simbaltrees: Simulate a set of balanced and unbalanced trees.

Description Usage Arguments Value Examples

View source: R/simbaltrees.r

Description

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

Usage

1
2
3
4
5
  simbaltrees(tips_p = 10, metric, numtrees, cutlow,
    cuthigh, a, bounds, alpha, sigma, theta, alpha_eb,
    sigma_eb, rval = NULL, cval = NULL, asymm = 1,
    cores = 2, dumpmatrices = FALSE, matdir = "~",
    netmets = c("connectance", "links per species", "nestedness", "web asymmetry"))

Arguments

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.

Value

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

Examples

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)

sckott/treeshape documentation built on May 26, 2017, 3:50 a.m.