| year | trip_type | lat | lon | species_name | port_name | state_abb | state_full | kept | discarded |
|---|---|---|---|---|---|---|---|---|---|
| 1996 | COMMERCIAL | 41.67694 | -69.59028 | FLOUNDER, WINTER / BLACKBACK | CHATHAM | MA | Massachusetts | 350 | 0 |
| 1996 | COMMERCIAL | 42.54417 | -70.53750 | COD | GLOUCESTER | MA | Massachusetts | 850 | 0 |
| 1996 | COMMERCIAL | 41.37472 | -71.57028 | FLOUNDER, WINTER / BLACKBACK | POINT JUDITH | RI | Rhode Island | 72 | 0 |
About
This package contains various functions for accessing (pulling) and cleaning federal fisheries dependent and independent data. Many of these data sets are confidential and require a formal data request submission to the appropriate governing body. Information regarding metadata and access for most of these data sets can be accessed via inPort, see below:
InPort is the authoritative metadata repository and data inventory platform for NOAA Fisheries and the National Ocean Service. The system supports documentation of datasets and provides tools to facilitate data discovery, public access, and responsible stewardship of scientific data within these line offices.
As such, using species.shifts will require access to this data in order to use the cleaning and plotting functions. It is strongly recommended that this data be stored locally in a centralized repository. Please refer to the package README more information on recommended work flows.
Data sets
The functions in this package correspond to six federal fisheries data sets, each with its own respective pull_() function.
NOAA Fisheries Vessel Trip Reports
NEFSC Spring-Fall Bottom Trawl Survey
GARFO Dealer Reported Landings
NOAA Fisheries Marine Recreational Information Program
Vessel trip reports
vtr <- pull_vtr(proj_path = my_path)
*Trip ID information removed from demo to maintain confidentiality.
Fisheries Observer
observer <- pull_observer(proj_path = my_path)
| year | negear | comname | targspec1 | targspec2 | targspec3 | lat | lon | hailwt | live_wt | kept | decade |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1989 | 50 | MONKFISH (GOOSEFISH) | 5260 | 0 | 0 | 40.91 | -70.83083 | 25 | 25 | Kept | 1980 |
| 1989 | 50 | BUTTERFISH | 5260 | 0 | 0 | 40.91 | -70.83083 | 25 | 25 | Kept | 1980 |
| 1989 | 50 | FLOUNDER, YELLOWTAIL | 5260 | 0 | 0 | 40.91 | -70.83083 | 100 | 100 | Discarded | 1980 |
*Trip ID information removed from demo to maintain confidentiality.
NEFSC Bottom Trawl
nefsc <- pull_nefsc(proj_path = my_path)
| id | svspp | comname | year | est_month | est_day | season | lat | lon | est_towdate | total_biomass_kg |
|---|---|---|---|---|---|---|---|---|---|---|
| 1.97003e+12 | 23 | winter skate | 1970 | 3 | 0 | Spring | 41.58333 | -69.46667 | 3/12/70 8:00 | 3.128 |
| 1.97003e+12 | 28 | thorny skate | 1970 | 3 | 0 | Spring | 41.58333 | -69.46667 | 3/12/70 8:45 | 0.900 |
| 1.97003e+12 | 73 | atlantic cod | 1970 | 3 | 0 | Spring | 41.58333 | -69.46667 | 3/12/70 8:45 | 8.910 |
GARFO Federal Permits
permits <- pull_permits(proj_path = my_path)
| ap_year | ap_num | vp_num | pport | ppst | permit | target | category | lat | long | state_full | council |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1996 | 227829 | 221741 | GLOUCESTER | MA | lobster_1 | lobster | commercial | 42.61536 | -70.66246 | Massachusetts | New England |
| 1996 | 227830 | 127133 | GLOUCESTER | MA | lobster_1 | lobster | commercial | 42.61536 | -70.66246 | Massachusetts | New England |
| 1996 | 227831 | 231461 | RYE | NH | lobster_1 | lobster | commercial | 43.01202 | -70.77194 | New Hampshire | New England |
GARFO Dealer-reported landings
landings <- pull_landings(proj_path = my_path)
| year | portnm | state | species_name | land | live | value | confidential | comname | lat | long | state_full | council |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1996 | ADDISON | ME | clam, quahog, ocean | 26418 | 217965 | 98152 | NA | ocean clam, quahog | 44.61882 | -67.74445 | Maine | New England |
| 1996 | ADDISON | ME | lobster, american | 355359 | 355359 | 1178910 | NA | american lobster | 44.61882 | -67.74445 | Maine | New England |
| 1996 | ADDISON | ME | scallop, sea | 9704 | 80837 | 66560 | NA | sea scallop | 44.61882 | -67.74445 | Maine | New England |
Marine Recreational Information Program
Directed trips
mrip_directed_trips <- pull_mrip_directed_trips()
| year | wave | st | sub_reg | mode_fx | area_x | species | Trips | SE | PSE | state | mode | area |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2018 | 1 | 10 | 5 | 3 | 1 | striped bass | 23379.88 | 8886.435 | 38.0 | DE | Shore | State Territorial Seas (Ocean<=3 mi excluding Inland) |
| 2018 | 1 | 10 | 5 | 3 | 5 | striped bass | 169377.67 | 40817.095 | 24.1 | DE | Shore | Inland |
| 2018 | 1 | 10 | 5 | 7 | 1 | striped bass | 44944.57 | 38431.208 | 85.5 | DE | Private & Rental | State Territorial Seas (Ocean<=3 mi excluding Inland) |
Catch estimates
mrip_catch <- pull_mrip_catch()
| estimate_status | year | coast | region | state | common_name | sci_name | harvest_a_b1_numbers | pse_harvest_a_b1_numbers | harvest_a_b1_weight_lb | pse_harvest_a_b1_weight | released_alive_b2_numbers | released_alive_b2_lower_95_percent_confidence_limit | released_alive_b2_upper_95_percent_confidence_limit | total_catch_a_b1_b2_numbers | total_catch_a_b1_b2_lower_95_percent_confidence_limit | total_catch_a_b1_b2_upper_95_percent_confidence_limit | total_catch_pse | comname |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Final | 2024 | Atlantic Coast | Mid Atlantic | Delaware | rudderfish, banded | Seriola zonata | 0 | 0.0 | 0 | 0.0 | 23 | 0 | 56 | 23 | 0 | 56 | 73.9 | banded rudderfish |
| Final | 2024 | Atlantic Coast | Mid Atlantic | Delaware | shark, dogfish, spiny | Squalus acanthias | 0 | 0.0 | 0 | 0.0 | 35430 | 6611 | 64249 | 35430 | 6611 | 64249 | 41.5 | spiny dogfish |
| Final | 2024 | Atlantic Coast | Mid Atlantic | Delaware | bass, black sea | Centropristis striata | 105763 | 28.8 | 130995 | 28.1 | 1008441 | 290955 | 1725926 | 1114203 | 395720 | 1832686 | 32.9 | black sea bass |
Plotting
Once the data has been pulled and saved to the local environment, each data set has a respective plot_() or map_() function. More about those functions here.