Genomic analysis of feed efficiency traits in beef cattle using random regression models.

Feed efficiency plays a major role in the overall profitability and sustainability of the beef cattle industry, as it is directly related to the reduction of the animal demand for input and methane emissions. Traditionally, the average daily feed intake and weight gain are used to calculate feed efficiency traits. However, feed efficiency traits can be analysed longitudinally using random regression models (RRMs), which allow fitting random genetic and environmental effects over time by considering the covariance pattern between the daily records. Therefore, the objectives of this study were to: (1) propose genomic evaluations for dry matter intake (DMI), body weight gain (BWG), residual feed intake (RFI) and residual weight gain (RWG) data collected during an 84-day feedlot test period via RRMs; (2) compare the goodness-of-fit of RRM using Legendre polynomials (LP) and B-spline functions; (3) evaluate the genetic parameters behaviour for feed efficiency traits and their implication for new selection strategies. The datasets were provided by the EMBRAPA-GENEPLUS beef cattle breeding program and included 2920 records for DMI, 2696 records for BWG and 4675 genotyped animals. Genetic parameters and genomic breeding values (GEBVs) were estimated by RRMs under ssGBLUP for Nellore cattle using orthogonal LPs and B-spline. Models were compared based on the deviance information criterion (DIC). The ranking of the average GEBV of each test week and the overall GEBV average were compared by the percentage of individuals in common and the Spearman correlation coefficient (top 1%, 5%, 10% and 100%). The highest goodness-of-fit was obtained with linear B-Spline function considering heterogeneous residual variance. The heritability estimates across the test period for DMI, BWG, RFI and RWG ranged from 0.06 to 0.21, 0.11 to 0.30, 0.03 to 0.26 and 0.07 to 0.27, respectively. DMI and RFI presented within-trait genetic correlations ranging from low to high magnitude across different performance test-day. In contrast, BWG and RWG presented negative genetic correlations between the first 3 weeks and the other days of performance tests. DMI and RFI presented a high-ranking similarity between the GEBV average of week eight and the overall GEBV average, with Spearman correlations and percentages of individuals selected in common ranging from 0.95 to 1.00 and 93 to 100, respectively. Week 11 presented the highest Spearman correlations (ranging from 0.94 to 0.98) and percentages of individuals selected in common (ranging from 85 to 94) of BWG and RWG with the average GEBV of the entire period of the test. In conclusion, the RRM using linear B-splines is a feasible alternative for the genomic evaluation of feed efficiency. Heritability estimates of DMI, RFI, BWG and RWG indicate enough additive genetic variance to achieve a moderate response to selection. A new selection strategy can be adopted by reducing the performance test to 56 days for DMI and RFI selection and 77 days for BWG and RWG selection.

Modeling the evolution of deaths from infectious diseases with functional data models: The case of COVID-19 in Brazil.

In this paper, we apply statistical methods for functional data to explore the heterogeneity in the registered number of deaths of COVID-19, over time. The cumulative daily number of deaths in regions across Brazil is treated as continuous curves (functional data). The first stage of the analysis applies clustering methods for functional data to identify and describe potential heterogeneity in the curves and their functional derivatives. The estimated clusters are labeled with different "levels of alert" to identify cities in a possible critical situation. In the second stage of the analysis, we apply a functional quantile regression model for the death curves to explore the associations with functional rates of vaccination and stringency and also with several scalar geographical, socioeconomic and demographic covariates. The proposed model gave a better curve fit at different levels of the cumulative number of deaths when compared to a functional regression model based on ordinary least squares. Our results add to the understanding of the development of COVID-19 death counts.

Varying Coefficient Mediation Model and Application to Analysis of Behavioral Economics Data.

This article is concerned with causal mediation analysis with varying indirect and direct effects. We propose a varying coefficient mediation model, which can also be viewed as an extension of moderation analysis on a causal diagram. We develop a new estimation procedure for the direct and indirect effects based on B-splines. Under mild conditions, rates of convergence and asymptotic distributions of the resulting estimates are established. We further propose a F-type test for the direct effect. We conduct simulation study to examine the finite sample performance of the proposed methodology, and apply the new procedures for empirical analysis of behavioral economics data.

A Spatially Correlated Model with Generalized Autoregressive Conditionally Heteroskedastic Structure for Counts of Crimes.

Crime is a negative phenomenon that affects the daily life of the population and its development. When modeling crime data, assumptions on either the spatial or the temporal relationship between observations are necessary if any statistical analysis is to be performed. In this paper, we structure space-time dependency for count data by considering a stochastic difference equation for the intensity of the space-time process rather than placing structure on a latent space-time process, as Cox processes would do. We introduce a class of spatially correlated self-exciting spatio-temporal models for count data that capture both dependence due to self-excitation, as well as dependence in an underlying spatial process. We follow the principles in Clark and Dixon (2021) but considering a generalized additive structure on spatio-temporal varying covariates. A Bayesian framework is proposed for inference of model parameters. We analyze three distinct crime datasets in the city of Riobamba (Ecuador). Our model fits the data well and provides better predictions than other alternatives.

Estimate of the rate of unreported COVID-19 cases during the first outbreak in Rio de Janeiro.

In this work we fit an epidemiological model SEIAQR (Susceptible - Exposed - Infectious - Asymptomatic - Quarantined - Removed) to the data of the first COVID-19 outbreak in Rio de Janeiro, Brazil. Particular emphasis is given to the unreported rate, that is, the proportion of infected individuals that is not detected by the health system. The evaluation of the parameters of the model is based on a combination of error-weighted least squares method and appropriate B-splines. The structural and practical identifiability is analyzed to support the feasibility and robustness of the parameters' estimation. We use the Bootstrap method to quantify the uncertainty of the estimates. For the outbreak of March-July 2020 in Rio de Janeiro, we estimate about 90% of unreported cases, with a 95% confidence interval (85%, 93%).