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Structure
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├─ .gitattributes
├─ .github
│ ├─ PR_download_griis_checklist.md
│ ├─ PR_get_muskrat_data.md
│ ├─ PR_management_prep.md
│ ├─ PR_occ_indic_preprocessing.md
│ ├─ PR_update_eu_concern_list.md
│ ├─ PR_upload_files.md
│ └─ workflows
│ ├─ get_griis_checklist.yaml
│ ├─ get_muskrat_data.yaml
│ ├─ management-prep.yaml
│ ├─ update_eu_concern_list.yaml
│ ├─ update_indicators_preprocessing.yaml
│ ├─ upload_files_direct.yaml
│ └─ upload_files_processing.yaml
├─ .gitignore
├─ README.md
├─ aspbo.Rproj
├─ data
│ ├─ ETL_files
│ │ ├─ UAT_filelist.csv
│ │ └─ UAT_upload_log.csv
│ ├─ input
│ │ └─ scafold.txt
│ ├─ interim
│ │ ├─ corrupt_bl_eea_cell_codes.csv
│ │ ├─ intersect_EEA_ref_grid_protected_areas.tsv
│ │ ├─ locations_missing_coords.csv
│ │ ├─ no_degree_of_establishment.csv
│ │ ├─ no_native_continent.csv
│ │ ├─ scafold.txt
│ │ └─ timeseries_taxonomic_info.tsv
│ └─ output
│ ├─ UAT_direct
│ │ ├─ Lithobates_catesbeianus.csv
│ │ ├─ Ondatra_zibethicus.csv
│ │ ├─ Oxyura_jamaicensis.csv
│ │ └─ translations.csv
│ ├─ UAT_processing
│ │ ├─ Vespa_velutina_shape
│ │ │ ├─ aantal_gemelde_nesten.geojson
│ │ │ ├─ aantal_lente_nesten.csv
│ │ │ ├─ actieve_haarden.geojson
│ │ │ ├─ beheerde_nesten.geojson
│ │ │ ├─ nesten.geojson
│ │ │ ├─ onbehandelde_nesten.geojson
│ │ │ └─ points.geojson
│ │ ├─ be_alientaxa_cube.csv
│ │ ├─ be_alientaxa_info.csv
│ │ ├─ communes.geojson
│ │ ├─ data_input_checklist_indicators.tsv
│ │ ├─ eu_concern_species.tsv
│ │ ├─ grid
│ │ │ ├─ gewestbel.cpg
│ │ │ ├─ gewestbel.dbf
│ │ │ ├─ gewestbel.prj
│ │ │ ├─ gewestbel.sbn
│ │ │ ├─ gewestbel.sbx
│ │ │ ├─ gewestbel.shp
│ │ │ ├─ gewestbel.shx
│ │ │ ├─ utm10_bel_with_regions.gpkg
│ │ │ └─ utm1_bel_with_regions.gpkg
│ │ ├─ griis_checklist_version.txt
│ │ ├─ occurrenceCube
│ │ │ ├─ be_10km.dbf
│ │ │ ├─ be_10km.prj
│ │ │ ├─ be_10km.shp
│ │ │ ├─ be_10km.shx
│ │ │ ├─ be_1km.dbf
│ │ │ ├─ be_1km.prj
│ │ │ ├─ be_1km.shp
│ │ │ └─ be_1km.shx
│ │ ├─ provinces.geojson
│ │ └─ trendOccupancy
│ │ ├─ Compare_T's.Rmd
│ │ ├─ NARA_T0_Graphs.Rmd
│ │ ├─ T1_Belgium_Union_List_Species.cpg
│ │ ├─ T1_Belgium_Union_List_Species.dbf
│ │ ├─ T1_Belgium_Union_List_Species.prj
│ │ ├─ T1_Belgium_Union_List_Species.sbn
│ │ ├─ T1_Belgium_Union_List_Species.sbx
│ │ ├─ T1_Belgium_Union_List_Species.shp
│ │ ├─ T1_Belgium_Union_List_Species.shp.xml
│ │ ├─ T1_Belgium_Union_List_Species.shx
│ │ ├─ ias_belgium_t0_2016.geojson
│ │ ├─ ias_belgium_t0_2018.geojson
│ │ └─ ias_belgium_t0_2020.geojson
│ ├─ alien_taxa_without_occs.tsv
│ ├─ muskrat_data.csv
│ ├─ scafold.txt
│ └─ taxa_introduced_in_BE_before_1950.tsv
└─ src
├─ 05_occurrence_indicators_preprocessing.Rmd
├─ build_docker_environment.Rmd
├─ connect_to_bucket.R
├─ create_geojsons.Rmd
├─ download_griis_checklist.R
├─ get_muskrat_data.R
├─ install_alienSpecies.R
├─ install_packages_eu_concern_list.R
├─ install_packages_get_griis.R
├─ install_packages_management.R
├─ install_packages_muskrat.R
├─ install_packages_occ_indic.R
├─ install_packages_upload_files.R
├─ management_graphs.Rmd
├─ management_prep.Rmd
├─ run_management_prep.R
├─ run_occurrence_indicators_preprocessing.R
├─ tests
│ └─ scafold.txt
├─ update_eu_concern_list.R
├─ upload_direct_to_UAT.R
├─ upload_files_to_UAT.R
└─ upload_processing_to_UAT.R
©generated by Project Tree Generator
This folder contains issue templates, pull request layouts used in github actions & github actions workflow files.
This folder contains .yaml github actions workflow files. Most of these files trigger scheduled data harvesting, cleaning and mapping workflows.
Exceptions on this rule are:
- upload_files_direct.yaml: Uploads files as is to the buckets whenever changes are pushed to ./data/output/UAT_direct/1.
- upload_files_processing.yaml: Triggers processing by functions of the alienSpecies package whenever changes are pushed to ./data/output/UAT_processing/1.
1 If these changes are pushed to the uat - branch the data is uploaded to the UAT - bucket else if they are pushed to the main - branch the data is uploaded to the PROD - bucket.
This folder contains static or rarely updated input files for data flows
This folder contains intermediate results of data flows mainly used for error flagging & checking
This folder contains final results of data flows ready for upload to the AWS buckets of the alien species portal.
This folder contains the files that are uploaded as is to the buckets. These include datasets of the following invasive species: Oxyura jamaicensis, Lithobates catesbeianus, and Ondatra zibethicus. In addition, 3 translation files are stored here:
- translations.csv (columns: ID, title and description). Used for records that need to tie a description to the translated title (e.g. graphs in app).
- translations_simple.csv (columns: ID and title). Simple translations in 3 languages, which don't need a description (e.g. labels/choice options in app).
- translations_regions.csv (columns: ID and title). Translations of geographical regions (e.g. municipalities). Note that in this case translations are not required for all 3 languages. If a translation is missing, the dutch translation is taken automatically. A function has been created which can create this file based on all regions used in the app for reference.
This folder contains files that are processed by alienSpecies functions.
This folder contains the .R and .Rmd scripts that are directly or indirectly sourced by the .yaml files in the ./.github/workflows folder. Other scripts include:
- build_docker_environment.Rmd, which is used to test the alien species portal.
- create_geojsons.R, which is used once to create required .geojson files.
note: scripts that are not mentioned here are in the process of being (re)moved.
In the future, this folder will contain files and scripts related to testing parts of the code. Overall, these will be used to verify that all scripts are executed correctly and generate the expected output.
This folder contains the .R and .Rmd scripts that are directly or indirectly sourced by the get_vespa_velutina_management.yaml workflow, which creates and updates ouput related to Vespa velutina in Flanders.