Factor analysis for ranked data with application to a job selection attitude survey

Summary.  Factor analysis is a powerful tool to identify the common characteristics among a set of variables that are measured on a continuous scale. In the context of factor analysis for non-continuous-type data, most applications are restricted to item response data only. We extend the factor model to accommodate ranked data. The Monte Carlo expectation–maximization algorithm is used for parameter estimation at which the E-step is implemented via the Gibbs sampler. An analysis based on both complete and incomplete ranked data (e.g. rank the top q out of k items) is considered. Estimation of the factor scores is also discussed. The method proposed is applied to analyse a set of incomplete ranked data that were obtained from a survey that was carried out in GuangZhou, a major city in mainland China, to investigate the factors affecting people's attitude towards choosing jobs.     

Sensitivity Coefficient in Principal Component Analysis: Robust Case

In the classical principal component analysis (PCA), the empirical influence function for the sensitivity coefficient ρ is used to detect influential observations on the subspace spanned by the dominants principal components. In this article, we derive the influence function of ρ in the case where the reweighted minimum covariance determinant (MCD¹) is used as estimator of multivariate location and scatter. Our aim is to confirm the reliability in terms of robustness of the MCD¹ via the approach based on the influence function of the sensitivity coefficient.     

Data-driven sensitivity analysis to detect missing data mechanism with applications to structural equation modelling

Missing data are a common problem in almost all areas of empirical research. Ignoring the missing data mechanism, especially when data are missing not at random (MNAR), can result in biased and/or inefficient inference. Because MNAR mechanism is not verifiable based on the observed data, sensitivity analysis is often used to assess it. Current sensitivity analysis methods primarily assume a model for the response mechanism in conjunction with a measurement model and examine sensitivity to missing data mechanism via the parameters of the response model. Recently, Jamshidian and Mata (Post-modelling sensitivity analysis to detect the effect of missing data mechanism, Multivariate Behav. Res. 43 (2008), pp. 432–452) introduced a new method of sensitivity analysis that does not require the difficult task of modelling the missing data mechanism. In this method, a single measurement model is fitted to all of the data and to a sub-sample of the data. Discrepancy in the parameter estimates obtained from the the two data sets is used as a measure of sensitivity to missing data mechanism. Jamshidian and Mata describe their method mainly in the context of detecting data that are missing completely at random (MCAR). They used a bootstrap type method, that relies on heuristic input from the researcher, to test for the discrepancy of the parameter estimates. Instead of using bootstrap, the current article obtains confidence interval for parameter differences on two samples based on an asymptotic approximation. Because it does not use bootstrap, the developed procedure avoids likely convergence problems with the bootstrap methods. It does not require heuristic input from the researcher and can be readily implemented in statistical software. The article also discusses methods of obtaining sub-samples that may be used to test missing at random in addition to MCAR. An application of the developed procedure to a real data set, from the first wave of an ongoing longitudinal study on aging, is presented. Simulation studies are performed as well, using two methods of missing data generation, which show promise for the proposed sensitivity method. One method of missing data generation is also new and interesting in its own right.     

Optimal Bayesian two-phase designs

In this paper we present a Bayesian decision theoretic approach to the two-phase design problem. The solution of such sequential decision problems is usually difficult to obtain because of their reliance on preposterior analysis. In overcoming this problem, we adopt the Mont-Carlo-based approach of Müller and Parmigiani (1995) and develop optimal Bayesian designs for two-phase screening tests. A rather attractive feature of the Monte-Carlo approach is that it facilitates the preposterior analysis by replacing it with a sequence of scatter plot smoothing/regression techniques and optimization of the corresponding fitted surfaces. The method is illustrated for depression in adolescents using data from past studies.     

Probabilistic sensitivity analysis of complex models: a Bayesian approach

Summary.  In many areas of science and technology, mathematical models are built to simulate complex real world phenomena. Such models are typically implemented in large computer programs and are also very complex, such that the way that the model responds to changes in its inputs is not transparent. Sensitivity analysis is concerned with understanding how changes in the model inputs influence the outputs. This may be motivated simply by a wish to understand the implications of a complex model but often arises because there is uncertainty about the true values of the inputs that should be used for a particular application. A broad range of measures have been advocated in the literature to quantify and describe the sensitivity of a model's output to variation in its inputs. In practice the most commonly used measures are those that are based on formulating uncertainty in the model inputs by a joint probability distribution and then analysing the induced uncertainty in outputs, an approach which is known as probabilistic sensitivity analysis. We present a Bayesian framework which unifies the various tools of prob- abilistic sensitivity analysis. The Bayesian approach is computationally highly efficient. It allows effective sensitivity analysis to be achieved by using far smaller numbers of model runs than standard Monte Carlo methods. Furthermore, all measures of interest may be computed from a single set of runs.     

Local sensitivity approximations for selectivity bias

Observational data analysis is often based on tacit assumptions of ignorability or randomness. The paper develops a general approach to local sensitivity analysis for selectivity bias, which aims to study the sensitivity of inference to small departures from such assumptions. If M is a model assuming ignorability, we surround M by a small neighbourhood N defined in the sense of Kullback–Leibler divergence and then compare the inference for models in N with that for M . Interpretable bounds for such differences are developed. Applications to missing data and to observational comparisons are discussed. Local approximations to sensitivity analysis are model robust and can be applied to a wide range of statistical problems.     

Influence analysis on crossover design experiment in bioequivalence studies

Crossover designs are commonly used in bioequivalence studies. However, the results can be affected by some outlying observations, which may lead to the wrong decision on bioequivalence. Therefore, it is essential to investigate the influence of aberrant observations. Chow and Tse in 1990 discussed this issue by considering the methods based on the likelihood distance and estimates distance. Perturbation theory provides a useful tool for the sensitivity analysis on statistical models. Hence, in this paper, we develop the influence functions via the perturbation scheme proposed by Hampel as an alternative approach on the influence analysis for a crossover design experiment. Moreover, the comparisons between the proposed approach and the method proposed by Chow and Tse are investigated. Two real data examples are provided to illustrate the results of these approaches. Our proposed influence functions show excellent performance on the identification of outlier/influential observations and are suitable for use with small sample size crossover designs commonly used in bioequivalence studies. Copyright © 2013 John Wiley & Sons, Ltd.     

Sensitivity analysis of partially linear models with response missing at random

This article investigates case-deletion influence analysis via Cook’s distance and local influence analysis via conformal normal curvature for partially linear models with response missing at random. Local influence approach is developed to assess the sensitivity of parameter and nonparametric estimators to various perturbations such as case-weight, response variable, explanatory variable, and parameter perturbations on the basis of semiparametric estimating equations, which are constructed using the inverse probability weighted approach, rather than likelihood function. Residual and generalized leverage are also defined. Simulation studies and a dataset taken from the AIDS Clinical Trials are used to illustrate the proposed methods.     

A gradient approach to efficient design and analysis of multivariate EWMA control charts

Compared to the grid search approach to optimal design of control charts, the gradient-based approach is more computationally efficient as the gradient information indicates the direction to search the optimal design parameters. However, the optimal parameters of multivariate exponentially weighted moving average (MEWMA) control charts are often obtained by using grid search in the existing literature. Note that the average run length (ARL) performance of the MEWMA chart can be calculated based on a Markov chain model, making it feasible to estimate the ARL gradient from it. Motivated by this, this paper develops an ARL gradient-based approach for the optimal design and sensitivity analysis of MEWMA control charts. It is shown that the proposed method is able to provide a fast, accurate, and easy-to-implement algorithm for the design and analysis of MEWMA charts, as compared to the conventional design approach based on grid search.     

The impact of missing data on the results of a schizophrenia study

Missing data pose a serious challenge to the integrity of randomized clinical trials, especially of treatments for prolonged illnesses such as schizophrenia, in which long‐term impact assessment is of great importance, but the follow‐up rates are often no more than 50%. Sensitivity analysis using Bayesian modeling for missing data offers a systematic approach to assessing the sensitivity of the inferences made on the basis of observed data. This paper uses data from an 18‐month study of veterans with schizophrenia to demonstrate this approach. Data were obtained from a randomized clinical trial involving 369 patients diagnosed with schizophrenia that compared long‐acting injectable risperidone with a psychiatrist's choice of oral treatment. Bayesian analysis utilizing a pattern‐mixture modeling approach was used to validate the reported results by detecting bias due to non‐random patterns of missing data. The analysis was applied to several outcomes including standard measures of schizophrenia symptoms, quality of life, alcohol use, and global mental status. The original study results for several measures were confirmed against a wide range of patterns of non‐random missingness. Robustness of the conclusions was assessed using sensitivity parameters. The missing data in the trial did not likely threaten the validity of previously reported results. Copyright © 2014 John Wiley & Sons, Ltd.     

Application of sensitivity analysis to incomplete longitudinal CD4 count data

In this paper, we investigate the effect of tuberculosis pericarditis (TBP) treatment on CD4 count changes over time and draw inferences in the presence of missing data. We accounted for missing data and conducted sensitivity analyses to assess whether inferences under missing at random (MAR) assumption are sensitive to not missing at random (NMAR) assumptions using the selection model (SeM) framework. We conducted sensitivity analysis using the local influence approach and stress-testing analysis. Our analyses showed that the inferences from the MAR are robust to the NMAR assumption and influential subjects do not overturn the study conclusions about treatment effects and the dropout mechanism. Therefore, the missing CD4 count measurements are likely to be MAR. The results also revealed that TBP treatment does not interact with HIV/AIDS treatment and that TBP treatment has no significant effect on CD4 count changes over time. Although the methods considered were applied to data in the IMPI trial setting, the methods can also be applied to clinical trials with similar settings.     

A robust variable screening method for high-dimensional data

In practice, the presence of influential observations may lead to misleading results in variable screening problems. We, therefore, propose a robust variable screening procedure for high-dimensional data analysis in this paper. Our method consists of two steps. The first step is to define a new high-dimensional influence measure and propose a novel influence diagnostic procedure to remove those unusual observations. The second step is to utilize the sure independence screening procedure based on distance correlation to select important variables in high-dimensional regression analysis. The new influence measure and diagnostic procedure that we developed are model free. To confirm the effectiveness of the proposed method, we conduct simulation studies and a real-life data analysis to illustrate the merits of the proposed approach over some competing methods. Both the simulation results and the real-life data analysis demonstrate that the proposed method can greatly control the adverse effect after detecting and removing those unusual observations, and performs better than the competing methods.     

Influence and sensitivity measures in correspondence analysis

Since correspondence analysis appears to be sensitive to outliers, it is important to be able to evaluate the sensitivity of the data on the results. This article deals with measuring the influence of rows and columns on the results obtained with correspondence analysis. To establish the influence of individuals on the analysis, we use the notion of influence curve and we propose a general criterion based on the mean square error to measure the sensitivity of the correspondence analysis and its robustness. A numerical example is presented to illustrate the notions developed in this article.     

Evaluations of Bayesian and maximum likelihood methods in PK models with below‐quantification‐limit data

Pharmacokinetic (PK) data often contain concentration measurements below the quantification limit (BQL). While specific values cannot be assigned to these observations, nevertheless these observed BQL data are informative and generally known to be lower than the lower limit of quantification (LLQ). Setting BQLs as missing data violates the usual missing at random (MAR) assumption applied to the statistical methods, and therefore leads to biased or less precise parameter estimation. By definition, these data lie within the interval [0, LLQ], and can be considered as censored observations. Statistical methods that handle censored data, such as maximum likelihood and Bayesian methods, are thus useful in the modelling of such data sets. The main aim of this work was to investigate the impact of the amount of BQL observations on the bias and precision of parameter estimates in population PK models (non‐linear mixed effects models in general) under maximum likelihood method as implemented in SAS and NONMEM, and a Bayesian approach using Markov chain Monte Carlo (MCMC) as applied in WinBUGS. A second aim was to compare these different methods in dealing with BQL or censored data in a practical situation. The evaluation was illustrated by simulation based on a simple PK model, where a number of data sets were simulated from a one‐compartment first‐order elimination PK model. Several quantification limits were applied to each of the simulated data to generate data sets with certain amounts of BQL data. The average percentage of BQL ranged from 25% to 75%. Their influence on the bias and precision of all population PK model parameters such as clearance and volume distribution under each estimation approach was explored and compared. Copyright © 2009 John Wiley & Sons, Ltd.     

Combination of several matching adjusted indirect comparisons (MAICs) with an application in psoriasis

In health technology assessment (HTA), beside network meta‐analysis (NMA), indirect comparisons (IC) have become an important tool used to provide evidence between two treatments when no head‐to‐head data are available. Researchers may use the adjusted indirect comparison based on the Bucher method (AIC) or the matching‐adjusted indirect comparison (MAIC). While the Bucher method may provide biased results when included trials differ in baseline characteristics that influence the treatment outcome (treatment effect modifier), this issue may be addressed by applying the MAIC method if individual patient data (IPD) for at least one part of the AIC is available. Here, IPD is reweighted to match baseline characteristics and/or treatment effect modifiers of published data. However, the MAIC method does not provide a solution for situations when several common comparators are available. In these situations, assuming that the indirect comparison via the different common comparators is homogeneous, we propose merging these results by using meta‐analysis methodology to provide a single, potentially more precise, treatment effect estimate. This paper introduces the method to combine several MAIC networks using classic meta‐analysis techniques, it discusses the advantages and limitations of this approach, as well as demonstrates a practical application to combine several (M)AIC networks using data from Phase III psoriasis randomized control trials (RCT).     

Self-Consistency Estimation of Distributions Based on Truncated and Doubly Censored Survival Data with Applications to AIDS Cohort Studies

Gomez and Lagakos (1994) propose a nonparametric method for estimating the distribution of a survival time when the origin and end points defining the survival time suffer interval-censoring and right-censoring, respectively. In some situations, the end point also suffers interval-censoring as well as truncation. In this paper, we consider this general situation and propose a two-step estimation procedure for the estimation of the distribution of a survival time based on doubly interval-censored and truncated data. The proposed method generalizes the methods proposed by DeGruttola and Lagakos (1989) and Sun (1995) and is more efficient than that given in Gomez and Lagakos (1994). The approach is based on self-consistency equations. The method is illustrated by an analysis of an AIDS cohort study.     

Sensitivity to censored‐at‐random assumption in the analysis of time‐to‐event endpoints

Over the past years, significant progress has been made in developing statistically rigorous methods to implement clinically interpretable sensitivity analyses for assumptions about the missingness mechanism in clinical trials for continuous and (to a lesser extent) for binary or categorical endpoints. Studies with time‐to‐event outcomes have received much less attention. However, such studies can be similarly challenged with respect to the robustness and integrity of primary analysis conclusions when a substantial number of subjects withdraw from treatment prematurely prior to experiencing an event of interest. We discuss how the methods that are widely used for primary analyses of time‐to‐event outcomes could be extended in a clinically meaningful and interpretable way to stress‐test the assumption of ignorable censoring. We focus on a ‘tipping point’ approach, the objective of which is to postulate sensitivity parameters with a clear clinical interpretation and to identify a setting of these parameters unfavorable enough towards the experimental treatment to nullify a conclusion that was favorable to that treatment. Robustness of primary analysis results can then be assessed based on clinical plausibility of the scenario represented by the tipping point. We study several approaches for conducting such analyses based on multiple imputation using parametric, semi‐parametric, and non‐parametric imputation models and evaluate their operating characteristics via simulation. We argue that these methods are valuable tools for sensitivity analyses of time‐to‐event data and conclude that the method based on piecewise exponential imputation model of survival has some advantages over other methods studied here. Copyright © 2016 John Wiley & Sons, Ltd.     

On the Kaplan–Meier estimator based on ranked set samples

When quantification of all sampling units is expensive but a set of units can be ranked, without formal measurement, ranked set sampling (RSS) is a cost-efficient alternate to simple random sampling (SRS). In this paper, we study the Kaplan–Meier estimator of survival probability based on RSS under random censoring time setup, and propose nonparametric estimators of the population mean. We present a simulation study to compare the performance of the suggested estimators. It turns out that RSS design can yield a substantial improvement in efficiency over the SRS design. Additionally, we apply the proposed methods to a real data set from an environmental study.     

Evaluating fit in functional data analysis using model embeddings

The author proposes a general method for evaluating the fit of a model for functional data. His approach consists of embedding the proposed model into a larger family of models, assuming the true process generating the data is within the larger family, and then computing a posterior distribution for the Kullback‐Leibler distance between the true and the proposed models. The technique is illustrated on biomechanical data reported by Ramsay, Flanagan & Wang (1995). It is developed in detail for hierarchical polynomial models such as those found in Lindley & Smith (1972), and is also generally applicable to longitudinal data analysis where polynomials are fit to many individuals.     

Sampling methods and sensitivity analysis for large parameter sets

Models with large parameter (i.e., hundreds or thousands of parameters) often behave as if they depend upon only a few parameters, with the rest having comparatively little influence. One challenge of sensitivity analysis with such models is screening parameters to identify the influential ones, and then characterizing their influences.

Large models often require significant computing resources to evaluate their output, and so a good screening mechanism should be efficient: it should minimize the number of times a model must be exercised. This paper describes an efficient procedure to perform sensitivity analysis on deterministic models with specified ranges or probability distributions for each parameter.

It is based on repeated exercising of the model, which can be treated as a black box. Statistical checks can ensure that the screening identified parameters that account for the bulk of the model variation. Subsequent sensitivity analysis can use the screening information to reduce the investment required to characterize the influence of influential and other parameters.

The procedure exploits simplifications in the dependence of a model output on model inputs. It works best where a small number of parameters are much more influential than all the rest. The method is much more sensitive to the number of influential parameters than to the total number of parameters. It is most effective when linear or quadratic effects dominate higher order effects and complex interactions.

The paper presents a set of M athematica functions that can be used to create a variety of types of experimental designs useful for sensitivity analysis, including simple random, latin hypercube and fractional factorial sampling. Each sampling method can use discretization, folding, grouping and replication to create composite designs. These techniques have beencombined in a composite approach called Iterated Fractional Factorial Design (IFFD).

The procedure is applied to model of nuclear fuel waste disposal, and to simplified example models to demonstrate the concepts involved.