Changelog
Source:NEWS.md
bold 1.3.0
CRAN release: 2023-05-02
NEW FEATURES
New function
bold_identify_taxonomy()
to add taxonomic information to the output ofbold_identify()
and replacebold_identify_parents()
. Instead of taking the taxon names from thebold_identify()
output, and usebold_tax_name()
to get the taxonomic ID to then pass it tobold_tax_id()
to get the parent names, we take the process ids from thebold_identify()
output and then pass them tobold_specimens()
. This has the advantages of being faster and, more importantly, making sure the correct taxonomy is returned. The function has less arguments since the filtering of the result isn’t necessary anymore. Since the result now has only one line per row of input, the output is always in ‘wide’ format (like when usingbold_identify_parents()
withwide=TRUE
). There is one new argumenttaxOnly
which isTRUE
by default and return only the taxonomic data. However, sincebold_specimens()
also returns other data (habitat, country, image_url, etc), setting this argument toFALSE
will also join that data to the input.New function
bold_tax_id2()
which will eventually replacebold_tax_id()
. The main changes are in the format of the output. For thedataTypes
‘basic’, ‘stats’, ‘images’ and ‘thirdparty’, the output doesn’t change. For thedataTypes
‘sequencinglabs’, ‘geo’ and ‘depository’, instead of having one (sometimes very) wide data.frame, the result is now in ‘long’ format, with the columns ‘input’, ‘taxid’, ‘sequencinglabs|country|depository’ and ‘count’. For thedataTypes
‘all’ or when selecting more than one dataTypes, the output is a list for each data types containing their respective data.frame. When setting includeTree toTRUE
, the parents’ data is rbinded to their respective data.frame. The function also check that all arguments are the correct type and that thedataTypes
chosen are valid.The now deprecated
bold_tax_id()
has the same argument checks asbold_tax_id2()
but will throw warnings instead of errors to not affect existing workflows. Also, if a chosendataTypes
is invalid, it gets removed to not make unnecessary requests.Similarly, the now deprecated
bold_identify_parents()
has new argument checks and will throw warnings to not affect existing workflows.-
For
bold_tax_id2()
andbold_tax_name()
, when querying multiple taxa, if one fails, the loop won’t break and will instead throw the API error as a warning. The output object will also have 2 new attributes “errors” and “params” that will let you see what errors occurred for with request and what parameters were use for the request. To make it easy to retrieve these attributes, 3 new functions have been created:-
bold_get_attr()
will return a list of the two attributes -
bold_get_errors()
will return a list of the errors -
bold_get_params()
will return a list of parameters used
-
bold_specimens()
andbold_seqspec()
have a new parametercleanData
which, when set toTRUE
, replaces empty strings (““) by NAs and strings containing only duplicated values by their unique value (ex :”COI-5P|COI-5P|COI-5P” becomes “COI-5P”).New function
bold_read_trace()
to replaceread_trace()
. Can read one or multiple trace files from aboldtrace
object or provided file path(s).New function
b_sepFasta()
to use after a call tobold_seqspec()
wheresepFasta
wasn’t set toTRUE
.
MINOR IMPROVEMENTS
- made tests for the new functions
- made tests for the
bold_trace()
function - added test to existing functions to improved test coverage
- added/completed argument checks for every functions
-
bold_specimens()
andbold_seqspec()
can now also return partial output likebold_seq()
- using
data.table
when possible, removeddplyr
andreshape
dependencies - using
stringi
instead ofstringr
which removedstringr
’s other dependencies - added more details to the documentation of some functions
BUG FIXES
- changed how http responses are read so they throw warnings and return NAs instead of errors. This prevents a long request to stop and fail, loosing the already fetched data. (#74)
- added a note in the documentation of
bold_seq()
,bold_seqspec()
andbold_specimen()
that if thetaxon
doesn’t have public records, if using another parameter will return all data for that parameter. Users can verify the availability of public records withbold_stats()
. A note was also added inbold_tax_name()
that the column ‘specimenrecords’ relate to the records in the taxonomy browser and not in the public data portal. (#76) - fixed output of bold_seq() (#79)
- changed the function used to encode to UTF-8 (#81, #86)
- contacted bold so they would fix their typo in ‘depository’ which prevented fetching related data with
bold_tax_id()
(#83). Added a line in the function to change ‘depositories’ to ‘depository’ in case people had been using that. - added a check for ‘name’ in
bold_tax_name()
to double escape single quotes. Otherwise it doesn’t return the data (#84, #85). Since it’s related to the API, this means that the data that comes back also contains errors. So I added a function to repair the names of ‘taxon’, ‘taxonrep’ and ‘parentname’ in the returned object. The function is also used inpipe_params()
(which is used bybold_seq()
,bold_seqspec()
andbold_specimen()
) to repair thetaxon
parameter in case users use results from previous versions. - changed the way the response of
bold_seqspec()
is read (#87, #88) thanks @cjfields - added a note in
bold_stats()
documentation to specify that the record counts include all gene markers (#90).
bold 1.0.0
CRAN release: 2020-05-01
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()
andbold_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
CRAN release: 2019-06-27
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
CRAN release: 2018-12-14
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 forbold_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
CRAN release: 2018-10-26
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 useslapply
internally, so queries with lots of sequences can take a long time
BUG FIXES
- fix
bold_specimens()
: userawToChar()
on raw bytes instead ofparse()
fromcrul
(#47)
bold 0.5.0
CRAN release: 2017-07-21
BUG FIXES
-
marker
parameter inbold_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 inbold_specimens
and other fxns (#46) - fixed by switching to new BOLD v4 API (#30)
MINOR IMPROVEMENTS
- Namespace calls to base pkgs for
stats
andutils
- replacedis
withinherits
(#39)
bold 0.4.0
CRAN release: 2017-01-06
NEW FEATURES
- New function
bold_identify_parents()
to add taxonomic information to the output ofbold_identify()
. We take the taxon names frombold_identify
output, and usebold_tax_name
to get the taxonomic ID, passing it tobold_tax_id
to get the parent names, then attaches those to the input data. There are two options given what you put for thewide
parameter. IfTRUE
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 ifFALSE
you get a long data.frame. thanks @dougwyu for inspiring this (#36)
MINOR IMPROVEMENTS
- replace
xml2::xml_find_one
withxml2::xml_find_first
(#33) - Fix description of
db
options inbold_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
CRAN release: 2016-03-29
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
CRAN release: 2016-03-23
MINOR IMPROVEMENTS
- Switched to
xml2
fromXML
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 usingrawToChar(content(x))
, which works (#24)
bold 0.3.0
CRAN release: 2015-09-16
MINOR IMPROVEMENTS
- Explicitly import non-base R functions (#22)
- Better package level manual file
bold 0.2.6
CRAN release: 2015-04-18
MINOR IMPROVEMENTS
-
sangerseqR
package now in Suggests for reading trace files, and is only used inbold_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) andbold_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 inbold_search()
that use these two functions.
bold 0.2.0
CRAN release: 2014-08-20
NEW FEATURES
- Package gains two new functions for working with the BOLD taxonomy APIs:
bold_tax_name()
andbold_tax_id()
, which search for taxonomic data from BOLD using either names or BOLD identifiers, respectively. (#11) - Two new packages in Imports:
jsonlite
andreshape
.
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 tohttr::GET
is done via named parameters, e.g.,config=verbose()
. (#13) - Added examples of doing curl debugging throughout man pages.
bold 0.1.2
CRAN release: 2014-07-24
MINOR IMPROVEMENTS
- Improved the vignette (#8)
- Added small function to print helpful message when user inputs no parameters or zero length parameter values.