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Changelog

Source: NEWS.md

taxlist 0.4.0

New Features

  • New function reindex() to reassign identifiers to taxon concepts, taxon names and taxon views.
  • New function sort_taxa() for sorting taxonomic lists before producing prints.

Improvements

  • Summary provided by 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.
  • Arrangement of parental chains now is done by an internal fucntion, namely taxlist:::arrange_taxa().
  • Function 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.

taxlist 0.3.0

CRAN release: 2024-07-03

New Features

  • New function prune_levels() pruning levels that are not used in taxlist objects.
  • New function merge_to_parent() merging multiple taxa to their respective parents.
  • New function sort_backups() retrieving a sorted list of backups written by backup_object().
  • New function taxlist2df() for converting taxlist objects into data frames.
  • New function parents() retrieving parent taxa at a determined rank for selected taxon concepts.

Improvements

  • Function merge_taxa() can now be used to query a list of taxonomic ranks. This is enabled through the argument level.
  • A new argument delelte_nomatch in function merge_taxa() to delete top ranks and rankless taxa.
  • Function backup_object() retrieves an invisible vector with information about the written backup.
  • Function 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().
  • Function insert_rows() was redefined as a generic function.
  • New arguments in function print_name():
    • italics: a logical value that allows to unset italic format of names. This can be usefull for taxonomic ranks that are not written in italics (e.g. Family names in plant and animals).
    • collapse: a character value (or vector of lengh 2), used to collapse strings of names, for instance to mention more than one taxa in the text.

taxlist 0.2.4

CRAN release: 2023-03-12

New Features

  • New S3 class 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.
  • Character identifiers (primary keys) are enabled.
  • New functions id_generator() to create vectors of identifiers, either as numeric values (integers) or as character values by using random strings.
  • New function 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.
  • Coercion of taxlist objects to data.frame objects.

Improvements

  • The validation for taxlist objects is also looking if Parent IDs are missing in the object.
  • Function match_names() displays multiple matchings per name and also works comparing a string with itself.
  • Simplified coercion in form of to_class <- as(obj, from_class).
  • Function tnrs() deprecated.
  • Simplified coercion in form of to_class <- as(obj, from_class)
  • Function add_concept() with a method for data.frame objects.

taxlist 0.2.3

CRAN release: 2022-09-12

New Features

  • New arguments isolate and trim to prevent parts of scientific names to be formatted in italics.

Improvements

  • Function match_names() allows to sort output data frame in the 'character,taxlist-method'.
  • Slot taxonViews allowing class lib_df from package biblio.
  • In function summary(), when using text as query, a new parameter exact allow for querying the exact name, which is usefull when querying genera.
  • New style of scripts using the package styler.
  • Name of taxon attribute lf_behn_2018 changed to life_form.
  • Function print_name() is now working with more than one name (vectorized) and reset to an S3 method, including an option for character vectors.
  • Function df2taxlist() redefined to allow import from a single data frame.

taxlist 0.2.2

CRAN release: 2021-07-15

Bug Fixes

taxlist 0.2.1

CRAN release: 2021-03-29

New Features

Improvements

  • New argument repaste in function dissect_name() for re-pasting dissected names.
  • Function replace_idx() setting by default idx1 = x.
  • Functions replace_idx() and replace_na() setting by default idx2 = idx1.
  • Special characters corrected in data set Cyperus.
  • Validation allowing taxa without rank but parents.

taxlist 0.2.0

CRAN release: 2020-10-07

Improvements

  • Several improvements to meet ROpenSci requirements documented here.

taxlist 0.1.9

CRAN release: 2020-05-31

Bug Fixes

  • Problems with encoding of data set Easplist

taxlist 0.1.8

CRAN release: 2020-04-29

New Features

  • Function taxlist2taxmap() for the interaction between packages taxlist and taxmap.
  • Function taxmap2taxlist() for the conversion of Taxmap objects into taxlist ones.

Improvements

  • Roxygenized version.
  • Method formula for function count_taxa().
  • New argument fext in function backup_object() setting the extension of the backup file.

taxlist 0.1.7

CRAN release: 2020-01-10

New Features

Improvements

  • Warning in function tax2traits() for objects without taxonomic ranks.
  • Second argument in function [ applies only to slot taxonTraits.
  • Replacement method for functions [ and $ deprecated.
  • Method for function $ matches all taxon concepts when retrieving information from slot taxonTraits.
  • Missing argument idx2 will be set as idx1 in functions replace_idx() and replace_na().
  • Function replace_view() deprecated.
  • Example data set cleaned (specifically author names)

Bug Fixes

  • Function match_names() was not properly working for the option accepted_only=TRUE.
  • Function merge_taxa() caused orphaned children of replaced taxon concepts.
  • Function clean() not working for deleted names.

taxlist 0.1.6

CRAN release: 2019-01-21

New Features

Improvements

  • A new option style="knitr" for function print_name() (See this issue at Stack Overflow).
  • In function backup_object(), the message will be done after successful saving and not before.
  • New argument accepted_only in function match_names(), for comparing strings only with accepted names.
  • Error message for NA’s in argument x at function match_names()

Bugs Fixes

  • Function add_synonym() was not properly working for incomplete entries (missing variables in the replacement values.)
  • Function load_last() was not properly working for values of file without mention of subfolder.
  • Function accepted_name() with option show_traits=TRUE was not displaying taxa with no entries for taxon traits.
  • Prototype for object taxlist wrongly included a slot hierarchy.

taxlist 0.1.5

CRAN release: 2018-06-29

New Features

  • A CITATION file is included in the installation.
  • New method replace_view.
  • New method print_name for formatting taxon names to italic style.
  • New method update_name, for updating information in slot taxonNames.
  • New method synonyms retrieving synonyms for indicated concepts.
  • New method delete_name for deleting synonyms in taxlist objects.
  • New method basionym for handling basionyms.

Improvements

  • Function accepted_name retrieves also information on Level (taxonomic rank) and traits (optional in argument show_traits).
  • Function summary for single taxon is displaying the name of the parent taxon (accepted name) and optional a string for the taxon view.
  • Function backup_object prints a message in the console.
  • Related functions will join documentation files.
  • Data set Easplist adapted to new state of database SWEA-Dataveg.
  • Function match_names counts multiple best matchings and includes a new argument show_concepts for displaying the respective accepted names and taxon concept ID.

Bugs Fixes

  • Function load_last was not working for single files with suffix, neither for absolute path or paths with underscores.
  • Function summary for single taxa was not displaying names that are homonyms to the accepted name.
  • Re-organized documentation.

taxlist 0.1.4

CRAN release: 2018-05-03

New Features

  • New function load_last to load last backup in an R-session.
  • File inst/ChangeLog replaced by NEWS.md.
  • New function dissect_name for splitting names into their parts.
  • New function match_names matching character vectors with names of a taxlist object.

Improvements

  • Function backup_object is also working with relative paths.

Bugs Fixes

  • Function add_view was not adding new columns in the respective slot.
  • Function tv2taxlist does not modify slot taxonViews in prototype.
  • Function load_last was not working with values of filename having underscores.

taxlist 0.1.3

CRAN release: 2018-01-05

New Features

  • New function: add_trait.
  • New function: tax2traits.

Improvements

  • Argument level inserted in function merge_taxa.
  • Function clean also set keys to class integer.
  • Validation checks for the existence of accepted names in names list.

Bugs Fixes

  • Bug in add_concept: wrong assignment of AcceptedName.

taxlist 0.1.2

CRAN release: 2017-08-06

New Features

  • new function merge_taxa.

Improvements

  • Argument ConceptID in summary (taxlis-method) can be a character vector matching TaxonName.

taxlist 0.1.1

CRAN release: 2017-07-23

New Features

  • New vignette taxlist-intro.

Improvements

  • Package vegdata moved from Depends to Imports.
  • Function df2taxlist adapted to species lists with duplicated names.
  • Arguments keep_parents and keep_children implemented in function subset.

taxlist 0.1.0

CRAN release: 2017-06-14

New Features