hello everyone, I wanna calculate dissimilarity index on taxonomic basis in R studio, I have 202 species having plant diversity data of of different years. Please guide me.
Thanks in advance.
Hello Yaseen Muhammad Please see the links below
https://carpentries-incubator.github.io/metagenomics/08-hands_on-diversity/index.html
https://cran.r-project.org/web/packages/betapart/betapart.pdf
https://cran.r-project.org/web/packages/vegan/vegan.pdf
First you need a distance matrix (e.g. calculating Euclidean Distances between your observations if they contain continuous measurements or counts), and from the distance matrix you might apply a linkage criteria (for e.g. average linkage) to calculate dissimilarities. At least this would be the clustering approach to calculate dissimilarities.
A well-known measure of dissimilarity is "distance." Various metrics can represent it with varying norms within [1 , infinity], among which the Euclidean distance (norm l1) is the most common. Therefore, any 202 × 202 distance matrix calculator function in the R environment will give you a perspective of the dissimilarity.
You can then use functions for hierarchical clustering based on the distance matrix obtained. For more detailed, easy to understand information and how to implement, you may see:
https://stackoverflow.com/questions/35540059/how-to-insert-a-distance-matrix-into-r-and-run-hierarchical-clustering
- Badges
- Science topic