geiger (version 2.0.11)

r8s.phylo: call r8s from geiger

Description

call r8s, including a calibration file

Usage

r8s.phylo(phy, calibrations=NULL, base="r8srun", ez.run="none", rm=TRUE,
  blformat=c(lengths="persite", nsites=10000, ultrametric="no", round="yes"),
  divtime=c(method="NPRS", algorithm="POWELL"),
  cv=c(cvStart=0, cvInc=0.5, cvNum=8), do.cv=FALSE)

Arguments

phy

a phylogram to turn into a chronogram

calibrations

a set of calibrations

base

file name

ez.run

if set to "PL" or "NPRS", does the analysis with settings appropriate for each

rm

remove the output files

blformat

blformat options for r8s. Pay special attention to nsites.

divtime

divtime options for r8s

cv

cv options for r8s

do.cv

Boolean for whether to do cross validation or not

Author

JM Eastman & B O'Meara

Details

This function uses r8s and a calibration to make your tree ultrametric

References

SANDERSON r8s ____NEED TO ADD_____

Examples

if (FALSE) {
phy <- read.tree(text=paste0("(Marchantia:0.033817,",
  "(Lycopodium:0.040281,((Equisetum:0.048533",
  "Osmunda:0.033640,Asplenium:0.036526):0.000425):",
  "0.011806,((((Cycas:0.009460,Zamia:0.018847):",
  "0.005021,Ginkgo:0.014702):1.687e-86,((Pinus:",
  "0.021500,(Podocarpac:0.015649,Taxus:0.021081):",
  "0.006473):0.002448,(Ephedra:0.029965,(Welwitsch",
  ":0.011298,Gnetum:0.014165):0.006883):0.016663)",
  ":0.006309):0.010855,((Nymphaea:0.016835,(((((Saururus:",
  "0.019902,Chloranth:0.020151):1.687e-86,",
  "((Araceae:0.020003,(Palmae:0.006005,Oryza:0.031555):",
  "0.002933):0.007654,Acorus:0.038488):0.007844)",
  ":1.777e-83,(Calycanth:0.013524,Lauraceae:0.035902):",
  "0.004656):1.687e-86,((Magnolia:0.015119,Drimys:",
  "0.010172):0.005117,(Ranunculus:0.029027,((Nelumbo:",
  "0.006180,Platanus:0.002347):0.003958,(Buxaceae:",
  "0.013294,((Pisum:0.035675,(Fagus:0.009848,Carya:",
  "0.008236):0.001459):0.001994,(Ericaceae:0.019136,",
  "Solanaceae:0.041396):0.002619):1.687e-86):0.004803)",
  ":1.687e-86):0.006457):0.002918):0.007348,",
  "Austrobail:0.019265):1.687e-86):1.687e-86,Amborella:",
  "0.019263):0.003527):0.021625):0.012469):",
  "0.019372);"))

	calibrations <- data.frame(MRCA="LP", MaxAge=450, MinAge=450,
		taxonA="marchantia", taxonB="pisum", stringsAsFactors=FALSE)

	phy.nprs <- r8s.phylo(phy=phy, calibrations=calibrations, base="nprs_file", ez.run="NPRS")
	phy.pl <- r8s.phylo(phy=phy, calibrations=calibrations, base="pl_file", ez.run="PL")
	}