man-roxygen/Fleet_template.R

In Blue-Matter/MSEtool: Management Strategy Evaluation Toolkit

# This file is auto-generated by build_tools/write_class_definitions.R
# Do not edit by hand


#' @slot Name Identifying name for the fleet. Usually includes location and
#'  gear type.
#' @slot nyears The number of years for the historical simulation. Single
#'  value. For example, if the simulated population is assumed to be unfished in
#'  1975 and this is the year you want to start your historical simulations, and
#'  the most recent year for which there is data available is 2019, then nyears
#'  equals 45.
#' @slot CurrentYr The last historical year simulated before projections begin.
#'  Single value. Note that this should match the last historical year specified in
#'  the `Data` object, which is usually the last historical year for which data is
#'  available.
#' @slot EffYears Vector indicating the historical years where there is
#'  information available to infer the relative fishing effort expended.This vector
#'  is specified in terms of the position of the year in the vector rather than the
#'  calendar year. For example, say our simulation starts with an unfished stock in
#'  1975,and the current year (the last year for which there is data available) is
#'  2019. Then there are 45 historical years simulated, and EffYears should include
#'  numbers between 1 and 45. Note that there may not be information available for
#'  every historical year, especially for data poor fisheries. In these situations,
#'  the EffYears vector should include only the positions of the years for which
#'  there is information, and the vector may be shorter than the total number of
#'  simulated historical years (nyears).
#' @slot EffLower Lower bound on relative fishing effort corresponding to
#'  EffYears. EffLower must be a vector that is the same length as EffYears
#'  describing how fishing effort has changed over time. Information on relative
#'  fishing effort can be entered in any units provided they are consistent across
#'  the entire vector because the data provided will be scaled to 1 (divided by the
#'  maximum number provided).
#' @slot EffUpper Upper bound on relative fishing effort corresponding to
#'  EffYears. EffUpper must be a vector that is the same length as EffYears
#'  describing how fishing effort has changed over time. Information on relative
#'  fishing effort can be entered in any units provided they are consistent across
#'  the entire vector because the data provided will be scaled to 1 (divided by the
#'  maximum number provided).
#' @slot Esd Additional inter-annual variability in fishing mortality rate. For
#'  each historical simulation a single value is drawn from a uniform distribution
#'  specified by the upper and lower bounds provided. If this parameter has a
#'  positive (non-zero) value, the yearly fishing mortality rate is drawn from a
#'  log-normal distribution with a standard deviation (in log space) specified by
#'  the value of `Esd` drawn for that simulation. This parameter applies only to
#'  historical projections.
#' @slot qinc Mean temporal trend in catchability (also though of as the
#'  efficiency of fishing gear) parameter, expressed as a percentage change in
#'  catchability (q) per year. For each simulation a single value is drawn from a
#'  uniform distribution specified by the upper and lower bounds provided. Positive
#'  numbers indicate an increase and negative numbers indicate a decrease. q then
#'  changes by this amount for in each year of the simulation This parameter
#'  applies only to forward projections.
#' @slot qcv Inter-annual variability in catchability expressed as a
#'  coefficient of variation. For each simulation a single value is drawn from a
#'  uniform distribution specified by the upper and lower bounds provided. This
#'  parameter applies only to forward projections.
#' @slot L5 Shortest length at which 5% of the population is vulnerable to
#'  selection by the gear used in this fleet. Values can either be specified as
#'  lengths (in the same units used for the maturity and growth parameters in the
#'  stock object) or as a percentage of the size of maturity (see the parameter
#'  isRel for more information). For each simulation a single value is drawn from a
#'  uniform distribution specified by the upper and lower bounds provided. This
#'  value is the same in all years unless cpars is used to provide time-varying
#'  selection.
#' @slot LFS Shortest length at which 100% of the population is vulnerable to
#'  selection by the gear used by this fleet. Values can either be specified as
#'  lengths (in the same units used for the maturity and growth parameters in the
#'  stock object) or as a percentage of the size of maturity (see the parameter
#'  isRel for more information). For each simulation a single value is drawn from a
#'  uniform distribution specified by the upper and lower bounds provided. This
#'  value is the same in all years unless cpars is used to provide time-varying
#'  selection.
#' @slot Vmaxlen Proportion of fish selected by the gear at the asymptotic
#'  length (\code{Stock@Linf}). Upper and Lower bounds between 0 and 1.  A value of
#'  1 indicates that 100% of fish are selected at the asymptotic length, and the
#'  selection curve is logistic. If `Vmaxlen` is less than 1 the selection curve is
#'  dome shaped. For example, if `Vmaxlen` is 0.4, then only 40% of fish are
#'  vulnerable to the fishing gear at the asymptotic length.
#' @slot isRel Specify whether selection and retention parameters use absolute
#'  lengths or relative to the size of maturity. Single logical value (TRUE or
#'  FALSE).
#' @slot LR5 Shortest length at which 5% of the population is vulnerable to
#'  retention by the fleet. Values can either be specified as lengths (in the same
#'  units used for the maturity and growth parameters in the stock object) or as a
#'  percentage of the size of maturity (see the parameter isRel for more
#'  information). For each simulation a single value is drawn from a uniform
#'  distribution specified by the upper and lower bounds provided. This value is
#'  the same in all years unless cpars is used to provide time-varying selection.
#' @slot LFR Shortest length where 100% of the population is vulnerable to
#'  retention by the fleet. Values can either be specified as lengths (in the same
#'  units used for the maturity and growth parameters in the stock object) or as a
#'  percentage of the size of maturity (see the parameter `isRel` for more
#'  information). For each simulation a single value is drawn from a uniform
#'  distribution specified by the upper and lower bounds provided. This value is
#'  the same in all years unless cpars is used to provide time-varying selection.
#' @slot Rmaxlen Proportion of fish retained at the asymptotic length
#'  (\code{Stock@Linf}). Upper and Lower bounds between 0 and 1.  A value of 1
#'  indicates that 100% of fish are retained at the asymptotic length, and the
#'  selection curve is logistic. If `Rmaxlen` is less than 1 the retention curve is
#'  dome shaped. For example, if `Rmaxlen` is 0.4, then only 40% of fish at the
#'  asymptotic length are retained.
#' @slot DR Discard rate, defined as the proportion of fully selected fish that
#'  are discarded by the fleet. Upper and Lower bounds between 0 and 1, with a
#'  value of 1 indicates that 100% of selected fish are discarded. For each
#'  simulation a single value is drawn from a uniform distribution specified by the
#'  upper and lower bounds provided.
#' @slot Spat_targ Distribution of fishing in relation to vulnerable biomass
#'  (VB) across areas. The distribution of fishing effort is proportional to
#'  VB^Spat_targ. Upper and lower bounds of a uniform distribution. For each
#'  simulation a single value is drawn from a uniform distribution specified by the
#'  upper and lower bounds provided. This parameter allows the user to model either
#'  avoidance or spatial targeting behavior by the fleet. If the parameter value is
#'  1, fishing effort is allocated across areas in proportion to the population
#'  density of that area. Values below 1 simulate an avoidance behavior and values
#'  above 1 simulate a targeting behavior.
#' @slot MPA Logical argument (TRUE or FALSE). Creates an MPA in Area 1 for all
#'  years if true is selected. Defaults to FALSE.
#' @slot Misc Miscellaneous list for bio-economic parameters