get colour and phylogeny - Githubissues

bowlerbear / DanishBirdAbundance

Project to estimate the abundance of birds in Denmark using distance-sampling

MIT License

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get colour and phylogeny #1

Open bowlerbear opened 2 years ago

bowlerbear commented 2 years ago

see the text file Avonet_traits.txt There are columns Sequence Avibase.ID1 - do these help you get the phylogeny

I had to change some of the bird names to match the original data - see the avonet section in the format_traits.R script

Note: the abundance data distinguished the hooded and common crow but the trait data did not -so I just doubled it.

coreytcallaghan commented 2 years ago

just pushed a bunch of stuff.

here is the rundown.

"corey_script.R" does the following:

taxonomy matching again, matching with Species3 from AVONET (the Tip Label from Jetz phylogeny).
trims phylogenetic tree (big .tre is .gitignored) and builds a consensus tree
saved consensus tree as "consensus_tree.RDS"
saved out the traits matched as I needed them in the color script
Also fits an example phylogenetic model using the variable "Total.individuals" in the AVONET dataset

"calculate_color_distance.R" does the following:

reads in color data
filters to danish birds (N=71 species)
gets color distance from brown and brightness with a bunch of steps in between
I don't like the final version, so we might want to look through some of these and decide together best 'approach'. But all the parts are there in the R script already.