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| 2. |
- Alam, Moudud, 1976-, et al.
(author)
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Fitting conditional and simultaneous autoregressive spatial models in hglm
- 2015
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In: The R Journal. - 2073-4859. ; 7:2, s. 5-18
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Journal article (peer-reviewed)abstract
- We present a new version (> 2.0) of the hglm package for fitting hierarchical generalized linear models (HGLMs) with spatially correlated random effects. CAR() and SAR() families for conditional and simultaneous autoregressive random effects were implemented. Eigen decomposition of the matrix describing the spatial structure (e.g., the neighborhood matrix) was used to transform the CAR/SAR random effects into an independent, but eteroscedastic, Gaussian random effect. A linear predictor is fitted for the random effect variance to estimate the parameters in the CAR and SAR models. This gives a computationally efficient algorithm for moderately sized problems.
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| 3. |
- Alam, Moudud, et al.
(author)
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Fitting spatial models in the R package: hglm
- 2014
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Reports (other academic/artistic)abstract
- We present a new version of the hglm package for fittinghierarchical generalized linear models (HGLM) with spatially correlated random effects. A CAR family for conditional autoregressive random effects was implemented. Eigen decomposition of the matrix describing the spatial structure (e.g. the neighborhood matrix) was used to transform the CAR random effectsinto an independent, but heteroscedastic, gaussian random effect. A linear predictor is fitted for the random effect variance to estimate the parameters in the CAR model.This gives a computationally efficient algorithm for moderately sized problems (e.g. n<5000).
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| 4. |
- Alvarez-Castro, Jose, et al.
(author)
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Estimation and interpretation of genetic effects with epistasis using the NOIA model.
- 2012
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In: Methods in Molecular Biology. - Totowa, NJ : Humana Press. - 1064-3745 .- 1940-6029. ; 871, s. 191-204
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Journal article (peer-reviewed)abstract
- We introduce this communication with a brief outline of the historical landmarks in genetic modeling, especially concerning epistasis. Then, we present methods for the use of genetic modeling in QTL analyses. In particular, we summarize the essential expressions of the natural and orthogonal interactions (NOIA) model of genetic effects. Our motivation for reviewing that theory here is twofold. First, this review presents a digest of the expressions for the application of the NOIA model, which are often mixed with intermediate and additional formulae in the original articles. Second, we make the required theory handy for the reader to relate the genetic concepts to the particular mathematical expressions underlying them. We illustrate those relations by providing graphical interpretations and a diagram summarizing the key features for applying genetic modeling with epistasis in comprehensive QTL analyses. Finally, we briefly review some examples of the application of NOIA to real data and the way it improves the interpretability of the results.
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| 6. |
- Anglart, D, et al.
(author)
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Detecting and predicting changes in milk homogeneity using data from automatic milking systems.
- 2021
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In: Journal of Dairy Science. - : American Dairy Science Association. - 0022-0302 .- 1525-3198. ; 104:10, s. 11009-11017
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Journal article (peer-reviewed)abstract
- To ensure milk quality and detect cows with signs of mastitis, visual inspection of milk by prestripping quarters before milking is recommended in many countries. An objective method to find milk changed in homogeneity (i.e., with clots) is to use commercially available inline filters to inspect the milk. Due to the required manual labor, this method is not applicable in automatic milking systems (AMS). We investigated the possibility of detecting and predicting changes in milk homogeneity using data generated by AMS. In total, 21,335 quarter-level milk inspections were performed on 5,424 milkings of 624 unique cows on 4 farms by applying visual inspection of inline filters that assembled clots from the separate quarters during milking. Images of the filters with clots were scored for density, resulting in 892 observations with signs of clots for analysis (77% traces or mild cases, 15% moderate cases, and 8% heavy cases). The quarter density scores were combined into 1 score indicating the presence of clots during a single cow milking and into 2 scores summarizing the density scores in cow milkings during a 30-h sampling period. Data generated from the AMS, such as milk yield, milk flow, conductivity, and online somatic cell counts, were used as input to 4 multilayer perceptron models to detect or predict single milkings with clots and to detect milking periods with clots. All models resulted in high specificity (98-100%), showing that the models correctly classified cow milkings or cow milking periods with no clots observed. The ability to successfully classify cow milkings or cow periods with observed clots had a low sensitivity. The highest sensitivity (26%) was obtained by the model that detected clots in a single milking. The prevalence of clots in the data was low (2.4%), which was reflected in the results. The positive predictive value depends on the prevalence and was relatively high, with the highest positive predictive value (72%) reached in the model that detected clots during the 30-h sampling periods. The misclassification rate for cow milkings that included higher-density scores was lower, indicating that the models that detected or predicted clots in a single milking could better distinguish the heavier cases of clots. Using data from AMS to detect and predict changes in milk homogeneity seems to be possible, although the prediction performance for the definitions of clots used in this study was poor.
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| 7. |
- Besnier, Francois, et al.
(author)
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Fine mapping and replication of QTL in outbred chicken advanced intercross lines
- 2011
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In: Genetics Selection Evolution. - Paris : Springer Science and Business Media LLC. - 0999-193X .- 1297-9686. ; 43, s. 3-
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Journal article (peer-reviewed)abstract
- BACKGROUND: Linkage mapping is used to identify genomic regions affecting the expression of complex traits. However, when experimental crosses such as F2 populations or backcrosses are used to map regions containing a Quantitative Trait Locus (QTL), the size of the regions identified remains quite large, i.e. 10 or more Mb. Thus, other experimental strategies are needed to refine the QTL locations. Advanced Intercross Lines (AIL) are produced by repeated intercrossing of F2 animals and successive generations, which decrease linkage disequilibrium in a controlled manner. Although this approach is seen as promising, both to replicate QTL analyses and fine-map QTL, only a few AIL datasets, all originating from inbred founders, have been reported in the literature.METHODS: We have produced a nine-generation AIL pedigree (n = 1529) from two outbred chicken lines divergently selected for body weight at eight weeks of age. All animals were weighed at eight weeks of age and genotyped for SNP located in nine genomic regions where significant or suggestive QTL had previously been detected in the F2 population. In parallel, we have developed a novel strategy to analyse the data that uses both genotype and pedigree information of all AIL individuals to replicate the detection of and fine-map QTL affecting juvenile body weight.RESULTS: Five of the nine QTL detected with the original F2 population were confirmed and fine-mapped with the AIL, while for the remaining four, only suggestive evidence of their existence was obtained. All original QTL were confirmed as a single locus, except for one, which split into two linked QTL.CONCLUSIONS: Our results indicate that many of the QTL, which are genome-wide significant or suggestive in the analyses of large intercross populations, are true effects that can be replicated and fine-mapped using AIL. Key factors for success are the use of large populations and powerful statistical tools. Moreover, we believe that the statistical methods we have developed to efficiently study outbred AIL populations will increase the number of organisms for which in-depth complex traits can be analyzed.
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| 9. |
- Carling, Kenneth, et al.
(author)
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Is Firm Interdependence within Industries Important for Portfolio Credit Risk?
- 2004
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Reports (other academic/artistic)abstract
- A drawback of available portfolio credit risk models is that they fail to allow for default risk dependency across loans other than through common risk factors. Thereby, thesemodels ignore that close ties can exist between companies due to legal, financial and business relations. In this paper, we integrate the insights from theoretical models of default correlation into a commonly used model of default and portfolio credit risk by allowing for dependency between firm default risk through both common factors and industry specific errors in a duration model. An application using pooled data from two Swedish banks’ business loan portfolios over the period 1996-2000 shows that estimates of individual default risk are little affected by including industry specific errors. However, accounting for these industry effects increases VaR estimates by 50-200 percent. A traditional model with only systematic factors, although able to fit the broad trends in credit losses, cannot match these fluctuations because it fails to capture credit losses in bad times, when banks are typically hit by large unexpected credit losses. The model we propose manages to follow both the trend in credit losses and produce industry driven, time-varying, fluctuations in losses around that trend. Consequently, this model will better aid banks and regulators in determining the appropriate size of economic capital requirements. Capital buffers derived from our model will be larger for periods with large ”aggregate” disturbances and smaller in better times, and avoid both overcapitalization in good times and undercapitalization in bad times.
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| 10. |
- Casals, M., et al.
(author)
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Parameter estimation of Poisson generalized linear mixed models based on three different statistical principles : a simulation study
- 2015
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In: SORT - Statistics and Operations Research Transactions. - 1696-2281 .- 2013-8830. ; 39:2, s. 281-308
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Journal article (peer-reviewed)abstract
- Generalized linear mixed models are flexible tools for modeling non-normal data and are useful for accommodating overdispersion in Poisson regression models with random effects. Their main difficulty resides in the parameter estimation because there is no analytic solution for the maximization of the marginal likelihood. Many methods have been proposed for this purpose and many of them are implemented in software packages. The purpose of this study is to compare the performance of three different statistical principles - marginal likelihood, extended likelihood, Bayesian analysis-via simulation studies. Real data on contact wrestling are used for illustration.
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