A Bayesian hierarchical model for the analysis of visual analogue scaling tasks

In psychophysics and psychometrics, an integral method to the discipline involves charting how a person's response pattern changes according to a continuum of stimuli. For instance, in hearing science, Visual Analog Scaling tasks are experiments in which listeners hear sounds across a speech continuum and give a numeric rating between 0 and 100 conveying whether the sound they heard was more like word "a" or more like word "b" (i.e. each participant is giving a continuous categorization response). By taking all the continuous categorization responses across the speech continuum, a parametric curve model can be fit to the data and used to analyze any individual's response pattern by speech continuum. Standard statistical modeling techniques are not able to accommodate all of the specific requirements needed to analyze these data. Thus, Bayesian hierarchical modeling techniques are employed to accommodate group-level non-linear curves, individual-specific non-linear curves, continuum-level random effects, and a subject-specific variance that is predicted by other model parameters. In this paper, a Bayesian hierarchical model is constructed to model the data from a Visual Analog Scaling task study of mono-lingual and bi-lingual participants. Any nonlinear curve function could be used and we demonstrate the technique using the 4-parameter logistic function. Overall, the model was found to fit particularly well to the data from the study and results suggested that the magnitude of the slope was what most defined the differences in response patterns between continua.

Maximin design of cluster randomized trials with heterogeneous costs and variances

Cluster randomized trials evaluate the effect of a treatment on persons nested within clusters, with clusters being randomly assigned to treatment. The optimal sample size at the cluster and person level depends on the study cost per cluster and per person, and the outcome variance at the cluster and the person level. The variances are unknown in the design stage and can differ between treatment arms. As a solution, this paper presents a Maximin design that maximizes the minimum relative efficiency (relative to the optimal design) over the variance parameter space, for trials with two treatment arms and a quantitative outcome. This maximin relative efficiency design (MMRED) is compared with a published Maximin design which maximizes the minimum efficiency (MMED). Both designs are also compared with the optimal designs for homogeneous costs and variances (balanced design) and heterogeneous costs and homogeneous variances (cost-conscious design), for a range of variances based upon three published trials. Whereas the MMED is balanced under high uncertainty about the treatment-to-control variance ratio, the MMRED then tends towards a balanced budget allocation between arms, leading to an unbalanced sample size allocation if costs are heterogeneous, similar to the cost-conscious design. Further, the MMRED corresponds to an optimal design for an intraclass correlation (ICC) in the lower half of the assumed ICC range (optimistic), whereas the MMED is the optimal design for the maximum ICC within the ICC range (pessimistic). Attention is given to the effect of the Welch-Satterthwaite degrees of freedom for treatment effect testing on the design efficiencies.

Efficient design of cluster randomized trials with treatment-dependent costs and treatment-dependent unknown variances

Cluster randomized trials evaluate the effect of a treatment on persons nested within clusters, where treatment is randomly assigned to clusters. Current equations for the optimal sample size at the cluster and person level assume that the outcome variances and/or the study costs are known and homogeneous between treatment arms. This paper presents efficient yet robust designs for cluster randomized trials with treatment‐dependent costs and treatment‐dependent unknown variances, and compares these with 2 practical designs. First, the maximin design (MMD) is derived, which maximizes the minimum efficiency (minimizes the maximum sampling variance) of the treatment effect estimator over a range of treatment‐to‐control variance ratios. The MMD is then compared with the optimal design for homogeneous variances and costs (balanced design), and with that for homogeneous variances and treatment‐dependent costs (cost‐considered design). The results show that the balanced design is the MMD if the treatment‐to control cost ratio is the same at both design levels (cluster, person) and within the range for the treatment‐to‐control variance ratio. It still is highly efficient and better than the cost‐considered design if the cost ratio is within the range for the squared variance ratio. Outside that range, the cost‐considered design is better and highly efficient, but it is not the MMD. An example shows sample size calculation for the MMD, and the computer code (SPSS and R) is provided as supplementary material. The MMD is recommended for trial planning if the study costs are treatment‐dependent and homogeneity of variances cannot be assumed.

A marginalized two-part model with heterogeneous variance for semicontinuous data

Semicontinuous data, characterized by a point mass at zero followed by a positive, continuous distribution, arise frequently in medical research. These data are typically analyzed using two-part mixtures that separately model the probability of incurring a positive outcome and the distribution of positive values among those who incur them. In such a conditional specification, however, standard two-part models do not provide a marginal interpretation of covariate effects on the overall population. We have previously proposed a marginalized two-part model that yields more interpretable effect estimates by parameterizing the model in terms of the marginal mean. In the original formulation, a constant variance was assumed for the positive values. We now extend this model to a more general framework by allowing non-constant variance to be explicitly modeled as a function of covariates, and incorporate this variance into two flexible distributional assumptions, log-skew-normal and generalized gamma, both of which take the log-normal distribution as a special case. Using simulation studies, we compare the performance of each of these models with respect to bias, coverage, and efficiency. We illustrate the proposed modeling framework by evaluating the effect of a behavioral weight loss intervention on health care expenditures in the Veterans Affairs health system.

Efficient treatment allocation in 2 × 2 multicenter trials when costs and variances are heterogeneous

At the design stage of a study, it is crucial to compute the sample size needed for treatment effect estimation with maximum precision and power. The optimal design depends on the costs, which may be known at the design stage, and on the outcome variances, which are unknown. A balanced design, optimal for homogeneous costs and variances, is typically used. An alternative to the balanced design is a design optimal for the known and possibly heterogeneous costs, and homogeneous variances, called costs considering design. Both designs suffer from loss of efficiency, compared with optimal designs for heterogeneous costs and variances. For 2 × 2 multicenter trials, we compute the relative efficiency of the balanced and the costs considering designs, relative to the optimal designs. We consider 2 heterogeneous costs and variance scenarios (in 1 scenario, 2 treatment conditions have small and 2 have large costs and variances; in the other scenario, 1 treatment condition has small, 2 have intermediate, and 1 has large costs and variances). Within these scenarios, we examine the relative efficiency of the balanced design and of the costs considering design as a function of the extents of heterogeneity of the costs and of the variances and of their congruence (congruent when the cheapest treatment has the smallest variance, incongruent when the cheapest treatment has the largest variance). We find that the costs considering design is generally more efficient than the balanced design, and we illustrate this theory on a 2 × 2 multicenter trial on lifestyle improvement of patients in general practices.

Efficient treatment allocation in 2 × 2 cluster randomized trials, when costs and variances are heterogeneous

Typically, clusters and individuals in cluster randomized trials are allocated across treatment conditions in a balanced fashion. This is optimal under homogeneous costs and outcome variances. However, both the costs and the variances may be heterogeneous. Then, an unbalanced allocation is more efficient but impractical as the outcome variance is unknown in the design stage of a study. A practical alternative to the balanced design could be a design optimal for known and possibly heterogeneous costs and homogeneous variances. However, when costs and variances are heterogeneous, both designs suffer from loss of efficiency, compared with the optimal design. Focusing on cluster randomized trials with a 2 × 2 design, the relative efficiency of the balanced design and of the design optimal for heterogeneous costs and homogeneous variances is evaluated, relative to the optimal design. We consider two heterogeneous scenarios (two treatment arms with small, and two with large, costs or variances, or one small, two intermediate, and one large costs or variances) at each design level (cluster, individual, and both). Within these scenarios, we compute the relative efficiency of the two designs as a function of the extents of heterogeneity of the costs and variances, and the congruence (the cheapest treatment has the smallest variance) and incongruence (the cheapest treatment has the largest variance) between costs and variances. We find that the design optimal for heterogeneous costs and homogeneous variances is generally more efficient than the balanced design and we illustrate this theory on a trial that examines methods to reduce radiological referrals from general practices. Copyright © 2016 John Wiley & Sons, Ltd.

The effect of heterogeneous variance on efficiency and power of cluster randomized trials with a balanced 2 × 2 factorial design

Sample size calculation for cluster randomized trials (CRTs) with a [Formula: see text] factorial design is complicated due to the combination of nesting (of individuals within clusters) with crossing (of two treatments). Typically, clusters and individuals are allocated across treatment conditions in a balanced fashion, which is optimal under homogeneity of variance. However, the variance is likely to be heterogeneous if there is a treatment effect. An unbalanced allocation is then more efficient, but impractical because the optimal allocation depends on the unknown variances. Focusing on CRTs with a [Formula: see text] design, this paper addresses two questions: How much efficiency is lost by having a balanced design when the outcome variance is heterogeneous? How large must the sample size be for a balanced allocation to have sufficient power under heterogeneity of variance? We consider different scenarios of heterogeneous variance. Within each scenario, we determine the relative efficiency of a balanced design, as a function of the level (cluster, individual, both) and amount of heterogeneity of the variance. We then provide a simple correction of the sample size for the loss of power due to heterogeneity of variance when a balanced allocation is used. The theory is illustrated with an example of a published 2 x2 CRT.

Across-country test-day model evaluations for Holstein, Nordic Red Cattle, and Jersey

Three random regression models were developed for routine genetic evaluation of Danish, Finnish, and Swedish dairy cattle. Data included over 169 million test-day records with milk, protein, and fat yield observations from over 8.7 million dairy cows of all breeds. Variance component analyses showed significant differences in estimates between Holstein, Nordic Red Cattle, and Jersey, but only small to moderate differences within a breed across countries. The obtained variance component estimates were used to build, for each breed, their own set of covariance functions. The covariance functions describe the animal effects on milk, protein, and fat yields of the first 3 lactations as 9 different traits, assuming the same heritabilities and a genetic correlation of unity across countries. Only 15, 27, and 7 eigenfunctions with the largest eigenvalues were used to describe additive genetic animal effects and nonhereditary animal effects across lactations and within later lactations, respectively. These reduced-rank covariance functions explained 99.0 to 99.9% of the original variances but reduced the number of animal equations to be solved by 44%. Moderate rank reduction for nonhereditary animal effects and use of one-third-smaller measurement error correlations than obtained from variance component estimation made the models more robust against extreme observations. Estimation of the genetic levels of the countries' subpopulations within a breed was found sensitive to the way the breed effects were modeled, especially for the genetically heterogeneous Nordic Red Cattle. Means to ensure that only additive genetic effects entered the estimated breeding values were to describe the crossbreeding effects by fixed and random cofactors and the calving age effect by an age × breed proportion interaction, and to model phantom parent groups as random effects. To ensure that genetic variances were the same across the 3 countries in breeding value estimation, as suggested by the variance component estimates, the applied multiplicative heterogeneous variance adjustment method had to be tailored using country-specific reference measurement error variances. Results showed the feasibility of across-country genetic evaluation of cows and sires based on original test-day phenotypes. Nevertheless, applying a thorough model validation procedure is essential throughout the model building process to obtain reliable breeding values.