raw commercial lengths

[andybeet]

Data

• Compiles length data without any borrowing of length samples. Aggregated to level of Year, Season, market code, gear type (fleet). realFisheryLencompRaw.rda
• Updated realFisheryLencomp.rda and realFisheryAgecompRaw.rda. Conversion of Lbs to kg was omitted

Code

• Added create_real_fishery_lencomp_raw.r

Documentation

• Added frequency plots. Too convoluted to create on the fly in the rmd
• nested plots in RMD (GBaLandingsByLength.rmd)

Other

• Simulated data files (since i branched from master and not dev, and last pull request went straight to master.) Alternatively we can merge this into master then just update dev. That might be easier

[sgaichas]

I first started plotting abundance at length in the catch rather than biomass. I think there are missing abundance values (all years and gears) for several species in realFisheryLencompRaw: Atlantic cod Haddock And there are others that are missing years that it looks like they should have length data according to the plots in the vignette (unless they are all length samples and not just Georges Bank?)

> mskeyrun::realFisheryLencompRaw %>% dplyr::filter(Name %in% "Atlantic cod")
# A tibble: 11,384 × 9
   ModSim  year   Code Name         fishery   lenbin variable  value units      
   <chr>  <int>  <dbl> <chr>        <chr>      <dbl> <chr>     <dbl> <chr>      
 1 Actual  1964 164712 Atlantic cod demersal      NA biomass   9364. metric tons
 2 Actual  1964 164712 Atlantic cod demersal      NA abundance   NA  numbers    
 3 Actual  1964 164712 Atlantic cod fixedGear     NA biomass   1003. metric tons
 4 Actual  1964 164712 Atlantic cod fixedGear     NA abundance   NA  numbers    
 5 Actual  1965 164712 Atlantic cod demersal      NA biomass   8675. metric tons
 6 Actual  1965 164712 Atlantic cod demersal      NA abundance   NA  numbers    
 7 Actual  1965 164712 Atlantic cod fixedGear     NA biomass    931. metric tons
 8 Actual  1965 164712 Atlantic cod fixedGear     NA abundance   NA  numbers    
 9 Actual  1966 164712 Atlantic cod demersal      NA biomass   8518. metric tons
10 Actual  1966 164712 Atlantic cod demersal      NA abundance   NA  numbers    
# … with 11,374 more rows
# ℹ Use `print(n = ...)` to see more rows
> mskeyrun::realFisheryLencompRaw %>% dplyr::filter(Name %in% "Haddock")
# A tibble: 5,876 × 9
   ModSim  year   Code Name    fishery   lenbin variable   value units      
   <chr>  <int>  <dbl> <chr>   <chr>      <dbl> <chr>      <dbl> <chr>      
 1 Actual  1964 164744 Haddock demersal      NA biomass   40012. metric tons
 2 Actual  1964 164744 Haddock demersal      NA abundance    NA  numbers    
 3 Actual  1964 164744 Haddock fixedGear     NA biomass     758. metric tons
 4 Actual  1964 164744 Haddock fixedGear     NA abundance    NA  numbers    
 5 Actual  1965 164744 Haddock demersal      NA biomass   45641. metric tons
 6 Actual  1965 164744 Haddock demersal      NA abundance    NA  numbers    
 7 Actual  1965 164744 Haddock fixedGear     NA biomass     696. metric tons
 8 Actual  1965 164744 Haddock fixedGear     NA abundance    NA  numbers    
 9 Actual  1966 164744 Haddock demersal      NA biomass   45334. metric tons
10 Actual  1966 164744 Haddock demersal      NA abundance    NA  numbers    
# … with 5,866 more rows

[andybeet]

@sgaichas The NA's in cod and Haddock for abundance (in 1964,1965, 1966 as shown above) are because there are no length samples for that year. The plots in the vignette show the frequency of lengths for GB. Can you give examples where you see length samples but NA for abundance? This obviously shouldn't be the case, if so i have a bug

[sgaichas]

ok, I see what I did--apologies, it was my summary and plotting code. here is Atlantic cod numbers summarized by year (all gears)