laser-package: LASER

In laser: Likelihood Analysis of Speciation/Extinction Rates from Phylogenies

Description

Maximum likelihood-based methods for analyzing lineage diversification rates

Details

Package:	laser
Type:	Package
Version:	2.4-0
Date:	2013-05-05
License:	GPL 2.0
LazyLoad:	yes

Author(s)

Dan Rabosky Klaus Schliep Maintainer: Dan Rabosky <[e-mail]>

Examples

	data(warblers)
	fitSPVAR(warblers)
	fitEXVAR(warblers)
	gamStat(warblers)
	mccrTest(CladeSize=50, NumberMissing=10, NumberOfReps=50, ObservedGamma=-2.1)

Example output

Loading required package: ape
Loading required package: geiger
$model
[1] "SPVAR"

$LH
[1] 14.31441

$aic
[1] -22.62882

$lam0
[1] 1.901438

$k
[1] 0.7466968

$mu0
[1] 0.04446222

$model
[1] "EXVAR"

$LH
[1] 3.514663

$aic
[1] -1.029326

$lam0
[1] 0.280729

$mu0
[1] 0.001

$z
[1] 0.001

------------------------------
Calculated gamma: -4.202036
pvalue: 1.322628e-05 
test: one-tailed; Ho: rates have not decreased over time 
*assumes complete taxon sampling.
$gamstat
[1] -4.202036

$pval
[1] 1.322628e-05

$test
[1] "one-tailed; Ho: rates have not decreased over time"

$null.gamma
 [1] -1.18341205 -0.18254078 -1.30132885  0.44898904 -1.26517780 -1.13140697
 [7] -0.70762659 -1.12033130  1.43763666  1.00937917 -0.17408049 -1.04261211
[13] -0.33608283 -0.93646385  0.20536109  0.87079298 -2.68380903 -0.28610121
[19] -0.46015737 -0.40191398 -0.35412094  0.72173962  0.53675528  0.02804166
[25] -0.62448506 -1.25440403 -1.53194951  1.06810721  0.20322437  0.82579553
[31]  0.54656398 -0.09458359 -2.06046163 -0.66429530 -1.62638966 -0.86676442
[37]  0.79356906 -0.14200828 -0.55961818  1.46376455 -0.90613534  0.93298942
[43]  0.43493270 -0.18322055 -0.04591010 -0.10128066  0.60288521 -0.72797326
[49] -0.99033672  0.49806677

$critical.value
[1] -1.583892

$p.value
[1] 0.03921569

laser documentation built on Jan. 15, 2017, 4:49 p.m.