Forest tree species distribution for Europe 2000-2020: mapping potential and realized distributions using spatiotemporal Machine Learning

Abstract

Paper describes a data-driven framework based on spatio-temporal ensemble machine learning to produce distribution maps for 16 forest tree species (Abies alba Mill., Castanea sativa Mill. , Corylus avellana L., Fagus sylvatica L., Olea europaea L., Picea abies L. H. Karst., Pinus halepensis Mill., Pinus nigra J. F. Arnold, Pinus pinea L., Pinus sylvestris L., Prunus avium L., Quercus cerris L., Quercus ilex L., Quercus robur L., Quercus suber L. and Salix caprea L.) at high spatial resolution (30 m). Tree occurrence data for a total of 3 million of points was used to train different Machine Learning (ML) algorithms: random forest, gradient-boosted trees, generalized linear models, k-nearest neighbors, CART and an artificial neural network. A stack of 585 coarse and high resolution covariates representing spectral reflectance (Landsat bands, spectral indices; time-series of seasonal composites), different biophysical conditions (i.e. temperature, precipitation, elevation, lithology) and biotic competition (other species distribution maps) was used as predictors for realized distributions, while potential distribution was modelled with environmental predictors only. Logloss and computing time were used to select the three best algorithms to train an ensemble model based on stacking with a logistic regressor as a meta-learner for each species. High resolution (30 m) probability and model uncertainty maps of realized distribution were produced for each species using a time window of 4 years for a total of 6 distribution maps per species for the studied period, while for potential distributions only one map per species was produced. Results of spatial cross validation show that Olea europaea and Quercus suber achieved the best performances in both potential and realized distribution, while Pinus sylvestris and Salix caprea achieved the worst. Further analysis shows that fine-resolution models consistently outperformed coarse resolution models (250 m) for realized distribution (average decrease in logloss: +53%). Realized distribution models achieved higher predictive performances than potential distribution ones. Importance of predictor variables differed across species and models, with the green band for summer and the NDWI and NDVI for fall for realized distribution and the diffuse irradiation and precipitation of the driest quarter being the most important and frequent for potential distribution. The ensemble model outperformed or performed as good as the best individual model in all potential species distributions, while for ten species it performed worse than the best individual model in modeling realized distributions. The framework shows how combining continuous and consistent EO time series data with state of the art ML can be used to derive dynamic distribution maps. The produced time-series occurrence predictions can be used to quantify temporal trends and detect potential forest degradation.

Biomes of the world under climate change scenarios: increasing aridity and higher temperatures lead to significant shifts in natural vegetation

“…All the analysis were performed using R (version 4.1.1) (R Core Team, 2021) and, specifically, the mlr package (Bischl et al, 2016). For more details on the hyperparameter space used for the other component models and the overall architecture of the ensemble model, see Bonannella et al (2022).…”

Ecodatacube.eu: Analysis-ready open environmental data cube for Europe

“…This loss in precision may lead to similar limitations, especially in the case of infrared for vegetation-related modeling. However, Bonannella et al (2022) achieved high accuracy (0.81-0.89) using the Byte-scale Landsat data when classifying multiple different tree species, suggesting this may not be a significant limitation.…”

“…and realized distribution of 16 tree species (Bonannella et al, 2022), monthly airborne fine particulate matter levels (Ibrahim et al, 2022), 43 CORINE land cover classes (Witjes et al, 2022), and daily aerosol optical depth levels (Ibrahim et al, 2021). We aim to continuously extend the feature space of the data cube, both by producing new datasets and hosting harmonized products created by third parties.…”

Forest tree species distribution for Europe 2000-2020: mapping potential and realized distributions using spatiotemporal Machine Learning

“…We implemented the workflow in the Python (Van Rossum and Drake, 2009) and R (R Core Team, 2021) programming languages. More technical details on preprocessing steps and packages used according to ODMAP (Zurell et al, 2020) are presented in Table S1 (found in https://zenodo.org/record/6516728/preview/Supplementary_material.pdf# subsection.0.1) (Bonannella et al, 2022).…”

“…Results of this operation are shown in Table S2 and Fig. S1 (found in https://zenodo.org/record/6516728/preview/Supplementary_ material.pdf#subsection.0.2) (Bonannella et al, 2022).…”