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Changelog

Source: NEWS.md

etn (development version)

  • Add European Union as funder (for STRAITS) (#497).
  • 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).
  • New get_acoustic_deployment_logs() gets acoustic deployment log data, which can be helpful to figure out what happened with a receiver during deployment (#254).
  • New example_dataset() reads an example dataset ("2014_DEMER") as a Data Package (#530).
  • New 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:
    • The function writes the output file as 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.
    • The animal sex, life stage and weight are added to an Extended Measurement Or Facts extension file (emof.csv), for better support with OBIS (#555).
  • The function reference has been reorganized (#549)
  • New get_bibliography() creates a bibliography from a table of detections, with references for ETN, the etn R package, and animal and acoustic projects associated with the detections (#587).
  • get_package() now includes a bibliography resource built with get_bibliography(), replacing the previous references resource (#587).
  • Error messages now provide suggestions when providing an incorrect value to parameters such as animal_project_code or scientific_name (#587).
  • etn now relies on R >= 4.2.0 (because of the arrow dependency) (#611).

etn 3.0.0

Use etn on your computer 🎉

  • etn now connects to the ETN database with an API provided by the etnservice package (#280). This means you can use the package from your own computer. Note that this will be slower than running it from the ETN RStudio server.
  • etn will automatically switch to a local database connection when available (e.g. the ETN RStudio server). Use Sys.setenv(ETN_PROTOCOL = "opencpu") to override this behaviour and force the package to use the API (#398).
  • Queries via the API and the ETN RStudio Server will return the same results (#317).
  • When using a local database connection, etn will check if the installed helper package etnservice that is used to place these queries is up to date with the one deployed via the API. This is to ensure that queries placed via the API and via the local database connection always result in consistent results. If the installed version of etnservice is older, you will be prompted to install a newer version (#385).

Credentials

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.

Here is how you can migrate:

  1. 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.

  2. Follow the steps in vignette("authentication") to look up and store your credentials.

  3. 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)

Accessing data

Changes for developers

  • New vignette vignette("options") describes some developer options (#398).
  • Contributors can change the default domain of the API to the URL of a test server via the environmental variable ETN_TEST_API (#383).
  • Tests make use of vcr to record and replay HTTP requests to the API. These results are stored in /tests/fixtures (#432).
  • Tests have new helper functions, including 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).
  • Tests for download_acoustic_datasets() are updated for archival tags and SQL vs API calls and makes use of markdown snapshots (#366).
  • pkgdown website is now automatically build by a GitHub Action and is served from the 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).

Miscellaneous

  • etn now relies on R >= 4.1.0 (because of 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).
  • Previously deprecated functions 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).

etn 2.2.2

Bug fixes

Miscellaneous

  • Tests depending on local database connection are now skipped when it is absent on testing machine (#346).
  • Funder is updated and custom authors are removed (#311).
  • The README now has a Zenodo badge (#352, #355).
  • New CITATION.cff file (#337).
  • pkgdown website has been updated (#354).

etn 2.2.1

etn 2.2.0

etn 2.1.0

  • Funder and default README.Rmd are added (#247).
  • New function write_dwc() transforms acoustic telemetry data to Darwin Core that can be harvested by OBIS and GBIF (#257).

etn 2.0.0

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.
  • Old function names are deprecated.
  • New vignette("acoustic-telemetry") showcases an acoustic use case.
  • Test coverage is increased.