Class 'Fleet' — Fleet-class • MSEtool Functions

The component of the operating model that controls fishing dynamics

Slots

Name: Identifying name for the fleet. Usually includes location and gear type.
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.
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.
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).
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).
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).
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.
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.
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.
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.
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.
Vmaxlen: Proportion of fish selected by the gear at the asymptotic length (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.
isRel: Specify whether selection and retention parameters use absolute lengths or relative to the size of maturity. Single logical value (TRUE or FALSE).
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.
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.
Rmaxlen: Proportion of fish retained at the asymptotic length (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.
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.
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.
MPA: Logical argument (TRUE or FALSE). Creates an MPA in Area 1 for all years if true is selected. Defaults to FALSE.
Misc: Miscellaneous list for bio-economic parameters

Creating Object

Objects can be created by calls of the form new('Fleet')

Author

T. Carruthers and A. Hordyk

Examples

showClass('Fleet')
#> Class "Fleet" [package "MSEtool"]
#> 
#> Slots:
#>                                                                             
#> Name:       Name    nyears CurrentYr  EffYears  EffLower  EffUpper       Esd
#> Class: character   numeric   numeric   numeric   numeric   numeric   numeric
#>                                                                             
#> Name:       qinc       qcv        L5       LFS   Vmaxlen     isRel       LR5
#> Class:   numeric   numeric   numeric   numeric   numeric  char.log   numeric
#>                                                                   
#> Name:        LFR   Rmaxlen        DR Spat_targ       MPA      Misc
#> Class:   numeric   numeric   numeric   numeric  char.log      list
#> 
#> Known Subclasses: "OM"