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週次 |
日期 |
單元主題 |
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Week 0 |
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<font color="red"><b>The schedule is subject to change.</b></font>
<br><font color="green">If you have problem downloading a file, please let the instructor know.</font> |
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Week 1 |
2/19 |
Why care about experimental design and data analysis?
<br><br>
<font color="red">Required</font>
<br>
<li><a href="http://www.jstor.org/stable/3802789">Johnson DH, 1999. The insignificance of statistical significance
testing. Journal of Wildlife Management 63:763–772.</a>
<li><a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/Osenberg et al. 2002.pdf">Osenberg, CW, et al., 2002. Rethinking ecological inference: density dependence in reef fishes. Ecology Letters 5:715-721.</a>
<br><br>
<font color="red">Supplementary</font>
<li><a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/Yoccoz p-value.pdf">Yoccoz, NG, 1991. Use, overuse and misuse of significance tests in evolutionary biology and ecology. Bull. Ecol. Soc. Am. 72:106-111.</a>
<li><a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/Pigliucci-NH.pdf">Pigliucci, M, Reject that null hypothesis!</a>
<br><br>
<font color="red">Homework</font>
<ul>
<li> <a href="http://cran.csie.ntu.edu.tw/">Download R</a> and install it on your computer.
<li> Go over the first three topics (basic input, basic types, and basic operations) of <a href="http://www.cyclismo.org/tutorial/R/">R tutorial</a>.
</ul> |
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Week 2 |
2/26 |
Questions, Hypotheses, and Approaches
<br><br>
<font color="red">Required</font>
<li><a href="http://press.princeton.edu/titles/8335.html">Chapter 1. How to Do Ecology.</a>
<li><a href="http://www.theresearchassistant.com/tutorial/2-1.asp">The Relationship Between the Research Question, Hypotheses, Specific Aims, and Long-Term Goals of the Project</a>
<li><a href="http://www.bioone.org/doi/abs/10.1641/B570708">Elliott, LP and BW Brook, 2007. Revisiting Chamberlin: multiple working hypotheses for the 21st century. BioScience 57:608-614.</a>
<br><br>
<font color="red">Supplementary</font>
<li><a href="http://www.accessexcellence.org/RC/AB/BC/chamberlin.php">Chamberlin, TC, 1897. The method of multiple working hypotheses. Journal of Geology 5:837-48. Reprinted in Science 148: 754-59 (1965).</a>
<li><a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/strong inference.pdf">Platt, JR, 1964. Strong inference. Science 146:347-353.</a>
<li><a href="http://www.motokawa.bio.titech.ac.jp/sushi.html">Motokawa, T, 1989. Sushi science and hamburger science. Perspectives in Biology and Medicine 32:489-504.</a>
<li><a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/HM2.pdf">Hilborn, R and M. Mangel, 1997. Alternative views of the scientific method and of modeling. In <i>Ecological Detective</i>, Chapter 2, Princeton University Press.</a>
<br><br>
<font color="red">Homework</font>
<ul>
<li><a href="http://www.cyclismo.org/tutorial/R/plotting.html">R tutorial for "plotting"</a>
<li><a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/R2.pdf">R intro Chapter 2</a>
<small>Most of the chapter 2 should be a review for you.</small>
<li><a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/R3.pdf">R intro Chapter 3</a>
</ul>
<br>
<font color="red"><b>Assignment 1</b></font> Due March 8, 1pm. (<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/A1.pdf">PDF</a>)
<br><br>
<a href="http://www.statmethods.net/graphs">Basic Graphs</a> section in <a href="http://www.statmethods.net">Quick-R</a> has useful information on plotting. The site is nicely edited. |
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Week 3 |
3/05 |
Variation, Replication, and Sampling
<br><br>
<font color="red">Required</font>
<li><a href="http://www.jstor.org/stable/1942661">Hurlbert, SH, 1984. Pseudoreplication and the design of ecological field experiments. Ecological Monographs 54:187-211.</a>
<br><br>
<font color="red">Supplementary</font>
<li><a href="http://www.jstor.org/stable/2265754">Heffner, RA, et al., 1996. Pseudoreplication revisited. Ecology 77:2558-2562.</a>
<li><a href="http://www3.interscience.wiley.com/journal/119019007/abstract">Oksanen, L, 2001. Logic of experiments in ecology: is pseudoreplication a pseudoissue? Oikos 84:27-38.</a>
<li><a href="http://www3.interscience.wiley.com/journal/118834066/abstract">Cottenie, K and De Meester L, 2003, Comment to Oksanen (2001): reconciling Oksanen (2001) and Hurlbert (1984). Oikos 100:394-396.</a>
<br><br>
<font color="red">Homework</font>
<ul>
<li><a href="http://www.cyclismo.org/tutorial/R/probability.html">R tutorial for "Basic Probability"</a>
<li><a href="http://www.statmethods.net/management">Quick-R Data Management</a> All sections.
</ul>
<br><br>
<font color="red"><b>Assignment 2</b></font> Due March 16, 13:00. (<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/A2.pdf">PDF</a>) |
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Week 4 |
3/12 |
Experimental designs
<br><br>
<a href="http://www.bio.ic.ac.uk/research/crawley/statistics/exercises.htm">This page</a> has useful information on statistical analysis using R. Be aware that nested designs (including the split-plot design) should not be analyzed in the conventional way. You can see the detail in the <a href="http://www.bio.ic.ac.uk/research/crawley/statistics/exercises/R7Nesteddesigns.pdf">exercise 7</a>.
<br><br>
<font color="red">Homework</font>
<ul>
<li>Go over all the previous homeworks if you have not finished them yet.
</ul>
<br><br>
<font color="red"><b>Assignment 3</b></font> Due March 23, 1pm. (<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/A3.pdf">PDF</a>)
<br>
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/A3 sample code.txt">Sample code</a> |
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Week 5 |
3/19 |
Taking measurements
<br><br>
<font color="red">Required</font><br>
<a href="http://www.bio.ic.ac.uk/research/crawley/statistics/exercises/R7Nesteddesigns.pdf">Nested design ANOVA</a> First 17 pages.
<br><br>
<font color="red"><b>Assignment 4</b></font> Due March 30, 13:00. (<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/A4.pdf">PDF</a>)
<br>
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/A4 sample code.txt">Sample code</a> |
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Week 6 |
3/26 |
Miscellaneous topics
<br><br>
The last class before Exam 1. Come to class with questions.
<br><br>
<font color="purple"><b>Quiz 1</b></font>
<br><br>
<font color="red"><b>Assignment 5</b></font> Due April 6, 13:00. (<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/A5.pdf">PDF</a>)
<br>
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/A5 sample code.txt">Sample code</a> |
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Week 7 |
4/02 |
<a href="http://reg.aca.ntu.edu.tw/ereg2007/calendar.htm">Exam preparation break (NO CLASS)</a> |
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Week 8 |
4/09 |
Exam 1 |
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Week 9 |
4/16 |
R review, Least squares, and Bootstrap
<br />
Meet in <font color="red">計資中心 110室</font> from now on.
<br><br>
<font color="red">Supplementary</font><br />
Chapters 5 and 6. <a href="http://books.google.com/books?id=ApeNVhVl4HUC">The Ecological Detective</a>.
<br />
<font color="red">Class excercise</font><br />
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/FR.txt"><tt>Functional response data</tt></a><br />
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/FRcode.txt"><tt>Parameter estimation code</tt></a>
<br /><br />
<font color="red"><b>Assignment 6</b></font> Due April 23, 1pm. (<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/A6.pdf">PDF</a>)
<br />
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/a6data.txt"><tt>a6data.txt</tt></a>
<br>
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/A6 sample code.txt">Sample code</a> |
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Week 10 |
4/23 |
Probability distributions and Maximum Likelihood
<br /><br />
<font color="red">Resource</font><br />
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/HSDE.pdf">Hand-book on Statistical Distributions for experimentalists</a><br />
<font color="red">Supplementary</font><br />
Chapter 7. <a href="http://books.google.com/books?id=ApeNVhVl4HUC">The Ecological Detective</a>.
<br /><br />
<font color="red">In class examples</font><br />
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/Pdata.txt">Poisson data</a><br />
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/Gdata.txt">Gamma data</a><br />
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/PoissonE.txt">Poisson example</a><br />
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/GammaE.txt">Gamma example</a>
<br /><br />
<font color="red"><b>Assignment 7</b></font> Due April 30, 13:00. (<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/A7.pdf">PDF</a>)<br />
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/a7data.txt">a7data.txt</a><br />
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/A7sample.txt">Sample code</a> |
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Week 11 |
4/30 |
Generalized Linear Model I
<br /><br />
<font color="red">Supplementary</font><br />
Excercises 9 and 11. <a href="http://www.bio.ic.ac.uk/research/crawley/statistics/exercises.htm">Statistics: An introduction using R</a>.
<br />
<font color="red">In class example</font><br />
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/flower.txt"><tt>flower.txt</tt></a><br />
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/GLMP.txt"><tt>Example code</tt></a>
<br /><br />
<font color="red"><b>Assignment 8</b></font> Due May 7, 1pm. (<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/A8.pdf">PDF</a>)
<br /><a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/a8sample.txt">Sample code</a> |
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Week 12 |
5/07 |
Generalized Linear Model II
<br /><br />
<font color="red">Supplementary</font><br />
Excercise 10. <a href="http://www.bio.ic.ac.uk/research/crawley/statistics/exercises.htm">Statistics: An introduction using R</a>.
<br />
<font color="red">In class example</font><br />
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/overdispersion.txt">Overdispersion example</a><br />
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/seeds.txt"><tt>seeds.txt</tt></a>
<br />
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/BinomE.txt">Example code</a>
<br /><br />
<font color="red"><b>Assignment 9</b></font> Due May 14, 1pm. (<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/A9.pdf">PDF</a>)
<br /><a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/a9sample.txt">Sample code</a> |
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Week 13 |
5/14 |
Likelihood ratio test and model selection
<br /><br />
<font color="red">Supplementary</font>
<li><a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/modsel.pdf">TREE 19: 101-108.</a>
<br />
<font color="red">In class example</font><br />
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/PB.txt">Parametric bootstrap LRT</a><br />
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/LRT1.txt">LRT example 1</a>
<br />
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/LRT2.txt">LRT example 2</a>
<br />
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/LRT3.txt">LRT example 3</a>
<br /><br />
<font color="red"><b>Assignment 10</b></font> Due May 21, 13:00. (<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/A10.pdf">PDF</a>)
<br />
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/a10data.txt"><tt>a10data.txt</tt></a>
<br /><a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/a10sample.txt">Sample code</a> |
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Week 14 |
5/21 |
Generalized Linear Mixed Model
<br /><br />
<font color="red">Supplementary</font>
<li><a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/GLMMTREE.pdf">TREE 24: 127-135.</a>
<br />
<font color="red">In class example</font><br />
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/mmex1.txt"><tt>mmex1.txt</tt></a>
<br />
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/ME1.txt">MM Example 1</a>
<br />
<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/ME2.txt">MM Example 2</a>
<br /><br />
<font color="red"><b>Assignment 11</b></font> Due May 28, 13:00. (<a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/A11.pdf">PDF</a>)
<br /><a href="https://ceiba.ntu.edu.tw/course/de6366/PDF/a11sample.txt">Sample code</a> |
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Week 15 |
5/28 |
<a href="http://reg.aca.ntu.edu.tw/ereg2007/calendar.htm">Dragon boat festival (NO CLASS)</a> |
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Week 16 |
6/04 |
Review |
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Week 17 |
6/11 |
Exam 2 |