NEWS
rfishbase 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.
rfishbase 4.1.1 (2023-02-20)
- hotfix for bug in 4.1.0 on Windows --
duckdb
httpfs
on windows created segfault
rfishbase 4.1.0 (2023-02-12)
- 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.
rfishbase 4.0.0 (2021-12-14)
- 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
rfishbase 3.1.9 (2021-08-09)
- avoid GitHub API calls to determine versions.
rfishbase 3.1.8 (2021-06-07)
use collect()
on taxa_tbl()
rfishbase 3.1.7 (2021-04-08)
- Avoid needless warning about
arrange()
rfishbase 3.1.6 (2021-02-10)
- 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.
rfishbase 3.1.5 (2021-01-18)
- replace rappdirs with base R tools
rfishbase 3.1.4 (2021-01-13)
- Uses
arkdb
with duckdb
as database backend
- resolve compatibility issues
rfishbase 3.0.5
validate_names()
has been rewritten [#170]
rfishbase 3.0.4 (2019-06-27)
- use latest version by default [#164]
rfishbase 3.0.3 (2019-03-12)
- fix bug in sealifebase name resolution [#154]
rfishbase 3.0.2
- fix missing function endpoint for
diet_items()
[#158]
rfishbase 3.0.1 (2019-03-02)
- patch for upcoming R release with staged installs
- patch common_names to allow omitting species_list for full table (#156)
rfishbase 3.0.0 (2018-11-09)
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.
rfishbase 2.2.0
(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)
rfishbase 2.1.2 (2017-04-19)
- bugfix avoid spurious warning when using http instead of https API
- bugfix to for taxa table as used on sealifebase
rfishbase 2.1.1 (2016-07-22)
- 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)
rfishbase 2.1.0 (2015-11-10)
- improve sealifebase operations
- Updates for optimized version of fishbaseapi
- More stable tests
rfishbase 2.0.3 (2015-09-09)
- 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.)
rfishbase 2.0.2 (2015-09-02)
- bugfix for package unit tests on some platforms
rfishbase 2.0.1 (2015-08-15)
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.