NEWS.md

In rfishbase: R Interface to 'FishBase'

NEWS

For more fine-grained list of changes or to report a bug, consult

• The issues log
• The commit log

Versioning

Releases will be numbered with the following semantic versioning format:

..

And constructed with the following guidelines:

• Breaking backward compatibility bumps the major (and resets the minor and patch)
• New additions without breaking backward compatibility bumps the minor (and resets the patch)
• Bug fixes and misc changes bumps the patch

For more information on SemVer, please visit http://semver.org/.

v 5.0.0

Another streamlined re-design following new abilities for data hosting and access. This release relies on a HuggingFace datasets hosting for data and metadata hosting in parquet and schema.org.

Data access is simplified to use the simple HuggingFace datasets API instead of the previous contentid-based resolution. This allows metadata to be defined with directly alongside the data platform independent of the R package.

A simplified access protocol relies on duckdbfs for direct reads of tables. Several functions previously used only to manage connections are now deprecated or removed, along with a significant number of dependencies.

Core use still centers around the same package API using the fb_tbl() function, with legacy helper functions for common tables like species() are still accessible and can still optionally filter by species name where appropriate. As before, loading the full tables and sub-setting manually is still recommended.

Historic helper functions like load_taxa() (combining the taxonomic classification from Species, Genus, Family and Order tables), validate_names(), and common_to_sci() and sci_to_common() should be in working order, all using table-based outputs.

v 4.1.1

• hotfix for bug in 4.1.0 on Windows -- duckdb httpfs on windows created segfault

v 4.1.0

• New data release, v23.01 (fishbase & sealifebase)
• direct URL-based import supported, contentid now a fallback method.
• set option "rfishbase_local_db" = TRUE to create a local copy, otherwise will use a remote copy. Local copy will get better performance after initial import, but may experience conflicts when duckdb is upgraded or when multiple sessions attempt to access the directory. Remove the default storage directory (given by db_dir()) after upgrading duckdb if using a local copy.

Note that with hash-archive.org resolver is down, and software-heritage API has strict rate limits, so direct URL access is preferable.

v 4.0.0

• Major upgrade that introduces content-identifier based downloads and parquet-backed database interface. Provides improved access to all tables and improved performance.
• See README or details

v 3.1.9

• avoid GitHub API calls to determine versions.

v 3.1.8

use collect() on taxa_tbl()

v 3.1.7

• Avoid needless warning about arrange()

v 3.1.6

• ensure any test needing internet connection is "fails gracefully" with no warnings or errors whenever tests are run without internet or the CRAN test environment where internet connectivity may be unreliable.

v 3.1.5

• replace rappdirs with base R tools

v 3.1.4

• Uses arkdb with duckdb as database backend
• resolve compatibility issues

v 3.0.5

• validate_names() has been rewritten [#170]

v 3.0.4

• use latest version by default [#164]

v 3.0.3

• fix bug in sealifebase name resolution [#154]

v 3.0.2

• fix missing function endpoint for diet_items() [#158]

v 3.0.1

• patch for upcoming R release with staged installs
• patch common_names to allow omitting species_list for full table (#156)

v 3.0.0

v 3.0.0 accesses a new static API for fishbase with in-memory memoization that significantly improves performance, particularly for large queries.

• Functions no longer have default limits on returns, so pagination is never involved -- all functions now return full set of available results.
• Almost all functions can be called without arguments (e.g. without a species list) to return the complete record of the requested table.
• Various minor issues in some functions have been resolved, see https://github.com/ropensci/rfishbase/issues/ for details.

v2.2.0

(not released to CRAN, rolled into 3.0 release)

• bugfix for validate_names() (#121)
• bugfix for faoareas() (#123)
• add genetics() endpoint (#122)
• add taxonomy() endpoint (#126)

v2.1.2 (2017-04-19)

• bugfix avoid spurious warning when using http instead of https API
• bugfix to for taxa table as used on sealifebase

v2.1.1

• bugfix for endpoints with inconsistent spelling of SpecCode column (e.g. maturity, diet, ecosystem, morphology, morphometrics, popchar, poplf).
• Now properly queries by input species list
• Minor bug fixes for issues #77 #82 #83 #89 #93 #94 #95 #97 #99 #100 (see https://github.com/ropensci/rfishbase/issues)

v2.1.0

• improve sealifebase operations
• Updates for optimized version of fishbaseapi
• More stable tests

v2.0.3

• Use dontrun instead of \donttest in the documentation. Apparently CRAN has decided to run donttest blocks in the examples, which can fail on their test servers when transferring data files over a network connection (which is why they were marked donttest in the first place.)

v2.0.2

• bugfix for package unit tests on some platforms

v2.0.1

First official release of the new rfishbase package, a non-backwards compatible replacement to all earlier versions of FishBase. See the package vignette for a more detailed overview and introduction.

rfishbase documentation built on Sept. 11, 2024, 8:12 p.m.