Predicting forest cover in distinct ecosystems: the potential of multi-source sentinel-1 and -2 data fusion

The fusion of microwave and optical data sets is expected to provide great potential for the derivation of forest cover around the globe. As Sentinel-1 and Sentinel-2 are now both operating in twin mode, they can provide an unprecedented data source to build dense spatial and temporal high-resolution time series across a variety of wavelengths. This study investigates (i) the ability of the individual sensors and (ii) their joint potential to delineate forest cover for study sites in two highly varied landscapes located in Germany (temperate dense mixed forests) and South Africa (open savanna woody vegetation and forest plantations). We used multi-temporal Sentinel-1 and single time steps of Sentinel-2 data in combination to derive accurate forest/non-forest (FNF) information via machine-learning classifiers. The forest classification accuracies were 90.9% and 93.2% for South Africa and Thuringia, respectively, estimated while using autocorrelation corrected spatial cross-validation (CV) for the fused data set. Sentinel-1 only classifications provided the lowest overall accuracy of 87.5%, while Sentinel-2 based classifications led to higher accuracies of 91.9%. Sentinel-2 short-wave infrared (SWIR) channels, biophysical parameters (Leaf Area Index (LAI), and Fraction of Absorbed Photosynthetically Active Radiation (FAPAR)) and the lower spectrum of the Sentinel-1 synthetic aperture radar (SAR) time series were found to be most distinctive in the detection of forest cover. In contrast to homogenous forests sites, Sentinel-1 time series information improved forest cover predictions in open savanna-like environments with heterogeneous regional features. The presented approach proved to be robust and it displayed the benefit of fusing optical and SAR data at high spatial resolution

Towards Causal Inference for Spatio-Temporal Data: Conflict and Forest Loss in Colombia

In many data scientific problems, we are interested not only in modeling the behaviour of a system that is passively observed, but also in inferring how the system reacts to changes in the data generating mechanism. Given knowledge of the underlying causal structure, such behaviour can be estimated from purely observational data. To do so, one typically assumes that the causal structure of the data generating mechanism can be fully specified. Furthermore, many methods assume that data are generated as independent replications from that mechanism. Both of these assumptions are usually hard to justify in practice: datasets often have complex dependence structures, as is the case for spatio-temporal data, and the full causal structure between all involved variables is hardly known. Here, we present causal models that are adapted to the characteristics of spatio-temporal data, and which allow us to define and quantify causal effects despite incomplete causal background knowledge. We further introduce a simple approach for estimating causal effects, and a non-parametric hypothesis test for these effects being zero. The proposed methods do not rely on any distributional assumptions on the data, and allow for arbitrarily many latent confounders, given that these confounders do not vary across time (or, alternatively, they do not vary across space). Our theoretical findings are supported by simulations and code is available online. This work has been motivated by the following real-world question: how has the Colombian conflict influenced tropical forest loss? There is evidence for both enhancing and reducing impacts, but most literature analyzing this problem is not using formal causal methodology. When applying our method to data from 2000 to 2018, we find a reducing but insignificant causal effect of conflict on forest loss. Regionally, both enhancing and reducing effects can be identified.Comment: 29 pages, 8 figure

Global apparent temperature sensitivity of terrestrial carbon turnover modulated by hydrometeorological factors

We are in debt to FLUXNET principal investigators and researchers for the fundamental measurements and synthesis datasets used to build the upscaled and in situ flux datasets used in this study. The work used eddy covariance data from La Thuile Synthesis Dataset, which were provided by the FLUXNET community. In particular, we thank A. Altaf, J. Beringer, P. Blanken, C. Brümmer, S. Burns, J. Cleverly, E. Cremonese, T. Grünwald, P. Kolari, W. Jans, M. Leonardo, T. Manise, M. Mund, A. Noormets, E. Pendall, C. Pio, S. Prober, L. Šigut, A. Varlagin and W. Woodgate, who provided us with site-level measurements of soil carbon and vegetation biomass, and B. Amiro, J. Ardö, S. Arndt, D. Baldocchi, L. Belelli, F. Bosveld, D. Bowling, N. Buchmann, A. Christen, M. Cuntz, A. Desai, B. Drake, I. Goded, A. Goldstein, C. Gough, S. Ivan, L. Hutley, I. Janssens, M. Karan, H. Kobayashi, M. Korkiakoski, B. Kruijt, S. Linder, B. Loubet, I. Mammarella, S. Minerbi, W. Munger, Z. Nagy, D. Papale, A. Richardson, B. Ruiz, E.P. Sanchez-Canete, FCE. Silva, E. Veenendaal, S. Wharton, G. Wohlfahrt, J. Wood, D. Yakir and D. Zona, who provided contacts and/or references for us to find site-level measurements of soil carbon and vegetation biomass. We are thankful to S. Bao and S. Besnard for helping with collected and processed site-level FLUXNET and vegetation biomass data. We thank M. Migliavacca and M. Schrumpf for providing reference and useful resources for data collection. N.F. acknowledges support from the International Max Planck Research School for Global Biogeochemical Cycles. Publisher Copyright: © 2022, The Author(s).The ecosystem carbon turnover time—an emergent ecosystem property that partly determines the feedback between the terrestrial carbon cycle and climate—is strongly controlled by temperature. However, it remains uncertain to what extent hydrometeorological conditions may influence the apparent temperature sensitivity of τ, defined as the factor by which the carbon turnover time increases with a 10 °C rise in temperature (Q10). Here, we investigate the responses of the ecosystem carbon turnover to temperature and hydrometeorological factors using an ensemble of observation-based global datasets and a global compilation of in situ measurements. We find that temperature and hydrometeorology are almost equally important in shaping the spatial pattern of ecosystem carbon turnover, explaining 60 and 40% of the global variability, respectively. Accounting for hydrometeorological effects puts a strong constraint on Q10 values with a substantial reduction in magnitude and uncertainties, leading Q10 to converge to 1.6 ± 0.1 globally. These findings suggest that hydrometeorological conditions modulate the apparent temperature sensitivity of terrestrial carbon turnover times, confounding the role of temperature in quantifying the response of the carbon cycle to climate change.publishersversionpublishe

Spatially autocorrelated training and validation samples inflate performance assessment of convolutional neural networks

Deep learning and particularly Convolutional Neural Networks (CNN) in concert with remote sensing are becoming standard analytical tools in the geosciences. A series of studies has presented the seemingly outstanding performance of CNN for predictive modelling. However, the predictive performance of such models is commonly estimated using random cross-validation, which does not account for spatial autocorrelation between training and validation data. Independent of the analytical method, such spatial dependence will inevitably inflate the estimated model performance. This problem is ignored in most CNN-related studies and suggests a flaw in their validation procedure. Here, we demonstrate how neglecting spatial autocorrelation during cross-validation leads to an optimistic model performance assessment, using the example of a tree species segmentation problem in multiple, spatially distributed drone image acquisitions. We evaluated CNN-based predictions with test data sampled from 1) randomly sampled hold-outs and 2) spatially blocked hold-outs. Assuming that a block cross-validation provides a realistic model performance, a validation with randomly sampled holdouts overestimated the model performance by up to 28%. Smaller training sample size increased this optimism. Spatial autocorrelation among observations was significantly higher within than between different remote sensing acquisitions. Thus, model performance should be tested with spatial cross-validation strategies and multiple independent remote sensing acquisitions. Otherwise, the estimated performance of any geospatial deep learning method is likely to be overestimated

Kernel Methods and their derivatives: Concept and perspectives for the Earth system sciences

Kernel methods are powerful machine learning techniques which implement generic non-linear functions to solve complex tasks in a simple way. They Have a solid mathematical background and exhibit excellent performance in practice. However, kernel machines are still considered black-box models as the feature mapping is not directly accessible and difficult to interpret.The aim of this work is to show that it is indeed possible to interpret the functions learned by various kernel methods is intuitive despite their complexity. Specifically, we show that derivatives of these functions have a simple mathematical formulation, are easy to compute, and can be applied to many different problems. We note that model function derivatives in kernel machines is proportional to the kernel function derivative. We provide the explicit analytic form of the first and second derivatives of the most common kernel functions with regard to the inputs as well as generic formulas to compute higher order derivatives. We use them to analyze the most used supervised and unsupervised kernel learning methods: Gaussian Processes for regression, Support Vector Machines for classification, Kernel Entropy Component Analysis for density estimation, and the Hilbert-Schmidt Independence Criterion for estimating the dependency between random variables. For all cases we expressed the derivative of the learned function as a linear combination of the kernel function derivative. Moreover we provide intuitive explanations through illustrative toy examples and show how to improve the interpretation of real applications in the context of spatiotemporal Earth system data cubes. This work reflects on the observation that function derivatives may play a crucial role in kernel methods analysis and understanding.Comment: 21 pages, 10 figures, PLOS One Journa

Drought, Heat, and the Carbon Cycle: a Review

Purpose of the Review Weather and climate extremes substantially affect global- and regional-scale carbon (C) cycling, and thus spatially or temporally extended climatic extreme events jeopardize terrestrial ecosystem carbon sequestration. We illustrate the relevance of drought and/or heat events (“DHE”) for the carbon cycle and highlight underlying concepts and complex impact mechanisms. We review recent results, discuss current research needs and emerging research topics. Recent Findings Our review covers topics critical to understanding, attributing and predicting the effects of DHE on the terrestrial carbon cycle: (1) ecophysiological impact mechanisms and mediating factors, (2) the role of timing, duration and dynamical effects through which DHE impacts on regional-scale carbon cycling are either attenuated or enhanced, and (3) large-scale atmospheric conditions under which DHE are likely to unfold and to affect the terrestrial carbon cycle. Recent research thus shows the need to view these events in a broader spatial and temporal perspective that extends assessments beyond local and concurrent C cycle impacts of DHE. Summary Novel data streams, model (ensemble) simulations, and analyses allow to better understand carbon cycle impacts not only in response to their proximate drivers (drought, heat, etc.) but also attributing them to underlying changes in drivers and large-scale atmospheric conditions. These attribution-type analyses increasingly address and disentangle various sequences or dynamical interactions of events and their impacts, including compensating or amplifying effects on terrestrial carbon cycling.publishedVersio

Decoupling between ecosystem photosynthesis and transpiration: a last resort against overheating

Ecosystems are projected to face extreme high temperatures more frequently in the near future. Various biotic coping strategies exist to prevent heat stress. Controlled experiments have recently provided evidence for continued transpiration in woody plants during high air temperatures, even when photosynthesis is inhibited. Such a decoupling of photosynthesis and transpiration would represent an effective strategy (‘known as leaf or canopy cooling’) to prevent lethal leaf temperatures. At the ecosystem scale, continued transpiration might dampen the development and propagation of heat extremes despite further desiccating soils. However, at the ecosystem scale, evidence for the occurrence of this decoupling is still limited. Here, we aim to investigate this mechanism using eddy-covariance data of thirteen woody ecosystems located in Australia and a causal graph discovery algorithm. Working at half-hourly time resolution, we find evidence for a decoupling of photosynthesis and transpiration in four ecosystems which can be classified as Mediterranean woodlands. The decoupling occurred at air temperatures above 35 °C. At the nine other investigated woody sites, we found that vegetation CO2 exchange remained coupled to transpiration at the observed high air temperatures. Ecosystem characteristics suggest that the canopy energy balance plays a crucial role in determining the occurrence of a decoupling. Our results highlight the value of causal-inference approaches for the analysis of complex physiological processes. With regard to projected increasing temperatures and especially extreme events in future climates, further vegetation types might be pushed to threatening canopy temperatures. Our findings suggest that the coupling of leaf-level photosynthesis and stomatal conductance, common in land surface schemes, may need be re-examined when applied to high-temperature events

Have precipitation extremes and annual totals been increasing in the world’s dry regions over the last 60 years?

Daily precipitation extremes and annual totals have increased in large parts of the global land area over the past decades. These observations are consistent with theoretical considerations of a warming climate. However, until recently these trends have not been shown to consistently affect dry regions over land. A recent study, published by Donat et al. (2016), now identified significant increases in annual-maximum daily extreme precipitation (Rx1d) and annual precipitation totals (PRCPTOT) in dry regions. Here, we revisit the applied methods and explore the sensitivity of changes in precipitation extremes and annual totals to alternative choices of defining a dry region (i.e. in terms of aridity as opposed to precipitation characteristics alone). We find that (a) statistical artifacts introduced by data pre-processing based on a time-invariant reference period lead to an overestimation of the reported trends by up to 40 %, and that (b) the reported trends of globally aggregated extremes and annual totals are highly sensitive to the definition of a "dry region of the globe". For example, using the same observational dataset, accounting for the statistical artifacts, and based on different aridity-based dryness definitions, we find a reduction in the positive trend of Rx1d from the originally reported +1.6 % decade−1 to +0.2 to +0.9 % decade−1 (period changes for 1981–2010 averages relative to 1951–1980 are reduced to −1.32 to +0.97 % as opposed to +4.85 % in the original study). If we include additional but less homogenized data to cover larger regions, the global trend increases slightly (Rx1d: +0.4 to +1.1 % decade−1), and in this case we can indeed confirm (partly) significant increases in Rx1d. However, these globally aggregated estimates remain uncertain as considerable gaps in long-term observations in the Earth's arid and semi-arid regions remain. In summary, adequate data pre-processing and accounting for uncertainties regarding the definition of dryness are crucial to the quantification of spatially aggregated trends in precipitation extremes in the world's dry regions. In view of the high relevance of the question to many potentially affected stakeholders, we call for a well-reflected choice of specific data processing methods and the inclusion of alternative dryness definitions to guarantee that communicated results related to climate change be robust.Have precipitation extremes and annual totals been increasing in the world’s dry regions over the last 60 years?publishedVersio

Imputing missing data in plant traits: A guide to improve gap‐filling

Aim: Globally distributed plant trait data are increasingly used to understand relationships between biodiversity and ecosystem processes. However, global trait databases are sparse because they are compiled from many, mostly small databases. This sparsity in both trait space completeness and geographical distribution limits the potential for both multivariate and global analyses. Thus, ‘gap-filling’ approaches are often used to impute missing trait data. Recent methods, like Bayesian hierarchical probabilistic matrix factorization (BHPMF), can impute large and sparse data sets using side information. We investigate whether BHPMF imputation leads to biases in trait space and identify aspects influencing bias to provide guidance for its usage. Innovation: We use a fully observed trait data set from which entries are randomly removed, along with extensive but sparse additional data. We use BHPMF for imputation and evaluate bias by: (1) accuracy (residuals, RMSE, trait means), (2) correlations (bi-and multivariate) and (3) taxonomic and functional clustering (valuewise, uni-and multivariate). BHPMF preserves general patterns of trait distributions but induces taxonomic clustering. Data set–external trait data had little effect on induced taxonomic clustering and stabilized trait–trait correlations. Main Conclusions: Our study extends the criteria for the evaluation of gap-filling beyond RMSE, providing insight into statistical data structure and allowing better informed use of imputed trait data, with improved practice for imputation. We expect our findings to be valuable beyond applications in plant ecology, for any study using hierarchical side information for imputation