Multispecies Stratified Survey Optimization for Gulf of Alaska Groundfishes

This repository provides the code used for an In Prep NOAA Technical Memorandum manuscript by Zack Oyafuso, Lewis Barnett, Margaret Siple, and Stan Kotwicki temporarily entitled "The expected performance and feasibility of a Gulf of Alaska groundfish bottom trawl survey optimized for abundance estimation."

Package Requirements

A handful of R packages are required. R version 4.0.2 was used for the analysis. Some conventional packages for plotting and manipulating data:

VAST version 3.6.1, and FishStatsUtils version 2.8.0 (2020-09-22).

library(tidyverse)
library(sp)
library(raster)
library(RColorBrewer)

The creation of the operating models was done using the VAST R package version 3.6.1 and FishStatsUtils version 2.8.0.

library(VAST)

The bulk of the optimization is done within the SamplingStrata R Package (https://github.com/barcaroli/SamplingStrata). There is one function in the package, BuildStrataDF() that I modify for this analysis, so it is best to use a forked version of the package that I modified:

library(devtools)
devtools::install_github(repo = "zoyafuso-NOAA/SamplingStrata")
library(SamplingStrata)

Lastly, the TSP package was imported to calculate the shortest path that visits each station.

library(TSP)

Species Included

The species set included in the survey optimization is a complex of fifteen Gulf of Alaska cods, flatfishes, and rockfishes:

Scientific Name	Common Name
Gadus chalcogrammus	Alaska or walleye pollock
Gadus macrocephalus	Pacific cod
Atheresthes stomias	arrowtooth flounder
Hippoglossoides elassodon	flathead sole
Glyptocephalus zachirus	rex sole
Lepidopsetta polyxystra	northern rock sole
Lepidopsetta bilineata	southern rock sole
Microstomus pacificus	Dover sole
Hippoglossus stenolepis	Pacific halibut
Sebastes alutus	Pacific ocean perch
Sebastes melanostictus/aleutianus	blackspotted and rougheye rockfishes*
Sebastes brevispinis	silvergrey rockfish
Sebastes variabilis	dusky rockfish
Sebastes polyspinis	northern rockfish
Sebastolobus alascanus	shortspine thornyhead

*Due to identification issues between two rockfishes these two species were combined into a species group we will refer as "BE and RS rockfishes" (blackspotted rockfish and rougheye rockfish, respectively).

In addtion, eleven species/species groups were included in the survey evaluations. These taxa were not included in the optimization but included when simulating surveys:

Scientific Name	Common Name
Anoplopoma fimbria	sablefish
Pleurogrammus monopterygius	Atka mackerel
Sebastes borealis	shortraker rockfish
Sebastes variegatus	harlequin rockfish
Sebastes ruberrimus	yelloweye rockfish
Species from Genera Hemitripterus, Hemilepidotus, and Myoxocephalus	sculpins (plain, great, and bigmouth sculpins and yellow Irish lord)
Beringraja binoculata	big skate
Raja rhina	longnose skate
Albatrossia Pectoralis	giant grenadier
Enteroctopus dofleini	giant octopus
Squalus suckleyi	Pacific spiny dogfish

Survey Optimization Scenarios

Survey Exploration	Scenario Option/Scenario Label	A	B	C	D	E	F	G	H	I	J	K	L	M
Spatial scale of optimization	gulf-wide	X
	area-level		X	X	X	X	X	X	X	X	X	X	X	X
Stratum variables	depth and longitude	X	X		X		X	X			X
	depth only			X		X			X	X		X
	existing STRS design												X	X
Sensitivity of data inputs	MLE	X	X	X	X	X					X	X	X	X
	measurement error simulated						X		X
	fixed and random effects simulated							X		X
One deep stratum: cells deeper than 300 m are set to 300 m	no	X	X	X			X	X	X	X	X	X	X	X
	yes				X	X
Maximum depth cutoff	1000 m	X	X	X	X	X	X	X	X	X			X
	700 m										X	X		X

Script Overview

Tasks are done modularly from data wrangling to VAST model fits to survey optimization to survey simulations to figure/table production. See the wiki page for a breakdown of the script workflow.