This repository contains the scripts for the analysis and visualisation of the monitoring of invertebrates as part of the Natura2000 Species directive (Art. 17 under the directive 43/92/ECC).
This work is funded by the Natural Environment & Climate Change Agency during the period 10-2024 until 07-2025.
- Scripts
- Species enrichment
- Spatial analysis
- Favourable Reference Values
- Natura2000 targets
- Data validation and quality control
- NECCA database
- Software
- Licence
The scripts in this repository are (with the order of execution):
- species_enrichment.R
This script facilitates species info and occurrences gathering and homogenisation from multiple
sources for Greek invertebrates. It starts by importing data from various sources,
including GBIF, previous monitoring data (E1X MDPP, E1X DB, E1X reference data),
IUCN redlist, NECCA redlist and other sources.
To ensure consistency across datasets, the script standardizes column names
based on Darwin Core (e.g., renaming decimalLongitude, decimalLatitude) and filters out incomplete records.
The main output of the is species_occurrences_art17_invertebrates.tsv file which
contains all data from the aformentioned resources.
For visualization, the script generates maps for each species, with points colored
based on their dataset source.
- spatial_analysis.R, spatial data trimming and final enrichment of species occurrences
- frvs_invertebrates_gr.R
- N2000_targets_invertebrates_gr.R
The script data_validation_qc.R is for the data validation of the data from the current samplings in order to find errors prior to submission.
The script necca_db_standards.R aims to construct all the data compliled from this work in a compatible form with the NECCA database.
| Name | Format | Content | Source |
|---|---|---|---|
| Species Taxonomy | Tabular (xlsx) | Species info | Manual curation - EIONET |
| Directive value | Tabular (xlsx) | Species info | ENVENCO |
| Current value | Tabular (xlsx) | Species info | Παραδοτέο Ανάδοχου |
| IUCN Red list | Tabular (tsv) | Species info | IUCN |
| IUCN Red list | Tabular (csv) | Species occurrences | IUCN |
| NECCA Redlist | Tabular (xlsx) | Species info | NECCA db |
| NECCA Redlist | Tabular (xlsx) | Species occurrences | NECCA db |
| Art 17 1.3.1 | Tabular (xlsx) | Species info | EIONET |
| Natura2000_v32 | Access | Species info | EIONET |
| Gbif | Tabular (tsv) | Species occurrences | Gbif |
| ΕΠΟΠΤΕΙΑ Ι | Tabular (xlsx) | Species occurrences | ENVENCO |
| ΕΠΟΠΤΕΙΑ Ι | Tabular (xlsx) | Species info | ENVENCO |
| ΟΦΥΠΕΚΑ έργα Μονάδων | Tabular (xlsx) | Species occurrences | NECCA db |
| Edaphobase 2.0 | Tabular (csv) | Species occurrences | Edaphobase 2.0 |
| National Report 2013-2018 | Shp | Species info | ENVENCO |
| Molluscabase | ? | Species occurrences | molluscabase.org |
| Worms Traits | Tabular (tsv) | Species info | |
| Genetic diversity | |||
| Species threats? |
Apatura metis Astacus astacus Austropotamobius torrentium Bolbelasmus unicornis Buprestis splendens Catopta thrips Cerambyx cerdo Coenagrion ornatum Cordulegaster heros Dioszeghyana schmidtii Eriogaster catax Euphydryas aurinia Euplagia quadripunctaria Hyles hippophaes Lindenia tetraphylla Lucanus cervus Lycaena dispar Maculinea arion Ophiogomphus cecilia Papilio alexanor Paracaloptenus caloptenoides Parnassius apollo Parnassius mnemosyne Polyommatus eroides Probaticus subrugosus Proserpinus proserpina Pseudophilotes bavius Rhysodes sulcatus Rosalia alpina Stenobothrus eurasius Stylurus flavipes Unio crassus Unio elongatulus Vertigo angustior Vertigo moulinsiana Zerynthia polyxena Morimus asper funereus Osmoderma eremita Complex Hirudo verbana
Endemic species and critically endangered are also studied in order to include them in future analyses.
Search in the website for the following: Taxonomy: Annelida - PhylumRemoveArthropoda - PhylumRemoveCnidaria - PhylumRemoveEchinodermata - PhylumRemoveMollusca - PhylumRemovePorifera - PhylumRemove Land Regions: Greece Include: Species
Didn't have any points data for the invertrebrate species of art 17.
Another search with redlist_species_data_f4d05b4d-bdbd-4b10-8c67-1523dffd9d0e id.
Geographical Scope: Global Land Regions: Greece Include: Species
All the data available from iunc Search on 2024-10-30 at 08:47:29
gawk -F"," '(NR>1){a[$3]++}END{for (i in a){print i "\t" a[i]}}' points_data.csv | sort -n -k 3
614 species with points data with 753110 occurrences.
This database doesn't have any occurrences of the species of interest.
Here we retrieve all the occurrences of the species from GBIF.
The download is manual with a registered account. Once the download is finished the user can filter based on species or country or some other field. Here we first filtered with country code of Greece to create a new file to further analyse it in R script.
gawk -F";" '(NR==1 || $7~"Greece"){print $0}' 2025-02-26-edaphobase-export.csv > 2025-02-26-edaphobase-export_GR.csv
This database doesn't have any occurrences of the species of interest.
| Name | Format | Content | Source |
|---|---|---|---|
| Natura 2000 Habitat types | shp | habitat | Κτηματολόγιο (ΕΚΧΑ) |
| Natura 2000 vegetation types | shp | vegetation | Διεύθυνση δασών |
| Corine Land Cover | shp | Land use | EEA |
| Natura2000 | shp | Natura2000 polygons | EIONET |
| EAA grid | shp | 1km², 10km² | EEA |
| Digital Elevation model | tiff | EEA | |
| Slope | |||
| Exposure | |||
| Springs | ? | ? | |
| WorldClim | tiff | WorldClim 2.0 | |
| GlobCover | ? | ? | |
| HildaPlus | tiff | Land cover change from 1960 | |
| Gadm | shp | Administrative units | Gadm |
| Υδρογραφικό δίκτυο Ελλάδα | shp | ? | |
| Natura2000 threats | ? | ||
| Elstat |
The MS access database has the schema of EEA Natura2000 in access format.
To retrieve each table run the following
mdb-export -d "\t" Natura2000DB_V32.mdb other_species > Natura2000DB_V32_other_species.tsv
The EEA Natura2000 data.
- digital elevation model over Europe (EU-DEM) eurostat DEM
- slope, aspect
The paper: Defining applying the concept of Favourable Reference Values for species and habitats defines the FRVs.
The following variables are used mostly:
- Altitude
- Slope
- Aspect
- Annual Mean Temperature
- Temperature Seasonality
- Mean Temp of Wettest Quarter
- Annual Precipitation
- Precipitation Seasonality
- Precipitation of Warmest Quarter
It is under development from AUTH. There is a script under development for the standardisation of data in order to be uploaded to NECCA database.
R version 4.4.3 (2025-02-28) with the packages:
- tidyr_1.3.1
- tibble_3.2.1
- ggplot2_3.5.1
- readr_2.1.5
- purrr_1.0.2
- dplyr_1.1.4
- readxl_1.4.3
- rgbif_3.8.1
- vegan_2.6-10
- taxize_0.10.0
- terra_1.8-15
- sf_1.0-19
GNU Awk 5.3.1
GNU GPLv3 license (for 3rd party scripts separate licenses apply).