perspectev.simulate: Simulate upper/lower level selection at different intensities and observe resulting p values.

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?