scholarly journals The algorithm of Bayesian estimation of maternal genetic and permanent maternal environmental variances in a two-trait binary threshold model

2011 ◽  
Vol 49 (No. 2) ◽  
pp. 58-63
Author(s):  
E. Skotarczak ◽  
M. Szyd ◽  
A. Dobek ◽  
K. Moli ◽  
T. Szwaczkowski
Keyword(s):  
Bayesian Estimation ◽  
Gibbs Sampling ◽  
Random Effects ◽  
Environmental Effects ◽  
Fixed Effects ◽  
Threshold Model ◽  
Sampling Procedure ◽  
Numerical Example ◽  
Estimation And Prediction

The paper presents an algorithm for the estimation and prediction of parameters in a two-trait binary threshold model. The model includes fixed effects and the following random effects: genetic direct additive, genetic maternal additive and permanent maternal environmental effects. The Gibbs sampling procedure was used to estimate the parameters. The algorithm was illustrated with a numerical example showing appropriateness of the proposed method.  

scholarly journals EFEITO DO MEIO E DA IDADE DA VACA SOBRE O GANHO DE PESO NA FASE DE CRIA, RECRIA E OS DIAS PARA SE OBTER 160 KG EM ANIMAIS DA RAÇA GUZERÁ

2004 ◽  
Vol 9 (1) ◽  
Author(s):  
E. GEMIN ◽  
J.C. SOUZA ◽  
L.O.C. SILVA ◽  
C.H.M. MALHADO ◽  
P.B. FERRAZ FILHO
Keyword(s):  
Environmental Factors ◽  
Statistical Model ◽  
Least Squares ◽  
Random Effects ◽  
Environmental Effects ◽  
Fixed Effects ◽  
Least Squares Method ◽  
Data Set ◽  
Quadratic Effect ◽  
Daily Gain

O objetivo deste trabalho foi avaliar a influência dos efeitos de meio e da idade da vaca sobre os ganhos de peso do nascimento ao desmame (GPD), período pós-desmame (GPS) e sobre o número de dias para se obter 160 kg (D160). O rebanho avaliado continha 1.747 animais, sendo os dados analisados pelo método dos quadrados mínimos utilizando-se um modelo estatístico contendo os efeitos fixos de mês, ano e sexo do bezerro, o efeito aleatório de touros na fazenda, e como covariável a idade da vaca ao parto. As médias ajustadas para ganho de peso pré e pós-desmame, e para dias para a obtenção 160 kg foram 0,604 ± 0,01 kg; 0,399 ± 0,01 kg; em 285 ± 5,3 dias, respectivamente. Os machos foram superiores às fêmeas relativo ao GPD = 6,0%; D160 = 5,8 %, GPS = 20,1%. Quanto ao mês, as maiores médias de ganho de peso no pré-desmame recaiu nos animais nascidos no mês de agosto. Com relação aos dias para se obter 160 kg, os melhores resultados foram dos animais nascidos nos meses julho a setembro. A idade da vaca influenciou as caracteristicas ganho de peso pré-desmame e no D160. Environmental effects and age of dam on pre- and post-weaning daily gain, and on number of days to gain 160 kg from birth to weaning on guzerath breed cattle Abstract The objective of this study was to evaluate the effects of environmental factors and age of dam on pre- (GPD) and post-weaning (GPS) daily gain, and on the were number of days to gain 160 kg (D160) from birth to weaning. The data set contained 1,747 animals, and were analyzed by the least squares method. The statistical model included the fixed effects of month and year of birth, and sex of the calf and age of the dam at calving. Sire nested within farm and the error were random effects. The pre- and post-weaning average daily gains, and days to gain 160 kg least squares means were 0.604 ± 0.01 kg, 0.399 ± 0.01 kg, and 285.0 ± 5.3 days, respectively. The males were 6.0, 21.1 and 5.8% superior to the females for GPD, GPS and D160, respectively. The highest pre-weaning gain was for the animals born August. Regarding D160, the best results were for the animals born from July to September. Age of the cow showed a significant quadratic effect on the traits. The best cows were the 94-month-old ones. First calving cows produced the lightest calves. The results showed the importance of the environmental effects on the traits studied, evidencing the need for them to be corrected.

scholarly journals A random effects population dynamics model based on proportions-at-age and removal data for estimating total mortality

2012 ◽  
Vol 69 (11) ◽  
pp. 1881-1893 ◽  
Author(s):  
Verena M. Trenkel ◽  
Mark V. Bravington ◽  
Pascal Lorance
Keyword(s):  
Population Dynamics ◽  
Random Effects ◽  
Fixed Effects ◽  
Random Effect ◽  
Total Mortality ◽  
Estimation Bias ◽  
Effective Sample Size ◽  
Dynamics Model ◽  
Population Dynamics Model ◽  
Study Parameter

Catch curves are widely used to estimate total mortality for exploited marine populations. The usual population dynamics model assumes constant recruitment across years and constant total mortality. We extend this to include annual recruitment and annual total mortality. Recruitment is treated as an uncorrelated random effect, while total mortality is modelled by a random walk. Data requirements are minimal as only proportions-at-age and total catches are needed. We obtain the effective sample size for aggregated proportion-at-age data based on fitting Dirichlet-multinomial distributions to the raw sampling data. Parameter estimation is carried out by approximate likelihood. We use simulations to study parameter estimability and estimation bias of four model versions, including models treating mortality as fixed effects and misspecified models. All model versions were, in general, estimable, though for certain parameter values or replicate runs they were not. Relative estimation bias of final year total mortalities and depletion rates were lower for the proposed random effects model compared with the fixed effects version for total mortality. The model is demonstrated for the case of blue ling (Molva dypterygia) to the west of the British Isles for the period 1988 to 2011.

scholarly journals Understanding, Choosing, and Unifying Multilevel and Fixed Effect Approaches

2020 ◽  
pp. 1-20
Author(s):  
Chad Hazlett ◽  
Leonard Wainstein
Keyword(s):  
Random Effects ◽  
Fixed Effects ◽  
Multilevel Models ◽  
Standard Errors ◽  
Point Estimate ◽  
Fe Model ◽  
Grouped Data ◽  
Coefficient Estimates ◽  
Political Science Education ◽  
Robust Standard Errors

Abstract When working with grouped data, investigators may choose between “fixed effects” models (FE) with specialized (e.g., cluster-robust) standard errors, or “multilevel models” (MLMs) employing “random effects.” We review the claims given in published works regarding this choice, then clarify how these approaches work and compare by showing that: (i) random effects employed in MLMs are simply “regularized” fixed effects; (ii) unmodified MLMs are consequently susceptible to bias—but there is a longstanding remedy; and (iii) the “default” MLM standard errors rely on narrow assumptions that can lead to undercoverage in many settings. Our review of over 100 papers using MLM in political science, education, and sociology show that these “known” concerns have been widely ignored in practice. We describe how to debias MLM’s coefficient estimates, and provide an option to more flexibly estimate their standard errors. Most illuminating, once MLMs are adjusted in these two ways the point estimate and standard error for the target coefficient are exactly equal to those of the analogous FE model with cluster-robust standard errors. For investigators working with observational data and who are interested only in inference on the target coefficient, either approach is equally appropriate and preferable to uncorrected MLM.

scholarly journals Association of bisphenol A with puberty timing: a meta-analysis

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Hui Meng ◽  
Yunping Zhou ◽  
Yunxia Jiang
Keyword(s):  
Bisphenol A ◽  
Confidence Intervals ◽  
Random Effects ◽  
Strong Correlation ◽  
Fixed Effects ◽  
Meta Analysis ◽  
Random Effects Models ◽  
Study Heterogeneity ◽  
The Relationship ◽  
Prevalence Ratios

AbstractObjectivesThe results of existing studies on bisphenol A (BPA) and puberty timing did not reach a consensus. Thereby we performed this meta-analytic study to explore the association between BPA exposure in urine and puberty timing.MethodsMeta-analysis of the pooled odds ratios (OR), prevalence ratios (PR) or hazards ratios (HR) with 95% confidence intervals (CI) were calculated and estimated using fixed-effects or random-effects models based on between-study heterogeneity.ResultsA total of 10 studies involving 5621 subjects were finally included. The meta-analysis showed that BPA exposure was weakly associated with thelarche (PR: 0.96, 95% CI: 0.93–0.99), while no association was found between BPA exposure and menarche (HR: 0.99, 95% CI: 0.89–1.12; OR: 1.02, 95% CI: 0.73–1.43), and pubarche (OR: 1.00, 95% CI: 0.79–1.26; PR: 1.00, 95% CI: 0.95–1.05).ConclusionsThere was no strong correlation between BPA exposure and puberty timing. Further studies with large sample sizes are needed to verify the relationship between BPA and puberty timing.

1 Effect of Conditioning, Rest, and Post-rest Transport Duration on Welfare Indicators of Beef Cattle Transported by Road

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 2-3
Author(s):  
Daniela M Melendez ◽  
Sonia Marti ◽  
Timothy D Schwinghamer ◽  
Derek B Haley ◽  
Karen S Schwartzkopf-Genswein
Keyword(s):  
Beef Cattle ◽  
Factorial Design ◽  
Random Effects ◽  
Fixed Effects ◽  
Rest Period ◽  
Flight Speed ◽  
Beef Calves ◽  
Welfare Indicators ◽  
Preliminary Results ◽  
And Performance

Abstract The aim of this study was to assess the effects of conditioning, rest, and post-rest transport duration on welfare indicators of 6–7 mo old beef calves. Three hundred and twenty-eight weaned calves (237 ± 29.7 kg BW) were randomly assigned to a 2 × 2 × 2 nested factorial design: conditioning, conditioned (C) or non-conditioned (N); rest, 0 (R0) or 8 (R8) h, and post-rest transport, 4 (T4) or 15 (T15) h. Calves were sampled prior to the first loading (L1), after 20h of transport, prior to and after the additional 4 or 15-h transport, and at 1, 2, 3, 5, 14, and 28 d after transport ended. Data were analyzed using the GLIMMIX procedure of SAS. Fixed effects included conditioning, transport and time nested within rest period, while random effects included animal and pen. Greater shrink (P < 0.01) was observed in C than N calves after the initial 20-h transport. The N calves had greater (P < 0.01) ADG than C calves between L1 and d 5, while C had greater (P < 0.01) ADG than N calves between 14 and 28 d. L-lactate concentrations and flight speed were greater (P ≤ 0.05) in C than N calves between L1 and d 5. The R8-T4 calves had greater (P < 0.01) ADG than R8-T15 calves between L1 and d 5. The R0-T4 calves had greater (P = 0.02) L-lactate concentrations than R0-T15 and R8-T4 calves on d 1. The R0 calves had greater (P < 0.01) ADG than R8 calves between 14 and 28 d. Preliminary results show physiological, behavioral, and performance differences across treatments, however, additional indicators are required to accurately assess the effect of conditioning, rest, and post-rest transport durations on calf welfare.

PSVIII-5 Genetic parameters of thrombin as a proxy for horn fly abundance in beef cattle

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 239-239
Author(s):  
Ashley S Ling ◽  
Taylor Krause ◽  
Amanda Warner ◽  
Jason Duggin ◽  
Bradley Heins ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Fixed Effects ◽  
Large Scale ◽  
Genetic Basis ◽  
Threshold Model ◽  
Economic Losses ◽  
Small Data ◽  
Horn Fly ◽  
Improvement Programs ◽  
Highest Posterior Density

Abstract Horn flies (Haematobia irritans) are a major nuisance to cattle, especially in warm, humid regions, and are estimated to cause economic losses in excess of $1 billion annually to the U.S. beef cattle industry. Variation in horn fly tolerance has been reported within and across breeds, and heritability estimates ranging between 10 and 80% show a clear genetic basis. However, collecting fly abundance phenotypes is costly and logistically demanding, which precludes large-scale implementation. Consequently, finding correlated phenotypes and endo-phenotypes that are heritable and relatively easy to measure would facilitate implementation of horn fly tolerance genetic improvement programs. Thrombin (TH), a blood coagulation precursor, has a reported association with horn fly count variation within and across cattle breeds. In this study, the genetic basis of thrombin in beef cattle was investigated. Blood samples and horn fly count were collected on 360 cows and heifers twice during the summer of 2019 (June and August). Due to uncertainty associated with assessment of horn fly abundance and thrombin and the fact that economic losses occur only when fly abundance exceeds a certain threshold, thrombin was categorized into 4 classes (1=TH > 500 ng/ml; 2=250< TH< 500 ng/ml; 3=100< TH< 250 ng/ml; and 4=TH< 100 ng/ml). The trait was analyzed using linear (continuous) and threshold (discrete) mixed models. Both models included farm, pregnancy status, and cow age as fixed effects and additive and permanent environment random effects. The pedigree included 642 animals. Estimates of heritability were 0.24 and 0.29 using linear and threshold models, respectively. Estimates of repeatability were slightly higher using the threshold model (0.21 vs 0.19). Despite the small data size, all estimates were non-zero based on their respective highest posterior density intervals. These results indicate reasonable genetic variation for thrombin that could be harnessed for improvement of horn fly tolerance in cattle.

The relationship between migraine and infant colic: A systematic review and meta-analysis

Cephalalgia ◽  
2014 ◽  
Vol 35 (1) ◽  
pp. 63-72 ◽  
Author(s):  
Amy A Gelfand ◽  
Peter J Goadsby ◽  
I Elaine Allen
Keyword(s):  
Systematic Review ◽  
Random Effects ◽  
Odds Ratio ◽  
Fixed Effects ◽  
Meta Analysis ◽  
Random Effects Model ◽  
Fixed Effects Model ◽  
Primary Analysis ◽  
Infant Colic ◽  
The Relationship

Context Infant colic is a common and distressing disorder of early infancy. Its etiology is unknown, making treatment challenging. Several articles have suggested a link to migraine. Objective The objective of this article was to perform a systematic review and, if appropriate, a meta-analysis of the studies on the relationship between infant colic and migraine. Data sources Studies were identified by searching PubMed and ScienceDirect and by hand-searching references and conference proceedings. Study selection For the primary analysis, studies specifically designed to measure the association between colic and migraine were included. For the secondary analysis, studies that collected data on colic and migraine but were designed for another primary research question were also included. Data extraction Data were abstracted from the original studies, through communication with study authors, or both. Two authors independently abstracted data. Main outcomes and measures The main outcome measure was the association between infant colic and migraine using both a fixed-effects model and a more conservative random-effects model. Results Three studies were included in the primary analysis; the odds ratio for the association between migraine and infant colic was 6.5 (4.6–8.9, p < 0.001) for the fixed-effects model and 5.6 (3.3–9.5, p = 0.004) for the random-effects model. In a sensitivity analysis wherein the study with the largest effect size was removed, the odds ratio was 3.6 (95% CI 1.7–7.6, p = 0.001) for both the fixed-effects model and random-effects model. Conclusions In this meta-analysis, infant colic was associated with increased odds of migraine. If infant colic is a migrainous disorder, this would have important implications for treatment. The main limitation of this meta-analysis was the relatively small number of studies included.

scholarly journals Selection of a suitable data set and model for the genetic evaluation of the linear description of conformation and type description in Old Kladruber horses

2012 ◽  
Vol 55 (2) ◽  
pp. 105-112
Author(s):  
L. Vostrý ◽  
K. Mach ◽  
J. Přibyl
Keyword(s):  
Random Effects ◽  
Fixed Effects ◽  
Genetic Parameters ◽  
Suitable Model ◽  
Residual Variance ◽  
Linear Type ◽  
Colour Variant ◽  
Repeated Evaluation ◽  
Estimation Of Genetic Parameters ◽  
Selection Of

Abstract. The objective of this paper was to select a suitable data subset and statistical model for the estimation of genetic parameters for 36 traits of the linear type in 977 Old Kladruber horses. Two subsets were tested to identify a suitable subset for analysis. One subset included repeated evaluation of certain individuals, whereas the other did not. The most suitable subset included repeated evaluation (n=1 390). The selection of a suitable model was made from 4 candidate models. These models comprised a number of random effects (direct individual effect and animal permanent environmental effect of the animal) and a number of fixed effects (colour variant, stud, colour variant × stud interaction, sex, age at description, year of birth, year of description). The model was selected based on the Akaike information criterion (AIC, Akaike 1974), residual variance and heritability coefficient. The model that included colour variant, stud, colour variant × stud interaction, sex, age at description, and year of description as fixed effects and direct individual and animal permanent environment as random effects was the most suitable model for the estimation of genetic parameters and for the subsequent estimation of breeding values.

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