Man pages for jcpayne/mice-models
Model of Intermediate Complexity for Ecosystem Assessment
| allplots | Show all plots in a result object |
| Anchovy-class | An S4 class for Anchovy. |
| calc_availability | Calculate prey Availability parameter |
| calc_B1P | Calculate age 1+ biomass |
| calc_Bev_Holt | Calculate recruits, using a Beverton-Holt model |
| calc_Bprey_agepreferred | Calculate the age-preferred biomass of a prey species... |
| calc_B_sp | Calculate spawning biomass (tons) |
| calc_catch | Calculate catch (biomass units) |
| calc_Dy | Calculate Dy. |
| calc_Ft | Calculate fishing mortality according to a fishing rule |
| calc_Fy | Calculate fishing mortality according to a fishing rule |
| calc_G | Create environmental driver, G |
| calc_mortality_t | Calculate total mortality rate |
| calc_mortality_y | Calculate total mortality rate |
| calc_Nt | Calculate Numbers at age at time t, for species tracked by... |
| calc_Ny | Calculate Numbers at age for year y, for species tracked by... |
| calc_other_R | Calculate recruits for Other_forage species |
| calc_p | Calculate impact of prey biomass on predator reproduction |
| calc_phi | Calculate phi (impact of prey on predator reproduction) |
| calc_predatorRecruits | Calculate Predator Recruits |
| calc_predicted | Calculate predicted values |
| calc_predRecruits_Punt | Calculate recruits using Punt method |
| calc_preyRecruits | Calculate Prey recruits |
| calc_recruits | Calculate recruits. |
| calc_R_error | Calculate stochastic recruitment errors |
| calc_Ricker | Calculate recruits per spawner (Ricker method) |
| calibrate | Do a calibration run. |
| compile_results | Compile results and generate graphs for one species. |
| distribute_byage | Distribute initial recruitment by age. |
| distribute_bytimestep | Distribute numbers-at-age by timestep |
| get_every_nth | Get every nth value of a time series |
| get_params | Set parameter values in a Species object |
| get_prefs | Set diet preference slots in a Predator object. |
| initialize_N | Initialize a Species object. |
| justplot | Show one type of plot for all species |
| load_residuals | Load anchovy recruitment residuals |
| make_4panel | Make a 4-panel plot |
| makeplot | Plot a time series (a utility function) |
| Other_forage-class | An S4 class for Other_forage |
| Pelican-class | An S4 class for Pelicans. |
| plot_fitted | Plot a fitted function (observed vs. expected) |
| plot_fitted_multipanel | Plot a multi-panel fitted function (observed vs. expected) |
| plot_function_only | Plot a function (expected values only) |
| plot_summed_by_year | Sum a by-timestep series by years and plot it. |
| Predator-class | An S4 parent class for Predators. |
| Prey-class | A S4 parent class for Prey. |
| runMICE | Run simulations |
| Sardine-class | An S4 class for Sardine |
| Sealion-class | An S4 class for Sea lions |
| set_lesliematrix | Put survival rates into a Leslie matrix |
| set_simParam | Set parameter values in a simulationParams object. |
| set_species | Set initial parameter values in Species objects. |
| simulationParams-class | An S4 class to hold global parameters and input data for... |
| solve_age0_survival | Solve for age-0 survival |
| solve_fecundity | Solve for the scaling parameter for fecundity. |
| solve_for_Ft | Solve for F |
| Species-class | An S4 class to represent a generic species. |
