Crop modeling for assessing and mitigating the impacts of extreme climatic events on the US agriculture system

The US agriculture system is the world’s largest producer of maize and soybean, and typically supplies more than one-third of their global trading. Nearly 90% of the US maize and soybean production is rainfed, thus is susceptible to climate change stressors such as heat waves and droughts. Process-based crop and cropping system models are important tools for climate change impact assessments and risk management. As data- science is becoming a new frontier for agriculture growth, the incoming decade calls for operational platforms that use hyper-local growth monitoring, high-resolution real-time weather and satellite data assimilation and cropping system modeling to help stakeholders predict crop yields and make decisions at various spatial scales. The fundamental question addressed by this dissertation is: How crop and cropping system models can be “useful” to the agriculture production, given the recent advent of cloud computing and earth observatory power? This dissertation consists of four main chapters. It starts with a study that reviews the algorithms of simulating heat and drought stress on maize in 16 major crop models, and evaluates algorithm performances by incorporating these algorithms into the Agricultural Production Systems sIMulator (APSIM) and running an ensemble of simulations at typical farms from the US Midwest. Results show that current parameterizations in most models favor the use of daylight temperature even though the algorithm was designed for using daily mean temperature. Different drought algorithms considerably differed in their patterns of water shortage over the growing season, but nonetheless predicted similar decreases in annual yield. In the next chapter of climate change assessment study, I quantify the current and future yield responses of US rainfed maize and soybean to climate extremes with and without considering the effect of elevated atmospheric CO2concentrations, and for the first time characterizes spatial shifts in the relative importance of temperature, heat and drought stresses. Model simulations demonstrate that drought will continue to be the largest threat to rainfed maize and soybean production, yet shifts in the spatial pattern of dominant stressors are characterized by increases in the concurrent stress, indicating future adaptation strategies will have trade-offs between multiple objectives. Following this chapter, I presented a chapter that uses billion-scale simulations to identify the optimal combination of Genotype × Environment × Management for the purpose of minimizing the negative impact of climate extremes on the rainfed maize yield. Finally, I present a prototype of crop model and satellite imagery based within-field scale N sidedress prescription tool for the US rainfed maize system. As an early attempt to integrate advances in multiple areas for precision agriculture, this tool successfully captures the subfield variability of N dynamics and gives reasonable spatially explicit sidedress N recommendations. The prescription enhances zones with high yield potentials, while prevents over-fertilization at zones with low yield potentials

Iterative Training Sample Expansion to Increase and Balance the Accuracy of Land Classification from VHR Imagery

© 1980-2012 IEEE. Imbalanced training sets are known to produce suboptimal maps for supervised classification. Therefore, one challenge in mapping land cover is acquiring training data that will allow classification with high overall accuracy (OA) in which each class is also mapped onto similar user's accuracy. To solve this problem, we integrated local adaptive region and box-and-whisker plot (BP) techniques into an iterative algorithm to expand the size of the training sample for selected classes in this article. The major steps of the proposed algorithm are as follows. First, a very small initial training sample (ITS) for each class set is labeled manually. Second, potential new training samples are found within an adaptive region by conducting local spectral variation analysis. Lastly, three new training samples are acquired to capture information regarding intraclass variation; these samples lie in the lower, median, and upper quartiles of BP. After adding these new training samples to the ITS, classification is retrained and the process is continued iteratively until termination. The proposed approach was applied to three very high-resolution (VHR) remote-sensing images and compared with a set of cognate methods. The comparison demonstrated that the proposed approach produced the best result in terms of OA and exhibited superiority in balancing user's accuracy. For example, the proposed approach was typically 2%-10% more accurate than the compared methods in terms of OA and it generally yielded the most balanced classification

Mapping smallholder cashew plantations to inform sustainable tree crop expansion in Benin

Cashews are grown by over 3 million smallholders in more than 40 countries worldwide as a principal source of income. As the third largest cashew producer in Africa, Benin has nearly 200,000 smallholder cashew growers contributing 15% of the country's national export earnings. However, a lack of information on where and how cashew trees grow across the country hinders decision-making that could support increased cashew production and poverty alleviation. By leveraging 2.4-m Planet Basemaps and 0.5-m aerial imagery, newly developed deep learning algorithms, and large-scale ground truth datasets, we successfully produced the first national map of cashew in Benin and characterized the expansion of cashew plantations between 2015 and 2021. In particular, we developed a SpatioTemporal Classification with Attention (STCA) model to map the distribution of cashew plantations, which can fully capture texture information from discriminative time steps during a growing season. We further developed a Clustering Augmented Self-supervised Temporal Classification (CASTC) model to distinguish high-density versus low-density cashew plantations by automatic feature extraction and optimized clustering. Results show that the STCA model has an overall accuracy over 85% and the CASTC model achieved an overall accuracy of 76%. We found that the cashew area in Benin almost doubled from 2015 to 2021 with 60% of new plantation development coming from cropland or fallow land, while encroachment of cashew plantations into protected areas has increased by 55%. Only half of cashew plantations were high-density in 2021, suggesting high potential for intensification. Our study illustrates the power of combining high-resolution remote sensing imagery and state-of-the-art deep learning algorithms to better understand tree crops in the heterogeneous smallholder landscape

From cropland to cropped field: A robust algorithm for national-scale mapping by fusing time series of Sentinel-1 and Sentinel-2

Detailed and updated maps of actively cropped fields on a national scale are vital for global food security. Unfortunately, this information is not provided in existing land cover datasets, especially lacking in smallholder farmer systems. Mapping national-scale cropped fields remains challenging due to the spectral confusion with abandoned vegetated land, and their high heterogeneity over large areas. This study proposed a large-area mapping framework for automatically identifying actively cropped fields by fusing Vegetation-Soil-Pigment indices and Synthetic-aperture radar (SAR) time-series images (VSPS). Three temporal indicators were proposed and highlighted cropped fields by consistently higher values due to cropping activities. The proposed VSPS algorithm was exploited for national-scale mapping in China without regional adjustments using Sentinel-2 and Sentinel-1 images. Agriculture in China illustrated great heterogeneity and has experienced tremendous changes such as non-grain orientation and cropland abandonment. Yet, little is known about the locations and extents of cropped fields cultivated with field crops on a national scale. Here, we produced the first national-scale 20 m updated map of cropped and fallow/abandoned land in China and found that 77 % of national cropland (151.23 million hectares) was actively cropped in 2020. We found that fallow/abandoned cropland in mountainous and hilly regions were far more than we expected, which was significantly underestimated by the commonly applied VImax-based approach based on the MODIS images. The VSPS method illustrates robust generalization capabilities, which obtained an overall accuracy of 94 % based on 4,934 widely spread reference sites. The proposed mapping framework is capable of detecting cropped fields with a full consideration of a high diversity of cropping systems and complexity of fallow/abandoned cropland. The processing codes on Google Earth Engine were provided and hoped to stimulate operational agricultural mapping on cropped fields with finer resolution from the national to the global scale

The role of topography, soil, and remotely sensed vegetation condition towards predicting crop yield

Foreknowledge of the spatiotemporal drivers of crop yield would provide a valuable source of information to optimize on-farm inputs and maximize profitability. In recent years, an abundance of spatial data providing information on soils, topography, and vegetation condition have become available from both proximal and remote sensing platforms. Given the wide range of data costs (between USD $0−50/ha), it is important to understand where often limited financial resources should be directed to optimize field production. Two key questions arise. First, will these data actually aid in better fine-resolution yield prediction to help optimize crop management and farm economics? Second, what level of priority should stakeholders commit to in order to obtain these data? Before fully addressing these questions a remaining challenge is the complex nature of spatiotemporal yield variation. Here, a methodological framework is presented to separate the spatial and temporal components of crop yield variation at the subfield level. The framework can also be used to quantify the benefits of different data types on the predicted crop yield as well to better understand the connection of that data to underlying mechanisms controlling yield. Here, fine-resolution (10 m) datasets were assembled for eight 64 ha field sites, spanning a range of climatic, topographic, and soil conditions across Nebraska. Using Empirical Orthogonal Function (EOF) analysis, we found the first axis of variation contained 60–85 % of the explained variance from any particular field, thus greatly reducing the dimensionality of the problem. Using Multiple Linear Regression (MLR) and Random Forest (RF) approaches, we quantified that location within the field had the largest relative importance for modeling crop yield patterns. Secondary factors included a combination of vegetation condition, soil water content, and topography. With respect to predicting spatiotemporal crop yield patterns, we found the RF approach (prediction RMSE of 0.2−0.4 Mg/ha for maize) was superior to MLR (0.3−0.8 Mg/ha). While not directly comparable to MLR and RF the EOF approach had relatively low error (0.5–1.7 Mg/ha) and is intriguing as it requires few calibration parameters (2–6 used here) and utilizes the climate-based aridity index, allowing for pragmatic long-term predictions of subfield crop yield

Causality guided machine learning model on wetland CH4 emissions across global wetlands

Wetland CH4 emissions are among the most uncertain components of the global CH4 budget. The complex nature of wetland CH4 processes makes it challenging to identify causal relationships for improving our understanding and predictability of CH4 emissions. In this study, we used the flux measurements of CH4 from eddy covariance towers (30 sites from 4 wetlands types: bog, fen, marsh, and wet tundra) to construct a causality-constrained machine learning (ML) framework to explain the regulative factors and to capture CH4 emissions at sub -seasonal scale. We found that soil temperature is the dominant factor for CH4 emissions in all studied wetland types. Ecosystem respiration (CO2) and gross primary productivity exert controls at bog, fen, and marsh sites with lagged responses of days to weeks. Integrating these asynchronous environmental and biological causal relationships in predictive models significantly improved model performance. More importantly, modeled CH4 emissions differed by up to a factor of 4 under a +1C warming scenario when causality constraints were considered. These results highlight the significant role of causality in modeling wetland CH(4 )emissions especially under future warming conditions, while traditional data-driven ML models may reproduce observations for the wrong reasons. Our proposed causality-guided model could benefit predictive modeling, large-scale upscaling, data gap-filling, and surrogate modeling of wetland CH4 emissions within earth system land models

Causality guided machine learning model on wetland CH4 emissions across global wetlands

Wetland CH4 emissions are among the most uncertain components of the global CH4 budget. The complex nature of wetland CH4 processes makes it challenging to identify causal relationships for improving our understanding and predictability of CH4 emissions. In this study, we used the flux measurements of CH4 from eddy covariance towers (30 sites from 4 wetlands types: bog, fen, marsh, and wet tundra) to construct a causality-constrained machine learning (ML) framework to explain the regulative factors and to capture CH4 emissions at sub -seasonal scale. We found that soil temperature is the dominant factor for CH4 emissions in all studied wetland types. Ecosystem respiration (CO2) and gross primary productivity exert controls at bog, fen, and marsh sites with lagged responses of days to weeks. Integrating these asynchronous environmental and biological causal relationships in predictive models significantly improved model performance. More importantly, modeled CH4 emissions differed by up to a factor of 4 under a +1C warming scenario when causality constraints were considered. These results highlight the significant role of causality in modeling wetland CH(4 )emissions especially under future warming conditions, while traditional data-driven ML models may reproduce observations for the wrong reasons. Our proposed causality-guided model could benefit predictive modeling, large-scale upscaling, data gap-filling, and surrogate modeling of wetland CH4 emissions within earth system land models.Peer reviewe

Causality guided machine learning model on wetland CH4 emissions across global wetlands

Wetland CH4 emissions are among the most uncertain components of the global CH4 budget. The complex nature of wetland CH4 processes makes it challenging to identify causal relationships for improving our understanding and predictability of CH4 emissions. In this study, we used the flux measurements of CH4 from eddy covariance towers (30 sites from 4 wetlands types: bog, fen, marsh, and wet tundra) to construct a causality-constrained machine learning (ML) framework to explain the regulative factors and to capture CH4 emissions at sub -seasonal scale. We found that soil temperature is the dominant factor for CH4 emissions in all studied wetland types. Ecosystem respiration (CO2) and gross primary productivity exert controls at bog, fen, and marsh sites with lagged responses of days to weeks. Integrating these asynchronous environmental and biological causal relationships in predictive models significantly improved model performance. More importantly, modeled CH4 emissions differed by up to a factor of 4 under a +1C warming scenario when causality constraints were considered. These results highlight the significant role of causality in modeling wetland CH(4 )emissions especially under future warming conditions, while traditional data-driven ML models may reproduce observations for the wrong reasons. Our proposed causality-guided model could benefit predictive modeling, large-scale upscaling, data gap-filling, and surrogate modeling of wetland CH4 emissions within earth system land models.Peer reviewe