Description Usage Arguments Value Examples

Could use this in asking questions aobut how phylogenetic tree balance influences ____ (madlib it).

1 2 3 4 5 |

`tips_p` |
Number of plant species to simulate in each tree - will be same for all trees. The number of animal species will be calculated based on the value of the asymm parameter. |

`metric` |
Methods to use to generate trees, one of "colless", "beta", or gamma (see details). Defaults to "colless". |

`numtrees` |
Number of trees to produce. Defaults to 10 trees. |

`cutlow` |
Value at which to filter trees on the low (e.g., unbalanced) side of the metric. |

`cuthigh` |
Value at which to filter trees on the high (e.g., balanced) side of the metric. |

`a` |
If model = "bm", a value for ancestral state at the root node. |

`bounds` |
If model = "bm", a vector with the lower and upper bounds (respectively) for bounded Brownian simulation - by default simulation is unbounded. |

`alpha` |
If model = "ou", a value for the Ornstein-Uhlenbeck model of trait evolution. From ape documentation: "a numeric vector giving the strength of the selective constraint for each branch (can be a single value)." |

`sigma` |
If model = "ou", is the single value of the standard-deviation of the random component for each branch (can be a single value). |

`theta` |
If model = "ou", a numeric vector giving the optimum for each branch (can be a single value) |

`alpha_eb` |
If model = "eb", is the exponent of the relationship between rate and time in the exponentialchange model. |

`sigma_eb` |
If model = "eb", the single value of the standard-deviation of the random component for each branch (can be a single value). This sigma means the same as for the OU model, but this allows to specify it separately. |

`rval` |
Value for the ratio model for constructing interaction network matrices. |

`cval` |
Value for the complimentarity model for constructing interation network matrices. |

`asymm` |
An asymmetry value in terms of ratio of animals:plants instead of the traditional definition like (Na-Np/Na+Np), where Na is number of animal species, and Np is number of plant species. For example, asymm=2 would mean twice as many animal as plant species. |

`cores` |
Number of cores to use in mcmapply in simulating networks form traits. |

`dumpmatrices` |
If FALSE (default) matrices are not spit out to file, but if TRUE, then matrices are written to file in separate folders for each (logical) |

`matdir` |
Directory to output matrices to. Ignored if dumpmatrices=FALSE. |

`netmets` |
Network structure metrics to calculate - only use those that calculate single values for each matrix. |

A data.frame of network structure metrics for balanced and unbalanced trees.

1 2 3 4 5 6 7 | ```
## Not run:
netmets <- c("connectance", "nestedness","nodf2")
temp <- simbaltrees(tips_p=15, metric="colless", numtrees=5, cutlow=-0.5, cuthigh=0.5, a=10, bounds=c(0,100), alpha=1, sigma=1, alpha_eb=-0.8, sigma_eb=3, cval=0.5, asymm=2, cores=4, dumpmatrices=TRUE, matdir="~/newfiles2", netmets=netmets)
head(temp[[1]]) # traits data.frame
head(temp[[2]]) # network structure output data.frame
## End(Not run)
``` |

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