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Rhode Island Natural History Survey » PRIMER Workshop
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Events &News RINHS on 17 Jun 2005 03:30 pm

PRIMER Workshop

Analysis of Multivariate Data from Ecology and Environmental Science using PRIMER v6

Training Workshop held at the Environmental Protection Agency – Atlantic Ecology Division
in conjunction with University of Rhode Island Bay Campus

A PRIMER v6 workshop is being officially organised by the Rhode Island Natural History Survey, and co-organised by the U. S. Environmental Protection Agency- Atlantic Ecology Division and the University of Rhode Island Bay Campus for 13-17 June 2005. This training will take place over five days and will cover the statistical analysis of assemblage data (species by samples matrices) and/or multi-variable environmental data, which arise in a wide range of applications in ecology and environmental science. The methods covered are generic and applicable in terrestrial, freshwater and palaeontological contexts, though the examples used in the workshop will all be from marine and estuarine studies. Many of these are of hard substrate, soft sediment or fish assemblages monitored for environmental impacts, but also covered are more fundamental studies, linking biotic patterns to physico-chemical variables and testing in field or mesocosm experiments. Many of the methods are equally applicable to environmental studies analysing suites of biomarkers, tissue/water contaminants, particle size analyses etc.

The workshop will be led by Dr K R Clarke (Director, PRIMER-E and an honorary fellow of the Plymouth Marine Laboratory). Bob Clarke is a researcher in ecological statistics and has worked for many years at the PML, where he was responsible for adapting and developing the methods underlying the PRIMER package. The schedule will be a mixture of lectures on the methodology and computer lab sessions, analysing real case studies, combined with the opportunity for participants to bring some of their own data to the workshop. The emphasis throughout is on practical application and interpretation, the theoretical aspects (e.g. the multivariate statistical methods which are the core of the course) being carefully selected to be those that are simple to describe, robust to operate and easy to interpret, so that no prior statistical knowledge is assumed.

The exposition will cover all features of the current (v5) Windows PRIMER package (Plymouth Routines In Multivariate Ecological Research), which exploits a range of univariate, graphical and multivariate routines: hierarchical clustering into sample (or species) groups (CLUSTER); ordination by non-metric multidimensional scaling (MDS) and principal components (PCA) to summarise patterns in species composition and environmental variables; permutation-based hypothesis testing (ANOSIM), an analogue of univariate ANOVA which tests for differences between groups of (multivariate) samples from different times, locations, experimental treatments etc; identifying the species primarily providing the discrimination between two observed sample clusters (SIMPER); the linking of multivariate biotic patterns to suites of environmental variables (BIO-ENV); comparative (Mantel-type) tests on similarity matrices (RELATE); standard diversity indices; dominance plots; species abundance distributions and simple species-area curves; aggregation of arrays to allow data analysis at higher taxonomic levels; and matching of sample patterns from different biotic arrays (BVSTEP, a stepwise algorithm generalising BIO-ENV which can be used, for example, to find ‘influential species’, and 2STAGE, a second-stage MDS in which relationships between a large set of ordinations can be visualised). A further unique feature of PRIMER v5 is the ability to calculate and test (TAXDTEST) biodiversity indices based on the taxonomic distinctness of the species making up a quantitative sample or species list, indices whose statistical properties are robust to variations in sampling effort.

Lectures will also include techniques available in a new PRIMER version (v6), which will be the workshop software. Therefore, purchase of a v6 single-user licence, or upgrade from v5, is mandatory for participation*. Techniques include: dispersion-weighted similarities, which exploit replication to improve the explanatory power of multivariate displays, by downweighting contributions from common but ‘noisy’ species and upweighting less common species which are consistently observed; new global permutation tests for the significance of dominance curves and biota-environment relations found by BIO-ENV (adjusting for selection bias); generalisation of similarity percentage breakdowns (SIMPER) to environmental variables and two-way layouts; non-parametric linkage trees, which relax the implicit constraint in BIO-ENV of additive environmental effects on biotic composition; a new class of taxonomically-based similarity measures, which extend the concept of taxonomic distinctness to multivariate analyses, etc. This is combined with many improvements to v5 features: calculation of a wider range of similarity coefficients, better treatment of missing data, facilities to navigate and save the workspace, improved MDS plots and diagnostics, merging sheets with non-matching species lists etc.


  • PRIMER: For any queries on current licence status, contact Cathy at admin@primer-e.com.
  • Enquiries about course accommodation (etc): Suzanne Ayvazian at ayvazian.suzanne@ epamail.epa.gov, (EPA, Narragansett) tel: 401-782:3027.
  • Registration and Payment of course and licence fees: Kira Stillwell, Program Administrator, Rhode Island Natural History Survey,
  • PO Box 1858, Kingston, RI 02881 phone: 401-874-5800, fax 401-874-5868 email kstillwell@rinhs.org

Kira Stillwell
Program Administrator
RI Natural History Survey

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