Description Usage Arguments Value
Calculates abundance and biomass survey indices based on length classes for a particular species in a given year.
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.
1 2 | calc_indices(st, le, lwcoeff = c(0.01, 3), stratas, std.towlength = 4,
std.area = 4 * 17/1852, std.cv = 1)
|
st |
A dataframe with station information. Required columns are id (unique station id), year, towlength and strata (the strata identifyer). |
le |
A dataframe with length frequency measurements. Required columns are id (station id), length (the length class) and n (the number of fish measured) where the latter are the "raised" numbers. |
lwcoeff |
A vector of length 2, containing parameter a and b of the length weight relationship. |
stratas, |
A dataframe containing columns strata (the strata identifyer) and area (the strata area). |
std.towlength |
Standard tow length in nautical miles. |
std.area |
Standardized area swept in nautical square miles. |
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. |
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
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