- Now using BOLD’s v4 API throughout the package. This was essentially just a change of the BASE URL for each request (#30)
- Now using
crul for HTTP requests. Only really affects users in that specifying curl options works slightly differenlty (#42)
marker parameter in
bold_seqspec was and maybe still is not working, in the sense that using the parameter doesn’t always limit results to the marker you specify. Not really fixed - watch out for it, and filter after you get results back to get markers you want. (#25)
- Fixed bug in
bold_identify_parents - was failing when no match for a parent name. (#41) thx @VascoElbrecht
tsv results were erroring in
bold_specimens and other fxns (#46) - fixed by switching to new BOLD v4 API (#30)
- Namespace calls to base pkgs for
utils - replaced
- New function
bold_identify_parents() to add taxonomic information to the output of
bold_identif(). We take the taxon names from
bold_identify output, and use
bold_tax_name to get the taxonomic ID, passing it to
bold_tax_id to get the parent names, then attaches those to the input data. There are two options given what you put for the
wide parameter. If
TRUE you get data.frames of the same dimensions with parent rank name and ID as new columns (for each name going up the hierarchy) - while if
FALSE you get a long data.frame. thanks @dougwyu for inspiring this (#36)
- Fix description of
db options in
bold_identify man file - COX1 and COX1_SPECIES were switched (#37) thanks for pointing that out @dougwyu
- Fix to
bold_tax_id for when some elements returned from the BOLD API were empty/
NULL (#32) thanks @fmichonneau !!
- Added more tests to the test suite (#28)
- Fixed a bug in an internal data parser (#27)
- Switched to
XML as the XML parser for this package (#26)
- Fixes to
bold_trace() to create dir and tar file when it doesn’t already exist
- Fixed odd problem where sometimes resulting data from HTTP request was garbled on
content(x, "text"), so now using
rawToChar(content(x)), which works (#24)
- Explicitly import non-base R functions (#22)
- Better package level manual file
sangerseqR package now in Suggests for reading trace files, and is only used in
- General code tidying, reduction of code duplication.
bold_trace() gains two new parameters:
overwrite to choose whether to overwrite an existing file of the same name or not,
progress to show a progress bar for downloading or not.
bold_trace() gains a print method to show a tidy summary of the trace file downloaded.
- Fixed similar bugs in
bold_tax_name() (#17) and
bold_tax_id() (#18) in which species that were missing from the BOLD database returned empty arrays but 200 status codes. Parsing those as failed attempts now. Also fixes problem in taxize in
bold_search() that use these two functions.
- Package gains two new functions for working with the BOLD taxonomy APIs:
bold_tax_id(), which search for taxonomic data from BOLD using either names or BOLD identifiers, respectively. (#11)
- Two new packages in Imports:
- Added new taxonomy API functions to the vignette (#14)
- Added reference URLS to all function doc files to allow easy reference for the appropriate API docs.
callopts parameter changed to
... throughout the package, so that passing on options to
httr::GET is done via named parameters, e.g.,
- Added examples of doing curl debugging throughout man pages.
- Improved the vignette (#8)
- Added small function to print helpful message when user inputs no parameters or zero length parameter values.
- Fixed some broken tests with the new
httr (v0.4) (#9), and added a few more tests (#7)