Community Ecology analysis using R: basic intro

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! Let’s get some richness estimators>richnessrichnessHere we calculate the Chao1 and ACE estimators and we seethe actual species/OTU numbers.
Rarefaction(script http://www.jennajacobs.org/R/rarefaction.html)>source("http://www.jennajacobs.org/R/rarefaction.txt") #source thefunction from the website>rarefaction(ABUND_OTU_counts, subsample=1000, plot=TRUE,color=TRUE, error=FALSE, legend=TRUE, symbol) # needs OTUtable with counts and subsample sizePooled samplesThis can take a whileto run.Mean OTU Richness0 2000 60000 500 1500 25000 1,000,000 2,000,000 3,000,000 4,000,000 5,000,000Individual samples0 100,000 200,000 300,000 400,000 500,000Reads (iTags)
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 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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