High-Performance Open-Source Archive
reindex() to reassign identifiers to taxon
concepts, taxon names and taxon views.sort_taxa() for sorting taxonomic lists
before producing prints.summary() (and
print()) produces an indented list for the hierarchical
levels (taxonomic ranks). This list is now inverted (top to bottom). The
hierarchical display of concepts also lists number of concepts per
rank.taxlist:::arrange_taxa().indented_list() will follow the order of
taxonomic concepts in slot taxonRelations when
alphabetical = FALSE. This function was formely sorting
according to taxonConceptID in the same situation.vegdata.prune_levels() pruning levels that are not
used in taxlist objects.merge_to_parent() merging multiple taxa to
their respective parents.sort_backups() retrieving a sorted list of
backups written by backup_object().taxlist2df() for converting
taxlist objects into data frames.parents() retrieving parent taxa at a
determined rank for selected taxon concepts.merge_taxa() can now be used to query a list
of taxonomic ranks. This is enabled through the argument
level.merge_taxa() to delete top ranks and rankless taxa.backup_object() retrieves an invisible vector
with information about the written backup.load_last() retrieves an invisible data frame
with information about the imported backup. It also include a new
argument choice to select a different backup from the list
produced by sort_backups().insert_rows() was redefined as a generic
function.print_name():
matched_names inheriting data frame
properties. This class will be used for an interactive selection of
multiple choices, when a name matches more than one candidate.id_generator() to create vectors of
identifiers, either as numeric values (integers) or as character values
by using random strings.id_solver() to compare vectors of
identifiers between a recipient database and a data set to be inserted
into the mentioned database. This function will propose a modified
vector for the new data to avoid conflicts by duplicated IDs.taxlist objects to data.frame
objects.taxlist objects is also looking if
Parent IDs are missing in the object.match_names() displays multiple matchings per
name and also works comparing a string with itself.to_class <- as(obj, from_class).tnrs() deprecated.to_class <- as(obj, from_class)add_concept() with a method for
data.frame objects.isolate and trim to prevent
parts of scientific names to be formatted in italics.match_names() allows to sort output data frame
in the 'character,taxlist-method'.lib_df
from package biblio.summary(), when using text as query, a new
parameter exact allow for querying the exact name, which is
usefull when querying genera.styler.print_name() is now working with more than one
name (vectorized) and reset to an S3 method, including an option for
character vectors.df2taxlist() redefined to allow import from a
single data frame.taxlist2taxmap() and
taxmap2taxlist() temporarily deprecated due to conflicts
with release of taxa v.
0.4.0indented_list() to print taxonomic ranks
in indented lists.repaste in function
dissect_name() for re-pasting dissected names.replace_idx() setting by default
idx1 = x.replace_idx() and replace_na()
setting by default idx2 = idx1.Easplisttaxlist2taxmap() for the interaction between
packages taxlist and taxmap.taxmap2taxlist() for the conversion of
Taxmap objects into taxlist ones.formula for function
count_taxa().fext in function
backup_object() setting the extension of the backup
file.match_names().replace_x(), replace_idx(),
replace_na(), and insert_rows().clean() with new argument
times for repeat cleaning of taxlist
objects.tax2traits() for objects without
taxonomic ranks.[ applies only to slot
taxonTraits.[ and $
deprecated.$ matches all taxon concepts when
retrieving information from slot taxonTraits.replace_idx() and
replace_na().replace_view() deprecated.match_names() was not properly working for the
option accepted_only=TRUE.merge_taxa() caused orphaned children of
replaced taxon concepts.clean() not working for deleted names.count_taxa()style="knitr" for function
print_name() (See this
issue at Stack Overflow).backup_object(), the message will be done
after successful saving and not before.accepted_only in function
match_names(), for comparing strings only with accepted
names.x at function
match_names()add_synonym() was not properly working for
incomplete entries (missing variables in the replacement values.)load_last() was not properly working for
values of file without mention of subfolder.accepted_name() with option
show_traits=TRUE was not displaying taxa with no entries
for taxon traits.taxlist wrongly included a slot
hierarchy.replace_view.print_name for formatting taxon names to
italic style.update_name, for updating information in
slot taxonNames.synonyms retrieving synonyms for indicated
concepts.delete_name for deleting synonyms in
taxlist objects.basionym for handling basionyms.accepted_name retrieves also information on
Level (taxonomic rank) and traits (optional in argument
show_traits).summary for single taxon is displaying the
name of the parent taxon (accepted name) and optional a string for the
taxon view.backup_object prints a message in the
console.Easplist adapted to new state of database
SWEA-Dataveg.match_names counts multiple best matchings and
includes a new argument show_concepts for displaying the
respective accepted names and taxon concept ID.load_last was not working for single files
with suffix, neither for absolute path or paths with underscores.summary for single taxa was not displaying
names that are homonyms to the accepted name.load_last to load last backup in an
R-session.dissect_name for splitting names into
their parts.match_names matching character vectors
with names of a taxlist object.backup_object is also working with relative
paths.add_view was not adding new columns in the
respective slot.tv2taxlist does not modify slot
taxonViews in prototype.load_last was not working with values of
filename having underscores.add_trait.tax2traits.level inserted in function
merge_taxa.clean also set keys to class
integer.add_concept: wrong assignment of
AcceptedName.merge_taxa.ConceptID in summary
(taxlis-method) can be a character vector matching
TaxonName.taxlist-intro.vegdata moved from Depends to Imports.df2taxlist adapted to species lists with
duplicated names.keep_parents and keep_children
implemented in function subset.
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