matrices in
method	The model to be used to construct interaction matrices. One of "complementarity", "barrier", or "twomethods" (for combined complementarity/barrier).
includetraitvar	Include trait variation in the simulation or not. Defaults to FALSE.
value	Value at which to determine if species interact or not - this value depends on the model you are using.
output	One of matrix or edgelist.

Value

A data.frame of network structure metrics for balanced and unbalanced trees (if output="matrix"), or an edgelist (if output="edgelist").

Examples

## Not run: 
trees <- rmtree(N=100, n=15)
trees2 <- rmtree(N=100, n=30)
library(doMC)
registerDoMC(4)
traitvecs <- llply(trees, fastBM, bounds=c(0,Inf), .parallel=TRUE)
traitvecs2 <- llply(trees2, fastBM, bounds=c(0,Inf), .parallel=TRUE)
alltraits <- list(traitvecs, traitvecs2)
sim_traits_nets_par(listoftraitvecs=alltraits, method="c", value=0.5, type="bal", traitm="bm", matdir="~/testtest", includetraitvar = TRUE)
sim_traits_nets_par(listoftraitvecs=alltraits, method="b", type="bal", traitm="bm", matdir="~/newfiles2")
length(out)

## End(Not run)

sckott/treeshape documentation built on May 29, 2019, 4:07 p.m.