larvaldispersal: Disperse and recruits larvae

Description Usage Arguments Examples

Description

This function uses the dispersal function to disperse the recruits, but also applies both natural mortality and that linked to habitat carrying capacity.

Usage

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larvaldispersal(recruits, cml, lM, CCs, fish)

Arguments

recruits

a vector of the number of recruits per cell

cml

A connectivity matrix containing the probability of dispersing from each starting location (rows) to each end location (columns). Can easily be generated by initcm

lM

A vector of natural larval mortality to be selected from

CCs

Habitat carrying capacity, in kg

fish

a matrix of fish numbers by site (rows) and by age (columns). Can easily be generated by initpop

Examples

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# create a fish matrix
fish <- initpop(initial_abun=250*10^6,cells=length(BESTMPA_domain),maxage=50,rate=0.7)
# identify nearby breeding grounds
breeding_near <- apply(gDistance(spTransform(Breeding,proj),p,byid = T),1,which.min)
# generate recruits vector
recruits <- reproduction(fish,fecundity=5e+05,age_mat_steepness=2.5,age_mat_sigmoid=4,l_to_w_int=1.1e-05,l_to_w_power=2.91,Linf_mean=112.03,Linf_SD=5.336735,k_mean=0.13,k_SD= 0.01071429,t0=0.18,breeding_near=breeding_near,domain=BESTMPA_domain)
# exponential dispersal kernal
cm <- initcm(domain=BESTMPA_domain,e_fold=75000,cell_size=20000)
recruits <- larvaldispersal(recruits=recruits,cml=cml,lM=rnorm(10000,0.5,0.1),CCs=rnorm(length(recruits),0.5,0.1))

remi-daigle/BESTMPA documentation built on May 27, 2019, 4:55 a.m.