Community Ecology analysis using R: basic intro

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! Other packages:! Labdsv (http://ecology.msu.montana.edu/labdsv/R/)! APE (Analysis of Phylogenetics and Evolution; http://ape.mpl.ird.fr/)! Picante (Phylocom integration, community analyses, null-models, traitsand evolution; http://picante.r-forge.r-project.org/)! Bioconductor (http://www.bioconductor.org/install/)
! Tutorial: try to perform the following tasks <strong>using</strong> what is includedin this presentation! OBS: Vegan needs to be installed.! TIP: you can install the R interpreter if you don’t want to use theterminal! Get an OTU-table into R. Which are the dimensions?! Obtain the number of reads per sample! Subsample the OTU table to a chosen value. Why did you choosethat value?! Produce collector curves! Fit data to different rank-abundance models, including Preston! Generate a NMDS. Do you see any specific clustering?! Generate a UPGMA. Do results agree with NMDS?! Generate a DCA and compare with previous results
Page 1 and 2: Community Ecology analysisusing R:
Page 3: ! Where to get R:! http://www.r-pro
Page 6 and 7: ! To see the variables that were de
Page 8 and 9: ! Working with tables:> getwd() #ge
Page 10 and 11: ! Analysis using Vegan (R functions
Page 12 and 13: owSums(OTU_table) # Find the sample
Page 14 and 15: ! Let’s get some richness estimat
Page 16 and 17: ! Accumulation curves (using Ugland
Page 18 and 19: ! We can also fit several rank-abun
Page 20 and 21: * Shannon H index (considers richne
Page 22 and 23: ! We use a subsampled OTU table in
Page 24 and 25: plot(OTU_ss_n.bray.nmds)>stressplot
Page 26 and 27: ! Detrended Correspondence Analysis
Page 28 and 29: ! A linear regression model can be

Community Ecology analysis using R: basic intro

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