man/glossary.md

In catarinawor/ERAR: This package is a loose translation of the Chinook Technical committee ERA model

Variable definition for the ERA CIS code

Objects are split in three groups: subs (or functions), variables and flags. All objects are listed in alphabetic order within the two groups. uncertain definitions are marked with IDK

Subs/functions

Age: ages associated with antural mortlity rates

GetCASStocks: function that Get the array of CASStocks corresponding to the current ERAStock (e.g. ANB,ACI,ALP,ADM,AHC for ERA stock AKS).

GetFirstAndLastBY: Get first and last brood years for the CASStocks corresponding to the current ERAstock.

GetIMData:

GetInterDamSurvival: This function retrieves the inter dam survival for a specific ERA stock, if inter dam survival data does not exist (i.e. no dams), then sets the interdam survival to 1

GetMaxReleaseSize: Returns the maximum amount (counts) amount of releases for each stock.

GetSuperStockData: Function that reads in the data from the SuperStock table in the database.

GetSurvivalRates: Retrieves Natural mortality rate from the database and the associated vector of ages.

GetTaggedReleaseByBrood: Recovers the information about hatchery releases by brood year - BroodYear CWTRelease TotalRelease.

GetWithinBYWeightFlagAndPNVRegionAndAvgMatRates:

MainSub: Main routine that calls most of the data reading and calculations subroutines.

NaturalMortalityRate: What it says. For each ERA stock

SetTerminalFishery: Populates a matrix that is PSCfishe ry x Age, with flags indicating if fish is caught at a terminal fishery.

Variables

AdultInterDamSurvivalRate: What is says. by calendar year

AverageMatRate: vector of length 4 that includes either maturity rate values or NA for the internally calculated maturity rates.

CalendarYear: Calendar year for which there is incidental mortality data

CASStockString: vector containing three letter identifiers of CAS Stocks for a specific ERAStock. Many CAS stocks can correspond to a single ERAStock (e.g.CAS stocks ANB,ACI,ALP,ADM,AHC for ERA stock AKS)

CNREffort: Catch non release effort

CNRLegalEncounterEst: Catch non release legal encounter estimate. Numeric ,CalendarYear x PSCFishery matrix.

CNRMethod: Catch non retention method, numrical, either 9, 1, 2, or 3 ("HAR"). CalendarYear x PSCFishery matrix.

CNRSeasonLength: Catch non retention season length?

CNRSubLegalEncounterEst: Catch non release sub legal encounter estimate. Numeric ,CalendarYear x PSCFishery matrix.

CurrentStock: holder of the three letter ERA stock code from ERAStockArray

DropoffRate: Dropoff Incidental mortality rate. CalendarYear x PSCFishery matrix. CalendarYear x PSCFishery matrix.

ERAStock: Counter for loop over all ERA stocks pa

ERAStockArray: Vector containing the 3-letter code that specifies the ERA stock identifier. Read from table CASStock in CIS.

ExtraLegalIMRate: ExtraLegal incidental mortality rate (Is this larger than the legal size, for the slot limit case?). CalendarYear x PSCFishery matrix.

ExtraLegalSelectivityFactor: Extra legal selectivity factor IDK. CalendarYear x PSCFishery matrix.

ExtraLegalShakerEst: Extra legal shaker estimate. CalendarYear x PSCFishery matrix.

FirstBY: First brood year for a given CASStockString

InterDamSurvival_CalendarYear: Calendar year for the interdamSurvival data.

JackInterDamSurvivalRate: What is says. by calendar year

LandedCatchEst: Landed catch estimate.CalendarYear x PSCFishery matrix.

LegalShakerEst: Legal Shaker estimate. CalendarYear x PSCFishery matrix.

LastAvailableBY: Last available brood year for a given CASStockString

LastBY: Last Brood Year, either equal to LastAvailableBY or LastPossibleBY depending on which one is lower.

LastPossibleBY: LastCalendarYear - OceanStartAge

LastCalendarYear: Variable that stores the last calendar year in the database. It is initially set by the user, but then gets adjusted in the Get_IMData function.

LegalCatchabilityCoefficient: Legal Catchability Coefficient. PSCFishery xAge.

LegalIMRate: Legal incidental mortality rate. CalendarYear x PSCFishery matrix.

LegalSelectivityFactor: Legal selectivity factor IDK numerical: 0.34, 0.20, 0.00, or 1.00. CalendarYear x PSCFishery matrix.

MaxAge: Maximum age assigned to a given Superstock.

MaxCalendarYear: variable used to store the last calendar year set initially by the user.

MeanMatType: Variable indicating what method is used to calculate average maturity rates. Options are: "ArithmeticMean" and or other (defaults to geometric mean).

MonitoredLegalCatch: that. CalendarYear x PSCFishery matrix.

MonitoredLegalReleases: that. CalendarYear x PSCFishery matrix.

OceanStartAge: The first age in which a given Superstock appears in the fishery.

PNV: Proportion non vulnerable CalendarYear x PSCFishery x Age array

PNVRegion: 5? IDK

PSCFishery: List of Integeres indicating PSC fisheries, current CIS data incluse 78 fisheries.

PV: Proportion vulnerable, CalendarYear x PSCFishery x Age array

Reavailability: IDK one of these: 0 78 1 92 125 60 for "HAR"

RetentionEffort: IDK What are the units for this? all 0s. CalendarYear x PSCFishery matrix.

RetentionMethod: Either NA or 0, CalendarYear x PSCFishery matrix.

SeasonLength: Numerical (high numbers) CalendarYear x PSCFishery matrix.

SeasonUnits: Either NA or 0 for harrison, CalendarYear x PSCFishery matrix.

SubLegalCatchabilityCoeificient: Sub legal catchability. PSCFishery xAge.

SublegalIMRate: Sub legal incidental mortality rate. CalendarYear x PSCFishery matrix.

SublegalSelectivityFactor: IDK either 1 or 0. CalendarYear x PSCFishery marix.

SubLegalShakerEst: Sub Legal shaker estimate. CalendarYear x PSCFishery marix.

SuperStock: 3-4 letter code indicating Superstock identifier

SurvivalRate: Survival rate at age for the CASStockString

terminal: Matrix with flags indicating is a fishery is terminal or not.

TermNetSwitchAge: Any age older than this age will be marked in the "terminal" flag. IDK I am not sure but I think the terminal flag will be used to indicate that aging should not occur for fish caught in certain net fisheries.

TimeStep: IDK Not functional and set to 1 in the current CIS code. Maybe time steps within a year?

TimePeriod: IDK Not functional and set to 1 in the current CIS code. Maybe periods larger than year?

youngestAge: Youngest age for a given set of CASStockString

Flags

ArithmeticMeanFlag: Flag indicating if Arithmetic Average Maturity Rates is used. Alternative is geometric mean. Note: In the R code this flag is given by the M$MeanMatType variable.

isreplicate2016URBdata: Flag used to make CIS match CAS, since some data was missing in the 2016 CAS database but was present in the C files. - This flag will probabaly go away once the review of the CIS prgram is complete.

isTraceCalc: IDK Some sort of verbose flag?

isTraceByBroodYr: IDK Some sort of verbose flag?

isTraceByCalendarYr: IDK Some sort of verbose flag?

traceThisShakerMethod: IDK Some sort of verbose flag?

ShakCalcFlg: Flag indicating which shaker method should be used. 'C' is the default.

isCombineAge2And3: indicates whether age 2 and 3 should be combined. Combination only applies if Oceanstartage is 3

WithinBYWeightFlag: Flag used to calculate Landed catch and escapenet method

catarinawor/ERAR documentation built on Sept. 21, 2019, 8:25 a.m.