simbaltrees_topy: Simulate a set of balanced and unbalanced trees.
In sckott/treeshape: treeshape fxns

Description Usage Arguments Value Examples

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

  simbaltrees_topy(networksize = 10, metric, numtrees,
    cutlow, cuthigh, a, bounds, alpha, sigma, theta,
    alpha_eb, sigma_eb, rval = NULL, cval = NULL,
    asymm = 2.47, cores = 2, dumpmatrices = TRUE,
    matdir = "~", modeltorun = "complementarity",
    output = "matrix", includetraitvar = FALSE)

`networksize`	Number of total species to simulate in each tree - will be same for all trees. The number of plant and 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.
`output`	One of matrix or edgelist.

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

## Not run: 
temp <- simbaltrees_topy(networksize=30, metric="colless", numtrees=5, cutlow=-0.7,
		cuthigh=0.7, a=10, bounds=c(0,100), alpha=10, sigma=3,
		alpha_eb=-1.1, sigma_eb=3, cval=0.5, asymm=2.47, matdir="~/testtest",
		modeltorun="twomethods", output="edgelist", includetraitvar = TRUE)
head(temp) # traits data.frame

## End(Not run)