Hi Matt, all,
The other machine is also linux, but 64 bit. I've also tested it on a third linux machine, which is running R-2.10 instead of R2.13, (but is 64 bit), and it works fine there too. Only on my 32 bit linux have I observed the error. I don't seem to have another 32 bit machine lying around though. Not sure why that should matter, but it's the only clear difference I can see. should have mentioned that the problem occurs (drops all tips) even when death rate is 0, in both geiger and TreeSim. playing with tolerance on prune.extinct.taxa doesn't seem to prevent this either. Here's it's sessionInfo() > sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] geiger_1.3-1 ouch_2.7-1 subplex_1.1-3 msm_0.9.5 mvtnorm_0.9-8 [6] MASS_7.3-7 ape_2.7-1 socialR_0.0-1 loaded via a namespace (and not attached): [1] gee_4.13-16 grid_2.13.0 lattice_0.19-26 nlme_3.1-101 [5] splines_2.13.0 survival_2.36-9 tools_2.13.0 > On Wed, May 18, 2011 at 9:00 AM, Matthew Vavrek <matt...@matthewvavrek.com>wrote: > Carl, > was the other machine this was working on a Linux box? I just ran into this > exact problem two days ago, and it seems to have something to do with the > tolerance level in Linux, as it came up in a course and I was surrounded by > non-Linux computers that seemed to have no problem with the same code. > Setting the tolerance worked when I was doing it, but for some reason it > doesn't with your code. It could be something to do with differing > birth/death rates from my simulation? > > Luke Harmon knows about this bug too, as he was teaching the course, so we > may see some sort of fix at some point. It does seem to be a Linux specific > problem though, and I'm not sure what's going on. > > Cheers > Matthew > > > > > On 11-05-18 09:42 AM, Carl Boettiger wrote: > >> Hi List, >> >> On one of my computers I get anomalous results from various birth-death >> simulations, which behave fine on my other machine. I'm quite puzzled. >> >> For instance, running the example code in geiger's birthdeath.tree and >> then >> pruning extinct taxa drops all the taxa every time, (does not happen on >> machine2) >> >> p2<-birthdeath.tree(b=0.2, d=0.05, time.stop=20, >>> >> return.all.extinct=FALSE) >> >>> plot(p2) >>> # Previous tree with extinct taxa removed >>> prune.extinct.taxa(p2)->p3 >>> p3 >>> >> NULL >> >> >> I get a similar problem when running the equivalent command in TreeSim: >> >> >> age<-2 >>> lambda<- 2.0 >>> mu<- 0.5 >>> frac<-0.6 >>> numbsim<-3 >>> >> >> sim.bd.age(age,numbsim,lambda,mu,frac,mrca=FALSE,complete=FALSE) >>> >> [[1]] >> [1] 0 >> >> [[2]] >> [1] 0 >> >> [[3]] >> [1] 0 >> >> >>> >> I get no error messages to indicate something is wrong with the >> simulations, >> and the output trees (i.e. p2, above), look normal, etc. My guess is >> these >> two errors are related, and hence points to the treatment of phylo object >> from ape, but I can't be sure. Another error that occurs only on the >> problem machine is in the last example in the help file of sim.bd.taxa. >> >> >>> sim.bd.taxa(n=3,numbsim,lambda,mu,frac,complete=FALSE,stochsampling=FALSE) >> Error in drop.tip(temp, droptips) : object "phy" is not of class "phylo" >> >> Here's the output of sessionInfo() on the problem machine. Any >> suggestions >> for tracking down the cause of this? >> >>> sessionInfo() >>> >> R version 2.13.0 (2011-04-13) >> Platform: i486-pc-linux-gnu (32-bit) >> >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices datasets utils methods base >> >> other attached packages: >> [1] TreeSim_1.3 geiger_1.3-1 ouch_2.7-1 subplex_1.1-3 >> [5] msm_1.0 mvtnorm_0.9-999 MASS_7.3-13 ape_2.7-1 >> >> loaded via a namespace (and not attached): >> [1] gee_4.13-16 grid_2.13.0 lattice_0.19-26 nlme_3.1-101 >> [5] splines_2.13.0 survival_2.36-9 tools_2.13.0 >> >>> >>> >> >> >> >> >> >> >> >> > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > -- Carl Boettiger UC Davis http://www.carlboettiger.info/ [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
