Fixing minor CRAN check issues.
Fixing minor CRAN check issues.
'' instead of NA
for missing values at the suggestion of Davis Vaughan (issue #212).vctrs update.Minor update
taxonomy printing errordefault.stringsAsFactors since it is
depreciated.LARGE CHANGES:
The beginning of a complete rewrite of the taxa package
to make the more basic component classes more like base R vectors. The
taxmap class is not yet reimplemented, but will be similar
to the class in the previous versions of taxa. The old version of
taxa has been incorporated into the metacoder
package until this version of taxa is mature, at which time
metacoder will also use this version.
n_obs that would cause an error when used
on an object with tables with columns named by numbers.taxmap are now
supportedtaxonomy_table option add_id_col now works
(issue
#191).parse_tax_data option class_col now
accepts negative column indexes, meaning “all other columns”.taxonomy_table function that converts the
information in a taxmap or taxonomy object
into a table with taxa as rows and ranks as columns.print_tree function that prints text-based
trees of taxmap or taxonomy objects (issue #173).get_dataset function to get a single data set
from taxmap objects. Useful for piping with
%>%.filter_taxa and filter_obs can now subset
anything that has names, length, and can be subset, not just tables,
lists, and vectors. For example, DNAbin objects from the
ape package can now be used in taxmap objects
(issue
#178).taxmap and taxonomy parsers now treat taxa
with the same name and same place in the taxonomy, but different ranks,
database IDs, or authorities, as different taxa.filter_obs can now filter multiple datasets at once if
they are the same length (issue #179).select_obs and arrange_obs can now work on
multiple datasets at once."taxon_rank" value for the
class_key options work with
extract_tax_data.taxmap print method when printing tables
with only a taxon ID column (issue #181).target in many functions renamed to
data to make it more intuitive.parse_tax_data can now incorporate rank information
which can be accessed by result$taxon_ranks() (issue #113).taxmap print methods now have more information and
color (issue
#124).leaves_apply function that works like
subtaxa_apply, but on leaves (issue #126).value option now return named taxon
indexes by default, instead of unnamed taxon indexes (issue #128).lookup_tax_data and extract_tax_data can
now use “fuzzy” matching when looking up taxon names, so taxon names can
be misspelled and still be founds.lookup_tax_data and extract_tax_data now
only look up unique sequence IDs, improving download speed.filter_obs now can filter out observations in
non-target data sets that are associated with taxa that are removed when
drop_taxa = TRUE (issue #143). This
is done using filter_taxa, so the supertaxa,
subtaxa, and reassign_obs options are now
available to filter_obs to control how taxon removal is
done.lookup_tax_data and extract_tax_data now
have progress bars instead of printing lots of text when downloading
information.mutate_obs now creates new vector/tables if the data
set specified does not exist (issue #121).filter_taxa option keep_order that
preserves input taxon order. It is TRUE by default, which
changes how it used to work. Set to FALSE for old
behavior.simplify option in many functions is now always
handled the same way: If all vectors in a list are names, then unique
key-value pairs are returned. Otherwise, names are ignored and unique
values are returned.leaves option now behaves like
subtaxa, returning all leaves for each taxon. The old
behavior can be replicated by setting the new simplify
option to TRUE (issue #127).filter_taxa now has better error messages for invalid
inputs (issue
#117).filter_taxa when no
taxa pass filter (issue #116).parse_tax_data when
class_key was not named (issue #131).hierarchy print method with
taxon_id class was not used (issue #138).parse_tax_data when all classification
data is NA.taxmap print method when printing
zero-length lists and vectors (issue #148).subset (issue #88, issue #89)lookup_tax_data and
extract_tax_data that caused an error when one of the
queries failed too download.obs_apply to
not work when passed as a variable (issue #97)map_data_ for mapping without using NSE.n_obs and n_obs_1
and make them available for NSE (issue #91parse_tax_data/extract_tax_data can now
parse things like
phylum;Nitrosopumilales;order;Nitrosopumilaceae;family; and
split out the rank and taxon names by using multiple matches to the
class_regex when class_sep is NULL.extract_tax_data now gives warnings if a regex does not
match.n_supertaxa_1 function to get number of immediate
supertaxa (always 1 or 0).branches function to go with roots,
leaves, and stems. (issue #56)internodes and is_internode
functions to go with roots, leaves,
branches, and stems. Useful for removing
uninformative taxonomic ranks/taxa.taxon,
taxon_name, taxon_id, taxon_rank,
and taxa to handle NULL inputs as first class
citizens to handle cases when you have essentially a blank taxon (use
case comes from taxize package) #95 #107classification as an abstraction to get
either hierarchy of taxon indexes, names, or ids (issue #57)get_data_frame for both
Taxonomy and Taxmap objects that wraps around
get_data to coerce into a data.frame. (issue #58) (PR #105)parse_tax_data, I moved “taxon_id” and “input_index”
columns to front and “input” to rear. Also “tax_data” now comes before
“class_data”.
Need a high-speed mirror for your open-source project?
Contact our mirror admin team at info@clientvps.com.
This archive is provided as a free public service to the community.
Proudly supported by infrastructure from VPSPulse , RxServers , BuyNumber , UnitVPS , OffshoreName and secure payment technology by ArionPay.