Calculating ecological diversity using R
- Initially I was using R library ecodist
- library(ecodist)
- bray_curtis_via_ecodist<-as.matrix(bcdist(mat,rmzero=TRUE));
- sorenson_via_ecodist<-as.matrix(distance(mat,method="sorensen"));
- R library vegan seems to have more options (and is preferred by Steve Kembel??)
- bray_curtis_via_vegan<-vegdist(mat,method="bray")
- Wrote col_betadiversity.R to calculate beta diversity using several measurements and outputs the data in several formats
- Results in this directory contain different beta diversity measurements between GOS (and other) samples using PFAM counts.
- This command generates the output files: ./col_betadiversity.R camera_proteins_vs_pfam.txt beta_diversity
- The output files are labeled "beta_diversity_" followed by the name of the dissimilarity measurement.
- "norm" means that the matrix was normalized by dividing each count by the total number of counts in each column.
- Each diversity metric is output in three files:
- "matrix" is a simple dissimilarity matrix (upper triangular is redundant)/
- "pairwise" outputs each dissimilarity score on its on line with the name of the samples in the first two columns.
- "hclust.pdf" is a pdf showing the results of doing hiearchael clustering using the distances.
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