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Files and Datasets | Schedule
 

Files for multivariate class

Jan 16 - Introduction to R, data management

• Download and install R
• List of R packages
• R manuals (the "Introduction to R" and "R Data Import/Export" will be most useful)
• After installing R, run the program and select Packages->Install packages from the menu
• Pick a CRAN mirror (reliable server with updated packages), USA (MO) run by Washington University in St.Louis is a good one
• Install the following packages (you can select all of them at once)
• vegan
• xlsReadWrite
• labdsv
• BiodiversityR
• car
• Rcmdr
• Note that some of these may require other packages, the program will compile a list of dependincies and ask permission to install those packages. Say yes.
• When you are done, enter the command installed.packages() and you should see a list of all installed packages (see above link if you want to know what some of these do).
• The library() command will load a specific package (eg. see script below).
• Sample dataset
• Basic data loading and manipulation script
• Recommended (optional) text editor with syntax highlighting of R commands
• Powerpoint presentation from class
• Script from class
• Update - For Mac users
  There is not a XLSReadWrite package so from here on out we will read all data as comma separated files
  • Basic data loading and manipulation script using csv files
  • Sample dataset, community part in csv form (right-lick, save as community.csv)
  • Sample dataset, factor part in csv form (right-lick, save as factors.csv)

Jan 23 - Analyses of diversity, diversity and similarity indices

• Sample dataset, community part in csv form (same as last week)
• Sample dataset, factors part in csv form (same as last week)
• Diversity, species accumulation, rarefaction and community similarity script.
• Powerpoint presentation from class
• Matthews, W.J. , R. Cashner and F. P. Gelwick. 1988. Stability and persistence of fish faunas and assemblages in three midwestern streams. Copeia 1988(4):945-955
• Hughes, J.B., J.J. Hellmann, T.H. Ricketts and B.J. Bohannan. 2001. Counting the uncountable: Statistical approaches to estimating microbial diversity. Applied and Environmental Microbiology. 67(10): 4399-4406.

Jan 30 - Analyses of similarity matrices (ANOSIM, MRPP, Analysis of Variance using distance matrix)

• Bird community dataset, community part in csv form
• Bird community dataset, factors part in csv form
• ANOSIM, MRPP and Multivariate Analysis of Variance for Similarity Matricies script.
• Powerpoint presentation from class
• Paszkowski, C.A. and W.M. Tonn. 2000. Community oncordance between the fish and aquatic birds of lakes in northern Alberta, Canada: the relative importance of environmental and biotic factors. Freshwater Biology 43:421-437

Feb 6 - Matrix comparisons (Mantel test)

• Zip file with 7 csv matrices and a script to run Mantel tests
  • Genetic distance and geographic distance for all individuals
  • Genetic distance and geographic distance for each of two subspecies
  • Matrix with within vs among subspecies comparisons as factors for partial Mantel
• Powerpoint presentation from class
• Jones, M.E. and L.A. Barmuta. 1998. Diet Overlap and Relative Abundance of Sympatric Dasyurid Carnivores: A Hypothesis of Competition. The Journal of Animal Ecology 67(3) 410-421.
• Vormisto, J., O. L. Phillips, K. Ruokolainen, H. Tuomisto, R. Vásquez. A Comparison of Fine-Scale Distribution Patterns of Four Plant Groups in an Amazonian Rainforest. Ecography 23(3) 349-359.

Feb 13 - Clustering

• Meristic data on 6 species in the genus Profundulus
• Species membership as a factor for the Profundulus data
• Cluster analysis of Profundulus meristic data script.
• Powerpoint presentation from class
• Smith, S. A. and E. Bermingham. 2005. The biogeography of lower Mesoamerican freshwater fishes. Journal of biogeography 32:1835-1854.

Feb 20 - PCoA - Principle Coordinates

• Community dataset for small first order streams in the upper Pascagoula (81 samples x 40 species).
• Principle Coordinates (PCoA) script
• Powerpoint presentation from class
• Elwa, A. 2004. Quantitative analysis and palaeoecology of Eocene Ostracoda and benthic foraminifera from Gebel Mokattam, Cairo, Egypt. Palaeogeography, Palaeoclimatology, Palaeoecology. 211: 309-323.

Feb 27 - PCA - Principle Components

• Community dataset for small first order streams in the upper Pascagoula (81 samples x 40 species).
• Principle Components (PCA) script
• Powerpoint presentation from class
• McPeek, M.A. 1990. Behavioral differences between Enallagma species (Odonata) influencing differential vulnerability to predators. Ecology 71(5):1714-1726
• Nash, D.R., T.D. Als, R. Maile, G.R. Jones, J.J. Boomsma. 2007. A mosaic of chemical coevolution in a large blue butterfly. Science 319:88-91

March 5 - NMDS - Non Metric Multidimensional Scaling

• Community dataset for small first order streams in the upper Pascagoula (81 samples x 40 species).
• Non metric multidimensional scaling script
• Powerpoint presentation from class
• Yrjala, K., R. Katainen, G. Jurgens, U. Saarela, A. Saano, M. Romantschuk and H. Fritze. 2004. Wood ash fertilization alters the forest humus Archaea community. Soil Biology and Biochemistry 36:199-201.
• Packham, J.M., T. May, M. Brown, T. Wardlaw and A Mills. 2002. Macrofungal diversity and community ecology in mature and regrowth wet eucalypt forest in Tasmania: A multivariate study. Austral Ecology 27:149-161.

March 19 - CA and DCA - Correspondence Analysis (CA, reciprocal averaging) and Detrended Correspondence Analysis (DCA)

• Community dataset for small first order streams in SE MO and SW IL (16 samples x 30 species).
• CA and DCA script
• Powerpoint presentation from class
• Luczkovich, J.L., G. P. Ward, J.C. Johnson, R.C. Christian, D. Baird, H. Neckles and W. M. Rizzo. 2002. Determining the trophic guilds of fishes and macroinvertebrates in a sea grass food web. Estuaries 25(6A) 1143-1163.

April 2 - CCA and RDA - Canonical Correspondence Analysis (CCA) and Redundancy Analysis (RDA)

• Community dataset for small first order streams in SE MO and SW IL (16 samples x 30 species).
• Environmental data for community samples. Variables include pH, conductivity (COND(S/m)), dissolved oxygen(DO(mg/L)), Temp, total dissolved solutes (TDS(g/L)), ORP(mV), depth, mean current velocity (flow), mean substrate size (substrate), mean percent cover (cover), mean percent emergent vegetation (veg), bank stability (bank), stream width (width), mean percent canopy cover (canopy), coefficient of variability in depth, current, substrate and width (cv_dep cv_flow cv_sub cv_width).
• CCA script
• Powerpoint presentation from class
• Smith, T.A. and C.E. Kraft. 2005. Stream fish assemblages in relation to landscape position and local habitat variables. Transactions of the American Fisheries Society. 134:430-440.

April 9 - Partial CCA and RDA

• Community dataset for small first order streams in SE MO and SW IL (16 samples x 30 species).
• Environmental data for community samples, includes variable designating stream. Variables include pH, conductivity (COND(S/m)), dissolved oxygen(DO(mg/L)), Temp, total dissolved solutes (TDS(g/L)), ORP(mV), depth, mean current velocity (flow), mean substrate size (substrate), mean percent cover (cover), mean percent emergent vegetation (veg), bank stability (bank), stream width (width), mean percent canopy cover (canopy), coefficient of variability in depth, current, substrate and width (cv_dep cv_flow cv_sub cv_width).
• Partial CCA script
• Powerpoint presentation from class
• Titeux, N., M. Dufrêne, J. Jacob, M. Paquay, P. Defourny. 2004. Multivariate analysis of a fine-scale breeding bird atlas using a geographical information system and partial canonical correspondence analysis: environmental and spatial effects. Journal of Biogeography 31(11): 1841-1856

April 16 - Indicator Species Analysis

• Community dataset from ichthyology class (fall 2006). Rows are sites, columns are species. The first and last rows (ICH06-01 and ICH06-16) are collections in MS, ICH06-02 through ICH06-07 are from the St. Francis Drainage in MO, ICH06-08 through ICH06-15 are from coastal streams in AL.
• Indicator Species Analysis script
• Powerpoint presentation from class
• Wilson, R.R. and D.J. Twedt. 2003. Spring bird migration in Mississippi alluvial valley forests. American Midland Naturalist 149(1):163-175.

April 23 - Model Selection and Regression/Classification Trees

• Ecological trait matrix. Matrix includes "reservoir ratio" and 32 ecological traits for 103 species in the full dataset. See class notes for details.
• Model Selection and Regression Tree Script
• Powerpoint presentation from class
• Neumann,D.W., B. Rajagopalan, E. Zagona. 2003. Regression model for daily maximum stream temperature. Journal of Environmental Engineering 129 (7):667-674.
• Note - Because this is our last meeting I have organized things a little differently. The example analyses in the notes are the same as done in the above script. Since we will not have a meeting to go over potential problems and output from this analysis I will cover as much of that as possible in class. It might be beneficial to run this analysis before class. If you run it later and have questions you can email me for help.