So the Weecology folks have published a large dataset on mammal communities in a data paper in Ecology. I know nothing about mammal communities, but that doesn't mean one can't play with the data...
Their dataset consists of five csv files: communities, references, sites, species, and trapping data.
Where are these sites, and by the way, do they vary much in altitude?
Let's zoom in on just 'the states'?
![](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj4EwxxlshXhfedLvLpZLFldHc7cNnC4fD0419tnSD1m5ylLNhhTFwffzm1Ozgl1HVMLWD6phX0b4gKHuMqyi-VVds4yX2w46Cvsq8I4k6Dh4pVk0Uu1fGMsuOPOdd9FZh4-v0OltAdY7qA/s400/usmap.png)
What phylogenies can we get for the species in this dataset?
We can use the rOpenSci package treebase to search the online phylogeny repository TreeBASE. Limiting to returning a max of 1 tree (to save time), we can see that X species are in at least 1 tree on the TreeBASE database. Nice.
So there are 321 species in the database with at least 1 tree in the TreeBASE database. Of course there could be many more, but we limited results from TreeBASE to just 1 tree per query.
Here's the code:
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