otndata is a wrapper around the Ocean Tracking Network’s Plone content
management system setup.
You can install the development version of otndata from GitHub with:
# install.packages("pak")
pak::pak("mhpob/otndata")There are a few things that can be accessed without logging in. Mainly all of the information presented via the leaflet map that can be seen on https://members.oceantrack.org.
library(otndata)
otn_list_species() |>
head()
#> scientificname commonname
#> 1 Abramis brama common bream
#> 2 Acanthocybium solandri wahoo
#> 3 Acanthurus bahianus cirujano pardo
#> 4 Acanthurus blochii ringtail surgeonfish
#> 5 Acanthurus chirurgus doctorfish
#> 6 Acanthurus coeruleus blue tang
otn_list_projects() |>
head()
#> node collectioncode country longitude latitude
#> 1 ETN Usk:2021-2024 UNITED KINGDOM -4.035 52.405
#> 2 ETN V2LTROT NORWAY 10.945 63.605
#> 3 ETN OTN-Tosenfjorden NORWAY 6.140 68.715
#> 4 ETN ST08SWE SWEDEN 10.960 58.465
#> 5 OTN RNP NORWAY 10.385 63.420
#> 6 OTN V2LBFC MEXICO, BELIZE -87.650 18.625
#> shortname
#> 1 River Usk receiver network 2021-2024
#> 2 OTN-Loan_Salmonids in Trondheimsfjorden
#> 3 OTN-Tosenfjorden,OTN-Tosenfjorden
#> 4 sea trout_2018-9_gullmarn,sea trout_2018-9_gullmarn
#> 5 NTNU River Nidelva Project
#> 6 Big Fish Caribbean
#> longname
#> 1 River Usk receiver network 2021-2024
#> 2 OTN_Loan_Salmonids in Trondheimsfjorden
#> 3 Marine migrations and area use of brown trout in Tosenfjorden, Bindal municipality 2015-2017
#> 4 Sea trout <i>Salmo trutta</i> connectivity in Gullmarn fjord, Skagerrak
#> 5 Migration of anadromous brown trout between river and fjord, Nidelva, Norway
#> 6 Big Fish: Cooperative monitoring network for fish spawning aggregations in the wider Caribbean
#> ocean website datacenter_infourl id
#> 1 NE ATLANTIC http://www.lifewatch.be/en/imis?dasid=6491&show=json http://www.lifewatch.be/etn/ <NA>
#> 2 NE ATLANTIC http://www.lifewatch.be/en/imis?dasid=8311&show=json http://www.lifewatch.be/etn/ <NA>
#> 3 NE ATLANTIC http://www.lifewatch.be/en/imis?dasid=6201&show=json http://www.lifewatch.be/etn/ <NA>
#> 4 NE ATLANTIC http://www.lifewatch.be/en/imis?dasid=8137&show=json http://www.lifewatch.be/etn/ <NA>
#> 5 NE ATLANTIC <NA> https://members.oceantrack.org <NA>
#> 6 NW ATLANTIC http://geo.gcoos.org/restore/ https://members.oceantrack.org <NA>
otn_list_stats()
#> $project_count
#> [1] 1601
#>
#> $contributor_count
#> [1] 2435
#>
#> $inst_count
#> [1] 467
#>
#> $species_count
#> [1] 457
#>
#> $rcvr_count
#> [1] 2973You can also query projects according to code, country of origin, species, institution, node, or point of contact.
otn_search_node("ACT") |>
head()
#> node collectioncode country longitude latitude shortname
#> 1 ACT NJDEPMR USA -73.8185 38.0705 NJDEP Mullica River Array
#> 2 ACT CTSEC6 USA -73.8150 38.0700 CT DEEP Sturgeon movements in CT, 2010-2017
#> 3 ACT CT001 USA -72.2500 41.6450 CT DEEP LIS array (Sec. 6 2018-2022)
#> 4 ACT RIWFCC USA -73.8185 38.0705 Narragansett Bay Cable Corridor Monitoring
#> 5 ACT CBASR USA -73.8150 38.0700 SERC Atlantic Stingray Study
#> 6 ACT TNCCVOW USA -73.8185 38.0705 TNC / NEFSC CVOW tagging and array
#> longname
#> 1 NJDEP Mullica River Array
#> 2 Identification of summering and foraging habitats of Atlantic Sturgeon in Connecticut waters and within Long Island Sound
#> 3 CT DEEP array of VEMCO receivers in Long Island Sound and lower Connecticut River, 2018-2023.
#> 4 Narragansett Bay Wind Farm Cable Corridor Monitoring
#> 5 Atlantic Stingray Habitat Use and Migration
#> 6 TNC / NEFSC CVOW tagging and array
#> ocean website datacenter_infourl
#> 1 NW ATLANTIC <NA> https://matos.asascience.com/
#> 2 NW ATLANTIC <NA> https://matos.asascience.com/
#> 3 NW ATLANTIC <NA> https://matos.asascience.com/
#> 4 NW ATLANTIC <NA> https://matos.asascience.com/
#> 5 NW ATLANTIC <NA> https://matos.asascience.com/
#> 6 NW ATLANTIC <NA> https://matos.asascience.com/
otn_search_code("tail")
#> node collectioncode country longitude latitude shortname
#> 1 ACT TAILWINDS USA -73.8185 38.0705 UMCES TailWinds
#> longname ocean
#> 1 TailWinds: Team for Assessing Impacts to Living resources from offshore WIND turbineS NW ATLANTIC
#> website datacenter_infourl
#> 1 https://tailwinds.umces.edu/ https://matos.asascience.com/
otn_search_contact("Mike O'Brien")
#> node collectioncode country longitude latitude shortname
#> 1 ACT CBBBMB USA -73.8150 38.0700 UMCES Chesapeake Backbone, Mid-Bay
#> 2 ACT TAILWINDS USA -73.8185 38.0705 UMCES TailWinds
#> 3 ACT MAMBON USA -73.8185 38.0705 Mid-Atlantic MBON
#> 4 ACT NAVYKENN USA -69.7800 43.7750 Navy Kennebec ME Telemetry Array
#> longname
#> 1 Building a Mainstem Chesapeake Bay Telemetry Array: Mid-Bay Segment
#> 2 TailWinds: Team for Assessing Impacts to Living resources from offshore WIND turbineS
#> 3 Mid-Atlantic MBON: Dynamic Biodiversity and Telemetry Data for a Changing Coast
#> 4 Naval Undersea Warfare Center (NUWC) Kennebec River and Offshore Acoustic Telemetry Monitoring
#> ocean website datacenter_infourl
#> 1 NW ATLANTIC <NA> https://matos.asascience.com/
#> 2 NW ATLANTIC https://tailwinds.umces.edu/ https://matos.asascience.com/
#> 3 NW ATLANTIC https://marinebon.org/us-mbon/mid-atlantic-mbon/ https://matos.asascience.com/
#> 4 NW ATLANTIC <NA> https://matos.asascience.com/You’ll likely need to log in to access other parts of the CMS. You can
set your username and password for your system using the
otn_set_credentials helper function.
otn_set_credentials()After that, you can just log in using otn_login. This package is meant
to interface with any node’s Plone instance. You can switch between them
using the server argument.
otn_login(server = 'devel')
#> ✔ Login successful!List your project’s files:
otn_project_files(project = 'nsbs', server = 'devel', batch_size = 5)
#> name description
#> 1 Copy of otn_tagging_metadata_2019.xls Manu tagging
#> 2 NSBS_otn_metadata_tagging_2019 Reel Deal.xls
#> 3 Tagging Metadata - Original
#> 4 Tagging Metadata - Quality Controlled
#> 5 Satellite Tagging Metadata - Original
#> url
#> 1 https://members.devel.oceantrack.org/data/repository/nsbs/data-and-metadata/2019/copy-of-otn_tagging_metadata_2019.xls
#> 2 https://members.devel.oceantrack.org/data/repository/nsbs/data-and-metadata/2019/nsbs_otn_metadata_tagging_2019-reel-deal.xls
#> 3 https://members.devel.oceantrack.org/data/repository/nsbs/data-and-metadata/2014/tagging-metadata-original
#> 4 https://members.devel.oceantrack.org/data/repository/nsbs/data-and-metadata/2014/tagging-metadata-qc
#> 5 https://members.devel.oceantrack.org/data/repository/nsbs/data-and-metadata/2014/satellite-tagging-metadata-original
#> created modified creator size type
#> 1 2020-01-27 16:31:22 2020-01-27 16:31:23 cbate 714.0 KB File
#> 2 2019-09-09 17:33:09 2019-09-16 18:13:28 ntress 794.5 KB File
#> 3 2016-11-07 20:16:10 2014-10-07 17:54:57 badavis 725.0 KB File
#> 4 2016-11-07 20:16:15 2014-10-09 14:18:29 badavis 721.5 KB File
#> 5 2016-11-07 20:16:20 2014-10-08 18:11:06 badavis 713.5 KB File
otn_extract_files(project = 'nsbs', server = 'devel', batch_size = 5)
#> name
#> 1 Matched to Animals 2018
#> 2 Matched to Animals 2019
#> 3 Matched to Animals 2015
#> 4 Matched to Animals 2013
#> 5 Matched to Animals 2014
#> description
#> 1 These detections have been mapped to animals tagged by your project and detected by any receiver projects, including your own. This file includes the initial release of the tagged animals.
#> 2 These detections have been mapped to animals tagged by your project and detected by any receiver projects, including your own. This file includes the initial release of the tagged animals.
#> 3 For Trackers: All detections of all tags released by the project no matter where they occurred. Detections classified as false but with a transmitter belonging to this project will be included in the future. All single detections are considered false. There may be detections of some of your tag ids which have not been matched. There can be many reasons for this. To check if any of your tags may have been missed please see the mystery tag list for your region or series. For Deployment Operators: Sets of sentinel tag detections, sets of detections mapped to animals without the animal details, sets of 'UNQUALIFIED' detections.
#> 4 These detections have been mapped to animals tagged by your project and detected by any receiver projects, including your own. This file includes the initial release of the tagged animals.
#> 5
#> url
#> 1 https://members.devel.oceantrack.org/data/repository/nsbs/detection-extracts/nsbs_matched_detections_2018.zip
#> 2 https://members.devel.oceantrack.org/data/repository/nsbs/detection-extracts/nsbs_matched_detections_2019.zip
#> 3 https://members.devel.oceantrack.org/data/repository/nsbs/detection-extracts/nsbs_matched_detections_2015.zip
#> 4 https://members.devel.oceantrack.org/data/repository/nsbs/detection-extracts/nsbs_matched_detections_2013.zip
#> 5 https://members.devel.oceantrack.org/data/repository/nsbs/detection-extracts/nsbs_matched_detections_2014.zip
#> created modified creator size type
#> 1 2018-10-10 18:57:31 2020-10-23 18:27:39 otnbot 42.5 KB File
#> 2 2019-11-04 18:57:48 2020-10-23 18:27:39 otnbot 34.0 KB File
#> 3 2016-11-07 20:17:57 2017-04-10 14:54:25 fwhoriskey 170.0 KB File
#> 4 2016-12-21 15:42:11 2020-10-23 18:27:38 otnbot 141.0 KB File
#> 5 2016-12-21 15:42:15 2016-12-13 17:56:30 fwhoriskey 353.5 KB FileOr, just grab the ones modified more recently using the since
argument:
otn_project_files(
project = 'nsbs',
since = "2020-01-01",
server = 'devel',
batch_size = 5
)
#> name description
#> title NSBS_project_metadata.txt
#> url
#> title https://members.devel.oceantrack.org/data/repository/nsbs/data-and-metadata/nsbs_project_metadata.txt
#> created modified creator size type
#> title 2020-06-04 19:00:12 2020-06-04 19:00:15 ntress 2.6 KB File
otn_extract_files(
project = 'nsbs',
since = "2020-01-01",
server = 'devel',
batch_size = 5
)
#> name
#> 1 Matched to Animals 2018
#> 2 Matched to Animals 2019
#> 3 Matched to Animals 2013
#> 4 Matched to Animals 2016
#> 5 Matched to Animals 2017
#> description
#> 1 These detections have been mapped to animals tagged by your project and detected by any receiver projects, including your own. This file includes the initial release of the tagged animals.
#> 2 These detections have been mapped to animals tagged by your project and detected by any receiver projects, including your own. This file includes the initial release of the tagged animals.
#> 3 These detections have been mapped to animals tagged by your project and detected by any receiver projects, including your own. This file includes the initial release of the tagged animals.
#> 4 These detections have been mapped to animals tagged by your project and detected by any receiver projects, including your own. This file includes the initial release of the tagged animals.
#> 5 These detections have been mapped to animals tagged by your project and detected by any receiver projects, including your own. This file includes the initial release of the tagged animals.
#> url
#> 1 https://members.devel.oceantrack.org/data/repository/nsbs/detection-extracts/nsbs_matched_detections_2018.zip
#> 2 https://members.devel.oceantrack.org/data/repository/nsbs/detection-extracts/nsbs_matched_detections_2019.zip
#> 3 https://members.devel.oceantrack.org/data/repository/nsbs/detection-extracts/nsbs_matched_detections_2013.zip
#> 4 https://members.devel.oceantrack.org/data/repository/nsbs/detection-extracts/nsbs_matched_detections_2016.zip
#> 5 https://members.devel.oceantrack.org/data/repository/nsbs/detection-extracts/nsbs_matched_detections_2017.zip
#> created modified creator size type
#> 1 2018-10-10 18:57:31 2020-10-23 18:27:39 otnbot 42.5 KB File
#> 2 2019-11-04 18:57:48 2020-10-23 18:27:39 otnbot 34.0 KB File
#> 3 2016-12-21 15:42:11 2020-10-23 18:27:38 otnbot 141.0 KB File
#> 4 2016-12-21 15:42:19 2020-08-18 17:38:32 otnbot 42.0 KB File
#> 5 2017-05-05 18:21:55 2020-10-23 18:27:39 otnbot 74.4 KB FileYou can download a file via its URL. This is a BIG work in progress and the API will likely change multiple times in the coming weeks.
otn_get_file(
"https://members.devel.oceantrack.org/data/repository/nsbs/detection-extracts/nsbs_matched_detections_2017.zip"
)