R: Extended DPR population dynamics model to include homerange...

DPRHomerangeGravity {ConnMatTools}

R Documentation

Extended DPR population dynamics model to include homerange movement

Description

This function implements the marine population dynamics model described in Gruss et al. (2011). The model is an extension of the dispersal-per-recruit model in Kaplan et al. (2006) to include movement in a homerange and a gravity model for fishing effort redistribution.

Usage

DPRHomerangeGravity(
  larval.mat,
  adult.mat,
  recruits0,
  f0,
  timesteps = 10,
  settler.recruit.func = hockeyStick,
  LEP.of.f = function(f) 1 - f,
  YPR.of.f = function(f) f,
  gamma = 0,
  gravity.ts.interval = 1,
  ...
)

Arguments

`larval.mat`	a square larval connectivity matrix. `dim(larval.mat) = rep(length(recruits0),2)`
`adult.mat`	a square adult homerange movement matrix. `dim(adult.mat) = rep(length(recruits0),2)`. adult.mat must be properly normalized so that each column sums to 1.
`recruits0`	a vector of initial recruitment values for each site.
`f0`	a vector of initial real fishing mortalities for each site.
`timesteps`	a vector of timesteps at which to record egg production, settlement and recruitment.
`settler.recruit.func`	a function to calculate recruitment from the number of settlers at each site. Defaults to `hockeyStick`.
`LEP.of.f`	a function that returns lifetime-egg-productions given a vector of fishing rates.
`YPR.of.f`	a function that returns yields-per-recruit given a vector of fishing rates.
`gamma`	exponent for the gravity model. Defaults to 0, i.e., no gravity model.
`gravity.ts.interval`	number of timesteps between updates of gravity model. Defaults to 1, i.e., every timestep.
`...`	additional arguments to settler.recruit.func.

Value

A list with the following elements:

`eggs`	egg production for the timesteps in `timesteps`
`settlers`	Similar for settlement
`recruits`	Similar for recruitment
`fishing.mortality`	Real spatial distribution of fishing mortality
`effective.fishing.mortality`	Effective fishing mortality taking into account adult movement
`yield`	Real spatial distribution of yield
`effective.yield`	Effective yield indicating where fish biomass caught originates from

Author(s)

David M. Kaplan dmkaplan2000@gmail.com

References

Gruss A, Kaplan DM, Hart DR (2011) Relative Impacts of Adult Movement, Larval Dispersal and Harvester Movement on the Effectiveness of Reserve Networks. PLoS ONE 6:e19960

Kaplan, D. M., Botsford, L. W., and Jorgensen, S. 2006. Dispersal per recruit: An efficient method for assessing sustainability in marine reserve networks. Ecological Applications, 16: 2248-2263.