Effectiveness of spatial analysis in Cryptomeria japonica D. Don (sugi) forward selection revealed by validation using progeny and clonal tests

International audienceAbstractKey messageAccurate evaluation of genetic performances of trees is crucial in order to improve the efficiency of forest tree breeding. We revealed that spatial analysis is effective for predicting individual tree breeding values at the forward selection stage ofCryptomeria japonicaD. Don (sugi) breeding program by using a novel validation approach.ContextIn the process of selecting genetically superior trees for breeding, appropriate handling of environmental effects is important in order to precisely evaluate candidate trees. Spatial analysis has been an effective statistical approach for genetic evaluation at sites with heterogeneous microenvironments. However, the efficiency of spatial analysis on forward selection has not been validated on a practical scale to date.AimsThis study aimed to reveal the effectiveness of spatial analysis, which incorporates spatially autocorrelated residuals into mixed models, for the prediction of breeding values at the forward selection stage by validation using progeny or clonal tests of forward-selected individuals.MethodsTree height was analyzed by ordinary randomized complete block design models and spatial models incorporating spatially autocorrelated residuals in a linear mixed model framework, and model selection was conducted at thirty Cryptomeria japonica D. Don breeding population sites having various topographical ruggedness. For validation, three clonal tests and one progeny test of individuals selected from three and four breeding populations, respectively, were used. The effectiveness of forward selection using the two models was evaluated based on the correlation between individual breeding values at the stage of forward selection and genotypic and breeding values that were estimated by clonal and progeny tests.ResultsSpatial models were more predictive than ordinary models in all cases. Spatial correlation parameters tend to increase with the topographical ruggedness index of each site. The correlation coefficients between breeding values at the time of forward selection and genotypic or breeding values evaluated in succeeding clonal and progeny tests were significantly higher in spatial models than in ordinary models in six out of nine cases.ConclusionValidation using progeny and clonal tests of forward-selected individual trees revealed that spatial analysis is more effective for the evaluation of genetic performance of individuals at the stage of forward selection in Cryptomeria japonica

The use of distributed hydrological models for the Gard 2002 flash flood event: Analysis of associated hydrological processes

Summary This paper presents a detailed analysis of the September 8-9, 2002 flash flood event in the Gard region (southern France) using two distributed hydrological models: CVN built within the LIQUID® hydrological platform and MARINE. The models differ in terms of spatial discretization, infiltration and water redistribution representation, and river flow transfer. MARINE can also account for subsurface lateral flow. Both models are set up using the same available information, namely a DEM and a pedology map. They are forced with high resolution radar rainfall data over a set of 18 sub-catchments ranging from 2.5 to 99 km2 and are run without calibration. To begin with, models simulations are assessed against post field estimates of the time of peak and the maximum peak discharge showing a fair agreement for both models. The results are then discussed in terms of flow dynamics, runoff coefficients and soil saturation dynamics. The contribution of the subsurface lateral flow is also quantified using the MARINE model. This analysis highlights that rainfall remains the first controlling factor of flash flood dynamics. High rainfall peak intensities are very influential of the maximum peak discharge for both models, but especially for the CVN model which has a simplified overland flow transfer. The river bed roughness also influences the peak intensity and time. Soil spatial representation is shown to have a significant role on runoff coefficients and on the spatial variability of saturation dynamics. Simulated soil saturation is found to be strongly related with soil depth and initial storage deficit maps, due to a full saturation of most of the area at the end of the event. When activated, the signature of subsurface lateral flow is also visible in the spatial patterns of soil saturation with higher values concentrating along the river network. However, the data currently available do not allow the assessment of both patterns. The paper concludes with a set of recommendations for enhancing field observations in order to progress in process understanding and gather a larger set of data to improve the realism of distributed models

Predicting spatiotemporal yield variability to aid arable precision agriculture in New Zealand : a case study of maize-grain crop production in the Waikato region : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Agriculture and Horticulture at Massey University, Palmerston North, New Zealand

Precision agriculture attempts to manage within-field spatial variability by applying suitable inputs at the appropriate time, place, and amount. To achieve this, delineation of field-specific management zones (MZs), representing significantly different yield potentials are required. To date, the effectiveness of utilising MZs in New Zealand has potentially been limited due to a lack of emphasis on the interactions between spatiotemporal factors such as soil texture, crop yield, and rainfall. To fill this research gap, this thesis aims to improve the process of delineating MZs by modelling spatiotemporal interactions between spatial crop yield and other complementary factors. Data was collected from five non-irrigated field sites in the Waikato region, based on the availability of several years of maize harvest data. To remove potential yield measurement errors and improve the accuracy of spatial interpolation for yield mapping, a customised filtering algorithm was developed. A supervised machine-learning approach for predicting spatial yield was then developed using several prediction models (stepwise multiple linear regression, feedforward neural network, CART decision tree, random forest, Cubist regression, and XGBoost). To provide insights into managing spatiotemporal yield variability, predictor importance analysis was conducted to identify important yield predictors. The spatial filtering method reduced the root mean squared errors of kriging interpolation for all available years (2014, 2015, 2017 and 2018) in a tested site, suggesting that the method developed in R programme was effective for improving the accuracy of the yield maps. For predicting spatial yield, random forest produced the highest prediction accuracies (R² = 0.08 - 0.50), followed by XGBoost (R² = 0.06 - 0.39). Temporal variables (solar radiation, growing degree days (GDD) and rainfall) were proven to be salient yield predictors. This research demonstrates the viability of these models to predict subfield spatial yield, using input data that is inexpensive and readily available to arable farms in New Zealand. The novel approach employed by this thesis may provide opportunities to improve arable farming input-use efficiency and reduce its environmental impact

The effects of CO2, climate and land-use on terrestrial carbon balance, 1920-1992: An analysis with four process-based ecosystem models

The concurrent effects of increasing atmospheric CO2 concentration, climate variability, and cropland establishment and abandonment on terrestrial carbon storage between 1920 and 1992 were assessed using a standard simulation protocol with four process-based terrestrial biosphere models. Over the long-term(1920–1992), the simulations yielded a time history of terrestrial uptake that is consistent (within the uncertainty) with a long-term analysis based on ice core and atmospheric CO2 data. Up to 1958, three of four analyses indicated a net release of carbon from terrestrial ecosystems to the atmosphere caused by cropland establishment. After 1958, all analyses indicate a net uptake of carbon by terrestrial ecosystems, primarily because of the physiological effects of rapidly rising atmospheric CO2. During the 1980s the simulations indicate that terrestrial ecosystems stored between 0.3 and 1.5 Pg C yr−1, which is within the uncertainty of analysis based on CO2 and O2 budgets. Three of the four models indicated (in accordance with O2 evidence) that the tropics were approximately neutral while a net sink existed in ecosystems north of the tropics. Although all of the models agree that the long-term effect of climate on carbon storage has been small relative to the effects of increasing atmospheric CO2 and land use, the models disagree as to whether climate variability and change in the twentieth century has promoted carbon storage or release. Simulated interannual variability from 1958 generally reproduced the El Niño/Southern Oscillation (ENSO)-scale variability in the atmospheric CO2 increase, but there were substantial differences in the magnitude of interannual variability simulated by the models. The analysis of the ability of the models to simulate the changing amplitude of the seasonal cycle of atmospheric CO2 suggested that the observed trend may be a consequence of CO2 effects, climate variability, land use changes, or a combination of these effects. The next steps for improving the process-based simulation of historical terrestrial carbon include (1) the transfer of insight gained from stand-level process studies to improve the sensitivity of simulated carbon storage responses to changes in CO2 and climate, (2) improvements in the data sets used to drive the models so that they incorporate the timing, extent, and types of major disturbances, (3) the enhancement of the models so that they consider major crop types and management schemes, (4) development of data sets that identify the spatial extent of major crop types and management schemes through time, and (5) the consideration of the effects of anthropogenic nitrogen deposition. The evaluation of the performance of the models in the context of a more complete consideration of the factors influencing historical terrestrial carbon dynamics is important for reducing uncertainties in representing the role of terrestrial ecosystems in future projections of the Earth system

Dynamic attention priors: a new and efficient concept for improving object detection

Recent psychophysical evidence in humans suggests that visual attention is a highly dynamic and predictive process involving precise models of object trajectories. We present a proof-of-concept that such predictive spatial attention can benefit a technical system solving a challenging visual object detection task. To this end, we introduce a Bayes-like integration of the so-called dynamic attention priors (DAPs) and dense detection likelihoods, which get enhanced at predicted object positions obtained by the extrapolation of trajectories. Using annotated video sequences of pedestrians in a parking lot setting, we quantitatively show that DAPs can improve detection performance significantly as compared to a baseline condition relying purely on pattern analysis

Landslide riskscapes in the Colorado Front Range: a quantitative geospatial approach for modeling human-environment interactions

2021 Spring.Includes bibliographical references.This research investigated the application of riskscapes to landslides in the context of geospatial inquiry. Riskscapes are framed as a landscape of risk to represent risk spatially. Geospatial models for landslide riskscapes were developed to improve our understanding of the spatial context for landslides and their risks as part of the system of human-environment interactions. Spatial analysis using Geographic Information Systems (GIS) leveraged modeling methods and the distributed properties of riskscapes to identify and preserve these spatial relationships. This dissertation is comprised of four separate manuscripts. These projects defined riskscapes in the context of landslides, applied geospatial analyses to create a novel riskscape model to introduce spatial autocorrelation methods to the riskscape framework, compared geostatistical analysis methods in these landslide riskscape assessments, and described limitations of spatial science identified in the riskscape development process. The first project addressed the current literature for riskscapes and introduced landslides as a measurable feature for riskscapes. Riskscapes are founded in social constructivist theory and landslide studies are frequently based on quantitative risk assessment practices. The uniqueness of a riskscape is the inclusion of human geography and environmental factors, which are not consistently incorporated in geologic or natural hazard studies. I proposed the addition of spatial theory constructs and methods to create spatially measurable products. I developed a conceptual framework for a landslide riskscape by describing the current riskscape applications as compared to existing landslide and GIS risk model processes. A spatial modeling formula to create a weighted sum landslide riskscape was presented as a modification to a natural hazard risk equation to incorporate the spatial dimension of risk factors. The second project created a novel method for three geospatial riskscapes as an approach to model landslide susceptibility areas in Boulder and Larimer Counties, Colorado. This study synthesized physical and human geography to create multiple landslide riskscape models using GIS methods. These analysis methods used a process model interface in GIS. Binary, ranked, and human factor weighted sum riskscapes were created, using frequency ratio as the basis for developing a weighting scheme. Further, spatial autocorrelation was introduced as a recommended practice to quantify the spatial relationships in landslide riskscape development. Results demonstrated that riskscapes, particularly those for ranked and human factor riskscapes, were highly autocorrelated, non-random, and exhibited clustering. These findings indicated that a riskscape model can support improvements to response modeling, based on the identification of spatially significant clustering of hazardous areas. The third project extended landslide riskscapes to measurable geostatistical comparisons using geostatistical tools within a GIS platform. Logistic regression, weights of evidence, and probabilistic neural networks methods were used to analyze the weighted sum landslide riskscape models using ArcGIS and Spatial Data Modeler (ArcSDM). Results showed weights of evidence models performed better than both logistic regression and neural networks methods. Receiver Operator Characteristic (ROC) curves and Area Under the Curve validation tests were performed and found the weights of evidence model performed best in both posterior probability prediction and AUC validation. A fourth project was developed based on the limitations discovered during the analytical process evaluations from the riskscape model development and geostatistical analysis. This project reviewed the issues with data quality, the variations in results predicated on the input parameters within the analytical toolsets, and the issues surrounding open-source application tools. These limitations stress the importance of parameter selection in a geospatial analytical environment. These projects collectively determined methods for riskscape development related to landslide features. The models presented demonstrate the importance and influence of spatial distributions on landslide riskscapes. Based on the proposed conceptual framework of a spatial riskscape for landslides, weighted sum riskscapes can provide a basis for prioritization of resources for landslides. Ranked and human factor riskscapes indicate the need to provide planning and protection for areas at increased risk for landslides. These studies provide a context for riskscapes to further our understanding of the benefits and limitations of a quantitative riskscape approach. The development of a methodological framework for quantitative riskscape models provides an approach that can be applied to other hazards or study areas to identify areas of increased human-environment interaction. Riskscape models can then be evaluated to inform mitigation and land-use planning activities to reduce impacts of natural hazards in the anthropogenic environment

Data assimilation of in situ soil moisture measurements in hydrological models: first annual doctoral progress report, work plan and achievements

Water scarcity and the presence of water of good quality is a serious public concern since it determines the availability of water to society. Water scarcity especially in arid climates and due to extreme droughts related to climate change drive water use technologies such as irrigation to become more efficient and sustainable. Plant root water and nutrient uptake is one of the most important processes in subsurface unsaturated flow and transport modeling, as root uptake controls actual plant evapotranspiration, water recharge and nutrient leaching to the groundwater, and exerts a major influence on predictions of global climate models. To improve irrigation strategies, water flow needs to be accurately described using advanced monitoring and modeling. Our study focuses on the assimilation of hydrological data in hydrological models that predict water flow and solute (pollutants and salts) transport and water redistribution in agricultural soils under irrigation. Field plots of a potato farmer in a sandy region in Belgium were instrumented to continuously monitor soil moisture and water potential before, during and after irrigation in dry summer periods. The aim is to optimize the irrigation process by assimilating online sensor field data into process based models. Over the past year, we demonstrated the calibration and optimization of the Hydrus 1D model for an irrigated grassland on sandy soil. Direct and inverse calibration and optimization for both heterogeneous and homogeneous conceptualizations was applied. Results show that Hydrus 1D closely simulated soil water content at five depths as compared to water content measurements from soil moisture probes, by stepwise calibration and local sensivity analysis and optimization the Ks, n and α value in the calibration and optimization analysis. The errors of the model, expressed by deviations between observed and modeled soil water content were, however, different for each individual depth. The smallest differences between the observed value and soil-water content were attained when using an automated inverse optimization method. The choice of the initial parameter value can be optimized using a stepwise approach. Our results show that statistical evaluation coefficients (R2, Ce and RMSE) are suitable benchmarks to evaluate the performance of the model in reproducing the data. The degree of water stress simulated with Hydrus 1D suggested to increase irrigation at least one time, i.e. at the beginning of the simulation period and further distribute the amount of irrigation during the growing season, instead of using a huge amount of irrigation later in the season. In the next year, we will further look for to the best method (using soft data and methods for instance PTFs, EMI, Penetrometer) to derive and predict the spatial variability of soil hydraulic properties (saturated hydraulic conductivity) of the soil and link to crop yield at the field scale. Linear and non-linear pedotransfer functions (PTFs) have been assessed to predict penetrometer resistance of soils from their water status (matric potential, ψ and degree of saturation, S) and bulk density, ρb, and some other soil properties such as sand content, Ks etc. The geophysical EMI (electromagnetic induction) technique provides a versatile and robust field instrument for determining apparent soil electrical conductivity (ECa). ECa, a quick and reliable measurement, is one of ancillary properties (secondary information) of soil, can improve the spatial and temporal estimation of soil characteristics e.g., salinity, water content, texture, prosity and bulk density at different scales and depths. According to previous literature on penetrometer measurements, we determined the effective stress and used some models to find the relationships between soil properties, especially Ks, and penetrometer resistance as one of the prediction methods for Ks. The initial results obtained in the first yearshowed that a new data set would be necessary to validate the results of this part. In the third year, quasi 3D-modelling of water flow at the field scale will be conducted. In this modeling set -up, the field will be modeled as a collection of 1D-columns representing the different field conditions (combination of soil properties, groundwater depth, root zone depth). The measured soil properties are extrapolated over the entire field by linking them to the available spatially distributed data (such as the EMI-images). The data set of predicted Ks and other soil properties for the whole field constructed in the previous steps will be used for parameterising the model. Sensitivity analysis ‘SA’ is essential to the model optimization or parametrization process. To avoid overparameterization, the use of global sensitivity analysis (SA) will be investigated. In order to include multiple objectives (irrigation management parameters, costs, …) in the parameter optimization strategy, multi-objective techniques such as AMALGAM have been introduced. We will investigate multi-objective strategies in the irrigation optimization

Use of mixed-type data clustering algorithm for characterizing temporal and spatial distribution of biosecurity border detections of terrestrial non-indigenous species

Appropriate inspection protocols and mitigation strategies are a critical component of effective biosecurity measures, enabling implementation of sound management decisions. Statistical models to analyze biosecurity surveillance data are integral to this decision-making process. Our research focuses on analyzing border interception biosecurity data collected from a Class A Nature Reserve, Barrow Island, in Western Australia and the associated covariates describing both spatial and temporal interception patterns. A clustering analysis approach was adopted using a generalization of the popular k-means algorithm appropriate for mixed-type data. The analysis approach compared the efficiency of clustering using only the numerical data, then subsequently including covariates to the clustering. Based on numerical data only, three clusters gave an acceptable fit and provided information about the underlying data characteristics. Incorporation of covariates into the model suggested four distinct clusters dominated by physical location and type of detection. Clustering increases interpretability of complex models and is useful in data mining to highlight patterns to describe underlying processes in biosecurity and other research areas. Availability of more relevant data would greatly improve the model. Based on outcomes from our research we recommend broader use of cluster models in biosecurity data, with testing of these models on more datasets to validate the model choice and identify important explanatory variables