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Filter length-weight outliers

Source: R/StoxBaselineFunctions.R
FilterWeightLengthOutliersStoxBiotic.Rd

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

FilterWeightLengthOutliersStoxBiotic(
  StoxBioticData,
  FilterUpwards = FALSE,
  logalfa = numeric(),
  beta = numeric(),
  sigma = numeric(),
  kAl = numeric(),
  kAu = numeric()
)

Arguments

StoxBioticData

StoxBioticData to be filtered

FilterUpwards

Whether the filter action will propagate in the upwards direction (removing Samples, Stations, etc. for which all fish records are removed). Default to FALSE.

logalfa

The alfa parameter (on a log scale) for the log-linear model. See details for units.

beta

The beta parameter for the log-linear model. See details for units.

sigma

The standard deviation of weight for the log-linear model. See details for units.

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

Value

StoxBioticData with individuals outside the acceptable region removed.

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.

Parameters 'logalfa', 'beta' and 'sigma' must be appropriate for weights recorded in gram, and lengths recorded in cm.

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.

Some parameterizations that have been used for some stocks at IMR:

cod.27.1-2 (Gadus morhua)

logalfa = -5.0061, beta = 3.0716, sigma = 0.1454, kAl = kAu = 4

had.27.1-2 (Melanogrammus aeglefinus)

logalfa = -4.9620, beta = 3.0919, sigma = 0.1282, kAl = kAu = 4

pok.27.1-2 (Pollachius virens)

logalfa = -4.7718, beta = 3.0287, sigma = 0.1338, kAl = kAu = 4

See also

FilterAgeLengthOutliersStoxBiotic