/working/auteur/R/calibrate.jumpsize.R

http://github.com/eastman/auteur · R · 13 lines · 9 code · 2 blank · 2 comment · 4 complexity · aedd07fd0b4331e238e7f98b0bb9ecef MD5 · raw file 

    

  1. #rjmcmc utility for initiating a proposal width for Markov sampling
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  2. #author: JM EASTMAN 2010
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  4. calibrate.jumpsize <-
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  5. function(phy, dat, nsteps=100, jumpsizes=NULL) {
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  6. 	if(!withinrange(nsteps, 100, 1000)) {
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  7. 		if(nsteps>1000) nsteps=1000 else nsteps=100
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  8. 	}
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  9. 	if(is.null(jumpsizes)) jumpsizes=2^(-2:3)
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  10. 	acceptance.rates=sapply(jumpsizes, function(x) rjmcmc.bm(phy=phy, dat=dat, ngen=nsteps, jumpsize=x, summary=FALSE, fileBase="jumpsize", internal.only=FALSE)$acceptance.rate)
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  11. 	return(sum(jumpsizes*(acceptance.rates/sum(acceptance.rates))))
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  12. }
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