During a recent run I discovered several issues with our species processing scripts. These need to be more flexible if we have missing columns and such - this is an initial attempt to solve this.
What changes have been made?
functions/processFieldNotes.R - when column eventID not present, eventID created from locality and date
functions/processFieldNotesOslo.R - sseparate script created for Oslo/Agder style datasets
pipeline/integration/utils/defineProcessing.R - allows for new function
pipeline/integration/speciesDataProcessing.R - change to remove any datasets with no data
General changes to all fieldNotes scripts
Species outside of relevant taxa are not checked for absences
coordinateUncertaintyInMetres is filtered much earlier
individualCount is set to one for all occurrence data, then subsequent NAs produced by creation of absences are set to 0
Additional bug fixes
functions/taxaCheck.R and functions/findGBIFName.R - stupid error whereby GBIF backbone won't find the name if there's no capitalised genus name, so I've capitalised the genus name if need be
pipeline/integration/speciesDataProcessing.R and pipeline/models/speciesModelRuns.R - focalTaxon import done locally
pipeline/integration/utils/metadataProduction.Rmd - fixed DOI object
Why have changes been made?
During a recent run I discovered several issues with our species processing scripts. These need to be more flexible if we have missing columns and such - this is an initial attempt to solve this.
What changes have been made?
General changes to all fieldNotes scripts
Additional bug fixes