In NOAA-EDAB/ms-keyrun: All information for keyrun review

knitr::opts_chunk$set(echo = TRUE)
library(magrittr)
library(mskeyrun)
options(warn=-1)

Any Statistical catch at age model will require input data in the form of numbers of fish over a range of ages. This data is obtained in a three step process:

• The catch is first expanded to a composition of lengths

• An age length key is estimated using the expanding catch and age-length data. The method follows that of @gerritsen_simple_2006. The source of the age-length data is often up to the discretion of the assessment scientist and is species dependent.

• The numbers of fish at age is then calculated using the age-length key, the expanded catch and the length-weight relationship. This is explained in mscatch

For the mskeyrun project the final data product is aggregated (over quarter or semester) to annual numbers. This data set is exported in the package as realFisheryAgecomp using the function:

create_real_fishery_agecomp()

A sample of the output for Atlantic cod is shown below.

mskeyrun::realFisheryAgecomp %>%
  dplyr::filter(Code == 172414,
                year == 2000) %>%
  dplyr::arrange(fishery,age) %>%
  head(.,10) %>%
  flextable::flextable() %>% 
  flextable::colformat_num(j=c("Code","year"), big.mark = "" , digits=0 )

References

NOAA-EDAB/ms-keyrun documentation built on April 20, 2024, 10:07 a.m.