Comparison of Different Count Models for Investigation of Some Environmental Factors Affecting Stillbirth in Holsteins

Background: The objective of this study is comparing different count data models for stillbirth data. In modeling this type of data, Poisson regression or alternative models can be preferred. Methods: The poisson, negative binomial, zero-inflated poisson, zero-inflated negative binomial, poisson-logit hurdle and negative binomial-logit hurdle regressions were compared and used to examine the effects of the gender, parity and herd-year-season independent variables on stillbirth. Furthermore, the Log-Likelihood statistics, Akaike Information Criteria, Bayesian Information Criteria and rootogram graphs were used as comparison criteria for performance of the models. According to these criteria, Negative Binomial-Logit Hurdle Regression model was chosen as the best model. Result: The parameter estimates obtained by Negative Binomial-Logit Hurdle Regression model in relation to the effects of the gender, parity and herd-year-season independent variables on stillbirth were found to be significant (p less than 0.01). It was found that while stillbirth incidence was higher in males than females, it was found to decrease as the parity increased. As a result, the Negative Binomial Logit Hurdle model was found the best model for stillbirth count data with overdispersion.

The effect of mainland dynamics on data and parameter estimates in island biogeography

Understanding macroevolution on islands requires knowledge of the closest relatives of island species on the mainland. The evolutionary relationships between island and mainland species can be reconstructed using phylogenies, to which models can be fitted to understand the dynamical processes of colonisation and diversification. But how much information on the mainland is needed to gain insight into macroevolution on islands? Here we first test whether species turnover on the mainland and incomplete mainland sampling leave recognisable signatures in community phylogenetic data. We find predictable phylogenetic patterns: colonisation times become older and the perceived proportion of endemic species increases as mainland turnover and incomplete knowledge increase. We then analyse the influence of these factors on the inference performance of the island biogeography model DAISIE, a whole-island community phylogenetic model that assumes that mainland species do not diversify, and that the mainland is fully sampled in the phylogeny. We find that colonisation and diversification rate are estimated with little bias in the presence of mainland extinction and incomplete sampling. By contrast, the rate of anagenesis is overestimated under high levels of mainland extinction and incomplete sampling, because these increase the perceived level of island endemism. We conclude that community-wide phylogenetic and endemism datasets of island species carry a signature of mainland extinction and sampling. The robustness of parameter estimates suggests that island diversification and colonisation can be studied even with limited knowledge of mainland dynamics.

Devil in the details: how can we avoid potential pitfalls of CATS regression when our data do not follow a Poisson distribution?

Background Community assembly by trait selection (CATS) allows for the detection of environmental filtering and estimation of the relative role of local and regional (meta-community-level) effects on community composition from trait and abundance data without using environmental data. It has been shown that Poisson regression of abundances against trait data results in the same parameter estimates. Abundance data do not necessarily follow a Poisson distribution, and in these cases, other generalized linear models should be fitted to obtain unbiased parameter estimates. Aims This paper discusses how the original algorithm for calculating the relative role of local and regional effects has to be modified if Poisson model is not appropriate. Results It can be shown that the use of the logarithm of regional relative abundances as an offset is appropriate only if a log-link function is applied. Otherwise, the link function should be applied to the product of local total abundance and regional relative abundances. Since this product may be outside the domain of the link function, the use of log-link is recommended, even if it is not the canonical link. An algorithm is also suggested for calculating the offset when data are zero-inflated. The relative role of local and regional effects is measured by Kullback-Leibler R2. The formula for this measure presented by Shipley (2014) is valid only if the abundances follow a Poisson distribution. Otherwise, slightly different formulas have to be applied. Beyond theoretical considerations, the proposed refinements are illustrated by numerical examples. CATS regression could be a useful tool for community ecologists, but it has to be slightly modified when abundance data do not follow a Poisson distribution. This paper gives detailed instructions on the necessary refinement.

What underlies the observed hospital volume-outcome relationship?

Background Studies of the hospital volume-outcome relationship have highlighted that a greater volume activity improves patient outcomes. While this finding has been known for years, most studies to date have failed to delve into what underlies this relationship. Objective This study aimed to shed light on the basis of the hospital volume effect on patient outcomes by comparing treatment modalities for epithelial ovarian carcinoma patients. Data An exhaustive dataset of 355 patients in first-line treatment for Epithelial Ovarian Carcinoma (EOC) in 2012 in three regions of France was used. These regions account for 15% of the metropolitan French population. Methods In the presence of endogeneity induced by a reverse causality between hospital volume and patient outcomes, we used an instrumental variable approach. Hospital volume of activity was instrumented by the distance from patients’ homes to their hospital, the population density, and the median net income of patient municipalities. Results Based on our parameter estimates, we found that the rate of complete tumor resection would increase by 15.5 percentage points with centralized care, and by 8.3 percentage points if treatment decisions were coordinated by high-volume centers compared to decentralized care. Conclusion As volume alone is an imperfect correlate of quality, policy-makers need to know what volume is a proxy for in order to devise volume-based policies.

Sustainable Intensification of Beef Production in the Tropics: The Role of Genetically Improving Sexual Precocity of Heifers

Increasing productivity through continued animal genetic improvement is a crucial part of implementing sustainable livestock intensification programs. In Zebu cattle, the lack of sexual precocity is one of the main obstacles to improving beef production efficiency. Puberty-related traits are complex, but large-scale data sets from different “omics” have provided information on specific genes and biological processes with major effects on the expression of such traits, which can greatly increase animal genetic evaluation. In addition, genetic parameter estimates and genomic predictions involving sexual precocity indicator traits and productive, reproductive, and feed-efficiency related traits highlighted the feasibility and importance of direct selection for anticipating heifer reproductive life. Indeed, the case study of selection for sexual precocity in Nellore breeding programs presented here show that, in 12 years of selection for female early precocity and improved management practices, the phenotypic means of age at first calving showed a strong decreasing trend, changing from nearly 34 to less than 28 months, with a genetic trend of almost −2 days/year. In this period, the percentage of early pregnancy in the herds changed from around 10% to more than 60%, showing that the genetic improvement of heifer’s sexual precocity allows optimizing the productive cycle by reducing the number of unproductive animals in the herd. It has a direct impact on sustainability by better use of resources. Genomic selection breeding programs accounting for genotype by environment interaction represent promising tools for accelerating genetic progress for sexual precocity in tropical beef cattle.

MEMS Accelerometer Noises Analysis Based on Triple Estimation Fractional Order Algorithm

This paper is devoted to identifying parameters of fractional order noises with application to noises obtained from MEMS accelerometer. The analysis and parameters estimation will be based on the Triple Estimation algorithm, which can simultaneously estimate state, fractional order, and parameter estimates. The capability of the Triple Estimation algorithm to fractional noises estimation will be confirmed by the sets of numerical analyses for fractional constant and variable order systems with Gaussian noise input signal. For experimental data analysis, the MEMS sensor SparkFun MPU9250 Inertial Measurement Unit (IMU) was used with data obtained from the accelerometer in x, y and z-axes. The experimental results clearly show the existence of fractional noise in this MEMS’ noise, which can be essential information in the design of filtering algorithms, for example, in inertial navigation.

GENERALIZED AUTOREGRESSIVE CONDITIONAL HETEROSCEDASTICITY (GARCH) MODELS AND OPTIMAL FOR NIGERIAN STOCK EXCHANGE

This paper focused on comparative performance of GARCH models, ascertaining the best model fit, estimating the parameters and making prediction from optimal model. The study used UBA daily stock exchange prices sourced from the official websites of www.investing.com,on the daily basis of the Nigeria stock exchange rate over a period of ten years from 06/06/2012 – 04/06/2021. Five GARCH models (SGARCH, GJRGARCH or TGARCH, EGARCH, APGARCH and IGARCH) were fitted to the secondary data set of the Nigerian Stock exchange market for the period of June 2012- June 2021 and the results of the findings were obtained. The AIC results were SGARCH (1,1) (-6.1784), GJRGARCH (1,1) (-6.1778), EGARCH (1,1) (-6.1714) , APGARCH (1,1) (-6.1245) and IGARCH(1,1) with the value of AIC -6.1793. The EGARCH (1, 1) was found to be the optimal model with AIC value of -6.1714. The further findings indicated volatility clustering and leverage effect. The result of the analysis equally showed parameter estimates of the EGARCH (1,1) model and all the parameters were significant including mean and alpha. Prediction using the optimal model was made with an initial out of sample of 200 and n ahead of 200 with predicted values within the 95% confidence interval resulting there is no sign of volatility and clustering. Based on the findings of the study, other time series packages should be compared with GARCH models, data should be making available for easy access and investors should be encouraged to invest in United Bank for Africa (UBA, Nigeria).

Influence of model selection and data structure on the estimation of genetic parameters in honeybee populations

Estimating genetic parameters of quantitative traits is a prerequisite for animal breeding. In honeybees, the genetic variance separates into queen and worker effects. However, under data paucity, parameter estimations that account for this peculiarity often yield implausible results. Consequently, simplified models which attribute all genetic contributions to either the queen (queen model) or the workers (worker model) are often used to estimate variance components in honeybees. However, the causes for estimations with the complete model (colony model) to fail and the consequences of simplified models for variance estimates are little understood. We newly developed the necessary theory to compare parameter estimates that were achieved by the colony model with those of the queen and worker models. Furthermore, we performed computer simulations to quantify the influence of model choice, estimation algorithm, true genetic parameters, rates of controlled mating, apiary sizes, and phenotype data completeness on the success of genetic parameter estimations. We found that successful estimations with the colony model were only possible if at least some of the queens mated controlledly on mating stations. In that case, estimates were largely unbiased if more than 20% of the colonies had phenotype records. The simplified queen and worker models proved more stable and yielded plausible parameter estimates for almost all settings. Results obtained from these models were unbiased when mating was uncontrolled, but with controlled mating, the simplified models consistently overestimated heritabilities. This work elucidates the requirements for variance component estimation in honeybees and provides the theoretical groundwork for simplified honeybee models.

Growth Parameters and Spawning Season Estimation of Four Important Flyingfishes in the Kuroshio Current Off Taiwan and Implications From Comparisons With Global Studies

Growth shapes the life history of fishes. Establishing appropriate aging procedures and selecting representative growth models are important steps in developing stock assessments. Flyingfishes (Exocoetidae) have ecological, economic, and cultural importance to many coastal countries including Taiwan. There are 29 species of flyingfishes found in the Kuroshio Current off Taiwan and adjacent waters, comprising 56% of the flyingfishes taxa recorded worldwide. Among the six dominant species in Taiwan, four are of special importance. This study reviews aging data of these four species, documents major points of the aging methods to address three aging issues identified in the literature, and applies multi-model inference to estimate sex-combined and sex-specific growth parameters for each species. The candidate growth models examined included von Bertalanffy, Gompertz, Logistic, and Richards models, and the resulting optimal model tended to be the von Bertalanffy model for sex-combined data and Gompertz and von Bertalanffy models for sex-specific cases. The study also estimates hatch dates from size data collected from 2008 to 2017; the results suggest that the four flyingfishes have two spawning seasons per year. Length-weight relationships are also estimated for each species. Finally, the study combines the optimal growth estimates from this study with estimates for all flyingfishes published globally, and statistically classifies the estimates into clusters by hierarchical clustering analysis of logged growth parameters. The results demonstrate that aging materials substantially affect growth parameter estimates. This is the first study to estimate growth parameters of flyingfishes with multiple model consideration. This study provides advice for aging flyingfishes based on the three aging issues and the classification analysis, including a recommendation of using the asterisci for aging flyingfishes to avoid complex otolith processing procedures, which could help researchers from coastal countries to obtain accurate growth parameters for many flyingfishes.