Abstract:

Cluster ensembles have emerged as a powerful meta-learning paradigm that provides improved accuracy and robustness by aggregating several input data clusterings. In particular, link-based similarity methods have recently been introduced with superior performance to the conventional co-association approach. This paper presents a MATLAB package, LinkCluE, that implements the link-based cluster ensemble framework. A variety of functional methods for evaluating clustering results, based on both internal and external criteria, are also provided. Additionally, the underlying algorithms together with the sample uses of the package with interesting real and synthetic datasets are demonstrated herein.

Abstract:

The 3-dimensional representation and inspection of complex data is a frequently used strategy in many data analysis domains. Existing data mining software often lacks functionality that would enable users to explore 3D data interactively, especially if one wishes to make dynamic graphical representations directly viewable on the web.

In this paper we present vrmlgen, a software package for the statistical programming language R to create 3D data visualizations in web formats like the Virtual Reality Markup Language (VRML) and LiveGraphics3D. vrmlgen can be used to generate 3D charts and bar plots, scatter plots with density estimation contour surfaces, and visualizations of height maps, 3D object models and parametric functions. For greater flexibility, the user can also access low-level plotting methods through a unified interface and freely group different function calls together to create new higher-level plotting methods. Additionally, we present a web tool allowing users to visualize 3D data online and test some of vrmlgen's features without the need to install any software on their computer.

Graphics for Statistics and Data Analysis with R
Kevin J. Keen
Chapman and Hall/CRC, 2010
ISBN: 9781584880875

R in a Nutshell
Joseph Adler
O'Reilly, 2010
ISBN: 978-0-596-80170-0

Bayesian Analysis for Population Ecology
Ruth King, Byron J. T. Morgan, Olivier Gimenez, Stephen P. Brooks
Chapman and Hall/CRC, 2010
ISBN: 978-1-4398-1187-0

Abstract:

depmixS4 implements a general framework for defining and estimating dependent mixture models in the R programming language. This includes standard Markov models, latent/hidden Markov models, and latent class and finite mixture distribution models. The models can be fitted on mixed multivariate data with distributions from the glm family, the (logistic) multinomial, or the multivariate normal distribution. Other distributions can be added easily, and an example is provided with the exgaus distribution. Parameters are estimated by the expectation-maximization (EM) algorithm or, when (linear) constraints are imposed on the parameters, by direct numerical optimization with the Rsolnp or Rdonlp2 routines.

Abstract:

The amei package for R is a tool that provides a flexible statistical framework for generating optimal epidemiological interventions that are designed to minimize the total expected cost of an emerging epidemic. Uncertainty regarding the underlying disease parameters is propagated through to the decision process via Bayesian posterior inference. The strategies produced through this framework are adaptive: vaccination schedules are iteratively adjusted to reflect the anticipated trajectory of the epidemic given the current population state and updated parameter estimates. This document briefly covers the background and methodology underpinning the implementation provided by the package and contains extensive examples showing the functions and methods in action.

Abstract:

The tolerance package for R provides a set of functions for estimating and plotting tolerance limits. This package provides a wide-range of functions for estimating discrete and continuous tolerance intervals as well as for estimating regression tolerance intervals. An additional tool of the tolerance package is the plotting capability for the univariate and regression settings as well as for the multivariate normal setting. The tolerance package's capabilities are illustrated using simulated data sets. Formulas used for the estimation procedures are also presented.

Abstract:

To simulate fractional Brownian motion indexed by a manifold poses serious numerical problems: storage, computing time and choice of an appropriate grid. We propose an effective and fast method, valid not only for fractional Brownian fields indexed by a manifold, but for any Gaussian fields indexed by a manifold. The performance of our method is illustrated with different manifolds (sphere, hyperboloid).

Abstract:

The metafor package provides functions for conducting meta-analyses in R. The package includes functions for fitting the meta-analytic fixed- and random-effects models and allows for the inclusion of moderators variables (study-level covariates) in these models. Meta-regression analyses with continuous and categorical moderators can be conducted in this way. Functions for the Mantel-Haenszel and Peto's one-step method for meta-analyses of 2 x 2 table data are also available. Finally, the package provides various plot functions (for example, for forest, funnel, and radial plots) and functions for assessing the model fit, for obtaining case diagnostics, and for tests of publication bias.

Abstract:

For right-censored data perhaps the most commonly used tests are weighted logrank tests, such as the logrank and Wilcoxon-type tests. In this paper we review several generalizations of those weighted logrank tests to interval-censored data and present an R package, interval, to implement many of them. The interval package depends on the perm package, also presented here, which performs exact and asymptotic linear permutation tests. The perm package performs many of the tests included in the already available coin package, and provides an independent validation of coin. We review analysis methods for interval-censored data, and we describe and show how to use the interval and perm packages.

Abstract:

Since zero-coupon rates are rarely directly observable, they have to be estimated from market data. In this paper we review several widely-used parametric term structure estimation methods. We propose a weighted constrained optimization procedure with analytical gradients and a globally optimal start parameter search algorithm. Moreover, we introduce the R package termstrc, which offers a wide range of functions for term structure estimation based on static and dynamic coupon bond and yield data sets. It provides extensive summary statistics and plots to compare the results of the different estimation methods. We illustrate the application of the package through practical examples using market data from European government bonds and yields.

ggplot2: Elegant Graphics for Data Analysis
Hadley Wickham
Springer-Verlag, 2009
ISBN: 978-0-387-98140-6