In iantaylor-NOAA/Lingcod_2021: Estimate the Status of Lingcod off the US West Coast in 2021

Length and age compositions from commercial landings for the TW and FG fleets were developed from the PacFIN database using PacFIN.Utilities. r ifelse(params$area == "North", "Many more length and age samples were available for the northern stock than the southern stock. Both the differences in sampling programs by \\gls{wdfw} and \\gls{odfw} compared to \\gls{cdfw} and larger commercial catches in the north compared to the south contributed to the differences in sample sizes", "" ).

Length and age samples from west coast groundfish commercial fisheries are typically expanded to account for variability in the number of fish sampled per trip relative to the total catch. This allows greater weight to be given to samples from a very large trip compared to one with a small catch. However, the commercial data for r spp, as represented in the PacFIN database, have a large fraction of trips without trip weights. This leads to large variability in the expanded sample sizes among trips and implausible amounts of variability in the resulting composition data among length bins within a given fleet and year. Unexpanded data did not show this variability, and thus, models were fit to unexpanded composition data for the commercial fisheries.

Commercial TW length-composition data started in r ifelse(params$area == "North", 1965, 1977) (Table \ref{tab:sample-size-length}; Figure \ref{fig:comp-lenfit--page1-multi-fleet-comparison}). Commercial FG length-composition data started in r ifelse(params$area == "North", 1986, 1992), with additional samples in r ifelse(params$area == "North", "1971, 1980, and 1982", "1988 and 1989") r ifelse(params$area == "North", "(Tables \\ref{tab:sample-size-length} and \\ref{tab:sample-size-length-byState}; Figures \\ref{fig:comp-lenfit--page1-multi-fleet-comparison}-\\ref{fig:comp-lenfit--page2-multi-fleet-comparison})", "(Table \\ref{tab:sample-size-length}; Figure \\ref{fig:comp-lenfit--page1-multi-fleet-comparison})" ).

Commercial age samples covered r ifelse(params$area == "North", "43 years for TW and 35 years for FG", "10 years for TW and 2 years for FG") years, starting in r ifelse(params$area == "North", "1978 for TW and 1986 for FG", "1993 for TW and 1993 for FG") r ifelse(params$area == "North", "(Tables \\ref{tab:sample-size-age} and \\ref{tab:sample-size-age-byState})", "(Table \\ref{tab:sample-size-age})" ). The commercial age data were processed as both marginal and conditional age-at-length compositions to allow explorations of either format in the models. Unsexed fish were represented as separate compositions in addition to the compositions of fish with known sex.

Length compositions and mean body weight observations were also available from commercial discards for the years 2004 to 2019. These observations were all unsexed and represented in the model as independent vectors to facilitate estimation of retention functions for the TW and FG fleets. The mean body weight observations were calculated from counted baskets of discarded fish and represented a larger number of individuals than the subsamples from which lengths were available but in general they provide similar information (Figures \ref{fig:discard-fitcommercialtrawl}-\ref{fig:bodywt-fit-fltcommercialfixed-gear}).

iantaylor-NOAA/Lingcod_2021 documentation built on Oct. 30, 2024, 6:42 p.m.