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Kosmos
Astronomia Astrofizyka
Inne

Kultura
Sztuka dawna i współczesna, muzea i kolekcje

Metoda
Metodologia nauk, Matematyka, Filozofia, Miary i wagi, Pomiary

Materia
Substancje, reakcje, energia
Fizyka, chemia i inżynieria materiałowa

Człowiek
Antropologia kulturowa Socjologia Psychologia Zdrowie i medycyna

Wizje
Przewidywania Kosmologia Religie Ideologia Polityka

Ziemia
Geologia, geofizyka, geochemia, środowisko przyrodnicze

Życie
Biologia, biologia molekularna i genetyka

Cyberprzestrzeń
Technologia cyberprzestrzeni, cyberkultura, media i komunikacja

Działalność
Wiadomości | Gospodarka, biznes, zarządzanie, ekonomia

Technologie
Budownictwo, energetyka, transport, wytwarzanie, technologie informacyjne

Journal of Statistical Software

Vol. 60, Issue 6, Sep 2014Abstract: This article surveys currently available implementations in R for continuous global optimization problems. A new R package globalOptTests is presented that provides a set of standard test problems for continuous global optimization based on C functions by Ali, Khompatraporn, and Zabinsky (2005). 48 of the objective functions contained in the package are used in empirical comparison of 18 R implementations in terms of the quality of the solutions found and speed.

http://www.jstatsoft.org/v60/i06/paper 2014/10/01 - 02:10

Vol. 60, Issue 5, Sep 2014Abstract: Convex optimization now plays an essential role in many facets of statistics. We briefly survey some recent developments and describe some implementations of these methods in R . Applications of linear and quadratic programming are introduced including quantile regression, the Huber M-estimator and various penalized regression methods. Applications to additively separable convex problems subject to linear equality and inequality constraints such as nonparametric density estimation and maximum likelihood estimation of general nonparametric mixture models are described, as are several cone programming problems. We focus throughout primarily on implementations in the R environment that rely on solution methods linked to R, like MOSEK by the package Rmosek. Code is provided in R to illustrate several of these problems. Other applications are available in the R package REBayes, dealing with empirical Bayes estimation of nonparametric mixture models.

http://www.jstatsoft.org/v60/i05/paper 2014/10/01 - 02:10

Vol. 60, Issue 4, Sep 2014Abstract: Trust region algorithms are nonlinear optimization tools that tend to be stable and reliable when the objective function is non-concave, ill-conditioned, or exhibits regions that are nearly flat. Additionally, most freely-available optimization routines do not exploit the sparsity of the Hessian when such sparsity exists, as in log posterior densities of Bayesian hierarchical models. The trustOptim package for the R programming language addresses both of these issues. It is intended to be robust, scalable and efficient for a large class of nonlinear optimization problems that are often encountered in statistics, such as finding posterior modes. The user must supply the objective function, gradient and Hessian. However, when used in conjunction with the sparseHessianFD package, the user does not need to supply the exact sparse Hessian, as long as the sparsity structure is known in advance. For models with a large number of parameters, but for which most of the cross-partial derivatives are zero (i.e., the Hessian is sparse), trustOptim offers dramatic performance improvements over existing options, in terms of computational time and memory footprint.

http://www.jstatsoft.org/v60/i04/paper 2014/10/01 - 02:10

Vol. 60, Issue 3, Sep 2014Abstract: Over the last two decades, it has been observed that using the gradient vector as a search direction in large-scale optimization may lead to efficient algorithms. The effectiveness relies on choosing the step lengths according to novel ideas that are related to the spectrum of the underlying local Hessian rather than related to the standard decrease in the objective function. A review of these so-called spectral projected gradient methods for convex constrained optimization is presented. To illustrate the performance of these low-cost schemes, an optimization problem on the set of positive definite matrices is described.

http://www.jstatsoft.org/v60/i03/paper 2014/10/01 - 02:10

Vol. 60, Issue 2, Sep 2014Abstract: R (R Core Team 2014) provides a powerful and flexible system for statistical computations. It has a default-install set of functionality that can be expanded by the use of several thousand add-in packages as well as user-written scripts. While R is itself a programming language, it has proven relatively easy to incorporate programs in other languages, particularly Fortran and C. Success, however, can lead to its own costs:

Users face a confusion of choice when trying to select packages in approaching a problem.
A need to maintain workable examples using early methods may mean some tools offered as a default may be dated.
In an open-source project like R, how to decide what tools offer "best practice" choices, and how to implement such a policy, present a serious challenge.

We discuss these issues with reference to the tools in R for nonlinear parameter estimation (NLPE) and optimization, though for the present article `optimization` will be limited to function minimization of essentially smooth functions with at most bounds constraints on the parameters. We will abbreviate this class of problems as NLPE. We believe that the concepts proposed are transferable to other classes of problems seen by R users.

http://www.jstatsoft.org/v60/i02/paper 2014/10/01 - 02:10

Vol. 60, Issue 1, Sep 2014Abstract: Numerical optimization is often an essential aspect of mathematical analysis in science, technology and other areas. The function optim() provides basic optimization capabilities and is among the most widely used functions in R . Additionally, there are various packages and functions for solving various types of optimization problem (the optimization task view on Comprehensive R Archive Network provides a comprehensive list of available options for solving optimization problems in R). In this special volume, four papers are presented which discuss some of the areas in numerical optimization where significant developments have been made recently to enhance the capabilities in R . This introduction provides a brief overview of the volume.

http://www.jstatsoft.org/v60/i01/paper 2014/10/01 - 02:10

Vol. 59, Issue 13, Sep 2014Abstract: The R package structSSI provides an accessible implementation of two recently developed simultaneous and selective inference techniques: the group Benjamini-Hochberg and hierarchical false discovery rate procedures. Unlike many multiple testing schemes, these methods specifically incorporate existing information about the grouped or hierarchical dependence between hypotheses under consideration while controlling the false discovery rate. Doing so increases statistical power and interpretability. Furthermore, these procedures provide novel approaches to the central problem of encoding complex dependency between hypotheses.
We briefly describe the group Benjamini-Hochberg and hierarchical false discovery rate procedures and then illustrate them using two examples, one a measure of ecological microbial abundances and the other a global temperature time series. For both procedures, we detail the steps associated with the analysis of these particular data sets, including establishing the dependence structures, performing the test, and interpreting the results. These steps are encapsulated by R functions, and we explain their applicability to general data sets.

http://www.jstatsoft.org/v59/i13/paper 2014/09/13 - 18:37

Vol. 59, Issue 12, Sep 2014Abstract: R package mixAK originally implemented routines primarily for Bayesian estimation of finite normal mixture models for possibly interval-censored data. The functionality of the package was considerably enhanced by implementing methods for Bayesian estimation of mixtures of multivariate generalized linear mixed models proposed in Komárek and Komárková (2013). Among other things, this allows for a cluster analysis (classification) based on multivariate continuous and discrete longitudinal data that arise whenever multiple outcomes of a different nature are recorded in a longitudinal study. This package also allows for a data-driven selection of a number of clusters as methods for selecting a number of mixture components were implemented. A model and clustering methodology for multivariate continuous and discrete longitudinal data is overviewed. Further, a step-by-step cluster analysis based jointly on three longitudinal variables of different types (continuous, count, dichotomous) is given, which provides a user manual for using the package for similar problems.

http://www.jstatsoft.org/v59/i12/paper 2014/09/13 - 18:37

Vol. 59, Issue 11, Sep 2014Abstract: In this paper we show how complete hierarchical multinomial marginal (HMM) models for categorical variables can be defined, estimated and tested using the R package hmmm. Models involving equality and inequality constraints on marginal parameters are needed to define hypotheses of conditional independence, stochastic dominance or notions of positive dependence, or when the parameters are allowed to depend on covariates. The hmmm package also serves the need of estimating and testing HMM models under equality and inequality constraints on marginal interactions.

http://www.jstatsoft.org/v59/i11/paper 2014/09/13 - 18:37

Vol. 59, Issue 10, Sep 2014Abstract: A huge amount of effort is spent cleaning data to get it ready for analysis, but there has been little research on how to make data cleaning as easy and effective as possible. This paper tackles a small, but important, component of data cleaning: data tidying. Tidy datasets are easy to manipulate, model and visualize, and have a specific structure: each variable is a column, each observation is a row, and each type of observational unit is a table. This framework makes it easy to tidy messy datasets because only a small set of tools are needed to deal with a wide range of un-tidy datasets. This structure also makes it easier to develop tidy tools for data analysis, tools that both input and output tidy datasets. The advantages of a consistent data structure and matching tools are demonstrated with a case study free from mundane data manipulation chores.

http://www.jstatsoft.org/v59/i10/paper 2014/09/13 - 18:37

Vol. 59, Issue 9, Sep 2014Abstract: When testing for reduction of the mean value structure in linear mixed models, it is common to use an asymptotic χ2 test. Such tests can, however, be very poor for small and moderate sample sizes. The pbkrtest package implements two alternatives to such approximate χ2 tests: The package implements (1) a Kenward-Roger approximation for performing F tests for reduction of the mean structure and (2) parametric bootstrap methods for achieving the same goal. The implementation is focused on linear mixed models with independent residual errors. In addition to describing the methods and aspects of their implementation, the paper also contains several examples and a comparison of the various methods.

http://www.jstatsoft.org/v59/i09/paper 2014/09/13 - 18:37

Vol. 59, Issue 8, Sep 2014Abstract: dglars is a publicly available R package that implements the method proposed in Augugliaro, Mineo, and Wit (2013), developed to study the sparse structure of a generalized linear model. This method, called dgLARS, is based on a differential geometrical extension of the least angle regression method proposed in Efron, Hastie, Johnstone, and Tibshirani (2004). The core of the dglars package consists of two algorithms implemented in Fortran 90 to efficiently compute the solution curve: a predictor-corrector algorithm, proposed in Augugliaro et al. (2013), and a cyclic coordinate descent algorithm, proposed in Augugliaro, Mineo, and Wit (2012). The latter algorithm, as shown here, is significantly faster than the predictor-corrector algorithm. For comparison purposes, we have implemented both algorithms.

http://www.jstatsoft.org/v59/i08/paper 2014/09/13 - 18:37

Vol. 59, Issue 7, Sep 2014Abstract: Equating is a family of statistical models and methods that are used to adjust scores on two or more versions of a test, so that the scores from different tests may be used interchangeably. In this paper we present the R package SNSequate which implements both standard and nonstandard statistical models and methods for test equating. The package construction was motivated by the need of having a modular, simple, yet comprehensive, and general software that carries out traditional and new equating methods. SNSequate currently implements the traditional mean, linear and equipercentile equating methods, as well as the mean-mean, mean-sigma, Haebara and Stocking-Lord item response theory linking methods. It also supports the newest methods such as local equating, kernel equating, and item response theory parameter linking methods based on asymmetric item characteristic functions. Practical examples are given to illustrate the capabilities of the software. A list of other programs for equating is presented, highlighting the main differences between them. Future directions for the package are also discussed.

http://www.jstatsoft.org/v59/i07/paper 2014/09/13 - 18:37

Vol. 59, Issue 6, Sep 2014Abstract: The R package phtt provides estimation procedures for panel data with large dimensions n, T, and general forms of unobservable heterogeneous effects. Particularly, the estimation procedures are those of Bai (2009) and Kneip, Sickles, and Song (2012), which complement one another very well: both models assume the unobservable heterogeneous effects to have a factor structure. Kneip et al. (2012) considers the case in which the time-varying common factors have relatively smooth patterns including strongly positively auto-correlated stationary as well as non-stationary factors, whereas the method of Bai (2009) focuses on stochastic bounded factors such as ARMA processes. Additionally, the phtt package provides a wide range of dimensionality criteria in order to estimate the number of the unobserved factors simultaneously with the remaining model parameters.

http://www.jstatsoft.org/v59/i06/paper 2014/09/13 - 18:37

Vol. 59, Issue 5, Sep 2014Abstract: In this paper, we describe the R package mediation for conducting causal mediation analysis in applied empirical research. In many scientific disciplines, the goal of researchers is not only estimating causal effects of a treatment but also understanding the process in which the treatment causally affects the outcome. Causal mediation analysis is frequently used to assess potential causal mechanisms. The mediation package implements a comprehensive suite of statistical tools for conducting such an analysis. The package is organized into two distinct approaches. Using the model-based approach, researchers can estimate causal mediation effects and conduct sensitivity analysis under the standard research design. Furthermore, the design-based approach provides several analysis tools that are applicable under different experimental designs. This approach requires weaker assumptions than the model-based approach. We also implement a statistical method for dealing with multiple (causally dependent) mediators, which are often encountered in practice. Finally, the package also offers a methodology for assessing causal mediation in the presence of treatment noncompliance, a common problem in randomized trials.

http://www.jstatsoft.org/v59/i05/paper 2014/09/13 - 18:37

Vol. 59, Issue 4, Aug 2014Abstract: Object orientation provides a flexible framework for the implementation of the convolution of arbitrary distributions of real-valued random variables. We discuss an algorithm which is based on the fast Fourier transform. It directly applies to lattice-supported distributions. In the case of continuous distributions an additional discretization to a linear lattice is necessary and the resulting lattice-supported distributions are suitably smoothed after convolution.
We compare our algorithm to other approaches aiming at a similar generality as to accuracy and speed. In situations where the exact results are known, several checks confirm a high accuracy of the proposed algorithm which is also illustrated for approximations of non-central χ2 distributions.
By means of object orientation this default algorithm is overloaded by more specific algorithms where possible, in particular where explicit convolution formulae are available. Our focus is on R package distr which implements this approach, overloading operator + for convolution; based on this convolution, we define a whole arithmetics of mathematical operations acting on distribution objects, comprising operators +, -, *, /, and ^.

http://www.jstatsoft.org/v59/i04/paper 2014/09/13 - 18:37

Vol. 59, Issue 3, Aug 2014Abstract: Today, many experiments in the field of behavioral sciences are conducted using a computer. While there is a broad choice of computer programs facilitating the process of conducting experiments as well as programs for statistical analysis there are relatively few programs facilitating the intermediate step of data aggregation. ART has been developed in order to fill this gap and to provide a computer program for data aggregation that has a graphical user interface such that aggregation can be done more easily and without any programming. All “rules” that are necessary to extract variables can be seen “at a glance” which helps the user to conduct even complex aggregations with several hundreds of variables and makes aggregation more resistant against errors. ART runs with Windows XP, Vista, 7, and 8 and it is free. Copies (executable and source code) are available at http://www.psychologie.hhu.de/arbeitsgruppen/allgemeine-psychologie-und-....

http://www.jstatsoft.org/v59/i03/paper 2014/09/13 - 18:37

Vol. 59, Issue 2, Aug 2014Abstract: We present an R package for the simulation of simple and complex survival data. It covers different situations, including recurrent events and multiple events. The main simulation routine allows the user to introduce an arbitrary number of distributions, each corresponding to a new event or episode, with its parameters, choosing between the Weibull (and exponential as a particular case), log-logistic and log-normal distributions.

http://www.jstatsoft.org/v59/i02/paper 2014/09/13 - 18:37

Vol. 59, Issue 1, Aug 2014Abstract: Progress in molecular high-throughput techniques has led to the opportunity of a comprehensive monitoring of biomolecules in medical samples. In the era of personalized medicine, these data form the basis for the development of diagnostic, prognostic and predictive tests for cancer. Because of the high number of features that are measured simultaneously in a relatively low number of samples, supervised learning approaches are sensitive to overfitting and performance overestimation. Bioinformatic methods were developed to cope with these problems including control of accuracy and precision. However, there is demand for easy-to-use software that integrates methods for classifier construction, performance assessment and development of diagnostic tests. To contribute to filling of this gap, we developed a comprehensive R package for the development and validation of diagnostic tests from high-dimensional molecular data. An important focus of the package is a careful validation of the classification results. To this end, we implemented an extended version of the multiple random validation protocol, a validation method that was introduced before. The package includes methods for continuous prediction scores. This is important in a clinical setting, because scores can be converted to probabilities and help to distinguish between clear-cut and borderline classification results. The functionality of the package is illustrated by the analysis of two cancer microarray data sets.

http://www.jstatsoft.org/v59/i01/paper 2014/09/13 - 18:37

Vol. 7, Issue 9, Sep 2002Abstract: Recurrence plots are graphical devices specially suited to detect hidden dynamical patterns and nonlinearities in data. However, there are few programs available to apply such a mehodology. This paper reviews one of the best free programs to apply nonlinear time series analysis: Visual Recurrence Analysis (VRA). This program is targeted to recurrence analysis and the so-called Recurrence Quantitative Analysis (RQA, the quantitative counterpart of recurrence plots), although it includes many procedures in a friendly visual environment. Comparisons with alternative programs are performed.

http://www.jstatsoft.org/v07/i09/paper 2014/06/12 - 21:19

Vol. 57, Issue 14, May 2014Abstract: Problems with truncated data occur in many areas, complicating estimation and inference. Regarding linear regression models, the ordinary least squares estimator is inconsistent and biased for these types of data and is therefore unsuitable for use. Alternative estimators, designed for the estimation of truncated regression models, have been developed. This paper presents the R package truncSP. The package contains functions for the estimation of semi-parametric truncated linear regression models using three different estimators: the symmetrically trimmed least squares, quadratic mode, and left truncated estimators, all of which have been shown to have good asymptotic and finite sample properties. The package also provides functions for the analysis of the estimated models. Data from the environmental sciences are used to illustrate the functions in the package.

http://www.jstatsoft.org/v57/i14/paper 2014/05/07 - 19:44

Vol. 57, Issue 13, May 2014Abstract: Inference in quantile analysis has received considerable attention in the recent years. Linear quantile mixed models (Geraci and Bottai 2014) represent a flexible statistical tool to analyze data from sampling designs such as multilevel, spatial, panel or longitudinal, which induce some form of clustering. In this paper, I will show how to estimate conditional quantile functions with random effects using the R package lqmm. Modeling, estimation and inference are discussed in detail using a real data example. A thorough description of the optimization algorithms is also provided.

http://www.jstatsoft.org/v57/i13/paper 2014/05/07 - 19:44

Vol. 57, Issue 12, May 2014Abstract: The R package compareGroups provides functions meant to facilitate the construction of bivariate tables (descriptives of several variables for comparison between groups) and generates reports in several formats (LATEX, HTML or plain text CSV). Moreover, bivariate tables can be viewed directly on the R console in a nice format. A graphical user interface (GUI) has been implemented to build the bivariate tables more easily for those users who are not familiar with the R software. Some new functions and methods have been incorporated in the newest version of the compareGroups package (version 1.x) to deal with time-to-event variables, stratifying tables, merging several tables, and revising the statistical methods used. The GUI interface also has been improved, making it much easier and more intuitive to set the inputs for building the bivariate tables. The first version (version 0.x) and this version were presented at the 2010 useR! conference (Sanz, Subirana, and Vila 2010) and the 2011 useR! conference (Sanz, Subirana, and Vila 2011), respectively. Package compareGroups is available from the Comprehensive R Archive Network at http://CRAN.R-project.org/package=compareGroups.

http://www.jstatsoft.org/v57/i12/paper 2014/05/07 - 19:44

Vol. 57, Issue 11, May 2014Abstract: The R package pdfCluster performs cluster analysis based on a nonparametric estimate of the density of the observed variables. Functions are provided to encompass the whole process of clustering, from kernel density estimation, to clustering itself and subsequent graphical diagnostics. After summarizing the main aspects of the methodology, we describe the features and the usage of the package, and finally illustrate its application with the aid of two data sets.

http://www.jstatsoft.org/v57/i11/paper 2014/05/07 - 19:44

Vol. 57, Issue 10, May 2014Abstract: In this paper we present PaCAL, a Python package for arithmetical computations on random variables. The package is capable of performing the four arithmetic operations: addition, subtraction, multiplication and division, as well as computing many standard functions of random variables. Summary statistics, random number generation, plots, and histograms of the resulting distributions can easily be obtained and distribution parameter fitting is also available. The operations are performed numerically and their results interpolated allowing for arbitrary arithmetic operations on random variables following practically any probability distribution encountered in practice. The package is easy to use, as operations on random variables are performed just as they are on standard Python variables. Independence of random variables is, by default, assumed on each step but some computations on dependent random variables are also possible. We demonstrate on several examples that the results are very accurate, often close to machine precision. Practical applications include statistics, physical measurements or estimation of error distributions in scientific computations.

http://www.jstatsoft.org/v57/i10/paper 2014/05/07 - 19:44

Vol. 57, Issue 9, Apr 2014Abstract: Two-phase designs, in which for a large study a dichotomous outcome and partial or proxy information on risk factors is available, whereas precise or complete measurements on covariates have been obtained only in a stratified sub-sample, extend the standard case-control design and have been proven useful in practice. The application of two-phase designs, however, seems to be hampered by the lack of appropriate, easy-to-use software. This paper introduces sas-twophase-package, a collection of SAS-macros, to fulfill this task. sas-twophase-package implements weighted likelihood, pseudo likelihood and semi- parametric maximum likelihood estimation via the EM algorithm and via profile likelihood in two-phase settings with dichotomous outcome and a given stratification.

http://www.jstatsoft.org/v57/i09/paper 2014/04/23 - 15:43

Vol. 57, Issue 8, Apr 2014Abstract: We describe the R package multiPIM, including statistical background, functionality and user options. The package is for variable importance analysis, and is meant primarily for analyzing data from exploratory epidemiological studies, though it could certainly be applied in other areas as well. The approach taken to variable importance comes from the causal inference field, and is different from approaches taken in other R packages. By default, multiPIM uses a double robust targeted maximum likelihood estimator (TMLE) of a parameter akin to the attributable risk. Several regression methods/machine learning algorithms are available for estimating the nuisance parameters of the models, including super learner, a meta-learner which combines several different algorithms into one. We describe a simulation in which the double robust TMLE is compared to the graphical computation estimator. We also provide example analyses using two data sets which are included with the package.

http://www.jstatsoft.org/v57/i08/paper 2014/04/23 - 15:43

Vol. 57, Issue 7, Apr 2014Abstract: The R package ThreeWay is presented and its main features are illustrated. The aim of ThreeWay is to offer a suit of functions for handling three-way arrays. In particular, the most relevant available functions are T3 and CP, which implement, respectively, the Tucker3 and Candecomp/Parafac methods. They are the two most popular tools for summarizing three-way arrays in terms of components. After briefly recalling both techniques from a theoretical point of view, the functions T3 and CP are described by considering three real life examples.

http://www.jstatsoft.org/v57/i07/paper 2014/04/23 - 15:43

Vol. 57, Issue 6, Apr 2014Abstract: PySSM is a Python package that has been developed for the analysis of time series using linear Gaussian state space models. PySSM is easy to use; models can be set up quickly and efficiently and a variety of different settings are available to the user. It also takes advantage of scientific libraries NumPy and SciPy and other high level features of the Python language. PySSM is also used as a platform for interfacing between optimized and parallelized Fortran routines. These Fortran routines heavily utilize basic linear algebra and linear algebra Package functions for maximum performance. PySSM contains classes for filtering, classical smoothing as well as simulation smoothing.

http://www.jstatsoft.org/v57/i06/paper 2014/04/09 - 13:57

Vol. 57, Issue 6, Apr 2014Abstract: PySSM is a Python package that has been developed for the analysis of time series using linear Gaussian state space models. PySSM is easy to use; models can be set up quickly and efficiently and a variety of different settings are available to the user. It also takes advantage of scientific libraries NumPy and SciPy and other high level features of the Python language. PySSM is also used as a platform for interfacing between optimized and parallelized Fortran routines. These Fortran routines heavily utilize basic linear algebra and linear algebra Package functions for maximum performance. PySSM contains classes for filtering, classical smoothing as well as simulation smoothing.

http://www.jstatsoft.org/v57/i06/paper 2014/04/09 - 13:57

Vol. 57, Issue 5, Apr 2014Abstract: Rating scales, such as Likert scales, are very common in marketing research, customer satisfaction studies, psychometrics, opinion surveys, population studies, and numerous other fields. We recommend diverging stacked bar charts as the primary graphical display technique for Likert and related scales. We also show other applications where diverging stacked bar charts are useful. Many examples of plots of Likert scales are given. We discuss the perceptual and programming issues in constructing these graphs. We present two implementations for diverging stacked bar charts. Most examples in this paper were drawn with the likert function included in the HH package in R. We also have a dashboard in Tableau.

http://www.jstatsoft.org/v57/i05/paper 2014/04/09 - 13:57

Vol. 57, Issue 5, Apr 2014Abstract: Rating scales, such as Likert scales, are very common in marketing research, customer satisfaction studies, psychometrics, opinion surveys, population studies, and numerous other fields. We recommend diverging stacked bar charts as the primary graphical display technique for Likert and related scales. We also show other applications where diverging stacked bar charts are useful. Many examples of plots of Likert scales are given. We discuss the perceptual and programming issues in constructing these graphs. We present two implementations for diverging stacked bar charts. Most examples in this paper were drawn with the likert function included in the HH package in R. We also have a dashboard in Tableau.

http://www.jstatsoft.org/v57/i05/paper 2014/04/09 - 13:57

Vol. 57, Issue 4, Apr 2014Abstract: The YUIMA Project is an open source and collaborative effort aimed at developing the R package yuima for simulation and inference of stochastic differential equations. In the yuima package stochastic differential equations can be of very abstract type, multidimensional, driven by Wiener process or fractional Brownian motion with general Hurst parameter, with or without jumps specified as Lévy noise. The yuima package is intended to offer the basic infrastructure on which complex models and inference procedures can be built on. This paper explains the design of the yuima package and provides some examples of applications.

http://www.jstatsoft.org/v57/i04/paper 2014/04/09 - 13:57

Vol. 57, Code Snippet 1, Mar 2014

http://www.jstatsoft.org/v57/c01/paper 2014/03/14 - 22:19

Vol. 57, Issue 3, Mar 2014Abstract: We introduce growcurves for R that performs analysis of repeated measures multiple membership (MM) data. This data structure arises in studies under which an intervention is delivered to each subject through the subject’s participation in a set of multiple elements that characterize the intervention. In our motivating study design under which subjects receive a group cognitive behavioral therapy (CBT) treatment, an element is a group CBT session and each subject attends multiple sessions that, together, comprise the treatment. The sets of elements, or group CBT sessions, attended by subjects will partly overlap with some of those from other subjects to induce a dependence in their responses. The growcurves package offers two alternative sets of hierarchical models: 1. Separate terms are specified for multivariate subject and MM element random effects, where the subject effects are modeled under a Dirichlet process prior to produce a semi-parametric construction; 2. A single term is employed to model joint subject-by-MM effects. A fully non-parametric dependent Dirichlet process formulation allows exploration of differences in subject responses across different MM elements. This model allows for borrowing information among subjects who express similar longitudinal trajectories for flexible estimation. growcurves deploys “estimation” functions to perform posterior sampling under a suite of prior options. An accompanying set of “plot” functions allows the user to readily extract by-subject growth curves. The design approach intends to anticipate inferential goals with tools that fully extract information from repeated measures data. Computational efficiency is achieved by performing the sampling for estimation functions using compiled C++ code.

http://www.jstatsoft.org/v57/i03/paper 2014/03/14 - 22:19

Vol. 57, Issue 2, Mar 2014Abstract: The computer program DixonText.CriticalValues is written in VB.NET to extend the quadrature approach to calculate the critical values with accuracy up to 6 significant digits for Dixon’s ratios. Its use in creating the critical values tables in Excel is illustrated.

http://www.jstatsoft.org/v57/i02/paper 2014/03/14 - 22:19

Vol. 57, Issue 1, Mar 2014Abstract: This paper introduces the R package lavaan.survey, a user-friendly interface to design-based complex survey analysis of structural equation models (SEMs). By leveraging existing code in the lavaan and survey packages, the lavaan.survey package allows for SEM analyses of stratified, clustered, and weighted data, as well as multiply imputed complex survey data. lavaan.survey provides several features such as SEMs with replicate weights, a variety of resampling techniques for complex samples, and finite population corrections, features that should prove useful for SEM practitioners faced with the common situation of a sample that is not iid.

http://www.jstatsoft.org/v57/i01/paper 2014/03/14 - 22:19