base_model: Base Model

In vquennessen/densityratio: Using Density Ratios to Help Manage Fisheries In And Around Marine Reserves

Base Model

Description

base_model runs one simulation of the density ratio base model, based on Babcock & MacCall (2011).

Usage

base_model(
  Species,
  R0 = 1e+05,
  A = 5,
  MPA = 3,
  Time1 = 50,
  Time2 = 20,
  Recruitment_mode = "regional_DD",
  M_Error = 0.05,
  Sampling_Var = TRUE,
  Recruitment_Var = TRUE,
  Surveys = TRUE,
  Fishery_management = TRUE,
  Fishing = TRUE,
  Transects = 24,
  Adult_movement = TRUE,
  Final_DRs,
  Years_sampled = 1,
  Areas_sampled = "all",
  Ind_sampled = "all",
  Floor_DR = 0.2,
  Allocation = "IFD",
  BM = FALSE,
  LDP = 0.1,
  Output.N = FALSE,
  Output.Abundance = FALSE,
  Output.Biomass = FALSE,
  Output.SSB = FALSE,
  Output.Yield = FALSE,
  Output.Effort = FALSE,
  Output.Density.Ratio = TRUE
)

Arguments

Species	character value, the species to analyze. Species names are in the format species abbreviation.state or stock.year assessed. Example: BR.CA.2003 is the California black rockfish stock assessed in 2003.
R0	numeric value, the unfished recruitment, set arbitrarily. Default value is 1e+5.
A	numeric value, the number of total areas in the model. Default value is 5.
MPA	numeric value, the area number to be designated as a marine reserve at Time1. Default value is 3.
Time1	numeric value, the number of years to run the model before a marine reserve is implemented. Default value is 50.
Time2	numeric value, the number of years to run the model after a marine reserve is implemented. Default value is 20.
Recruitment_mode	character value, values can be: 'closed' - the recruits in each area originate from adults in that area. 'pool' - the recruits in each area come from a pool of larvae produced by adults in all areas. 'regional_DD' - larvae experience regional density dependence before settling evenly across all areas 'local_DD' - larvae experience local density dependence before settling evely across all areas Default value is 'regional_DD'.
M_Error	numeric value, the error between estimated and correct natural mortality.
Sampling_Var	logical value, is there any variability in sampling? Default value is TRUE.
Recruitment_Var	logical vector, is there any variability in recruitment? Default value is TRUE.
Surveys	logical value, are surveys being conducted? Default value is TRUE.
Fishery_management	logical value, is the fishery being managed using the control rules? Default value is TRUE.
Fishing	logical value, is fishing occurring? Default value is TRUE.
Transects	numerical value, the number of sampling transects conducted in each area to estimate density ratio. Default value is 24.
Adult_movement	logical value, do adults move between areas? Default value is TRUE.
Final_DRs	numeric vector, the final target density ratios.
Years_sampled	numeric value, the number of years of sampling upon which to base the estimate of density ratio. Default value is 1.
Areas_sampled	character value, the areas to be sampled to calculate density ratio. Values can be: 'all' - sample all areas. 'far' - sample only the first and last areas (assuming the reserve is somewhere in the middle. Default value is 'all'.
Ind_sampled	character value, the individuals to be sampled to calculate density ratio. Values can be: 'all' - sample all individuals. 'mature' - sample only mature individuals. Default value is 'all'.
Floor_DR	numeric value, the DR value under which effort will be reduced to 10% of its starting value. Default value is 0.2.
Allocation	character value, how effort is to be allocated. Values can be: 'IFD' - the ideal free distribution. Effort is allocated proportional to the yield caught in each area in the previous timestep. 'equal' - Effort is allocated equally between all areas. Default value is 'IFD'.
BM	logical value, are the control rules from Babcock and MacCall 2011? Default value is FALSE.
LDP	numeric value, the proportion of larvae that drift to adjacent areas. Default value is 0.1.
Output.N	logical value, should the output include N? Default value is FALSE.
Output.Abundance	logical value, should the output include Abundance? Default value is FALSE.
Output.Biomass	logical value, should the output include biomass? Default value is FALSE.
Output.SSB	logical value, should the output include spawning stock biomass? Default value is FALSE.
Output.Yield	logical value, should the output include yield? Default value is FALSE.
Output.Effort	logical value, should the output include effort? Default value is FALSE.
Output.Density.Ratio	logical value, should the output include density ratios? Default value is TRUE.

Value

a list, containing numerical arrays of the relative biomass, yield, and spawning stock biomass, as well as the true density ratios over time and the transient target density ratios over time

Examples

base_model(Species = 'BR_CA_2003', R0 = 1e+5, A = 5, MPA = 3, Time1 = 50,
   Time2 = 20, Recruitment_mode = 'regional_DD', M_Error = 0.05,
   Sampling_Var = TRUE, Recruitment_Var = TRUE, Surveys = TRUE,
   Fishery_management = TRUE, Fishing = TRUE, Transects = 24,
   Adult_movement = TRUE, Final_DRs = c(0.6, 0.8), Years_sampled = 1,
   Areas_sampled = 'all', Ind_sampled = 'all', Floor_DR = 0.2,
   Allocation = 'IFD', BM = FALSE, LDP = 0.1, Output.N = FALSE,
   Output.Abundance = FALSE, Output.Biomass = FALSE, Output.SSB = FALSE,
   Output.Yield = FALSE, Output.Effort = FALSE, Output.Density.Ratio = TRUE)

vquennessen/densityratio documentation built on Aug. 28, 2022, 5:36 p.m.