Community Ecology analysis using R: basic intro

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! Analysis <strong>using</strong> Vegan (R functions for <strong>analysis</strong> of communityecology: http://cc.oulu.fi/~jarioksa/softhelp/vegan.html) #Don’t get confused with MEGAN or MEGA.> install.packages("vegan",repos="http://r-forge.r-project.org")#installs Vegan> library(vegan)Get ready your OTU table è the easiest is to copy-paste from excelto a text file with no formatting; this table will be tab-separatedSample_1 Sample_2 Sample_3 Sample_41 2443 546 43 02 4355 43 433 56653 322 45544 5 4345
OTU_table head(OTU_table) # check if the table looks OK> OTU_table
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 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
Page 30 and 31: ! Other packages:! Labdsv (http://e

Community Ecology analysis using R: basic intro

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