Handling Taxonomic Lists

Handling taxonomic lists through objects of class 'taxlist'. This package provides functions to import species lists from 'Turboveg' (< https://www.synbiosys.alterra.nl/turboveg>) and the possibility to create backups from resulting R-objects. Also quick displays are implemented as summary-methods.


News

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).

taxlist 0.0.0.9014

New Features

  • New method as.list.

Improvements

  • New validation rule: duplicated combinations TaxonName and AuthorName not allowed in slot taxonNames.
  • Data Easplist modified to fulfil the latter rule.

Reference manual

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install.packages("taxlist")

0.1.6 by Miguel Alvarez, 3 months ago


https://cran.r-project.org/package=taxlist, https://github.com/kamapu/taxlist


Report a bug at https://github.com/kamapu/taxlist/issues


Browse source code at https://github.com/cran/taxlist


Authors: Miguel Alvarez [aut, cre]


Documentation:   PDF Manual  


GPL (>= 2) license


Imports foreign, grDevices, methods, taxize, stringdist, vegdata

Depends on stats, utils

Suggests devtools, knitr, stringi, taxa, rmarkdown


Depended on by vegtable.


See at CRAN