filterLogLinear: Filter length-weight outliers

In StoXProject/RstoxFDA: Fisheries Dependent Analysis with RstoX

Filter length-weight outliers

Description

Removes fish records that fall outside an acceptable weight-length region defined by the log-linear model

weight=alfa\*length^beta\*exp(epsilon); epsilon~N(0,sigma^2)

with alfa=exp(logalfa), logalfa and other parameters corresponding to arguments to this function.

Usage

filterLogLinear(
  individuals,
  logalfa,
  beta,
  sigma,
  kAl,
  kAu = kAl,
  weightCol = "IndividualRoundWeight",
  lengthCol = "IndividualTotalLength"
)

Arguments

individuals	data.table of fish records
logalfa	The alfa parameter (on a log scale) for the log-linear model
beta	The beta parameter for the log-linear model
sigma	The standard deviation of weight for the log-linear model
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
weightCol	name of column in 'individuals' that contain fish weight (in a unit corresponding to alfa and beta). Default correspond to the Individual level of StoxBioticData, but see details.
lengthCol	name of column in 'individuals' that contain fish length (in a unit corresponding to alfa and beta). 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 a log-linear weight-length model, and function arguments are named to correspond to the naming convention used in ECA.

Records are removed if their weights that outside the range from: alfa\*L^beta\*exp(kAu\*sigma) to alfa\*L^beta\*exp(-kAl\*sigma)

any records with missing length or weight is not removed.

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 Jan. 13, 2024, 12:32 a.m.