I am required to do distance decay analysis for my NGS bacterial community along a geographical gradient. What metadata fields are required for the gradient. Will the geographical co-ordinates (lat long) be enough together with the otu table. Can anyone help me with the R code for doing the same and obtaining a distance decay plot for the same.
Not sure there is an "out of the box" way of doing this. But it should be pretty straight forward to get started:
1. Pick your favorite distance measure between your bacterial communities. Unifrac is a popular one, though i'd go for a simple euclidean distance on the logged abundances of your taxa.
2. Plot these distances against the geographical distances. You can get these from your lat-long measurements by something like: https://conservationecology.wordpress.com/2013/06/30/distance-between-two-points-in-r/
Hope this helps.
Not sure there is an "out of the box" way of doing this. But it should be pretty straight forward to get started:
1. Pick your favorite distance measure between your bacterial communities. Unifrac is a popular one, though i'd go for a simple euclidean distance on the logged abundances of your taxa.
2. Plot these distances against the geographical distances. You can get these from your lat-long measurements by something like: https://conservationecology.wordpress.com/2013/06/30/distance-between-two-points-in-r/
Hope this helps.
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