hydraDataList: Data for Hydra dat and pin files (hydradata)
In NOAA-EDAB/hydradata: Manipulate input data for the hydra multispecies model
Description
Usage
Format
Details
Source
See Also
Description
All the required information for creating dat and pin files are stored in this list. This
data list is used to create documentation and to create dat and pin files for use in simulaion with Hydra
This data List contains the parameter values to enable reproduction of the material presented at the CIE review.
Usage
1
2
3
Format
A list containing 117 elements
- alphaBH
Numeric Vector: slope at origin (alpha) for Beverton Holt Stock recruitment relationship
- alphaDS
Numeric Vector: slope at origin (alpha) for Deriso-Schnute Stock recruitment relationship
- alphaEggRicker
Numeric Vector: slope at origin (alpha) for Ricker stock-egg production relationship
- alphaGamma
Numeric Vector: slope at origin (alpha) for Gamma Stock recruitment relationship
- alphaHockey
Numeric Vector: slope at origin (alpha) for Hockey Stick recruitment relationship
- alphaRicker
Numeric Vector: slope at origin (alpha) for Ricker Stock recruitment relationship
- alphaSegmented
Numeric Vector: slope at origin (alpha) for Segmented (linear) recruitment relationship
- alphaShepherd
Numeric Vector: slope at origin (alpha) for Shepherd Stock recruitment relationship
- ARParameters
Numeric Vector: Auto-regressive parameters for error strucure of Survey, Recruitment, & Catch (Default = (0,0,0))
- assessmentPeriod
Integer scalar: length of time (years) between assessment of stocks
- avgFPhase
??
- avgRecPhase
??
- B0
Numeric Vector: Levels of unfished biomass (metric tonnes)
- bandwidthMetric
Integer scalar: number of years used to calculate standard deviation of catch and biomass (past bandwidthMeric years used in calculation)
- baselineThreshold
Numeric scalar: Proportion of unfished biomass at which landings are prohibited
- betaBH
Numeric Vector: (beta) for Beverton Holt Stock recruitment relationship
- betaDS
Numeric Vector: (beta) for Deriso-Schnute Stock recruitment relationship
- betaEggRicker
Numeric Vector: (beta) for Ricker stock-egg production relationship
- betaGamma
Numeric Vector: (beta) for Gamma Stock recruitment relationship
- betaHockey
Numeric Vector: (beta) for Hockey Stick recruitment relationship (Note: beta = -alpha for Hockey stick)
- betaRicker
Numeric Vector: (beta) for Ricker Stock recruitment relationship
- betaSegmented
Numeric Vector: (beta) for Segmented (linear) recruitment relationship
- betaShepherd
Numeric Vector: (beta) for Shepherd Stock recruitment relationship
- binwidth
Integer matrix (Nspecies x Nsizebins): width of each size class (cm)
- csigPhase
??
- debugState
Integer scalar: Type of debugging. (Values 1, 2, 3, 4). Default = 3
- devFPhase
??
- devRecPhase
??
- discardCoef
Numeric matrix (Nspecies.Nfleets x Nsizebins): Proportion of catch that is discarded for each species/fleet/size class combination
- discardSurvival
Numeric matrix (Nspecies.Nfleets x Nsizebins): Proportion of catch that survives given it is discarded for each species/fleet/size class combination
- exploitationOptions
Numeric matrix (Nthresholds x Nscenarios): Step function for assessments for different scenarios. Each column defines exploitation rates for each threshold defined by thresholds
- fecundityd
Numeric Vector: parameter (d) used to calculate fecundity at length (cm)
- fecundityh
Numeric Vector: parameter (h) used to calculate fecundity at length (cm)
- fecundityTheta
Numeric Vector: parameter (theta) used to calculate fecundity at length (cm)
- fisheryq
Numeric matrix (Nspecies x Nfleets): Fish caught per fish available per unit effort and per unit time. Worded in a different way it represents the probability of any single fish being caught
- fisherySelectivityc
Numeric matrix (Nspecies x Nfleets): parameter c. These are a measure of the selection process by fishing gear which causes the catch composition to be different from the general population. Worded in a different way it represents the probability of a fish remaining in the gear as a function of its size. It is used to control the impact of fishing on juveniles
- fisherySelectivityd
Numeric matrix (Nspecies x Nfleets): parameter d. These are a measure of the selection process by fishing gear which causes the catch composition to be different from the general population. Worded in a different way it represents the probability of a fish remaining in the gear as a function of its size. It is used to control the impact of fishing on juveniles
- fisherySigma
Numeric matrix (Nspecies x Nfleets): Standard deviation applied to catch (assumed log normal distribution)
- flagLinearRamp
Integer scalar: Determins if a step function or a linear function is used to calculate exploitation rates during an assessment. Values: 0 (Step function) or 1 (linear function). Default = 1
- flagMSE
Integer scalar: Determins whether an MSE is being performed. Values: 0 (no, extensive output files) or 1 (yes, limited output files). 2 (yes, Darwinian, catch and biomass only). Default = 0
- fleetNames
Character vector: Names to characterize the fleets
- foodweb
Binary matrix (Nspecies x Nspecies): Predators in columns, prey in rows. Value of 1 indicates predator eats prey
- fqphase
??
- growthCov
Numeric matrix (NgrowthCov x Nyrs): Covariates that determine species growth
- growthCovEffects
Numeric matrix (Nspecies x NgrowthCov): Weight of each covariate for growth for each species
- growthK
Numeric Vector (Nspecies): Values of parameter k assuming von Bertalanfy growth
- growthKappa
Numeric Vector (Nspecies): Values of parameter kappa assuming exponential growth
- growthLinf
Numeric Vector (Nspecies): Values of parameter Linf assuming von Bertalanfy growth
- growthPsi
Numeric Vector (Nspecies): Values of parameter psi assuming exponential growth
- growthType
Numeric Vector (Nspecies): Type of growth for each species. Values 2 (exponential) or 4 (Von Bertalanfy)
- guildMembership
Numeric vector: (Nspecies): Determins guild membership for each species. (Values: 1 - numguilds). See guildNames
- guildNames
Character vector (numGuilds): Names of the guilds
- indicatorFisheryq
Binary matrix (Nspecies x Nfleets): Determins which species in each fleet are actually targeted catch (1) or not (0). This is used to determine exploitation rate durin an assessment
- intakeAlpha
Numeric vector (Nspecies): alpha parameter for functional form of food intake
- intakeBeta
Numeric vector (Nspecies): beta parameter (exponent) for functional form of food intake
- intakeStomach
Numeric matrix (Nspecies x Nsizebins): Each row repsents species stomach weight (g) for each size class. Note. It is assumed that stomach weight remains constant through time (only for creating data input files. Hydra is modelled to acept changes through time.)
- lenwta
Numeric vector (Nspecies): scale parameter for length to weight relationship
- lenwtb
Numeric vector (Nspecies): shape parameter for length to weight relationship
- LFISize
Numeric scalar: Length (cm) at which a fish is considered large. Used in health indices module
- M1
Numeric matrix (Nspecies x Nsizebins): Rate of M1 mortality (natural mortality unexplained by model) for each species in in each size class AT EACH TIME STEP.
- M2sizePrefMu
Numeric vector (Nspecies): size preference parameter (location parameter (mu) of the log normal distribution)
- M2sizePrefSigma
Numeric vector (Nspecies): size preference parameter (scale parameter (sigma) of the log normal distribution)
- maturityCov
Numeric matrix (NmaturityCov x Nyrs): Covariates that determine species maturity
- maturityCovEffects
Numeric matrix (Nspecies x NmaturityCov): Weight of each covariate for maturity for each species
- maturityNu
Numeric vector (Nspecies): maturity parameter (location)
- maturityOmega
Numeric vector (Nspecies): maturity parameter (scale)
- minMaxThresholds
Numeric vector (2): The minimum and maximum thresholds used during an assessment (as a proportion of unfished biomass). The maximum is the level at which effort is reduced (from maximum exploitation) due to overfishing. The minimum is the level in which minimum exploitation is reached. See minMaxExploitation
- Nareas
Integer scalar: Number of spatial regions in the model.
- Nfleets
Integer scalar: Number of fleets in the model. See fleetNames
- NgrowthCov
Integer scalar: Number of growth covariates. See growthCov
- NmaturityCov
Integer scalar: Number of maturity covatiates. See maturityCov
- NrecruitmentCov
Integer scalar: Number og recruitment covariates. See recruitmentCov
- Nsizebins
Integer scalar: Number of size classes (Each species must have same number of size classes, different widths.). See binwidth
- Nspecies
Integer scalar: Number of species in the model
- Nthresholds
Integer scalar: number of assessment threshold. See thresholds for thresholf values
- numGuilds
Integer scalar: Number of guilds. See guildNames
- Nyrs
Integer scalar: Number of years in the model
- observedBiomass
Numeric matrix (Nspecies+1) x Nyrs: Real biomass values (from data) for each species over time. First row is year. Currently these are model values from ALTANTIS. Only used in estimation
- observedCatch
Numeric matrix (Nspecies+1) x Nyrs: Real catch values (from data) for each species over time. First row is year. Currently these are model values from ALTANTIS. Only used in estimation
- observedEffort
Numeric matrix (Nfleets+1) x Nyrs: Real fishing effort data for each fleet in the model. First row is year.
- observedTemperature
Numeric matrix (2 x Nyrs): Real temperature values ('C) over time. First row is year.
- otherFood
Numeric scalar: Amount of other food (metric tonnes) available for species in the model. This represents other food sources not explicity accounted for in the model
- phimax
Numeric scalar: Scales the growth of fish to the rate of the fasting growing fish. This is set to 1 and shouldn't be a parameter. If the calculated growth rates are all < 1, then no species will grow out of a size class in the given time interval. In that case phimax = 1 is used.
- predOrPrey
Binary vector: Indicated which species is considered a predator or prey. (This is subjective). This is used in as part of a health index where the ratio of predator to prey is monitored
- recphase
??
- recruitCovEffects
Numeric matrix (Nspecies x NmaturityCov): Weight of each covariate for recruitment for each species
- recruitmentCov
Numeric matrix (NrecruitmentyCov x Nyrs): Covariates that determine species recruitment
- recSigma
Numeric vector: standard deviation associated with recruitment estimates (based on spawning stock biomass size). (0 = known perfectly, no error). See recStochastic
- recStochastic
Binary vector (Nspecies): A switch to turn on (1) and off (0) recruitment error
- recType
Integer vector (Nspecies): Determins which form of recruitment is to be used. Values (1= Egg production, 2= Deriso-Scnute, 3= Gamma, 4= Ricker, 5= Beverton holt, 6= Shepherd, 7= Hockey Stick, 8= Segmented Linear model, 9= recruitment deviations). Default = 8 (Segmented linear model)
- redundantAvgRec
Numeric vector (Nspecies): Average recruitment for each species
- redundantRecDevs
Numeric matrix (Nspecies x Nyrs): Recruitment deviations about the average (redundantAvgRec) over time
- scaledEffort
Numeric Vector (Nspecies): Amount by which to scale effort by species. Can be used if stock recruitment functions are calculated on an area larger or smaller than the region of interest. Default = 1's
- scaleInitialN
Numeric scalar: Amount by which to scale the initial values of Y1N. Default = 1.
- sexRatio
Numeric vector (Nspecies): Proportion of females for each species. Default = 0.5 for all species
- shapeBH
Numeric Vector: (shape) for Beverton Holt Stock recruitment relationship
- shapeDS
Numeric Vector: (shape) for Deriso-Schnute Stock recruitment relationship
- shapeEggRicker
Numeric Vector: (shape) for Ricker stock-egg production relationship
- shapeGamma
Numeric Vector: (shape) for Gamma Stock recruitment relationship
- shapeHockey
Numeric Vector: (shape) for Hockey Stick recruitment relationship
- shapeRicker
Numeric Vector: (shape) for Ricker Stock recruitment relationship
- shapeSegmented
Numeric Vector: (shape) for Segmented (linear) recruitment relationship
- shapeShepherd
Numeric Vector: (shape) for Shepherd Stock recruitment relationship
- speciesList
Character vector: names of species in model
- sqphase
??
- ssigPhase
??
- surveyq
Numeric vector (Nspecies): Proportion of true biomass sampled on a survey. (q = 1 equates to known exactly)
- surveySigma
Numeric vector (Nspecies): The uncertainty (standard deviation) of estimate of survey biomass (0 = known perfectly, no error)
- thresholds
Numeric vector (Nthresholds): The proportions of unfished biomass at which exploitation is decreased
- thresholdSpecies
Numeric vector (Nspecies): A proportion in excess of the current thresholds. These species have reduced exploitaion at higher proportions of B/B0
- wtconv
Numeric Scalar: conversion factor from weight (g) to biomass
- Y1N
Numeric Vector (Nspecies x Nsizebins): initial abundance estimates (milions) for each species in each size class
- yr1Nphase
??
- minMaxExploitation
Numeric Vector (2): The minimum and maximum values of exploitation permissable during an assessment (as a proportion of unfished biomass). The maximum is the level at which all stocks are healthy. The minimum is the lowest level due to overfishing. See minMaxThresholds
- assessmentOn
Binary Scalar: Assessment scenario on (1) or not (0). This is set in create_datpin_files
- assessmentWithSpeciesOn
Binary Scalar: Assessment with extra protection for selected species. on (1) or not (0). This is set in create_datpin_files
- exploitationLevels
Numeric Vector (Nthresholds): The values of exploitation at each threshold (Only used in step function Ramp). This is set in create_datpin_files. See flagLinearRamp
A list containing 117 elements
- alphaBH
Numeric Vector: slope at origin (alpha) for Beverton Holt Stock recruitment relationship
- alphaDS
Numeric Vector: slope at origin (alpha) for Deriso-Schnute Stock recruitment relationship
- alphaEggRicker
Numeric Vector: slope at origin (alpha) for Ricker stock-egg production relationship
- alphaGamma
Numeric Vector: slope at origin (alpha) for Gamma Stock recruitment relationship
- alphaHockey
Numeric Vector: slope at origin (alpha) for Hockey Stick recruitment relationship
- alphaRicker
Numeric Vector: slope at origin (alpha) for Ricker Stock recruitment relationship
- alphaSegmented
Numeric Vector: slope at origin (alpha) for Segmented (linear) recruitment relationship
- alphaShepherd
Numeric Vector: slope at origin (alpha) for Shepherd Stock recruitment relationship
- ARParameters
Numeric Vector: Auto-regressive parameters for error strucure of Survey, Recruitment, & Catch (Default = (0,0,0))
- assessmentPeriod
Integer scalar: length of time (years) between assessment of stocks
- avgFPhase
??
- avgRecPhase
??
- B0
Numeric Vector: Levels of unfished biomass (metric tonnes)
- bandwidthMetric
Integer scalar: number of years used to calculate standard deviation of catch and biomass (past bandwidthMeric years used in calculation)
- baselineThreshold
Numeric scalar: Proportion of unfished biomass at which landings are prohibited
- betaBH
Numeric Vector: (beta) for Beverton Holt Stock recruitment relationship
- betaDS
Numeric Vector: (beta) for Deriso-Schnute Stock recruitment relationship
- betaEggRicker
Numeric Vector: (beta) for Ricker stock-egg production relationship
- betaGamma
Numeric Vector: (beta) for Gamma Stock recruitment relationship
- betaHockey
Numeric Vector: (beta) for Hockey Stick recruitment relationship (Note: beta = -alpha for Hockey stick)
- betaRicker
Numeric Vector: (beta) for Ricker Stock recruitment relationship
- betaSegmented
Numeric Vector: (beta) for Segmented (linear) recruitment relationship
- betaShepherd
Numeric Vector: (beta) for Shepherd Stock recruitment relationship
- binwidth
Integer matrix (Nspecies x Nsizebins): width of each size class (cm)
- csigPhase
??
- debugState
Integer scalar: Type of debugging. (Values 1, 2, 3, 4). Default = 3
- devFPhase
??
- devRecPhase
??
- discardCoef
Numeric matrix (Nspecies.Nfleets x Nsizebins): Proportion of catch that is discarded for each species/fleet/size class combination
- discardSurvival
Numeric matrix (Nspecies.Nfleets x Nsizebins): Proportion of catch that survives given it is discarded for each species/fleet/size class combination
- exploitationOptions
Numeric matrix (Nthresholds x Nscenarios): Step function for assessments for different scenarios. Each column defines exploitation rates for each threshold defined by thresholds
- fecundityd
Numeric Vector: parameter (d) used to calculate fecundity at length (cm)
- fecundityh
Numeric Vector: parameter (h) used to calculate fecundity at length (cm)
- fecundityTheta
Numeric Vector: parameter (theta) used to calculate fecundity at length (cm)
- fisheryq
Numeric matrix (Nspecies x Nfleets): Fish caught per fish available per unit effort and per unit time. Worded in a different way it represents the probability of any single fish being caught
- fisherySelectivityc
Numeric matrix (Nspecies x Nfleets): parameter c. These are a measure of the selection process by fishing gear which causes the catch composition to be different from the general population. Worded in a different way it represents the probability of a fish remaining in the gear as a function of its size. It is used to control the impact of fishing on juveniles
- fisherySelectivityd
Numeric matrix (Nspecies x Nfleets): parameter d. These are a measure of the selection process by fishing gear which causes the catch composition to be different from the general population. Worded in a different way it represents the probability of a fish remaining in the gear as a function of its size. It is used to control the impact of fishing on juveniles
- fisherySigma
Numeric matrix (Nspecies x Nfleets): Standard deviation applied to catch (assumed log normal distribution)
- flagLinearRamp
Integer scalar: Determins if a step function or a linear function is used to calculate exploitation rates during an assessment. Values: 0 (Step function) or 1 (linear function). Default = 1
- flagMSE
Integer scalar: Determins whether an MSE is being performed. Values: 0 (no, extensive output files) or 1 (yes, limited output files). 2 (yes, Darwinian, catch and biomass only). Default = 0
- fleetNames
Character vector: Names to characterize the fleets
- foodweb
Binary matrix (Nspecies x Nspecies): Predators in columns, prey in rows. Value of 1 indicates predator eats prey
- fqphase
??
- growthCov
Numeric matrix (NgrowthCov x Nyrs): Covariates that determine species growth
- growthCovEffects
Numeric matrix (Nspecies x NgrowthCov): Weight of each covariate for growth for each species
- growthK
Numeric Vector (Nspecies): Values of parameter k assuming von Bertalanfy growth
- growthKappa
Numeric Vector (Nspecies): Values of parameter kappa assuming exponential growth
- growthLinf
Numeric Vector (Nspecies): Values of parameter Linf assuming von Bertalanfy growth
- growthPsi
Numeric Vector (Nspecies): Values of parameter psi assuming exponential growth
- growthType
Numeric Vector (Nspecies): Type of growth for each species. Values 2 (exponential) or 4 (Von Bertalanfy)
- guildMembership
Numeric vector: (Nspecies): Determins guild membership for each species. (Values: 1 - numguilds). See guildNames
- guildNames
Character vector (numGuilds): Names of the guilds
- indicatorFisheryq
Binary matrix (Nspecies x Nfleets): Determins which species in each fleet are actually targeted catch (1) or not (0). This is used to determine exploitation rate durin an assessment
- intakeAlpha
Numeric vector (Nspecies): alpha parameter for functional form of food intake
- intakeBeta
Numeric vector (Nspecies): beta parameter (exponent) for functional form of food intake
- intakeStomach
Numeric matrix (Nspecies x Nsizebins): Each row repsents species stomach weight (g) for each size class. Note. It is assumed that stomach weight remains constant through time (only for creating data input files. Hydra is modelled to acept changes through time.)
- lenwta
Numeric vector (Nspecies): scale parameter for length to weight relationship
- lenwtb
Numeric vector (Nspecies): shape parameter for length to weight relationship
- LFISize
Numeric scalar: Length (cm) at which a fish is considered large. Used in health indices module
- M1
Numeric matrix (Nspecies x Nsizebins): Rate of M1 mortality (natural mortality unexplained by model) for each species in in each size class AT EACH TIME STEP.
- M2sizePrefMu
Numeric vector (Nspecies): size preference parameter (location parameter (mu) of the log normal distribution)
- M2sizePrefSigma
Numeric vector (Nspecies): size preference parameter (scale parameter (sigma) of the log normal distribution)
- maturityCov
Numeric matrix (NmaturityCov x Nyrs): Covariates that determine species maturity
- maturityCovEffects
Numeric matrix (Nspecies x NmaturityCov): Weight of each covariate for maturity for each species
- maturityNu
Numeric vector (Nspecies): maturity parameter (location)
- maturityOmega
Numeric vector (Nspecies): maturity parameter (scale)
- minMaxThresholds
Numeric vector (2): The minimum and maximum thresholds used during an assessment (as a proportion of unfished biomass). The maximum is the level at which effort is reduced (from maximum exploitation) due to overfishing. The minimum is the level in which minimum exploitation is reached. See minMaxExploitation
- Nareas
Integer scalar: Number of spatial regions in the model.
- Nfleets
Integer scalar: Number of fleets in the model. See fleetNames
- NgrowthCov
Integer scalar: Number of growth covariates. See growthCov
- NmaturityCov
Integer scalar: Number of maturity covatiates. See maturityCov
- NrecruitmentCov
Integer scalar: Number og recruitment covariates. See recruitmentCov
- Nsizebins
Integer scalar: Number of size classes (Each species must have same number of size classes, different widths.). See binwidth
- Nspecies
Integer scalar: Number of species in the model
- Nthresholds
Integer scalar: number of assessment threshold. See thresholds for thresholf values
- numGuilds
Integer scalar: Number of guilds. See guildNames
- Nyrs
Integer scalar: Number of years in the model
- observedBiomass
Numeric matrix (Nspecies+1) x Nyrs: Real biomass values (from data) for each species over time. First row is year. Currently these are model values from ALTANTIS. Only used in estimation
- observedCatch
Numeric matrix (Nspecies+1) x Nyrs: Real catch values (from data) for each species over time. First row is year. Currently these are model values from ALTANTIS. Only used in estimation
- observedEffort
Numeric matrix (Nfleets+1) x Nyrs: Real fishing effort data for each fleet in the model. First row is year.
- observedTemperature
Numeric matrix (2 x Nyrs): Real temperature values ('C) over time. First row is year.
- otherFood
Numeric scalar: Amount of other food (metric tonnes) available for species in the model. This represents other food sources not explicity accounted for in the model
- phimax
Numeric scalar: Scales the growth of fish to the rate of the fasting growing fish. This is set to 1 and shouldn't be a parameter. If the calculated growth rates are all < 1, then no species will grow out of a size class in the given time interval. In that case phimax = 1 is used.
- predOrPrey
Binary vector: Indicated which species is considered a predator or prey. (This is subjective). This is used in as part of a health index where the ratio of predator to prey is monitored
- recphase
??
- recruitCovEffects
Numeric matrix (Nspecies x NmaturityCov): Weight of each covariate for recruitment for each species
- recruitmentCov
Numeric matrix (NrecruitmentyCov x Nyrs): Covariates that determine species recruitment
- recSigma
Numeric vector: standard deviation associated with recruitment estimates (based on spawning stock biomass size). (0 = known perfectly, no error). See recStochastic
- recStochastic
Binary vector (Nspecies): A switch to turn on (1) and off (0) recruitment error
- recType
Integer vector (Nspecies): Determins which form of recruitment is to be used. Values (1= Egg production, 2= Deriso-Scnute, 3= Gamma, 4= Ricker, 5= Beverton holt, 6= Shepherd, 7= Hockey Stick, 8= Segmented Linear model, 9= recruitment deviations). Default = 8 (Segmented linear model)
- redundantAvgRec
Numeric vector (Nspecies): Average recruitment for each species
- redundantRecDevs
Numeric matrix (Nspecies x Nyrs): Recruitment deviations about the average (redundantAvgRec) over time
- scaledEffort
Numeric Vector (Nspecies): Amount by which to scale effort by species. Can be used if stock recruitment functions are calculated on an area larger or smaller than the region of interest. Default = 1's
- scaleInitialN
Numeric scalar: Amount by which to scale the initial values of Y1N. Default = 1.
- sexRatio
Numeric vector (Nspecies): Proportion of females for each species. Default = 0.5 for all species
- shapeBH
Numeric Vector: (shape) for Beverton Holt Stock recruitment relationship
- shapeDS
Numeric Vector: (shape) for Deriso-Schnute Stock recruitment relationship
- shapeEggRicker
Numeric Vector: (shape) for Ricker stock-egg production relationship
- shapeGamma
Numeric Vector: (shape) for Gamma Stock recruitment relationship
- shapeHockey
Numeric Vector: (shape) for Hockey Stick recruitment relationship
- shapeRicker
Numeric Vector: (shape) for Ricker Stock recruitment relationship
- shapeSegmented
Numeric Vector: (shape) for Segmented (linear) recruitment relationship
- shapeShepherd
Numeric Vector: (shape) for Shepherd Stock recruitment relationship
- speciesList
Character vector: names of species in model
- sqphase
??
- ssigPhase
??
- surveyq
Numeric vector (Nspecies): Proportion of true biomass sampled on a survey. (q = 1 equates to known exactly)
- surveySigma
Numeric vector (Nspecies): The uncertainty (standard deviation) of estimate of survey biomass (0 = known perfectly, no error)
- thresholds
Numeric vector (Nthresholds): The proportions of unfished biomass at which exploitation is decreased
- thresholdSpecies
Numeric vector (Nspecies): A proportion in excess of the current thresholds. These species have reduced exploitaion at higher proportions of B/B0
- wtconv
Numeric Scalar: conversion factor from weight (g) to biomass
- Y1N
Numeric Vector (Nspecies x Nsizebins): initial abundance estimates (milions) for each species in each size class
- yr1Nphase
??
- minMaxExploitation
Numeric Vector (2): The minimum and maximum values of exploitation permissable during an assessment (as a proportion of unfished biomass). The maximum is the level at which all stocks are healthy. The minimum is the lowest level due to overfishing. See minMaxThresholds
- assessmentOn
Binary Scalar: Assessment scenario on (1) or not (0). This is set in create_datpin_files
- assessmentWithSpeciesOn
Binary Scalar: Assessment with extra protection for selected species. on (1) or not (0). This is set in create_datpin_files
- exploitationLevels
Numeric Vector (Nthresholds): The values of exploitation at each threshold (Only used in step function Ramp). This is set in create_datpin_files. See flagLinearRamp
Details
All the required information for creating dat and pin files are stored in this list. This
data list is used to create documentation and to create dat and pin files for use in simulaion with Hydra
Source
Gaichas et al. + publication (currently being written up)
Gaichas et al. + publication (currently being written up)
See Also
To visualize this data please run create_documentation
To visualize this data please run create_documentation
NOAA-EDAB/hydradata documentation built on Feb. 3, 2021, 9:02 p.m.
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Description Usage Format Details Source See Also
Description
All the required information for creating dat and pin files are stored in this list. This data list is used to create documentation and to create dat and pin files for use in simulaion with Hydra
This data List contains the parameter values to enable reproduction of the material presented at the CIE review.
Usage
1 2 3 |
Format
A list containing 117 elements
- alphaBH
Numeric Vector: slope at origin (alpha) for Beverton Holt Stock recruitment relationship
- alphaDS
Numeric Vector: slope at origin (alpha) for Deriso-Schnute Stock recruitment relationship
- alphaEggRicker
Numeric Vector: slope at origin (alpha) for Ricker stock-egg production relationship
- alphaGamma
Numeric Vector: slope at origin (alpha) for Gamma Stock recruitment relationship
- alphaHockey
Numeric Vector: slope at origin (alpha) for Hockey Stick recruitment relationship
- alphaRicker
Numeric Vector: slope at origin (alpha) for Ricker Stock recruitment relationship
- alphaSegmented
Numeric Vector: slope at origin (alpha) for Segmented (linear) recruitment relationship
- alphaShepherd
Numeric Vector: slope at origin (alpha) for Shepherd Stock recruitment relationship
- ARParameters
Numeric Vector: Auto-regressive parameters for error strucure of Survey, Recruitment, & Catch (Default = (0,0,0))
- assessmentPeriod
Integer scalar: length of time (years) between assessment of stocks
- avgFPhase
??
- avgRecPhase
??
- B0
Numeric Vector: Levels of unfished biomass (metric tonnes)
- bandwidthMetric
Integer scalar: number of years used to calculate standard deviation of catch and biomass (past
bandwidthMericyears used in calculation)- baselineThreshold
Numeric scalar: Proportion of unfished biomass at which landings are prohibited
- betaBH
Numeric Vector: (beta) for Beverton Holt Stock recruitment relationship
- betaDS
Numeric Vector: (beta) for Deriso-Schnute Stock recruitment relationship
- betaEggRicker
Numeric Vector: (beta) for Ricker stock-egg production relationship
- betaGamma
Numeric Vector: (beta) for Gamma Stock recruitment relationship
- betaHockey
Numeric Vector: (beta) for Hockey Stick recruitment relationship (Note: beta = -alpha for Hockey stick)
- betaRicker
Numeric Vector: (beta) for Ricker Stock recruitment relationship
- betaSegmented
Numeric Vector: (beta) for Segmented (linear) recruitment relationship
- betaShepherd
Numeric Vector: (beta) for Shepherd Stock recruitment relationship
- binwidth
Integer matrix (Nspecies x Nsizebins): width of each size class (cm)
- csigPhase
??
- debugState
Integer scalar: Type of debugging. (Values 1, 2, 3, 4). Default = 3
- devFPhase
??
- devRecPhase
??
- discardCoef
Numeric matrix (Nspecies.Nfleets x Nsizebins): Proportion of catch that is discarded for each species/fleet/size class combination
- discardSurvival
Numeric matrix (Nspecies.Nfleets x Nsizebins): Proportion of catch that survives given it is discarded for each species/fleet/size class combination
- exploitationOptions
Numeric matrix (Nthresholds x Nscenarios): Step function for assessments for different scenarios. Each column defines exploitation rates for each threshold defined by
thresholds- fecundityd
Numeric Vector: parameter (d) used to calculate fecundity at length (cm)
- fecundityh
Numeric Vector: parameter (h) used to calculate fecundity at length (cm)
- fecundityTheta
Numeric Vector: parameter (theta) used to calculate fecundity at length (cm)
- fisheryq
Numeric matrix (Nspecies x Nfleets): Fish caught per fish available per unit effort and per unit time. Worded in a different way it represents the probability of any single fish being caught
- fisherySelectivityc
Numeric matrix (Nspecies x Nfleets): parameter c. These are a measure of the selection process by fishing gear which causes the catch composition to be different from the general population. Worded in a different way it represents the probability of a fish remaining in the gear as a function of its size. It is used to control the impact of fishing on juveniles
- fisherySelectivityd
Numeric matrix (Nspecies x Nfleets): parameter d. These are a measure of the selection process by fishing gear which causes the catch composition to be different from the general population. Worded in a different way it represents the probability of a fish remaining in the gear as a function of its size. It is used to control the impact of fishing on juveniles
- fisherySigma
Numeric matrix (Nspecies x Nfleets): Standard deviation applied to catch (assumed log normal distribution)
- flagLinearRamp
Integer scalar: Determins if a step function or a linear function is used to calculate exploitation rates during an assessment. Values: 0 (Step function) or 1 (linear function). Default = 1
- flagMSE
Integer scalar: Determins whether an MSE is being performed. Values: 0 (no, extensive output files) or 1 (yes, limited output files). 2 (yes, Darwinian, catch and biomass only). Default = 0
- fleetNames
Character vector: Names to characterize the fleets
- foodweb
Binary matrix (Nspecies x Nspecies): Predators in columns, prey in rows. Value of 1 indicates predator eats prey
- fqphase
??
- growthCov
Numeric matrix (NgrowthCov x Nyrs): Covariates that determine species growth
- growthCovEffects
Numeric matrix (Nspecies x NgrowthCov): Weight of each covariate for growth for each species
- growthK
Numeric Vector (Nspecies): Values of parameter k assuming von Bertalanfy growth
- growthKappa
Numeric Vector (Nspecies): Values of parameter kappa assuming exponential growth
- growthLinf
Numeric Vector (Nspecies): Values of parameter Linf assuming von Bertalanfy growth
- growthPsi
Numeric Vector (Nspecies): Values of parameter psi assuming exponential growth
- growthType
Numeric Vector (Nspecies): Type of growth for each species. Values 2 (exponential) or 4 (Von Bertalanfy)
- guildMembership
Numeric vector: (Nspecies): Determins guild membership for each species. (Values: 1 - numguilds). See
guildNames- guildNames
Character vector (numGuilds): Names of the guilds
- indicatorFisheryq
Binary matrix (Nspecies x Nfleets): Determins which species in each fleet are actually targeted catch (1) or not (0). This is used to determine exploitation rate durin an assessment
- intakeAlpha
Numeric vector (Nspecies): alpha parameter for functional form of food intake
- intakeBeta
Numeric vector (Nspecies): beta parameter (exponent) for functional form of food intake
- intakeStomach
Numeric matrix (Nspecies x Nsizebins): Each row repsents species stomach weight (g) for each size class. Note. It is assumed that stomach weight remains constant through time (only for creating data input files. Hydra is modelled to acept changes through time.)
- lenwta
Numeric vector (Nspecies): scale parameter for length to weight relationship
- lenwtb
Numeric vector (Nspecies): shape parameter for length to weight relationship
- LFISize
Numeric scalar: Length (cm) at which a fish is considered large. Used in health indices module
- M1
Numeric matrix (Nspecies x Nsizebins): Rate of M1 mortality (natural mortality unexplained by model) for each species in in each size class AT EACH TIME STEP.
- M2sizePrefMu
Numeric vector (Nspecies): size preference parameter (location parameter (mu) of the log normal distribution)
- M2sizePrefSigma
Numeric vector (Nspecies): size preference parameter (scale parameter (sigma) of the log normal distribution)
- maturityCov
Numeric matrix (NmaturityCov x Nyrs): Covariates that determine species maturity
- maturityCovEffects
Numeric matrix (Nspecies x NmaturityCov): Weight of each covariate for maturity for each species
- maturityNu
Numeric vector (Nspecies): maturity parameter (location)
- maturityOmega
Numeric vector (Nspecies): maturity parameter (scale)
- minMaxThresholds
Numeric vector (2): The minimum and maximum thresholds used during an assessment (as a proportion of unfished biomass). The maximum is the level at which effort is reduced (from maximum exploitation) due to overfishing. The minimum is the level in which minimum exploitation is reached. See
minMaxExploitation- Nareas
Integer scalar: Number of spatial regions in the model.
- Nfleets
Integer scalar: Number of fleets in the model. See
fleetNames- NgrowthCov
Integer scalar: Number of growth covariates. See
growthCov- NmaturityCov
Integer scalar: Number of maturity covatiates. See
maturityCov- NrecruitmentCov
Integer scalar: Number og recruitment covariates. See
recruitmentCov- Nsizebins
Integer scalar: Number of size classes (Each species must have same number of size classes, different widths.). See
binwidth- Nspecies
Integer scalar: Number of species in the model
- Nthresholds
Integer scalar: number of assessment threshold. See
thresholdsfor thresholf values- numGuilds
Integer scalar: Number of guilds. See
guildNames- Nyrs
Integer scalar: Number of years in the model
- observedBiomass
Numeric matrix (Nspecies+1) x Nyrs: Real biomass values (from data) for each species over time. First row is year. Currently these are model values from ALTANTIS. Only used in estimation
- observedCatch
Numeric matrix (Nspecies+1) x Nyrs: Real catch values (from data) for each species over time. First row is year. Currently these are model values from ALTANTIS. Only used in estimation
- observedEffort
Numeric matrix (Nfleets+1) x Nyrs: Real fishing effort data for each fleet in the model. First row is year.
- observedTemperature
Numeric matrix (2 x Nyrs): Real temperature values ('C) over time. First row is year.
- otherFood
Numeric scalar: Amount of other food (metric tonnes) available for species in the model. This represents other food sources not explicity accounted for in the model
- phimax
Numeric scalar: Scales the growth of fish to the rate of the fasting growing fish. This is set to 1 and shouldn't be a parameter. If the calculated growth rates are all < 1, then no species will grow out of a size class in the given time interval. In that case phimax = 1 is used.
- predOrPrey
Binary vector: Indicated which species is considered a predator or prey. (This is subjective). This is used in as part of a health index where the ratio of predator to prey is monitored
- recphase
??
- recruitCovEffects
Numeric matrix (Nspecies x NmaturityCov): Weight of each covariate for recruitment for each species
- recruitmentCov
Numeric matrix (NrecruitmentyCov x Nyrs): Covariates that determine species recruitment
- recSigma
Numeric vector: standard deviation associated with recruitment estimates (based on spawning stock biomass size). (0 = known perfectly, no error). See
recStochastic- recStochastic
Binary vector (Nspecies): A switch to turn on (1) and off (0) recruitment error
- recType
Integer vector (Nspecies): Determins which form of recruitment is to be used. Values (1= Egg production, 2= Deriso-Scnute, 3= Gamma, 4= Ricker, 5= Beverton holt, 6= Shepherd, 7= Hockey Stick, 8= Segmented Linear model, 9= recruitment deviations). Default = 8 (Segmented linear model)
- redundantAvgRec
Numeric vector (Nspecies): Average recruitment for each species
- redundantRecDevs
Numeric matrix (Nspecies x Nyrs): Recruitment deviations about the average (
redundantAvgRec) over time- scaledEffort
Numeric Vector (Nspecies): Amount by which to scale effort by species. Can be used if stock recruitment functions are calculated on an area larger or smaller than the region of interest. Default = 1's
- scaleInitialN
Numeric scalar: Amount by which to scale the initial values of
Y1N. Default = 1.- sexRatio
Numeric vector (Nspecies): Proportion of females for each species. Default = 0.5 for all species
- shapeBH
Numeric Vector: (shape) for Beverton Holt Stock recruitment relationship
- shapeDS
Numeric Vector: (shape) for Deriso-Schnute Stock recruitment relationship
- shapeEggRicker
Numeric Vector: (shape) for Ricker stock-egg production relationship
- shapeGamma
Numeric Vector: (shape) for Gamma Stock recruitment relationship
- shapeHockey
Numeric Vector: (shape) for Hockey Stick recruitment relationship
- shapeRicker
Numeric Vector: (shape) for Ricker Stock recruitment relationship
- shapeSegmented
Numeric Vector: (shape) for Segmented (linear) recruitment relationship
- shapeShepherd
Numeric Vector: (shape) for Shepherd Stock recruitment relationship
- speciesList
Character vector: names of species in model
- sqphase
??
- ssigPhase
??
- surveyq
Numeric vector (Nspecies): Proportion of true biomass sampled on a survey. (q = 1 equates to known exactly)
- surveySigma
Numeric vector (Nspecies): The uncertainty (standard deviation) of estimate of survey biomass (0 = known perfectly, no error)
- thresholds
Numeric vector (Nthresholds): The proportions of unfished biomass at which exploitation is decreased
- thresholdSpecies
Numeric vector (Nspecies): A proportion in excess of the current
thresholds. These species have reduced exploitaion at higher proportions of B/B0- wtconv
Numeric Scalar: conversion factor from weight (g) to biomass
- Y1N
Numeric Vector (Nspecies x Nsizebins): initial abundance estimates (milions) for each species in each size class
- yr1Nphase
??
- minMaxExploitation
Numeric Vector (2): The minimum and maximum values of exploitation permissable during an assessment (as a proportion of unfished biomass). The maximum is the level at which all stocks are healthy. The minimum is the lowest level due to overfishing. See
minMaxThresholds- assessmentOn
Binary Scalar: Assessment scenario on (1) or not (0). This is set in
create_datpin_files- assessmentWithSpeciesOn
Binary Scalar: Assessment with extra protection for selected species. on (1) or not (0). This is set in
create_datpin_files- exploitationLevels
Numeric Vector (Nthresholds): The values of exploitation at each threshold (Only used in step function Ramp). This is set in
create_datpin_files. SeeflagLinearRamp
A list containing 117 elements
- alphaBH
Numeric Vector: slope at origin (alpha) for Beverton Holt Stock recruitment relationship
- alphaDS
Numeric Vector: slope at origin (alpha) for Deriso-Schnute Stock recruitment relationship
- alphaEggRicker
Numeric Vector: slope at origin (alpha) for Ricker stock-egg production relationship
- alphaGamma
Numeric Vector: slope at origin (alpha) for Gamma Stock recruitment relationship
- alphaHockey
Numeric Vector: slope at origin (alpha) for Hockey Stick recruitment relationship
- alphaRicker
Numeric Vector: slope at origin (alpha) for Ricker Stock recruitment relationship
- alphaSegmented
Numeric Vector: slope at origin (alpha) for Segmented (linear) recruitment relationship
- alphaShepherd
Numeric Vector: slope at origin (alpha) for Shepherd Stock recruitment relationship
- ARParameters
Numeric Vector: Auto-regressive parameters for error strucure of Survey, Recruitment, & Catch (Default = (0,0,0))
- assessmentPeriod
Integer scalar: length of time (years) between assessment of stocks
- avgFPhase
??
- avgRecPhase
??
- B0
Numeric Vector: Levels of unfished biomass (metric tonnes)
- bandwidthMetric
Integer scalar: number of years used to calculate standard deviation of catch and biomass (past
bandwidthMericyears used in calculation)- baselineThreshold
Numeric scalar: Proportion of unfished biomass at which landings are prohibited
- betaBH
Numeric Vector: (beta) for Beverton Holt Stock recruitment relationship
- betaDS
Numeric Vector: (beta) for Deriso-Schnute Stock recruitment relationship
- betaEggRicker
Numeric Vector: (beta) for Ricker stock-egg production relationship
- betaGamma
Numeric Vector: (beta) for Gamma Stock recruitment relationship
- betaHockey
Numeric Vector: (beta) for Hockey Stick recruitment relationship (Note: beta = -alpha for Hockey stick)
- betaRicker
Numeric Vector: (beta) for Ricker Stock recruitment relationship
- betaSegmented
Numeric Vector: (beta) for Segmented (linear) recruitment relationship
- betaShepherd
Numeric Vector: (beta) for Shepherd Stock recruitment relationship
- binwidth
Integer matrix (Nspecies x Nsizebins): width of each size class (cm)
- csigPhase
??
- debugState
Integer scalar: Type of debugging. (Values 1, 2, 3, 4). Default = 3
- devFPhase
??
- devRecPhase
??
- discardCoef
Numeric matrix (Nspecies.Nfleets x Nsizebins): Proportion of catch that is discarded for each species/fleet/size class combination
- discardSurvival
Numeric matrix (Nspecies.Nfleets x Nsizebins): Proportion of catch that survives given it is discarded for each species/fleet/size class combination
- exploitationOptions
Numeric matrix (Nthresholds x Nscenarios): Step function for assessments for different scenarios. Each column defines exploitation rates for each threshold defined by
thresholds- fecundityd
Numeric Vector: parameter (d) used to calculate fecundity at length (cm)
- fecundityh
Numeric Vector: parameter (h) used to calculate fecundity at length (cm)
- fecundityTheta
Numeric Vector: parameter (theta) used to calculate fecundity at length (cm)
- fisheryq
Numeric matrix (Nspecies x Nfleets): Fish caught per fish available per unit effort and per unit time. Worded in a different way it represents the probability of any single fish being caught
- fisherySelectivityc
Numeric matrix (Nspecies x Nfleets): parameter c. These are a measure of the selection process by fishing gear which causes the catch composition to be different from the general population. Worded in a different way it represents the probability of a fish remaining in the gear as a function of its size. It is used to control the impact of fishing on juveniles
- fisherySelectivityd
Numeric matrix (Nspecies x Nfleets): parameter d. These are a measure of the selection process by fishing gear which causes the catch composition to be different from the general population. Worded in a different way it represents the probability of a fish remaining in the gear as a function of its size. It is used to control the impact of fishing on juveniles
- fisherySigma
Numeric matrix (Nspecies x Nfleets): Standard deviation applied to catch (assumed log normal distribution)
- flagLinearRamp
Integer scalar: Determins if a step function or a linear function is used to calculate exploitation rates during an assessment. Values: 0 (Step function) or 1 (linear function). Default = 1
- flagMSE
Integer scalar: Determins whether an MSE is being performed. Values: 0 (no, extensive output files) or 1 (yes, limited output files). 2 (yes, Darwinian, catch and biomass only). Default = 0
- fleetNames
Character vector: Names to characterize the fleets
- foodweb
Binary matrix (Nspecies x Nspecies): Predators in columns, prey in rows. Value of 1 indicates predator eats prey
- fqphase
??
- growthCov
Numeric matrix (NgrowthCov x Nyrs): Covariates that determine species growth
- growthCovEffects
Numeric matrix (Nspecies x NgrowthCov): Weight of each covariate for growth for each species
- growthK
Numeric Vector (Nspecies): Values of parameter k assuming von Bertalanfy growth
- growthKappa
Numeric Vector (Nspecies): Values of parameter kappa assuming exponential growth
- growthLinf
Numeric Vector (Nspecies): Values of parameter Linf assuming von Bertalanfy growth
- growthPsi
Numeric Vector (Nspecies): Values of parameter psi assuming exponential growth
- growthType
Numeric Vector (Nspecies): Type of growth for each species. Values 2 (exponential) or 4 (Von Bertalanfy)
- guildMembership
Numeric vector: (Nspecies): Determins guild membership for each species. (Values: 1 - numguilds). See
guildNames- guildNames
Character vector (numGuilds): Names of the guilds
- indicatorFisheryq
Binary matrix (Nspecies x Nfleets): Determins which species in each fleet are actually targeted catch (1) or not (0). This is used to determine exploitation rate durin an assessment
- intakeAlpha
Numeric vector (Nspecies): alpha parameter for functional form of food intake
- intakeBeta
Numeric vector (Nspecies): beta parameter (exponent) for functional form of food intake
- intakeStomach
Numeric matrix (Nspecies x Nsizebins): Each row repsents species stomach weight (g) for each size class. Note. It is assumed that stomach weight remains constant through time (only for creating data input files. Hydra is modelled to acept changes through time.)
- lenwta
Numeric vector (Nspecies): scale parameter for length to weight relationship
- lenwtb
Numeric vector (Nspecies): shape parameter for length to weight relationship
- LFISize
Numeric scalar: Length (cm) at which a fish is considered large. Used in health indices module
- M1
Numeric matrix (Nspecies x Nsizebins): Rate of M1 mortality (natural mortality unexplained by model) for each species in in each size class AT EACH TIME STEP.
- M2sizePrefMu
Numeric vector (Nspecies): size preference parameter (location parameter (mu) of the log normal distribution)
- M2sizePrefSigma
Numeric vector (Nspecies): size preference parameter (scale parameter (sigma) of the log normal distribution)
- maturityCov
Numeric matrix (NmaturityCov x Nyrs): Covariates that determine species maturity
- maturityCovEffects
Numeric matrix (Nspecies x NmaturityCov): Weight of each covariate for maturity for each species
- maturityNu
Numeric vector (Nspecies): maturity parameter (location)
- maturityOmega
Numeric vector (Nspecies): maturity parameter (scale)
- minMaxThresholds
Numeric vector (2): The minimum and maximum thresholds used during an assessment (as a proportion of unfished biomass). The maximum is the level at which effort is reduced (from maximum exploitation) due to overfishing. The minimum is the level in which minimum exploitation is reached. See
minMaxExploitation- Nareas
Integer scalar: Number of spatial regions in the model.
- Nfleets
Integer scalar: Number of fleets in the model. See
fleetNames- NgrowthCov
Integer scalar: Number of growth covariates. See
growthCov- NmaturityCov
Integer scalar: Number of maturity covatiates. See
maturityCov- NrecruitmentCov
Integer scalar: Number og recruitment covariates. See
recruitmentCov- Nsizebins
Integer scalar: Number of size classes (Each species must have same number of size classes, different widths.). See
binwidth- Nspecies
Integer scalar: Number of species in the model
- Nthresholds
Integer scalar: number of assessment threshold. See
thresholdsfor thresholf values- numGuilds
Integer scalar: Number of guilds. See
guildNames- Nyrs
Integer scalar: Number of years in the model
- observedBiomass
Numeric matrix (Nspecies+1) x Nyrs: Real biomass values (from data) for each species over time. First row is year. Currently these are model values from ALTANTIS. Only used in estimation
- observedCatch
Numeric matrix (Nspecies+1) x Nyrs: Real catch values (from data) for each species over time. First row is year. Currently these are model values from ALTANTIS. Only used in estimation
- observedEffort
Numeric matrix (Nfleets+1) x Nyrs: Real fishing effort data for each fleet in the model. First row is year.
- observedTemperature
Numeric matrix (2 x Nyrs): Real temperature values ('C) over time. First row is year.
- otherFood
Numeric scalar: Amount of other food (metric tonnes) available for species in the model. This represents other food sources not explicity accounted for in the model
- phimax
Numeric scalar: Scales the growth of fish to the rate of the fasting growing fish. This is set to 1 and shouldn't be a parameter. If the calculated growth rates are all < 1, then no species will grow out of a size class in the given time interval. In that case phimax = 1 is used.
- predOrPrey
Binary vector: Indicated which species is considered a predator or prey. (This is subjective). This is used in as part of a health index where the ratio of predator to prey is monitored
- recphase
??
- recruitCovEffects
Numeric matrix (Nspecies x NmaturityCov): Weight of each covariate for recruitment for each species
- recruitmentCov
Numeric matrix (NrecruitmentyCov x Nyrs): Covariates that determine species recruitment
- recSigma
Numeric vector: standard deviation associated with recruitment estimates (based on spawning stock biomass size). (0 = known perfectly, no error). See
recStochastic- recStochastic
Binary vector (Nspecies): A switch to turn on (1) and off (0) recruitment error
- recType
Integer vector (Nspecies): Determins which form of recruitment is to be used. Values (1= Egg production, 2= Deriso-Scnute, 3= Gamma, 4= Ricker, 5= Beverton holt, 6= Shepherd, 7= Hockey Stick, 8= Segmented Linear model, 9= recruitment deviations). Default = 8 (Segmented linear model)
- redundantAvgRec
Numeric vector (Nspecies): Average recruitment for each species
- redundantRecDevs
Numeric matrix (Nspecies x Nyrs): Recruitment deviations about the average (
redundantAvgRec) over time- scaledEffort
Numeric Vector (Nspecies): Amount by which to scale effort by species. Can be used if stock recruitment functions are calculated on an area larger or smaller than the region of interest. Default = 1's
- scaleInitialN
Numeric scalar: Amount by which to scale the initial values of
Y1N. Default = 1.- sexRatio
Numeric vector (Nspecies): Proportion of females for each species. Default = 0.5 for all species
- shapeBH
Numeric Vector: (shape) for Beverton Holt Stock recruitment relationship
- shapeDS
Numeric Vector: (shape) for Deriso-Schnute Stock recruitment relationship
- shapeEggRicker
Numeric Vector: (shape) for Ricker stock-egg production relationship
- shapeGamma
Numeric Vector: (shape) for Gamma Stock recruitment relationship
- shapeHockey
Numeric Vector: (shape) for Hockey Stick recruitment relationship
- shapeRicker
Numeric Vector: (shape) for Ricker Stock recruitment relationship
- shapeSegmented
Numeric Vector: (shape) for Segmented (linear) recruitment relationship
- shapeShepherd
Numeric Vector: (shape) for Shepherd Stock recruitment relationship
- speciesList
Character vector: names of species in model
- sqphase
??
- ssigPhase
??
- surveyq
Numeric vector (Nspecies): Proportion of true biomass sampled on a survey. (q = 1 equates to known exactly)
- surveySigma
Numeric vector (Nspecies): The uncertainty (standard deviation) of estimate of survey biomass (0 = known perfectly, no error)
- thresholds
Numeric vector (Nthresholds): The proportions of unfished biomass at which exploitation is decreased
- thresholdSpecies
Numeric vector (Nspecies): A proportion in excess of the current
thresholds. These species have reduced exploitaion at higher proportions of B/B0- wtconv
Numeric Scalar: conversion factor from weight (g) to biomass
- Y1N
Numeric Vector (Nspecies x Nsizebins): initial abundance estimates (milions) for each species in each size class
- yr1Nphase
??
- minMaxExploitation
Numeric Vector (2): The minimum and maximum values of exploitation permissable during an assessment (as a proportion of unfished biomass). The maximum is the level at which all stocks are healthy. The minimum is the lowest level due to overfishing. See
minMaxThresholds- assessmentOn
Binary Scalar: Assessment scenario on (1) or not (0). This is set in
create_datpin_files- assessmentWithSpeciesOn
Binary Scalar: Assessment with extra protection for selected species. on (1) or not (0). This is set in
create_datpin_files- exploitationLevels
Numeric Vector (Nthresholds): The values of exploitation at each threshold (Only used in step function Ramp). This is set in
create_datpin_files. SeeflagLinearRamp
Details
All the required information for creating dat and pin files are stored in this list. This data list is used to create documentation and to create dat and pin files for use in simulaion with Hydra
Source
Gaichas et al. + publication (currently being written up)
Gaichas et al. + publication (currently being written up)
See Also
To visualize this data please run create_documentation
To visualize this data please run create_documentation
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