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JamesDMSpeed / PhyloTroph

Phylogenetic diversity across trophic levels
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Phylogeny #7

Open kjerstrs opened 4 years ago

kjerstrs commented 4 years ago

I've uploaded the file 'CommunityMat' that works as a community matrix for the animals. Together with the nwk file from TimeTree, I'm able to calculate the phylogenetic diversity for the animals with the pd function in picante. I was just wondering how I can include the plants into my community matrix when i don't have the polygon layer and can extract which species are within each cell, as I have done with the animals? @damarismm @JamesDMSpeed

damarismm commented 4 years ago

With the file you have, it is not possible to get the species information out. I will upload soon what you need, I am still working on it.

damarismm commented 4 years ago

The rasterbrick is too big and is saved in the NTNU box. Here is the link: https://ntnu.box.com/s/050j37osuazm4ezl9rlz9oc3srdwz9kb. Download this on your local, I added the plants in your script (Phylogeny animals) already.

kjerstrs commented 4 years ago

Thank you!

kjerstrs commented 4 years ago

Just a couple of questions regarding the phylogenies. The phylogeny for the animals, retrieved from TimeTree, is ultrametric, while the phylogeny for the plants is not, what is preferred? And I noticed that it is common to include the root when calculating the phylogenetic diversity. Do I then have to combine the two phylogenies in order to get the correct and comparable values for PD? If so, is there an easy way to do that in R?
@JamesDMSpeed @damarismm

damarismm commented 4 years ago

I am not sure if an ultrametric or non-ultrametric tree is preferred. They show relationships different, so I would think you want both trees either ultrametric or non-ultrametric. @JamesDMSpeed has probably a better answer to that. You do not nee to combine the two trees, but work with them separately. And look e.g. at areas with high PD of plants and how they relate to mammal PD and/or SR.