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EUNIS-ESy: Expert system for automatic classification of European vegetation plots to EUNIS habitats

Chytrý, Milan; Tichý, Lubomír; Hennekens, Stephan M.; Knollová, Ilona; Janssen, John A. M.; Rodwell, John S.; Peterka, Tomáš; Marcenò, Corrado; Landucci, Flavia; Danihelka, Jiří; Hájek, Michal; Dengler, Jürgen; Novák, Pavel; Zukal, Dominik; Jiménez-Alfar

Publisher
Zenodo
DOI
10.5281/zenodo.16895007
Repository
zenodo.org
Language
en

Abstract

EUNIS-ESy is an expert system for automatic classification of European vegetation plots to habitat types of the EUNIS Habitat Classification. The EUNIS classification and the principles of the expert system are described by Chytrý et al. (2020). The classification of a set of vegetation plots can be run using the JUICE program (Tichý 2002; https://www.sci.muni.cz/botany/juice/), TURBOVEG 3 program (Hennekens 2015) and an R script (Bruelheide et al. 2021). This dataset contains two parts: (1) the expert system and related files necessary for running it; (2) characterization of EUNIS habitats based on the results of the expert system classification. 1. Expert system and related files necessary to run it 1.1. EUNIS-ESy-2025-10-03.txt – a file containing the script for the classification of vegetation plots by EUNIS-ESy. This version contains tested definitions for the revised EUNIS classification of vegetated Marine (MA), Coastal (N), Wetland (Q), Grassland (R), Shrubland (S), Forest (T), Inland sparsely vegetated (U) and Man-made (V). It also contains tested definitions of Aquatic plant communities (P3) and Springs (P2N). This file is different from the analogous file in the previous versions. 1.2. Nomenclature-translation-from-Turboveg-2-databases.zip – an archive containing the scripts for automatic translation of taxon concepts and names used in individual European Turboveg 2 databases (Hennekens & Schaminée 2001; https://www.synbiosys.alterra.nl/turboveg/) to the nomenclature that can be used as an input for EUNIS-ESy. This file is the same as in the previous versions. 1.3. EUNIS-ESy-User-Guide.pdf – a brief user guide to the classification of vegetation plots by EUNIS-ESy using the JUICE program. Please read this guide carefully before running the expert system to avoid misclassifications. This file is the same as in the previous versions. 2. Characterization of the EUNIS habitats based on the results of the EUNIS-ESy classification 2.1. EUNIS-habitats-2025-10-03.xlsx – the current list of EUNIS habitats. This file is different from the analogous file in the previous versions. 2.2. EUNIS-EuroVegChecklist-crosswalk-2025-10-03.xlsx – a crosswalk between the EUNIS habitat classification and phytosociological alliances of EuroVegChecklist (Mucina et al. 2016; https://floraveg.eu/vegetation/). 2.3. EUNIS-habitats-Characteristic-species-combintation-2025-10-03.xlsx – a database of habitats' characteristic species combinations in a spreadsheet format. These species combinations are based on the analysis of vegetation plots from the European Vegetation Archive (EVA; Chytrý et al. 2016; http://euroveg.org/eva-database) and other databases classified by EUNIS-ESy v2025-10-03. Analytical methods are described in Chytrý et al. (2020). This file is different from the analogous file in the previous versions. 2.4. EUNIS-habitats-Distribution-maps-2025-10-03.xlsx – a set of distribution maps in the TIFF format based on the analysis of vegetation plots from the European Vegetation Archive (EVA; Chytrý et al. 2016; http://euroveg.org/eva-database) and other databases classified by EUNIS-ESy v2025-10-03. 2.5. Data-sources-EUNIS-classification-2025-10-03.pdf – a list of data sources used to produce the distribution maps and characteristic species combinations. ----------------------------------------------------------------------------------------------------- Differences from the previous version (2021-06-01) Aquatic plant communities (P3), spring (P2N), some wetland (Q61-Q63) and some inland sparsely vegetated (U71-U72) habitats were added to the EUNIS-ESy expert system. Plant taxon concepts and nomenclature were extensively revised. Some previously included habitat definitions were slightly refined. New vegetation-plot records added to the EVA database by 8 August 2025 were used to characterize habitat types. Unlike in the previous version, this version does not provide Habitat factsheets because summarized information about each habitat is now available in the FloraVeg.EU database at https://floraveg.eu/habitat/. ----------------------------------------------------------------------------------------------------- Recommended citation of this version of the EUNIS-ESy expert system Chytrý et al. (2020), version 2025-10-03 Chytrý M., Tichý L., Hennekens S.M., Knollová I., Janssen J.A.M., Rodwell J.S., Peterka T., Marcenò C., Landucci F., Danihelka J., Hájek M., Dengler J., Novák P., Zukal D., Jiménez-Alfaro B., Mucina L., Abdulhak S., Aćić S., Agrillo E., Attorre F., Bergmeier E., Biurrun I., Boch S., Bölöni J., Bonari G., Braslavskaya T., Bruelheide H., Campos J.A., Čarni A., Casella L., Ćuk M., Ćušterevska R., De Bie E., Delbosc P., Demina O., Didukh Y., Dítě D., Dziuba T., Ewald J., Gavilán R.G., Gégout J.-C., Giusso del Galdo G.P., Golub V., Goncharova N., Goral F., Graf U., Indreica A., Isermann M., Jandt U., Jansen F., Jansen J., Jašková A., Jiroušek M., Kącki Z., Kalníková V., Kavgacı A., Khanina L., Korolyuk A.Yu., Kozhevnikova M., Kuzemko A., Küzmič F., Kuznetsov O.L., Laiviņš M., Lavrinenko I., Lavrinenko O., Lebedeva M., Lososová Z., Lysenko T., Maciejewski L., Mardari C., Marinšek A., Napreenko M.G., Onyshchenko V., Pérez-Haase A., Pielech R., Prokhorov V., Rašomavičius V., Rodríguez Rojo M.P., Rūsiņa S., Schrautzer J., Šibík J., Šilc U., Škvorc Ž., Smagin V.A., Stančić Z., Stanisci A., Tikhonova E., Tonteri T., Uogintas D., Valachovič M., Vassilev K., Vynokurov D., Willner W., Yamalov S., Evans D., Palitzsch Lund M., Spyropoulou R., Tryfon E., Schaminée J.H.J. (2020) EUNIS Habitat Classification: expert system, characteristic species combinations and distribution maps of European habitats. Applied Vegetation Science, 23, 648–675. https://doi.org/10.1111/avsc.12519

Full text

Suppo ing in o ma ion o he pape Chy ý M. e al., EUNIS Habi a Classi ica ion: expe sys em, cha ac e is ic species combina ions and dis ibu ion maps o Eu opean habi a s. Applied Vege a ion Science. Appendix S5. B ie use guide o he classi ica ion o ege a ion plo s by he expe sys em EUNIS-ESy using he JUICE p og am. B ie use guide o he classi ica ion o ege a ion plo s by he expe sys em EUNIS-ESy using he JUICE p og am 1. P epa a ion and upload o inpu iles EUNIS-ESy is op imized o da a iles om he Eu opean Vege a ion A chi e (EVA), which a e expo ed om he TURBOVEG 3 p og am. These iles con ain axon concep s and names ha co espond o he Eu o+Med Plan Base and all he in o ma ion ha is equi ed o he p ope unc ioning o EUNIS-ESy. Howe e , EUNIS-ESy can also be applied o he iles expo ed om TURBOVEG 2 o any o he da abase managemen p og am, p o ided he axon concep s and names a e uni ied acco ding o Eu o+Med, and he equi ed in o ma ion is p esen in heade da a. 1.1. Inpu iles om EVA EVA da a a e s o ed in he TURBOVEG 3 p og am and expo ed in wo iles wi h he ex ensions *.hea and *.cs . These iles a e impo ed o JUICE using: File / Impo / Table / om TURBOVEG3 and Simple Tex File (Da abase Reco ds) Fill he numbe s o columns wi h he equi ed da a in he o m (see he sc eensho below). The column names can be shown by un icking he box Omi he i s line. As a minimum, he ollowing h ee columns mus be impo ed: 1. Rele é numbe 2. Ma ched concep – his column con ains he name con e ed o Eu o+Med Plan Base nomencla u e 3. Co e alue (%) EUNIS-ESy does no conside in o ma ion on ege a ion laye s. The e o e, eco ds o he same axon in di e en laye s ha e o be me ged by icking he box Me ge same SN (= species name), LC (= laye code) and SD1 (= species da a) when impo ing he da a. I you wan o check how o iginal axon names we e ansla ed o Eu o+Med, impo he o iginal names om he sou ce da abases in he column “Tu bo eg2 concep ” o he ield wi h species da a in JUICE: 1.2. Inpu iles om TURBOVEG 2 and o he da abases Make su e ha he ile con ains in o ma ion in he ollowing heade da a ields: • Coun y – a quali a i e a iable con aining coun y names spelled as ollows: Albania, Ando a, A menia, Aus ia, Bela us, Belgium, Bosnia-He zego ina, Bulga ia, Canada, C oa ia, Cyp us, Czech Republic, Denma k, Es onia, Fa oe Islands, Finland, F ance, Geo gia, Ge many, G eece, Hunga y, Iceland, I eland, I aly, Kazakhs an, Koso o, La ia, Liech ens ein, Li huania, Luxembou g, Mal a, Moldo a, Monaco, Mon eneg o, Ne he lands, No h Macedonia, No way, Poland, Po ugal, Romania, Russian Fede a ion, San Ma ino, Se bia, Slo ak Republic, Slo enia, Spain, S alba d and Jan Mayen Is, Sweden, Swi ze land, Tu key, Uk aine, Uni ed Kingdom • ECOREG_WWF – con aining h ee-le e codes o e es ial eco egions acco ding o Dine s ein e al. (2017; h ps://eco egions2017.appspo .com/) • COAST_EEA – in o ma ion whe he he si e is a he coas (including coas al habi a s such as dunes, sea cli s o coas al sal ma shes) wi h he ollowing ca ego ies (explana ion in b acke s): • ARC_COAST (A c ic) • ATL_COAST (A lan ic) • BAL_COAST (Bal ic) • BLA_COAST (Black Sea) • MED_COAST (Medi e anean) • N_COAST (Ou side he coas al a ea) • DUNES_BOHN – in o ma ion whe he he si e is in coas al dunes (including dune sc ub and dune o es ); he ca ego ies a e Y_DUNES and N_DUNES o he occu ences in and ou side dunes, espec i ely • DEG_LAT, DEG_LON – deg ees o la i ude and longi ude o he plo in he coo dina e sys em WGS 84, o ma DD.DDDD; wes e n longi udes a e indica ed wi h a minus sign • Al i ude (m) – a quan i a i e a iable con aining he al i ude o he plo in me es abo e sea le el Upload he ege a ion-plo da ase o JUICE. Remo e laye in o ma ion o all he axa by selec ing “0” laye in: Species / Renumbe Laye s o COLOUR Species Find a ile in Zenodo eposi o y (h p://doi.o g/10.5281/zenodo.3841729) ha co esponds o he species lis used in you da abase. Open his ile using: Analysis / Expe Sys em Classi ica o P ess he bu on Modi y Species Names. A e he p ocess inishes, which is indica ed by he appea ance o he lis o modi ica ions in he whi e window, p ess Me ge Same Spec. Names. The eco ds ela ed o he same species name will be me ged, and hei co e s will be summed using he Jennings–Fische o mula assuming he andom o e lap o co e s (Jennings 2009, Ecological Monog aphs; Fische 2015, Applied Vege a ion Science), i.e. he esul ing alue will ne e exceed 100%. As a esul , each axon will occu only once in he able. 2. Classi ica ion Check i he colou o plo s (Rele és) on he op o he JUICE sc een is se o whi e: Open: Analysis / Expe Sys em Classi ica o To s a he classi ica ion, p ess he bu on Classi y WHITE Rele és. Al e na i ely, you can colou selec ed plo s and classi y only hese plo s. The classi ica ion p ocess can ake se e al minu es. In he case o da ase s con aining mo e han 1 million plo s, i will ake a leas wo hou s o e en mo e, depending on he quali y o he p ocesso o you compu e . When he p ocess is inished, codes o indi idual habi a s appea in he heade o each plo . Fo u he analyses, hese heade s should be expo ed o a ile using File / Expo / Expo Sho Heade s. The classi ied plo s can be g ouped and sepa a ed using: So ing / So Sho Heade s Sepa a o s / Make Sepa a o s / Wi hin Sho Heade s