perspectev.simulate: Simulate upper/lower level selection at different intensities...

In perspectev: Permutation of Species During Turnover Events

Description

Perform simulations of natural selection on a data set, and observe what p values result. Performs linear transformation of trait vs. survivorship (using provided or fitted slope and intercept) and then transforms into survviorship probabilites using inv.logit function.

Usage

perspectev.simulate(data,simulations,cores,traitfun=mcpRange,vlist=NULL,
	binary=NA,intercept=NA,slope=NA,level=NA,noise=0,fit=FALSE,quiet=FALSE)

Arguments

data	Dataframe in perspectev format. See ?perspectev.read for more information.
simulations	Number of simulations to perform. At least 1000 is recommended but can be slow.
cores	Number of cores over which to parallelize the simulations.
traitfun	Function for calculating trait value at each level.
vlist	Optional variable list for trait function.
intercept	Intercept of the regression between range and survivorship. Can be manually provided or, if not provided, is fit to the data set. Will attempt to set automatically if unspecified.
slope	Slope of the regression between range and survivorship. Can be manually provided or, if not provided, is fit to the data set. Will attempt to set automatically if unspecified.
level	Simulate either upper or lower level selection. Accepts either "lower" or "upper" respectively. Will set to 'upper' if unspecified.
noise	Extra stochasticity to the simulation.
fit	Fit simulation to observed parameters? Will do automatically if intercept or slope are not specified.
binary	Is survivorship binary or continuous? Will attempt to set automatically if unspecified.
quiet	Suppress information messages?

Value

correlation_simulated	Correlation between trait and surivovorship from permuted groups at each simulation.
correlation_observed	Observed correlation between trait and surivovorship from simulated groups.
pvalue	p value observed under simulation of selection.
level	Level of simulated selection.
intercept	Intercept of simulation.
slope	Slope of the simulation.
noise	Noise level selected for simulation.
fitted_model	Was the model fitted to the data set?

Note

See original publication and tutorial for more information on simulation.

Author(s)

Kenneth B. Hoehn <[e-mail]>

perspectev documentation built on May 1, 2019, 6:32 p.m.