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 developed within the TrIAS project are:
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:
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:
The workflow is divided in two steps:
1 Assessing emerging status of alien species 2. Ranking species by emerging status
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:
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 : Find appearing and reappearing taxa in the last years
│ ├── 07_occurrence_indicators_modelling.Rmd : Apply GAM and decision rules models to assess partial emerging scores
│ ├── 08_ranking_emerging_status.Rmd : Rank alien taxa based on their emerging status derived by the emerging scores
│ ├── 09_define_overlay_grid_belgium_with_protected_areas.Rmd : Visualize Belgian protected areas, superimpose the EEA reference grid and the protected areas
│ ├── 10_occurrence_species_protected_areas_level.Rmd : 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 : to find number of alien taxa and observations in protected areas and number of protected areas each alien taxon is present