NEWS.md

In EcologicalTraitData/traitdataform: Formatting and Harmonizing Ecological Trait-Data

traitdataform 0.6.8

• fix test value for changed dependencies: new taxon names on gbif.org.
• add suppdata to NAMESPACE

traitdataform 0.6.7

Dependency on external data has been revised to comply with CRAN policy: - demo data are now delivered with the package, to enable offline package testing, examples and vignette building; also more detailled documentation on these data was added. - calls on external data for research purposes now fail with an informative message without causing errors or warnings when the resource is not available - download URLs for research data are resolved from DOIs using package 'suppdata' (where possible) to provide higher stability for external resources

traitdataform 0.6.6

• fix external URLs to Dryad (pull request #45 by @Rekyt)

traitdataform 0.6.5

• update Rd documentation pages to include return value

traitdataform 0.6.4

• fix tidyverse URL in README

traitdataform 0.6.3

• fix: reference to doi in Rd documentation syntax

traitdataform 0.6.2

• update call to package units (pull request #42 by Iñaki Ucar)
• update new taxon names in tests

traitdataform 0.6.1

• fix to comply to CRAN policy: Packages which use Internet resources should fail gracefully with an informative message if the resource is not available or has changed (and not give a check warning nor error).

traitdataform 0.6.0

Major changes:

• update internal terms to v0.10 of the Ecological Trait-data Standard (ETS). In ETS v0.10 the assignment of user-defined and standardised measurement values and trait and taxon assignments has been updated, to match labelling practice in DwC and provide a more intuitive content for those fields. Accordingly
  • the v0.9.1 terms scientificName, traitName, traitValue, and traitUnit have been renamed into verbatimScientificName, verbatimTraitName, verbatimTraitValue, and verbatimTraitUnit with new identifiers.
  • the terms scientificNameStd, traitNameStd, traitValueStd, and traitUnitStd have been renamed into scientificName, traitName, traitValue, and traitUnit and now form the default suggested content for trait data complying with the ETS. Definitions have been harmonized. The original *Std identifiers now resolve to these new terms.

This causes the output file to differ from earlier outputs. To maintain compatibility with earlier versions, an option conformsTo has been added to as.traitdata() to return the data table in terms of version 0.9. By default, output is returned in ETS version 0.10. Data releases created by traitdataform should always be labelled with the version of ETS that applies to the data!

traitdataform 0.5.7

• Preparing for R 4.0.0 change to read.table() and data.frame(): handling of factor data (trait and taxon names) is now locale-independent
• updating download links for Data Dryad

traitdataform 0.5.6

• fix broken data calls to datadryad.org

traitdataform 0.5.5

• upgrading vignette to knitr v1.23 upon request of CRAN

traitdataform 0.5.4

• enforce UTF-8 environment in Latin-1 locale now works for

traitdataform 0.5.3 (released on CRAN 2019-04-16)

• character issues in strict Latin-1 locale have been resolved (apostrophe and en-dash)
• a dependency on an external resource (ETS.csv) is now static.

traitdataform 0.5.2 (released on CRAN 30.12.2018)

• solve minor compliance issues with CRAN: use LICENSE template

traitdataform 0.5.1

• thorough spell-checking
• set heavy examples to 'dontrun'

traitdataform 0.5.0 (released 04.12.2018)

stable, for submission on CRAN. From this point on, backwards compatibility will be maintained.

minor changes (since v0.4):

• complete package vignette
• improved unit handling
• solid demo data import

traitdataform 0.4.4

• finalize vignette (include section on writing data)

traitdataform 0.4.3

• update rbind.traitdataform() to specify metadata handling

traitdataform 0.4.2

• finalize package vignette
• simplify demo data calls
• fix handling of measurementID as factor
• fix return of output in standardize()

traitdataform 0.4.1

• update package vignette
• fix print methods
• fix thesaurus function
• set helper functions internal (not exported)
• fix file import for carabids

traitdataform 0.4.0 (released 26.11.2018)

bugfixes

• fix locale issues with pulldata() on linux (still not solved on Mac OS X)
• eliminate dependency on 'reshape' package

Minor changes

• the functions cast.traitdata() and mutate.traitdata() now support units.

traitdataform 0.3.4

• update as.trait() and as.thesaurus() as well as print methods
• update dependencies on units()

traitdataform 0.3.3

• rename and update standardize_taxa() <- standardize.taxonomy()
• rename standardize_traits() <- standardize.traits()
• fix environment issues with pulldata()

traitdataform 0.3.1

• clean rewrite of get_gbif_taxonomy()
• test_that implementation
• Travis CI implementation
• add Code of Conduct and CONTRIBUTING

traitdataform 0.3.0

• solve all errors, warnings and notes on R CHECK
• complete man pages
• fix matching bug for get_gbif_taxonomy()

traitdataform 0.2.6

• fix function mutate.traitdata() (remove method dependency to dplyr)
• update documentation for as.trait()
• successful build of vignette

traitdataform 0.2.5

• fix export of get_gbif_taxonomy()
• handle subspecies and superspecies cases
• handle warnings in taxon mapping output
• update documentation on taxon mapping

traitdataform 0.2.4

• fix export of standardize.exploratories() to include all columns by default.
• start fixing install warnings

traitdataform 0.2.3

• fixing broken NAMESPACE export
• update documentation website

traitdataform 0.2.2

• fix bug in standardize.taxonomy(): reset row.names.
• update data attributes in dataset carabids for handling in as.traitdata().

traitdataform 0.2.1

• add function as.metadata() for templating of metadata into an object class, including method print.metadata()
• update as.traitdata, print.traitdata, rbind.traitdata to make use of as.metadata
• provide metadata and thesaurus as attributes in data object 'carabids'
• update as.traitdata(): enable forwarding of attributes of input object (for metadata etc. )

traitdataform 0.2

Major changes

• updated terms to traitdata standard v0.6.
• datasets are not loaded by default, but wait for a prompt using data(). Also added documentation for all datasets and added more datasets.
• adding function method rbind.traitdata() for merging standardised datasets into a unified table. includes handling of metadata object in attributes
• metadata can be stored in the attributes of a dataset and will be preserved when updating the dataset. Information will be handled when merging or combining multiple datasets.
• trait thesauri can be added more easily from a data frame or from a list of 'trait' objects.

Minor changes

• update vignette: add section on merging and combining data.
• added print methods for traits and thesaurus objects.

traitdataform 0.1.7

Major changes

• add function standardize.exploratories() to extract georeference data for a plotID.
• add function read.service() (provided by Dennis Heimann & Andreas Ostrowski) for access of datasets on BExIS. I added a secure masked prompt using the 'getPass' package.

Bug fixes

• Spelling of 'occurrence'

EcologicalTraitData/traitdataform documentation built on June 12, 2022, 5:57 a.m.