Estimates of genetic parameters for scrotal circumference using random regression models in Nelore cattle

A total of 15,901 scrotal circumference (SC) records from 5300 Nelore bulls, ranging from 229 to 560 days of age, were used with the objective of estimating (co)variance functions for SC, using random regression models. Models included the fixed effects of contemporary group and age of dam at calving as covariable (linear and quadratic effects). To model the population mean trend, a third order Legendre polynomial on animal age was utilized. The direct additive genetic and animal permanent environmental random effects were modeled by Legendre polynomials on animal age, with orders of fit ranging from 1 to 5. Residual variances were modeled considering 1 (homogeneity of variance) or 4 age classes. Results obtained with the random regression models were compared to multi-trait analysis. (Co)variance estimates using multi-trait and random regression models were similar. The model considering a third- and fifth-order Legendre polynomials for additive genetic and animal permanent environmental effects, respectively, was the most adequate to model changes in variance of SC with age. Heritability estimates for SC ranged from 0.24 (229 days of age) to 0.47 (300 days of age), remained almost constant until 500 days of age (0.52), decreasing thereafter (0.44). In general, the genetic correlations between measures of scrotal circumference obtained from 229 to 560 days of age decreased with increasing distance between ages. For genetic evaluation scrotal circumference could be measured between 400 and 500 days of age. (C) 2010 Elsevier B.V. All rights reserved.

Estimation models of variance components for farrowing interval in swine

Este trabalho teve como objetivo principal avaliar a importância da inclusão dos efeitos genético materno, comum de leitegada e de ambiente permanente no modelo de estimação de componentes de variância para a característica intervalo de parto em fêmeas suínas. Foram utilizados dados que consistiam de 1.013 observações de fêmeas Dalland (C-40), registradas em dois rebanhos. As estimativas dos componentes de variância foram realizadas pelo método da máxima verossimilhança restrita livre de derivadas. Foram testados oito modelos, que continham os efeitos fixos (grupos de contemporâneo e covariáveis) e os efeitos genético aditivo direto e residual, mas variavam quanto à inclusão dos efeitos aleatórios genético materno, ambiental comum de leitegada e ambiental permanente. O teste da razão de verossimilhança (LR) indicou a não necessidade da inclusão desses efeitos no modelo. No entanto observou-se que o efeito ambiental permanente causou mudança nas estimativas de herdabilidade, que variaram de 0,00 a 0,03. Conclui-se que os valores de herdabilidade obtidos indicam que esta característica não apresentaria ganho genético como resposta à seleção. O efeito ambiental comum de leitegada e o genético materno não apresentaram influência sobre esta característica. Já o ambiental permanente, mesmo sem ter sido significativo o seu efeito pelo LR, deve ser considerado nos modelos genéticos para essa característica, pois sua presença causou mudança nas estimativas da variância genética aditiva.

Computed success rates of various carrier phase integer estimation solutions and their comparison with statistical success rates

The success rate of carrier phase ambiguity resolution (AR) is the probability that the ambiguities are successfully fixed to their correct integer values. In existing works, an exact success rate formula for integer bootstrapping estimator has been used as a sharp lower bound for the integer least squares (ILS) success rate. Rigorous computation of success rate for the more general ILS solutions has been considered difficult, because of complexity of the ILS ambiguity pull-in region and computational load of the integration of the multivariate probability density function. Contributions of this work are twofold. First, the pull-in region mathematically expressed as the vertices of a polyhedron is represented by a multi-dimensional grid, at which the cumulative probability can be integrated with the multivariate normal cumulative density function (mvncdf) available in Matlab. The bivariate case is studied where the pull-region is usually defined as a hexagon and the probability is easily obtained using mvncdf at all the grid points within the convex polygon. Second, the paper compares the computed integer rounding and integer bootstrapping success rates, lower and upper bounds of the ILS success rates to the actual ILS AR success rates obtained from a 24 h GPS data set for a 21 km baseline. The results demonstrate that the upper bound probability of the ILS AR probability given in the existing literatures agrees with the actual ILS success rate well, although the success rate computed with integer bootstrapping method is a quite sharp approximation to the actual ILS success rate. The results also show that variations or uncertainty of the unit–weight variance estimates from epoch to epoch will affect the computed success rates from different methods significantly, thus deserving more attentions in order to obtain useful success probability predictions.

Low-density koala (Phascolarctos cinereus) populations in the mulgalands of south-west Queensland. IV. Abundance and conservation status

Urban encroachment on dense, coastal koala populations has ensured that their management has received increasing government and public attention. The recently developed National Koala Conservation Strategy calls for maintenance of viable populations in the wild. Yet the success of this, and other, conservation initiatives is hampered by lack of reliable and generally accepted national and regional population estimates. In this paper we address this problem in a potentially large, but poorly studied, regional population in the State that is likely to have the largest wild populations. We draw on findings from previous reports in this series and apply the faecal standing-crop method (FSCM) to derive a regional estimate of more than 59 000 individuals. Validation trials in riverine communities showed that estimates of animal density obtained from the FSCM and direct observation were in close agreement. Bootstrapping and Monte Carlo simulations were used to obtain variance estimates for our population estimates in different vegetation associations across the region. The most favoured habitat was riverine vegetation, which covered only 0.9% of the region but supported 45% of the koalas. We also estimated that between 1969 and 1995 -30% of the native vegetation associations that are considered as potential koala habitat were cleared, leading to a decline of perhaps 10% in koala numbers. Management of this large regional population has significant implications for the national conservation of the species: the continued viability of this population is critically dependent on the retention and management of riverine and residual vegetation communities, and future vegetation-management guidelines should be cognisant of the potential impacts of clearing even small areas of critical habitat. We also highlight eight management implications.

Using simulation techniques to investigate methods to determine resistance of helminths to anthelmintic treatment

The widespread and increasing resistance of internal parasites to anthelmintic control is a serious problem for the Australian sheep and wool industry. As part of control programmes, laboratories use the Faecal Egg Count Reduction Test (FECRT) to determine resistance to anthelmintics. It is important to have confidence in the measure of resistance, not only for the producer planning a drenching programme but also for companies investigating the efficacy of their products. The determination of resistance and corresponding confidence limits as given in anthelmintic efficacy guidelines of the Standing Committee on Agriculture (SCA) is based on a number of assumptions. This study evaluated the appropriateness of these assumptions for typical data and compared the effectiveness of the standard FECRT procedure with the effectiveness of alternative procedures. Several sets of historical experimental data from sheep and goats were analysed to determine that a negative binomial distribution was a more appropriate distribution to describe pre-treatment helminth egg counts in faeces than a normal distribution. Simulated egg counts for control animals were generated stochastically from negative binomial distributions and those for treated animals from negative binomial and binomial distributions. Three methods for determining resistance when percent reduction is based on arithmetic means were applied. The first was that advocated in the SCA guidelines, the second similar to the first but basing the variance estimates on negative binomial distributions, and the third using Wadley’s method with the distribution of the response variate assumed negative binomial and a logit link transformation. These were also compared with a fourth method recommended by the International Co-operation on Harmonisation of Technical Requirements for Registration of Veterinary Medicinal Products (VICH) programme, in which percent reduction is based on the geometric means. A wide selection of parameters was investigated and for each set 1000 simulations run. Percent reduction and confidence limits were then calculated for the methods, together with the number of times in each set of 1000 simulations the theoretical percent reduction fell within the estimated confidence limits and the number of times resistance would have been said to occur. These simulations provide the basis for setting conditions under which the methods could be recommended. The authors show that given the distribution of helminth egg counts found in Queensland flocks, the method based on arithmetic not geometric means should be used and suggest that resistance be redefined as occurring when the upper level of percent reduction is less than 95%. At least ten animals per group are required in most circumstances, though even 20 may be insufficient where effectiveness of the product is close to the cut off point for defining resistance.

Essays on Risk Modeling. Applications to Portfolio and Risk Management (summary section only)

In this thesis we deal with the concept of risk. The objective is to bring together and conclude on some normative information regarding quantitative portfolio management and risk assessment. The first essay concentrates on return dependency. We propose an algorithm for classifying markets into rising and falling. Given the algorithm, we derive a statistic: the Trend Switch Probability, for detection of long-term return dependency in the first moment. The empirical results suggest that the Trend Switch Probability is robust over various volatility specifications. The serial dependency in bear and bull markets behaves however differently. It is strongly positive in rising market whereas in bear markets it is closer to a random walk. Realized volatility, a technique for estimating volatility from high frequency data, is investigated in essays two and three. In the second essay we find, when measuring realized variance on a set of German stocks, that the second moment dependency structure is highly unstable and changes randomly. Results also suggest that volatility is non-stationary from time to time. In the third essay we examine the impact from market microstructure on the error between estimated realized volatility and the volatility of the underlying process. With simulation-based techniques we show that autocorrelation in returns leads to biased variance estimates and that lower sampling frequency and non-constant volatility increases the error variation between the estimated variance and the variance of the underlying process. From these essays we can conclude that volatility is not easily estimated, even from high frequency data. It is neither very well behaved in terms of stability nor dependency over time. Based on these observations, we would recommend the use of simple, transparent methods that are likely to be more robust over differing volatility regimes than models with a complex parameter universe. In analyzing long-term return dependency in the first moment we find that the Trend Switch Probability is a robust estimator. This is an interesting area for further research, with important implications for active asset allocation.

Assessment of cobia, Rachycentron canadum, in the waters of the U.S. Gulf of Mexico

This assessment applies to cobia (Rachycentron canadum) located in the territorial waters of the U.S. Gulf of Mexico. Separation of the Gulf of Mexico and Atlantic Ocean is defined by the seaward extension of the Dade/Monroe county line in south Florida. Mixing of fish between the Atlantic and Gulf of Mexico occurs in the Florida Keys during winter months. Cobia annually migrate north in early spring in the Gulf to spawning grounds in the northern Gulf of Mexico, returning to the Florida Keys by winter. Catches of cobia in the Gulf of Mexico are dominated by recreational landings, accounting for nearly 90% of the total. Since 1980, the landings of cobia in the recreational fishery have remained fairly stable at around 400-600 mt with a slight peak of 1,014 mt in 1997. The recreational fishery was estimated to have landed 471 mt in 2000. The landings from the commercial fishery have shown a steady increase from 45 mt in 1980 to a peak of 120 mt in 1994, followed by a decline to 62 mt in 2000. The previous assessment of cobia occurred in 1996 using a virtual population analysis (VPA) model. For this analysis a surplus-production model (ASPIC) and a forward-projecting, age-structured population model programmed in the AD Model Builder (ADMB) software were applied to cobia data from the Gulf of Mexico. The primary data consisted of four catch-per-unit-effort (CPUE) indices derived from the Marine Recreational Fisheries Statistics Survey (MRFSS) (1981-1999), Southeast region headboat survey (1986-1999), Texas creel survey (1983-1999), and shrimp bycatch estimates (1980-1999). Length samples were available from the commercial (1983-2000) and recreational (1981-2000) fisheries. The ASPIC model applied to the cobia data provided unsatisfactory results. The ADMB model fit described the observed length composition data and fishery landings fairly well based on graphical examination of model residuals. The CPUE indices indicated some disagreement for various years, but the model fit an overall increasing trend from 1992-1997 for the MRFSS, headboat, and Texas creel indices. The shrimp bycatch CPUE was treated as a recruitment index in the model. The fit to these data followed an upward trend in recruitment from 1988-1997, but did not fit the 1994-1997 data points very well. This was likely the result of conflicting information from other data sources. Natural mortality (M) for cobia is unknown. As a result, a range of values for M from 0.2-0.4, based on longevity and growth parameters, were selected for use in the age-structured model. The choice of natural mortality appears to greatly influence the perceived status of the population. Population status as measured by spawning stock biomass in the last year relative to the value at maximum sustainable yield (SSB2000/SSBMSY), spawning stock biomass in the last year relative to virgin spawning stock biomass (SSB2000/S0), and static spawning stock biomass per recruit (SSBR) all indicate the population is either depleted, near MSY, or well above MSY depending on the choice of M. The variance estimates for these benchmarks are very large and in most cases ranges from depleted to very healthy status. The only statement that can be made with any degree of certainty about cobia in the Gulf of Mexico is that the population has increased since the 1980s. (PDF contains 61 pages)

An evaluation of length-frequency sampling procedures and subsequent data analysis for purse seine-caught yellowfin tuna in the Eastern Pacific Ocean

ENGLISH: A two-stage sampling design is used to estimate the variances of the numbers of yellowfin in different age groups caught in the eastern Pacific Ocean. For purse seiners, the primary sampling unit (n) is a brine well containing fish from a month-area stratum; the number of fish lengths (m) measured from each well are the secondary units. The fish cannot be selected at random from the wells because of practical limitations. The effects of different sampling methods and other factors on the reliability and precision of statistics derived from the length-frequency data were therefore examined. Modifications are recommended where necessary. Lengths of fish measured during the unloading of six test wells revealed two forms of inherent size stratification: 1) short-term disruptions of existing pattern of sizes, and 2) transition zones between long-term trends in sizes. To some degree, all wells exhibited cyclic changes in mean size and variance during unloading. In half of the wells, it was observed that size selection by the unloaders induced a change in mean size. As a result of stratification, the sequence of sizes removed from all wells was non-random, regardless of whether a well contained fish from a single set or from more than one set. The number of modal sizes in a well was not related to the number of sets. In an additional well composed of fish from several sets, an experiment on vertical mixing indicated that a representative sample of the contents may be restricted to the bottom half of the well. The contents of the test wells were used to generate 25 simulated wells and to compare the results of three sampling methods applied to them. The methods were: (1) random sampling (also used as a standard), (2) protracted sampling, in which the selection process was extended over a large portion of a well, and (3) measuring fish consecutively during removal from the well. Repeated sampling by each method and different combinations indicated that, because the principal source of size variation occurred among primary units, increasing n was the most effective way to reduce the variance estimates of both the age-group sizes and the total number of fish in the landings. Protracted sampling largely circumvented the effects of size stratification, and its performance was essentially comparable to that of random sampling. Sampling by this method is recommended. Consecutive-fish sampling produced more biased estimates with greater variances. Analysis of the 1988 length-frequency samples indicated that, for age groups that appear most frequently in the catch, a minimum sampling frequency of one primary unit in six for each month-area stratum would reduce the coefficients of variation (CV) of their size estimates to approximately 10 percent or less. Additional stratification of samples by set type, rather than month-area alone, further reduced the CV's of scarce age groups, such as the recruits, and potentially improved their accuracy. The CV's of recruitment estimates for completely-fished cohorts during the 198184 period were in the vicinity of 3 to 8 percent. Recruitment estimates and their variances were also relatively insensitive to changes in the individual quarterly catches and variances, respectively, of which they were composed. SPANISH: Se usa un diseño de muestreo de dos etapas para estimar las varianzas de los números de aletas amari11as en distintos grupos de edad capturados en el Océano Pacifico oriental. Para barcos cerqueros, la unidad primaria de muestreo (n) es una bodega de salmuera que contenía peces de un estrato de mes-área; el numero de ta11as de peces (m) medidas de cada bodega es la unidad secundaria. Limitaciones de carácter practico impiden la selección aleatoria de peces de las bodegas. Por 10 tanto, fueron examinados los efectos de distintos métodos de muestreo y otros factores sobre la confiabilidad y precisión de las estadísticas derivadas de los datos de frecuencia de ta11a. Se recomiendan modificaciones donde sean necesarias. Las ta11as de peces medidas durante la descarga de seis bodegas de prueba revelaron dos formas de estratificación inherente por ta11a: 1) perturbaciones a corto plazo en la pauta de ta11as existente, y 2) zonas de transición entre las tendencias a largo plazo en las ta11as. En cierto grado, todas las bodegas mostraron cambios cíclicos en ta11a media y varianza durante la descarga. En la mitad de las bodegas, se observo que selección por ta11a por los descargadores indujo un cambio en la ta11a media. Como resultado de la estratificación, la secuencia de ta11as sacadas de todas las bodegas no fue aleatoria, sin considerar si una bodega contenía peces de un solo lance 0 de mas de uno. El numero de ta11as modales en una bodega no estaba relacionado al numero de lances. En una bodega adicional compuesta de peces de varios lances, un experimento de mezcla vertical indico que una muestra representativa del contenido podría estar limitada a la mitad inferior de la bodega. Se uso el contenido de las bodegas de prueba para generar 25 bodegas simuladas y comparar los resultados de tres métodos de muestreo aplicados a estas. Los métodos fueron: (1) muestreo aleatorio (usado también como norma), (2) muestreo extendido, en el cual el proceso de selección fue extendido sobre una porción grande de una bodega, y (3) medición consecutiva de peces durante la descarga de la bodega. EI muestreo repetido con cada método y distintas combinaciones de n y m indico que, puesto que la fuente principal de variación de ta11a ocurría entre las unidades primarias, aumentar n fue la manera mas eficaz de reducir las estimaciones de la varianza de las ta11as de los grupos de edad y el numero total de peces en los desembarcos. El muestreo extendido evito mayormente los efectos de la estratificación por ta11a, y su desempeño fue esencialmente comparable a aquel del muestreo aleatorio. Se recomienda muestrear con este método. El muestreo de peces consecutivos produjo estimaciones mas sesgadas con mayores varianzas. Un análisis de las muestras de frecuencia de ta11a de 1988 indico que, para los grupos de edad que aparecen con mayor frecuencia en la captura, una frecuencia de muestreo minima de una unidad primaria de cada seis para cada estrato de mes-área reduciría los coeficientes de variación (CV) de las estimaciones de ta11a correspondientes a aproximadamente 10% 0 menos. Una estratificación adicional de las muestras por tipo de lance, y no solamente mes-área, redujo aun mas los CV de los grupos de edad escasos, tales como los reclutas, y mejoró potencialmente su precisión. Los CV de las estimaciones del reclutamiento para las cohortes completamente pescadas durante 1981-1984 fueron alrededor de 3-8%. Las estimaciones del reclutamiento y sus varianzas fueron también relativamente insensibles a cambios en las capturas de trimestres individuales y las varianzas, respectivamente, de las cuales fueron derivadas. (PDF contains 70 pages)

Adjusted jackknife for imputation under unequal probability sampling without replacement

Imputation is commonly used to compensate for item non-response in sample surveys. If we treat the imputed values as if they are true values, and then compute the variance estimates by using standard methods, such as the jackknife, we can seriously underestimate the true variances. We propose a modified jackknife variance estimator which is defined for any without-replacement unequal probability sampling design in the presence of imputation and non-negligible sampling fraction. Mean, ratio and random-imputation methods will be considered. The practical advantage of the method proposed is its breadth of applicability.

A practical approach to a multi-level analysis with a sparse binary outcome within a large surgical trial

Objectives: To assess the potential source of variation that surgeon may add to patient outcome in a clinical trial of surgical procedures. Methods: Two large (n = 1380) parallel multicentre randomized surgical trials were undertaken to compare laparoscopically assisted hysterectomy with conventional methods of abdominal and vaginal hysterectomy; involving 43 surgeons. The primary end point of the trial was the occurrence of at least one major complication. Patients were nested within surgeons giving the data set a hierarchical structure. A total of 10% of patients had at least one major complication, that is, a sparse binary outcome variable. A linear mixed logistic regression model (with logit link function) was used to model the probability of a major complication, with surgeon fitted as a random effect. Models were fitted using the method of maximum likelihood in SAS((R)). Results: There were many convergence problems. These were resolved using a variety of approaches including; treating all effects as fixed for the initial model building; modelling the variance of a parameter on a logarithmic scale and centring of continuous covariates. The initial model building process indicated no significant 'type of operation' across surgeon interaction effect in either trial, the 'type of operation' term was highly significant in the abdominal trial, and the 'surgeon' term was not significant in either trial. Conclusions: The analysis did not find a surgeon effect but it is difficult to conclude that there was not a difference between surgeons. The statistical test may have lacked sufficient power, the variance estimates were small with large standard errors, indicating that the precision of the variance estimates may be questionable.

Estimação de parâmetros genéticos para produção de leite de cabras da raça Alpina

Foram utilizados 9.374 registros semanais de produção de leite de 302 primeiras lactações de cabras da raça Alpina. A produção de leite no dia do controle foi analisada por meio de um modelo animal, unicarater, de regressão aleatória, em que as funções de covariâncias para os componentes genéticos aditivos e de ambiente permanente foram modeladas por meio das funções de Wilmink, Ali e Schaeffer e por polinômios ortogonais, em uma escala de Legendre de ordens cúbica e quíntica. Assumiu-se, ainda, variância residual homogênea durante toda a lactação e heterogênea com três e quatro classes de variância residual. Os modelos foram comparados pelo critério de informação de Akaike (AIC), pelo critério de informação Bayesiano de Schwar (BIC), pela função de verossimilhança (Ln L), pela visualização das estimativas de variâncias genéticas, de ambiente permanente, fenotípicas e residuais e pelas herdabilidades. O polinômio de Legendre de ordem quíntica, com quatro e três classes de variâncias residuais, e a função de Ali e Schaeffer, com quatro classes de variâncias residuais, foram indicados como os mais adequados pelo AIC, BIC e Ln L. Estes modelos diferiram na partição da variância fenotípica para as variâncias de ambiente permanente, genética e residual apenas no início e no final da lactação. Contudo, a função de Ali e Schaeffer resultou em estimativas negativas de correlação genética entre os controles mais distantes. O polinômio de Legendre de ordem quíntica, assumindo variância residual heterogênea, mostrou-se mais adequado para ajustar a produção de leite no dia do controle de cabras da raça Alpina.

Bayesian analysis of random regression models using B-splines to model test-day milk yield of Holstein cattle in Brazil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Estimation of genetic parameters for milk yield in Murrah buffaloes by Bayesian inference

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Estudo de simulação de modelos lineares mistos com distribuição normal contaminada no melhoramento genético animal

Objetivou-se com esse trabalho comparar estimativas de componentes de variâncias obtidas por meio de modelos lineares mistos Gaussianos e Robustos, via Amostrador de Gibbs, em dados simulados. Foram simulados 50 arquivos de dados com 1.000 animais cada um, distribuídos em cinco gerações, em dois níveis de efeito fixo e três valores fenotípicos distintos para uma característica hipotética, com diferentes níveis de contaminação. Exceto para os dados sem contaminação, quando os modelos foram iguais, o modelo Robusto apresentou melhores estimativas da variância residual. As estimativas de herdabilidade foram semelhantes em todos os modelos, mas as análises de regressão mostraram que os valores genéticos preditos com uso do modelo Robusto foram mais próximos dos valores genéticos verdadeiros. Esses resultados sugerem que o modelo linear normal contaminado oferece uma alternativa flexível para estimação robusta em melhoramento genético animal.