calc_length_indices: Calculate length based survey indices

In fishvice/pax: tidy fish data wrangling functions

Description

Calculates abundance and biomass survey indices based on length classes for a particular species in a given year.

The minimum arguments needed are a Station table, a Strata table, Species code and length-weight coefficient, with the rest of the data read in from fjolst.

The function does in principle three things

• Standardizes value (e.g. number of fish) by tow length.

• Calculates stratified indices.

• Aggregates the stratified indices to the total area.

Usage

calc_length_indices(Station, Stratas, SPECIES, lwcoeff, Sex, Length,
  Subsampling, std.towlength = 4, std.towwidth = 17, std.cv = 1,
  oracle = FALSE)

Arguments

Station	A dataframe with station information. Required columns are id (unique station id), year, towlength and strata (the strata identifyer).
Stratas	A dataframe containing columns strata (the strata identifyer) and area (the strata area).
SPECIES	Species code
lwcoeff	A vector of length 2, containing parameter a and b of the length weight relationship.
Sex	Specify sex (1 or 2) to limit calulation. Useful e.g. if one is interested in calculatin indices for "Raudmagi" or "Grasleppa". If missing (default) one gets the ususal non-sexed indices.
Length	A dataframe with length frequency measurements. If missing (default) the data are read in using fjolst::lesa.lengdir based on the id (synis.id) in Station table. This is the recomended method, but if a length dataframe is passed to the function the required columns are id (station id), length (the length class) and n (the number of fish measured), the latter not being raised.
Subsampling	A dataframe containing a raising factor (r) for each sample id (synis.id) for the SPECIES. If missing (default) the data are read using the fjolst::lesa.numer based on the id (synis.id) in the Station table. This is the recomended method.
std.towlength	Standard tow length in nautical miles (default 4)
std.towwidth	Standardized tow width in meters (defalt 17)
std.cv	A multipler (default is 1) on the mean abundance/biomass if only one tow in a strata. In such cases the cv is set equivalent to the "mean" value.
oracle	A boolean, if FALSE (default) reads data from fjolst-package, if TRUE reads data from Oracle database

Value

Returns a list with the following data.frames:

• base that contains the statistics by each strata

  • year: Names/number of the strata

  • ... TODO

• aggr The total survey index. The columns are:

  • year: Survey year

  • length: The length class

  • n: Abundance index for the given length class

  • n.cv: cv of the abundance index for a given length class

  • b: Biomass index for the given length class

  • b.cv: cv of the biomass index for a given length class

  • cn: Abundance index of fish smaller than or equal to a given length class.

  • cn.cv: cv of the abundance index of fish smaller than or equal to a given length class

  • cb: Biomass index of fish greater than or equal to a given length class.

  • cb.cv: cv of the biomass index of fish greater than or equal to a given length class

fishvice/pax documentation built on May 16, 2019, 1:13 p.m.