rase-package: Range Ancestral State Estimation

In ignacioq/rase: Range Ancestral State Estimation for Phylogeography and Comparative Analyses

Description

The rase package primarily implements the Range Ancestral State Estimation for phylogeography described in Quintero, I., Keil, P., Jetz, W., Crawford, F. W. 2015 Historical Biogeography Using Species Geographical Ranges. Systematic Biology. doi: 10.1093/sysbio/syv057. It also includes Bayesian inference of ancestral states under a Brownian Motion model of character evolution and Maximum Likelihood estimation of rase for n-dimensional data. Visualizing functions in 3D are implemented using the rgl package.

Details

Package:	rase
Type:	Package
Version:	0.3-2
Date:	2017-03-21
License:	GLP (>=2)

Author(s)

Ignacio Quintero, Forrest Crawford, Petr Keil

Maintainer: Ignacio Quintero <[e-mail]>

References

Quintero, I., Keil, P., Jetz, W., Crawford, F. W. 2015 Historical Biogeography Using Species Geographical Ranges. Systematic Biology.doi: 10.1093/sysbio/syv057

Examples

  # Here the application in the paper of Quintero et al.,
  # on the Psophia trumpeters 
  # is shown using rase package.
  	
  #load data
  data(rase_data, package = 'rase')  
  	
  ## Not run: 
    # check the data we are going to use
    # the phylogenetic tree
    psophia_tree
    	
    # the GPC polygons of Psophia distribution.
    psophia_poly

    # Species names of polygons (in order)
    pnames <- c('dextralis', 'viridis', 'leucoptera', 'interjecta', 
      'obscura', 'crepitans', 'ochroptera', 'napensis')

    # name the polygons
    psophia_poly <- name.poly(psophia_poly, psophia_tree, 
      poly.names = pnames)

    # Run rase for 10 iterations
    rase_results <- rase(psophia_tree, psophia_poly, niter = 100)
    # Run with higher number of iterations
    # rase_results <- rase(psophia_tree, polygons)
     # Use the amazing 'coda' package to explore the MCMC
    require(coda)

    # post-MCMC handling
    rasemcmc <- coda::mcmc(rase_results)
      
    #plot the traces for all the parameters 
    plot(rasemcmc)
  
## End(Not run)

ignacioq/rase documentation built on Feb. 20, 2022, 3:16 p.m.