calc_recruits: Calculate the number of recruits
In LeMaRns: Length-Based Multispecies Analysis by Numerical Simulation

Description Usage Arguments Value References See Also Examples

Calculates the number of recruits of each species in a year.

1	calc_recruits(SSB, stored_rec_funs, rec_args)

`SSB`	A numeric vector of length `nfish` representing the Spawning Stock Biomass (SSB) of each species.
`stored_rec_funs`	A list object of length `nfish` that is used to store the generated stock recruitment functions.
`rec_args`	A list object of length `nfish` that is used to store the parameters of the stock recruitment functions.

A numeric vector of length nfish representing the number of new recruits of each species.

Barrowman, N.J., Myers, R.A. (2000). Still more spawner-recruit curves: the hockey stick and its generalisations. Canadian Journal of Fisheries and Aquatic Science, 57:665–676.

Beverton, R.J.H., Holt, S.J. (1957). On the Dynamics of Exploited Fish Populations, volume 19 of Fisheries Investigations (Series 2). United Kingdom Ministry of Agriculture and Fisheries.

Hall, S. J., Collie, J. S., Duplisea, D. E., Jennings, S., Bravington, M., & Link, J. (2006). A length-based multispecies model for evaluating community responses to fishing. Canadian Journal of Fisheries and Aquatic Sciences, 63(6):1344-1359.

Ogle, D.H. (2016). Introductory Fisheries Analyses with R. CRC Press.

Ricker, W.E. (1954). Stock and recruitment. Journal of the Fisheries Research Board of Canada, 11:559-623.

Thorpe, R.B., Le Quesne, W.J.F., Luxford, F., Collie, J.S., Jennings, S. (2015). Evaluation and management implications of uncertainty in a multispecies size-structured model of population and community responses to fishing. Methods in Ecology and Evolution, 6:49-58.

get_rec_fun, make_rec_fun, rec_BH, rec_Ricker, rec_hockey, rec_const, rec_linear and calc_SSB

# Set up the inputs to the function - species-independent parameters
nfish <- nrow(NS_par)
nsc <- 32
maxsize <- max(NS_par$Linf)*1.01 # the biggest size is 1% bigger than the largest Linf
l_bound <- seq(0, maxsize, maxsize/nsc); l_bound <- l_bound[-length(l_bound)]
u_bound <- seq(maxsize/nsc, maxsize, maxsize/nsc)
mid <- l_bound+(u_bound-l_bound)/2

# Set up the inputs to the function - species-specific parameters
Linf <- NS_par$Linf # the von-Bertalanffy asymptotic length of each species (cm).
W_a <- NS_par$W_a # length-weight conversion parameter.
W_b <- NS_par$W_b # length-weight conversion parameter.
k <- NS_par$k # the von-Bertalnaffy growth parameter.
Lmat <- NS_par$Lmat # the length at which 50\% of individuals are mature (cm).

# Get phi_min
tmp <- calc_phi(k, Linf, nsc, nfish, u_bound, l_bound, calc_phi_min=FALSE,
                  phi_min=0.1) # fixed phi_min
phi_min <- tmp$phi_min

# Run calc_ration_growthfac()
tmp <- calc_ration_growthfac(k, Linf, nsc, nfish, l_bound, u_bound, mid, W_a, W_b, phi_min)
sc_Linf <- tmp$sc_Linf
wgt <- tmp$wgt

# Calculate maturity
mature <- calc_mature(Lmat, nfish, mid, kappa=rep(10, nfish), sc_Linf)

# Create recruitment functions
stored_rec_funs <- get_rec_fun(rep("hockey-stick", nfish))
recruit_params <- do.call("Map", c(c, list(a=NS_par$a, b=NS_par$b)))

# Get an initial population
N0 <- get_N0(nsc, nfish, mid, wgt, sc_Linf, intercept=1e10, slope=-5)

# Calculate the SSB
SSB <- calc_SSB(mature, N0, wgt)

# Calculate the number of recruits
R <- calc_recruits(SSB, stored_rec_funs, recruit_params)