filterVonBsigma: Filter length-age outliers

In StoXProject/RstoxFDA: Fisheries Dependent Analysis with RstoX

Filter length-age outliers

Description

Removes fish records that fall outside an acceptable age-length region defined by a von-Bertalanffy growth curve:

length=Linf(1-exp(-K\*age))\*exp(epsilon); epsilon~N(0,sigma^2)

with parameters corresponding to arguments to this function.

Usage

filterVonBsigma(
  individuals,
  Linf,
  K,
  sigma,
  kAl,
  kAu = kAl,
  ageCol = "IndividualAge",
  lengthCol = "IndividualTotalLength"
)

Arguments

individuals	data.table of fish records
Linf	Asymptotic length for the von-Bertalanffy growth curve
K	The growth coefficient for the von-Bertalanffy growth curve
sigma	The standard deviation of length for the von-Bertalanffy growth curve
kAl	Number of standard deviations (on a log scale) that defines the lower limit of the acceptable region
kAu	Number of standard deviations (on a log scale) that defines the upper limit of the acceptable region
ageCol	name of column in 'individuals' that contain fish age in decimal years. Default correspond to the Individual level of StoxBioticData, but see details.
lengthCol	name of column in 'individuals' that contain fish length in the same unit as Linf and sigma. Default correspond to the Individual level of StoxBioticData

Details

This function is intended to provide the same filtering that is offered in ECA 3.x and ECA 4.x for removing outliers based on von-Bertalanffy growth relationships, and function arguments are named to correspond to the naming convention used in ECA.

Fish with lengths that fall outside the range from: Linf\*(1-exp(-K\*(AGE)))\*exp(kAu\*sigma) to Linf\*(1-exp(-K\*(AGE)))\*exp(-kAl\*sigma) are removed

any records with missing length or age is not removed.

The filtering may be sensitive to the resolution of age for small fish. When age is counting completed winter-ring growth, an acceptable resolution may be achieved by adding M/12 to the age of each fish, where M is the month-number for the date of catch.

Note that kAl and kAu are given on a log scale, so that the acceptable region is not symmetric around the growth curve when kAl=kAu.

Value

data.table, like individuals, but with some records removed.

StoXProject/RstoxFDA documentation built on Nov. 12, 2024, 3:42 a.m.