Predicting the spatial distribution of ground flora on large domains using a hierarchical Bayesian model

Accomodation of important sources of uncertainty in ecological models is essential to realistically predicting ecological processes. The purpose of this project is to develop a robust methodology for modeling natural processes on a landscape while accounting for the variability in a process by utilizing environmental and spatial random effects. A hierarchical Bayesian framework has allowed the simultaneous integration of these effects. This framework naturally assumes variables to be random and the posterior distribution of the model provides probabilistic information about the process. Two species in the genus Desmodium were used as examples to illustrate the utility of the model in Southeast Missouri, USA. In addition, two validation techniques were applied to evaluate the qualitative and quantitative characteristics of the predictions.This revised version was published online in May 2005 with corrections to the Cover Date.     

基于MCMC模拟的MGPD模型及其在地质灾害风险度量中的应用

基于马尔科夫链蒙特卡洛(简记为MCMC)模拟的参数贝叶斯估计,对改进的广义帕累托分布(简记为MGPD)模型进行了优化,并利用该模型得到了地质灾害损失的在险损失值(简记为VaR)和条件损失值(简记为CVaR).以湖南娄底市地质灾害损失数据进行实证分析及模型适应性检验,结果表明:优化后的模型不仅具有很好的极值数据描述能力,而且具有较强的适用性.     

基于信号博弈的阳澄湖大闸蟹绿色标签市场应用分析

水产品绿色标签对消费者来说是高质量的信号,对卖家来说则是卖出高价的资本.但是欺诈行为的存在损害了消费者和其他卖家的利益,扰乱了市场秩序.以阳澄湖大闸蟹为例,通过信号博彝理论,对螃蟹市场中关卖双方的消费行为进行博彝分析,得到了精炼贝叶斯Nash均衡.     

Bayesian estimation of diagnostic accuracy of a new bead-based antibody detection test to reveal Toxoplasma gondii infections in pig populations

The success of a Toxoplasma gondii surveillance program in European pig production systems depends partly on the quality of the test to detect infection in the population. The test accuracy of a recently developed serological bead-based assay (BBA) was investigated earlier using sera from experimentally infected animals. In this study, the accuracy of the BBA was determined by the use of sera from animals from two field subpopulations. As no T. gondii infection information of these animals was available, test accuracy was determined through a Bayesian approach allowing for conditional dependency between BBA and an ELISA test. The priors for prevalence were based on available information from literature, whereas for specificity vague non-informative priors were used. Priors for sensitivity were based either on available information or specified as non-informative. Posterior estimates for BBA sensitivity and specificity were (mode) 0.855 (Bayesian 95% credibility interval (bCI) 0.702–0.960) and 0.913 (bCI 0.893–0.931), respectively. Comparing the results of BBA and ELISA, sensitivity was higher for the BBA while specificity was higher for ELISA. Alternative priors for the sensitivity affected posterior estimates for sensitivity of both BBA and ELISA, but not for specificity. Because the difference in prevalence between the two subpopulations is small, and the number of infected animals is small as well, the precision of the posterior estimates for sensitivity may be less accurate in comparison to the estimates for specificity. The estimated value for specificity of BBA is at least optimally defined for testing pigs from conventional and organic Dutch farms.     

金融时间序列指标判别框架：以特质波动率为例

基于拐点集合判别的TBUD方法主要思路是分析拐点集合间的关系，并在高维空间进行划分，从而搭建判别模型，并将分析框架应用在特质波动率等若干指标上，利用实证数据得到结论。应用TBUD判别框架可以发现，特质波动率等指标无法对拐点集合进行清晰划分，因而并不具有预测能力。     

A global sensitivity analysis of cultivar trait parameters in a sugarcane growth model for contrasting production environments in Queensland,Australia

New sugarcane cultivars are continuously developed to improve sugar industry productivity. Despite this sugarcane crop models such as the ‘Sugar’ module in the Agricultural Productions System sIMulator (APSIM-Sugar) have not been updated to reflect the most recent cultivars. The implications of misrepresenting cultivar parameters in APSIM-Sugar is difficult to judge as little research has been published on the likely values of these parameters and how uncertainty in parameter values may affect model outputs. A global sensitivity analysis can be used to better understand how cultivar parameters influence simulated yields. A Gaussian emulator was used to perform a global sensitivity analysis on simulated biomass and sucrose yield at harvest for two contrasting sugarcane-growing regions in Queensland, Australia. Biomass and sucrose yields were simulated for 42 years to identify inter-annual variability in output sensitivities to 10 parameters that represent physiological traits and can be used to simulated differences between sugarcane cultivars. Parameter main effect (S_i) and total effect (ST_i) sensitivity indices and emulator accuracy were calculated for all year-region-output combinations. When both regions were considered together parameters representing radiation use efficiency (rue), number of green leaves (green_leaf_no) and a conductance surrogate parameter (k_L) were the most influential parameters for simulated biomass in APSIM-Sugar. Simulated sucrose yield was most sensitive to rue, sucrose_fraction (representing the fraction of biomass partitioned as sucrose in the stem) and green_leaf_no. However, climate and soil differences between regions changed the level of influence cultivar parameters had on simulation outputs. Specifically, model outputs were more sensitive to changes in the transp_eff_cf and k_L parameters in the Burdekin region due to lower rainfall and poor simulated soil conditions. Collecting data on influential traits that are relatively simple to measure (e.g. number of green leaves) during cultivar development would greatly contribute to the simulation of new cultivars in crop models. Influential parameters that are difficult to measure directly such as transp_eff_cf and sucrose_fraction are ideal candidates for statistical calibration. Calibrating crop models either through direct observation or statistical calibration would allow crop modellers to better test how new cultivars will perform in a range of production environments.     

Genomic prediction for meat and carcass traits in Nellore cattle using a Markov blanket algorithm

This study was carried out to evaluate the advantage of preselecting SNP markers using Markov blanket algorithm regarding the accuracy of genomic prediction for carcass and meat quality traits in Nellore cattle. This study considered 3675, 3680, 3660 and 524 records of rib eye area (REA), back fat thickness (BF), rump fat (RF), and Warner–Bratzler shear force (WBSF), respectively, from the Nellore Brazil Breeding Program. The animals have been genotyped using low-density SNP panel (30 k), and subsequently imputed for arrays with 777 k SNPs. Four Bayesian specifications of genomic regression models, namely Bayes A, Bayes B, Bayes Cπ and Bayesian Ridge Regression methods were compared in terms of prediction accuracy using a five folds cross-validation. Prediction accuracy for REA, BF and RF was all similar using the Bayesian Alphabet models, ranging from 0.75 to 0.95. For WBSF, the predictive ability was higher using Bayes B (0.47) than other methods (0.39 to 0.42). Although the prediction accuracies using Markov blanket of SNP markers were lower than those using all SNPs, for WBSF the relative gain was lower than 13%. With a subset of informative SNPs markers, identified using Markov blanket, probably, is possible to capture a large proportion of the genetic variance for WBSF. The development of low-density and customized arrays using Markov blanket might be cost-effective to perform a genomic selection for this trait, increasing the number of evaluated animals, improving the management decisions based on genomic information and applying genomic selection on a large scale.     

江苏省小麦籽粒蛋白质达标弱筋小麦的适生性分析与评价

【目的】弱筋小麦是制作饼干糕点类食品的原料,其烘烤特性很大程度上取决于蛋白质的质和量。小麦籽粒蛋白质含量（GPC,%）不仅由品种的遗传特性决定,还受到气候、土壤、栽培措施等影响。明确江苏省弱筋小麦适宜种植区域以及其地理、气候影响因素,可为江苏弱筋小麦的种植区划提供理论依据。【方法】在2年江苏省小麦品质抽样调查数据的基础上,利用随机森林算法筛选重要性指标,结合单组率Meta分析及其亚组分析,探究地理位置及气象因子对江苏省小麦籽粒蛋白质含量（GPC）达到弱筋小麦标准可能性的影响。【结果】2个年度江苏省小麦GPC平均值为13.92 %,其中2018年、2019年小麦GPC变幅分别为11.06%—18.09%、10.20%—16.50%,平均值分别为14.52%、13.33%,GPC<12.5%的样品分别占比10%、29.71%。从地理分布看,江苏的东南沿湖沿海地区小麦GPC达到弱筋小麦标准的可能性最高,达标可能性最高可达92%,其次是江苏东部沿海地区以及江苏西北部沿河一带。种植地距离一级河流和湖泊或者海岸线的最短距离为20—30 km时,达标可能性相对较高,为23.95%。从气象因子方面看,生育前期特别是出苗期和拔节期,降雨量对江苏弱筋小麦的形成影响较为重要;生育后期尤其是开花期以及灌浆期后期,积温对小麦GPC的影响更重要;且出苗和拔节期的日照时数及开花期的降雨量对江苏弱筋小麦的形成亦很重要,其中,江苏小麦GPC达标弱筋小麦标准的可能性与出苗期的降雨量呈正相关,而与出苗和拔节期的日照时数、拔节期的降雨量以及灌浆后期积温则呈负相关。【结论】江苏弱筋小麦适宜的种植范围受到水系分布与气象因素的共同制约,主要集中在东部沿海和东南沿海沿湖地区。在出苗、拔节期降雨量和开花灌浆期积温适宜的情况下,西北沿河一带的小麦GPC也可达标弱筋小麦标准。品质区划应重点考虑地理位置（水系分布等）和气候分布。     

Meta-analysis of fungicide efficacy on soybean target spot and cost–benefit assessment

Target spot of soybean has spread in Brazil, the southeastern United States and Argentina in the last decade. A collaborative network of field Uniform Fungicide Trials (UFT) in Brazil was created in 2011 to study the target spot control efficacy of fungicides, including azoxystrobin + benzovindiflupyr (AZ_BF), carbendazim (CZM), fluxapyroxad + pyraclostrobin (FLUX_PYRA), epoxiconazole + FLUX_PYRA (EPO_FLUX_PYRA), mancozeb (MZB) and prothioconazole + trifloxystrobin (PROT_TRIF). Network meta-analysis was used to conduct a quantitative synthesis of UFT data collected from 2012 to 2016 and to evaluate the effects of disease pressure (DP, low ≤ 35% target spot severity in the nontreated control < high) and year of experiment on the overall mean efficacy and yield response to each of the tested fungicides. Based on mean percentage control of target spot severity, the tested fungicides fall into three efficacy groups (EG): high EG, FLUX_PYRA (76.2% control relative to the nontreated control) and EPO_FLUX_PYRA (75.7% control); intermediate EG, PROT_TRIF (66.5% control) and low EG, MZB (49.6% control), AZ_BF (46.7% control) and CZM (32.4% control). DP had a significant effect on yield response. At DP_Low, the highest response was due to PROT_TRIF (+342 kg ha⁻¹, +12.8%) and EPO_FLUX_PYRA (+295.5 kg ha⁻¹, +11.2%), whereas at DP_High, EPO_FLUX_PYRA and FLUX_PYRA outperformed the other treatments, with yield responses of 503 kg ha⁻¹ (+20.2%) and 469 kg ha⁻¹ (+19.1%), respectively. The probability of a positive return on fungicide investment ranged from 0.26 to 0.56 at DP_Low and from 0.34 to 0.66 at DP_High.