# Script file for reformatting ant data for sample-based rarefaction # 10 June 2012 NJG # Uses BlackRock data with multiple samples from 3 habitats # Data are nest counts # Read ant data set Complete.Ant.Data <- read.csv("MAantsampledata.csv",header=TRUE) Grassland.Matrix <-subset(Complete.Ant.Data,CommunityType..Habitat.== "Cultural Grassland") Grassland.Matrix <-table(Grassland.Matrix$Code..Species.,Grassland.Matrix$Site..Sample.) Grassland.Matrix <- Grassland.Matrix[,colSums(Grassland.Matrix)>0] print(Grassland.Matrix) # Save results to a .csv file OutputFile <- "Cultural Grassland Matrix.csv" outfile <- file(OutputFile, "w") write.csv(file=outfile, Grassland.Matrix,row.names=TRUE) # Clean up close(outfile) Oak.Matrix <-subset(Complete.Ant.Data,CommunityType..Habitat.== "Oak-Hickory-WhitePine Forest") Oak.Matrix <-table(Oak.Matrix$Code..Species.,Oak.Matrix$Site..Sample.) Oak.Matrix <- Oak.Matrix[,colSums(Oak.Matrix)>0] print(Oak.Matrix) # Save results to a .csv file OutputFile <- "Oak Hickory WhitePine Matrix.csv" outfile <- file(OutputFile, "w") write.csv(file=outfile, Oak.Matrix,row.names=TRUE) # Clean up close(outfile) Successional.Matrix <-subset(Complete.Ant.Data,CommunityType..Habitat.== "Successional Shrubland") Successional.Matrix <-table(Successional.Matrix$Code..Species.,Successional.Matrix$Site..Sample.) Successional.Matrix <- Successional.Matrix[,colSums(Successional.Matrix)>0] print(Successional.Matrix) # Save results to a .csv file OutputFile <- "Successional Shrubland Matrix.csv" outfile <- file(OutputFile, "w") write.csv(file=outfile, Successional.Matrix,row.names=TRUE) # Clean up close(outfile)