trias-project/occ-cube

🗺 Occurrence cube for countries

occ-cube's Issues

Error at last command in 1_download.Rmd

At the end of running 1_download.Rmd this command is run however the result is an error

update_download_list(
  file = here::here("data", "raw", "gbif_downloads.tsv"), 
  download_to_add = gbif_download_key, 
  input_checklist = ""
)

The error message

Rows: 9 Columns: 5
-- Column specification ----------------------------------------------------------------------------------------
Delimiter: "\t"
chr  (4): gbif_download_key, input_checklist, gbif_download_status, gbif_download_doi
dttm (1): gbif_download_created

i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
[1] "https://doi.org/10.15468/dl.4r7trg"
Error in match.arg(escape) : 'arg' must be NULL or a character vector
> 

Save all outputs as csv instead of tsv

This will make preview of files on Zenodo available.

Rewrite workflows with arrow package

The use of the Very promising.arrow package should make the workflows more readable, fast and less cumbersome: no SQL syntax, dplyr verbs apply.
To be tested.

Discard occurrences with identificationVerificationStatus = unverified

Similar to trias-project/occ-cube-alien#24.
This will improve quality and remove unverified observations, e.g. https://www.gbif.org/occurrence/2631775528 (Natuurpunt:Waarnemingen:190863847)

Wrong data in Belgian cube

See trias-project/occ-cube-alien#44.
A new zenodo release will be done soon.

Generate an occurrence cube for entire Europe

This very big cube should contain an extra column with countryCode so that it would be easy for scientists to filter by country.

This pipeline would run on cluster computers of UGent for computation speed. @amyjsdavis will take care of running it.