This is a repository for combining trawl survey datasets from NOAA and Fisheries and Oceans Canada in the Northeast Pacific Ocean.
A pkgdown site is available here.
This data includes surveys conducted by the Northwest Fisheries Science Center (NWFSC) off the west coast of the United States, surveys collected by Fisheries and Oceans Canada (DFO) in the waters of British Columbia, and surveys conducted by the Alaska Fisheries Science Center (AFSC) in Alaska.
There are 55 species included in the initial version of the package, focusing on species that are occurring in multiple regions.
Installing
# install.packages("pak")
pak::pkg_install("DFO-NOAA-Pacific/surveyjoin")Basic use
library(surveyjoin)On first use, download the data and load it into a local SQL database:
Find available species:
## # A tibble: 55 × 3
## common_name scientific_name itis
## <chr> <chr> <dbl>
## 1 aleutian skate bathyraja aleutica 160935
## 2 arrowtooth flounder atheresthes stomias 172862
## 3 big skate raja binoculata 160848
## 4 bigfin eelpout lycodes cortezianus 550588
## 5 bigmouth sculpin hemitripterus bolini 167287
## 6 black eelpout lycodes diapterus 165261
## 7 blackbelly eelpout lycodes pacificus 630999
## 8 bocaccio sebastes paucispinis 166733
## 9 canary rockfish sebastes pinniger 166734
## 10 capelin mallotus villosus 162035
## # ℹ 45 more rowsLoad data for a species:
d <- get_data("pacific cod")
dplyr::glimpse(d, width = 72)## Rows: 58,889
## Columns: 21
## $ survey_name <chr> "Aleutian Islands", "Aleutian Islands", "Aleut…
## $ event_id <dbl> -21893, -21764, -21455, -18280, -18259, -18094…
## $ date <chr> "2022-08-07", "2022-07-28", "2022-07-03", "201…
## $ pass <int> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…
## $ vessel <chr> "OCEAN EXPLORER", "OCEAN EXPLORER", "ALASKA PR…
## $ lat_start <dbl> 52.01721, 53.11242, 51.96523, 52.67577, 52.507…
## $ lon_start <dbl> -175.8889, -170.9027, -172.6282, -172.7522, -1…
## $ lat_end <dbl> 52.00690, 53.10904, 51.96874, 52.67061, 52.516…
## $ lon_end <dbl> -175.9017, -170.9244, -172.6096, -172.7648, -1…
## $ depth_m <dbl> 184, 98, 216, 184, 167, 133, 225, 80, 186, 111…
## $ effort <dbl> 2.3745, 2.5268, 2.6409, 1.7392, 1.8012, 1.8531…
## $ effort_units <chr> "ha", "ha", "ha", "ha", "ha", "ha", "ha", "ha"…
## $ performance <chr> "0", "0", "5", "4", "4", "0", "4", "0", "0", "…
## $ bottom_temp_c <dbl> 4.6, 4.9, 4.5, 4.5, 4.6, 4.6, 4.3, 5.5, 4.8, 4…
## $ region <chr> "afsc", "afsc", "afsc", "afsc", "afsc", "afsc"…
## $ year <int> 2022, 2022, 2022, 2018, 2018, 2018, 2018, 2018…
## $ itis <dbl> 164711, 164711, 164711, 164711, 164711, 164711…
## $ catch_numbers <dbl> 0, 0, 0, 7, 11, 4, 11, 30, 12, 56, 2, 0, 0, 3,…
## $ catch_weight <dbl> 0.00, 0.00, 0.00, 24.65, 31.22, 14.61, 34.22, …
## $ scientific_name <chr> "gadus macrocephalus", "gadus macrocephalus", …
## $ common_name <chr> "pacific cod", "pacific cod", "pacific cod", "…Citations
Citing the surveyjoin package can be done with the DOI linked above, though more detailed citations may be needed for specific surveys or methodology. For citations pertaining to surveys run by the Alaska Fisheries Science Center (AFSC), see https://github.com/afsc-gap-products/citations. Metadata for surveys conducted by the AFSC can be found at https://afsc-gap-products.github.io/gap_products.
Background and additional citations on surveys run by the Northwest Fisheries Science Center (NWFSC) can be found in Keller et al. 2017.
What species are included?
We first divided the joined datasets into 4 major areas: Eastern Bering Sea, Gulf of Alaska, British Columbia, and west coast of California / Oregon / Washington states.
Within each region, we identified the species that occurred in at least 5% of all tows (resulting in 4 lists, 1 for each region). Because our interests are in cross-regional work, we identified species meeting our occurrence threshold that also occurred in 2 or more regions. This resulted in the following list of 55 species:
| Common name | Scientific name |
|---|---|
| Aleutian Skate | Bathyraja aleutica |
| Arrowtooth Flounder | Atheresthes stomias |
| Big Skate | Raja binoculata |
| Bigfin Eelpout | Lycodes cortezianus |
| Bigmouth Sculpin | Hemitripterus bolini |
| Black Eelpout | Lycodes diapterus |
| Blackbelly Eelpout | Lycodes pacificus |
| Bocaccio | Sebastes paucispinis |
| Canary Rockfish | Sebastes pinniger |
| Capelin | Mallotus villosus |
| Curlfin Sole | Pleuronichthys decurrens |
| Darkblotched Rockfish | Sebastes crameri |
| Darkfin Sculpin | Malacocottus zonurus |
| Dover Sole | Microstomus pacificus |
| English Sole | Parophrys vetulus |
| Eulachon | Thaleichthys pacificus |
| Flathead Sole | Hippoglossoides elassodon |
| Giant Grenadier | Albatrossia pectoralis |
| Great Sculpin | Myoxocephalus polyacanthocephalus |
| Greenstriped Rockfish | Sebastes elongatus |
| Harlequin Rockfish | Sebastes variegatus |
| Kamchatka Flounder | Atheresthes evermanni |
| Lingcod | Ophiodon elongatus |
| Longnose Skate | Raja rhina |
| North Pacific Hake | Merluccius productus |
| Northern Rock Sole | Lepidopsetta polyxystra |
| Pacific Cod | Gadus macrocephalus |
| Pacific Halibut | Hippoglossus stenolepis |
| Pacific Herring | Clupea pallasii |
| Pacific Ocean Perch | Sebastes alutus |
| Pacific Sanddab | Citharichthys sordidus |
| Pacific Spiny Dogfish | Squalus suckleyi |
| Petrale Sole | Eopsetta jordani |
| Redbanded Rockfish | Sebastes babcocki |
| Rex Sole | Glyptocephalus zachirus |
| Rock Sole | Lepidopsetta bilineata |
| Rosethorn Rockfish | Sebastes helvomaculatus |
| Sablefish | Anoplopoma fimbria |
| Sandpaper Skate | Bathyraja interrupta |
| Sawback Poacher | Sarritor frenatus |
| Searcher | Bathymaster signatus |
| Sharpchin Rockfish | Sebastes zacentrus |
| Shortfin Eelpout | Lycodes brevipes |
| Shortspine Thornyhead | Sebastolobus alascanus |
| Slender Sole | Lyopsetta exilis |
| Spinyhead Sculpin | Dasycottus setiger |
| Splitnose Rockfish | Sebastes diploproa |
| Spotted Ratfish | Hydrolagus colliei |
| Sturgeon Poacher | Podothecus accipenserinus |
| Threadfin Sculpin | Icelinus filamentosus |
| Walleye Pollock | Gadus chalcogrammus |
| Wattled Eelpout | Lycodes palearis |
| Widow Rockfish | Sebastes entomelas |
| Yellow Irish Lord | Hemilepidotus jordani |
| Yellowtain Rockfish | Sebastes flavidus |
