r8s.phylo: call r8s from geiger

In mwpennell/geiger-v2: Analysis of Evolutionary Diversification

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

Details

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

Author(s)

JM Eastman & B O'Meara

References

SANDERSON r8s ____NEED TO ADD_____

Examples

## Not run: 
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")
	
## End(Not run)

mwpennell/geiger-v2 documentation built on Feb. 26, 2023, 1:19 a.m.