Description Usage Arguments Details Value References Examples

Calculates the proportion of individuals that are mature for each species and length class.

1 | ```
calc_mature(Lmat, nfish, mid, kappa, sc_Linf, eps = 1e-05, force_mature = TRUE)
``` |

`Lmat` |
A numeric vector of length |

`nfish` |
A numeric value representing the number of species in the model. |

`mid` |
A numeric vector of length |

`kappa` |
A numeric vector of length |

`sc_Linf` |
A numeric vector of length |

`eps` |
A numeric value specifying a numerical offset. The default is |

`force_mature` |
A logical statement indicating whether to force all fish in the largest length class to be mature. The default is |

The proportion of individuals in the `j`

th length class of the `i`

th species that are mature is described by a logistic model

`1/(1+exp(-kappa[i]*(mid[j]-Lmat[i])))`

A matrix with dimensions `nsc`

and `nfish`

and elements in the range 0-1 representing the proportion of individuals that are mature for each species and length class.

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.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | ```
# 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 <- tmp$phi
phi_min <- tmp$phi_min
# Calculate growth increments
tmp <- calc_ration_growthfac(k, Linf, nsc, nfish, l_bound, u_bound, mid, W_a, W_b, phi_min)
sc_Linf <- tmp$sc_Linf
# Calculate the proportion of mature individuals
mature <- calc_mature(Lmat, nfish, mid, kappa=rep(10, nfish), sc_Linf)
``` |

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