NEWS.md

In LimaRAF/plantR: Managing Species Records from Biological Collections

plantR NEWS

version 0.1.6

• Fixing the functions prepSpecies(), prepFamily() and formatTax() related to issues #90 and #96 (Plant List website was discontinued)

• Fixing the function checkCoord() related to an issue of a same coordinate overlaying more than one polygon using GADM maps (related to issue #91)

• Minor improvements in functions prepDup() and readData(), this last one related to issue #95.

• Minor fix in prepCoord() related to the new approach to handle non-ASCII characters in R>4.2 in Windows

version 0.1.5

• Fixing a small bug function prepDup() related to issues #86 and #87

• Minor improvements in functions fixLoc(), prepCoord(), prepFamily() and getYear().

• Minor changes in several package functions related to the internal use of functions from the package stringr.

version 0.1.4

• Fixing an issue related to non-NA type specifications in validateTax() and checkList() used to validate species identifications and detect type specimens.

• Fixing a small issue related to non-preserved specimens observation in validateTax() to assign confidence levels to species identifications.

• New (simple) internal function plotCoord() to help the visualization of the coordinate validation process

• New (simple) internal function fixEncoding() to help solving common encoding problems of text in 'latin1'

• Inclusion of an argument to make optional the prints of functions: prepFamily(), summaryData(), summaryFlags() and validateTax()

• Major updates on the plant collection code dictionary and minor changes in the plant taxonomist dictionary

• Function getDup() now makes the distinction between physical and purely virtual duplicates

• Function mergeDup() now provides the reference specimens used to homogenize the information within groups of duplicates. The reference specimen is provided separately for the taxonomic, locality and coordinate information. We also fixed a bug related to the homogenization of the geographical and locality information

• Function prepTDWG() (and consequently prepName()) now provides the argument 'pretty' which controls how the output names are presented. By default the function returns, as before, names in a 'pretty' way (i.e. only the first letter of names capitalized, initials separated by points and no spaces, and family name prepositions in lower cases). But now the function also returns the names in the desired format but presented in the same way as the input names

• Function formatDwc() now accepts data downloaded from the BIEN database and it includes a dataset-specific option to solve common latin1 encoding problems

• Function fixName() now includes an option to detect and solve potentially problematic cases when the name notation uses commas to separate multiple people's names. This option is controlled by the new argument bad.comma

• Minor improvements in checkList(), fixSpecies(), prepName(), getPrep(), getInit(), getYear(), colNumber(), lastName(), checkCoord(), mahalanobisDist(), prepFamily() and addRank().

• Adding tests to most of the package functions

• Solving some minor problems in the world map objects to make them compatible to the use of the spherical geometry operators of package s2, which is now the default of package sf version >= 1.0

version 0.1.3

• Fixing bugs in formatDwc() related to the difference in the number of columns that speciesLink returns for queries using different taxa and for the binding of columns with different data types.

• rgbif2() now has warnings and workarounds related to the maximum limit of 100,000 records per query

• fixes in formatOcc(), validateCoord(), validateDup(), and summaryFlags() for the particular case of only one record per species

• minor fix in prepFamily() to get missing family names based on genera

• small improvements in prepCoord(), getYear(), addRank() and formatTax()

version 0.1.2

• New tutorial on how plantR can be used to update databases of biological collections (currently in Portuguese, only)

• rspeciesLink() now supports download at the family level

• rgbif2() now supports download at any taxonomic level and using user-defined maximum number of records for download

• New accessory functions added to better handle taxonomic information

• fixSpecies() with several improvements related to scientific name casing and authorities

• saveData() now supports user-specified file names

• getYear() improved to handle more date formats

• mergeDup() now also takes into account the scientific name status to prioritize the merge of taxonomic information within duplicates

• minor bug fixes and improvements in prepSpecies() and a small update of the list of taxonomists related to the new tutorial

version 0.1.1

• New function readData() to read DwC-A zip files from GBIF

• checkCoord() now supports user provided maps

• prepSpecies() adapted to the new Taxonstand version 2.3

• Added a NEWS.md file to track changes to the package.

version 0.1.0

• The first public version of the package in GitHub.

LimaRAF/plantR documentation built on Jan. 1, 2023, 10:18 a.m.