Skip to content

Commit

Permalink
update news and cran comments
Browse files Browse the repository at this point in the history
  • Loading branch information
sckott committed Aug 13, 2020
1 parent f157085 commit a98fd4b
Show file tree
Hide file tree
Showing 2 changed files with 19 additions and 5 deletions.
22 changes: 18 additions & 4 deletions NEWS.md
Original file line number Diff line number Diff line change
Expand Up @@ -3,10 +3,24 @@ taxizedb 0.2.0

## NEW FEATURES

* support for the NCBI taxonomy database added
* gains ports of `taxize` functions to `taxizedb` (NCBI & ITIS supported): `children`, `classification`, `downstream`. beware when both `taxize` and `taxizedb` loaded in the same R session to namespace calls to these three functions.
* gains mapping functions: `name2taxid` (scientific or common name to taxonomy ID); `taxid2name` (taxonomy ID to scientific name); `taxid2rank` (taxonomy ID to rank)
*
* gains 3 new data sources: NCBI taxonomy, World Flora Online, Wikidata (#18) (#49) (#37)
* gains ports of `taxize` functions to `taxizedb` (NCBI & ITIS supported): `children`, `classification`, `downstream`. beware when both `taxize` and `taxizedb` loaded in the same R session to namespace calls to these three functions (#19) (#25) (#44) (#48)
* gains mapping functions: `name2taxid` (scientific or common name to taxonomy ID); `taxid2name` (taxonomy ID to scientific name); `taxid2rank` (taxonomy ID to rank) (#41) (#42)
* intro vignette added (#17)
* GBIF and COL data sources are not updated daily in the repos https://github.com/ropenscilabs/gbif-backbone-sql and https://github.com/ropenscilabs/col-sql/ via GithHub Actions. See those repos for details (#26)
* update package level manual file (`?taxizedb-package`) with details on each data source, their update schedules, and examples
* all data sources now use SQLite as the database storage engine. passwords/ports/usernames/etc are no longer needed! note that some `db_download*` functions download already created SQLite databases, whereas for other data sources the database is built locally on your machine from other data formats downloaded (see also #36, #46)
* a copy of the taxonomic ranks information from taxize package was ported over for internal use to be able to make `downstream()` work for most data sources

## MINOR IMPROVEMENTS

* remove check for whether SQLite is installed (#5 #29)
* all `src_*` functions now only have two paramters: `path` and `...`. where path by default figures out the path for you using the function `db_path()`, and `...` allows the user to pass on parameters to `DBI::dbConnect`

## DEFUNCT

* `db_load()` is now defunct. Now just use `db_download*` then `src*` for your data source (see also #43)


taxizedb 0.1.4
==============
Expand Down
2 changes: 1 addition & 1 deletion cran-comments.md
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ There are no reverse dependencies.

---

This version xxxx.
This version fixes many bugs and adds additional data sources.

Thanks!
Scott Chamberlain

0 comments on commit a98fd4b

Please sign in to comment.