Indicators

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:

1. checklist-based indicators
2. occurrence-based indicators

Checklist-based indicators

Checklist based indicators developed within the TrIAS project are:

1. number of introduced species present in Belgium as function of time shown as graphs
2. cumulative number of introduced species present in Belgium as function of time shown as graphs
3. 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

Occurrence-based indicators can be divided in three groups:

1. assessment of appearing and reappearing alien taxa during the last year
2. ranking of alien taxa based on an emerging status assessment
3. 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.

Appearing and reappearing alien taxa

This analysis is performed in pipeline Appearing-reappearing species.

Ranking of alien taxa based on an emerging status assessment

In order to calculate an emergency index, we take into account:

1. number of occurrences per year, or simply occurrences
2. area of occupancy (AOO), or simply occupancy

The workflow is divided in three steps:

1. Assessing emerging status of alien species
2. Ranking species by emerging status
3. 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.

Protected areas analysis

This analysis is divided in three steps:

1. 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
2. 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
3. Status of invasion of Belgian protected areas

Repo structure

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.

├── README.md              : Description of this repository
├── LICENSE                : Repository license
├── indicators.Rproj       : RStudio project file
├── .gitignore             : Files and directories to be ignored by git
│
├── data
│   ├── input
│   │   ├── modelling_species.csv               : List of species for risk modelling
│   ├── interim
|       ├── data_input_checklist_indicators.tsv : Data for making checklist indicators. Output of 'get_data_input_checklist_indicators.Rmd'
│   └── output
|   |   ├── GAM_outputs                         : Output and graphs with GAM modelling for occurrence and occupancy in both entire Belgium and Belgian protected areas 
|   |   ├── decision_rules_outputs              : Output of decision rules for occurrence and occupancy in both entire Belgium and Belgian protected areas
|   |   ├── protected_areas_analysis            : Files generated by protected areas analysis
|       ├── gbif_downloads.csv                  : List of triggered GBIF occurrence downloads 
|       └── intersect_EEA_ref_grid_protected_areas.tsv  : Membership of reference grid cells to (one or more) protected areas.
│   │   ├── Belgian_Natura2000_protected_areas.gpkg: Geopackage containing the Belgian Natura2000 protected areas with added regional distribution 
│   ├── external
│   |   ├── utm_1_bel       : Belgian reference grid of European Environmental Agency (EEA) at 1km<sup>2</sup> resolution
│   |   ├── utm_10_bel      : Belgian reference grid of European Environmental Agency (EEA) at 10km<sup>2</sup> resolution
│   |   ├── utm_100_bel     : Belgian reference grid of European Environmental Agency (EEA) at 100km<sup>2</sup> resolution
│   |   └── utm_5_bel       : Belgian reference grid at 5km<sup>2</sup> resolution created by INBO
│
└── src
│   ├── gbif_download.Rmd         : Script to trigger and verify a GBIF occurrence download
│   ├── 01_get_data_input_checklist_indicators.Rmd : Script to manipulate taxonomic data from the Global Register of Introduced and Invasive Species - Belgium
│   ├── 02_indicator_introductions_per_year.Rmd : Script to generate graphs with number of new introduced species per year
│   ├── 03_indicator_cumulative_number.Rmd : Script to generate graphs with cumulative number of introduced species per year
│   ├── 04_indicator_pathways.Rmd : Script to generate tables with pathways of introduction
│   ├── 05_occurrence_indicators_preprocessing.Rmd : Script to produce time series from the occurrence cube
│   ├── 06_occurrence_indicators_appearing_taxa.Rmd : Script to find appearing and reappearing taxa in the last years
│   ├── 07_occurrence_indicators_modelling.Rmd : Script to apply GAM and decision rules models to assess partial emerging scores
│   ├── 08_ranking_emerging_status.Rmd : Script to rank alien taxa based on their emerging status derived by the emerging scores
│   ├── 09_define_overlay_grid_belgium_with_protected_areas.Rmd : Script to visualize Belgian protected areas, superimpose the EEA reference grid and the protected areas
│   ├── 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
│   ├── 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
│   └── 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

Contributors

List of contributors

License

MIT License