Training workshop on
Analysis of Multivariate Data from Ecology and Environmental Science, using PRIMER v6
Institute of Biology (Room U99), University of Southern Denmark, Odense
16th May – 20th May 2011
Course content
● This five day workshop will cover the statistical analysis of assemblage data (species by samples matrices of
abundance, area cover etc) and/or multi-variable environmental data which arise in a wide range of applications in
environmental science and ecology, from environmental impact assessments, through fundamental community ecology
studies and monitoring of widescale biodiversity change, to biomarker studies and purely physical or chemical analyses
● Based on the PRIMER package (Plymouth Routines In Multivariate Ecological Research), a worldwide standard
software tool used in over 6000 SCI-listed papers for analysis of aquatic assemblages and, increasingly, terrestrial,
paleontological, microbial and genetic data, also for model output, in ecotoxicology, epidemiology, sociology etc
● The workshop covers definitions of similarity, clustering (CLUSTER), ordination by non-metric multi-dimensional
scaling (MDS) and principal components analysis (PCA), hypothesis testing on similarity matrices (ANOSIM) and
other permutation tests (RELATE), linking biotic patterns to environmental variables (BEST), identifying species
responsible for the observed community pattern (SIMPER, BEST), comparison of ordinations (2STAGE, eg 2nd
stage MDS), dominance curves and (bio)diversity indices, including measures based on taxonomic relatedness of
species (TAXDTEST). All other features of PRIMER v6 are also covered: choice between over 50 (dis)similarity
measures, including dispersion-weighted and relatedeness-based coefficients, new 'exploratory' permutation tests for
structure in a priori unstructured samples (SIMPROF) and optimal biota-environment relationships (the latter also
examined by non-parametric multivariate regression trees, LINKTREE). Also covered are tests for dominance
curves (DOMDIS), SIMPER analyses for 2-way layouts and abiotic variables, missing data algorithms for environmental data, merging of non-matching species lists etc.
● Also briefly demonstrated (though not covered in detail, since they require another 5-day course!) will be the ‘addon’ PERMANOVA+ routines to PRIMER6, which add 'semi-parametric' multivariate analyses, e.g. the extension of
permutation tests to complex designs (PERMANOVA), regression (DISTLM) and dispersion tests (PERMDISP).
● The workshop will be led by Dr Paul J Somerfield (Plymouth Marine Lab, UK). Paul is a senior researcher in
community ecology and quantitative methods at the PML, spearheading the laboratory's biodiversity research. He
has been responsible for some of the methodology in the current version of PRIMER and has much experience of
using the package creatively in a wide range of applications (marine and terrestrial, microbial and genetic, etc)
● ‘Hands-on’ lab sessions will use real literature case studies, analysed with PRIMER. Participants are also encouraged
to bring some of their own data to the course. 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 and understand. No prior statistical knowledge is assumed
● The workshop will be held on the main campus of the University of Southern Denmark, at Campusvej 55, 5230
Odense M (http://sdu.dk/servicenavigation/left/Vejviser/Odense/KrakIFrameCampusvej.aspx). Parking is free and
available around the buildings. The workshop will take place in room U99 near the main entrance (“hoved indgang”)
http://sdu.dk/servicenavigation/left/Vejviser/Odense/ParkeringerIndgangeCampusvej.aspx.
● There is a fairly good bus service from and to the university http://www.fynbus.dk/wm141234 so that
accommodation can be arranged all over the city. However, we advise bed and breakfast or hotels in Odense M (for
Middle), Odense C (Centret) or Odense SØ (Syd Øst). We do have special prices in different hotels located in the
city centre. Please contact mdelefosse@biology.sdu.dk for more information.
● The course will take place in a conference room, not a computer laboratory, so participants are expected to bring their
own laptop computers to use during the lab sessions, analysing literature data sets and some of their own data (with Paul
Somerfield’s help). Not every participant needs a laptop and you may prefer to share with a colleague – one machine
between two people is very workable (in fact, has some benefits in terms of livelier interactions!). The laptop requires a
registered PRIMER6 licence already installed, or purchased (at discount) for delivery and installation at the start of the
workshop (CD/DVD drive and administrator access required). PRIMER6 is a Windows-only product (no native Mac
version), running on 2000/XP (needs 256Mb RAM) or Vista/7 (needs 1Gb RAM), either 32- or 64-bit machines (also
needs Internet Explorer 5 or later to install the .Net2 framework, if not already present).
Workshop costs
● Course fee: 4750 DKK (3200 DKK for full-time students) for a full five days. The fee includes the course book,
coffees/teas and lunches but not the cost of PRIMER software or accommodation.
● Software licence for PRIMER6. The PRIMER v6 software will be used throughout and, to register, participants are
expected to already own a licence for this version or purchase in connection with the course*. Below are single-user
licence fees for participants (at 20% discount on list price - they subsume any further discounts for bulk purchase). The
usual additional carriage charges will also be waived if software is picked up at the start of the workshop.
New academic, single-user licence (i.e. universities and colleges only):
1900 DKK
New public sector, single-user licence (government labs, museums, 'not-for-profits' etc):
2850 DKK
New private sector, single-user licence (fully commercial activity):
3800 DKK
Licensed v5 users can upgrade** to v6 at 50% of the above prices
The add-on PERMANOVA+ package can additionally be ordered***, at standard list prices (1200/1800/2400 DKK for
academic/public-sector/private-sector single-user licences), for delivery at the workshop
Courier (200 DKK) or air mail (100 DKK) charges will be added if software is to be sent in advance of the workshop
● VAT: EU invoice addresses are exempt from VAT for both course fee and software, provided a valid VAT number is
given on registration. For participants with UK addresses VAT will be added at 20% on both components
* An exception can be made for a student who will, in future, always use their supervisor’s PC (and their supervisor has a registered v6
licence), or they will be using a machine covered by a v6 teaching licence at their university
** If upgrading, please first check with Cathy or Marg (at admin@primer-e.com) that you hold a valid v5 licence
*** PERMANOVA+ add-on licence is not required for this course - it will only be briefly demonstrated, not used in the lab sessions
Registration
● E-mail/post the booking form below to the local organiser, Matthieu Delefosse (phone: +45 60 47 79 50; contact
mdelefosse@biology.sdu.dk). He will e-mail you a programme for the course, and can answer queries on local issues.
● You will then be sent confirmation of your registration from Cathy or Marg at the PRIMER-E office in Plymouth, UK
(admin@primer-e.com), along with a payment invoice for course and software (please indicate below if these need to be
separate invoices, or if either needs to go to a different invoice address and e-mail than your own). If you require a
proforma invoice (a formal quote) before your institution permits you to register, please contact Cathy or Marg prior to
sending in the registration form to Matthieu. Ensure that any Purchase Order number is included on the booking form.
● All payments are to PRIMER-E and can be by credit card (Mastercard and Visa only), cheque or bank transfer (full
details will be on the invoice). They should be received in Plymouth by the payment deadline of 15 April. If there are
institutional rules which prevent payment from purchase orders being made in advance of the workshop, please discuss
these with Cathy or Marg at PRIMER-E (admin@primer-e.com)
● The workshop can cater for up to about 30 participants. Places will be allocated in order of receipt of booking forms
by Matthieu. Registrations after the payment deadline will be accepted, space permitting, but if the workshop is oversubscribed, participants who have not paid by the payment deadline risk losing their place to someone on the waiting list.
----------------------------------------------------------------------------------------------------------------------------- ----------------------------BOOKING FORM: Please e-mail/post the following information to Matthieu Delefosse at E-mail: mdelefosse@biology.sdu.dk;
Post: Institute of Biology Campusvej, 55 DK-5230 Odense M, Denmark.
Name: …………………………………………. Organisation: …………….…………..…..……………………………………....…………..
E-mail: ………………………………………… Address: …………………………...………………………………………………..……….
Tel: …………..………… ………....
…………………………...…………………………………………………..
Please cross the boxes [ x ], as appropriate
……………………………………………………………………….……....
I wish to be invoiced for the following (see prices above, all in DKK): [ ] Full course fee or [ ] Full-time student course fee
[ ] New PRIMER6 licence or [ ] Upgraded PRIMER6 licence from PRIMER5 and/or [ ] PERMANOVA+ 'add-on' licence
[ ] Software picked up at the workshop or Software sent in advance to the above address by: [ ] Courier or [ ] Air mail
[ ] I am from a (non-UK) EU institution whose VAT number is ………………………………………………………….……..
[ ] I require the invoice to be sent elsewhere (please specify): ………………………………………………….……………..…
……………………………………………………………………………………………………………………….……………..
[ ] Please include my Purchase Order number on the invoice ………………………………………………………………….…