Community Ecology analysis using R: basic intro

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! We can also fit several rank-abundance distribution models to ourdata:> modmodsum
! Let’s fit our data to the Preston model>prestonprestondistr plot(preston)> lines(prestondistr, line.col="blue3")Quasi-Poisson fit to octavesMaximized likelihood to log2 abundancesQuasi-Poison fit:Extrapolated Observed Veiled13925.938 9007.000 4918.938Maximum Likelihood fit:Extrapolated Observed Veiled13433.634 9007.000 4426.634OTUs0 500 1000 15001 2 4 8 32 128 512 2048 8192 65536 524288Frequency
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 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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