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"calc_M2" ] }, { "page": "calc_mature", "title": "Calculate the proportion of mature individuals", "topics": [ "calc_mature" ] }, { "page": "calc_phi", "title": "Calculate the proportion of individuals that leave each length class for each species each length class each time step.", "topics": [ "calc_phi" ] }, { "page": "calc_prefs", "title": "Calculate predator-prey size preferences", "topics": [ "calc_prefs" ] }, { "page": "calc_Q", "title": "Calculate gear catchability", "topics": [ "calc_Q", "get_Q", "knife_edge_catch", "logistic_catch", "log_gaussian_catch" ] }, { "page": "calc_ration_growthfac", "title": "Calculate growth increments", "topics": [ "calc_ration_growthfac" ] }, { "page": "calc_recruits", "title": "Calculate the number of recruits", "topics": [ "calc_recruits" ] }, { "page": "calc_SSB", "title": "Calculate Spawning Stock Biomass (SSB) or total biomass", "topics": [ "calc_biomass", "calc_SSB" ] }, { "page": "calc_suit_vect", "title": "Combines prey preference and prey suitability", "topics": [ "calc_suit_vect" ] }, { "page": "comb_LeMans_run", "title": "Combine two 'LeMans_outputs' objects", "topics": [ "comb_LeMans_run" ] }, { "page": "get_annual_catch", "title": "Get annual catch for each species, catch per unit effort or catch per gear", "topics": [ "get_annual_catch", "get_annual_catch,LeMans_param,LeMans_outputs-method", "get_annual_catch,LeMans_param,missing-method", "get_annual_catch,missing,LeMans_outputs-method", "get_annual_catch,missing,missing-method", "get_CPG", "get_CPG,LeMans_param,LeMans_outputs-method", "get_CPG,LeMans_param,missing-method", "get_CPG,missing,LeMans_outputs-method", "get_CPG,missing,missing-method", "get_CPUE", "get_CPUE,LeMans_param,LeMans_outputs-method", "get_CPUE,LeMans_param,missing-method", "get_CPUE,missing,LeMans_outputs-method", "get_CPUE,missing,missing-method" ] }, { "page": "get_indicators", "title": "Calculate indicators", "topics": [ "get_indicators", "get_indicators,LeMans_param,LeMans_outputs-method", "get_indicators,LeMans_param,missing-method", "get_indicators,missing,LeMans_outputs-method", "get_indicators,missing,missing-method", "get_LFI", "get_LFI,LeMans_param,LeMans_outputs-method", "get_LFI,LeMans_param,missing-method", "get_LFI,missing,LeMans_outputs-method", "get_LFI,missing,missing-method", "get_LQ", "get_LQ,LeMans_param,LeMans_outputs-method", "get_LQ,LeMans_param,missing-method", "get_LQ,missing,LeMans_outputs-method", "get_LQ,missing,missing-method", "get_MML", "get_MML,LeMans_param,LeMans_outputs-method", "get_MML,LeMans_param,missing-method", "get_MML,missing,LeMans_outputs-method", "get_MML,missing,missing-method", "get_TyL", "get_TyL,LeMans_param,LeMans_outputs-method", "get_TyL,LeMans_param,missing-method", "get_TyL,missing,LeMans_outputs-method", "get_TyL,missing,missing-method" ] }, { "page": "get_N0", "title": "Generate a starting value for N", "topics": [ "get_N0" ] }, { "page": "get_rec_fun", "title": "Collate the stock recruitment functions", "topics": [ "get_rec_fun" ] }, { "page": "get_SSB", "title": "Calculate Spawning Stock Biomass (SSB) or total biomass", "topics": [ "get_biomass", "get_biomass,LeMans_param,LeMans_outputs-method", "get_biomass,LeMans_param,missing-method", "get_biomass,missing,LeMans_outputs-method", "get_biomass,missing,missing-method", "get_SSB", "get_SSB,LeMans_param,LeMans_outputs-method", "get_SSB,LeMans_param,missing-method", "get_SSB,missing,LeMans_outputs-method", "get_SSB,missing,missing-method" ] }, { "page": "LeMans_outputs-class", "title": "An S4 class representing the outputs of the LeMans model", "topics": [ "LeMans_outputs-class" ] }, { "page": "LeMans_param-class", "title": "An S4 class representing the inputs of the LeMans model", "topics": [ "LeMans_param-class" ] }, { "page": "LeMansParam", "title": "A constructor for the 'LeMansParam' class", "topics": [ "LeMansParam", "LeMansParam,ANY,ANY-method", "LeMansParam,missing,ANY-method", "LeMansParam,missing,missing-method" ] }, { "page": "make_rec_fun", "title": "Generate the stock recruitment functions", "topics": [ "make_rec_fun" ] }, { "page": "NS_eta", "title": "The steepness of the slope of the catchability curve", "topics": [ "NS_eta" ] }, { "page": "NS_L50", "title": "The length at 50% of the maximum catchability of the catchability curve", "topics": [ "NS_L50" ] }, { "page": "NS_mixed_fish", "title": "Gear selectivity data frame", "topics": [ "NS_mixed_fish" ] }, { "page": "NS_other", "title": "Other food for the North Sea", "topics": [ "NS_other" ] }, { "page": "NS_par", "title": "North Sea data", "topics": [ "NS_par" ] }, { "page": "NS_tau", "title": "North Sea interaction matrix", "topics": [ "NS_tau" ] }, { "page": "plot_indicators", "title": "Plot indicators", "topics": [ "plot_indicators", "plot_indicators,LeMans_param,LeMans_outputs-method", "plot_indicators,LeMans_param,missing-method", "plot_indicators,missing,LeMans_outputs-method", "plot_indicators,missing,missing-method", "plot_LFI", "plot_LFI,LeMans_param,LeMans_outputs-method", "plot_LFI,LeMans_param,missing-method", "plot_LFI,missing,LeMans_outputs-method", "plot_LFI,missing,missing-method", "plot_LQ", "plot_LQ,LeMans_param,LeMans_outputs-method", "plot_LQ,LeMans_param,missing-method", "plot_LQ,missing,LeMans_outputs-method", "plot_LQ,missing,missing-method", "plot_MML", "plot_MML,LeMans_param,LeMans_outputs-method", "plot_MML,LeMans_param,missing-method", "plot_MML,missing,LeMans_outputs-method", "plot_MML,missing,missing-method", "plot_TyL", "plot_TyL,LeMans_param,LeMans_outputs-method", "plot_TyL,LeMans_param,missing-method", "plot_TyL,missing,LeMans_outputs-method", "plot_TyL,missing,missing-method" ] }, { "page": "plot_SSB", "title": "Plot Spawning Stock Biomass (SSB)", "topics": [ "plot_biomass", "plot_biomass,LeMans_param,LeMans_outputs-method", "plot_biomass,LeMans_param,missing-method", "plot_biomass,missing,LeMans_outputs-method", "plot_biomass,missing,missing-method", "plot_SSB", 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