search for: matzk

...ad 2 packages that have a function with the same name, how do I tell R to run one or the other? (Instead of having R automatically use the first- or last-loaded one, whichever it is. (Which is it, by the way.)) Cheers! Nick -- ==================================================== Nicholas J. Matzke Ph.D. Candidate, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Graduate Student Instructor, IB200B Principles of Phylogenetics: Ecology and Ev...

..." "d" "f" > exists("z") [1] TRUE > exists("z$a") [1] FALSE ======================= ...basically, I want something that returns TRUE if the $a exists in z... Thanks! Nick -- ==================================================== Nicholas J. Matzke Ph.D. Candidate, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Graduate Student Instructor, IB200B Principles of Phylogenetics: Ecology and Ev...

...ngle column so I can do e.g. hist and mean on it without writing my own function. There must be a simple function for this, but I'm stumped -- reshape, dim, etc. don't seem to do it... Help appreciated! Thanks!! Nick -- ==================================================== Nicholas J. Matzke Ph.D. Candidate, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Graduate Student Instructor, IB200A Principles of Phylogenetics: Systematics htt...

...orgot to store the output in a variable. Is there a hidden variable somewhere that stores the result, so that one doesn't have to re-run the analysis for an hour? E.g., x <- whatever_the_last_output_was Thanks! Nick -- ==================================================== Nicholas J. Matzke Ph.D. student, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Lab websites: http://ib.berkeley.edu/people/lab_detail.php?lab=54 http://fisher.be...

...get strings to display e.g. tab or newline characters as they should be displayed, rather than as e.g. \n or \t? e.g.: > x="\t" > x="\t" > x [1] "\t" > print(x) [1] "\t" -- ==================================================== Nicholas J. Matzke Ph.D. student, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Lab websites: http://ib.berkeley.edu/people/lab_detail.php?lab=54 http://fisher.be...

...scientific format, 0.3523e10, and another, 0.3523e-10, and a negative, -313.1" How could I get R to just give me a list of numerics containing the numbers therein? Thanks very much to the regexp wizards! Cheers, Nick -- ==================================================== Nicholas J. Matzke Ph.D. Candidate, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Graduate Student Instructor, IB200B Principles of Phylogenetics: Ecology and Ev...

...perhaps with some other command-line utility)? E.g., I have a map in postscript format with lots of features, but I just want to extract the coastline and it's coordinates. Any help very much appreciated! Cheers! Nick -- ==================================================== Nicholas J. Matzke Ph.D. Candidate, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Graduate Student Instructor, IB200B Principles of Phylogenetics: Ecology and Ev...

...oaded as a library before running. For some reason, just putting require(phangorn) into the sourced function doesn't do anything. This must be simple, but I can't figure it out! Any help appreciated... Cheers! Nick -- ==================================================== Nicholas J. Matzke Ph.D. Candidate, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Graduate Student Instructor, IB200B Principles of Phylogenetics: Ecology and Ev...

...filename0003 filename0004 filename0005 filename0006 filename0007 filename0008 filename0009 filename0010 filename0011 ...etc.. Basically I want to produce strings like "0010" without an elaborate hack. Thanks! Nick -- ==================================================== Nicholas J. Matzke Ph.D. Candidate, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Graduate Student Instructor, IB200A Principles of Phylogenetics: Systematics htt...

...(species stratigraphic ranges). Basically I want a scatterplot to plot x,y data points, except with vertical bars instead of points. I've tried hacking hist() but so far without luck. Any help greatly appreciated! Nick -- ==================================================== Nicholas J. Matzke Ph.D. Student, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Graduate Student Instructor, IB200A Principles of Phylogenetics: Systematics http:...

...124x124 output matrix that comes out with the rows & columns in alphabetical order, I want them in a pre-specified order I can get from the input file, but the above is an example of the conceptual issue) Thanks! Nick -- ==================================================== Nicholas J. Matzke Ph.D. student, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Lab websites: http://ib.berkeley.edu/people/lab_detail.php?lab=54 http://fisher.be...

...s message: Warning message: In gregion$name = "North America" : Coercing LHS to a list ...although it appears to work, I'd rather not have disturbing mysterious error messages (what's LHS?)... Cheers! Nick -- ==================================================== Nicholas J. Matzke Ph.D. Candidate, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Graduate Student Instructor, IB200A Principles of Phylogenetics: Systematics htt...

...} PS: I have to go through this rigamarole: expr = "y1 = x$c[1]" eval(parse(text=print(expr))) Because the following doesn't work, even though it seems like it should: expr = "y = x$c[2]" eval(expr) -- ==================================================== Nicholas J. Matzke Ph.D. Candidate, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Lab websites: http://ib.berkeley.edu/people/lab_detail.php?lab=54 http://fisher....

...ewraps after about 70 characters, this occurs even if I increase the window size. (I want to output some simple tables to screen for students in a computer lab course) I am running R2.9, i.e. R.app, in Mac OS X. Cheers! Nick -- ==================================================== Nicholas J. Matzke Ph.D. Candidate, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Lab websites: http://ib.berkeley.edu/people/lab_detail.php?lab=54 http://fisher....

...20790/r-script-determine-whether-the-script-is-run-in-the-gui-or-from-command-line Which says to use: interactive() ...but that doesn't work. Interactive R is fine (e.g. starting R from Mac Terminal), only R.app is not. -- ==================================================== Nicholas J. Matzke Ph.D. Candidate, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Graduate Student Instructor, IB200B Principles of Phylogenetics: Ecology and Ev...

...ile_location) system(cmd1) system(cmd2) ============ ...but if I do it this way, the sourcing of .bash_profile from the first system() call does not carry over to the 2nd system() call. Any help appreciated!! Cheers, Nick -- ==================================================== Nicholas J. Matzke Ph.D. student, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Lab websites: http://ib.berkeley.edu/people/lab_detail.php?lab=54 http://fisher.be...

..." there. Surely there must be a way to get R.app to synonymize these two keys? All that moving over to the number pad is driving me nuts. Thanks so much!! Apologies if it is something obvious which I missed!! Nick -- ==================================================== Nicholas J. Matzke Ph.D. Candidate, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Graduate Student Instructor, IB200A Principles of Phylogenetics: Systematics htt...

...l ...but it doesn't seem to specify where to find the file in which a property like this would be set: ======== <key>Enable line wrapping if TRUE</key> <string>YES</string> ======== Cheers! Nick -- ==================================================== Nicholas J. Matzke Ph.D. Candidate, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Graduate Student Instructor, IB200A Principles of Phylogenetics: Systematics htt...

...t to flip between them. However, Quartz seems to hold a maximum of about 15 plots, and then discards anything plotted before that. This is pretty annoying, does anyone know of way to change this default setting? Cheers, Nick -- ==================================================== Nicholas J. Matzke Ph.D. Candidate, Graduate Student Researcher Huelsenbeck Lab Center for Theoretical Evolutionary Genomics 4151 VLSB (Valley Life Sciences Building) Department of Integrative Biology University of California, Berkeley Graduate Student Instructor, IB200B Principles of Phylogenetics: Ecology and Ev...

..., "/Library/Frameworks/R.framework/Resources/library/", NULL, type='source', configure.args="--with-geos-config=/usr/local/bin/geos-config") library(rgeos) # (You may have to remove old .o and .so files from previous install attempts...) On 10/25/11 1:09 PM, Nick Matzke wrote: > Hi all, > > I have almost gotten rgeos to install, however I'm getting a > peculiar error about a (successfully installed) other > package, stringr: > > "Error : package 'stringr' does not have a name space" > > I have asked the r-sig-geo l...