R for Ecologists
BIOL 7901, Section 1, Fall 2009
Fridays 9:10 - 10:00 a.m.
Life Sciences Annex, A663

Seminar Leader: Dr. Kyle E. Harms



Click on the underlined links below to view or download course materials
(the links are often named with filename extensions only)
     "csv" = Comma-separated values file
     "doc" & "docx" = Microsoft Word document format
     "pdf" = Portable document format
     "r" = R file
     "txt" = Text file



Syllabus - pdf



Remaining Schedule

Self-tutorial Introduction to R

     R Self-tutorial, an Introduction to R Programming (K. Harms, 2009) - doc
          Data set to accompany R Self-tutorial - txt



Focused self-tutorials created this semester by seminar participants
(contact individual authors for details, questions, or suggestions;
an e-mail address for the author is provided in each Word document)

     ANOVA, i.e., aov()
          (T. Hmielowski, 11/13/09) - doc
               Data set to accompany ANOVA - biomass.txt

     Factor Analysis, i.e., factanal()
          (M. Brooks, 10/16/09) - doc
               Data set to accompany Factor Analysis - bacsred.csv

     Histogram Function, i.e., hist()
          (L. Wieland, 10/16/09) - docx

     Kolmogorov-Smirnov Test, i.e., ks.test()
          (K. Harms, 09/30/09) - doc

     Maps Library, plotting latitude & longitude data using map()
          (M. Monk, 10/23/09) - doc
               Data set to accompany Maps Library - mapdata210.txt
               R code used in Maps Library - mapping210.r

     Monte Carlo Simulations for Population Genetics, to illustrate for(), runif() & while()
          (C. Prada, 10/30/09) - doc

     Picante Package, selected functions
          (M. Gavilanez, 10/30/09) - docx
               Data sets to accompany Picante Package - comun.txt; comun6.txt; newick_tree_COOPER.txt

     Principal Components Analysis, i.e., prcomp() & princomp()
          (D. Anderson, 10/26/09) - docx
               Data set to accompany Principal Components Analysis - Anderson_PCA_data.txt

     Randomization Test used in DeWalt et al. (2006)
          (K. Harms, 10/29/09) - doc
               Data set to accompany Rand. Test DeWalt et al. (2006) - Sepilokliana.txt
               R code used in Rand. Test DeWalt et al. (2006) - DeWalt_etal_2006_R_code.txt

     Regression & Variable Selection, e.g., lm() & glm()
          (M. Sagot, 11/20/09) - docx
               Data set to accompany Regression & Variable Selection - habitat.txt

     Scatterplots (and Box Plots), i.e., plot()
          (C. Saari, 11/13/09) - docx
               Data set to accompany Scatterplots (and Box Plots) - body.csv

     Scatterplots - 3D, selected functions from scatterplot3D & rgl packages
          (L. Patrick, 11/20/09) - docx
               Data sets to accompany Scatterplots - 3D - Guild10.txt; meche.txt

     Tinn-R, a useful text editor for R programming
          (M. Monk, 10/23/09) - docx



Useful web sites for R programming

     R Project web site: The R Project for Statistical Computing


     Bolker - Ben Bolker's web site: www.zoology.ufl.edu/bolker

     BUGS (Bayesian inference Using Gibbs Sampling) web site: www.mrc-bsu.cam.ac.uk/bugs

     Burns - Patrick Burns' web site (including "The R Inferno"): www.burns-stat.com

     Cadotte - Marc Cadotte's web site: www.utsc.utoronto.ca/~mcadotte/lab.html

     Clark - Jim Clark's web site: www.nicholas.duke.edu/people/faculty/clark

     Crawley - Mick Crawley's web site: www.bio.ic.ac.uk/research/mjcraw/crawley.htm

     Fox - John Fox's web site (home of "R Commander"): http://socserv.mcmaster.ca/jfox
    
     Johnson - Paul Johnson's "Rtips" (under "Documentation Wiki"): http://pj.freefaculty.org

     Kabacoff - Rob Kabacoff's "Quick-R" web site: www.statmethods.net

     Maindonald - John Maindonald’s web site: wwwmaths.anu.edu.au/~johnm

     McCarthy - Brian C. McCarthy's web site: www.plantbio.ohiou.edu/epb/faculty/faculty/bcm.htm

     McGill - Brian McGill’s web site (including "R cheat sheet"): www.brianmcgill.org

     NCEAS R Programming Resource Center: www.nceas.ucsb.edu/scicomp/RProgTutorialsLatest.html

     New York Times article on R: www.nytimes.com

     Review of R books: ecotope.org/blogs/page/R-Book-Review

     R Seek (a useful way to search for R code, packages, etc.): www.rseek.org

     R-sig-ecology (discussion re ecological data analysis in R): stat.ethz.ch/pipermail/r-sig-ecology

     R-sig-phylo (discussion re phylogenetic & compariative methods in R): stat.ethz.ch/pipermail/r-sig-phylo

     Sanderson - Alastair Sanderson's web site: www.sr.bham.ac.uk/~ajrs

     Short - Tom Short's "R Reference Card" (available at R Project web site): Short-refcard.pdf

     Stevens - Hank Stevens' web site: www.cas.muohio.edu/~stevenmh

     SpringerLink's R books: www.springerlink.com

     Tinn-R - A useful text editor for R programming: sourceforge.net/projects/tinn-r

     USGS "Learn R" web site: www.fort.usgs.gov/BRDScience/LearnR.htm

     Verzani - John Verzani's web site: wiener.math.csi.cuny.edu/verzani