Report the location of the Data Files

Description

A function that returns the location of the example CSV files

Usage

DataDir()

Author(s)

A. Hordyk modified (i.e., stolen) from T. Carruthers' code (DLMtool package)

Kalman filter and Rauch-Tung-Striebel smoother

Description

A function that applies a filter and smoother to estimates

Usage

FilterSmooth(RawEsts, R = 1, Q = 0.1, Int = 100)

Arguments

Value

a vector of smoothed values

LBSPR Optimization function for age-based selectivity model

Description

Internal optimization function

Usage

LBSPR_NLLabsel(
  starts,
  x,
  P,
  LMids,
  LBins,
  LDat,
  MK,
  Linf,
  FecB,
  L50,
  L95,
  maxsd,
  CVLinf,
  Nage,
  usePen
)

Arguments

Value

negative log-likelihood value

Author(s)

A. Hordyk

LBSPR Optimization function for GTG model

Description

Internal optimization function

Usage

LBSPR_NLLgtg(
  starts,
  LMids,
  LBins,
  LDat,
  gtgLinfs,
  MKMat,
  MK,
  Linf,
  ngtg,
  recP,
  usePen
)

Arguments

Value

negative log-likelihood value

Author(s)

A. Hordyk

Fit LBSPR model to length data

Description

A function that fits the LBSPR model to length data

Usage

LBSPRfit(
  LB_pars = NULL,
  LB_lengths = NULL,
  yrs = NA,
  Control = list(),
  pen = TRUE,
  verbose = TRUE,
  useCPP = TRUE,
  ...
)

Arguments

Details

The Control options are:

modtype

Model Type: either Growth-Type-Group Model (default: "GTG") or Age-Structured ("absel")

maxsd

Maximum number of standard deviations for length-at-age distribution (default is 2)

ngtg

Number of groups for the GTG model. Default is 13

P

Proportion of survival of initial cohort for maximum age for Age-Structured model. Default is 0.01

Nage

Number of pseudo-age classes in the Age Structured model. Default is 101

maxFM

Maximum value for F/M. Estimated values higher than this are trunctated to maxFM. Default is 4

Value

a object of class 'LB_obj'

Author(s)

A. Hordyk

Examples

## Not run: 
MyFit <- LBSPRfit(LBparameters, LBlengths)
MyFit@Ests

## End(Not run)

Internal function to fit LBSPR model to length data

Description

An internal function that fits the LBSPR model to a single year of length data

Usage

LBSPRfit_(
  yr = 1,
  LB_pars = NULL,
  LB_lengths = NULL,
  Control = list(),
  pen = TRUE,
  useCPP = TRUE,
  verbose = TRUE
)

Arguments

Details

The Control options are:

modtype

Model Type: either Growth-Type-Group Model (default: "GTG") or Age-Structured ("absel")

maxsd

Maximum number of standard deviations for length-at-age distribution (default is 2)

ngtg

Number of groups for the GTG model. Default is 13

P

Proportion of survival of initial cohort for maximum age for Age-Structured model. Default is 0.01

Nage

Number of pseudo-age classes in the Age Structured model. Default is 101

maxFM

Maximum value for F/M. Estimated values higher than this are trunctated to maxFM. Default is 4

Value

a object of class 'LB_obj'

Author(s)

A. Hordyk

Optimisation Routine for fitting LBSPR

Description

A function that calculate the negative log-likelihood of the LBSPR model

Usage

LBSPRopt(
  trypars,
  yr = 1,
  LB_pars = NULL,
  LB_lengths = NULL,
  Control = list(),
  pen = TRUE
)

Arguments

Details

The Control options are:

modtype

Model Type: either Growth-Type-Group Model (default: "GTG") or Age-Structured ("absel")

maxsd

Maximum number of standard deviations for length-at-age distribution (default is 2)

ngtg

Number of groups for the GTG model. Default is 13

P

Proportion of survival of initial cohort for maximum age for Age-Structured model. Default is 0.01

Nage

Number of pseudo-age classes in the Age Structured model. Default is 101

maxFM

Maximum value for F/M. Estimated values higher than this are trunctated to maxFM. Default is 4

Value

a NLL value

Author(s)

A. Hordyk

LBSPR Simulation Model

Description

Function that generates the expected equilbrium size composition given biological parameters, and fishing mortality and selectivity pattern.

Usage

LBSPRsim(LB_pars = NULL, Control = list(), verbose = TRUE)

Arguments

Details

The Control options are:

modtype

Model Type: either Growth-Type-Group Model (default: "GTG") or Age-Structured ("absel")

maxsd

Maximum number of standard deviations for length-at-age distribution (default is 2)

ngtg

Number of groups for the GTG model. Default is 13

P

Proportion of survival of initial cohort for maximum age for Age-Structured model. Default is 0.01

Nage

Number of pseudo-age classes in the Age Structured model. Default is 101

maxFM

Maximum value for F/M. Estimated values higher than this are trunctated to maxFM. Default is 4

Value

a object of class 'LB_obj'

Author(s)

A. Hordyk

Examples

 LB_pars <- new("LB_pars")
 LB_pars@MK <- 1.5
 LB_pars@Linf <- 100
 LB_pars@L50 <- 50
 LB_pars@L95 <- 55
 LB_pars@SL50 <- 60
 LB_pars@SL95 <- 65
 LB_pars@FM <- 1
 Sim <- LBSPRsim(LB_pars)
 Sim@SPR

Internal LBSPR Simulation Model

Description

A internal function that generates the expected equilbrium size composition given biological parameters, and fishing mortality and selectivity pattern. Typically only used by other functions in the package.

Usage

LBSPRsim_(LB_pars = NULL, Control = list(), verbose = TRUE, doCheck = TRUE)

Arguments

Details

The Control options are:

modtype

Model Type: either Growth-Type-Group Model (default: "GTG") or Age-Structured ("absel")

maxsd

Maximum number of standard deviations for length-at-age distribution (default is 2)

ngtg

Number of groups for the GTG model. Default is 13

P

Proportion of survival of initial cohort for maximum age for Age-Structured model. Default is 0.01

Nage

Number of pseudo-age classes in the Age Structured model. Default is 101

maxFM

Maximum value for F/M. Estimated values higher than this are trunctated to maxFM. Default is 4

Value

a object of class 'LB_obj'

Author(s)

A. Hordyk

An S4 class containing length data

Description

An S4 class containing length data

Slots

LMids

A numeric vector containing the mid-points of the length bins

LData

A numeric matrix containing length data

L_units

Character descrbing units of the length measurements

Years

A numeric vector containing the year indices

NYears

A length-one numeric vector for number of years

Elog

A error log

An S4 class containing all parameters for the LBSPR model

Description

An S4 class containing all parameters for the LBSPR model

Slots

SPR

The Spawning Potential Ratio

Yield

Relative yield

YPR

Yield per recruit

SSB

Spawning stock biomass (relative only)

SSB0

Unfished spawning stock biomass

B0

Unfished biomass

LMids

A numeric vector containing the mid-points of the length bins

pLCatch

A numeric vector containg expected proportion for each length class in the catch

pLPop

A numeric vector containg expected proportion for each length class in the population

RelRec

Relative recruitment

Ests

A matrix of estimated values

Vars

A vector of estimated variance for SL50, SL95, F/M and SPR

NLL

A numeric NLL values

maxFM

A numeric of maximum estimated F/M value (note this is apical F)

SPRatsize

A vector of cumulative SPR at length (currently only works for GTG model)

fitLog

A vector of error logs for each fit. 0 means everything is okay.

An S4 class containing life history and other parameters

Description

An S4 class containing life history and other parameters

Slots

Species

Character vector of species name

MK

A length-one numeric vector for M/K ratio

M

An optional value for natural mortality (M)

Linf

A length-one numeric vector for Linf

L_units

Character describing units of length parameters

CVLinf

A length-one numeric vector for CV of length-at-age

L50

A length-one numeric vector for length at 50% maturity

L95

A length-one numeric vector for length at 95% maturity

Walpha

A length-one numeric vector for alpha parameter of length-weight relationship

Walpha_units

Character describing units for weight scaling parameter

Wbeta

A length-one numeric vector for beta parameter of length-weight relationship

FecB

A length-one numeric vector for beta parameter of length-fecundity relationship

Steepness

A length-one numeric vector for steepness of SRR

Mpow

A length-one numeric vector for M at length

R0

A length-one numeric vector for initial number of recruits (1 for per-recruit)

SL50

A length-one numeric vector for length at 50% selectivity

SL95

A length-one numeric vector for length at 95% selectivity

MLL

Minimum legal length (inflection point)

sdLegal

Standard deviation of MLL curve

fDisc

Fraction discarded that die

FM

A length-one numeric vector for F/M ratio (note this is apical F)

SPR

A length-one numeric vector for SPR

BinMin

A length-one numeric vector for minimum length bin

BinMax

A length-one numeric vector for maximum length bin

BinWidth

A length-one numeric vector for width of length bins

Run a Shiny Application

Description

Shiny runs one of the Shiny Applications that are included in the package

Usage

Shiny(app)

Arguments

References

Modified from Deal Attali's code: https://deanattali.com/2015/04/21/r-package-shiny-app/

Calculate Relative Yield, YPR, SPR, SSB, and Recruitment curves for F/M

Description

A function that takes a LB_pars or LB_obj object and returns a data frame of values for relative Yield, YPR, SPR, SSB, and Recruitment at different values of F/M

Usage

calcCurves(LB_obj)

Arguments

Value

a dataframe with YPR, Yield, SSB, Rec, and FM

Author(s)

A. Hordyk

Calculate F/M given SPR and other parameters

Description

A internal function that optimizes for F/M when SPR is provided in the simulation parameters.

Usage

getFMfun(FM, LB_pars, Control = list())

Arguments

Details

The Control options are:

modtype

Model Type: either Growth-Type-Group Model (default: "GTG") or Age-Structured ("absel")

maxsd

Maximum number of standard deviations for length-at-age distribution (default is 2)

ngtg

Number of groups for the GTG model. Default is 13

P

Proportion of survival of initial cohort for maximum age for Age-Structured model. Default is 0.01

Nage

Number of pseudo-age classes in the Age Structured model. Default is 101

maxFM

Maximum value for F/M. Estimated values higher than this are trunctated to maxFM. Default is 4

Value

sum of squares value

Author(s)

A. Hordyk

Create a new LB_lengths object

Description

Function

Usage

## S4 method for signature 'LB_lengths'
initialize(
  .Object,
  file = "none",
  LB_pars = NULL,
  dataType = c("raw", "freq"),
  header = FALSE,
  verbose = TRUE,
  ...
)

Arguments

Value

a object of class 'LB_lengths'

Author(s)

A. Hordyk

Create a new LB_obj object

Description

Function

Usage

## S4 method for signature 'LB_obj'
initialize(.Object, defaults = FALSE, verbose = FALSE)

Arguments

Value

a object of class 'LB_obj'

Author(s)

A. Hordyk

Create a new LB_pars object

Description

Function

Usage

## S4 method for signature 'LB_pars'
initialize(.Object, file = "none", defaults = TRUE, verbose = TRUE)

Arguments

Value

a object of class 'LB_pars'

Author(s)

A. Hordyk

Plot the Relative Yield, YPR, SPR, SSB, and Recruitment curves

Description

A function that plots the Relative Yield, YPR, SPR, SSB, and Recruitment curves

Usage

plotCurves(
  LB_obj,
  X = c("FM", "SSB", "SPR"),
  Y = c("SPR", "SSB", "Yield"),
  size.axtex = 12,
  size.title = 14,
  size.leg = 12,
  size.pt = 4,
  inc.pts = TRUE
)

Arguments

Value

a ggplot object

Author(s)

A. Hordyk

Plot LBSPR model estimates

Description

A function that plots the estimates of the LBSPR with a smoother line

Usage

plotEsts(
  LB_obj = NULL,
  pars = c("Sel", "FM", "SPR"),
  Lwd = 2.5,
  ptCex = 1.25,
  axCex = 1.45,
  labCex = 1.55,
  doSmooth = TRUE,
  incL50 = FALSE,
  CIcol = "darkgray",
  L50col = "gray"
)

Arguments

Author(s)

A. Hordyk

Plot the maturity-at-length and selectivity-at-length curves

Description

A function that plots the maturity-at-length and selectivity-at-length curves

Usage

plotMat(
  LB_obj = NULL,
  size.axtex = 12,
  size.title = 14,
  size.leg = 12,
  useSmooth = TRUE,
  Title = NULL
)

Arguments

Value

a ggplot object

Author(s)

A. Hordyk

Circle of estimated SPR and target and limit points

Description

A function that creates a circle plot showing the estimated SPR relative to the target and limit reference points

Usage

plotSPRCirc(
  LB_obj = NULL,
  SPRTarg = 0.4,
  SPRLim = 0.2,
  useSmooth = TRUE,
  Title = FALSE,
  Leg = TRUE,
  limcol = "#ff1919",
  targcol = "#f2ff02",
  abtgcol = "#32ff36",
  labcol = NULL,
  bgcol = "#FAFAFA",
  labcex = 2,
  texcex = 1.3
)

Arguments

Author(s)

A. Hordyk

General plotting function for simulated data

Description

A general function that plots the simulation object. Includes four different plots: equilbrium size structure, maturity and selectivity curves, growth curves, and relative Yield, YPR, SPR, SSB, and Recruitment curves.

Usage

plotSim(
  LB_obj = NULL,
  type = c("all", "len.freq", "growth", "maturity.select", "yield.curve"),
  lf.type = c("catch", "pop"),
  growth.type = c("LAA", "WAA"),
  y.type = c("SPR", "SSB", "Yield", "YPR"),
  x.type = c("FM", "SSB", "SPR"),
  perRec = FALSE,
  inc.SPR = TRUE,
  Cols = NULL,
  size.axtex = 12,
  size.title = 14,
  size.SPR = 4,
  size.leg = 12,
  inc.pts = TRUE,
  size.pt = 4
)

Arguments

Value

a ggplot object

Author(s)

A. Hordyk

Examples

 LB_pars <- new("LB_pars")
 LB_pars@MK <- 1.5
 LB_pars@Linf <- 100
 LB_pars@L50 <- 50
 LB_pars@L95 <- 55
 LB_pars@SL50 <- 60
 LB_pars@SL95 <- 65
 LB_pars@FM <- 1
 Sim <- LBSPRsim(LB_pars)
 plotSim(Sim)

Plot the size data and model fits

Description

A function that plots size data and the fitted LBSPR model

Usage

plotSize(
  LB_obj = NULL,
  size.axtex = 12,
  size.title = 14,
  Title = NULL,
  scales = c("fixed", "free_x", "free_y", "free"),
  inc.text = FALSE,
  warn.size = 0.8
)

Arguments

Value

a ggplot object

Author(s)

A. Hordyk

Plot sampled length structure against target simulated size composition

Description

A function that plots the observed size structure against the expected size composition at the target SPR

Usage

plotTarg(
  LB_pars = NULL,
  LB_lengths = NULL,
  yr = 1,
  Cols = NULL,
  title = NULL,
  targtext = TRUE,
  size.axtex = 12,
  size.title = 14,
  scales = c("fixed", "free_x", "free_y", "free")
)

Arguments

Value

a ggplot object

Author(s)

A. Hordyk