NEWS.md

In ropensci/taxlist: Handling Taxonomic Lists

taxlist 0.4.0

New Features

• New function reindex() to reassign identifiers to taxon concepts, taxon names and taxon views.

taxlist 0.3.0

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

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

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

Bug Fixes

• Functions taxlist2taxmap() and taxmap2taxlist() temporarily deprecated due to conflicts with release of taxa v. 0.4.0

taxlist 0.2.1

New Features

• New function indented_list() to print taxonomic ranks in indented lists.

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

Improvements

• Several improvements to meet ROpenSci requirements documented here.

taxlist 0.1.9

Bug Fixes

• Problems with encoding of data set Easplist

taxlist 0.1.8

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

New Features

• Method for character values in function match_names().
• Set of functions for data manipulation, namely replace_x(), replace_idx(), replace_na(), and insert_rows().
• Function clean() with new argument times for repeat cleaning of taxlist objects.

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

New Features

• New function count_taxa()

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

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

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

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

New Features

• new function merge_taxa.

Improvements

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

taxlist 0.1.1

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

New Features

• Released to CRAN (https://cran.r-project.org/package=taxlist).

ropensci/taxlist documentation built on Sept. 17, 2024, 3:39 p.m.