bold 1.2.0
MINOR IMPROVEMENTS
bold 1.1.0
MINOR IMPROVEMENTS
bold 1.0.0
MINOR IMPROVEMENTS
- change base url for all requests to https from http (#70)
- fixed a warning arising from use of
bold_seqspec() - we now set the encoding to “UTF-8” before parsing the string to XML (#71)
bold_seqspec() fix: capture “Fatal errors” returned by BOLD servers and pass that along to the user with advice (#66)- add “Marker” and “Large requests” documentation sections to both
bold_seq() and bold_seqspec(). the marker section details that the marker parameter doesn’t actually filter results that you get - but you can filter them yourself. the large requests section gives some caveats associated with large data requests and outlines how to sort it out (#61)
bold 0.9.0
MINOR IMPROVEMENTS
- improved test coverage (#58)
- allow curl options to be passed into
bold_identify_parents() (#64)
- fix instructions in README for package
sangerseqR - instructions depend on which version of R is being used (#65) thanks @KevCaz
BUG FIXES
- fixes in package for
_R_CHECK_LENGTH_1_LOGIC2_ (#57)
bold_identify() fix: ampersands needed to be escaped (#62) thanks @devonorourke
bold 0.8.6
MINOR IMPROVEMENTS
- tests that make HTTP requests now use package
vcr to cache responses, speeds up tests significantly, and no longer relies on an internet connection (#55) (#56)
bold_seq(): sometimes on large requests, the BOLD servers time out, and give back partial output but don’t indicate that there was an error. We catch this kind of error now, throw a message for the user, and the function gives back the partial output given by the server. Also added to the documentation for bold_seq() and in the README that if you run into this problem try to do many queries that will result in smaller set of results instead of one or fewer larger queries (#52) (#53)bold_seq(): remove return characters (\r and \n) from sequences (#54)
bold 0.8.0
MINOR IMPROVEMENTS
- link to taxize bookdown book in readme and vignette (#51)
bold_identify_parents() gains many new parameters (taxid, taxon, tax_rank, tax_division, parentid, parentname, taxonrep, specimenrecords) to filter parents based on any of a number of fields - should solve problem where multiple parents found for a single taxon, often in different kingdoms (#50)- add note in docs of
bold_identify() that the function uses lapply internally, so queries with lots of sequences can take a long time
BUG FIXES
- fix
bold_specimens(): use rawToChar() on raw bytes instead of parse() from crul (#47)
bold 0.5.0
NEW FEATURES
- 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)
BUG FIXES
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)
MINOR IMPROVEMENTS
- Namespace calls to base pkgs for
stats and utils - replaced is with inherits (#39)
bold 0.4.0
NEW FEATURES
- 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)
MINOR IMPROVEMENTS
- replace
xml2::xml_find_one with xml2::xml_find_first (#33)
- Fix description of
db options in bold_identify man file - COX1 and COX1_SPECIES were switched (#37) thanks for pointing that out @dougwyu
BUG FIXES
- Fix to
bold_tax_id for when some elements returned from the BOLD API were empty/NULL (#32) thanks @fmichonneau !!
bold 0.3.5
MINOR IMPROVEMENTS
- Added more tests to the test suite (#28)
BUG FIXES
- Fixed a bug in an internal data parser (#27)
bold 0.3.4
NEW FEATURES
MINOR IMPROVEMENTS
- Switched to
xml2 from 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
BUG FIXES
- 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)
bold 0.3.0
MINOR IMPROVEMENTS
- Explicitly import non-base R functions (#22)
- Better package level manual file
bold 0.2.6
MINOR IMPROVEMENTS
sangerseqR package now in Suggests for reading trace files, and is only used in bold_trace() function.- 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.
BUG FIXES
- 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.
bold 0.2.0
NEW FEATURES
- Package gains two new functions for working with the BOLD taxonomy APIs:
bold_tax_name() and bold_tax_id(), which search for taxonomic data from BOLD using either names or BOLD identifiers, respectively. (#11)
- Two new packages in Imports:
jsonlite and reshape.
MINOR IMPROVEMENTS
- 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., config=verbose(). (#13)- Added examples of doing curl debugging throughout man pages.
bold 0.1.2
MINOR IMPROVEMENTS
- Improved the vignette (#8)
- Added small function to print helpful message when user inputs no parameters or zero length parameter values.
BUG FIXES
- Fixed some broken tests with the new
httr (v0.4) (#9), and added a few more tests (#7)
bold 0.1.0
NEW FEATURES