rase-package: Range Ancestral State Estimation

In 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)

Example output

Loading required package: ape
Loading required package: polyCub
Loading required package: spatstat
Loading required package: spatstat.data
Loading required package: nlme
Loading required package: rpart

spatstat 1.64-1       (nickname: ‘Help you I can, yes!’) 
For an introduction to spatstat, type ‘beginner’ 


Note: spatstat version 1.64-1 is out of date by more than 11 months; we recommend upgrading to the latest version.

Attaching package: ‘spatstat’

The following objects are masked from ‘package:ape’:

    edges, rotate

Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'. 
3: no DISPLAY variable so Tk is not available 

Phylogenetic tree with 8 tips and 7 internal nodes.

Tip labels:
  crepitans, ochroptera, napensis, interjecta, dextralis, obscura, ...

Rooted; includes branch lengths.
[[1]]
window: polygonal boundary
enclosing rectangle: [-58.54078, -51.71649] x [-11.924656, -1.559724] units

[[2]]
window: polygonal boundary
enclosing rectangle: [-65.40391, -54.85738] x [-13.258487, -2.225402] units

[[3]]
window: polygonal boundary
enclosing rectangle: [-77.70858, -58.197] x [-17.952688, -2.541395] units

[[4]]
window: polygonal boundary
enclosing rectangle: [-53.60102, -47.93829] x [-14.303673, -0.997727] units

[[5]]
window: polygonal boundary
enclosing rectangle: [-49.6515, -44.28343] x [-5.794721, -0.636049] units

[[6]]
window: polygonal boundary
enclosing rectangle: [-67.83677, -49.64817] x [-2.994571, 6.856398] units

[[7]]
window: polygonal boundary
enclosing rectangle: [-66.38054, -60.21097] x [-4.003335, -0.339092] units

[[8]]
window: polygonal boundary
enclosing rectangle: [-78.00182, -65.55248] x [-5.175934, 3.772616] units

Iteration sigma2x sigma2y
10 19.05881 2.610033 
20 34.57503 6.22391 
30 36.36247 3.662895 
40 34.10856 3.581334 
50 27.34076 3.354031 
60 27.34076 3.354031 
70 32.16536 4.003249 
80 28.96824 3.70687 
90 32.62004 4.086902 
100 30.65832 4.797053 
Loading required package: coda

rase documentation built on May 2, 2019, 12:46 p.m.