Hi all- Thanks for calling these issues to my attention. An updated version of laser should be on cran within the next few days (I just uploaded the package).
Many thanks in particular to Klaus Schliep for fixing a number of dependency issues and for improving several of the functions. Klaus, I apologize for missing your original email that included your fixes (I was in the field without email for an extended period of time earlier this year and missed a number of messages that arrived during that time). A comprehensive revision of the package is underway, but the version I just uploaded largely maintains the functionality of the package as it existed before being kicked off of CRAN a few months ago. ~Dan Rabosky On Sep 4, 2013, at 6:20 AM, Emmanuel Paradis wrote: > Hi Mariana, > > You may try the function bd.time in ape. The companion paper gives examples > similar to what laser does. > > Best, > > Emmanuel > -----Original Message----- > From: Mariana Vasconcellos <marian...@utexas.edu> > Sender: r-sig-phylo-boun...@r-project.org > Date: Tue, 3 Sep 2013 23:20:17 > To: Liam J. Revell<liam.rev...@umb.edu> > Cc: <r-sig-phylo@r-project.org> > Subject: Re: [R-sig-phylo] Substitute for functions on the laser package > > Thanks, Liam! But, unfortunately I don't know how to build from source. I > downloaded Xcode and the laser_2.3.tar.gz. But, I have no idea of how to > install from source. If someone could help with any advise, that would be > great! Also, does anyone have another option to calculate decreasing > speciation rate, increasing extinction rate or both using a different package? > > Thank you very much! > > ---------------------- > Mariana Vasconcellos > Ecology, Evolution & Behavior > Integrative Biology > The University of Texas at Austin > > > > > On Sep 3, 2013, at 10:05 PM, Liam J. Revell <liam.rev...@umb.edu> wrote: > >> Hi Mariana. >> >> You can download old versions of laser from the CRAN archive >> (http://cran.r-project.org/src/contrib/Archive/laser/); however you will >> have to build from source. This is easy if you have Xcode (for Mac OS) or a >> gcc compiler installed. If you do not, and cannot figure out how to install >> from source, then respond to the list & I'm sure someone will help out & >> post a package binary for you. >> >> - Liam >> >> Liam J. Revell, Assistant Professor of Biology >> University of Massachusetts Boston >> web: http://faculty.umb.edu/liam.revell/ >> email: liam.rev...@umb.edu >> blog: http://blog.phytools.org >> >> On 9/3/2013 10:39 PM, Mariana Vasconcellos wrote: >>> Dear all: >>> I just performed a test of the gamma-statistic on my tree and I found that >>> diversification is not constant in time. So, I would like to perform the >>> function fitSPVAR, fitEXVAR and fitBOTHVAR using the laser package. But, I >>> just saw that the laser package was removed from the CRAN repository. Could >>> anyone tell me what other alternative package I could use to develop and >>> test models of decreasing speciation rate, increasing extinction rate or >>> both? Does MEDUSA do this sort of analyses? >>> >>> Thank you for your help! >>> Mariana >>> >>> >>> >>> >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> R-sig-phylo mailing list - R-sig-phylo@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo >>> Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ >>> > > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ > _______________________________________________ > R-sig-phylo mailing list - R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/ _____________________ Dan Rabosky Assistant Professor & Curator of Herpetology Museum of Zoology & Department of Ecology and Evolutionary Biology University of Michigan Ann Arbor, MI 48109-1079 USA drabo...@umich.edu http://www-personal.umich.edu/~drabosky http://www.lsa.umich.edu/ummz/ [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
