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Filter outliers

Source: R/StoxBaselineFunctions.R
FilterAgeLengthOutliersStoxBiotic.Rd

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

FilterAgeLengthOutliersStoxBiotic(
  StoxBioticData,
  FilterUpwards = FALSE,
  Linf = numeric(),
  K = 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.

Linf

Asymptotic length for the von-Bertalanffy growth curve (in cm)

K

The growth coefficient for the von-Bertalanffy growth curve

sigma

The standard deviation of length for the von-Bertalanffy growth curve (in cm)

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. Defaults to the same value as kAl.

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 von-Bertalanffy growth curves, and function arguments are named to correspond to the naming convention used in ECA.

Records are removed if the length fall outside the range from: Linf\*(1-exp(-K\*(AGE)))\*exp(kAu\*sigma) to Linf\*(1-exp(-K\*(AGE)))\*exp(-kAl\*sigma)

Age is provided with a resolutation of 1/12 year, which is approximated by adding M/12 to the integer age, where M is the number of the month of catch (e.g. 2 for february). For this reason, 'DateTime' must be provided for all 'Stations' in 'StoxBioticData'

any records with missing length or age 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.

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

cod.27.1-2 (Gadus morhua)

Linf=232.98028344, K=0.05284384 sigma=0.16180306 kAl=kAu=4

had.27.1-2 (Melanogrammus aeglefinus)

Linf=69.7075536, K=0.2158570, sigma=0.1441575 kAl=kAu=4

pok.27.1-2 (Pollachius virens)

Linf=100.5282683, K=0.1392982, sigma=0.0996507 kAl=kAu=4

pelagic stocks North Atlantic

Linf=37.2490509 K=0.3128122 sigma=0.009681094 kAl=kAu=4

See also

FilterWeightLengthOutliersStoxBiotic