SimulatorFn: Simulate double reading data

In nwfsc-assess/nwfscAgeingError: Estimating ageing error with 'TMB' from double reads

Simulate double reading data

Description

A function to generate simulated double reading data with given properties

Usage

SimulatorFn(
  Nreaders,
  M,
  SelexForm,
  ErrorParams,
  BiasParams,
  SelexParams,
  ReadsMat,
  RecCv = 0.6,
  RecAr1 = 0.8,
  Amax = 100
)

Arguments

Nreaders	The number of ageing readers
M	True natural mortality
SelexForm	Form of selectivity-at-age (logistic selex-at-age is the only one that is implemented).
ErrorParams	Error type CV in the following equation: VarAgeRead = (CV*TrueAge)^2
BiasParams	Bias type b in the following equation: EAgeRead = b*TrueAge
SelexParams	Selectivity parameters, which are standard to the logistic equation.
ReadsMat	Matrix describing number of reads per reader combination. Where each row specifies how many reads (in the first column) have a particular pattern of double reads (in the second through Nreaders+1 columns).
RecCv	CV of recruitment, and it shoudl be noted that recruitment is assumed to be stationary over time.
RecAr1	First-order autoregressive coefficient for recruitment
Amax	True maximum age

Value

Returns a simulated double read matrix

Author(s)

James T. Thorson

References

Punt, A.E., Smith, D.C., KrusicGolub, K., and Robertson, S. 2008. Quantifying age-reading error for use in fisheries stock assessments, with application to species in Australias southern and eastern scalefish and shark fishery. Can. J. Fish. Aquat. Sci. 65: 1991-2005.

Examples

# Parameters for generating data
# This represents 2 unique readers
# Row 1 -- Otoliths read only once by reader
# Row 2 -- Otoliths read twice by reader 1
# Row 2 -- Otoliths read only once by reader 2
# Row 4 -- Otoliths read twice by reader 2
# Row 5 -- Otoliths read once by reader 1 and once by reader 2
ReadsMat <- structure(matrix(
  nrow = 5, ncol = 5,
  c(
    rep(25, 5),
    1, 1, 0, 0, 1,
    0, 1, 0, 0, 0,
    0, 0, 1, 1, 1,
    0, 0, 0, 1, 0
  )
), dimnames = list(
  c(
    "Reader1_Only", "Reader1_DoubleReads",
    "Reader2_Only", "Reader2_DoubleReads",
    "Reader1_&_Reader2"
  ),
  c(
    "NumberOfReads",
    "Reader1", "Reader1_DoubleReads",
    "Reader2", "Reader2_DoubleReads"
  )
))

# Generate data
set.seed(2)
AgeReads <- SimulatorFn(
  Nreaders = 4, M = 0.2,
  SelexForm = "Logistic",
  SelexParams = c(5, 0.2), BiasParams = c(1, 1, 1.1, 1.1),
  ErrorParams = c(0.2, 0.2, 0.2, 0.2), ReadsMat = ReadsMat,
  RecCv = 0.6, RecAr1 = 0.8, Amax = 100
)

nwfsc-assess/nwfscAgeingError documentation built on July 4, 2025, 9:49 a.m.