Exxon Valdez   Perna viridis    Scotian Shelf     Galeta oilspil

MV Statistical Methods for Prediction & Hypothesis-testing: Case Studies

                                                Roger H. Green

                    Fredericton NB Canada       March 7-8 2011

Louisiana bayou  Sungei Buloh Park    Presqu'ile Bay   Gulf of Mexico

     Background expected:  a statistics half-course covering ANOVA & regression, and some field ecology experience 











.........Website Menu               [Last updated March 03]

























Philosophy of workshop:

   It will be assumed that attendees are familiar with ordination and clustering (not exhaustively - just what they do), and the principles of hypothesis-testing study designs. But multivariate (MV) statistical analysis includes much more than ordination and clustering. Other kinds of MV analysis, of the hypothesis-testing and predictive kind, will be presented with examples. All classical linear model statistics (regression, ANOVA, ANCOVA and their variants) can be done with multiple response variables. Such MV analyses include MANOVA, MANCOVA, Canonical Correlation, General Linear Models, Multi-way Contingency Tables, and others. Then we will consider 5 or 6 environmental case studies which combine MV statistical analysis & interpretation with good study design, prediction and hypothesis-testing. Throughout there will be a comparison with biotic index approaches. The general subject of relating biotic response variables to environmental predictors will come in naturally. Case studies that will be presented include:
- Lower Great Lakes studies, cluster on biota to group reference sites, CDA clusters on environmental variables, plot test site on p=0.95 ordination ellipse (Reynoldson's BEAST).
- MANOVA design & analysis for GOOMEX oil platforms (Kennicutt et al 1996), Sediment Quality Triad (SQT) approach (Green and Montagna)
- Various MV analyses used on Southern Gulf of St. Lawrence community-based data (DFO Technical Report in prep)
- Cluster biota, MANOVA & CDA on clusters in MV environmental space
- Patalas Experimental Lakes plankton data (Green & Vascotto)
- A variety of MV analysis sequences modeled on SQT to explain biotic response to a pollution gradien
- Vancouver Harbour data (Green, Boyd and Macdonald) .


Short bio of instructor:

   Dr. Roger Green is an environmental biologist whose own research focuses on the use of freshwater and marine invertebrates for biomonitoring. He has consulted on study design and statistical analysis of results for numerous impact and monitoring studies of oil spills, oil and gas development, and contaminant discharges. Dr. Green's 1979 book "Sampling Design and Statistical Methods for Environmental Biologists" (Wiley) is well known and still widely used. He has conducted environmental study design & analysis workshops all over the world, and is an Emeritus Professor at the University of Western Ontario, is affiliated with the Environment and Natural Resources Institute of the University of Alaska (Anchorage), and with the Watershed Graduate Studies program at Trent University (Peterborough Ontario). He is a member of the Scientific Advisory Committee of the Prince William Sound Regional Citizens Advisory Council, and an environmental advisory panel for Atlantic Canada offshore oil operations.


Guest experts:

    Two experienced professionals in the subject area, Dr. Robert Bailey and Dr. Simon Courtenay, will be present for parts of the workshop,
in addition to Dr. Roger Green.  Plans are that Dr. Courtenay will be with us for Day 1 (Monday), and Dr. Bailey will be with us for both days.


Cost of attendance at workshop:

  Most costs are fixed and not related to the number of attendees, so the attendance fee is a function of the number of attendees. If the
number was around 20 the attendance fee would be $296. A maximum number would be 30, for which the fee would be $197.
 ***** The workshop is full so the fee has been set at $200 *****
What you will get for that will be:
- a 2 full days workshop on the UNB campus in Fredricton NB
- a lot of workshop-related material - mostly electronically
- access to a workshop website with references, case study data, and communication capabilities
- The website will be available from a month before the workshop until several months after it.
- 1-on-1 assistance with attendees' study design & analysis problems during, and for a reasonable period of time after, the workshop



















New information


The General info & philosophical approach material has been updated.

I have revised the workshop schedule somewhat, changing and rearranging examples (case studies). As a result
what is to be covered on Day 1 according to the schedule will probably go into Day 2. But not to worry - there
will be less additional material to cover on Day 2.

We have provided you with 8 e-papers (full-text). They are (check the References):
- Green and Chapman in press                - Anderson and Clements 2000
- Green 1986                                  - Hurlbert 1971
- Green and Montagna 1996                  - Reynoldson et al 1997
- Diaz et al 2004                             - Kennicutt et al 1996  

Try to read Green and Chapman in press, Diaz et al 2004 and Hurlbert 1971, before Monday.

Workshop schedule & venue

-Dates: Mon March 7 & Tue March 8, 2011

-Venue:  UNB Fredricton campus,  Room 22 Bailey Hall, 10 Bailey Drive

-Daily schedule: a 9am-5pm day, with a 12:30-1:30pm lunch break and 30 min breaks at 10:30am and 3:00pm.   

 (We will keep to the schedule i.e. we will start and re-start on time!)



-Tentative schedule of topics

Day 1: 9:00am-10:30am:   1.  Introduction and general review of environmental study designs; Problems with indices

   "   : 11:00am-12:30pm:   2. "Search for structure" MV methods - ordination & clustering and their misuses

   "   :    1:30pm-3:00pm:    3. "Samples in a priori groups" MV methods e.g. MANOVA,  Canonical Discriminant Analysis;

   "    :   3:30pm-5:00pm:    4. "Variables in a priori groups" MV methods; MV methods applied in sequence
 

Day 2: 9:00am-10:30am:    5. "Samples in a priori groups" MV methods:  MV methods applied in sequence 

   "   : 11:00am-12:30pm:   6. Cluster reference sites on biota, use CDA to relate to natural environmental variation,
                                             calculate probability ellipses for reference sites (Reference Condition Approach)

   "   :  1:30pm-3:00pm:    7. M.J. Anderson's Multivariate Control Charts                                       

   "   :  3:30pm-5:00pm    8. Southern Gulf of St. Lawrence biological community monitoring





























Useful references - books & papers

Current people to revere (anything they write or say will be good):

- K.R. (Bob) Clarke (Plymouth Marine Lab, UK) - of Primer fame
- M.J. (Marti) Anderson (Massey Univ., NZ) - of PERMANOVA fame, which is now part of Primer
- Pierre Legendre (Univ. de Montreal) - check his website - references, software - English or Francais
- A.J. (Tony) Underwood (Sydney Uni.) - was Marti Anderson's Ph.D. supervisor. His book pulls together his papers
- C.H. (Pete) Peterson (U. of NC Marine Lab) - an integrator, the guy you ask to pull a big project together

(All these people professionally relate, e.g. co-author, are in workshops together, send each other drafts of papers.)


 Books
 
Anderson, M.J., R.N. Gorley, and K.R. Clarke. 2008. PERMANOVA+ for PRIMER: Guide to Software
and Statistical Methods. PRIMER-E: Plymouth, UK. (See her papers.  This brings together and
implements her MV analysis with permutation tests, accompanying the PRIMER package. See Clarke
and Warwick 2001, and Clarke and Gorley 2006.)

Bailey, R.C.,  R.H. Norris, and T.B. Reynoldson. 2003. Bioassessment of freshwater ecosystems: Using
the reference condition approach. Springer, New York.  (See also Reynoldson et al 1997.)

Borcard, D., F. Gillet, and P. Legendre. 2011. Numerical ecology with R. Springer. (Also see book
Legendre and Legendre 1998.)

Clarke, K.R., and R.N. Gorley. 2006. PRIMER v6: User Manual / Tutorial. PRIMER-E Ltd, Plymouth UK

Clarke, K.R., and R.M. Warwick. 2001. Change in marine communities: an approach to statistical
analysis and interpretation. PRIMER-E Ltd, Plymouth UK.

Cochran, W.G. 1963. Sampling techniques, 2nd Ed. Wiley, N.Y. (First edition was 1953. It's still the
classic reference on the subject. "The Bible")

Cochran, W.G. 1983. Planning and analysis of observational studies. Wiley, New York. (A nice short
treatment of principles of design and statistical analysis - including power analysis - for the kinds
of studies ecologists most commonly do, i.e. studies that are not designed experiments.)

Crowder, M.J., and D.J. Hand. 1990. Analysis of repeated measures. Chapman and Hall, London. (This
is the bible on the subject. There are worked examples, discussion of procedures as implemented in
various statistical packages, and discussion of assumptions and consequences of their violation.)

Draper, N.R., and H. Smith. 1981. Applied regression analysis, 2nd Ed. Wiley, New York. (The bible on
regression analysis and modelling, examining residuals, nonlinear models, etc. Worked examples.)

Edgington, E.S. 1995. Randomization tests, 3rd Ed. Marcel Dekker, New York. (See comments on Manly
1991.)

Elliott, J.M. 1977. Some methods for the statistical analysis of samples of benthic invertebrates. FBA
Sci. Publ. No.25, Windermere, Cumbria, U.K. (A "best buy". Good on spatial distributions, sampling
designs, transformations.)

Gower, J.C., and D.J. Hand. 1996. Biplots. Chapman & Hall, London UK.  (See Gabriel 1971 and refs
referred to.)

Gower, J.C.,  S. Lubbe, and N. le Roux. 2011. Understanding biplots. Wiley. (See Gabriel 1971 and refs
referred to.)

Green, R.H. 1979. Sampling design and statistical methods for environmental biologists. Wiley, N.Y.
(A "handbook" with examples, univariate and multivariate approaches, my prejudices, and a large
topic-coded bibliography which is now rather out of date. It's still in print!)

Harris, R.J. 1985. A primer of multivariate statistics, 2nd Ed. Academic Press, N.Y. (A good multivariate
stats text and reference, but “primer” is misleading. Don't start with it - start with Pielou 1984,
Pimentel 1978 or Manly 1994.)

Jongman, R.H.G., C.J.F. ter Braak, and O.F.R. van Tongeren. 1987. Data analysis in community and
landscape ecology.  Pudoc Wageningen, The Hague.  (Offspring of a mating between a Dutch school and
"the Cornell school".  (Re. the latter see papers by Gauch and Whittaker.)  Gives rationale for methods
implemented in CANOCO, e.g. Canonical Correspondence Analysis - ter Braak 1986.)

Karr, J.R., and E.W. Chu. 1999. Restoring life in running waters: better biological monitoring. Island
Press. Washington DC (The "bible" of biotic indices.)

Keough, M.J., and B.D. Mapstone. 1995. Protocols for designing marine ecological monitoring programs
associated with BEK mills. Report No. 11. CSIRO, Canberra. (It’s a book-size report. Excellent coverage
of general principles and practice of environmental study design. A non-commercially published
word-of-mouth gem, like Elliott 1977. If you write to CSIRO in Canberra they’ll probably mail you a
copy for free. But see Quinn and Keough 2002 for similar, often more extensive, coverage.)

Kirk, R.E. 1982. Experimental design: procedures for the behavioral sciences. Brooks/Cole, Monterey,
California. (Another good reference on experimental and observational study design. His fans, who
tend to be fanatics, always ask "But what does Captain Kirk say?" (apologies to Trekkies). One of his
cleverer efforts is to show how to do "pseudo-F tests" by constructing composite error terms. SAS will
sometimes do this for complex designs without being asked. See Winer 1971 or Underwood 1997 for a
more classical treatment of the subject.)

Legendre, L., and P. Legendre. 1998. Numerical ecology. 2nd English Edition. Elsevier,Amsterdam.
(Very thorough text/reference. Covers matrix algebra diversity indices, multivariate analyses, time series,
matrix population models, etc. Check out Pierre Legendre's website
www.bio.umontreal.ca/legendre/indexEn.html  for his publications and a variety of computer programs.
See book just out Borcard et al 2011. Also see Legendre's website for publications and computer
programs: www.bio.umontreal.ca/legendre/indexEn.html .  N.B. - publications were last updated in 2007. )

Levins, R. 1968. Evolution in changing environments. Princeton University Press, Princeton NJ (Told us
that truth is the intersection of independent lies)

Manly, B.F.J. 1991. Randomization and Monte Carlo methods in biology. Chapman and Hall, London.
(Randomization tests have largely replaced “nonparametric” tests. This is a good reference to them,
and Manly’s RT package implements them. Also see Edgington 1995.)

Manly, B.F.J. 1994. Multivariate statistical methods: a primer. Chapman and Hall, London. (Another good
one is Pielou 1984.)

Pielou, E.C. 1984. The interpretation of ecological data. Wiley, N.Y. (The subtitle is "A primer on
classification and ordination". It's a good introduction to descriptive multivariate statistics
applied to ecology. There are clear worked examples. Another good one is Manly 1994.)

Quinn, G.P., and M.J. Keough. 2002. Experimental design and data analysis for biologists. Cambridge.
(A good reference by two good Australians. Available in soft cover.)

Schmitt, R.J., and C.W. Osenberg. 1996. Detecting ecological impacts caused by human activities. Academic
Press, New York. (It’s a mixed bag, with chapters by various people. But the people are mostly very good
- e.g. Stewart-Oaten, Underwood, Keough, Jones & Kaly, Mapstone, Kingsford - and the topics are mostly
very current and important. I totally disagree with some of it, but that’s OK - some of the chapter
authors disagree with other chapter authors within the book.)

Schneider, D.C. 1994. Quantitative ecology: spatial and temporal scaling. Academic Press, San Diego.
(Nice coverage of how temporal and spatial scales of observations, and of what is being observed,
influences results and interpretations of studies.)

Seber, G.A.F. 1984. Multivariate observations. Wiley, New York. (A "bible" for multivariate
statistics, including the math theory and algorithms that underlie it.)

Snedecor, G.W., and W.G. Cochran. 1989. Statistical methods, 8th ed. Iowa State Univ. Press, Ames, Iowa.
(Perhaps the best biologically oriented statistics text. See Zar 1996 for a more introductory level text.)

Sokal, R.R., and F.J. Rohlf. 1995. Biometry: the principles and practice of statistics in biological research,
3rd Edition. (A good 2nd level text. Their smaller "Biostatistics" is introductory. Topics this one is
good on include: problems with derived ratio variables, and rules for pooling error terms in Model II
(nested) ANOVA, and ANOVA designs in general. I think this book is better as a reference than as a text for
learning statistics.)

Underwood, A.J. 1997. Experiments in ecology: their logical design and interpretation using
analysis of variance. Cambridge Univ. Press. (Finally we have the book which brings together all the
ecological study design and statistics principles scattered throughout Underwood’s papers. Available in
soft cover.)

Wald, A. 1947. Sequential analysis. Wiley, New York (A not-well-known and under-used sampling/analysis
design. Dover soft-cover edition 1973. See Anderson and Thompson 2004 paper for a multivariate version.)

Winer, B.J. 1971. Statistical principles in experimental design, 2nd Ed. McGraw-Hill, New York. (One of
the classics on experimental design, from a social sciences perspective but that doesn’t matter very much.)

Zar, J.H. 1996. Biostatistical analysis, 3rd Ed. Prentice-Hall, Englewood Cliffs, N.J. (Introductory
biostatistics, and a well-done job. Besides a good introduction to all the obvious things, there is
also power analysis, circular distribution statistics (e.g., times of day, stages of the tide,
directions of animal movement and orientation, etc.), nested ANOVA, and other gems.)

 

Papers

Anderson, M.J. 2008. Animal-sediment relationships revisited: characterizing species' distributions along an 
environmental gradient using canonical analysis and quantile regression splines. J. Exper. Mar. Biol. Ecol. 366: 
16-27.

Anderson, M.J. 2006. Distance-based tests for homogeneity of multivariate dispersions. Biometrics 62: 245-253.

Anderson, M.J, K.E. Ellingsen, and B.H. McArdle. 2006. Multivariate dispersion as a measure of beta diversity. 
Ecology Letters 9: 683-693.

Anderson, M.J., R.B. Millar, W.M. Blom, and C.E. Diebel. 2005. Nonlinear multivariate models of successional 
change in community structure using the von Bertalanffy curve. Oecologia 146: 279-286.  (It is worth checking out 
Marti Jane Anderson's website at  www.massey.ac.nz/massey/learning/departments/iims/staff/stat-team-member/
en/m_j_anderson_complete.cfm .)

Anderson, M.J., and A.A. Thompson. 2004. Multivariate control charts for ecological and environmental monitoring. 
Ecological Applications 14: 1921-1935. ( Control charts are a version of sequential analysis.  See Wald's 1947 
book.) 

Anderson, M.J., and J. Robinson. 2001. Permutation tests for linear models. Austr. NZ J. Statistics 43: 75-88.
  
Anderson, M. J., and J. Robinson. 2003. Generalized discriminant analysis based on distances. Australian & New 
Zealand Journal of Statistics 45: 301-318.  

Anderson, M.J., and CJF ter Braak. 2003. Permutation tests for multi-factorial analysis of variance. J. Statist. 
Comp. Simul. 73: 85-113.

Anderson, M.J., and A. Clements. 2000. Resolving environmental disputes: a statistical method for choosing among 
competing cluster models. Ecological Applications 10: 1341-1355. (This is about as far as I would go with the idea 
of "testing cluster analysis solutions"). 

Anderson, M.J. and T.J. Willis. 2003. Canonical analysis of principal coordinates: a useful method of constrained 
ordination for ecology. Ecology 84: 511-525.  

Anderson, M.J. 2001a. Permutation tests for univariate or multivariate analysis of variance and regression. 
Canadian Journal of Fisheries and Aquatic Sciences 58: 629-636.  (See Anderson et al 2008  PERMANOVA+ for 
Primer book.)

Anderson, M.J. 2001b. A new method for non-parametric multivariate analysis of variance. Austral Ecology 26: 32-
46. 

Arana, H.A.H., R.M. Warwick, M.J. Attrill, A.A. Rowden, and G. Gold-Bouchot. 2005. Assessing the impact of oil-
related activities on benthic macroinfauna assemblages of the Campeche shelf, southern Gulf of Mexico.  Mar. 
Ecol. Progr. Ser. 289: 89-107.  (Uses Primer package e.g. BIO-ENV.)

Atchley, W.R., C.T. Gaskins, and D. Anderson. 1976. Statistical properties of ratios 1. Empirical results. 
Systematic Zoology 25: 137-148. (Indices are often built on or around ratio variables.)

Auclair, A.N., and F.G. Goff. 1971. Diversity relations of upland forests in the western Great Lakes area. American 
Naturalist 105: 499-528. (Correlations among indices are provided and a PCA can be done from them. The PCA 
shows that the information in the different indices is largely redundant.)

Bailey, R.C., R.H. Norris, T.B. Reynoldson. 2001. Taxonomic resolution of benthic macroinvertebrate communities 
in bioasessments. J. North Amer. Benthol. Soc. 20: 280-286. (The freshwater side of the "what taxonomic level?" 
issue.  For the marine side see Somerfield and Clarke 1995).

Bergen, M., D. Cadien, A. Dalkey, D. E. Montagne, R.W. Smith, J.K. Stull, R.G. Velarde, and S.B. Weisberg. 2000. 
Assessment of benthic faunal condition on the mainland shelf of Southern California. Environm. Monit. Assessm. 
64: 421-434. (Using Smith's Benthic Response Index (BRI), an index based on indicator species. See also Smith et 
al 2001.)

Bernstein, B.B., and R.W. Smith. 1986. Community approaches to monitoring. Oceans '86 3:934-939. Marine 
Technology Society, Washington DC. (Great quote on MV methods vs single species indicators & derived variables
i.e. indices.)

Borja, A., J. Franco, and V.Perez. 2000. A marine biotic index to establish the ecological quality of soft-bottom
benthos within European estuarine and coastal environments. Marine Pollution Bulletin 40:1100-1114. (The paper 
that proposed AMBI (sounds to me like a cross between a baby deer and an amphibious vehicle), now a popular 
index used by the European marine folk.  It borders onto an indicator species approach. See also Green and 
Chapman in press, Diaz et al 2004, Borja et al 2008, Warwick et al 2010,  Bergen et al 2000, and Smith et al 2001.)

Borja, A., D.M Dauer, R.Diaz, R.J. Llanso, I. Muxika, J.G. Rodriguez, and L. Schaffner. 2008. Assessing 
estuarine benthic quality conditions in Chesapeake Bay: a comparison of three indices. Ecological indicators
395-403. (In a new journal, sort of like the Devil starting his own New Testament. Sigh. The authors are an uneasy 
mix of the Basque index mafia and Virginia Chesapeake Bay folk.  Be sure to read Diaz et al 2004.)

Cairns, J., Jr., 1974. Indicator species vs. the concept of community structure as an index of population. Water
Research Bulletin 10: 338-347.

Cattell, R.B. 1965. Factor analysis: an introduction to essentials. 1. The purpose and underlying models. 
Biometrics 21: 190-215. (This and the following paper are the original Factor Analysis papers.) 

Cattell, R.B. 1965. Factor analysis: an introduction to essentials. 2. The role of factor analysis in research.
Biometrics 21: 405-435.

Chapman, P.M. 1996. Presentation and interpretation of Sediment Quality Triad data. Ecotoxicology 5:327-339.
(Chapman's updating of the SQT in response to other papers on it.)

Chapman, P.M., R.N. Dexter, and E.R. Long. 1987. Synoptic measures of sediment contaminantion, toxicity and 
infaunal community composition (the Sediment Quality Triad) in San Francisco Bay. Marine Ecology-Progress 
Series 37: 75-96. (Early SQT paper. See also Long and Chapman 1985.)

Chapman, P.M., B. Anderson, R.S. Carr, V. Engle, R.H. Green, J. Hameedi, M. Harmon, P.S. Haverland, J. Hyland, 
C.G. Ingersoll, E.R. Long, J. Rodgers Jr.,  M.H. Salazar, P.K. Sibley, P.J. Smith, R.C. Swartz, B. Thompson, and 
H. Windom. 1997. General guidelines for using the Sediment Quality Triad.  Marine Pollution Bulletin 34: 
368-372.

Clarke, K.R. 1993. Nonparametric multivariate analysis of changes in community structure. Austr. J. Ecol. 18: 
117-143.  (From a 1992 workshop organized by A.J. Underwood at Sydney University on "Solutions to 
Environmental Problems".)

Clarke, K.R. 1999. Nonmetric multivariate analysis in community-level ecotoxicology. Envir. Toxicol. Chem. 18:
118-127. (Uses NM-MDS and Mantel tests on similarity matrices. Presents oil impact example. Kind of forerunner 
to Marti Anderson's nonparametric multivariate analysis e.g. Anderson 2001a,b.)

Clarke, K. R. and R. H. Green. 1988. Statistical design and analysis for a 'biological effects' study. Mar. 
Ecol. Prog. Ser. 46: 213-226.

Clarke, K.R., and M. Ainsworth. 1993. A method of linking multivariate community structure to environmental 
variables. Marine Ecology Progress Series 92: 205-219.  (A classic - implemented in Primer. Matches rank-
orders of between-variable similarities underlying ordinations on biotic and on environmental variables, by 
finding the environmental variables subset that best explains the biotic structure. 3 worked examples.)

Clarke, K.R., and R.M. Warwick. 1998a. A taxonomic distinctiveness index and its statistical properties. J. Appl. 
Ecol. 35: 523-531. (Can be used to assess impact - example presented. See also Warwick and Clarke 1998.)

Clarke, K.R., and R.M. Warwick. 1998b. Quantifying structural redundancy in ecological communities. Oecologia
113: 278-298.

Clarke, K.R., and R.M. Warwick. 1994. Similarity-based testing for community pattern: the two-way layout with 
no replication. Marine Biology 118: 167-176.  (Implemented in Primer.)

Clarke, K.R., P.J. Somerfield, L. Airoldi, R.M. Warwick. 2006. Exploring interactions by second-stage community 
analyses. J. Exp. Mar. Biol. Ecol. 338: 179-192. (Anything Bob Clarke publishes is worth taking seriously.  
This addresses the problems of interpreting interactions in factorial ANOVA designs, of which the BACI design is 
one.)

Clarke, K.R., P.J. Somerfield, and R.N. Gorley. 2008. Testing of null hypotheses in exploratory community 
analysis: similarity profiles and biota-environment linkage. J. Exper. Mar. Biol. Ecol.  36: 56-69.

DeBenedictis, P.A. 1973. Correlations between certain diversity indices. American Naturalist 107: 295-302. 
(Supposedly different diversity indices are often redundant i.e. highly correlated in practice.)

De Caceres, M., and P. Legendre. 2009. Associations between species and groups of sites: indices and statistical
inference. Ecology 90: 3566-3574.

De Caceres, M., P. Legendre, and M. Moretti. 2010. Improving indicator species analysis by combining groups of 
sites. OIKOS 119:1674-1684.

de Leeuw, Jan, and Patrick Mair.  Simple and Canonical Correspondence Analysis using the R Package anacor. 
Cran.R-project. (But see McCune 1997 re. Can Corresp Anal, as well as ter Braak 1986.)

Dennis, B. 1996. Discussion: Should ecologists become Bayesians? Ecological Applications 6: 1095-1103 (An 
excellent critique of Bayesian statistics enthusiasts especially in ecology and environmentsal studies. It's the 8th of 
a set of 8 papers in this issue, under the heading "Bayesian Inference".  This paper captures my viewpoint.  For 
other views see Suter 1996, and Walters' view in Walters and Green 1997.)

Diaz, R.J., M. Solan, and R.M Valente. 2004. A review of approaches for classifying benthic habitats and evaluating 
habitat quality. J. Environm. Man. 73: 165-181. (Among other things it's an excellent review of use of indices in the 
marine environment.  Should have been cited by  Chapman and Green in press  but I missed it.)

Douglas, M. E., and J. A. Endler. 1982. Quantitative matrix comparisons in ecological and evolutionary investigations.
J. Theor. Biol. 99: 777-795. (A great example (Trinidad stream fish) of using matrix descriptions of biological
response and various classes of predictor variables and then applying Mantel's procedure to such data. The 
appendix is the worked example.) 

Dray, S, and P. Legendre. 2008. Testing the species traits-environment relationships: the fourth-corner problem 
revisited. Ecologyy 89: 3400-3412. 

Dufrene, M., and P. Legendre. 1997.  Species assemblages and indicator species: the need for a flexible asymmetrical 
approach.  Ecological Monographs 67: 345-366. (A MV criterion for selecting indicator species. Could also use 
Orloci's (1973) method, or PCA, instead.) 

Eberhardt, L. L. 1976. Quantitative ecology and impact assessment. J. Envir. Man. 4: 27-70. (A classic that 
should be more famous than it is. Many current issues were considered in this paper two and a half decades 
ago.  I didn’t know this paper when I wrote my 1979 book. See Eberhardt and Thomas 1991.) 

Eberhardt, L.L., and J.M. Thomos. 1991. Designing environmental field studies. Ecological Monographs 61: 53-73.
(Very worth reading as is anything by Eberhardt.)

Field, J.G., K.R. Clarke, and R.M. Warwick. 1982. a A practical strategy for analysing multispecies distribution 
patterns.  Marine Ecology Progress Series 8: 37-52.  (See Clarke 1993 for evaluation 11 yrs later. It's a two-stage 
approach, uses NMMDS on biota and then relates biota to environmental variables.)

Gabriel, K.R. 1971. The biplot graphic display of matrices with application to principal component analysis. 
Biometrika 58: 453-467.  (The original paper. Also see ter Braak 1983, book by Gower and Hand 1996, Legendre 
and Gallagher 2001, Makarenkov and Legendre 2002, Greenacre 2010, book by Gower et al 2011.)

Gauch, H.G., Jr.  1974. Ordination of vegetation samples by Gaussian species distributions. Ecology 55: 1382-1390.
(Based on the reality that species generally are most abundant at their optima on environmental gradients.)

Gauch, H.G., Jr, and R.H. Whittaker. 1972. Comparison of ordination techniques. Ecology 53: 868-875. (Done on
simulated species abundance data on an environmental gradient. PCA and Euclidean distance are worst.  That 
makes sense. I think PCA is great but not on species abundance data whith its nonlinear relationships.  Bob 
Clarke and Primer agree - PCA is fine on environmental data but not on biota.  But see Legendre and Gallagher 
2001.)

Gauch, H.G., Jr, and R.H. Whitaker. 1981. Hierarchical classification of community data. Journal of Ecology 69:
537-557.  (Good example of application of different flavours of cluster analysis, which plant ecologists call 
"classification".  No-one else does, and in most of the statistical world "classification" means something else 
entirely. In this and some other ways plant ecologists are a bit odd.) 

Gauch, H.G. Jr, R.H. Whittaker, and S.B. Singer. 1981. A comparative study of nonmetric ordinations. Journal of 
Ecology 69: 135-152.  (Also includes application of Reciprocal Averaging (RA) and Detrended Correspondence 
Analysis (DCA).  The latter has been criticized, and isn't recommended.  For RA see Hill 1973, and Gauch et al 
1977.)

Gauch, H.G., Jr, R.H. Whittaker, and T.R. Wentworth. 1977. Comparative study of reciprocal averaging and 
other ordinatioin techniques. Journal of Ecology 65: 157-174.  (For RA see Hill 1973, and Gauch et al 1981.)

Graham, M.H. 2003. Confronting multicollinearity in ecological multiple regression. Ecology 84: 2809-2815.
(The problem when observational data are used to predict biological responses from values of environmental 
variables, which are inevitably correlated. )

Grassle, J.F., and W. Smith. 1976. A similarity measure sensitive to the contribution of rare species and its 
use in investigation of variation in marine benthic communities. Oecologia 25: 13-22.

Gray, J.S., P. Dayton, S. Thrush, and M.J. Kaiser. 2006. On effects of trawling, benthos and sampling design. 
Mar. Pollut. Bull. 52: 840-843. (These are good authors.  The paper is on bottom trawling done 
experimentally, demonstrated effects on the benthic community, and misinterpretation of results.)

Green, R.H. 1971. A multivariate statistical approach to the Hutchinsonian niche: bivalve molluscs of central 
Canada. Ecology 52: 543-556. (Reproduced in G.E. Hutchinson's 1979 book "Introduction to population 
ecology" Yale Univ. Press)

Green, R.H. 1972. Distribution and morphological variation of Lampsilis radiata in some central Canadian 
lakes: a multivariate statistical approach. J. Fish. Res. Board Can. 29:1565-1570. (An application of 
Canonical Correlation Analysis to relate shell morphology to environment.)
 
Green, R.H. 1984. Statistical and nonstatistical considerations for environmental monitoring studies. 
Environ. Monit. Assessm. 4: 293-301.

Green, R.H. 1986. Some applications of linear models for analysis of contaminants in aquatic biota. In 
"Statistical aspects of water quality monitoring", p. 231-245. A.H. El-Shaarawi and R.E. Kwiatowski, Eds. 
Elsevier, New York.  (Shows how to display ratio variable data using log-log plots, and then statistically 
analyze the data by Regression & ANCOVA, with three worked examples. I used Model 1 (OLS) 
regression & ANCOVA but you might like to use the Model 2 version - see Mcardle 1988.)  I will try to 
provide you with a soft copy of this paper. 

Green, R.H. 1989. Power analysis and practical strategies for environmental monitoring. Environm. Res. 50: 
195-205.

Green, R.H. 1993a. Application of repeated measures designs in environmental impact and monitoring studies. 
Austr. J. Ecol. 18: 81-98.

Green, R.H. 1993b. Relating two sets of variables in environmental studies. In: "Multivariate analysis: future 
directions", C.R. Rao, Ed., p.151-165.  Elsevier.  (Includes Mantel Test and Procrustes Analysis. See also 
Green et al 1993.)

Green, R.H. 1994. Aspects of power analysis in environmental monitoring. In “Statistics in Ecology and 
Environmental Monitoring”, D. J. Fletcher and B. F. J. Manly, eds., p. 173-182, Otago Conference Series. 
University of Otago Press, Otago, New Zealand.

Green, R.H., J.M. Boyd, and J.S. Macdonald.  1993.  Relating sets of variables in environmental studies: 
the Sediment Quality Triad as a paradigm.  Environmetrics 4:439-457.  (The data analyzed here are from 
Vancouver Harbour BC. See also Green 1993b, and Green and Montagna 1996.)

Green, R.H., and P.M. Chapman. in press. The problem with indices. Marine Pollution Bulletin (accepted 29 
Jan 2011) (Lots of references covering the history of diversity and biotic indices. I am planning to go to 
NABS 2011 at Providence RI May 22-26, and I expect this paper (and myself) to be much abused by those 
whose professional lives are invested in indices. But there are people who like it a lot who out-vote 
everyone else, as far as I'm concerned.)

Green, R.H., B.A. McArdle, and R. van Woesik. in press. Sampling state and process variables on coral reefs.
Environmental Monitoring & Assessment (accepted 6 Sept 2010)

Green, R.H., and P. A. Montagna. 1996. Implications for monitoring: study designs and interpretation 
of results. Can. J. Fish. Aquat. Sci. 53:2629-2636. (In the GOOMEX 8-paper set. Three applications to 
GOOMEX data: sediment quality triad, increased error variance as result of impact, future study 
design recommendations.)

Green, R.H. and S. R. Smith. 1997. Sample program design and environmental impact assessment on coral 
reefs. Proc. 8th Int. Coral Reef Symp. 2: 1459-1464. (Repeated measures design for coral reefs, with 
examples.)

Green, R.H., and G.L. Vascotto. 1978. A method for the analysis of environmental factors controlling 
patterns of species composition in aquatic communities. Water Research 12: 583:590. (Clustering on 
biota (plankton in lakes) then MANOVA & CDA among clusters in environmental variable space.)

Green, R. H., and R. C. Young. 1993. Sampling to detect rare species. Ecol. Appl. 3: 351-356. (This 
resulted from a request to help with a contract from the U.S. Office of Endangered Species, re. how 
to sample when trying to findif a species is in a habitat.  The answer turned out to be simple and 
elegant. The database is unionid molluscs in Tennessee and Virginia rivers.)

Greenacre, M. 2010. Biplots in practice. BBVA Foundation. Madrid, Spain.  (This is available free 
online! Go to  www.multivariatestatistics.org/biplots.html  Also see Gabriel 1971 and refs referred to. )

Hart, C.W., and S.L.H. Fuller. 1974. Pollution ecology of freshwater invertebrates. Academic Press, 
New York.

Hart, C.W., and S.L.H. Fuller. 1979. Pollution ecology of estuarine invertebrates. Academic Press, 
New York.

Hewitt, J.E., M.J. Anderson, and S.F. Thrush. 2005. Assessing and monitoring ecological community health 
in marine systems. Ecological Applications 15: 942-953.

Hewitt, J.E., M.J. Anderson, C.W. Hickey, S. Kelly, and SF Thrush. 2009. Enhancing the ecological 
significance of sediment contamination guidelines through integration with community analysis. Environm.
Sci. Technol. 43: 2118-2123.

Hill, M.O. 1973. Reciprocal Averaging: an eigenvector method of ordination. Journal of Ecology 61: 237-
249. (See also Gauch et al 1977, and Gauch et al 1981.)

Hilsenhoff, W.L. 1987. An improved biotic index of organic stream pollution. Great Lakes Entomology 20: 
31-40.  (In a sense the mother paper of biotic indices. See also Hilsenhoff 1988, 1998.)

Hilsenhoff, W.L. 1988. Seasonal corection factors for the biotic index. Great Lakes Entomology 21: 9-13.

Hilsenhoff, W.L. 1998. A modification of the biotic index of organic stream pollution to remedy problems 
and permit its use throughout the year. Great Lakes Entomology 31: 1-12.

Hurlbert, S.H. 1971. The nonconcept of species diversity: a critique and alternative parameters. Ecology 52: 
577-586.

Jackson, D.A. 1995. PROTEST: A PROcrustean randomization TEST of community environment 
concordance. EcoScience 2: 297-303.  (Uses randomization test based on Procrustes Analysis. Gives 
examples based on lake biota and environment. Compares results to those from Mantel Test. See also 
Jackson and Harvey 1993.)

Jackson, D.A. 1997. Compositional data in community ecology: the paradigm or peril of proportions. 
Ecology 78: 929-940. (Gets at the ratio variables problem, as often occurs with indices and with coding 
abundance data as proportions.  He thinks Correspondence Analysis is best.) 

Jackson, D.A., and H.H. Harvey. 1993. Fish and benthic invertebrates: community concordance and 
community-environment relationships.  Can. J. Fish. Aquat. Sci. 50: 2641-2651.  (See also Jackson 1995.)

Jones, G.P. and Kaly, U.L. 1996. Criteria for selecting marine organisms in biomonitoring studies. 
In: “Detecting Ecological Impacts: Concepts and Applications in Coastal Habitats”, R. J. Schmitt and C. W. 
Osenberg, eds., p. 29-48. Academic, New York.

Karr, J.R.  1967. Biological monitoring and environmental assessment: a conceptual framework. 
Environmental Management 11: 249-256. (This is the seminal pro- biotic indices paper.  It is totally 
wrong-headed for a number of reasons.  See also Kerans and Karr 1994. This sort of thing has led 
environmental biologists badly astray. I would rather that young scientists in our field spent their days 
watching hard-core porn. For the contrary view see Green and Chapman in press and references cited 
therein (especially Diaz et al 2004), and p.95-110 of the Green 1979 book for that matter.)

Kennicutt, M.C., II, R.H. Green, P. Montagna and P.F. Rosigno.  1996.  Gulf of Mexico Offshore Operations 
Monitoring Experiment (GOOMEX), Phase I: sublethal responses to contaminant exposure - introduction 
and review.  Can. J. Fish. Aquat. Sci. 53:2540-2553.  (See comments on Peterson et al 1996, below.  This 
one is the introductory paper of the 8-paper set.  It presents the overall study design and planned 
statistical analysis, which was my responsibility in the project.)

Kerans, B.L., and J.R. Karr. 1994. A benthic index of biotic integrity (B-IBI) for rivers of the Tennessee 
Valley. Ecological Applications 4: 768-785.

Laliberte, E., and P. Legendre. 2010. A distance-based framework for measuring functional diversity from 
multiple traits. Ecology 91: 299-305.

Legendre, P. 1987. Constrained clustering. In "Developments in Numerical Ecology", Eds. P. Legendre 
and L. Legendre, p.289-302. Springer-Verlag. (Relates to spatial pattern - samples are constrained to be 
spatially contiguous. See also Legendre and Legendre 1998 book, Laliberte and Legendre 2010, 
De Caceres and Legendre 2009, Dray and Legendre 2008, and De Caceres et al 2010)

Legendre, P., and M.J. Anderson. 1999. Distance-based redundancy analysis: Testing multispecies 
responses in multifactorial experiments. Ecol. Monogr. 69: 1-24. (See McArdle and Anderson 2001.)

Legendre, P., and E.D. Gallagher. 2001. Ecologically meaningful transformations for ordination of 
species data. Oecologia 129: 271-280.  (Species biplots using transformations for species data tables, so 
euclidean-based ordinations, such as PCA, can be used for the analysis of community data. (Avoid CA 
and CCA which present problems of their own in some cases.) Allows test for relationships with 
explanatory environmental variables. Biplots can display the relationships of the species to the 
explanatory variables. Re. biplots see Gabriel 1971 and refs referred to. )

Legendre, P., M. De Caceres, and D. Borcard. 2010. Community surveys through space and time: testing 
the space-time interaction in the absence of replication. Ecology 91: 262-272. (Including MV, and 
presenting two applications.)

Lincoln-Smith, M.P., K.A. Pitt, J.D. Bell, and B.D. Mapstone. 2006. Using impact assessment methods to 
determine the effects of a marine reserve on abundances and sizes of valuable tropical invertebrates. Can. 
J. Fish. Aquat. Sci. 63: 1251-1266.  (An example of a "beyond-BACI design, with different spatial 
scales.)

Long, E,R,, and P.M. Chapman. 1985.  A sediment quality triad: measures of sediment contamination, 
toxicity and infaunal community composition in Puget Sound. Marine Pollution Bulletin 16: 405-415.  
(See Chapman papers also on SQT, e.g. Chapman et al 1987.)

Makarenkov, V., and P. Legendre. 2002. Nonlinear redundancy analysis and canonical correlation 
analysis based on polynomial regression. Ecology 83: 1146-1161.  (Deals with the reality that few 
species-environmental relationships are linear, by using polynomial functions of the explanatory 
(environmental) variables - in RDA (an extension of multiple regression) and CCA. New ways of 
representing the variables in biplots are presented. Examples are given. Programs are available. See 
McArdle and Anderson 2001 re. RDA.)

Mantel, N. 1967. The detection of disease clustering and a generalized regression approach. Cancer 
Research 27: 209-220.  (The original & classic "Mantel Test" paper. See also Mantel 1970.)

Mantel, N, R.S. Valand. 1970. A technique of nonparametric multivariate analysis. Biometrics 26: 
547-558.

Mapstone, B. D. 1995. Scalable decision rules for environmental impact studies: effect size, Type I, and 
Type II errors. Ecol. Appl. 5: 401-410.

McArdle, B.H. 1988. The structural relationship: regression in biology. Can. J. Zool. 66: 2329-2339.
(Regression when both Y and X variables are response variables i.e. measured with error. See also 
McArdle 2003.) 

McArdle, B.H. 2003. Lines, models, and errors: regression in the field. Limnol. Oceanogr. 48: 1363-
1366. (Follow-up to McArdle 1988.)

McArdle, B.H., and M.J. Anderson. 2001. Fitting multivariate models to community data: A comment on
distance-based redundancy analysis. Ecology 82: 290-297. (Redundancy Analysis = RDA. See Legendre 
and Anderson 1999.  RDA is similar to Canonical Correlation Analysis but deriving a minimal set of 
synthetic variables from one set (the "independent" set) of variables that explains as much variance 
as possible in the other set (the dependent set). It is a MV analogue of regression. )

McArdle, B.H., and M.J. Anderson. 2004. Variance heterogeneity, transformations and models of species 
abundances: a cautionary tale. Can. J. Fish. Aquat. Sci. 61: 1294-1302.

McCune, B. 1997. Influence of noisy environmental data on Canonical Correspondence Analysis. Ecology 
78: 2617-2623.  ("- - one of the most potentially misleading multivariate methods for community 
analysis. Inclusion of noisy or irrelevant environmental variables can distort the representation of 
gradients". Says better to do ordination on biotic variables first then relate ordination results to 
environmental variables (Yea for 2-step analyses!).  Says Can Corresp Anal can be OK for decribing 
how biota respond to particular envir vars once you know they are predictive, in situations where 
species responses are unimodal on the environmental gradient. See ter Braak 1986.)

McDonald, L. L. and W. P. Erickson. 1994. Testing for bioequivalence in field studies: Has a disturbed 
site been adequately reclaimed? In “Statistics in Ecology and Environmental Monitoring”, D. J. Fletcher 
and B. F. J. Manly, eds., p. 183-197, Otago Conference Series. University of Otago Press, Otago, New 
Zealand.

Metcalfe-Smith, J.L., R.H. Green, and L.C. Grapentine. 1996. Influence of biological factors on 
concentrations of metals in the tissues of freshwater mussels (Elliptio complanata and Lampsilis radiata 
radiata) from the St. Lawrence River. Can. J. Fish. Aquat. Sci. 53: 205-219. (Describing components of 
biological variation caused by metal vector patterns.)

Millar,R.B., M.J. Anderson, and and G. Zunun.  2005. Fitting nonlinear environmental gradients to 
community data: a general distance-based approach. Ecology 86: 2245-2251.

Olsgard, F., P. J. Somerfield, and M. R. Carr. 1997. Relationships between taxonomic resolution and 
data transformations in analyses of a macrobenthic community along a established pollution gradient. Mar. 
Ecol. Prog. Ser.: 1-9. (Patterns of macrobenthic data in vicinity of North Sea oilfield show high degree 
of consistency up to taxonomic level of order.)

Orloci, L. 1973. Ranking characters by a dispersion criterion. Nature (London) 244: 371-373. (A "most-
cited" paper, describing an easy-to-use MV method for choosing a subset of variables which best predict 
the whole set.  Good for selecting indicator species.)  

Peterman, R. M. 1990. Statistical power analysis can improve fisheries research and management. Can. J. 
Fish. Aquat. Sci. 47: 2-15.

Peterson, C. H. 1993. Improvement of environmental impact analysis by application of principles derived 
from manipulative ecology: Lessons from coastal marine case studies. Austr. J. Ecol. 18: 21-52.

Peterson, C.H., M.C. Kennicutt, II, R.H. Green, P. Montagna, D.E. Harper, Jr., E.N. Powell, and P.F. 
Rosigno. 1996. Ecological consequences of environmental perturbations associated with offshore hydrocarbon 
production:  a perspective on long-term exposures in the Gulf of Mexico.  Can. J. Fish. Aquat. Sci. 53:
2637-2654.  (This is the “summary of results & implications” paper, the 8th of an 8-paper set reporting 
the results of a 2-3 year study by a half-dozen principal investigators.  This set of papers has had a 
major impact, and its conclusions are somewhat controversial -- for example that there is no apparent 
biological impact beyond a few hundred meters from drilling platforms.)

Peterson, C.H., L.L. Macdonald, R.H. Green, and W.P. Erickson.  2001.  Sampling design begets conclusions: 
the statistical basis for detection of injury to and recovery of shoreline communities after the Exxon 
Valdez oil spill.  Marine Ecology Progress Series 210: 255-283. (This is a major review paper.  Its main 
theme is that the Exxon-funded study design whatever the intentions were and whatever their design’s other 
virtues, was bound to have low power to detect impacts by the oilspill on the biological community.  And it 
did, in comparison with the government-funded & supervised studies.  Mind you, I was Chair of the 
Statistical Working Group for the latter and Peterson was Chief Scientist, so we can’t claim to be 
disinterested.)

Pinedo, S., M. Garcia, M.P. Satta, M. De Torres, and E. Ballesteros. 2007. Rocky-shore communities as 
indicators of water quality: a case study in the Northwestern Mediterranean.  Mar. Pollut. Bull. 55: 126-135. 
(Example of using MV stats to interpret patterns of community taxa.)

Reynoldson, T. B., R.H. Norris, V.H. Resch, K.E. Day, and D.M. Rosenberg. 1997. The reference condition: 
a comparison of multimetric and multivariate approaches to assess water-quality impairment using benthic 
macroinvertebrates. J. North Amer. Benthol. Soc. 16: 833-852.  (A good paper to start with re. the 
Reference Condition approach.  See also the book Bailey et al 2003.)

Salmon, A., and R.H. Gren. 1983. Environmental determinants of unionid clam distribution in the Middle 
Thames River Ontario. Can. J. Zool. 61: 832-838. (A MV approach to species "niches" in this habitat, 
including the "unclam" - where no unionids occurred.)

Schonemann, P.H., and R.M. Carroll. 1970. Fitting one matrix to another under choice of a central dilation 
and a rigid motion. Psychometrika 35:245-255.  (Early Procrustes Analysis paper.)

Sims, M., S. Wanless, M.P. Harris, P.I. Mitchell, and D.A. Elston. 2066. Evaluating the power of monitoring 
plot designs for detecting long-term trends in the numbers of common guillemots. J. Applied Ecology 43: 
537-546. (Power to detect time trends in monitoring design options, by assessing sources and sizes of 
variance components.  Better to count birds in more plots than increasing the number of counts at existing 
plots.)

Skilleter, G.A., A. Pryor, S. Miller, and B. Cameron. 2006. Detecting the effects of physical disturbance 
on benthic assemblages in a subtropical estuary: a Beyond BACI approach. (Nice on addressing different 
spatial scales, and an example of where BACI has gone.) 

Smith, R.W., and J.F. Grassle. 1977. Sampling properties of a family of diversity measures. Biometrics 33: 
283-292.

Smith, R.W., M. Bergen, S.B. Weisberg, D. Cadien, A. Dalkey, D. Montagne, J.K. Stull, and R.G. Velarde. 
2001. Benthic Response Index for assessing infaunal communities on the Southern California mainland 
shelf.  Ecological Applications 11: 1073-1087. (See also Bergen et al 2000.)

Somerfield, P.J., and K.R. Clarke. 1995. Taxonomic levels, in marine community studies, revisited. Marine 
Ecology Progress Series 127: 113-119.  (How much information is retained as you go to higher taxonomic 
levels. Cites earlier work along the same line. See Bailey et al 2001 for the freshwater side of this issue.)

Stewart-Oaten, A. 1986. Environmental impact assessment: "psuedoreplication" in time? Ecology 67: 
929-940. (So-called BACI-P, where there is only one Control site and one supposedly replicates in time.)

Suter, G. W. 1996. Abuse of hypothesis testing statistics in ecological risk assessment. Human and 
Ecological Risk Assessment 2: 331-347. (Not my viewpoint - this is a Bayesian attitude. It's FYI. My view 
is well expressed by Dennis 1996.)

ter Braak, C.J.F, 1983. Principal components biplots and alpha and beta diversity. Ecology 64:454-462. (re. 
biplots see also Legendre and Gallagher 2001, Makarenkov and Legendre 2002, Gabriel 1971 and refs 
referred to.)

ter Braak, C.J.F. 1986. Canonical correspondence analysis: a new eigenvector technique for multivariate 
direct gradient analysis. Ecology 67: 1167-1179. (See book Jongman et al 1987. See critique by McCune 
1997.)

Thomas, W.A., G. Goldstein, and W.H. Wilcox. 1973. Biological indicators of environmental quality: a 
bibliography of abstracts. Ann Arbor Science, Ann Arbor, Michigan.

Underwood, A. J. 1981. Techniques of analysis of variance in experimental marine biology and ecology. Ann. 
Rev. Oceanogr. Mar. Biol 19: 513-605.

Underwood, A. J. 1991. Beyond BACI: experimental designs for detecting human environmental impacts on 
temporal variations in natural populations. Austr. J. Mar. Freshw. Res. 42: 569-587.

Underwood, A. J. 1992. Beyond BACI: the detection of environmental impacts on populations in the real, but 
variable, world. J. Exp. Mar. Biol. Ecol. 161: 145-178.

Underwood, A. J. 1993. The mechanics of spatially replicated sampling programmes to detect environmental 
impacts in a variable world. Austr. J. Ecol. 18: 99-116..

Underwood, A. J. 1994. Things environmental scientists (and statisticians) need to know to receive (and 
give) better statistical advice. 33-61.

Underwood, A. J. 1994. On beyond BACI: sampling designs that might reliably detect environmental 
disturbances. Ecol. Appl. 4: 3-15.

Underwood, A.J., and M.G. Chapman. 2003. Power, precaution, Type II error and sampling design in assessment 
of environmental impacts. J. Exper. Mar. Ecol. 296: 49-70.  (Good general recommendations on design 
choices for detection of different kinds of impacts.)

Verlaan, P.A. 2007. Experimental activities that intentionally perturb the marine environment: implications 
for the marine environmental protection and marine scientific research provisions of the 1982 United Nations 
Convention on the Law of the Sea.  Marine Policy 31: 210-216. (I argue that experimental manipulation is 
valuable, even necessary, to do good science.  Experimental oil spills would be an example, but so would 
mesocosm experiments or field recoprocal transplant experiments.  Field observational studies are often not 
enough. )
 
Walters, C.J. and R.H. Green. 1997.  Valuation of experimental management options for ecological systems.  
J. Wildl. Man. 61(4):987-1006.  (Roughly bashed together during a sabbatical period I spent at UBC, then 
finished using fax and email.  Walters and I come from opposite philosophical directions re. estimation vs. 
testing: Bayesian vs. Fisherian.  This paper is an attempt to reconcile these philosophically different 
approaches in ecological applications. I'm not sure that it succeeded very well. See Dennis 1996.)

Warwick, R.M., and K.R. Clarke. 1995. New 'biodiversity' measures reveal a decrease in taxonomic 
distinctness with increasing stress. Mar. Ecol. Progr. Ser. 129: 301-305.

Warwick, R.M., and K.R. Clarke. 1998. Taxonomic distinctness and environmental assessment. J. Appl. Ecol.
35: 532-543. (See also Clarke and Warwick 1998a,b.)

Warwick, R.M., K.R. Clarke, and P.J. Somerfield. 2010. Exploring the marine biotic index (AMBI): variations 
on a theme by Angel Borja. Marine Pollution Bulletin 60: 554-559.

Wilhm, J., and T.C. Dorris. 1968. Biological parameters for water quality criteria. BioScience 18: 477-481.

Williams,W.T., and J.M. Lambert. 1959. Multivariate methods in plant ecology. I. Association-analysis in 
plant communities.  Journal of Ecology 47: 83-101. (A really good easy-to-use cluster analysis method based 
on species presence-absence data.  You start by calculating the species x species chi-square matrix.  Since 
it's a divisive method you only have to determine the first few levels.  Since it's for presence-absence data you 
want a large number of small samples.  Or you could score above median abundance samples as "present" 
and below median abundance samples as "absent".  It works very well - see the examples in the paper.) 

Wright, J.F. 1995. Development and use of a system for predicting the macroinvertebrate fauna in flowing 
waters. Australian Journal of Ecology 20: 181-197. (John Wright's work in the UK was the predecessor of the
Reference Sites => Reference Condition Approach which is now a big deal in Canada & Australia.)

Wright, J.F., D.W. Sutcliffe, and M.T. Furse. 2000. Assessing the biological quality of fresh waters: RIVPACS
and other techniques. Freshwater Biological Association of the UK, Ambleside, Cumbria, UK.

Zettler, M.L., D. Schiedek, and B. Bobertz. 2007. Benthic biodiversity indices versus salinity gradient in 
the southern Baltic Sea. Mar. Pollut. Bull. 55:258-270.  (I'm not a fan of biotic indices.  I rather think 
that MV analyses should be used in most cases.  One problem is often confounding with natural environmental 
gradients.  This is an example of govt-driven biotic indices used where there's a salinity gradient.)




























































Short professional resume – Roger H. Green

Academic qualifications:
- Bachelor of Science in Biology, College of William & Mary, 1961
- Ph.D. in Zoology, Cornell University, 1965
- Fulbright Postdoctoral Fellowship, University of Queensland, 1965-66
- Resident Ecologist, Marine Biological Laboratory, Woods Hole, 1966-68
- Asst. and Assoc. Professor, Department of Zoology, University of Manitoba, 1968-76
- Assoc. Professor and Professor, Department of Zoology, University of Western Ontario, 1977-99
- Professor Emeritus and member Faculty of Graduate Studies, Department of Zoology (now
   Biology), University of Western Ontario, 1999-
- Visiting Professor with Centre for Marine and Coastal Studies (CEMACS), University Science
   Malaysia, Penang Malaysia, May 2001 - May 2002
- Research Affiliate, Environment and Natural Resources Institute, University of Alaska Anchorage
   2003-present
- Research Associate, Watershed Ecosystems Graduate Program, Trent University, 2006-present

Publications:
- 59 papers in refereed journals
- 25 papers in refereed conference or workshop proceedings
- 1 book: Sampling Design and Statistical Methods for Environmental Biologists. 1979. Wiley, New York  
- 8 contributions to a book or document
- 4 invited book reviews

Invited contributions to conferences or workshops (since 2000):
- Sable Offshore Energy Program workshop, Dartmouth Nova Scotia, March 2000
- Fisheries & Oceans Canada/, Ministry of Natural Resources Ontario workshop on environmental
   monitoring of fish habitat, March 2001
- U.S. National Science Foundation sponsored Conference on Environmental Statistics, Seattle Washington,
   June 2001
- Asia-Pacific Conference on Marine Science and Technology, Kuala Lumpur, May 2002
- Invited participant in British Columbia provincial workshop “Biomonitoring: A Decision Support Tool for
   Resource Management”, Vancouver BC, May 2003
- Keynote speaker and workshop rapporteur at international workshop on Offshore Oil & Gas Environmental
   Effects Monitoring sponsored by Fisheries and Oceans Canada, the Program for Energy Research and
   Development, and the Atlantic Canada Petroleum Institute, Halifax, May 2003
- Invited participant in US National Oceanographic and Atmospheric Administration workshop to develop an
   R&D strategy for oil spills, Durham NH, November 2003
- Attending annual meetings of Society for Environmental Toxicology and Chemistry, as representative of
   Prince William Sound Regional Citizens Advisory Council, Austin TX, November 2003, and Montreal QC
   2006
- Invited speaker at international ecological modeling conference ECOMOD 2004, at University Science
   Malaysia, Penang Malaysia, September 2004.

Workshops I organized, and other external teaching and academic duties (since 2000):
- Workshop on Environmental Study Design and Statistics, Vancouver BC, April 2001
- Workshop on Multivariate Analysis in Environmental Studies, University Science Malaysia, January 2002
    (for USM and Penang)
- Workshop on Environmental Study Design and Analysis, University Science Malaysia, April 2002
    (for Malaysia and neighboring countries)
- Workshops on Environmental Study Design study in Watershed Environment Graduate Program, Trent
    University, Peterborough Ontario, March and October 2006
- Workshop on design and statistical analysis of ecological data, University of North Carolina Institute of
    Marine Sciences, Morehead City, North Carolina, September 2003
- Workshop on design and statistical analysis, San Diego California, April 2004
- Workshop on Environmental Study Design, sponsored by Prince William Sound Regional Citizens Advisory
    Council and University of Alaska Anchorage, Anchorage Alaska, February 2007 (and repeated May 2007 in
    Juneau Alaska)
- Workshop on Statistical Approaches to Environmental Study Data, sponsored by Prince William Sound
    Regional Citizens Advisory Council and University of Alaska Anchorage, Anchorage Alaska, March 2008
- Workshop on Multivariate Methods for Prediction & Hypothesis Testing: Case Studies, sponsored by
    University of New Brunswick, Fredricton NB, March 7-8 2011

Graduate and postdoctoral students supervised
- Masters students: 15 completed
- Ph.D. students: 8 completed
- Postdoctoral students: 3 completed

Research grants & contracts since 2000:
- Research grants from Natural Sciences & Engineering Research Council of Canada, for studies on
    freshwater and marine biological communities, to 2003, and extended to 2005 to fund continued studies on the
    estuarine bivalve mollusc Macoma balthica in Hudson Bay and south-central Alaska – research done on
    Hudson Bay in July 2004 and in Alaska throughout the year
- Co-principal investigator on research grant from Exxon Valdez Oil Spill Trustee Council, on “Development
    of a strategy for monitoring Exxon Valdez oil and other contamination in Prince William Sound", 2004

Consulting services provided (since 2000):
- Jacques Whitford Ltd. (Nova Scotia) - advised re. design of, assisted with statistical analysis & interpretation
    for, and helped prepare reports on offshore field environmental monitoring design for Sable Offshore Energy
    Program (1998-2000)
- LGL Ltd/U.S. Minerals Management - advising on design & analysis for study on feeding by bowhead whales
    on Alaska north slope (1998-2000)
- RL&L Environmental Services, Castlegar British Columbia - analysis and modeling of temperature data for
    Consulting services provided (2000-2002)
- Regional Centre for Forest Management, Kuala Lumpur Malaysia – reviewing documents and advising on
    design aspects of managing SE Asian forests to maintain biodiversity, and periodic reviewing and advising re.
    environmental concerns & forest management practice (1999-2001)
- University of Guelph, Ontario Hydro, and Chippewa First Nation - member of Advisory Committee for
    project on “Whitefish Interactions with Nuclear Generating Stations” (2000-2001)
- Ontario Ministry of Environment, reviewer of research document on mine-waste contamination in Moira
    River (2000)
- Assisted with statistical analysis of Ph.D. research data on Malayan monitor lizards in Sungei Buloh Nature
    Park, Singapore (2000-02)
- International Council for Science, member of scientific panel assessing impact of uranium mining near
    Kakadu National Park Australia - a World Heritage Site (2000)
- Alberta Ministry of Environment, Terrestrial Environmental Effects Monitoring Program (re. high stack
    emissions at tar sands development) – modeling and statistical analysis issues (2000-2001), and March
    2006 technical experts workshop to review reports (Edmonton)
- Member Scientific Advisory Committee of Prince William Sound Regional Citizens Advisory Council,
    from March 2003 (see website www.pwsrcac.org )
- Member of advisory committee re. environmental effects monitoring program for White Rose offshore oil
    & gas development (Grand Banks of Nfld), for Husky Energy, from June 2003 - still continuing in 2011.
    (see website www.huskywhiterose.com )
- Consultant to Breedlove, Dennis, Young & Associates Tennessee & Florida on mitigation issues in
    litigation, re. one issue April 2005 and another issue Sept-Oct 2005 (see website www.bda-inc.com)
- Consultant re. design/statistics for World Bank funded project on status and potential management of
    world’s coral reefs, from 2004 (funded 5 yrs, planned for 15 yrs) (See website
    www.gefonline.org/projectDetails.cfm?projID=1531 )
- Reviewer of marine/estuarine contracted reports for Applied Marine Sciences, California (3 in 2006, 1 in
    2007) (see website www.amarine.com )
- Chair of Local Arrangements Committee for June 2006 meeting of North American Benthological Society
    (NABS) in Anchorage Alaska, 900 attendees
- Reviewing a report to Environment Canada of an application of two different study designs to environmental
    impact assessment of mining discharges in northern Ontario, April-June 2007
- Consultant to Alberta Environment on aquatic monitoring design re. northern Alberta tar sands
    development impacts, 2007-2008
- Reviewing & analyzing community-based environmental monitoring results for southern Gulf of
    St. Lawrence, coordinated by Fisheries & Oceans Canada, Moncton NB, February-April 2010.

(A summary of consulting services provided before 2000, back to 1989, is available in another document.)


February 2011