This repository contains pipelines to generate alien species indicators, i.e. graphs or tables analyzing specific aspects of their stage of invasion. Indicators can be divided in two groups:
- checklist-based indicators
- occurrence-based indicators
Checklist based indicators developed within the TrIAS project are:
- number of introduced species present in Belgium as function of time shown as graphs
- cumulative number of introduced species present in Belgium as function of time shown as graphs
- pathways of introduction shown as graphs and tables
The indicators are built upon the taxa published in the Global Register of Introduced and Invasive Species - Belgium.
Occurrence-based indicators can be divided in three groups:
- assessment of appearing and reappearing alien taxa during the last year
- ranking of alien taxa based on an emerging status assessment
- state of invasion of protected areas
All of them start from data as preprocessed in pipeline Preprocessing for occurrence-based indicators. The starting point are the occurrence cube at species level as produced in TrIAS repository occ-cube and published on Zenodo and the occurrence cube of alien taxa as produced in TrIAS repository occ-cube-alien and published on Zenodo.
This analysis is performed in pipeline Appearing-reappearing species.
In order to calculate an emergency index, we take into account:
- number of occurrences per year, or simply occurrences
- area of occupancy (AOO), or simply occupancy
The workflow is divided in three steps:
- Assessing emerging status of alien species
- Ranking species by emerging status
- Assess the taxonomic distribution of emerging species
We work with GAM (Generalized Additive Models) and decision rules to assess the emerging status of a species.
This analysis is divided in three steps:
- Belgian protected areas and EEA grid of Belgium to preprocess geospatial data, visualize the Natura2000 protected areas and overlay the EEA 1kmx1km reference grid to protected areas
- Belgian protected areas: observations and occupancy to assess the number of observations, the area of occupancy and the coverage of Belgian protected areas for all species and year
- Status of invasion of Belgian protected areas
The repository structure is based on Cookiecutter Data Science. Files indicated with GENERATED
should not be edited manually. This list can be not complete as the content of this repository is still in progress.
โโโ README.md : Description of this repository
โโโ LICENSE : Repository license
โโโ indicators.Rproj : RStudio project file
โโโ .gitignore : Files and directories to be ignored by git
โ
โโโ data
โ โโโ input
โ โ โโโ modelling_species.csv : List of species for risk modelling
โ โโโ interim
| โโโ data_input_checklist_indicators.tsv : Data for making checklist indicators. Output of 'get_data_input_checklist_indicators.Rmd'
โ โโโ output
| | โโโ GAM_outputs : Output and graphs with GAM modelling for occurrence and occupancy in both entire Belgium and Belgian protected areas
| | โโโ decision_rules_outputs : Output of decision rules for occurrence and occupancy in both entire Belgium and Belgian protected areas
| | โโโ protected_areas_analysis : Files generated by protected areas analysis
| โโโ gbif_downloads.csv : List of triggered GBIF occurrence downloads
| โโโ intersect_EEA_ref_grid_protected_areas.tsv : Membership of reference grid cells to (one or more) protected areas.
โ โ โโโ Belgian_Natura2000_protected_areas.gpkg: Geopackage containing the Belgian Natura2000 protected areas with added regional distribution
โ โโโ external
โ | โโโ utm_1_bel : Belgian reference grid of European Environmental Agency (EEA) at 1km<sup>2</sup> resolution
โ | โโโ utm_10_bel : Belgian reference grid of European Environmental Agency (EEA) at 10km<sup>2</sup> resolution
โ | โโโ utm_100_bel : Belgian reference grid of European Environmental Agency (EEA) at 100km<sup>2</sup> resolution
โ | โโโ utm_5_bel : Belgian reference grid at 5km<sup>2</sup> resolution created by INBO
โ
โโโ src
โ โโโ gbif_download.Rmd : Script to trigger and verify a GBIF occurrence download
โ โโโ 01_get_data_input_checklist_indicators.Rmd : Script to manipulate taxonomic data from the Global Register of Introduced and Invasive Species - Belgium
โ โโโ 02_indicator_introductions_per_year.Rmd : Script to generate graphs with number of new introduced species per year
โ โโโ 03_indicator_cumulative_number.Rmd : Script to generate graphs with cumulative number of introduced species per year
โ โโโ 04_indicator_pathways.Rmd : Script to generate tables with pathways of introduction
โ โโโ 05_occurrence_indicators_preprocessing.Rmd : Script to produce time series from the occurrence cube
โ โโโ 06_occurrence_indicators_appearing_taxa.Rmd : Script to find appearing and reappearing taxa in the last years
โ โโโ 07_occurrence_indicators_modelling.Rmd : Script to apply GAM and decision rules models to assess partial emerging scores
โ โโโ 08_ranking_emerging_status.Rmd : Script to rank alien taxa based on their emerging status derived by the emerging scores
โ โโโ 09_define_overlay_grid_belgium_with_protected_areas.Rmd : Script to visualize Belgian protected areas, superimpose the EEA reference grid and the protected areas
โ โโโ 10_occurrence_species_protected_areas_level.Rmd : Sript to assess number of observations, area of occupancy, coverage of Belgian protected areas for all species and year
โ โโโ 11_status_alien_species_in_protected_areas.Rmd : Script to find number of alien taxa and observations in protected areas and number of protected areas each alien taxon is present
โ โโโ 12_taxonomic_distribution_emerging_species.Rmd : Script to produce summary tables and graphs about the taxonomic distribution of the species labelled as emerging in 07_occurrence_indicators_modelling.Rmd