LeMansParam | R Documentation |
LeMansParam
classA constructor for the LeMansParam
class.
LeMansParam(df, gdf, ...) ## S4 method for signature 'ANY,ANY' LeMansParam( df, gdf, nfish = nrow(df), nsc = 32, pred_mu = -2.25, pred_sigma = 0.5, other = 1e+12, bounds = NULL, calc_phi_min = FALSE, phi_min = 0.1, vary_growth = TRUE, growth_eff = 0.5, growth_eff_decay = 0.11, eps = 1e-05, force_mature = TRUE, species_names = paste("species", 1:nfish, sep = "_"), kappa = rep(10, nfish), tau = matrix(1, nfish, nfish), rec_fun = rep("hockey-stick", nfish), recruit_params = list(a = 18.835 - 4.133 * df$Linf, b = rep(1000/nfish, nfish)), natmort_opt = rep("std_RNM", nfish), Nmort = rep(0.8, nfish), prop = rep(3/4, nfish), curve = rep("logistic", nfish), catch_species = ((0:(length(curve) - 1))%%nfish) + 1, max_catchability = rep(1, length(curve)), gear_name = paste("gear_", 1:length(curve), sep = ""), custom = NULL, ... ) ## S4 method for signature 'missing,ANY' LeMansParam( gdf, nfish = length(Linf), nsc = 32, pred_mu = -2.25, pred_sigma = 0.5, other = 1e+12, bounds = NULL, calc_phi_min = FALSE, phi_min = 0.1, vary_growth = FALSE, growth_eff = 0.5, growth_eff_decay = 0.11, eps = 1e-05, force_mature = TRUE, Linf, k, W_a, W_b, Lmat, species_names = paste("species", 1:nfish, sep = "_"), kappa = rep(10, nfish), tau = matrix(1, nfish, nfish), rec_fun = rep("hockey-stick", nfish), recruit_params = list(a = 18.835 - 4.133 * Linf, b = rep(1000/nfish, nfish)), natmort_opt = rep("std_RNM", nfish), Nmort = rep(0.8, nfish), prop = rep(3/4, nfish), curve = rep("logistic", nfish), catch_species = ((0:(length(curve) - 1))%%nfish) + 1, max_catchability = rep(1, length(curve)), gear_name = paste("gear_", 1:length(curve), sep = ""), custom = NULL, ... ) ## S4 method for signature 'missing,missing' LeMansParam( df, gdf, nfish = length(Linf), nsc = 32, pred_mu = -2.25, pred_sigma = 0.5, other = 1e+12, bounds = NULL, calc_phi_min = TRUE, phi_min = 0.1, vary_growth = FALSE, growth_eff = 0.5, growth_eff_decay = 0.11, eps = 1e-05, force_mature = TRUE, species_names = paste("species", 1:nfish, sep = "_"), Linf, k, W_a, W_b, Lmat, kappa = rep(10, nfish), tau = matrix(1, nfish, nfish), rec_fun = rep("hockey-stick", nfish), recruit_params = list(a = 18.835 - 4.133 * Linf, b = rep(1000/nfish, nfish)), natmort_opt = rep("std_RNM", nfish), Nmort = rep(0.8, nfish), prop = rep(3/4, nfish), curve = rep("logistic", nfish), catch_species = ((0:(length(curve) - 1))%%nfish) + 1, max_catchability = rep(1, length(curve)), gear_name = paste("gear_", 1:length(curve), sep = ""), custom = NULL, ... )
df |
A data frame with |
gdf |
A data frame with |
... |
Additional arguments for calculating catchability curves. See |
nfish |
A numeric value representing the number of fish species in the model. |
nsc |
A numeric value representing the number of length classes in the model. |
pred_mu |
A numeric value representing the preferred predator-prey mass ratio. |
pred_sigma |
A numeric value representing the width of the weight preference function. |
other |
A numeric value representing the amount of other food (g) available from prey that is not explicitly represented in the model. The default is |
bounds |
An optional argument specifying the bounds of the length classes. |
calc_phi_min |
A logical statement indicating whether |
phi_min |
A fixed numeric value of |
vary_growth |
A logical statement indicating whether growth efficiency should vary for each species ( |
growth_eff |
If |
growth_eff_decay |
A numeric value specifying the rate at which growth efficiency decreases as length increases to |
eps |
A numeric value specifying a numerical offset. The default value is |
force_mature |
A logical statement indicating whether to force maturity for all fish in the largest length class. The default is |
species_names |
A numeric or character vector of length |
kappa |
A numeric vector of length |
tau |
A matrix with dimensions |
rec_fun |
A character vector representing the stock recruitment function to be applied to each species. The default value is |
recruit_params |
A list object of length |
natmort_opt |
A character vector of length |
Nmort |
A numeric vector of length |
prop |
A numeric vector of length |
curve |
A character vector of almost any length describing the type of curve to be used to determine the catchability of each species by fishing gear. By default, |
catch_species |
A numeric value or character string describing the species to apply the catchability curve to. |
max_catchability |
A numeric vector of length |
gear_name |
A character vector of the same length as |
custom |
An array with dimensions |
Linf |
A numeric vector of length |
k |
k A numeric vector of length |
W_a |
A numeric vector representing the parameter |
W_b |
A numeric vector representing the parameter |
Lmat |
A numeric vector of length |
Converts objects of class data frame or vector to class LeMansParams for use in the LeMans model. Linf
, W_a
, W_b
, k
and Lmat
are required as either a data frame or as vectors.
An object of class LeMansParam
for use in the LeMans model.
run_LeMans
, LeMans_param
# To run the model with all inputs specified explicitly: # Set up 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). NS_params <- LeMansParam(species_names=NS_par$species_names, Linf=Linf, k=k, W_a=W_a, W_b=W_b, Lmat=Lmat, tau=NS_tau, recruit_params=list(a=NS_par$a, b=NS_par$b), eta=rep(0.25, 21), L50=Lmat, other=NS_other) ############################################### # Alternatively: NS_params <- LeMansParam(NS_par, tau=NS_tau, eta=rep(0.25, 21), L50=NS_par$Lmat, other=NS_other)
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