Cluster analysis is a set of statistical methods for discovering new group/class structure when exploring datasets. This article reviews the following popular libraries/commands in the R software language for applying different types of cluster analysis: from the stats library, the kmeans and hclust functions; the mclust library; the poLCA library; and the clustMD library. The packages/functions cover a variety of cluster analysis methods for continuous data, categorical data or a collection of the two. The contrasting methods in the different packages are briefly introduced and basic usage of the functions is discussed. The use of the different methods is compared and contrasted and then illustrated on example data. In the discussion, links to information on other available libraries for different clustering methods and extensions beyond basic clustering methods are given. The code for the worked examples in Section 2 is available at http://www.stats.gla.ac.uk/˜nd29c/Software/ClusterReviewCode.R.

BackgroundObesity and diabetes are global public health concerns. Studies indicate a relationship between socioeconomic, demographic and environmental variables and the spatial patterns of diet-related chronic disease. In this paper, we propose a methodology using model-based clustering and variable selection to predict rates of obesity and diabetes. We test this method through an application in the northeastern United States.MethodsWe use model-based clustering, an unsupervised learning approach, to find latent clusters of similar US counties based on a set of socioeconomic, demographic, and environmental variables chosen through the process of variable selection. We then use Analysis of Variance and Post-hoc Tukey comparisons to examine differences in rates of obesity and diabetes for the clusters from the resulting clustering solution.ResultsWe find access to supermarkets, median household income, population density and socioeconomic status to be important in clustering the counties of two northeastern states. The results of the cluster analysis can be used to identify two sets of counties with significantly lower rates of diet-related chronic disease than those observed in the other identified clusters. These relatively healthy clusters are distinguished by the large central and large fringe metropolitan areas contained in their component counties. However, the relationship of socio-demographic factors and diet-related chronic disease is more complicated than previous research would suggest. Additionally, we find evidence of low food access in two clusters of counties adjacent to large central and fringe metropolitan areas. While food access has previously been seen as a problem of inner-city or remote rural areas, this study offers preliminary evidence of declining food access in suburban areas.ConclusionsModel-based clustering with variable selection offers a new approach to the analysis of socioeconomic, demographic, and environmental data for diet-related chronic disease prediction. In a test application to two northeastern states, this method allows us to identify two sets of metropolitan counties with significantly lower diet-related chronic disease rates than those observed in most rural and suburban areas. Our method could be applied to larger geographic areas or other countries with comparable data sets, offering a promising method for researchers interested in the global increase in diet-related chronic disease.Electronic supplementary materialThe online version of this article (doi:10.1186/s12942-015-0017-5) contains supplementary material, which is available to authorized users.

Recently there has been significant work in the social sciences involving ensembles of social networks, that is, multiple, independent, social networks such as students within schools or employees within organizations. There remains, however, very little methodological work on exploring these types of data structures. We present methods for clustering social networks with observed nodal class labels, based on statistics of walk counts between the nodal classes. We extend this method to consider only non-backtracking walks, and introduce a method for normalizing the counts of long walk sequences using those of shorter ones. We then present a method for clustering networks based on these statistics to explore similarities among networks. We demonstrate the utility of this method on simulated network data, as well as on advice-seeking networks in education.

Agreement indices are commonly used to summarize the performance of both classification and clustering methods. The easy interpretation/intuition and desirable properties that result from the Rand and adjusted Rand indices, has led to their popularity over other available indices. While more algorithmic clustering approaches like k-means and hierarchical clustering produce hard partition assignments (assigning observations to a single cluster), other techniques like model-based clustering include information about the certainty of allocation of objects through class membership probabilities (soft partitions). To assess performance using traditional indices, e.g. the adjusted Rand index (ARI), the soft partition is mapped to a hard set of assignments, which commonly overstates the certainty of correct assignments. This paper proposes an extension of the ARI, the soft adjusted Rand index (sARI), with similar intuition and interpretation but also incorporating information from one or two soft partitions. It can be used in conjunction with the ARI, comparing the similarities of hard to soft, or soft to soft, partitions to the similarities of the mapped hard partitions. Simulation study results support the intuition that, in general, mapping to hard partitions tends to increase the measure of similarity between partitions. In applications, the sARI more accurately reflects the cluster boundary overlap commonly seen in real data. Keywords adjusted Rand index • model-based clustering • mixture models • soft partition • posterior probabilities • class membership probabilities Mathematics Subject Classification (2000) 62H30 • 91C20 • 62H86 Address(es) of author(s) should be given

No abstract