manageSetup: Setup Management Structure

In gabackus/rcomms: Simulate Randomized Metacommunities under Stochastic Climate Change

Description

This sets up the management options for a simulation. It creates a list of several lists that include paramaters for each management option. Many of these don't bother to check for errors, so make sure you're careful.

Usage

manageSetup(P, X, years = 100, AM = NULL, corridor = NULL,
  habQual = NULL, locHet = NULL, velocHet = NULL, targs = NULL,
  eta = 50, tCD = 5, rho = 0.8, mu = 0.8, zEst = P$zo,
  xLoc = 10, recRad = 2, donor = 1, recipient = 1, tLR = NULL,
  randPick = F)

Arguments

P	List of biotic parameters
X	List of abiotic parameters
years	The number of years that the model is going to be run.
AM	Assisted migration. TRUE or FALSE determine whether the model runs through AM during each time step. If left NULL, this function will not define any parameters for AM.
corridor	Corridor establishment. TRUE or FALSE determine whether the model runs through corridor management during each time step. If left NULL, this function will not define any parameters for corridor.
habQual	Change habitat quality. TRUE or FALSE determine whether the model runs through changing habitat quality during each time step. If left NULL, this function will not define any parameters for habQual.
locHet	Change local heterogeneity. TRUE or FALSE determine whether the model runs through changing local heterogeneity during each time step. If left NULL, this function will not define any parameters for locHet.
velocHet	Change heterogeneity climate velocity. TRUE or FALSE determine whether the model runs through changing heterogeneity in climate velocity during each time step. If left NULL, this function will not define any parameters for velocHet.
targs	Which species are specifically targeted for assisted migration? A list of 0s (for not targeted) and 1s (for targeted). Must be a vector of length S. Could also be a vector of species number (index from P parameters). Lastly, can just be "all" to include all species.
eta	Relocation threshold. Any population of a target species that falls below this is relocated. Should be a nonnegative single integer or a vector of length S.
tCD	Cooldown time between relocations. AM is not repeated if tCD has not passed since the last AM event. Should be a single nonnegative integer or a vector of length S.
rho	Proportion of the total population moved when AM is triggered. Should be a single number from 0 to 1 or a vector of length S.
mu	Probability of surviving AM. Should be a single number from 0 to 1 or a vector of length S.
zEst	Estimate of species' thermal optimum. Should be a vector of length S.
xLoc	How far ahead (in the direction of the leading edge) of the location closest to the thermal optimum estimate are we centering the relocation? Should be a single integer or a vector of length S.
recRad	How wide is the recipient location? The recipient location consists of the center location (xLoc in front of the thermal optimum) and each patch +/- recRad from this center. Should be a single positive integer or a vector of length S.
donor	Which individuals do we take from the donor community? 1: randomly (from the "top"), 2: from the trailing edge, 3: from the leading edge. Possible future extensions are 4: from the middle and 5: randomly from the old donor population. Should be a single integer.
recipient	What shape should the recipient population look like? 1: an evenly distributed box. Possible future extensions are 2: rounded, 3: triangular, 4: thermal tolerance shaped. Should be a single integer.
tLR	When was the last time the species was relocated? Should be an integer vector of length S.
randPick	Do you want to pick exactly rho of the population (rounded down) or would you rather randomly pick from a binomial distribution with rho as the probability? If you want to do this randomly, set randPick to T. By default, it is set to F.

Value

A list of parameters that tell the model when and how to enact various managment techniques.

Examples

cSetup<-commSetup(S=32,L=512,W=4,years=202)
P<-cSetup$P
X<-cSetup$X
mSetup<-manageSetup(P,X,AM=T,targs = "all",eta=40,rho=0.6)
n0 <- nSetup(8,32,512,4)
initSim <- commSimulate(n0,P,X,y=1,years=100,init=T)
n1 <- initSim$n
ccSim <- commSimulate(n1,P,X,y=101,years=100,init=F)
vComTime(ccSim$N)

gabackus/rcomms documentation built on Nov. 4, 2019, 1 p.m.