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[AUTO] update cube_preprocessing #230

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[AUTO] update cube_preprocessing #230

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Brief description

This is an automatically generated PR.
The following steps are all automatically performed:

  • rerun occurrence_indicators_preprocessing to create and upload
    df_timeseries.rData to the UAT bucket.
  • df_timeseries.rData is combined with grid.RData from the UAT bucket using
    alienSpecies::createTimeseries(). The result is also stored on the UAT bucket.

Note to the reviewer: the workflow automation is still in a development phase.
Please, check the output thoroughly before merging to main.
run_occurrence_indicators_preprocessing.r downloads
./data/interim/intersect_EEA_ref_grid_protected_areas.tsv from
trias-project/indicators then it runs
./src/05_occurrence_indicators_preprocessing.Rmd based on the script from trias-project/indicators/.

@soriadelva
Create test_be_alientaxa_cube_species.R
25f6fce
@soriadelva
Keep only GRIIS species with occurrences in Belgium, last observed af…
42634b6 
…ter 1950, and Animalia or Plantae
@soriadelva
Add necessary packages wk and rgbif
1b13a9e
@soriadelva
Update description of steps
153d545
@soriadelva
Add necessary packages
5b0e460
@soriadelva
Update explanation
56a312a
@soriadelva
Use same download parameters as in alien taxa cube
53cdd6d
@soriadelva
add alientaxa cube rationale
483e620
@soriadelva
Remove last_observed filter for GRIIS
23162f0
@soriadelva
Add taxonomic info of be_alientaxa_cube
8fb20bc
@soriadelva
Filter out synonyms as indicated in the includes column of the cube i…
8f1c032 
…nfo file
@soriadelva
Update info
5d95c60
@soriadelva
Use information of GRIIS checklist to print missing taxonkeys and sci…
697e60b 
…entificnames
@soriadelva
Remove old code
e1057e6
@soriadelva
Provide more info
6f28138
@soriadelva
Save results of test in log that can be consulted
c260639
@soriadelva
Add test to cube_preprocessing.yaml
4af7474
@soriadelva
Write !grepl more efficiently
a344488
@soriadelva
Merge branch 'uat' into 214-add-check-to-highlight-species-on-griis-m…
bdff433 
…issing-from-be_alientaxa_cube
@FaunabeheerenInvasieveSoorten FaunabeheerenInvasieveSoorten linked an issue Aug 9, 2024 that may be closed by this pull request
Add check to highlight species on GRIIS missing from be_alientaxa_cube #214
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SanderDevisscher
SanderDevisscher requested changes Aug 12, 2024
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use correct secrets to supply username, pswd & email to rgbif functions

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@SanderDevisscher SanderDevisscher SanderDevisscher requested changes

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Add check to highlight species on GRIIS missing from be_alientaxa_cube
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@FaunabeheerenInvasieveSoorten @SanderDevisscher @soriadelva