elements

elements is a R package containing correlative, realised Ecological Niche Models (ENMs) for the most prevalent vascular plants, bryophytes, and terricolous lichens in the European Vegetation Archive (EVA) (Chytrý et al., 2016).

The code used to produce the models is available here https://github.com/NERC-CEH/elementsAnalysis.

Methods

The ENMs adhere to Hutchinsonian conceptualisation of the ecological niche as an n-dimensional hypervolume (Hutchinson, 1957). The environmental variables forming the dimensions of each hypervolume consist of:

  • Seven unweighted, plot-mean Ecological Indicator Values (EIVs):
    • M - Soil Moisture1
    • R - Reaction1
    • N - Soil Nitrogen1
    • L - Light1
    • GP - Grazing Pressure2
    • SD - Soil Disturbance2
    • S - Salinity3
  • Four bioclimatic variables:
    • bio05 - Maximum temperature in the warmest month4
    • bio06 - Minimum temperature in the coldest month4
    • bio16 - Precipitation in the wettest quarter4
    • bio17 - Precipitation in the driest quarter4

Support Vector Machine (SVM) models, which form a hyperplane between the presence and absence hypervolumes, were trained and tested using using the mlr3 ecosystem of R packages (Lang et al., 2019). The raw e1071 (Meyer et al., 2024) SVM models are bundled in elements.

For more information please see Marshall et al (in prep).

1(Dengler et al., 2023), 2(Midolo et al., 2023), 3(Tichy et al., 2023), 4(Copernicus Climate Change Service, 2021)

References

Chytrý, M., Hennekens, S.M., Jiménez-Alfaro, B., Knollová, I., Dengler, J., Jansen, F., Landucci, F., Schaminée, J.H.J., Aćić, S., Agrillo, E., Ambarlı, D., Angelini, P., Apostolova, I., Attorre, F., Berg, C., Bergmeier, E., Biurrun, I., Botta-Dukát, Z., Brisse, H., Campos, J.A., Carlón, L., Čarni, A., Casella, L., Csiky, J., Ćušterevska, R., Dajić Stevanović, Z., Danihelka, J., De Bie, E., de Ruffray, P., De Sanctis, M., Dickoré, W.B., Dimopoulos, P., Dubyna, D., Dziuba, T., Ejrnæs, R., Ermakov, N., Ewald, J., Fanelli, G., Fernández-González, F., FitzPatrick, Ú., Font, X., García-Mijangos, I., Gavilán, R.G., Golub, V., Guarino, R., Haveman, R., Indreica, A., Işık Gürsoy, D., Jandt, U., Janssen, J.A.M., Jiroušek, M., Kącki, Z., Kavgacı, A., Kleikamp, M., Kolomiychuk, V., Krstivojević Ćuk, M., Krstonošić, D., Kuzemko, A., Lenoir, J., Lysenko, T., Marcenò, C., Martynenko, V., Michalcová, D., Moeslund, J.E., Onyshchenko, V., Pedashenko, H., Pérez-Haase, A., Peterka, T., Prokhorov, V., Rašomavičius, V., Rodríguez-Rojo, M.P., Rodwell, J.S., Rogova, T., Ruprecht, E., Rūsiņa, S., Seidler, G., Šibík, J., Šilc, U., Škvorc, Ž., Sopotlieva, D., Stančić, Z., Svenning, J.-C., Swacha, G., Tsiripidis, I., Turtureanu, P.D., Uğurlu, E., Uogintas, D., Valachovič, M., Vashenyak, Y., Vassilev, K., Venanzoni, R., Virtanen, R., Weekes, L., Willner, W., Wohlgemuth, T., Yamalov, S., 2016. European Vegetation Archive (EVA): an integrated database of European vegetation plots. Applied Vegetation Science 19, 173–180. https://doi.org/10.1111/avsc.12191

Copernicus Climate Change Service, 2021. Downscaled bioclimatic indicators for selected regions from 1950 to 2100 derived from climate projections. https://doi.org/10.24381/CDS.0AB27596

Dengler, J., Jansen, F., Chusova, O., Hüllbusch, E., Nobis, M.P., Meerbeek, K.V., Axmanová, I., Bruun, H.H., Chytrý, M., Guarino, R., Karrer, G., Moeys, K., Raus, T., Steinbauer, M.J., Tichý, L., Tyler, T., Batsatsashvili, K., Bita-Nicolae, C., Didukh, Y., Diekmann, M., Englisch, T., Fernández-Pascual, E., Frank, D., Graf, U., Hájek, M., Jelaska, S.D., Jiménez-Alfaro, B., Julve, P., Nakhutsrishvili, G., Ozinga, W.A., Ruprecht, E.-K., Šilc, U., Theurillat, J.-P., Gillet, F., 2023. Ecological Indicator Values for Europe (EIVE) 1.0. Vegetation Classification and Survey 4, 7–29. https://doi.org/10.3897/VCS.98324

Hutchinson, G.E., 1957. Concluding Remarks. Cold Spring Harbor Symposia on Quantitative Biology 22, 415–427. https://doi.org/10.1101/SQB.1957.022.01.039

Lang, M., Binder, M., Richter, J., Schratz, P., Pfisterer, F., Coors, S., Au, Q., Casalicchio, G., Kotthoff, L., Bischl, B., 2019. mlr3: A modern object-oriented machine learning framework in R. Journal of Open Source Software 4, 1903. https://doi.org/10.21105/joss.01903

Meyer, D., Dimitriadou, E., Hornik, K., Weingessel, A., Leisch, F., 2024. e1071: Misc Functions of the Department of Statistics, Probability Theory Group (Formerly: E1071), TU Wien. https://doi.org/10.32614/CRAN.package.e1071

Midolo, G., Herben, T., Axmanová, I., Marcenò, C., Pätsch, R., Bruelheide, H., Karger, D.N., Aćić, S., Bergamini, A., Bergmeier, E., Biurrun, I., Bonari, G., Čarni, A., Chiarucci, A., De Sanctis, M., Demina, O., Dengler, J., Dziuba, T., Fanelli, G., Garbolino, E., Giusso del Galdo, G., Goral, F., Güler, B., Hinojos-Mendoza, G., Jansen, F., Jiménez-Alfaro, B., Lengyel, A., Lenoir, J., Pérez-Haase, A., Pielech, R., Prokhorov, V., Rašomavičius, V., Ruprecht, E., Rūsiņa, S., Šilc, U., Škvorc, Ž., Stančić, Z., Tatarenko, I., Chytrý, M., 2023. Disturbance indicator values for European plants. Global Ecology and Biogeography 32, 24–34. https://doi.org/10.1111/geb.13603

Tichý, L., Axmanová, I., Dengler, J., Guarino, R., Jansen, F., Midolo, G., Nobis, M.P., Van Meerbeek, K., Aćić, S., Attorre, F., Bergmeier, E., Biurrun, I., Bonari, G., Bruelheide, H., Campos, J.A., Čarni, A., Chiarucci, A., Ćuk, M., Ćušterevska, R., Didukh, Y., Dítě, D., Dítě, Z., Dziuba, T., Fanelli, G., Fernández-Pascual, E., Garbolino, E., Gavilán, R.G., Gégout, J.-C., Graf, U., Güler, B., Hájek, M., Hennekens, S.M., Jandt, U., Jašková, A., Jiménez-Alfaro, B., Julve, P., Kambach, S., Karger, D.N., Karrer, G., Kavgacı, A., Knollová, I., Kuzemko, A., Küzmič, F., Landucci, F., Lengyel, A., Lenoir, J., Marcenò, C., Moeslund, J.E., Novák, P., Pérez-Haase, A., Peterka, T., Pielech, R., Pignatti, A., Rašomavičius, V., Rūsiņa, S., Saatkamp, A., Šilc, U., Škvorc, Ž., Theurillat, J.-P., Wohlgemuth, T., Chytrý, M., 2023. Ellenberg-type indicator values for European vascular plant species. Journal of Vegetation Science 34, e13168. https://doi.org/10.1111/jvs.13168