Changes combined since v0.1.0

taxize 0.1.5

NEW FEATURES

classification() gains extension method classification.ids() to accept output from get_ids() - which attempts to get a taxonomic hierarchy from each of the taxon identifiers with the output from get_ids().
synonyms() gains extension method synonyms.ids() to accept output from get_ids() - which attempts to get synonyms from each of the taxon identifiers with the output from get_ids().

taxize 0.1.4

NEW FEATURES

Reworked functions that interact with the ITIS API so that lower level functions were grouped together into higher level functions. All the approximately 50 lower level functions are still exported but are not included in the index help file (due to @Keywords internal for each fxn) - but can still be used normally, and man files are avaialable at ?functionName.
New function itis_ping() to check if the ITIS API service is up, similar to eol_ping() for the EOL API.
New function itis_getrecord() to get a partial or full record, using a TSN or lsid.
New function itis_refs() to get references associated with a TSN.
New function itis_kingdomnames() to get all kingdom names, or kingdom name for a TSN.
New function itis_lsid() to get a TSN from an lsid, get a partial or full record from an lsid.
New function itis_native() to get status as native, exotic, etc. in various geographic regions.
New function itis_hierarchy() to get full hierarchy, or immediate up or downstream hierarchy.
New function itis_terms() to get tsn's, authors, common names, and scientific names from a given query.
New function sci2comm() to get common (vernacular) names from input scientific names from various data sources.
New function comm2sci() to get scientific names from input common (vernacular) names from various data sources.
New function get_ids() to get taxonomic identifiers across all sources.

MINOR IMPROVEMENTS

itis_taxrank() now outputs a character, not a factor; loses parameter verbose, and gains ..., which passes on further arguments to gettaxonomicranknamefromtsn.
tp_synonyms(), tp_summary(), plantminer(), itis_downstream(), gisd_isinvasive(), get_genes_avail(), get_genes(), eol_invasive(), eol_dataobjects(), andn tnrs() gain parameter verbose to optionally suppress messages.
phylomatic_tree() format changed so that names are passed in normall (e.g., Poa annua) instead of the slashpath format (family/genus/genus_species). Also, taxaformat parameter dropped.
itis_acceptname() gains ... to pass in further arguments to getacceptednamesfromtsn()
tp_namedistributions() loses parameter format.
get_tsn() and get_uid() return infomation about match as attribute.
clarified iucn-documentation

BUG FIXES

Fixed bug in synonyms() so that further arguments can be passed on to get_tsn() to suppress messages.
Removed test for ubio_classification_search(), a function that isn't operational yet.

NEW FEATURES

New functions added just like get_uid()/get_tsn() but for EOL, Catalogue of Life, and Tropicos, see get_eolid(), get_colid(), and get_tpsid(), respectively.
classification() methods added for EOL, Catalogue of Life, and Tropicos, see functions classification.eolid(), classification.colid(), and classification.tpsid() respectively.
New function col_search() to search for names in the Catalogue of Life.
User can turn off interactive mode in get_* functions. All get_* functions gain an ask argument, if TRUE (default) a user prompt is used for user to select which row they want, if FALSE, NA is returned when many results available; and added tests for the new argument. Affects downstream functions too.
New function eol_invasive() to search EOL collections of invasive species lists.
New function tp_search() to search for a taxonomic IDs from Tropicos.
New function tp_classification() to get a taxonomic hierarchy from Tropicos.
New function gbif_parse() to parse scientific names into their components, using the GBIF name parser API.
New function itis_searchcommon() to search for common names across both searchbycommonnamebeginswith, and searchbycommonnameendswith.

BUG FIXES

tax_name() and other function broke, because get_tsn() and get_uid() returned wrong value when a taxon was not found. Fixed.

MINOR IMPROVEMENTS

NOTES

Moved tests from inst/tests to tests/testthat according to new preferred location of tests.
Updated CITATION in inst/ with our F1000Research paper info.
Package repo name on Github changed from taxize_ to taxize - remember to use "taxize" in install_github() calls now instead of "taxize_"

NEW FEATURES

New function tpl_families() to get data.frame of families from The Plantlist.org site.
New function names_list() to get a random vector of species names using the
Added two new data sets, plantGenusNames.RData and plantNames.RData, to be used in names_list().
New function ldfast(), a replacement function for plyr::ldply that should be faster in all cases.
Changed API key names to be more consistent, now tropicosApiKey, eolApiKey, ubioApiKey, and pmApiKey - do change these in your .Rprofile if you store them there.
Added a startup message.

MINOR IMPROVEMENTS

Across most functions, removed dependencies on plyr, using ldfast() instead, for increased speed.
Across most functions, changed from using RCurl to using httr.
Across most functions, stop_for_status() now used directly after Curl call to check the http status code, stoping the function if appropriate code found.
Many functions changed parameter ... to callopts, which passes on additional Curl options, with default an empty list (list()), which makes function testing easier.
eol_search() gains parameters page, exact, filter_tid, filter_heid, filter_by_string, matching, cache_ttl, and callopts.
eol_hierarchy() gains parameter callopts, and loses parameter usekey (always using API key now).
eol_pages() gains parameters images, videos, sounds, maps, text, subject, licenses, details, common_names, synonyms, references, vetted, cache_ttl, and callopts.
gni_search(): parameter url lost, is defined inside the function now, and .Rd file gains url references.
phylomatic_tree() now checks to make sure family names were found for input taxa. If not, the function stops with message informing this.
tpl_get() updated with fixes/improvements by John Baumgartner - now gets taxa from all groups, whereas only retrieved from Angiosperms before. In addition, csv files from The Plantlist.org are downloaded directly rather than read into R and written out again.
tpl_search() now checks for missing data or errors, and stops function with error message.

BUG FIXES

capwords() fxn changed to taxize_capwords() to avoid namespace conflicts with other packages with a similar function.
ubio_namebank() was giving back base64 encoded data, now decoded appropriately.

NOTES