Description Usage Arguments Value Examples
View source: R/simbaltrees_topy.r
Could use this in asking questions aobut how phylogenetic tree balance influences ____ (madlib it).
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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.
1 2 3 4 5 6 7 8 | ## 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)
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