Articles | Volume 17, issue 15
https://doi.org/10.5194/gmd-17-6007-2024
© Author(s) 2024. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
https://doi.org/10.5194/gmd-17-6007-2024
© Author(s) 2024. This work is distributed under
the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Model evaluation paper
| 
14 Aug 2024
Model evaluation paper |
| 14 Aug 2024
| 14 Aug 2024
Random forests with spatial proxies for environmental modelling: opportunities and pitfalls
Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
Universitat Pompeu Fabra (UPF), Barcelona, Spain
Marvin Ludwig
Institute of Landscape Ecology, University of Münster, Münster, Germany
Edzer Pebesma
Institute for Geoinformatics, University of Münster, Münster, Germany
Cathryn Tonne
Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
Universitat Pompeu Fabra (UPF), Barcelona, Spain
CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
Hanna Meyer
Institute of Landscape Ecology, University of Münster, Münster, Germany
Related authors
Jan Linnenbrink, Carles Milà, Marvin Ludwig, and Hanna Meyer
Geosci. Model Dev., 17, 5897–5912, https://doi.org/10.5194/gmd-17-5897-2024, https://doi.org/10.5194/gmd-17-5897-2024, 2024
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Estimation of map accuracy based on cross-validation (CV) in spatial modelling is pervasive but controversial. Here, we build upon our previous work and propose a novel, prediction-oriented k-fold CV strategy for map accuracy estimation in which the distribution of geographical distances between prediction and training points is taken into account when constructing the CV folds. Our method produces more reliable estimates than other CV methods and can be used for large datasets.
Fabian Lukas Schumacher, Christian Knoth, Marvin Ludwig, and Hanna Meyer
EGUsphere, https://doi.org/10.5194/egusphere-2024-2730, https://doi.org/10.5194/egusphere-2024-2730, 2024
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Machine learning is increasingly used in environmental sciences for spatial predictions, but its effectiveness is challenged when models are applied beyond the areas they were trained on. We propose a Local Training Data Point Density (LPD) approach that considers how well a model's environment is represented by training data. This method provides a valuable tool for evaluating model applicability and uncertainties, crucial for broader scientific and practical applications.
Jan Linnenbrink, Carles Milà, Marvin Ludwig, and Hanna Meyer
Geosci. Model Dev., 17, 5897–5912, https://doi.org/10.5194/gmd-17-5897-2024, https://doi.org/10.5194/gmd-17-5897-2024, 2024
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Estimation of map accuracy based on cross-validation (CV) in spatial modelling is pervasive but controversial. Here, we build upon our previous work and propose a novel, prediction-oriented k-fold CV strategy for map accuracy estimation in which the distribution of geographical distances between prediction and training points is taken into account when constructing the CV folds. Our method produces more reliable estimates than other CV methods and can be used for large datasets.
Henning Teickner, Edzer Pebesma, and Klaus-Holger Knorr
EGUsphere, https://doi.org/10.5194/egusphere-2024-1739, https://doi.org/10.5194/egusphere-2024-1739, 2024
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The Holocene Peatland Model (HPM) is a widely used peatland model to understand and predict long-term peatland dynamics. Here, we test whether the HPM can predict Sphagnum litterbag decomposition rates from oxic to anoxic conditions. Our results indicate that decomposition rates change more gradually from oxic to anoxic conditions and may be underestimated under anoxic conditions, possibly because the effect of water table fluctuations on decomposition rates is not considered.
Henning Teickner, Edzer Pebesma, and Klaus-Holger Knorr
EGUsphere, https://doi.org/10.5194/egusphere-2024-1686, https://doi.org/10.5194/egusphere-2024-1686, 2024
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Decomposition rates for Sphagnum mosses, the main peat forming plants in northern peatlands, are often derived from litterbag experiments. Here, we estimate initial leaching losses from available Sphagnum litterbag experiments and analyze how decomposition rates are biased when initial leaching losses are ignored. Our analyses indicate that initial leaching losses range between 3 to 18 mass-% and that this may result in overestimated mass losses when extrapolated to several decades.
M. Ludwig, J. Bahlmann, E. Pebesma, and H. Meyer
Int. Arch. Photogramm. Remote Sens. Spatial Inf. Sci., XLIII-B3-2022, 135–141, https://doi.org/10.5194/isprs-archives-XLIII-B3-2022-135-2022, https://doi.org/10.5194/isprs-archives-XLIII-B3-2022-135-2022, 2022
Hanna Meyer, Marwan Katurji, Florian Detsch, Fraser Morgan, Thomas Nauss, Pierre Roudier, and Peyman Zawar-Reza
Earth Syst. Sci. Data Discuss., https://doi.org/10.5194/essd-2019-215, https://doi.org/10.5194/essd-2019-215, 2019
Preprint withdrawn
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Air temperature is an important baseline parameter for terrestrial Antarctica in the context of patterns and processes in climatology, hydrology or ecology. In this paper, we present AntAir, a new dataset of gridded air temperatures in 1 km spatial and daily temporal resolution that is available since 2003. AntAir was created by modelling daily air temperature from MODIS satellite-based land surface temperature using machine learning algorithms and measurements from 70 weather stations.
A. Joshi, E. Pebesma, R. Henriques, and M. Appel
Int. Arch. Photogramm. Remote Sens. Spatial Inf. Sci., XLII-5-W3, 43–47, https://doi.org/10.5194/isprs-archives-XLII-5-W3-43-2019, https://doi.org/10.5194/isprs-archives-XLII-5-W3-43-2019, 2019
Sergio Ibarra-Espinosa, Rita Ynoue, Shane O'Sullivan, Edzer Pebesma, María de Fátima Andrade, and Mauricio Osses
Geosci. Model Dev., 11, 2209–2229, https://doi.org/10.5194/gmd-11-2209-2018, https://doi.org/10.5194/gmd-11-2209-2018, 2018
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An emissions inventory is a compilation of the mass of pollutants released by different sources. The quantification of vehicular emissions is difficult because these sources are in movement across streets. Also, emissions processes are multiple and complex. In this paper, we present an open-source software for calculating spatial vehicular emissions, including exhaust, evaporation and wear, named VEIN. The software is an R package available at
https://github.com/atmoschem/vein.
Hanna Meyer, Johannes Drönner, and Thomas Nauss
Atmos. Meas. Tech., 10, 2009–2019, https://doi.org/10.5194/amt-10-2009-2017, https://doi.org/10.5194/amt-10-2009-2017, 2017
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A spatially explicit mapping of rainfall is required for southern Africa but obtaining accurate estimates is still a challenging task. We estimated hourly rainfall based on optical satellite data and neural networks. The results indicated that the majority of rainfall events could be captured by the model, but with a clear tendency to overestimate rainfall. Despite being a comparably simple approach, the presented rainfall retrieval could outperform a complex global rainfall product.
Related subject area
Earth and space science informatics
An improved global pressure and zenith wet delay model with optimized vertical correction considering the spatiotemporal variability in multiple height-scale factors
kNNDM CV: k-fold nearest-neighbour distance matching cross-validation for map accuracy estimation
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Focal-TSMP: deep learning for vegetation health prediction and agricultural drought assessment from a regional climate simulation
Tomofast-x 2.0: an open-source parallel code for inversion of potential field data with topography using wavelet compression
Functional analysis of variance (ANOVA) for carbon flux estimates from remote sensing data
The 4D reconstruction of dynamic geological evolution processes for renowned geological features
Machine learning for numerical weather and climate modelling: a review
Overcoming barriers to enable convergence research by integrating ecological and climate sciences: the NCAR–NEON system Version 1
Ensemble of optimised machine learning algorithms for predicting surface soil moisture content at a global scale
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A generalized spatial autoregressive neural network method for three-dimensional spatial interpolation
The Common Community Physics Package (CCPP) Framework v6
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A methodological framework for improving the performance of data-driven models: a case study for daily runoff prediction in the Maumee domain, USA
SHAFTS (v2022.3): a deep-learning-based Python package for simultaneous extraction of building height and footprint from sentinel imagery
Bayesian atmospheric correction over land: Sentinel-2/MSI and Landsat 8/OLI
Twenty-five years of the IPCC Data Distribution Centre at the DKRZ and the Reference Data Archive for CMIP data
Effectiveness and computational efficiency of absorbing boundary conditions for full-waveform inversion
LAND-SUITE V1.0: a suite of tools for statistically based landslide susceptibility zonation
Towards physics-inspired data-driven weather forecasting: integrating data assimilation with a deep spatial-transformer-based U-NET in a case study with ERA5
Fast infrared radiative transfer calculations using graphics processing units: JURASSIC-GPU v2.0
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A new methodological framework for geophysical sensor combinations associated with machine learning algorithms to understand soil attributes
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Chunhua Jiang, Xiang Gao, Huizhong Zhu, Shuaimin Wang, Sixuan Liu, Shaoni Chen, and Guangsheng Liu
Geosci. Model Dev., 17, 5939–5959, https://doi.org/10.5194/gmd-17-5939-2024, https://doi.org/10.5194/gmd-17-5939-2024, 2024
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With ERA5 hourly data, we show spatiotemporal characteristics of pressure and zenith wet delay (ZWD) and propose an empirical global pressure and ZWD grid model with a broader operating space which can provide accurate pressure, ZWD, zenith hydrostatic delay, and zenith tropospheric delay estimates for any selected time and location over globe. IGPZWD will be of great significance for the tropospheric augmentation in real-time GNSS positioning and atmospheric water vapor remote sensing.
Jan Linnenbrink, Carles Milà, Marvin Ludwig, and Hanna Meyer
Geosci. Model Dev., 17, 5897–5912, https://doi.org/10.5194/gmd-17-5897-2024, https://doi.org/10.5194/gmd-17-5897-2024, 2024
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Estimation of map accuracy based on cross-validation (CV) in spatial modelling is pervasive but controversial. Here, we build upon our previous work and propose a novel, prediction-oriented k-fold CV strategy for map accuracy estimation in which the distribution of geographical distances between prediction and training points is taken into account when constructing the CV folds. Our method produces more reliable estimates than other CV methods and can be used for large datasets.
Nikola Besic, Nicolas Picard, Cédric Vega, Lionel Hertzog, Jean-Pierre Renaud, Fajwel Fogel, Agnès Pellissier-Tanon, Gabriel Destouet, Milena Planells-Rodriguez, and Philippe Ciais
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2024-95, https://doi.org/10.5194/gmd-2024-95, 2024
Revised manuscript accepted for GMD
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The creation of advanced mapping models for forest attributes, utilizing remote sensing data and incorporating machine or deep learning methods, has become a key area of interest in the domain of forest observation and monitoring. This paper introduces a method where we blend and collectively interpret five models dedicated to estimating forest canopy height. We achieve this through Bayesian model averaging, offering a comprehensive approach to height estimation in forest ecosystems.
Ziyu Yin, Jiale Ding, Yi Liu, Ruoxu Wang, Yige Wang, Yijun Chen, Jin Qi, Sensen Wu, and Zhenhong Du
Geosci. Model Dev. Discuss., https://doi.org/10.5194/gmd-2024-62, https://doi.org/10.5194/gmd-2024-62, 2024
Revised manuscript accepted for GMD
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In geography, understanding how relationships between different factors change over time and space is crucial. This study implements two neural network-based spatiotemporal regression models as well as an open-sourced Python package named GNNWR, to accurately capture the varying relationships between factors. This makes it a valuable tool for researchers in various fields, such as environmental science, urban planning, and public health.
Marion N. Parquer, Eric A. de Kemp, Boyan Brodaric, and Michael J. Hillier
EGUsphere, https://doi.org/10.5194/egusphere-2024-1326, https://doi.org/10.5194/egusphere-2024-1326, 2024
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This is a proof-of-concept paper outlining a general approach to how 3D geological models would be checked to be geologically 'reasonable'. We do this with a consistency checking tool that looks at geological feature pairs and their spatial, temporal and internal polarity characteristics. The idea is to assess if geological relationships from a specific 3D geological model matches what is allowed in the real world, from the perspective of geological principals.
Lars Hoffmann, Kaveh Haghighi Mood, Andreas Herten, Markus Hrywniak, Jiri Kraus, Jan Clemens, and Mingzhao Liu
Geosci. Model Dev., 17, 4077–4094, https://doi.org/10.5194/gmd-17-4077-2024, https://doi.org/10.5194/gmd-17-4077-2024, 2024
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Lagrangian particle dispersion models are key for studying atmospheric transport but can be computationally intensive. To speed up simulations, the MPTRAC model was ported to graphics processing units (GPUs). Performance optimization of data structures and memory alignment resulted in runtime improvements of up to 75 % on NVIDIA A100 GPUs for ERA5-based simulations with 100 million particles. These optimizations make the MPTRAC model well suited for future high-performance computing systems.
Oriol Tintó Prims, Robert Redl, Marc Rautenhaus, Tobias Selz, Takumi Matsunobu, Kameswar Rao Modali, and George Craig
EGUsphere, https://doi.org/10.5194/egusphere-2024-753, https://doi.org/10.5194/egusphere-2024-753, 2024
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Advanced compression techniques can drastically reduce the size of meteorological datasets (by 5x to 150x) without compromising the data's scientific value. We developed a user-friendly tool called 'enstools-compression' that makes this compression simple for Earth scientists. This tool works seamlessly with common weather and climate data formats. Our work shows that lossy compression can significantly improve how researchers store and analyze large meteorological datasets.
Mohamad Hakam Shams Eddin and Juergen Gall
Geosci. Model Dev., 17, 2987–3023, https://doi.org/10.5194/gmd-17-2987-2024, https://doi.org/10.5194/gmd-17-2987-2024, 2024
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In this study, we use deep learning and a climate simulation to predict the vegetation health as it would be observed from satellites. We found that the developed model can help to identify regions with a high risk of agricultural drought. The main applications of this study are to estimate vegetation products for periods where no satellite data are available and to forecast the future vegetation response to climate change based on climate scenarios.
Vitaliy Ogarko, Kim Frankcombe, Taige Liu, Jeremie Giraud, Roland Martin, and Mark Jessell
Geosci. Model Dev., 17, 2325–2345, https://doi.org/10.5194/gmd-17-2325-2024, https://doi.org/10.5194/gmd-17-2325-2024, 2024
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We present a major release of the Tomofast-x open-source gravity and magnetic inversion code that is enhancing its performance and applicability for both industrial and academic studies. We focus on real-world mineral exploration scenarios, while offering flexibility for applications at regional scale or for crustal studies. The optimisation work described in this paper is fundamental to allowing more complete descriptions of the controls on magnetisation, including remanence.
Jonathan Hobbs, Matthias Katzfuss, Hai Nguyen, Vineet Yadav, and Junjie Liu
Geosci. Model Dev., 17, 1133–1151, https://doi.org/10.5194/gmd-17-1133-2024, https://doi.org/10.5194/gmd-17-1133-2024, 2024
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The cycling of carbon among the land, oceans, and atmosphere is a closely monitored process in the global climate system. These exchanges between the atmosphere and the surface can be quantified using a combination of atmospheric carbon dioxide observations and computer models. This study presents a statistical method for investigating the similarities and differences in the estimated surface–atmosphere carbon exchange when different computer model assumptions are invoked.
Jiateng Guo, Zhibin Liu, Xulei Wang, Lixin Wu, Shanjun Liu, and Yunqiang Li
Geosci. Model Dev., 17, 847–864, https://doi.org/10.5194/gmd-17-847-2024, https://doi.org/10.5194/gmd-17-847-2024, 2024
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This study proposes a 3D and temporally dynamic (4D) geological modeling method. Several simulation and actual cases show that the 4D spatial and temporal evolution of regional geological formations can be modeled easily using this method with smooth boundaries. The 4D modeling system can dynamically present the regional geological evolution process under the timeline, which will be helpful to the research and teaching on the formation of typical and complex geological features.
Catherine O. de Burgh-Day and Tennessee Leeuwenburg
Geosci. Model Dev., 16, 6433–6477, https://doi.org/10.5194/gmd-16-6433-2023, https://doi.org/10.5194/gmd-16-6433-2023, 2023
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Machine learning (ML) is an increasingly popular tool in the field of weather and climate modelling. While ML has been used in this space for a long time, it is only recently that ML approaches have become competitive with more traditional methods. In this review, we have summarized the use of ML in weather and climate modelling over time; provided an overview of key ML concepts, methodologies, and terms; and suggested promising avenues for further research.
Danica L. Lombardozzi, William R. Wieder, Negin Sobhani, Gordon B. Bonan, David Durden, Dawn Lenz, Michael SanClements, Samantha Weintraub-Leff, Edward Ayres, Christopher R. Florian, Kyla Dahlin, Sanjiv Kumar, Abigail L. S. Swann, Claire M. Zarakas, Charles Vardeman, and Valerio Pascucci
Geosci. Model Dev., 16, 5979–6000, https://doi.org/10.5194/gmd-16-5979-2023, https://doi.org/10.5194/gmd-16-5979-2023, 2023
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We present a novel cyberinfrastructure system that uses National Ecological Observatory Network measurements to run Community Terrestrial System Model point simulations in a containerized system. The simple interface and tutorials expand access to data and models used in Earth system research by removing technical barriers and facilitating research, educational opportunities, and community engagement. The NCAR–NEON system enables convergence of climate and ecological sciences.
Qianqian Han, Yijian Zeng, Lijie Zhang, Calimanut-Ionut Cira, Egor Prikaziuk, Ting Duan, Chao Wang, Brigitta Szabó, Salvatore Manfreda, Ruodan Zhuang, and Bob Su
Geosci. Model Dev., 16, 5825–5845, https://doi.org/10.5194/gmd-16-5825-2023, https://doi.org/10.5194/gmd-16-5825-2023, 2023
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Using machine learning, we estimated global surface soil moisture (SSM) to aid in understanding water, energy, and carbon exchange. Ensemble models outperformed individual algorithms in predicting SSM under different climates. The best-performing ensemble included K-neighbours Regressor, Random Forest Regressor, and Extreme Gradient Boosting. This is important for hydrological and climatological applications such as water cycle monitoring, irrigation management, and crop yield prediction.
Xiaoyi Shao, Siyuan Ma, and Chong Xu
Geosci. Model Dev., 16, 5113–5129, https://doi.org/10.5194/gmd-16-5113-2023, https://doi.org/10.5194/gmd-16-5113-2023, 2023
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Scientific understandings of the distribution of coseismic landslides, followed by emergency and medium- and long-term risk assessment, can reduce landslide risk. The aim of this study is to propose an improved three-stage spatial prediction strategy and develop corresponding hazard assessment software called Mat.LShazard V1.0, which provides a new application tool for coseismic landslide disaster prevention and mitigation in different stages.
Junda Zhan, Sensen Wu, Jin Qi, Jindi Zeng, Mengjiao Qin, Yuanyuan Wang, and Zhenhong Du
Geosci. Model Dev., 16, 2777–2794, https://doi.org/10.5194/gmd-16-2777-2023, https://doi.org/10.5194/gmd-16-2777-2023, 2023
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We develop a generalized spatial autoregressive neural network model used for three-dimensional spatial interpolation. Taking the different changing trend of geographic elements along various directions into consideration, the model defines spatial distance in a generalized way and integrates it into the process of spatial interpolation with the theories of spatial autoregression and neural network. Compared with traditional methods, the model achieves better performance and is more adaptable.
Dominikus Heinzeller, Ligia Bernardet, Grant Firl, Man Zhang, Xia Sun, and Michael Ek
Geosci. Model Dev., 16, 2235–2259, https://doi.org/10.5194/gmd-16-2235-2023, https://doi.org/10.5194/gmd-16-2235-2023, 2023
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The Common Community Physics Package is a collection of physical atmospheric parameterizations for use in Earth system models and a framework that couples the physics to a host model’s dynamical core. A primary goal for this effort is to facilitate research and development of physical parameterizations and physics–dynamics coupling methods while offering capabilities for numerical weather prediction operations, for example in the upcoming implementation of the Global Forecast System (GFS) v17.
Tobias Tesch, Stefan Kollet, and Jochen Garcke
Geosci. Model Dev., 16, 2149–2166, https://doi.org/10.5194/gmd-16-2149-2023, https://doi.org/10.5194/gmd-16-2149-2023, 2023
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A recent statistical approach for studying relations in the Earth system is to train deep learning (DL) models to predict Earth system variables given one or several others and use interpretable DL to analyze the relations learned by the models. Here, we propose to combine the approach with a theorem from causality research to ensure that the deep learning model learns causal rather than spurious relations. As an example, we apply the method to study soil-moisture–precipitation coupling.
Yao Hu, Chirantan Ghosh, and Siamak Malakpour-Estalaki
Geosci. Model Dev., 16, 1925–1936, https://doi.org/10.5194/gmd-16-1925-2023, https://doi.org/10.5194/gmd-16-1925-2023, 2023
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Data-driven models (DDMs) gain popularity in earth and environmental systems, thanks in large part to advancements in data collection techniques and artificial intelligence (AI). The performance of these models is determined by the underlying machine learning (ML) algorithms. In this study, we develop a framework to improve the model performance by optimizing ML algorithms and demonstrate the effectiveness of the framework using a DDM to predict edge-of-field runoff in the Maumee domain, USA.
Ruidong Li, Ting Sun, Fuqiang Tian, and Guang-Heng Ni
Geosci. Model Dev., 16, 751–778, https://doi.org/10.5194/gmd-16-751-2023, https://doi.org/10.5194/gmd-16-751-2023, 2023
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We developed SHAFTS (Simultaneous building Height And FootprinT extraction from Sentinel imagery), a multi-task deep-learning-based Python package, to estimate average building height and footprint from Sentinel imagery. Evaluation in 46 cities worldwide shows that SHAFTS achieves significant improvement over existing machine-learning-based methods.
Feng Yin, Philip E. Lewis, and Jose L. Gómez-Dans
Geosci. Model Dev., 15, 7933–7976, https://doi.org/10.5194/gmd-15-7933-2022, https://doi.org/10.5194/gmd-15-7933-2022, 2022
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The proposed SIAC atmospheric correction method provides consistent surface reflectance estimations from medium spatial-resolution satellites (Sentinel 2 and Landsat 8) with per-pixel uncertainty information. The outputs from SIAC have been validated against a wide range of ground measurements, and it shows that SIAC can provide accurate estimations of both surface reflectance and atmospheric parameters, with meaningful uncertainty information.
Martina Stockhause and Michael Lautenschlager
Geosci. Model Dev., 15, 6047–6058, https://doi.org/10.5194/gmd-15-6047-2022, https://doi.org/10.5194/gmd-15-6047-2022, 2022
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The Data Distribution Centre (DDC) of the Intergovernmental Panel on Climate Change (IPCC) celebrates its 25th anniversary in 2022. DDC Partner DKRZ has supported the IPCC Assessments and preserved the quality-assured, citable climate model data underpinning the Assessment Reports over these years over the long term. With the introduction of the IPCC FAIR Guidelines into the current AR6, the value of DDC services has been recognized. However, DDC sustainability remains unresolved.
Daiane Iglesia Dolci, Felipe A. G. Silva, Pedro S. Peixoto, and Ernani V. Volpe
Geosci. Model Dev., 15, 5857–5881, https://doi.org/10.5194/gmd-15-5857-2022, https://doi.org/10.5194/gmd-15-5857-2022, 2022
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We investigate and compare the theoretical and computational characteristics of several absorbing boundary conditions (ABCs) for the full-waveform inversion (FWI) problem. The different ABCs are implemented in an optimized computational framework called Devito. The computational efficiency and memory requirements of the ABC methods are evaluated in the forward and adjoint wave propagators, from simple to realistic velocity models.
Mauro Rossi, Txomin Bornaetxea, and Paola Reichenbach
Geosci. Model Dev., 15, 5651–5666, https://doi.org/10.5194/gmd-15-5651-2022, https://doi.org/10.5194/gmd-15-5651-2022, 2022
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LAND-SUITE is a software package designed to support landslide susceptibility zonation. The software integrates, extends, and completes LAND-SE (Rossi et al., 2010; Rossi and Reichenbach, 2016). The software is implemented in R, a free software environment for statistical computing and graphics, and gives expert users the possibility to perform easier, more flexible, and more informed statistically based landslide susceptibility applications and zonations.
Ashesh Chattopadhyay, Mustafa Mustafa, Pedram Hassanzadeh, Eviatar Bach, and Karthik Kashinath
Geosci. Model Dev., 15, 2221–2237, https://doi.org/10.5194/gmd-15-2221-2022, https://doi.org/10.5194/gmd-15-2221-2022, 2022
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There is growing interest in data-driven weather forecasting, i.e., to predict the weather by using a deep neural network that learns from the evolution of past atmospheric patterns. Here, we propose three components to add to the current data-driven weather forecast models to improve their performance. These components involve a feature that incorporates physics into the neural network, a method to add data assimilation, and an algorithm to use several different time intervals in the forecast.
Paul F. Baumeister and Lars Hoffmann
Geosci. Model Dev., 15, 1855–1874, https://doi.org/10.5194/gmd-15-1855-2022, https://doi.org/10.5194/gmd-15-1855-2022, 2022
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The efficiency of the numerical simulation of radiative transport is shown on modern server-class graphics cards (GPUs). The low-cost prefactor on GPUs compared to general-purpose processors (CPUs) enables future large retrieval campaigns for multi-channel data from infrared sounders aboard low-orbit satellites. The validated research software JURASSIC is available in the public domain.
Gregory E. Tucker, Eric W. H. Hutton, Mark D. Piper, Benjamin Campforts, Tian Gan, Katherine R. Barnhart, Albert J. Kettner, Irina Overeem, Scott D. Peckham, Lynn McCready, and Jaia Syvitski
Geosci. Model Dev., 15, 1413–1439, https://doi.org/10.5194/gmd-15-1413-2022, https://doi.org/10.5194/gmd-15-1413-2022, 2022
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Scientists use computer simulation models to understand how Earth surface processes work, including floods, landslides, soil erosion, river channel migration, ocean sedimentation, and coastal change. Research benefits when the software for simulation modeling is open, shared, and coordinated. The Community Surface Dynamics Modeling System (CSDMS) is a US-based facility that supports research by providing community support, computing tools and guidelines, and educational resources.
Danilo César de Mello, Gustavo Vieira Veloso, Marcos Guedes de Lana, Fellipe Alcantara de Oliveira Mello, Raul Roberto Poppiel, Diego Ribeiro Oquendo Cabrero, Luis Augusto Di Loreto Di Raimo, Carlos Ernesto Gonçalves Reynaud Schaefer, Elpídio Inácio Fernandes Filho, Emilson Pereira Leite, and José Alexandre Melo Demattê
Geosci. Model Dev., 15, 1219–1246, https://doi.org/10.5194/gmd-15-1219-2022, https://doi.org/10.5194/gmd-15-1219-2022, 2022
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We used soil parent material, terrain attributes, and geophysical data from the soil surface to test and compare different and unprecedented geophysical sensor combination, as well as different machine learning algorithms to model and predict several soil attributes. Also, we analyzed the importance of pedoenvironmental variables. The soil attributes were modeled throughout different machine learning algorithms and related to different geophysical sensor combinations.
Duncan Watson-Parris, Andrew Williams, Lucia Deaconu, and Philip Stier
Geosci. Model Dev., 14, 7659–7672, https://doi.org/10.5194/gmd-14-7659-2021, https://doi.org/10.5194/gmd-14-7659-2021, 2021
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The Earth System Emulator (ESEm) provides a fast and flexible framework for emulating a wide variety of Earth science datasets and tools for constraining (or tuning) models of any complexity. Three distinct use cases are presented that demonstrate the utility of ESEm and provide some insight into the use of machine learning for emulation in these different settings. The open-source Python package is freely available so that it might become a valuable tool for the community.
Chongyang Wang, Li Wang, Danni Wang, Dan Li, Chenghu Zhou, Hao Jiang, Qiong Zheng, Shuisen Chen, Kai Jia, Yangxiaoyue Liu, Ji Yang, Xia Zhou, and Yong Li
Geosci. Model Dev., 14, 6833–6846, https://doi.org/10.5194/gmd-14-6833-2021, https://doi.org/10.5194/gmd-14-6833-2021, 2021
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The turbidity maximum zone (TMZ) is a special phenomenon in estuaries worldwide. However, the extraction methods and criteria used to describe the TMZ vary significantly both spatially and temporally. This study proposes an new index, the turbidity maximum zone index, based on the corresponding relationship of total suspended solid concentration and Chl a concentration, which could better extract TMZs in different estuaries and on different dates.
Ranee Joshi, Kavitha Madaiah, Mark Jessell, Mark Lindsay, and Guillaume Pirot
Geosci. Model Dev., 14, 6711–6740, https://doi.org/10.5194/gmd-14-6711-2021, https://doi.org/10.5194/gmd-14-6711-2021, 2021
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We have developed a software that allows the user to extract and standardize drill hole information from legacy datasets and/or different drilling campaigns. It also provides functionality to upscale the lithological information. These functionalities were possible by developing thesauri to identify and group geological terminologies together.
David Meyer, Thomas Nagler, and Robin J. Hogan
Geosci. Model Dev., 14, 5205–5215, https://doi.org/10.5194/gmd-14-5205-2021, https://doi.org/10.5194/gmd-14-5205-2021, 2021
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A major limitation in training machine-learning emulators is often caused by the lack of data. This paper presents a cheap way to increase the size of training datasets using statistical techniques and thereby improve the performance of machine-learning emulators.
Mark Jessell, Vitaliy Ogarko, Yohan de Rose, Mark Lindsay, Ranee Joshi, Agnieszka Piechocka, Lachlan Grose, Miguel de la Varga, Laurent Ailleres, and Guillaume Pirot
Geosci. Model Dev., 14, 5063–5092, https://doi.org/10.5194/gmd-14-5063-2021, https://doi.org/10.5194/gmd-14-5063-2021, 2021
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We have developed software that allows the user to extract sufficient information from unmodified digital maps and associated datasets that we are able to use to automatically build 3D geological models. By automating the process we are able to remove human bias from the procedure, which makes the workflow reproducible.
Martí Bosch, Maxence Locatelli, Perrine Hamel, Roy P. Remme, Jérôme Chenal, and Stéphane Joost
Geosci. Model Dev., 14, 3521–3537, https://doi.org/10.5194/gmd-14-3521-2021, https://doi.org/10.5194/gmd-14-3521-2021, 2021
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The article presents a novel approach to simulate urban heat mitigation from land use/land cover data based on three biophysical mechanisms: tree shade, evapotranspiration and albedo. An automated procedure is proposed to calibrate the model parameters to best fit temperature observations from monitoring stations. A case study in Lausanne, Switzerland, shows that the approach outperforms regressions based on satellite data and provides valuable insights into design heat mitigation policies.
Quang-Van Doan, Hiroyuki Kusaka, Takuto Sato, and Fei Chen
Geosci. Model Dev., 14, 2097–2111, https://doi.org/10.5194/gmd-14-2097-2021, https://doi.org/10.5194/gmd-14-2097-2021, 2021
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This study proposes a novel structural self-organizing map (S-SOM) algorithm. The superiority of S-SOM is that it can better recognize the difference (or similarity) among spatial (or temporal) data used for training and thus improve the clustering quality compared to traditional SOM algorithms.
Batunacun, Ralf Wieland, Tobia Lakes, and Claas Nendel
Geosci. Model Dev., 14, 1493–1510, https://doi.org/10.5194/gmd-14-1493-2021, https://doi.org/10.5194/gmd-14-1493-2021, 2021
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Extreme gradient boosting (XGBoost) can provide alternative insights that conventional land-use models are unable to generate. Shapley additive explanations (SHAP) can interpret the results of the purely data-driven approach. XGBoost achieved similar and robust simulation results. SHAP values were useful for analysing the complex relationship between the different drivers of grassland degradation.
Juan A. Añel, Michael García-Rodríguez, and Javier Rodeiro
Geosci. Model Dev., 14, 923–934, https://doi.org/10.5194/gmd-14-923-2021, https://doi.org/10.5194/gmd-14-923-2021, 2021
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This work shows that it continues to be hard, if not impossible, to obtain some of the most used climate models worldwide. We reach this conclusion through a systematic study and encourage all development teams and research centres to make public the models they use to produce scientific results.
Prabhat, Karthik Kashinath, Mayur Mudigonda, Sol Kim, Lukas Kapp-Schwoerer, Andre Graubner, Ege Karaismailoglu, Leo von Kleist, Thorsten Kurth, Annette Greiner, Ankur Mahesh, Kevin Yang, Colby Lewis, Jiayi Chen, Andrew Lou, Sathyavat Chandran, Ben Toms, Will Chapman, Katherine Dagon, Christine A. Shields, Travis O'Brien, Michael Wehner, and William Collins
Geosci. Model Dev., 14, 107–124, https://doi.org/10.5194/gmd-14-107-2021, https://doi.org/10.5194/gmd-14-107-2021, 2021
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Detecting extreme weather events is a crucial step in understanding how they change due to climate change. Deep learning (DL) is remarkable at pattern recognition; however, it works best only when labeled datasets are available. We create
ClimateNet– an expert-labeled curated dataset – to train a DL model for detecting weather events and predicting changes in extreme precipitation. This work paves the way for DL-based automated, high-fidelity, and highly precise analytics of climate data.
Xiang Que, Xiaogang Ma, Chao Ma, and Qiyu Chen
Geosci. Model Dev., 13, 6149–6164, https://doi.org/10.5194/gmd-13-6149-2020, https://doi.org/10.5194/gmd-13-6149-2020, 2020
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This paper presents a spatiotemporal weighted regression (STWR) model for exploring nonstationary spatiotemporal processes in nature and socioeconomics. A value change rate is introduced in the temporal kernel, which presents significant model fitting and accuracy in both simulated and real-world data. STWR fully incorporates observed data in the past and outperforms geographic temporal weighted regression (GTWR) and geographic weighted regression (GWR) models in several experiments.
Sheri Mickelson, Alice Bertini, Gary Strand, Kevin Paul, Eric Nienhouse, John Dennis, and Mariana Vertenstein
Geosci. Model Dev., 13, 5567–5581, https://doi.org/10.5194/gmd-13-5567-2020, https://doi.org/10.5194/gmd-13-5567-2020, 2020
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Every generation of MIP exercises introduces new layers of complexity and an exponential growth in the amount of data requested. CMIP6 required us to develop a new tool chain and forced us to change our methodologies. The new methods discussed in this paper provided us with an 18 times faster speedup over our existing methods. This allowed us to meet our deadlines and we were able to publish more than half a million data sets on the Earth System Grid Federation (ESGF) for the CMIP6 project.
Benjamin Campforts, Charles M. Shobe, Philippe Steer, Matthias Vanmaercke, Dimitri Lague, and Jean Braun
Geosci. Model Dev., 13, 3863–3886, https://doi.org/10.5194/gmd-13-3863-2020, https://doi.org/10.5194/gmd-13-3863-2020, 2020
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Landslides shape the Earth’s surface and are a dominant source of terrestrial sediment. Rivers, then, act as conveyor belts evacuating landslide-produced sediment. Understanding the interaction among rivers and landslides is important to predict the Earth’s surface response to past and future environmental changes and for mitigating natural hazards. We develop HyLands, a new numerical model that provides a toolbox to explore how landslides and rivers interact over several timescales.
Jorge Vicent, Jochem Verrelst, Neus Sabater, Luis Alonso, Juan Pablo Rivera-Caicedo, Luca Martino, Jordi Muñoz-Marí, and José Moreno
Geosci. Model Dev., 13, 1945–1957, https://doi.org/10.5194/gmd-13-1945-2020, https://doi.org/10.5194/gmd-13-1945-2020, 2020
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The modeling of light propagation through the atmosphere is key to process satellite images and to understand atmospheric processes. However, existing atmospheric models can be complex to use in practical applications. Here we aim at providing a new software tool to facilitate using advanced models and to generate large databases of simulated data. As a test case, we use this tool to analyze differences between several atmospheric models, showing the capabilities of this open-source tool.
Jiali Wang, Prasanna Balaprakash, and Rao Kotamarthi
Geosci. Model Dev., 12, 4261–4274, https://doi.org/10.5194/gmd-12-4261-2019, https://doi.org/10.5194/gmd-12-4261-2019, 2019
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Parameterizations are frequently used in models representing physical phenomena and are often the computationally expensive portions of the code. Using model output from simulations performed using a weather model, we train deep neural networks to provide an accurate alternative to a physics-based parameterization. We demonstrate that a domain-aware deep neural network can successfully simulate the entire diurnal cycle of the boundary layer physics and the results are transferable.
Gianandrea Mannarini and Lorenzo Carelli
Geosci. Model Dev., 12, 3449–3480, https://doi.org/10.5194/gmd-12-3449-2019, https://doi.org/10.5194/gmd-12-3449-2019, 2019
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The VISIR ship-routing model is updated in order to deal with ocean currents.
The optimal tracks we computed through VISIR in the Atlantic ocean show great seasonal and regional variability, following a variable influence of surface gravity waves and currents. We assess how these tracks contribute to voyage energy-efficiency gains through a standard indicator (EEOI) of the International Maritime Organization. Also, the new model features are validated against an exact analytical benchmark.
Grzegorz Muszynski, Karthik Kashinath, Vitaliy Kurlin, Michael Wehner, and Prabhat
Geosci. Model Dev., 12, 613–628, https://doi.org/10.5194/gmd-12-613-2019, https://doi.org/10.5194/gmd-12-613-2019, 2019
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We present the automated method for recognizing atmospheric rivers in climate data, i.e., climate model output and reanalysis product. The method is based on topological data analysis and machine learning, both of which are powerful tools that the climate science community often does not use. An advantage of the proposed method is that it is free of selection of subjective threshold conditions on a physical variable. This method is also suitable for rapidly analyzing large amounts of data.
Christina Papagiannopoulou, Diego G. Miralles, Matthias Demuzere, Niko E. C. Verhoest, and Willem Waegeman
Geosci. Model Dev., 11, 4139–4153, https://doi.org/10.5194/gmd-11-4139-2018, https://doi.org/10.5194/gmd-11-4139-2018, 2018
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Common global land cover and climate classifications are based on vegetation–climatic characteristics derived from observational data, ignoring the interaction between the local climate and biome. Here, we model the interplay between vegetation and local climate by discovering spatial relationships among different locations. The resulting global
hydro-climatic biomescorrespond to regions of coherent climate–vegetation interactions that agree well with traditional global land cover maps.
Wendy Sharples, Ilya Zhukov, Markus Geimer, Klaus Goergen, Sebastian Luehrs, Thomas Breuer, Bibi Naz, Ketan Kulkarni, Slavko Brdar, and Stefan Kollet
Geosci. Model Dev., 11, 2875–2895, https://doi.org/10.5194/gmd-11-2875-2018, https://doi.org/10.5194/gmd-11-2875-2018, 2018
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Next-generation geoscientific models are based on complex model implementations and workflows. Next-generation HPC systems require new programming paradigms and code optimization. In order to meet the challenge of running complex simulations on new massively parallel HPC systems, we developed a run control framework that facilitates code portability, code profiling, and provenance tracking to reduce both the duration and the cost of code migration and development, while ensuring reproducibility.
Daojun Zhang, Na Ren, and Xianhui Hou
Geosci. Model Dev., 11, 2525–2539, https://doi.org/10.5194/gmd-11-2525-2018, https://doi.org/10.5194/gmd-11-2525-2018, 2018
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Geographically weighted regression is a widely used method to deal with spatial heterogeneity, which is common in geostatistics. However, most existing software does not support logistic regression and cannot deal with missing data, which exist extensively in mineral prospectivity mapping. This work generalized logistic regression to spatial statistics based on a spatially weighted technique. The new model also supports an anisotropic local window, which is another innovative point.
Thomas Block, Sabine Embacher, Christopher J. Merchant, and Craig Donlon
Geosci. Model Dev., 11, 2419–2427, https://doi.org/10.5194/gmd-11-2419-2018, https://doi.org/10.5194/gmd-11-2419-2018, 2018
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For calibration and validation purposes it is necessary to detect simultaneous data acquisitions from different spaceborne platforms. We present an algorithm and a software system which implements a general approach to resolve this problem. The multisensor matchup system (MMS) can detect simultaneous acquisitions in a large dataset (> 100 TB) and extract data for matching locations for further analysis. The MMS implements a flexible software infrastructure and allows for high parallelization.
David Hassell, Jonathan Gregory, Jon Blower, Bryan N. Lawrence, and Karl E. Taylor
Geosci. Model Dev., 10, 4619–4646, https://doi.org/10.5194/gmd-10-4619-2017, https://doi.org/10.5194/gmd-10-4619-2017, 2017
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We present a formal data model for version 1.6 of the CF (Climate and Forecast) metadata conventions that provide a description of the physical meaning of geoscientific data and their spatial and temporal properties. We describe the CF conventions and how they lead to our CF data model, and compare it other data models for storing data and metadata. We present cf-python version 2.1: a software implementation of the CF data model capable of manipulating any CF-compliant dataset.
Cited articles
Baddeley, A., Rubak, E., and Turner, R.: Spatial point patterns: methodology and applications with R, CRC Press, ISBN 9781482210200, 2015. a
Behrens, T. and Viscarra Rossel, R. A.: On the interpretability of predictors in spatial data science: The information horizon, Sci. Rep.-UK, 10, 16737, https://doi.org/10.1038/s41598-020-73773-y, 2020. a, b
Breiman, L.: Random forests, Mach. Learn., 45, 5–32, 2001. a
Breiman, L.: Manual on setting up, using, and understanding random forests v3.1, Statistics Department University of California Berkeley, CA, USA, 1, 3–42, https://www.stat.berkeley.edu/~breiman/Using_random_forests_V3.1.pdf (last access: 24 April 2023), 2002. a
Cracknell, M. J. and Reading, A. M.: Geological mapping using remote sensing data: A comparison of five machine learning algorithms, their response to variations in the spatial distribution of training data and the use of explicit spatial information, Comput. Geosci., 63, 22–33, https://doi.org/10.1016/j.cageo.2013.10.008, 2014. a, b, c, d
de Bruin, S., Brus, D. J., Heuvelink, G. B., van Ebbenhorst Tengbergen, T., and Wadoux, A. M.-C.: Dealing with clustered samples for assessing map accuracy by cross-validation, Ecol. Inform., 69, 101665, https://doi.org/10.1016/j.ecoinf.2022.101665, 2022. a
de Hoogh, K., Chen, J., Gulliver, J., Hoffmann, B., Hertel, O., Ketzel, M., Bauwelinck, M., van Donkelaar, A., Hvidtfeldt, U. A., Katsouyanni, K., Klompmaker, J., Martin, R. V., Samoli, E., Schwartz, P. E., Stafoggia, M., Bellander, T., Strak, M., Wolf, K., Vienneau, D., Brunekreef, B., and Hoek, G.: Spatial PM2.5, NO2, O3 and BC models for Western Europe – Evaluation of spatiotemporal stability, Environ. Int., 120, 81–92, https://doi.org/10.1016/j.envint.2018.07.036, 2018. a, b
Dormann, C. F., McPherson, J. M., Araújo, M. B., Bivand, R., Bolliger, J., Carl, G., Davies, R. G., Hirzel, A., Jetz, W., Daniel Kissling, W., Kühn, I., Ohlemüller, R., Peres-Neto, P. R., Reineking, B., Schröder, B., Schurr, F. M., and Wilson, R.: Methods to account for spatial autocorrelation in the analysis of species distributional data: a review, Ecography, 30, 609–628, https://doi.org/10.1111/j.2007.0906-7590.05171.x, 2007. a
Fourcade, Y., Besnard, A. G., and Secondi, J.: Paintings predict the distribution of species, or the challenge of selecting environmental predictors and evaluation statistics, Global Ecol. Biogeogr., 27, 245–256, https://doi.org/10.1111/geb.12684, 2018. a
Gebbers, R. and de Bruin, S.: Application of Geostatistical Simulation in Precision Agriculture, Springer Netherlands, Dordrecht, 269–303, https://doi.org/10.1007/978-90-481-9133-8_11, 2010. a
Georganos, S., Grippa, T., Gadiaga, A. N., Linard, C., Lennert, M., Vanhuysse, S., Mboga, N., Wolff, E., and Kalogirou, S.: Geographical random forests: a spatial extension of the random forest algorithm to address spatial heterogeneity in remote sensing and population modelling, Geocarto Int., 36, 121–136, https://doi.org/10.1080/10106049.2019.1595177, 2021. a, b
Hajjem, A., Bellavance, F., and Larocque, D.: Mixed effects regression trees for clustered data, Stat. Probabil. Lett., 81, 451–459, https://doi.org/10.1016/j.spl.2010.12.003, 2011. a
Hajjem, A., Bellavance, F., and Larocque, D.: Mixed-effects random forest for clustered data, J. Stat. Comput. Sim., 84, 1313–1328, https://doi.org/10.1080/00949655.2012.741599, 2014. a
Hengl, T.: A practical guide to geostatistical mapping of environmental variables, Office for Official Publications of the European Communities, ISBN 978-92-79-06904-8, 2007. a
Heuvelink, G. B. and Webster, R.: Spatial statistics and soil mapping: A blossoming partnership under pressure, Spat. Stat.-Neth., 50, 100639, https://doi.org/10.1016/j.spasta.2022.100639, 2022. a
Hijmans, R. J.: terra: Spatial Data Analysis, r package version 1.6-47, https://CRAN.R-project.org/package=terra (last access: 1 February 2023), 2022. a
Kattenborn, T., Schiefer, F., Frey, J., Feilhauer, H., Mahecha, M. D., and Dormann, C. F.: Spatially autocorrelated training and validation samples inflate performance assessment of convolutional neural networks, ISPRS Open Journal of Photogrammetry and Remote Sensing, 5, 100018, https://doi.org/10.1016/j.ophoto.2022.100018, 2022. a
Kloog, I., Nordio, F., Lepeule, J., Padoan, A., Lee, M., Auffray, A., and Schwartz, J.: Modelling spatio-temporally resolved air temperature across the complex geo-climate area of France using satellite-derived land surface temperature data, Int. J. Climatol., 37, 296–304, https://doi.org/10.1002/joc.4705, 2017. a
Kuhn, M.: caret: Classification and Regression Training, r package version 6.0-93, https://CRAN.R-project.org/package=caret (last access: 1 February 2023), 2022. a
Kuhn, M. and Johnson, K.: Feature engineering and selection: A practical approach for predictive models, Chapman and Hall/CRC, ISBN 978-1032090856, 2019. a
Lary, D. J., Alavi, A. H., Gandomi, A. H., and Walker, A. L.: Machine learning in geosciences and remote sensing, Geosci. Front., 7, 3–10, https://doi.org/10.1016/j.gsf.2015.07.003, 2016. a
Le Rest, K., Pinaud, D., Monestiez, P., Chadoeuf, J., and Bretagnolle, V.: Spatial leave-one-out cross-validation for variable selection in the presence of spatial autocorrelation, Global Ecol. Biogeogr., 23, 811–820, https://doi.org/10.1111/geb.12161, 2014. a
Li, L., Girguis, M., Lurmann, F., Wu, J., Urman, R., Rappaport, E., Ritz, B., Franklin, M., Breton, C., Gilliland, F., and Habre, R.: Cluster-based bagging of constrained mixed-effects models for high spatiotemporal resolution nitrogen oxides prediction over large regions, Environ. Int., 128, 310–323, https://doi.org/10.1016/j.envint.2019.04.057, 2019. a
Longley, P.: Geographic information systems and science, John Wiley & Sons, ISBN 9781118676950, 2005. a
Ludwig, M., Moreno-Martinez, A., Hölzel, N., Pebesma, E., and Meyer, H.: Assessing and improving the transferability of current global spatial prediction models, Global Ecol. Biogeogr., 32, 356–368, https://doi.org/10.1111/geb.13635, 2023. a
Ma, H., Mo, L., Crowther, T. W., Maynard, D. S., van den Hoogen, J., Stocker, B. D., Terrer, C., and Zohner, C. M.: The global distribution and environmental drivers of aboveground versus belowground plant biomass, Nature Ecology & Evolution, 5, 1110–1122, 2021. a
Meyer, H. and Pebesma, E.: Machine learning-based global maps of ecological variables and the challenge of assessing them, Nat. Commun., 13, 2208, https://doi.org/10.1038/s41467-022-29838-9, 2022. a
Meyer, H., Milà, C., Ludwig, M., and Linnenbrink, J.: CAST: 'caret' Applications for Spatial-Temporal Models, https://github.com/HannaMeyer/CAST (last access: 8 May 2023), https://hannameyer.github.io/CAST/ (last access: 5 September 2023), 2023. a
Milà, C.: Code and data for “Random forests with spatial proxies for environmental modelling: opportunities and pitfalls”, Zenodo [code], https://doi.org/10.5281/zenodo.10495234, 2024. a
Milà, C., Mateu, J., Pebesma, E., and Meyer, H.: Nearest neighbour distance matching Leave-One-Out Cross-Validation for map validation, Methods Ecol. Evol., 13, 1304–1316, https://doi.org/10.1111/2041-210X.13851, 2022. a, b
Pebesma, E.: Simple Features for R: Standardized Support for Spatial Vector Data, R J., 10, 439–446, https://doi.org/10.32614/RJ-2018-009, 2018. a
Pebesma, E. J.: Multivariable geostatistics in S: the gstat package, Comput. Geosci., 30, 683–691, https://doi.org/10.1016/j.cageo.2004.03.012, 2004. a
Ploton, P., Mortier, F., Réjou-Méchain, M., Barbier, N., Picard, N., Rossi, V., Dormann, C., Cornu, G., Viennois, G., Bayol, N., Lyapustin, A., Gourlet-Fleury, S., and Pélissier, R.: Spatial validation reveals poor predictive performance of large-scale ecological mapping models, Nat. Commun., 11, 4540, https://doi.org/10.1038/s41467-020-18321-y, 2020. a
Poggio, L., de Sousa, L. M., Batjes, N. H., Heuvelink, G. B. M., Kempen, B., Ribeiro, E., and Rossiter, D.: SoilGrids 2.0: producing soil information for the globe with quantified spatial uncertainty, SOIL, 7, 217–240, https://doi.org/10.5194/soil-7-217-2021, 2021. a
R Core Team: R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, Austria, https://www.R-project.org/ (last access: 1 February 2023), 2022. a
Roberts, D. R., Bahn, V., Ciuti, S., Boyce, M. S., Elith, J., Guillera-Arroita, G., Hauenstein, S., Lahoz-Monfort, J. J., Schröder, B., Thuiller, W., Warton, D. I., Wintle, B. A., Hartig, F., and Dormann, C. F.: Cross-validation strategies for data with temporal, spatial, hierarchical, or phylogenetic structure, Ecography, 40, 913–929, 2017. a
Saha, A., Basu, S., and Datta, A.: RandomForestsGLS: Random Forests for Dependent Data, r package version 0.1.4, https://CRAN.R-project.org/package=RandomForestsGLS (last access: 8 May 2023), 2022. a
Sekulić, A., Kilibarda, M., Heuvelink, G. B., Nikolić, M., and Bajat, B.: Random Forest Spatial Interpolation, Remote Sens.-Basel, 12, 1687, https://doi.org/10.3390/rs12101687, 2020. a, b
Telford, R. and Birks, H.: Evaluation of transfer functions in spatially structured environments, Quaternary Sci. Rev., 28, 1309–1316, https://doi.org/10.1016/j.quascirev.2008.12.020, 2009. a
Tennekes, M.: tmap: Thematic Maps in R, J. Stat. Softw., 84, 1–39, https://doi.org/10.18637/jss.v084.i06, 2018. a
Valavi, R., Elith, J., Lahoz-Monfort, J. J., and Guillera-Arroita, G.: blockCV: An r package for generating spatially or environmentally separated folds for k-fold cross-validation of species distribution models, Methods Ecol. Evol., 10, 225–232, https://doi.org/10.1111/2041-210X.13107, 2019. a
Wadoux, A. M. J.-C., Brus, D. J., and Heuvelink, G. B.: Sampling design optimization for soil mapping with random forest, Geoderma, 355, 113913, https://doi.org/10.1016/j.geoderma.2019.113913, 2019. a
Wadoux, A. M. J.-C., Minasny, B., and McBratney, A. B.: Machine learning for digital soil mapping: Applications, challenges and suggested solutions, Earth-Sci. Rev., 210, 103359, https://doi.org/10.1016/j.earscirev.2020.103359, 2020a. a, b, c
Wadoux, A. M. J.-C., Samuel-Rosa, A., Poggio, L., and Mulder, V. L.: A note on knowledge discovery and machine learning in digital soil mapping, Eur. J. Soil Sci., 71, 133–136, https://doi.org/10.1111/ejss.12909, 2020b. a
Wadoux, A. M. J.-C., Heuvelink, G. B., de Bruin, S., and Brus, D. J.: Spatial cross-validation is not the right way to evaluate map accuracy, Ecol. Model., 457, 109692, https://doi.org/10.1016/j.ecolmodel.2021.109692, 2021. a, b, c
Walsh, E. S., Kreakie, B. J., Cantwell, M. G., and Nacci, D.: A Random Forest approach to predict the spatial distribution of sediment pollution in an estuarine system, PLOS ONE, 12, 1–18, https://doi.org/10.1371/journal.pone.0179473, 2017. a
Wang, Y., Wu, G., Deng, L., Tang, Z., Wang, K., Sun, W., and Shangguan, Z.: Prediction of aboveground grassland biomass on the Loess Plateau, China, using a random forest algorithm, Sci. Rep.-UK, 7, 6940, https://doi.org/10.1038/s41598-017-07197-6, 2017. a
Wang, Y., Khodadadzadeh, M., and Zurita-Milla, R.: Spatial+: A new cross-validation method to evaluate geospatial machine learning models, Int. J. Appl. Earth Obs., 121, 103364, https://doi.org/10.1016/j.jag.2023.103364, 2023. a
Wenger, S. J. and Olden, J. D.: Assessing transferability of ecological models: an underappreciated aspect of statistical validation, Methods Ecol. Evol., 3, 260–267, https://doi.org/10.1111/j.2041-210X.2011.00170.x, 2012. a
Wickham, H.: ggplot2: Elegant Graphics for Data Analysis, Springer-Verlag New York, https://ggplot2.tidyverse.org (last access: 1 February 2023), 2016. a
Wright, M. N. and Ziegler, A.: ranger: A Fast Implementation of Random Forests for High Dimensional Data in C++ and R, J. Stat. Softw., 77, 1–17, https://doi.org/10.18637/jss.v077.i01, 2017. a
Wylie, B. K., Pastick, N. J., Picotte, J. J., and Deering, C. A.: Geospatial data mining for digital raster mapping, GISci. Remote Sens., 56, 406–429, https://doi.org/10.1080/15481603.2018.1517445, 2019. a
Zhan, Y., Luo, Y., Deng, X., Chen, H., Grieneisen, M. L., Shen, X., Zhu, L., and Zhang, M.: Spatiotemporal prediction of continuous daily PM2.5 concentrations across China using a spatially explicit machine learning algorithm, Atmos. Environ., 155, 129–139, https://doi.org/10.1016/j.atmosenv.2017.02.023, 2017. a
Short summary
Spatial proxies, such as coordinates and distances, are often used as predictors in random forest models for predictive mapping. In a simulation and two case studies, we investigated the conditions under which their use is appropriate. We found that spatial proxies are not always beneficial and should not be used as a default approach without careful consideration. We also provide insights into the reasons behind their suitability, how to detect them, and potential alternatives.
Spatial proxies, such as coordinates and distances, are often used as predictors in random...
