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In coupled human-environment systems where well established and proven general theories are often lacking cluster analysis provides the possibility to discover regularities – a first step in empirically based theory building. The aim of this report is to share the experiences and knowledge on cluster analysis we gained in several applications in this realm helping to avoid typical problems and pitfalls. In our description of issues and methods we will highlight well-known main-stream methods as well as promising new developments, referring to pertinent literature for further information, thus offering also some potential new insights for the more experienced. The following aspects are discussed in detail: data-selection and pre-treatment, selection of a distance measure in the data space, selection of clustering method, performing clustering (parameterizing the algorithm(s), determining the number of clusters etc.) and the interpretation and evaluation of results. We link our description – as far as tools for performing the analysis are concerned - to the R software environment and its associated cluster analysis packages. We have used this public domain software, together with own tailor-made extensions, documented in the appendix.