NEWS.md

In traits: Species Trait Data from Around the Web

traits 0.5.0

DEFUNCT

• tr_usda() is defunct. The API is down for good (#122)
• all coral_* functions are defunct (#124)

MINOR IMPROVEMENTS

• replace httr with crul (#89)
• fix BETYdb tess (#123)

BUG FIXES

• ncbi_searcher() fix: we weren't including the NCBI Entrez API key even when it was found (#120)

traits 0.4.2

MINOR IMPROVEMENTS

• betydb gains alias for API versions (#114)

BUG FIXES

• taxa_search: removed traitbank option because traits::traitbank() used internally has completely changed and it's no longer feasible to do a straight-forward taxon search for all traits in EOL's Traitbank (#115)

traits 0.4.0

NEW FEATURES

• New package author: Chris Black (@infotroph) (#106)
• betydb functions now can do pagination (#94)
• betydb functions gain progress parameter to optionally suppress the progress bar (#113)
• EOL Traitbank completely changed their query interface - function no longer works as it did before. for now, you have to specify your own query that's rather complex, see docs for help. Later on we can try to simplify queries for users (#112)

MINOR IMPROVEMENTS

• table in README for different sources and clarify what traits are (#110) (#111)
• fixed link to Birdlife (#108)

BUG FIXES

• fix to ncbi_searcher() to prevent failures in some cases (#107) thanks @zachary-foster
• fix to ncbi_byid(): ten new fields added to the output (#101) (#102) thanks @boopsboops

traits 0.3.0

DEFUNCT

• Four functions are now defunct - those involving getting data on whether a species if native/invasive in a particular region. See ?traits-defunct for more information. Deprecated functions: eol_invasive_(), fe_native(), g_invasive(), is_native() (#72)

NEW FEATURES

• Gains new function tr_ernest for a dataset of Amniote life history data (#60)
• Gains new function tr_usda for the USDA plants database (#61)
• Gains new function tr_zanne for a dataset of plant growth data (#73)
• BetyDB functions gain automatic paging of large requests where API supports it, i.e. not in v0 (#94)

MINOR IMPROVEMENTS

• Change Coral database base URL to https (#99)
• Now requiring readr > 1.0 (#76)
• Changed ncbi_*() functions to give back NA types that match data.frame column classes to make combining easier (#96)
• replace xml2::xml_find_one with xml2::xml_find_first throughout (#97)
• namespace all fxn calls for base pkgs, remove from Imports (#98)
• BetyDB cleanup (#25) (#77) (#82) (#88)

BUG FIXES

• Fixed birdlife* functions that needed to change URL structure due to changes in the Birdlife website (#100)
• Fixes to traitbank() (#79) (#80) thanks @dschlaep !
• ncbi_*() fxns now use https (#95)

traits 0.2.0

DEPRECATED

• Marked four functions as deprecated - those involving getting data on whether a species if native/invasive in a particular region. See ?traits-deprecated for more information. Deprecated functions: eol_invasive_(), fe_native(), g_invasive(), is_native() (#63)

MINOR IMPROVEMENTS

• Standardized outputs of all data - all data.frame column names should be lowercase now (#47)
• With all httr::content() calls now explicitly setting encoding to UTF-8, and parsing to text, then manually parsing either JSON or XML later (#65)
• Replaced XML with xml2 for XML parsing (#67)

traits 0.1.2

NEW FEATURES

• ncbi_searcher() gains new parameter fuzzy to toggle fuzzy taxonomic ID search or exact search. (#34) (thx @mpnelsen)

MINOR IMPROVEMENTS

• Importing only functions (via importFrom) used across all imports now. In addition, importFrom for all non-base R pkgs, including methods, stats and utils packages (#36)
• Changed the trait parameter in traitbank() function to pageid, because EOL expects a page identifier, which is associated with a taxon, not a trait. The previous parameter name was very misleading.

traits 0.1.0

NEW FEATURES

• released to CRAN

traits documentation built on Aug. 27, 2020, 9:07 a.m.