Hidden Markov Models for Real-Time Estimation of Corn Progress Stages Using MODIS and Meteorological Data

Abstract: Real-time estimation of crop progress stages is critical to the US agricultural economy and decision making. In this paper, a Hidden Markov Model (HMM) based method combining multisource features has been presented. The multisource features include mean Normalized Difference Vegetation Index (NDVI), fractal dimension, and Accumulated Growing Degree Days (AGDDs). In our case, these features are global variable, and measured in the state-level. Moreover, global feature in each Day of Year (DOY) would be impacted by multiple progress stages. Therefore, a mixture model is employed to model the observation probability distribution with all possible stage components. Then, a filtering based algorithm is utilized to estimate the proportion of each progress stage in the real-time. Experiments are conducted in the states of Iowa, Illinois and Nebraska in the USA, and our results are assessed and validated by the Crop Progress Reports (CPRs) of the National Agricultural Statistics Service (NASS). Finally, a quantitative comparison and analysis between our method and spectral pixel-wise based methods is presented. The results demonstrate the feasibility of the proposed method for the estimation of corn progress stages. The proposed method could be used as aRemote Sens. 2013, 5 173

Utilizing Collocated Crop Growth Model Simulations to Train Agronomic Satellite Retrieval Algorithms

Due to its worldwide coverage and high revisit time, satellite-based remote sensing provides the ability to monitor in-season crop state variables and yields globally. In this study, we presented a novel approach to training agronomic satellite retrieval algorithms by utilizing collocated crop growth model simulations and solar-reflective satellite measurements. Specifically, we showed that bidirectional long short-term memory networks (BLSTMs) can be trained to predict the in-season state variables and yields of Agricultural Production Systems sIMulator (APSIM) maize crop growth model simulations from collocated Moderate Resolution Imaging Spectroradiometer (MODIS) 500-m satellite measurements over the United States Corn Belt at a regional scale. We evaluated the performance of the BLSTMs through both k-fold cross validation and comparison to regional scale ground-truth yields and phenology. Using k-fold cross validation, we showed that three distinct in-season maize state variables (leaf area index, aboveground biomass, and specific leaf area) can be retrieved with cross-validated R2 values ranging from 0.4 to 0.8 for significant portions of the season. Several other plant, soil, and phenological in-season state variables were also evaluated in the study for their retrievability via k-fold cross validation. In addition, by comparing to survey-based United State Department of Agriculture (USDA) ground truth data, we showed that the BLSTMs are able to predict actual county-level yields with R2 values between 0.45 and 0.6 and actual state-level phenological dates (emergence, silking, and maturity) with R2 values between 0.75 and 0.85. We believe that a potential application of this methodology is to develop satellite products to monitor in-season field-scale crop growth on a global scale by reproducing the methodology with field-scale crop growth model simulations (utilizing farmer recorded field-scale agromanagement data) and collocated high-resolution satellite data (fused with moderate-resolution satellite data)

Hidden Markov Models for Real-Time Estimation of Corn Progress Stages Using MODIS and Meteorological Data

Real-time estimation of crop progress stages is critical to the US agricultural economy and decision making. In this paper, a Hidden Markov Model (HMM) based method combining multisource features has been presented. The multisource features include mean Normalized Difference Vegetation Index (NDVI), fractal dimension, and Accumulated Growing Degree Days (AGDDs). In our case, these features are global variable, and measured in the state-level. Moreover, global feature in each Day of Year (DOY) would be impacted by multiple progress stages. Therefore, a mixture model is employed to model the observation probability distribution with all possible stage components. Then, a filtering based algorithm is utilized to estimate the proportion of each progress stage in the real-time. Experiments are conducted in the states of Iowa, Illinois and Nebraska in the USA, and our results are assessed and validated by the Crop Progress Reports (CPRs) of the National Agricultural Statistics Service (NASS). Finally, a quantitative comparison and analysis between our method and spectral pixel-wise based methods is presented. The results demonstrate the feasibility of the proposed method for the estimation of corn progress stages. The proposed method could be used as a supplementary tool in aid of field survey. Moreover, it also can be used to establish the progress stage estimation model for different types of crops

Use of geospatial techniques to improve bee farming and bee health across four main agroecological zones in Kenya.

Doctoral Degree. University of KwaZulu-Natal, Pietermaritzburg.Amid augmented climate change and anthropogenic influence on natural environments and agricultural systems, the global socioeconomic and environmental value of bees is undisputed. Bee products such as honey, pollen, nectar, royal jelly and to a lesser extent bee venom are important supplemental sources of income generation especially in the underdeveloped rural African areas. Moreover, bee farming is an important incentive for forest conservation, biodiversity and ecosystem services in terms of pollination services. Bee pollination services play a vital role in crop production, hence directly contribute to food and nutritional security for African smallholder farmers. Nevertheless, bee farming and bee health in general are under threat from climate change, agricultural intensification and associated habitat alteration, agrochemicals intensification, bee pests and diseases. Therefore, there is need to establish spatial distribution of bees, their food substrates, floral cycle and biotic and abiotic threats, especially bee pests. Bee pests devastate bee colonies through physical injury and as vectors of pathogens, hence causing a considerable reduction in bee colony productivity. Thus, this study sought to establish geospatial techniques that could be used to improve bee farming and bee health in Kenya. Firstly, this study aimed to determine the spatial and temporal distribution of stingless bees in Kenya using six machine learning ecological niche approaches and non-conflating variables from both bioclimatic, vegetation phenology and topographic features. All machine learning algorithms used herein performed at an ‘excellent’ level with a true skills statistics (TSS) score of up to 0.91. Secondly, the study assessed the suitability of resampled multispectral data for mapping melliferous (flowering plants that produce substance used by bees to produce honey) plants in Kenya. Bi-temporal AISA Eagle hyperspectral images, resampled to four sensors’ (i.e., WorldView-2, RapidEye, Spot- 6 and Sentinel-2) spatial and spectral resolutions, and a RF classifier were used to map melliferous plants. Melliferous plants were successfully mapped with up to 93.33% overall accuracy using WorldView-2. Furthermore, the study predicted the distribution of four main bee pests (Aethina tumida, Galleria mellonella, Oplostomus haroldi and Varroa destructor) in Kenya using the maximum entropy (MaxEnt) model and random forest (RF) classifier. The effect of seasonality on the abundance of bee pests was apparent, as indicated by the Wilcoxon rank sum test, with up to 6.35 times more pests in the wet than the dry season. Furthermore, bioclimatic variables especially precipitation contributed the most (up to 77.8%) to all bee pest predictions, while vegetation phenology provided vital information needed to sharpen the prediction models at grain level due to their higher spatial resolution and seasonal and phenological features. Moreover, topography had a moderate influence (14.3%) on the distribution of bee pests. Also, there was a positive correlation between bee pests’ abundance, habitat suitability and high altitude. Anthropogenic influence (as depicted by human footprint data) on the distribution of bee pests was relatively low (1.2%) due to the availability of a variety of bee food substrate from the mixed land use/land cover (LULC) classes, especially farmlands. Using the Pearson correlation coefficient, the prediction models for all bee pests scored at an excellent level (0.84), except for the G. mellonella prediction model, which was ranked ‘fair’ (0.55). Due to the relatively high accuracy for models developed herein to map stingless bees’ distribution, melliferous plants and bee pests’ occurrence and abundance, this study concluded that the models developed could reliably be used to indicate high suitability areas for bee farming. They could also be used to predict high bee pests risk areas for mitigation and management purposes, hence improving bee health and hive productivity

ANALYSIS OF AGRO-ECOSYSTEMS EXPLOITING OPTICAL SATELLITE DATA TIME SERIES: THE CASE STUDY OF CAMARGUE REGION, FRANCE

The research activities presented in this manuscript were conducted in the frame of the international project SCENARICE, whose aim is to demonstrate the contribution of different technical and scientific competences, to assess current characteristics of analyzed cropping systems and to define sustainable future agricultural scenarios. Dynamic simulation crop models are used to evaluate the efficiency of current cropping systems and to predict their performances as consequence of climate change scenarios. In this context, a lack of information regarding the intra- and inter-annual variability of crop practices was highlighted for crops such as winter wheat, for the study area of Camargue. Moreover, a description of possible future cropping systems adaptation strategies was needed to formulate short term scenario farming system assessment. To perform this analysis it is fundamental to identify the different farm typologies representing the study area. Since it was required to take into account inter-annual variability of crop practices and farm diversities to build farm typologies, representative data of the study region in both time and space were needed. To address this issue, in this work long term time series of satellite data (2003-2013) were exploited with the specific aims to: (i) provide winter wheat sowing dates estimations variability on a long term period (11 years) to contribute in base line scenario definition and (ii) reconstruct farms land use changes through the analysis of time series of satellite data to provide helpful information for farm typologies definition. Two main research activities were carried out to address the defined objectives. Firstly a rule-based methodology was developed to automatically identify winter wheat cultivated areas in order to retrieve crop sowing occurrences in the satellite time series. Detection criteria were derived on the basis of agronomic expert knowledge and by interpretation of high confidence temporal signature. The distinction of winter wheat from other crops was based on the individuation of the crop heading and establishment periods and considering the length of the crop cycle. The detection of winter wheat cultivated areas showed that 56% of the target in the study area was correctly detected with low commissions (11%). Once winter wheat area was detected, additional rules were designed to identify sowing dates. The method was able to capture the seasonal variability of sowing dates with errors of \ub18 and \ub116 days in 45% and 65% of cases respectively. Extending the analysis to the 11 years period it was observed that in Camargue the most frequent sowing period was about October 31th (\ub14 days of uncertainty). The 2004 and 2006 seasons showed early sowings (late September) the 2003 and 2008 seasons were slightly delayed at the beginning of November. Sowing dates were not correlated to the seasonal rainfall events; this led us to formulate the hypothesis that sowing dates could be much more influenced by the harvest date of the preceding crop and soil moisture, which are related to rains but also to the date of last irrigations and to the wind. The second activity was related to define farm typologies. Temporal trajectories of winter and summer crops cultivated areas were estimated at farm scale level based on satellite data time series in the 2003-2013 periods. The validation demonstrated that the method was able to produce maps with high overall accuracy (OA 92%) and very low commission errors (3% for summer crops and 7% for winter crops). Omission errors were very low for summer crops (3%) and higher but within an acceptable level for winter crops (31%). Temporal trajectories of annual winter and summer crop land use at farm level were assumed as indicators of farm management (e.g. intensive monoculture farm or diversified crop producer). Trajectories were analysed through a hierarchical clustering procedure to identify farm management typologies. We were able to identify six typologies out of 140 farm samples, covering 75% of the arable land in the study area. A semantic interpretation of the farm types, allowed formulating hypothesis to describe farming systems. The size of the farms seemed to be an explanatory variable of the intensive or extensive farm management. The two main activities presented in this thesis highlighted the importance of time series spatial and temporal resolution for crop monitoring purposes. Currently, only heterogeneous remotely sensed data in terms of spatial and temporal resolutions are available for agricultural monitoring. Forthcoming sensors (i.e. ESA Sentinel-II A/B) will offer the chance to exploit coexisting high spatial and temporal resolutions for the first time. A preliminary application of an innovative methodology for the fusion of heterogeneous spatio-temporal resolution remotely sensed datasets was provided in the final section of the thesis with the aim to (i) produce high spatio-temporal resolution time series and (ii) verify the quality and the usefulness of the generated time series for monitoring the main European cultivated crops. The experiment positively demonstrated the contribution of data fusion techniques for the production of time series at high space-time resolution for crop monitoring purposes. The application of data fusion techniques in the main methodologies presented in this work appears to be beneficial. To conclude this thesis framework, satellite remotely sensed data properly analyzed has shown to be a reliable tool to study large-scale crop cultivations and to retrieve spatially and temporally distributed information of cropping systems. Remote sensing time series analyses lead to highlight patterns of intra- and inter-annual dynamics of agro-practices and were also useful to define farm typologies based on multi-temporal land use trajectories. Results contribute in enriching the studies and the characterization of the Camargue study area, in particular providing information such as sowing dates that are not available at present for the considered study area and represent a step forward in respect to the actual (static) available crop calendar informations. Moreover, the achieved results provide supplementary information layers for summarize and classify the diversity of the farm in the study area and to characterize farming systems

Improving Retrievals of Crop Vegetation Parameters from Remote Sensing Data

Agricultural systems are difficult to model because crop growth is driven by the strongly nonlinear interaction of Genotype x Environment x Management (G x E x M) factors. Due to the nonlinearity in the interaction of these factors, the amount of data necessary to develop and utilize models to accurately predict the performance of agricultural systems at an operational scale is large. Satellite remote sensing provides the potential to vastly increase the amount of data available for modelling agricultural systems as a result of its high revisit time and spatial coverage. Unfortunately, there have been significant difficulties in deploying remote sensing for many agricultural modelling applications because of the uncertainty involved in the retrievals. In this dissertation, we show that collecting farmer-provided agro-managment information has the potential to reduce the uncertainty in the retrieval products obtained from remote sensing observations. Specifically, both field-scale and regional-scale analysis are used to show that secondary factor variability is a very significant cause of uncertainty in both crop growth modelling and agricultural remote sensing that needs to be addressed through increased data collection. In order to address this need for increased data availability, a method is developed that allows geolocated crop growth model simulations to be used to train satellite-based crop state variable retrievals, which is then validated at regional scale. The method developed provides a general robust methodology to create a large-scale platform that would allow farmers to share data with government agencies and universities to improve crop state variable retrievals and crop growth modelling and provide farmers, government, industry, and researchers with insights and predictive capability into crop growth at both field and regional scales