Length-Based Multispecies Analysis by Numerical Simulation

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Documentation for package ‘LeMaRns’ version 0.1.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

calc_biomass	Calculate Spawning Stock Biomass (SSB) or total biomass
calc_growth	Calculate growth
calc_LFI	Calculate community indicators
calc_LQ	Calculate community indicators
calc_M1	Calculate background mortality
calc_M1_constRNM	Calculate background mortality
calc_M1_lin	Calculate background mortality
calc_M1_stdRNM	Calculate background mortality
calc_M2	Calculate predation mortality
calc_mature	Calculate the proportion of mature individuals
calc_phi	Calculate the proportion of individuals that leave each length class for each species each length class each time step.
calc_prefs	Calculate predator-prey size preferences
calc_Q	Calculate gear catchability
calc_ration_growthfac	Calculate growth increments
calc_recruits	Calculate the number of recruits
calc_SSB	Calculate Spawning Stock Biomass (SSB) or total biomass
calc_suit_vect	Combines prey preference and prey suitability
calc_TyL	Calculate community indicators
comb_LeMans_run	Combine two 'LeMans_outputs' objects
get_annual_catch	Get annual catch for each species, catch per unit effort or catch per gear
get_annual_catch-method	Get annual catch for each species, catch per unit effort or catch per gear
get_biomass	Calculate Spawning Stock Biomass (SSB) or total biomass
get_biomass-method	Calculate Spawning Stock Biomass (SSB) or total biomass
get_CPG	Get annual catch for each species, catch per unit effort or catch per gear
get_CPG-method	Get annual catch for each species, catch per unit effort or catch per gear
get_CPUE	Get annual catch for each species, catch per unit effort or catch per gear
get_CPUE-method	Get annual catch for each species, catch per unit effort or catch per gear
get_indicators	Calculate indicators
get_indicators-method	Calculate indicators
get_LFI	Calculate indicators
get_LFI-method	Calculate indicators
get_LQ	Calculate indicators
get_LQ-method	Calculate indicators
get_M1	Calculate background mortality
get_MML	Calculate indicators
get_MML-method	Calculate indicators
get_N0	Generate a starting value for N
get_Q	Calculate gear catchability
get_rec_fun	Collate the stock recruitment functions
get_SSB	Calculate Spawning Stock Biomass (SSB) or total biomass
get_SSB-method	Calculate Spawning Stock Biomass (SSB) or total biomass
get_TyL	Calculate indicators
get_TyL-method	Calculate indicators
knife_edge_catch	Calculate gear catchability
LeMansParam	A constructor for the 'LeMansParam' class
LeMansParam-method	A constructor for the 'LeMansParam' class
LeMans_outputs-class	An S4 class representing the outputs of the LeMans model
LeMans_param-class	An S4 class representing the inputs of the LeMans model
logistic_catch	Calculate gear catchability
log_gaussian_catch	Calculate gear catchability
make_rec_fun	Generate the stock recruitment functions
NS_eta	The steepness of the slope of the catchability curve
NS_L50	The length at 50% of the maximum catchability of the catchability curve
NS_mixed_fish	Gear selectivity data frame
NS_other	Other food for the North Sea
NS_par	North Sea data
NS_tau	North Sea interaction matrix
plot_biomass	Plot Spawning Stock Biomass (SSB)
plot_biomass-method	Plot Spawning Stock Biomass (SSB)
plot_indicators	Plot indicators
plot_indicators-method	Plot indicators
plot_LFI	Plot indicators
plot_LFI-method	Plot indicators
plot_LQ	Plot indicators
plot_LQ-method	Plot indicators
plot_MML	Plot indicators
plot_MML-method	Plot indicators
plot_SSB	Plot Spawning Stock Biomass (SSB)
plot_SSB-method	Plot Spawning Stock Biomass (SSB)
plot_TyL	Plot indicators
plot_TyL-method	Plot indicators
rec_BH	The Beverton-Holt stock recruitment function
rec_const	The constant stock recruitment function
rec_hockey	The hockey-stick stock recruitment function
rec_linear	The density-independent stock recruitment function
rec_Ricker	The Ricker stock recruitment function
run_LeMans	Project the LeMans model
run_LeMans-method	Project the LeMans model