get_acoustic_projects(), get_animal_projects() and get_cpod_projects() now have an optional argument citation, which adds the columns citation, doi, contact_name, contact_email and contact_affiliation to the data frame. This makes it easier to cite projects or contact the responsible. The citation information is obtained via MarineInfo (#518).example_dataset() reads an example dataset ("2014_DEMER") as a Data Package (#530).get_package() gets all data related to an animal project as a Data Package. Use this in combination with write_package() to download a dataset (#544).read_package(), write_package() and read_resource() are reexported from {frictionless} to read, write and access data from Data Packages (#525, #570).download_acoustic_dataset() is deprecated. Please use get_package() and then write_package() instead (#559).write_dwc() now uses a Data Package as input, rather than reading from the ETN database. This means the function can be used locally (#528). In addition:
occurrence.csv (previously dwc_occurrence.csv) and adds a meta.xml file.dwc:institutionCode is always set to "VLIZ" as maintainer of ETN. The institution_code parameter has been removed.dc:license is set to "CC-BY-4.0" or "CC0-1.0" rather than a URL. The input for the license parameter has been updated accordingly.dwc:identificationVerificationStatus has been added and is set to "verified by expert" for all records, since the taxon is assumed to be well-known before the tag was attached.emof.csv), for better support with OBIS (#555).Sys.setenv(ETN_PROTOCOL = "opencpu") to override this behaviour and force the package to use the API (#398).::: {.callout-important} Breaking change! Action required :::
Your credentials (username and password) to connect to the ETN database are no longer passed via the connection argument. They are asked or retrieved from your .Renviron file every time you run a function.
vignette("authentication").connection argument is deprecated in all functions (#301).connect_to_etn() is deprecated (#303).Here is how you can migrate:
Use the new ETN RStudio server (https://rstudio.europeantrackingnetwork.org). The LifeWatch RStudio server (https://rstudio.lifewatch.be) won't work with this version of etn and will be discontinued.
Follow the steps in vignette("authentication") to look up and store your credentials.
Update your scripts:
# Good
get_animals(animal_id = 305)
# Bad
connect_to_etn()
get_animals(con, animal_id = 305)
get_animals(connection = con, animal_id = 305)
get_acoustic_detections() now uses a different protocol to retrieve data. It can now reliably return 10M+ detections without timeouts (#384, #382, #323).get_acoustic_detections() now returns a progress bar for large queries (#384).get_acoustic_detections() now has a deployment_id filter argument (#382, #340).get_acoustic_detections() now has a tag_serial_number argument, which is more reliable than acoustic_tag_id (which is still supported). Thanks @lottepohl for the suggestion (#408, #386).get_acoustic_detections() may return fewer (erroneous) detections than before, due to fixes in the database.get_animals() now includes type_type = "archival" data (#365).vignette("options") describes some developer options (#398).ETN_TEST_API (#383).{vcr} to record and replay HTTP requests to the API. These results are stored in /tests/fixtures (#432).skip_if_not_localdb(), skip_if_http_error() and expect_protocol_agnostic(). The latter is used to compare SQL vs API calls in test-protocol_agnostic.R (#436).download_acoustic_datasets() are updated for archival tags and SQL vs API calls and makes use of markdown snapshots (#366).gh-pages branch. The docs/ directory has been removed (#456).vignette("acoustic-telemetry") is precompiled with vignettes/precompile.R, so it doesn't run for every build (#473).{arrow} and {vcr} dependencies) and uses base pipes (|> rather than %>%) (#327, #384).write_dwc() now invisibly returns the transformed data as a list of data frames (rather than a data frame) (#302).get_deployments(), get_detections(), get_projects(), get_receivers(), list_network_project_codes() are now removed.vignette("etn_fields") was outdated and has been removed (#468).check_value() now correctly formats NA values returned by list_ functions (#356, #357).list_receiver_ids() no longer return duplicate values (#357).write_dwc() now handles empty rights_holder (#356).CITATION.cff file (#337).write_dwc() now supports uppercase animal_project_codes (#289).write_dwc() no longer breaks on updated dependency (#293).NEWS.md file is added to communicate changes to the package.depth_in_meters field is added to get_acoustic_detections() (#261).download_acoustic_dataset() no longer breaks on missing fields in datapackage.json.write_dwc() transforms acoustic telemetry data to Darwin Core that can be harvested by OBIS and GBIF (#257).This releases updates the package to make use of the new model and scope of ETN. Have a look at this milestone for all issues that are included.
tag_serial_number is now the primary identifier for tags. Tags can have multiple types, subtypes and sensors. Acoustic information is related to the acoustic_tag_id.acoustic scope remains completely covered, but is now reflected in function names. This allows us to implement additional scopes (e.g. cpod) in the future.vignette("acoustic-telemetry") showcases an acoustic use case.