The most important aspect of your scientific paper is that it needs to hang together like a scientific paper. You need to have a central thesis, and everything needs to be related to this thesis.
As part of this class, you will be exploring the use of indirect and direct gradient analysis (and perhaps partial analysis) with your data. However, you may conclude that only one (or even none!) of these methods will be of use to you, and you should write the paper accordingly. And more often than not, your paper will need to include other kinds of analysis (e.g. summary statistics, univariate analysis, etc.).
You need to decide which journal is most appropriate for your paper. Please talk with colleagues, other students, or me about this, in case you have any doubts. Unless the journal is an ESA, SCB, BSA, OAS, ATB, SER or IAVS journal, please also hand in a photocopy of the instructions for authors (OR a URL of the instructions).
Except for following the format of the journal, there is no set structure or format for the project. You just need to try to be convincing with respect to your thesis.
Please submit an electronic copy as an attachment, along with an electronic cover letter (it can be the main body of the email).
Please include all of the co-authors, in the order given. In your cover letter, please (very briefly) indicate what each co-author was responsible for (especially for those outside of the class) - I do not wish to grade them! In general, it is not a good idea to submit a paper unless ALL co-authors have read and commented on the paper. However, for the first version (in the interest of time) I will not require this.
However, please have at least one other person read over your paper before handing it in, and incorporate their comments. It is perfectly fine if this person is a classmate. If not a coauthor, then make sure to acknowledge him or her. This means getting your paper done well in advance of the due date.
Please note that the first version is a full submission, not a draft. I will act as an editor and reviewers (as there will not be enough time for peer review!). I may (that is, probably will) request new analyses, in addition to changes in the text. I will grade the final version according to whether the requests are followed. Thus, it is entirely possible that the first version will have a high grade, and the second version a low grade. However, I don't think any of us want this to happen!
Pay special attention to the points raised by Gopen & Swan, and by Lertzman.
The principle of parsimony holds for scientific writing as well as it does for research. "It is vain to do with more what can be done with less". So the paper needs to be as short as possible, while still being complete.
Do not stress the methods; they are only tools. So a title like "A multivariate analysis of Oklahoma sand scrub communities" is not appropriate. There may be exceptions to this: for example, you may be introducing new techniques into a field - in which case your paper would be a methodological paper.
Although some journals prefer to have figures and tables in separate files, PLEASE include them in the same document as the text. Unless your journal dictates otherwise, I prefer to have line numbers in the left column.
Absolutely, under no circumstances, call your first submission a draft. It is better to hand the paper in late, than to hand in a draft. Calling it a draft is an admission that you don't consider it ready. Do not apologize for a paper upon submission.
After you are finished writing your first version, here is a checklist to help you avoid common mistakes:
Checklist for submission of scientific papers
Cover letter
Is the cover letter written, and addressed to the editor of the journal?
Are the roles of the
authors spelled out in the cover letter? This is necessary for the class,
but it is not often required in the 'real world'.
General
Did you avoid passive voice throughout the text, including in the methods?
Do you use subheaders to guide the reader? (make sure that if you use subheaders, there are more than one per section).
Did you follow the directions of the journal and (almost more important) read a number of papers in that journal, to insure you are using the right style?
Are you sure your paper is appropriate for that journal?
Are your pages numbered?
Avoid all suspicions of
plagiarism
Use singular and plural correctly for datum/data and axis/axes.
Are all species names
spelled correctly?
Do you provide the source of nomenclature for your species?
Did you acknowledge the person/people who read your paper?
Does the file name include your name?
Thesis
Is the thesis is a real
thesis (e.g. the operating verb is something like
argue,
show, demonstrate, test, determine – and not something weak and
noncommittal like explore, study, look
at, examine, investigate)
The thesis is in the
right place
The thesis is blatantly
obvious
Does the title reflect
the thesis?
Abstract
Is your thesis obvious in your abstract?
Is your abstract truly an abstract of your study? Does it include all aspects including methods and study system?
Do you state what you actually found?
Do you avoid uninformative phrases such as 'findings will be discussed' or 'we present implications for management'?
Introduction
Is the introduction a
real introduction, and not a review of the literature?
Is your justification
for the analysis based on real ecological principles, not merely “little
is known about…”
Use of Techniques
Are all methods and
computer programs spelled correctly?
When you refer to a DCA,
do not say “DCA Analysis” as it is redundant.
Likewise with CCA.
Is a rationale given for
how many axes you are discussing?
If you do a stepwise
analysis, do you avoid trusting the p-values?
Do you provide appropriate citations for the methods
used?
Results and Discussion
Is the discussion
session (if any) free of results material?
Is the interpretation of ordination diagrams simultaneous? That is, are the species scores interpreted along the same gradient as the sample scores?
Do you ever accept a
null hypothesis? (note that a sentence such as 'there was no effect of
grazing on species richness' is verbally accepting a null hypothesis).
Graphical output of ordinations
Are there too many
species to display clearly? If so, make sure to reduce the number of
species displayed and not the number in the analysis.
Is your choice of displaying results in scatter plots, biplots, or triplots appropriate to maximize legibility and interpretability?
When you present different graphs of the same analysis (e.g. one with species scores, and another with sample scores plus environmental arrows) do you give them different panels of the same figure? (for example, Fig. 2a and 2b). You should.
If you have multiple panels such as this, do you have only one figure header?
Are there reasonable
labels for species/samples/environment in the figures?
Are codes, if any, accessible to the reader without too much work ?
Are the different groups of symbols (e.g. species scores, sample scores, environmental scores) visually distinct from each other?
Are the figures visible in black on white format? (most journals will not allow color unless it is primarily an online journal, or unless you are willing to pay a large sum. However, for presentations and posters, judicious use of color is highly recommended).
Are environmental arrows
interpreted correctly? (that is,
species scores are imagined as projecting onto the axis – not by their
closeness to the axis).
Did you label the axes? Do the axes have the correct labels indicating the analysis type? (e.g. 'DCA Axis 1' or "pCCA Axis 2")
Literature cited
Is the literature cited in the correct format?
Are all references in
the references cited at least once?
Are all citations in the
literature cited section?
Are issue numbers
removed from the literature cited section?
Is the literature cited
section in alphabetical order?
Avoid citing URLs. Many internet sites (such as USDA Plants) have formal ways for citing them; search the sites for these.
If you must cite a URL, check with the journal about whether this is allowable, and if so, how to do it.
A sample cover letter could include (after appropriate addresses and date) text such as the following. Please address it directly to the editor of the journal. Of course, change the text as need be; don't just copy what I have:
"Dear ______
Please find enclosed (or attached if an email) a copy of our manuscript entitled, "*****". This paper describes the results of our research on "*****". We believe this research would be of great interest to readers of ***journal name in italics*** because it related directly to a number of recent contributions to the journal. Thus, we feel it would be of great interest to your readership. I look forward to hearing from you.
Sincerely,
*****"
The text might be longer if directly related to previous contributions, or if it is a revision. For revisions, make sure you respond to all of the editor's substantial suggestions in the cover letter.
Good luck, and I look forward to seeing your papers!
Grading scheme:
|
|
%
of grade
|
Conform to reader's
expectations: Grammar/punctuation/spelling, Sentence structure (including
avoidance of passive voice), page numbers, paragraph structure, appropriate use of
subheadings
|
10 |
Overall paper
structure: is the material where it should be?
|
5
|
Is the subject of the
paper the system, rather than the tools?
|
2
|
Title:
appropriateness, reflects thesis
|
2
|
Abstract: adequate summary, does not include vague items like “implications will be discussed” |
5
|
Introduction:
Overall quality, true introduction, and not a review?
|
8
|
Is
the thesis in the right location, blatantly obvious, and a real thesis?
|
4
|
Is
the thesis adequately addressed in the paper?
|
7
|
Methods:
Description of data collection and analytical methods
|
6 |
Correct
methods used, and methods used correctly
|
5
|
Citations
of methods appropriate
|
2
|
Results
and Discussion: Appropriate material (e.g. if separate sections, results
only in results), Interpretation correct and adequate, Focus on
biological instead of numerical results, Thesis fully addressed,
implications/summary clearly stated
|
15
|
Acknowledgments
|
1
|
Literature
cited: Correctness of Format
|
5
|
Appropriate
and adequate literature
|
5
|
Tables/Figures:
Appropriate material, Headers/legends adequate. Choice of graphs, quality
of graphics (including scaling of axes, labeling of axes, overall clutter
and legibility)
|
15 |
Instructions
for authors: Journal indicated, Manuscript conforms to style
|
2
|
Cover
letter handed in?
|
2
|
TOTAL
|
100
|
Papers to possibly cite for analytical methods. Your textbook may also be relevant.
General
theory:
ter
Braak, C. J. F., and I. C. Prentice. 1988. A theory of gradient analysis. Adv.
Ecol. Res. 18:271-313
ter
Braak, C. J. F. 1994.
Canonical community ordination. Part
I: Basic theory and linear methods. DLO-Agricultural Mathematics Group,
Wageningen.
Variance
partitioning:
Borcard,
D., P. Legendre, and P. Drapeau. 1992. Partialling out the spatial component of
ecological variation. Ecology 73:1045-55
φkland,
R. H. 1999. On the variation explained by ordination and constrained ordination
axes. J. Veg. Sci. 10:131-6
φkland,
R. H., and O. Eilertsen. 1994. Canonical correspondence analysis with variation
partitioning: some comments and an application. J. Veg. Sci. 5:117-26
Correspondence
Analysis:
Gauch,
H. G. J., R. H. Whittaker, and T. R. Wentworth. 1977. A comparative study of
reciprocal averaging and other ordination techniques. J. Ecol. 65:157-74
Gauch,
H. G., Jr. 1982.
Multivariate Analysis and Community Structure.
Legendre,
P., and L. Legendre. 1998.
Numerical Ecology, 2nd English Edition. Elsevier,
ter
Braak, C. J. F. 1987.
Ordination. p. 91-173 in Jongman, R.H., C.J.F. ter Braak and O.F.R. van
Tongeren, editors. Data analysis in community ecology. Pudoc, Wageningen, The
Detrended
Correspondence Analysis:
Gauch,
H. G., Jr. 1982.
Multivariate Analysis and Community Structure.
Hill,
M. O., and H. G. Gauch Jr. 1980. Detrended Correspondence analysis: an improved
ordination technique. Vegetatio 42:47-58
Legendre,
P., and L. Legendre. 1998.
Numerical Ecology, 2nd English Edition. Elsevier,
ter
Braak, C. J. F. 1987.
Ordination. p. 91-173 in Jongman, R.H., C.J.F. ter Braak and O.F.R. van
Tongeren, editors. Data analysis in community ecology. Pudoc, Wageningen, The
CCA:
Legendre,
P., and L. Legendre. 1998.
Numerical Ecology, 2nd English Edition. Elsevier,
ter
Braak, C. J. F. 1987.
Ordination. p. 91-173 in Jongman, R.H., C.J.F. ter Braak and O.F.R. van
Tongeren, editors. Data analysis in community ecology. Pudoc, Wageningen, The
ter
Braak, C. J. F. 1986. Canonical correspondence analysis: a new eigenvector
technique for multivariate direct gradient analysis. Ecology 67:1167-79
ter
Braak, C. J. F. 1987. The analysis of vegetation-environment relationships by
canonical correspondence analysis. Vegetatio 69:69-77
ter
Braak, C. J. F. 1988. CANOCO - an extension of DECORANA to analyze
species-environment relationships. Vegetatio 75:159-60
ter
Braak, C. J. F., and P. F. M. Verdonschot. 1995. Canonical correspondence
analysis and related multivariate methods in aquatic ecology. Aquatic Sciences
57:255-89
ter Braak, C. J. F., & P. Šmilauer. 2002. CANOCO reference manual and CanoDraw for Windows User's guide: Software for Canonical Community Ordination (version 4.5). Microcomputer Power (Ithaca , NY, USA), 500p.
Stepwise
CCA and partial analysis:
ter
Braak, C. J. F. 1988.
Partial canonical correspondence analysis. Pages 551-558 in H. H.
Bock, editor. Classification and related methods of data analysis.
North-Holland,
Hallgren,
E., M. W. Palmer, and P. Milberg. 1999. Data diving with cross validation: an
investigation of broad-scale gradients in Swedish weed communities. J. Ecol.
87:1037-51
ter Braak, C. J. F., & P. Šmilauer. 2002. CANOCO reference manual and CanoDraw for Windows User's guide: Software for Canonical Community Ordination (version 4.5). Microcomputer Power (Ithaca , NY, USA), 500p.
PCA:
ter
Braak, C. J. F. 1983. Principal components biplots and alpha and beta diversity.
Ecology 64:454-62
ter Braak, C. J. F., & P. Šmilauer. 2002. CANOCO reference manual and CanoDraw for Windows User's guide: Software for Canonical Community Ordination (version 4.5). Microcomputer Power (Ithaca , NY, USA), 500p.
RDA:
Legendre,
P., and L. Legendre. 1998.
Numerical Ecology, 2nd English Edition. Elsevier,
ter
Braak, C. J. F. 1987.
Ordination. p. 91-173 in Jongman, R.H., C.J.F. ter Braak and O.F.R. van
Tongeren, editors. Data analysis in community ecology. Pudoc, Wageningen, The
ter Braak, C. J. F., & P. Šmilauer. 2002. CANOCO reference manual and CanoDraw for Windows User's guide: Software for Canonical Community Ordination (version 4.5). Microcomputer Power (Ithaca , NY, USA), 500p.