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README.Rmd
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---
output:
github_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
# Gulf of Alaska Bottomfish
**Author:** Clay McKean (<clay.mckean@alaska.gov>)\
\
**Last updated:** December 2024\
\
**Local Directory** \
There are 2 local directories associated with this project:\
**Homer:** Main directory O:/DSF/GOAB/\
Locally, this repository is housed at O:/DSF/GOAB/Git/\
**Anchorage** Clay's S:/DSFShared/Groundfish Port Sampling program/\
\
## About this project
This project assesses the halibut, rockfish, and lingcod sport fisheries in Southcentral Alaska by collecting biological
samples and conducting angler interviews out of the ports of Homer, Seward, Whittier, Valdez, and Kodiak.
The operational plan for this project can be found here: <https://www.adfg.alaska.gov/FedAidPDFs/ROP.SF.2A.2022.24.pdf>
\
## Project Objectives
\
### Primary Objectives
1) Estimate the mean weight of Pacific halibut taken by each user in each area of Southcentral
Alaska (Kodiak, Lower Cook Inlet, Central Cook Inlet, North Gulf Coast, Eastern Prince
William Sound, and Western Prince William Sound), such that the mean weight estimates
for each user group in each area are within 0.20 of the true mean weight at least 90% of the
time.\
2) Estimate the length composition of the Pacific halibut harvest by area such that the
estimated proportions are within 0.20 of the true proportions at least 95% of the time.\
3) Estimate the species composition by port of the rockfish harvest landed at Kodiak, Homer,
Seward, Whittier, and Valdez during May through September such that the estimated
proportions of each species are within 0.20 of the true proportions at least 95% of the time.\
4) Estimate the age, length, and sex composition by port of the principal rockfishes landed at
Kodiak, Homer, Seward, Whittier, and Valdez during May through September such that
the estimated proportions are within 0.20 of the true proportions at least 95% of the time.\
5) Estimate the age, length, and sex composition by port of the lingcod harvest landed at
Kodiak, Homer, Seward, Whittier, and Valdez during July through September such that
the estimated proportions are within 0.20 of the true proportions at least 90% of the time.
### Secondary Objectives
1) Identify differences in the geographic distribution of groundfish effort and harvest between
user groups and across years for each port during May through September.\
2) Estimate the proportion of the Pacific halibut harvest that was cleaned (and carcasses
discarded) at sea at each port. These estimates will be used to stratify length and weight
estimates at ports where cleaning at sea is prevalent.\
3) Estimate the proportions of released Pacific halibut that were caught on circle hooks versus
other types of hooks at each port. This information is needed to refine estimates of halibut
release mortality in the sport fishery.\
4) To refine discard mortality estimates, gather data on the depths of capture for pelagic and
nonpelagic rockfish that were released.\
5) Estimate the proportions of released lingcod that were of sublegal (under 35 inches total
length) and legal size (35 inches and greater) for ports with a minimum size limit
regulation. These data will provide information on future recruitment and abundance
indices used for future stock assessments.\
6) Biological data will be collected from salmon sharks (Lamna ditropis), Pacific sleeper
sharks (Somniosus pacificus), and spiny dogfish (Squalus acanthias) harvested in the sport
fishery in order to estimate the age, length, sex composition, and spatial distribution of the
harvest. No sampling objectives are established for sharks because harvests are too small
to generate reliable estimates for any given year. It is expected that age, length, and sex
data will be compiled across a number of years and combined with commercial harvest
sampling and other research programs to estimate life history parameters.
## Repository Directory
- 1.`data/`: Data folder\
- i.`HAL/`: Halibut AWL data. Data is compiled each year from port sampling biological samples\
- ii.`Harvest/`: Rockfish and Lingcod harvest data, calculated by combining SWHS and logbook estimates\
* a.`LC/`: Lingcod harvest data by port and sport fish management area\
* b.`RF/`: Rockfish harvest data by port, sport fish management area, and species\
- iii.`Intervw/`: Port sampling interview data. Data is compiled each year from interview samples\
- iv.`LC/`: Lingcod AWL data. Data is compiled each year from port sampling biological samples\
- v.`RF/`: Rockfish AWL data. Data is compiled each year from port sampling biological samples\
- vi.`RF_Harvest_Reconstruction/`: Statewide rockfish harvest and release estimates using the Howard et al. method. This data is used for the annual rockfish harvest reconstruction.\
* This data comes from Phil Joy, and can be found at <https://github.com/ADFG-DSF/RockfishSportMort/output/>\
- 2.`Figures/`: Output figures\
\
- 3.`reports/`: Reports associated with this repository\
- i.`RF_Harvest_Reconstruction.R`: This file contains the output file of the rockfish harvest reconstruction, titled `RF_Removals_thruXX.xlsx`. This file is sent out to the members of the Statewide Rockfish Initiative in early October, once the harvest and release estimates are recieved from Phil Joy.\
- 4.`scripts/`: Scripts for running analyses\
- i.`Age_comps/`: Age composition data for Rockfish and Lingcod\
* a.`LC Age Comp bubble.R`: Lingcod age composition bubble plot\
* b.`LCAgeComp9622_port.R`: Lingcod age composition by port\
* c.`LCAgeComp9622_SFmgmtarea.R`: Lingcod age composition by sport fish management area\
* d.`RF Age Comp bubble.R`: Rockfish age composition bubble plot\
* b.`RFAgeComp9622_port.R`: Rockfish age composition by port\
* c.`RFAgeComp9622_SFmgmtarea.R`: Rockfish age composition by sport fish management area\
- ii.`Apportionment/`: Apportioning groundfish to sport fish management areas to assess proportion of harvest by port and management area\
* a.`Apportion halibut to mgmtareas.R`: Halibut apportionment\
* b.`Apportion lingcod to mgmtareas.R`: Lingcod apportionment\
* c.`Apportion rockfish to mgmtareas.R`: Rockfish apportionment\
- iii.`L.WRegression/`: Calculate yield of groundfish in kg, using length-weight regressions to estimate weights of fish when no weight is available in the data.\
Computation is based on the basic formula: Yield(s) = Harvest(all s) * SpeciesComp(s) * MeanWt(s).\
Estimates are preliminary because they are based on L-W regressions that haven't yet been tested for differences between years, ports, sexes, etc.\
* a.`LCYieldPrelim_SFmgmtarea.R`: Estimate of lingcod yield by sport fish management area by year\
* b.`RFYieldPrelim_byAssemb_port.R`: Estimate of rockfish yield by port and assemblage by year\
* c.`RFYieldPrelim_byAssemb_SFmgmtarea.R`: Estimate of rockfish yield by sport fish management area and assemblage by year\
- iv.`RF_Reconstruction`: Rockfish harvest reconstruction using harvest and release estimates from RTS.\
* a.`RF_removals`: Estimates the total removals in lbs. for Black and Yelloweye rockfish using harvest and release estimates from Phil Joy, using the Howard et al. method. This script should be run in early October after recieving the updated harvest and release estimates. Be sure to update the script to add the port sampling data for the current year and update the ouput file to state the current year.\
- v.`Spatial harvest and effort/`: Total harvest by port, user, and year from port sampling interview data. Used for providing harvest trends in managemnet reports/
* a.`LC/`: Lingcod data/
+ (i).`LC_report_spatial_subset.R`: Lingcod interview harvest data for lingcod report/
* b.`RF/`: Rockfish data. currently empty/
- vi.`Species_comp/`: Rockfish species composition data from port sampling biological sampling/
* a.`RF by assemblage.R`: Species compositon and average weights per year at the assemblage level. Predicted weights based on length used when weight is not available for a sample/
* b.`RF_simple_spcomp.R`: Simple species composition by sport fish management area. Useful for providing species comps to area managers\
* c.`RFspcomp9622.R`: Rockfish species composition in biological data. Uses Steve Fleischman version of composition equations\
- vii.`AWLsummaries.R`: Summary statistics of rockfish data. For rockfish report\
- viii.`FractionCleanedAtSea.R`: Calculates the fraction of harvest cleaned at sea by port for halibut, rockfish, and lingcod. Used in writing Op plan.\
- 5.`functions.R`: Functions used in R scripts. Accessed with `source("functions.R")`\