# Amazilia Analysis:
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In this dataset submission, I include data necessary to replicate the Amazilia analysis.


## Description of the Data and file structure

I am including:
-Phylogenetic trees: 
18866_tree.newick
18866distribution_simulated.data
amazilia_phylo.nex
hum_phylo.nex
-Geographic information of extant species:
humm_distribution.csv
-R scripts to run the analysis
additional_tools.R #includes important functions
aics_depths.R #routine to calculate AIC
count_areas_present.R # routine to calculate how many areas a species is present 
EF_lemad_amaziliatree_FIGURE.R # this file will create a plot showing the Ancestral states
functions_divalike.R # we can use some functions of BioGeoBear with this file
maintoSimulateCrown.R # roturine to simulate phylogenetic trees and geographic distributions
plot_simulated_data.R # script to make figures of the data
run.R # sets the lemad analysis for different rates of species extinction
Simul_CLAsecsse.R # this includes the main function for simulations
six.R # simular to run.R but with some additional options
some_tools.R #this file has a number of necessary functions to process lemad output
divalike_amazilia.RDS # in case you dont want to run the lemad routine, this file contains the output of it


## Sharing/access Information
Data is not shared elsewhere. However, it is important to know that the LEMAD package is available at:
https://github.com/leonelhalsina/lemad

And we have prepared a wiki page with additional information:
https://github.com/leonelhalsina/lemad/wiki

Was data derived from another source?
Data was provided by one of the authors (Ornelas, F) of this publication