r8s.phylo: call r8s from geiger

Description Usage Arguments Details Author(s) References Examples

View source: R/congruify.R

Description

call r8s, including a calibration file

Usage

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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

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## 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)

geiger documentation built on July 8, 2020, 7:12 p.m.