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1.
The simultaneous analysis of mixed discrete and continuous outcomes using nonlinear threshold models
Todd Coffey Chris Gennings 《Journal of Agricultural, Biological & Environmental Statistics》2007,12(1):55-77
Mixed discrete and continuous outcomes are commonly measured on each experimental unit in dose-response studies in toxicology.
The dose-response relationships for these outcomes often have dose thresholds and nonlinear patterns. In addition, the endpoints
are typically correlated, and a statistical analysis that incorporates the association may result in improved precision. We
propose an extension of the generalized estimating equation (GEE) methodology to simultaneously analyze binary, count, and
continuous outcomes with nonlinear threshold models that incorporates the intra-subject correlation. The methodology uses
a quasi-likelihood framework and a working correlation matrix, and is appropriate when the marginal expectation of each outcome
is of primary interest and the correlation between endpoints is a nuisance parameter. Because the derivatives of threshold
models are not continuous at each point of the parameter space, we describe the necessary modifications that result in asymptotically
normal and consistent estimators. Using dose-response data from a neurotoxicity experiment, the methodology is illustrated
by analyzing five outcomes of mixed type with nonlinear threshold models. In this example, the incorporation of the intra-subject
correlation resulted in decreased standard errors for the threshold parameters. 相似文献
2.
Helena Geys Meredith M. Regan Paul J. Catalano Geert Molenberghs 《Journal of Agricultural, Biological & Environmental Statistics》2001,6(3):340-355
Measurements of both continuous and discrete outcomes are encountered in many statistical problems. Here we consider the particular context of teratology studies, where quantitative risk asessment is aimed at determining the effect of dose on the probability that an individual fetus is malformed or of low birth weight, both being important measures of teratogenicity. We will introduce two different joint marginal mean models for outcomes of a mixed nature. First, we propose the Plackett-Dale approach, where for each binary outcome it is assumed that there exists an underlying glatent variable. The latent malformation outcomes are then assumed to follow a Plackett distribution. The second approach we consider is a probit approach. Here it is assumed that there exists an underlying continuous variable for each binary outcome, so the joint distribution for weight and malformation can be assumed to follow a multivariate normal distribution. In both cases, specification of the full distribution will be avoided using pseudolikelihood and generalized estimating equations methodology, respectively. Quantitative risk assessment is illustrated using data from two developmental toxicology experiments. 相似文献
3.
Susan M. Parker Chris Gennings 《Journal of Agricultural, Biological & Environmental Statistics》2008,13(3):334-354
Classical optimal design theory may produce experimental designs that are biologically or characteristically inappropriate.
Often, there is a particular study goal along with many practical experimental concerns that a researcher may wish to include
in the optimal design process. This article provides a technique that allows a researcher to incorporate desired experimental
characteristics into an adjusted optimal design criterion. This technique uses a weighted overall desirability function to
penalize the optimal design criterion. A researcher may define an overall desirability function using any number of individual
desirability functions to influence the properties of an optimal experimental design. The methodology is illustrated with
two dose-response examples. 相似文献
4.
Many disciplines conduct studies in which the primary objectives depend on inference based on a nonlinear relationship between
the treatment and response. In particular, interest often focuses on calibration—that is, estimating the best treatment level
to achieve a particular result. Often, data for such calibration come from experiments with split-plots or other features
that result in multiple error terms or other nontrivial error structures. One such example is the time-of-weed-removal study
in weed science, designed to estimate the critical period of weed control. Calibration, or inverse prediction, is not a trivial
problem with simple linear regression, and the complexities of experiments such as the time-of-weed-removal study further
complicate the procedure. In this article, we extend existing calibration techniques to nonlinear mixed effects models, and
illustrate the procedure using data from a time-of-weed-removal study. 相似文献
5.
Mariola Sánchez-González María Durbán Dae-Jin Lee Isabel Cañellas Hortensia Sixto 《Journal of Agricultural, Biological & Environmental Statistics》2017,22(1):23-41
Aboveground biomass estimation in short-rotation forestry plantations is an essential step in the development of crop management strategies as well as allowing the economic viability of the crop to be determined prior to harvesting. Hence, it is important to develop new methodologies that improve the accuracy of predictions, using only a minimum set of easily obtainable information i.e., diameter and height. Many existing models base their predictions only on diameter (mainly due to the complexity of including further covariates), or rely on complicated equations to obtain biomass predictions. However, in tree species, it is important to include height when estimating aboveground biomass because this will vary from one genotype to another. This work proposes the use of a more flexible and easy to implement model for predicting aboveground biomass (stem, branches and total) as a smooth function of height and diameter using smooth additive mixed models which preserve the additive property necessary to model the relationship within wood fractions, and allows the inclusion of random effects and interaction terms. The model is applied to the analysis of three trials carried out in Spain, where nine clones at three different sites are compared. Also, an analysis of slash pine data is carried out in order to compare with the approach proposed by Parresol (Can J For Res 31:865–878, 2001).Supplementary materials accompanying this paper appear on-line 相似文献
6.
Temperature dependence of organic matter decomposition: a critical review using literature data analyzed with different models 总被引:14,自引:0,他引:14
The literature was reviewed regarding laboratory incubation studies where C mineralization was measured. Experiments were
selected in which the same substrate was incubated at least at two different temperatures and where time-series were available
with at least four measurements for each substrate and temperature. A first-order one-component model and a parallel first-order
two-component model were fitted to the CO2–C evolution data in each experiment using a least-squares procedure. After normalising for a reference temperature, the temperature
coefficient (Q
10
) function and three other temperature response functions were fitted to the estimated rate constants. The two-component model
could describe the dynamics of the 25 experiments much more adequately than the one-component model (higher R2, adjusted for the number of parameters), even when the rate constants for both were assumed to be equally affected by temperature.
The goodness-of-fit did not differ between the temperature response models, but was affected by the choice of the reference
temperature. For the whole data set, a Q
10
of 2 was found to be adequate for describing the temperature dependence of decomposition in the intermediate temperature
range (about 5–35 °C). However, for individual experiments, Q
10
values deviated greatly from 2. At least at temperatures below 5 °C, functions not based on Q
10
are probably more adequate. However, due to the paucity of data from low-temperature incubations, this conclusion is only
tentative, and more experimental work is called for.
Received: 1 December 1997 相似文献
7.
C. J. Brien C. G. B. Demétrio 《Journal of Agricultural, Biological & Environmental Statistics》2009,14(3):253-280
Mixed models have become important in analyzing the results of experiments, particularly those that require more complicated
models (e.g., those that involve longitudinal data). This article describes a method for deriving the terms in a mixed model.
Our approach extends an earlier method by Brien and Bailey to explicitly identify terms for which autocorrelation and smooth
trend arising from longitudinal observations need to be incorporated in the model. At the same time we retain the principle
that the model used should include, at least, all the terms that are justified by the randomization. This is done by dividing
the factors into sets, called tiers, based on the randomization and determining the crossing and nesting relationships between
factors. The method is applied to formulate mixed models for a wide range of examples. We also describe the mixed model analysis
of data from a three-phase experiment to investigate the effect of time of refinement on Eucalyptus pulp from four different
sources. Cubic smoothing splines are used to describe differences in the trend over time and unstructured covariance matrices
between times are found to be necessary. 相似文献
8.
9.
Molly I. Hartfield Richard F. Gunst 《Journal of Agricultural, Biological & Environmental Statistics》2003,8(1):105-121
Environmental data routinely are collected at irregularly spaced monitoring stations and at intermittent times, times which
may differ by location. This article introduces a class of continuous-time, continuous-space statistical models that can accommodate
many of these more complex environmental processes. This class of models in corporates temporal and spatial variability in
a cohesive manner and is broad enough to include temporal processes that are assumed to be generated by stochastic differential
equations with possibly temporally and spatially correlated errors. A wide range of ARIMA temporal models and geostatistical
spatial models are included in the class of models investigated. Techniques for identifying the structure of the temporal
and spatial components of this class of models are detailed. Point estimates of model parameters, asymptotic distributions,
and Kalman-filter prediction methods are discussed. 相似文献
10.
Measurements of both continuous and categorical outcomes appear in many statistical problems. One such example is the study
of teratology and developmental toxicity, where both the probability that a live fetus is malformed (ordinal) or of low birth
weight (continuous) are important measures in the context of teratogenicity. Although multivariate methods of the analysis
of continuous outcomes are well understood, methods for jointly continuous and discrete outcomes are less familiar. We propose
a likelihood-based method that is an extension of the Plackett-Dale approach. Specification of the full likelihood will be
avoided using pseudo-likelihood methodology. The estimation of safe dose levels as part of quantitative risk assessment will
be illustrated based on a developmental toxicity experiment of diethylene glycol dimethyl ether in mice. 相似文献
11.
Piepho Hans-Peter McCulloch Charles E. 《Journal of Agricultural, Biological & Environmental Statistics》2004,9(2):123-137
An important trait in crop cultivar evaluation is stability of performance across environments. There are many different measures
of stability, most of which are related to variance components of a mixed model. We believe that stability measures assessing
yield risk are of particular relevance, because they integrate location and scale parameters in a meaningful way. A prerequisite
for obtaining valid risk estimates is an appropriate model for the distribution of yield across environments. Multienvironment
trials (MET) are often analyzed by mixed linear models, assuming that environments are a random sample from a target population,
and that random terms in the model are normally distributed. The normality assumption may not always be tenable, and consequently,
risk estimates may be biased. In this article, we suggest a transformation approach based on the Johnson system to cope with
nonnormality in mixed models. The methods are exemplified using an international wheat yield trial. The importance of accounting
for nonnormality in risk analyses based on MET is emphasized. We suggest that transformations should be routinely considered
in analyses to assess risk. 相似文献
12.
为设计和优化面粉输送设备,应用离散元法对面粉进行准确地工程建模和分析,需要对其接触参数进行必要的标定。该研究依据颗粒缩放理论,用“Hertz-Mindlin with Johnson-Kendall-Roberts”接触模型表征面粉颗粒间黏性的影响,提出了一种基于静/动态休止角的接触参数标定方法。运用正交试验方法,对接触参数的敏感性和方差分析,表明面粉颗粒间的滚动摩擦系数、面粉颗粒与不锈钢表面间的静摩擦系数、表面能对静态休止角的影响极显著(P<0.01),并且多组接触参数都可以模拟出与试验相同的静态休止角。进一步研究表明,面粉颗粒与不锈钢表面间的静摩擦系数的合理取值范围为0.2~0.4。通过2种填充率、4种转速下基于动态休止角的参数标定,将其中与试验最为吻合的一组参数作为标定结果,其值如下:面粉颗粒之间恢复系数为0.6、面粉颗粒之间静摩擦系数为0.2、面粉颗粒之间滚动摩擦系数为0.1、面粉颗粒与不锈钢容器表面之间恢复系数为0.6、面粉颗粒与不锈钢容器表面之间静摩擦系数为0.6、面粉颗粒与不锈钢容器表面之间滚动摩擦系数为0.5、表面能为0.12 J/m2。使用该组参数对矩形容器中物料自由坍塌试验进行仿真,其结果与试验结果相符,验证了该标定方法的有效性。该研究提出的标定方法简单、易执行,对粉料输送设备的设计及优化具有一定的工程应用价值。 相似文献
13.
14.
Conservation planning and management decisions often present trade-offs among habitats and species, generating uncertainty about the composition and configuration of habitat that will best meet management goals. The public acquisition of 5471 ha of salt ponds in San Francisco Bay for tidal-marsh restoration presents just such a challenge. Because the existing ponds support large numbers of waterbirds, restoring the entire area to tidal marsh could cause undesirable local declines for many species. To identify management strategies that simultaneously maximize abundances of marsh- and pond-associated species, we applied an integer programming approach to maximize avian abundance, comparing across two objectives, two models, and five species weightings (20 runs total). For each pond, we asked: should it be restored to a tidal marsh or kept as a managed pond, and with what salinity and depth? We used habitat relationship models as inputs to non-linear integer programs to find optimal or near-optimal solutions. We found that a simple linear objective, based on maximizing a weighted sum of standardized species’ abundance, led to homogeneous solutions (all-pond or all-marsh). Maximizing a log-linear objective yielded more heterogeneous configurations that benefit more species. Including landscape terms in the models resulted in slightly greater habitat aggregation, but generally favored pond-associated species. It also led to the placement of certain habitats near the bay’s edge. Using the log-linear objective, optimal restoration configurations ranged from 9% to 60% tidal marsh, depending on the species weighting, highlighting the importance of thoughtful a priori consideration of priority species. 相似文献
15.
16.
Einar Heegaard Trygve Nilsen Trygve Nilsen 《Journal of Agricultural, Biological & Environmental Statistics》2007,12(3):414-430
Clustered data, either as an explicit part of the study design or due to the natural distribution of habitats, populations,
and so on, are frequently encountered by biologists. Mixed effect models provide a framework that can handle clustered data
by estimating cluster-specific random effects and introducing correlated residual structures. General parametric models have
been shown not to suit all biological problems, resulting in an increased popularity for local regression procedures, such
as LOESS and splines. To evaluate similar biological problems for clustered data with cluster-specific random effects and
potential dependencies between within-cluster residuals, we suggest a local linear mixed model (LLMM). The LLMM approach is
a local version of a linear mixed-effect model (LME), and the LLMM approach produces: (1) local shared predictions, (2) local
cluster-specific predictions, and (3) estimates of cluster-specific random effects conditioned on the covariates. Thus, in
addition to the local estimates of the expected response, we obtain information about how the cluster-specific random variability
depends on the values of the covariate. Ovary data are used to illustrate the flexibility and potential of this procedure
in biological contexts. 相似文献
17.
J. A. Tracey J. Zhu K. Crooks 《Journal of Agricultural, Biological & Environmental Statistics》2005,10(1):1-18
The study of individual animal movement in relation to objects in a landscape is important in many areas of ecology and conservation
biology. Yet, many of the models used by ecologists do not account for landscape features and thus may not be conducive to
analysis of animal movement data. This article develops a set of nonlinear regression models for both move angles and move
distances in relation to a single object in the landscape. Our models incorporate the concept of perceptual range from theories
of animal movement behavior. We describe numerical methods for obtaining the maximum likelihood estimates of the model parameters.
For illustration, we show results from both computer simulated data and real movement data collected for a red diamond rattlesnake
(Crotalus ruber) via radio telemetry field techniques. 相似文献
18.
This article considers the analysis of experiments with missing data from various experimental designs frequently used in
agricultural research (randomized complete blocks, split plots, strip plots). We investigate the small sample properties of
REML-based Wald-type F tests using linear mixed models. Several methods for approximating the denominator degrees of freedom are employed, all of
which are available with the MIXED procedure of the SAS System (8.02). The simulation results show that the Kenward-Roger
method provides the best control of the Type I error rate and is not inferior to other methods in terms of power. 相似文献
19.
William L. Thompson Amy E. Miller Dorothy C. Mortenson Andrea Woodward 《Biological conservation》2011,(5):1270-1277
Monitoring natural resources in Alaskan national parks is challenging because of their remoteness, limited accessibility, and high sampling costs. We describe an iterative, three-phased process for developing sampling designs based on our efforts to establish a vegetation monitoring program in southwest Alaska. In the first phase, we defined a sampling frame based on land ownership and specific vegetated habitats within the park boundaries and used Path Distance analysis tools to create a GIS layer that delineated portions of each park that could be feasibly accessed for ground sampling. In the second phase, we used simulations based on landcover maps to identify size and configuration of the ground sampling units (single plots or grids of plots) and to refine areas to be potentially sampled. In the third phase, we used a second set of simulations to estimate sample size and sampling frequency required to have a reasonable chance of detecting a minimum trend in vegetation cover for a specified time period and level of statistical confidence. Results of the first set of simulations indicated that a spatially balanced random sample of single plots from the most common landcover types yielded the most efficient sampling scheme. Results of the second set of simulations were compared with field data and indicated that we should be able to detect at least a 25% change in vegetation attributes over 31 years by sampling 8 or more plots per year every five years in focal landcover types. This approach would be especially useful in situations where ground sampling is restricted by access. 相似文献
20.
目前,中国大多数沼气工程均采用农作物秸秆与畜禽粪便为主要原料,但对于实际沼气工程的工艺控制,尤其是对于沼气工程进料混配及发酵浓度等控制工艺仍缺少参考和支撑。该研究采用玉米秸秆与牛粪原料,在中温条件下,利用纯牛粪、纯秸秆以及秸秆与牛粪干物质比(S:CM)=1:1、1:3、3:1条件的混合原料,按照不同干物质浓度(total solid,TS)=3%、6%、8%,梯次启动CSTR反应器,系统探讨物料配比与发酵浓度对反应器产气量、甲烷体积分数、pH值、氧化还原电位(oxidation-reductionpotential,ORP)、挥发酸(volatilefattyacids,VFAs)含量等运行特征的影响。结果表明,正常运行时,纯秸秆与纯牛粪条件下厌氧发酵产气效果显著低于混合原料,且所有条件下反应器的产气量基本都随着发酵浓度升高而升高。在发酵浓度为8%条件下,S:CM=3:1和1:1的反应器容积产气率在运行130和150 d后分别达到峰值0.78和0.76 L/(L·d)。随着反应器的持续运行,170 d后各反应器的产气率与pH值降低,而VFAs与ORP升高。S:CM=3:1和1:1的反应器容积产气率降低至0.6 L/(L·d),pH值降低至6.5左右。这主要是由于恒定的搅拌功率条件下,随着反应器内TS升高,搅拌转速降低,进而在反应器内产生搅拌死区与浮渣等问题,导致反应器内局部酸化,造成系统整体失稳。在启动期间,所有5个条件下反应器内ORP呈缓慢上升趋势。运行172 d后,S:CM=1:1条件下ORP迅速增加至高于–300 mV。总体而言,厌氧系统中VFA浓度随着进料中秸秆比例增加而增加,且丙酸积累发生并变得更加严重。这也在一定程度上表明,与采用秸秆与粪便混合原料厌氧发酵相比,采用纯秸秆原料厌氧发酵生产沼气厌氧反应器的运行稳定性较差。 相似文献