-## mcmc.popsize.R (2004-12-02)
+## mcmc.popsize.R (2010-11-16)
## Run reversible jump MCMC to sample demographic histories
-## Copyright 2004 Rainer Opgen-Rhein and Korbinian Strimmer
+## Copyright 2004-2010 Rainer Opgen-Rhein and Korbinian Strimmer
## Portions of this function are adapted from rjMCMC code by
-## Karl Broman (see http://www.biostat.jhsph.edu/~kbroman/)
+## Karl W Broman (see http://www.biostat.wisc.edu/~kbroman/)
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
#BEGIN CALCULATION
- for(i in (1:nstep + 1)) {
-
- #progress bar
- if(i %% 100 == 0){
- z<-i/nstep
- zt<-(i-100)/(nstep)
- polygon(c(zt,zt,z,z), c(1,0,0,1), col="black")
-
+ for(i in (1:nstep + 1))
+ {
+ #progress bar
+ if(progress.bar==TRUE)
+ {
+ if(i %% 100 == 0)
+ {
+ z<-i/nstep
+ zt<-(i-100)/(nstep)
+ polygon(c(zt,zt,z,z), c(1,0,0,1), col="black")
+ }
}
# calculate jump probabilities without given lamda
}
if (i %% thinning == 0& i>burn.in) {count.i<-count.i+1}
}
- dev.off()
+
+ if(progress.bar==TRUE) dev.off()
list(pos=save.pos,h=save.h,loglik=save.loglik,
steptype=save.steptype,accept=save.accept)