Two robust estimators of the cross‐variogram for multivariate geostatistical analysis of soil properties

If we wish to describe the coregionalization of two or more soil properties for estimation by cokriging then we must estimate and model their auto‐ and cross‐variogram(s). The conventional estimates of these variograms, obtained by the method‐of‐moments, are unduly affected by outlying data which inflate the variograms and so also the estimates of the error variance of cokriging predictions. Robust estimators are less affected. Robust estimators of the auto‐variogram and the pseudo cross‐variogram have previously been proposed and used successfully, but the multivariate problem of estimating the cross‐variogram robustly has not yet been tackled. Two robust estimators of the cross‐variogram are proposed. These use covariance estimators with good robustness properties. The robust estimators of the cross‐variogram proved more resistant to outliers than did the method‐of‐moments estimator when applied to simulated fields which were then contaminated. Organic carbon and water content of the soil was measured at 256 sites on a transect and the method‐of‐moments estimator, and the two robust estimators, were used to estimate the auto‐variograms and cross‐variogram from a prediction subset of 156 sites. The data on organic carbon included a few outliers. The method‐of‐moments estimator returned larger values of the auto‐ and cross‐variograms than did either robust estimator. The organic carbon content at the 100 validation sites on the transect was estimated by cokriging from the prediction data plus a set of variograms fitted to the method‐of‐moments estimates and two sets of variograms fitted to the robust estimates. The ratio of the actual squared prediction error to the cokriging estimate of the error variance was computed at each validation site. These results showed that cokriging using variograms obtained by the method‐of‐moments estimator overestimated the error variance of the predictions. By contrast, cokriging with the robustly estimated variograms gave reliable estimates of the error variance of the predictions.     

Robust estimation of the pseudo cross‐variogram for cokriging soil properties

The pseudo cross‐variogram can be used for cokriging two or more soil properties when few or none of the sampling locations have values recorded for all of them. The usual estimator of the pseudo cross‐variogram is susceptible to the effects of extreme data (outliers). This will lead to overestimation of the error variance of predictions obtained by cokriging. A solution to this problem is to use robust estimators of the pseudo cross‐variogram, and three such estimators are proposed in this paper. The robust estimators were demonstrated on simulated data in the presence of different numbers of outlying data drawn from different contaminating distributions. The robust estimators were less sensitive to the outliers than the non‐robust one, but they had larger variances. Outliers tend to obscure the spatial structure of the cross‐correlation of the simulated variables as described by the non‐robust estimator. The several estimators of the pseudo cross‐variogram were applied to a multitemporal data set on soil water content. Since these were obtained non‐destructively, direct measurements of temporal change can be made. A prediction subset of the data was subsampled as if obtained by destructive analysis and the remainder used for validation. Estimators of the auto‐variogram and pseudo cross‐variogram were applied to the prediction data, then used to predict the change in water content at the validation sites by cokriging. The estimation variances of these predictions were best calculated with a robustly estimated model of coregionalization, although the validation set was too small to conclude that the non‐robust estimators were unsuitable in this instance.     

Estimating Distance Sampling Detection Functions When Distances Are Measured With Errors

Distance sampling methods assume that distances are known but in practice there are often errors in measuring them. These can have substantial impact on the bias and precision of distance sampling estimators. In this paper we develop methods that accommodate both systematic and stochastic measurement errors. We use the methods to estimate detection probability in two surveys with substantial measurement error. The first is a shipboard line transect survey in the North Sea in which information on measurement error comes from photographically measured distances to a subset of detections. The second is an aerial cue-counting survey off Iceland in which information on measurement error comes from pairs of independently estimated distances to a subset of detections. Different methods are required for measurement error estimation in the two cases. We investigate by simulation the properties of the new estimators and compare them to conventional estimators. They are found to perform better than conventional estimators in the presence of measurement error, more so in the case of cue-counting and point transect estimators than line transect estimators. An appendix on the asymptotic distributions of conditional and full likelihood estimators is available online.     

On the Akaike Information Criterion for choosing models for variograms of soil properties

A problem in the application of geostatistics to soil is to find satisfactory models for variograms of soil properties. It is usually solved by fitting plausible models to the sample variogram by weighted least squares approximation. The residual sum of squares can always be diminished, and the fit improved in that sense, by adding parameters to the model. A satisfactory compromise between goodness of fit and parsimony can be achieved by applying the Akaike Information Criterion (AIC). For a given set of data the variable part of the AIC is estimated by where n is the number of experimental points on the variogram, R is the residual sum of squares and p is the number of parameters in the model. The model to choose is the one for which  is least.
The AIC is closely related to Akaike's earlier final prediction error and the Schwarz criterion. It is also equivalent to an F test when adding parameters in nested models.     

A comparison of some robust estimators of the variogram for use in soil survey

The standard estimator of the variogram is sensitive to outlying data, a few of which can cause overestimation of the variogram. This will result in incorrect variances when estimating the value of a soil property by kriging or when designing a sampling grid to map the property to a required precision. Several robust estimators of the variogram, based on location and scale estimation, have been proposed as improvements. They seem to be suitable for analysis of soil data in circumstances where the standard estimator is likely to be affected by outliers. Robust estimators are based on assumptions about the distribution of the data which will not always hold and which need not be made in kriging or in estimating the variogram by the standard estimator. The estimators are reviewed. Simulation studies show that the robust estimators vary in their susceptibility to moderate skew in the underlying distribution, but that the effects of outliers are generally greater. The estimators are applied to some soil data, and the resulting variograms used for ordinary kriging at sites in a separate validation data set. In most cases the variograms derived from the standard estimator gave kriging variances which appeared to overestimate the mean squared error of prediction (MSEP). Kriging with variograms based on robust estimators sometimes gave kriging variances which underestimated the MSEP or did not differ significantly from it. Estimates of kriging variance and the MSEP derived from the validation data were generally close to estimates from cross‐validation on the prediction set used to derive the variograms. This indicates that variogram models derived from different estimators could be compared by cross‐validation.     

A Sequential Monte Carlo Approach for MLE in a Plant Growth Model

Parametric identification of plant growth models formalized as discrete dynamical systems is a challenging problem due to specific data acquisition (system observation is generally done with destructive measurements), non-linear dynamics, model uncertainties and high-dimensional parameter space. In this study, we present a novel idea of modeling plant growth in the framework of non-homogeneous hidden Markov models (Cappé, Moulines, and Rydén 2005), for a certain class of plants with known organogenesis (structural development). Unknown parameters of the models are estimated via a stochastic variant of a generalized EM (Expectation-Maximization) algorithm and approximate confidence intervals are given via parametric bootstrap. The complexity of the model makes both the E-step (expectation step) and the M-step (maximization step) non-explicit. For this reason, the E-step is approximated via a sequential Monte Carlo procedure (sequential importance sampling with resampling) and the M-step is separated into two steps (Conditional-Maximization), where before applying a numerical maximization procedure (quasi-Newton type), a large subset of unknown parameters is updated explicitly conditioned on the other subset. A simulation study and a case-study with real data from the sugar beet are considered and a model comparison is performed based on these data. Appendices are available online.     

应用土壤质地预测干旱区葡萄园土壤饱和导水率空间分布

田间表层土壤饱和导水率的空间变异性是影响灌溉水分入渗和土壤水分再分布的主要因素之一,研究土壤饱和导水率的空间变化规律,有助于定量估计土壤水分的空间分布和设计农田的精准灌溉管理制度。为了探究应用其他土壤性质如质地、容重、有机质预测土壤饱和导水率空间分布的可行性,试验在7.6 hm2的葡萄园内,采用均匀网格25 m×25 m与随机取样相结合的方式,测定了表层(0～10 cm)土壤饱和导水率、粘粒、粉粒、砂粒、容重和有机质含量,借助经典统计学和地统计学,分析了表层土壤饱和导水率的空间分布规律、与土壤属性的空间相关性,并对普通克里格法、回归法和回归克里格法预测土壤饱和导水率空间分布的结果进行了对比。结果表明:1)土壤饱和导水率具有较强的变异性,平均值为1.64 cm/d,变异系数为1.17;2)表层土壤饱和导水率60%的空间变化是由随机性或小于取样尺度的空间变异造成;3)土壤饱和导水率与粘粒、粉粒、砂粒和有机质含量具有一定空间相关性,而与土壤容重几乎没有空间相关性;4)在中值区以土壤属性辅助的回归克里格法对土壤饱和导水率的预测精度较好,在低值和高值区其与普通克里格法表现类似。研究结果将为更好地描述土壤饱和导水率空间变异结构及更准确地预测其空间分布提供参考。     

A Bayesian Approach to Spatial Prediction With Flexible Variogram Models

A Bayesian approach to covariance estimation and spatial prediction based on flexible variogram models is introduced. In particular, we consider black-box kriging models. These variogram models do not require restrictive assumptions on the functional shape of the variogram; furthermore, they can handle quite naturally non isotropic random fields. The proposed Bayesian approach does not require the computation of an empirical variogram estimator, thus avoiding the arbitrariness implied in the construction of the empirical variogram itself. Moreover, it provides a complete assessment of the uncertainty in the variogram estimation. The advantages of this approach are illustrated via simulation studies and by application to a well known benchmark dataset.     

On spatial prediction of soil properties in the presence of a spatial trend: the empirical best linear unbiased predictor (E-BLUP) with REML

Geostatistical estimates of a soil property by kriging are equivalent to the best linear unbiased predictions (BLUPs). Universal kriging is BLUP with a fixed‐effect model that is some linear function of spatial co‐ordinates, or more generally a linear function of some other secondary predictor variable when it is called kriging with external drift. A problem in universal kriging is to find a spatial variance model for the random variation, since empirical variograms estimated from the data by method‐of‐moments will be affected by both the random variation and that variation represented by the fixed effects. The geostatistical model of spatial variation is a special case of the linear mixed model where our data are modelled as the additive combination of fixed effects (e.g. the unknown mean, coefficients of a trend model), random effects (the spatially dependent random variation in the geostatistical context) and independent random error (nugget variation in geostatistics). Statisticians use residual maximum likelihood (REML) to estimate variance parameters, i.e. to obtain the variogram in a geostatistical context. REML estimates are consistent (they converge in probability to the parameters that are estimated) with less bias than both maximum likelihood estimates and method‐of‐moment estimates obtained from residuals of a fitted trend. If the estimate of the random effects variance model is inserted into the BLUP we have the empirical BLUP or E‐BLUP. Despite representing the state of the art for prediction from a linear mixed model in statistics, the REML–E‐BLUP has not been widely used in soil science, and in most studies reported in the soils literature the variogram is estimated with methods that are seriously biased if the fixed‐effect structure is more complex than just an unknown constant mean (ordinary kriging). In this paper we describe the REML–E‐BLUP and illustrate the method with some data on soil water content that exhibit a pronounced spatial trend.     

Optimal interpolation and isarithmic mapping of soil properties: I The semi‐variogram and punctual kriging

Kriging is a means of spatial prediction that can be used for soil properties. It is a form of weighted local averaging. It is optimal in the sense that it provides estimates of values at unrecorded places without bias and with minimum and known variance. Isarithmic maps made by kriging are alternatives to conventional soil maps where properties can be measured at close spacings. Kriging depends on first computing an accurate semi‐variogram, which measures the nature of spatial dependence for the property. Estimates of semi‐variance are then used to determine the weights applied to the data when computing the averages, and are presented in the kriging equations. The method is applied to three sets of data from detailed soil surveys in Central Wales and Norfolk. Sodium content at Plas Gogerddan was shown to vary isotropically with a linear semi‐variogram. Ordinary punctual kriging produced a map with intricate isarithms and fairly large estimation variance, attributed to a large nugget effect. Stoniness on the same land varied anisotropically with a linear semi‐variogram, and again the estimation error of punctual kriging was fairly large. At Hole Farm, Norfolk, the thickness of cover loam varied isotropically, but with a spherical semi‐variogram. Its parameters were estimated and used to krige point values and produce a map showing substantial short‐range variation.     

Spatial Variability in Slash Linear Modeling with Finite Second Moment

This article studies the dependence of spatial linear models using a slash distribution with a finite second moment. The parameters of the model are estimated with maximum likelihood by using the EM algorithm. To avoid identifiability problems, the cross-validation, the Trace and the maximum log-likelihood value are used to choose the parameter for adjusting the kurtosis of the slash distribution and the selection of the model to explain the spatial dependence. We present diagnostic techniques of global and local influences for exploring the sensibility of estimators and the presence of possible influential observations. A simulation study is developed to determine the performance of the methodology. The results showed the effectiveness of the choice criteria of the parameter for adjusting the kurtosis and for the selection of the spatial dependence model. It has also showed that the slash distribution provides an increased robustness to the presence of influential observations. As an illustration, the proposed model and its diagnostics are used to analyze an aquifer data. The spatial prediction with and without the influential observations were compared. The results show that the contours of the interpolation maps and prediction standard error maps showed low changes when we removed the influential observations. Thus, this model is a robust alternative in the spatial linear modeling for dependent random variables. Supplementary materials accompanying this paper appear online.     

Alternative methods in the development of pedotransfer functions for soil hydraulic characteristics

Soil hydraulic properties are needed in the modeling of water flow and solute movement in the vadose zone. Pedotransfer functions (PTFs) have received the attention of many researchers for indirect determination of hydraulic properties from basic soil properties as an alternative to direct measurement. The objective of this study was to compare the performance of cascade forward network (CFN), multiple-linear regression (MLR), and seemingly unrelated regression (SUR) methods using prediction capabilities of point and parametric PTFs developed by these methods. The point PTFs estimated field capacity (FC), permanent wilting point (PWP), available water capacity (AWC), and saturated hydraulic conductivity (Ks) and the parametric PTFs estimated the van Genuchten retention parameters. A total of 180 soil samples was extracted from the UNSODA database and divided into two groups as 135 for the development and 45 for the validation of the PTFs. The model performances were evaluated with three statistical tools: the maximum error (ME), the model efficiency (EF), and the D index (D) using the observed and predicted values of a given parameter. Despite the fact that the differences among the three methods in prediction accuracies of the point and parametric PTFs were not statistically significant (p > 0.05) except θ_r and α (p < 0.05) based on the ANOVA test, overall MLR and SUR were somewhat better than CFN in prediction of the point PTFs, whereas CFN performed better than the other two methods in prediction of the parametric PTFs. The F.F values of FC and θ_r for CFN, MLR, and SUR methods were 0.705. 0.805, 0.795 and 0.356, −0.290, −0.290, respectively, which refer to the best and worst predictions. Properties (Ks, θ_r, α) having some difficulty in prediction were better predicted by CFN and SUR methods, where these methods predict all hydraulic properties from basic soil properties simultaneously rather than individually as in MLR. This suggests that multivariate analysis using such functional relationships between hydraulic properties and basic soil properties can be utilized in developing more accurate point and parametric PTFs with less time and effort.     

Confidence intervals for fish out-migration estimates using stratified trap efficiency methods

Marked fish placed above a smolt trap allow fisheries biologists to estimate the efficiency of the trap and hence to estimate the number of smolts migrating past the trap. We compared stratified maximum likelihood estimators and confidence intervals of total numbers of fish migrating to two other well-known estimators and associated confidence intervals using simulation. The Bailey adjusted Lincoln-Petersen estimator and its bootstrap confidence interval performed well overall.     

Model‐based analysis using REML for inference from systematically sampled data on soil

The general linear model encompasses statistical methods such as regression and analysis of variance (anova ) which are commonly used by soil scientists. The standard ordinary least squares (OLS) method for estimating the parameters of the general linear model is a design‐based method that requires that the data have been collected according to an appropriate randomized sample design. Soil data are often obtained by systematic sampling on transects or grids, so OLS methods are not appropriate. Parameters of the general linear model can be estimated from systematically sampled data by model‐based methods. Parameters of a model of the covariance structure of the error are estimated, then used to estimate the remaining parameters of the model with known variance. Residual maximum likelihood (REML) is the best way to estimate the variance parameters since it is unbiased. We present the REML solution to this problem. We then demonstrate how REML can be used to estimate parameters for regression and anova ‐type models using data from two systematic surveys of soil. We compare an efficient, gradient‐based implementation of REML (ASReml) with an implementation that uses simulated annealing. In general the results were very similar; where they differed the error covariance model had a spherical variogram function which can have local optima in its likelihood function. The simulated annealing results were better than the gradient method in this case because simulated annealing is good at escaping local optima.     

Estimating variograms of soil properties by the method-of-moments and maximum likelihood

Variograms of soil properties are usually obtained by estimating the variogram for distinct lag classes by the method‐of‐moments and fitting an appropriate model to the estimates. An alternative is to fit a model by maximum likelihood to data on the assumption that they are a realization of a multivariate Gaussian process. This paper compares the two using both simulation and real data. The method‐of‐moments and maximum likelihood were used to estimate the variograms of data simulated from stationary Gaussian processes. In one example, where the simulated field was sampled at different intensities, maximum likelihood estimation was consistently more efficient than the method‐of‐moments, but this result was not general and the relative performance of the methods depends on the form of the variogram. Where the nugget variance was relatively small and the correlation range of the data was large the method‐of‐moments was at an advantage and likewise in the presence of data from a contaminating distribution. When fields were simulated with positive skew this affected the results of both the method‐of‐moments and maximum likelihood. The two methods were used to estimate variograms from actual metal concentrations in topsoil in the Swiss Jura, and the variograms were used for kriging. Both estimators were susceptible to sampling problems which resulted in over‐ or underestimation of the variance of three of the metals by kriging. For four other metals the results for kriging using the variogram obtained by maximum likelihood were consistently closer to the theoretical expectation than the results for kriging with the variogram obtained by the method‐of‐moments, although the differences between the results using the two approaches were not significantly different from each other or from expectation. Soil scientists should use both procedures in their analysis and compare the results.     

A simulation study for a linear measurement error model when error variances vary between measurements

When predicting scores in the Draize eye irritation test based on measurements of in vitro alternative tests, we are often faced with estimating parameters in a linear measurement error model with heterogeneous error variances. This article proposes a new statistical method for parameter estimation to address this issue. The proposed method is an extension of an earlier proposal that applied a linear measurement error model with homogeneous error variances, to cases with heterogeneous error variances. A simulation study to examine the performance of the proposed method was conducted in a framework that was adaptable to the data, which was obtained in a validation study of alternative methods to animal experiments conducted in Japan. The proposed method reduced the biases of estimates in comparison with an ordinary regression analysis method and three other methods under the assumption of homogeneous error variances. Although the proposed method did not fit the real data well, the resulting prediction formula was far better than those obtained by other methods.     

The Matérn variogram model: Implications for uncertainty propagation and sampling in geostatistical surveys

The Matérn variogram model has been advocated because it is flexible and can represent varied behaviour at small lags. We show how the constraints on the spherical and exponential variogram at short lags ignore a possible source of uncertainty in the variogram and so in kriging surveys, that the Matérn model can describe. Matérn, spherical and exponential variogram models were fitted by maximum likelihood to a set of log₁₀(K) observations made on a regular grid at Broom's Barn Farm, Suffolk, England. The likelihood profiles of the Matérn parameter estimates were asymmetric. Thus the uncertainty of these estimates could only be adequately assessed by a Bayesian approach. The uncertainty of estimated parameters of the Matérn variogram was larger than for the exponential variogram. This is an indication that the assumption of an exponential model limits the behaviour that may be described by the variogram. Thus uncertainty analyses where an exponential variogram is assumed may underestimate the uncertainty of kriged estimates. Bayesian analysis of the kriged estimates of log₁₀(K) at Broom's Barn Farm using the Matérn variogram revealed an observable component of uncertainty due to variogram uncertainty. When an exponential variogram model was used, the estimate of this component of uncertainty was negligible. The Matérn variogram should therefore be used rather than the exponential model when assessing the adequacy of a variogram estimate. A method of designing sample schemes which is suitable for both estimating a Matérn variogram and interpolation is suggested.     

区域土壤质地层次三维空间分布的地统计模拟方法比较

为了定量化描述冲积平原区土壤剖面质地层次的复杂变异性,本研究根据华北冲积平原一块面积约15 km2区域内的139个土壤剖面（0 ~ 2 m）观测数据,分别应用顺序指示模拟和多点地统计学模拟方法分析了区域内土壤质地层次的三维空间分布特征。前者的结果显示土壤质地层在水平方向上的分布具有很强的随机特性,而后者的结果表明土壤质地层在水平方向上的分布具有一定的规律性。将转移概率函数得到的各向同性分布比例和各向异性平均长度（厚度）用来生成三维训练图像,然后将生成的训练图像用于多点地统计学模拟,并与传统的顺序指示模拟结果进行了对比。结果表明,多点地统计学模拟在估计精度以及垂直方向上土壤质地层次连贯性的再现性上优于传统顺序指示模拟,所得结果能更好地反映土壤质地层次的空间分布特征。     

Comparison of spatial variables over subregions using a block bootstrap

In environmental and agricultural studies, it is often of interestto compare spatial variables across different regions. Traditional statistical tools that assume independent samples are inadequate because of potential spatial correlations. In this article, spatial dependence is accounted for by a random field model, and a non parametric test is developed to compare the overall distributions of variables in two neighboring regions. Sampling distribution of the test statistic is estimated by a spatial block bootstrap. For illustration, the procedure is applied to study root-lesion nematode populations on a production farm in Wisconsin. Choices of the bootstrap block size are investigated via a simulation study and results of the test are compared to traditional approaches.     

Reducing sampling intensity in order to investigate spatial variability of soil pH,organic matter and available phosphorus using co-kriging techniques. A case study of acid soils in Eastern Croatia

Soil pH, hydrolytic acidity (HA), organic matter (OM) and plant available phosphorus (AP) are factors controlling the environmental-friendly soil management in agroecosystems. These parameters are highly variable in space. The objective of this work is to study spatial variability of pH, HA, OM and AP using several interpolation methods in Eastern Croatia. A total of 1004 (0–30 cm) soil samples were collected, and several univariate and multivariate interpolation performances were tested. The results showed that soils of the study area had high HA and AP, while pH and OM were low. The variogram analysis revealed different spatial structures among studied soil properties and demonstrate a need for variable-rate management. Soil pH and OM had lower spatial variability compared to AP and HA. Ordinary kriging was the most accurate method to estimate the studied variables. The incorporation of auxiliary variables increased the precision of the estimations for HA. Soil AP and OM showed different results for spatial prediction obtained by co-kriging. Overall, the incorporation of pH as auxiliary variable increased the prediction of the models. However, more co-variates should be incorporated in further models, in order to identify with more precision areas that need to be restored.