doAssessment: Do assessment

In wStockhausen/rPIBKC: Package to run the PIBKC stock assessment

Do assessment

Description

Function to do the assessment.

Usage

doAssessment(
  assYr = 2014,
  recentYear = 1990,
  srvData = NULL,
  fshData = NULL,
  avgTypeForMMB = "IV",
  yrsForBmsy = c(1980:1984, 1990:1997),
  nYrsSrvIV = 3,
  nYrsTheta = 3,
  M = 0.18,
  t.sf = 3/12,
  t.fm = 4/12,
  hm.pot = 0.5,
  hm.trl = 0.8,
  pct.male = 0.5,
  gamma = 1,
  alpha = 0.1,
  beta = 0.25,
  pdfType = "lognormal",
  ci = 0.95,
  verbose = FALSE,
  showPlot = FALSE
)

Arguments

assYr	year of assessment
recentYear	recent year to set time axis for some plots
srvData	survey data dataframe, path to csv file, or NULL
fshData	fisheries data dataframe, path to csv file, or NULL
avgTypeForMMB	flag indicating averaging type for survey data ('raw', 'IV' or 'RE')
yrsForBmsy	years for B_{MSY} calculation
nYrsSrvIV	number of years to include in inverse variance averages
nYrsTheta	number of years to average for \theta calculation
M	rate of natural mortality
t.sf	time from survey to fishery
t.fm	time from fishery to mating
hm.pot	pot fisheries handling mortality rate
hm.trl	trawl fisheries handling mortality rate
pct.male	assumed male percentage
gamma	value for the Tier 4 \gamma constant (in Tier 4: F_{OFL_{max}} = \gamma \cdot M)
alpha	value for the Tier 4 \alpha constant (the x-intercept of the sloping control rule)
beta	value for the Tier 4 \beta constant (the threshold for MMB/B_{MSY} to allow directed fishing)
pdfType	probability distribution for error bars
ci	confidence interval for error bar plots
verbose	flag (T/F) to print intermediate output
showPlot	flag (T/F) to plot results

Details

Output units are in t for biomass, ones for abundance.

Value

list consisting of the following elements:

• data - list with elements:

  • fshData - dataframe with fishery data

  • srvData - dataframe with 'raw' survey data

  • avgSrvData - dataframe with 'smoothed' survey data

  • plots.RawData - list of ggplot2 objects

  • plots.AvgdData - list of ggplot2 objects

• lstMMB - list from calcMMBMating:

  • mmbMat = MB at maturity (t)

  • mmbFsh = MMB at fishery time (t)

  • mmbSrv = MMB at survey time (t)

  • retM = retained mortality (t)

  • dscM = list with elements:

    • tot = total discard mortality (t)

    • gft = groundfish trawl fisheries mortality (t)

    • gfp = groundfish pot fisheries mortality (t)

    • crb = crab fisheries discard mortality (t)

  • plots = list with elements:

    • MMB = MMB time series ggplot2 plot object

• inputs.OFL - list of inputs to calcOFL, with elements:

  • mmbSrvCurr - "current" value of MMB at survey time

  • Bmsy - B_{MSY} from calcBmsy

  • theta - \theta, from calcTheta

  • M - rate of natural mortality, M

  • gamma - value for the Tier 4 \gamma constant (in Tier 4: F_{OFL_{max}} = \gamma \cdot M)

  • alpha - value for the Tier 4 \alpha constant

  • beta - value for the Tier 4 \beta constant

  • t.sf - time from survey to fishery (as fraction of year)

  • t.fm - time from fishery to mating (as fraction of year)

• lstOFL - list result from calcOFL, with elements:

  • maxFofl = max allowed F_{OFL_{max}} (= \gamma \cdot M))

  • Bmsy = B_{MSY} (in t)

  • Fofl = F_{OFL} (in t)

  • prjMMB = projected MMB (in t)

  • retOFL = retained portion of total OFL (in t)

  • dscOFL = discard portion of total OFL (in t)

wStockhausen/rPIBKC documentation built on April 25, 2023, 6:50 p.m.