[R] Ordination plot option missing from PCA dialog
Hello, I am trying to learn how to do PCA. I found a tutorial online, but what I'm seeing in my installation does not match what is in the tutorial. Specifically, if I select Statistics:Dimensional Analysis: Principal-components analysis, the dialog I am presented with does not include an option to create an ordination plot. My question is why not? Is this a problem with my data set, local computer configuration (I am having trouble with the rgl package), or something else? I have R-2.11.1 installed on SuSE SLES 10.1. thanks, Bill -- - William C. Nelson, PhD Research Asst Professor University of Southern California, College of Letters, Arts and Sciences, Department of Biological Sciences, Marine Environmental Biology Division, Wrigley Institute for Environmental Studies 310-510-4097 wcnel...@usc.edu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Ordination plot option missing from PCA dialog
Hi Bill, R does not have a standard menu-driven interface, but rather several contributed interfaces including Rcommander, RKward, Deducer, and others. In order or anyone on this list to help you we are going to need to know which one you're using... -Ista On Thu, Oct 21, 2010 at 6:46 PM, William C. Nelson wcnel...@usc.edu wrote: Hello, I am trying to learn how to do PCA. I found a tutorial online, but what I'm seeing in my installation does not match what is in the tutorial. Specifically, if I select Statistics:Dimensional Analysis: Principal-components analysis, the dialog I am presented with does not include an option to create an ordination plot. My question is why not? Is this a problem with my data set, local computer configuration (I am having trouble with the rgl package), or something else? I have R-2.11.1 installed on SuSE SLES 10.1. thanks, Bill -- - William C. Nelson, PhD Research Asst Professor University of Southern California, College of Letters, Arts and Sciences, Department of Biological Sciences, Marine Environmental Biology Division, Wrigley Institute for Environmental Studies 310-510-4097 wcnel...@usc.edu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Ista Zahn Graduate student University of Rochester Department of Clinical and Social Psychology http://yourpsyche.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Ordination plot option missing from PCA dialog
My apologies for the too-brief description of my problem. Let me start again. As I said before, I have R-2.11.1 installed on SLES 10.1. I have installed on top of that Rcmdr v 1.6.0 and many associated packages (the default suggestions during Rcmdr installation). Upon starting Rcmdr, I get the following in the parent R terminal: library(Rcmdr) Loading required package: tcltk Loading Tcl/Tk interface ... done Loading required package: car Loading required package: MASS Loading required package: nnet Loading required package: survival Loading required package: splines I also get a dialog box saying that rgl is missing and some functions may not be available (hrm...). If I request that rgl be installed, rgl is downloaded, appears to compile with no errors, but at the end I see: ** testing if installed package can be loaded Error : .onLoad failed in loadNamespace() for 'rgl', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared library '/data/packages/R-2.11.1/library/rgl/libs/rgl.so': libpng14.so.14: cannot open shared object file: No such file or directory ERROR: loading failed * removing â/data/packages/R-2.11.1/library/rglâ I would like to be able to create an ordination plot for a PCA. I found a tutorial ([1]R with Rcmdr BASIC INSTRUCTIONS); it seemed like a good place to start. Following along its section on PCA, I navigated to Statistics:Dimensional Analysis:Principal-components analysis, which brings up a dialog box. In the tutorial there is an image of the dialog box, and it shows an option to create an ordination plot, however in the dialog box that comes up on my installation, the Ordination Plot option is missing. Is my problem with rgl related to the missing option? Any other suggestions as to why the option is missing? Any ideas as to why rgl won't load? thanks, Bill -- - William C. Nelson, PhD Research Asst Professor University of Southern California, College of Letters, Arts and Sciences, Department of Biological Sciences, Marine Environmental Biology Division, Wrigley Institute for Environmental Studies 310-510-4097 [2]wcnel...@usc.edu References 1. http://www.mzandee.net/%7Ezandee/statistiek/R/Rmanual_paper.pdf 2. mailto:wcnel...@usc.edu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Ordination plot option missing from PCA dialog
Bill, this may be a long shot, but the error you report is extremely close to what you get on a Mac when trying to load rgl when X11 is missing. Bryan ** Bryan Hanson Professor of Chemistry Biochemistry DePauw University 602 S. College Avenue Greencastle, IN 46135 PHONE 765-658-4602 FAX 765-658-6084 han...@depauw.edu academic.depauw.edu/~hanson/deadpezsociety.html www.depauw.edu/acad/chemistry/ academic.depauw.edu/~hanson/UMP/index.html On 10/22/10 12:59 PM, William C. Nelson, PhD wcnel...@usc.edu wrote: My apologies for the too-brief description of my problem. Let me start again. As I said before, I have R-2.11.1 installed on SLES 10.1. I have installed on top of that Rcmdr v 1.6.0 and many associated packages (the default suggestions during Rcmdr installation). Upon starting Rcmdr, I get the following in the parent R terminal: library(Rcmdr) Loading required package: tcltk Loading Tcl/Tk interface ... done Loading required package: car Loading required package: MASS Loading required package: nnet Loading required package: survival Loading required package: splines I also get a dialog box saying that rgl is missing and some functions may not be available (hrm...). If I request that rgl be installed, rgl is downloaded, appears to compile with no errors, but at the end I see: ** testing if installed package can be loaded Error : .onLoad failed in loadNamespace() for 'rgl', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared library '/data/packages/R-2.11.1/library/rgl/libs/rgl.so': libpng14.so.14: cannot open shared object file: No such file or directory ERROR: loading failed * removing â/data/packages/R-2.11.1/library/rglâ I would like to be able to create an ordination plot for a PCA. I found a tutorial ([1]R with Rcmdr BASIC INSTRUCTIONS); it seemed like a good place to start. Following along its section on PCA, I navigated to Statistics:Dimensional Analysis:Principal-components analysis, which brings up a dialog box. In the tutorial there is an image of the dialog box, and it shows an option to create an ordination plot, however in the dialog box that comes up on my installation, the Ordination Plot option is missing. Is my problem with rgl related to the missing option? Any other suggestions as to why the option is missing? Any ideas as to why rgl won't load? thanks, Bill -- - William C. Nelson, PhD Research Asst Professor University of Southern California, College of Letters, Arts and Sciences, Department of Biological Sciences, Marine Environmental Biology Division, Wrigley Institute for Environmental Studies 310-510-4097 [2]wcnel...@usc.edu References 1. http://www.mzandee.net/%7Ezandee/statistiek/R/Rmanual_paper.pdf 2. mailto:wcnel...@usc.edu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
