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
- fix external URLs to Dryad (pull request #45 by @Rekyt)
- update Rd documentation pages to include return value
- fix tidyverse URL in README
- fix: reference to doi in Rd documentation syntax
- update call to package
units (pull request #42 by Iñaki Ucar)
- update new taxon names in tests
- 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).
- 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
This causes the output file to differ from earlier outputs. To maintain compatibility with earlier versions, an option
- the v0.9.1 terms
traitUnit have been renamed into
verbatimTraitUnit with new identifiers.
- the terms
traitUnitStd have been renamed into
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.
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!
- 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
- fix broken data calls to datadryad.org
- upgrading vignette to knitr v1.23 upon request of CRAN
- enforce UTF-8 environment in Latin-1 locale now works for
- 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.
- solve minor compliance issues with CRAN: use LICENSE template
- thorough spell-checking
- set heavy examples to ‘dontrun’
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
- finalize vignette (include section on writing data)
- update rbind.traitdataform() to specify metadata handling
- finalize package vignette
- simplify demo data calls
- fix handling of measurementID as factor
- fix return of output in standardize()
- update package vignette
- fix print methods
- fix thesaurus function
- set helper functions internal (not exported)
- fix file import for carabids
- fix locale issues with pulldata() on linux (still not solved on Mac OS X)
- eliminate dependency on ‘reshape’ package
- the functions cast.traitdata() and mutate.traitdata() now support units.
- update as.trait() and as.thesaurus() as well as print methods
- update dependencies on units()
- rename and update standardize_taxa() <- standardize.taxonomy()
- rename standardize_traits() <- standardize.traits()
- fix environment issues with pulldata()
- clean rewrite of get_gbif_taxonomy()
- test_that implementation
- Travis CI implementation
- add Code of Conduct and CONTRIBUTING
- solve all errors, warnings and notes on R CHECK
- complete man pages
- fix matching bug for get_gbif_taxonomy()
- fix function mutate.traitdata() (remove method dependency to dplyr)
- update documentation for as.trait()
- successful build of vignette
- fix export of get_gbif_taxonomy()
- handle subspecies and superspecies cases
- handle warnings in taxon mapping output
- update documentation on taxon mapping
- fixing broken NAMESPACE export
- update documentation website
- add function
as.metadata() for templating of metadata into an object class, including method
- update as.traitdata, print.traitdata, rbind.traitdata to make use of
- provide metadata and thesaurus as attributes in data object ‘carabids’
as.traitdata(): enable forwarding of attributes of input object (for metadata etc. )
- 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.
- update vignette: add section on merging and combining data.
- added print methods for traits and thesaurus objects.
- 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.