Re: [R] Speed up R
Matthew Keller wrote: So Mike, let me ask you a question. If R runs out of RAM, does it begin to use virtual RAM, and hence begin to swap from the hard drive? If so, I could see how a faster hard drive would speed R up when you don't have enough RAM... Yes. Virtual memory management is done by any modern operating system. The slowdown will be extreme. (Therefore, a minimum of 2Gb is a good idea for serious crunching -- I'd recommend 3 or 4 if possible. Don't forget that any programming language may have two copies of some arrays in memory during certain operations.) But even when R itself is not using VM, any significant I/O load on a Windows CPU (when (S)ATA disks are used) slows down *at least* all other I/O, and it seems to me that it slows down other interrupt servicing (e.g., responding to mouse clicks) as well. Even if the latter is not strictly true, it may be that the mouse click requires paging something in, like the stupid animation that plays when files are copied. Aside: On a old PC, copying files from the command line was fine, but if I forgot did it from the Windows Explorer, the stupid animation swapped in from disk and the machine froze for ~30 seconds.) Windows Vista can take advantage of a new gizmo Intel has introducted with a 1 Gb solid-state disk cache. That might reduce such problems. Mike Mike Prager Southeast Fisheries Science Center, NOAA Beaufort, North Carolina USA __ R-help@stat.math.ethz.ch 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] TCL/TK and R documentation?
I am hoping something has changed since I last asked about this. Is there any good source of documentation, including examples, of using tcl/tk as a gui for R applications? __ R-help@stat.math.ethz.ch 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] Matrix dimnames
Daniel Gatti wrote: How does one assign names to the columns of a matrix so that the columns can be accesses using the '$' operator? It seem that x$c1 below should return column 1. x = matrix(1:4,2) dimnames(x) = list(c(r1, r2), c(c1, c2)) x c1 c2 r1 1 3 r2 2 4 x$c1 NULL x$c2 NULL Is this useful?-- x[,c1] r1 r2 1 2 I have only seen $ used with lists. A data frame is a kind of list, but a matrix isn't. From the R Reference Manual: The form [of indexing] using $ applies to recursive objects such as lists and pairlists. HTH Mike Prager Southeast Fisheries Science Center, NOAA Beaufort, North Carolina USA __ R-help@stat.math.ethz.ch 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] Saving a function
Matt,
patopatasfrias wrote:
Hey, I'm a real novice... how do I go about saving a function that I created
eg. If I created this function: Fun-function(x1,X2) {..}, how can I
store it so that the next time I use R I can load it and not have to type it
out again
If you search the list archives, you may find a solution to
this that I posted several months ago. It involves moving
one's own functions to a dedicated directory, saving them in
an R workspace in that directory, and then loading that
workspace in the .Rprofile file.
My method is a LOT simpler than making an R package but it is
more complex than saving the functions with dput or otherwise
in a file to be reloaded. Its advantage is that (like making
a package) it makes the functions available to you even when
you open R in a different directory.
HTH
Mike Prager
Southeast Fisheries Science Center, NOAA
Beaufort, North Carolina USA
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and provide commented, minimal, self-contained, reproducible code.
[R] Package development on Windows - latest guidance?
I would like to start building R packages under Windows XP. I have programming experience and a minimal but working knowlege of many Unix (-like) programming tools. The package functions (for now) will be from R source, not C or Fortran. I've installed Rtools, Perl, the MS hhc, and so on. I am setting up a command shell with the correct PATH for building packages. (The master Windows PATH points to different versions of make and grep that I prefer for my usual work.) Two questions: 1. GUIDANCE. Is the Peter Rossi document now the best place to look for detailed guidance? I have located it at http://www1.appstate.edu/~arnholta/Software/MakingPackagesUnderWindows.pdf The links to it on the R Project Website are no longer good. I am also reading at the latest version of Writing R Extensions. 2. LATEX. In Rossi's paper, fpTeX is recommended (I use VTeX in everyday work). However, fpTeX has been discontinued by the author. What is the best way to get an R-compatible TeX installation for this work? (or might I get VTeX working -- its command line is idiosyncratic but it can create PDF, DVI, or HTML directly from LaTeX source)? Mike Prager Southeast Fisheries Science Center, NOAA Beaufort, North Carolina USA __ R-help@stat.math.ethz.ch 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] Package development on Windows - latest guidance?
Thanks to Gabor G., Duncan M., and Hong O. for helpful replies. I've made some progress, but have two questions. Can anyone explain *how* R CMD searches for latex? I have provided a batch file (shell script) and and alias (I use a Windows command shell with aliasing) that each provide the proper VTeX command when latex is typed from the command line. The batch file in on my PATH, but R CMD check still fails when it searches for latex. Is there any way around this, or will I have to relent and install MikTeX solely for this purpose? Also, R CMD build makes a tarball. Can I simply ZIP the same material that's in the tarball to make a working Windows installable package? Mike Prager Southeast Fisheries Science Center, NOAA Beaufort, North Carolina USA __ R-help@stat.math.ethz.ch 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] Package development on Windows - latest guidance?
Thanks again to D. M. and G. G. for help. I have built a small package successfully, although latex is not working quite right. I might be able to get it working, but I'm unclear what the latex compiler is used for when building a package. Otherwise, I'll just install MikTeX and treat it as a black box. M Mike Prager Southeast Fisheries Science Center, NOAA Beaufort, North Carolina USA __ R-help@stat.math.ethz.ch 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] Command equivalent of rgui File, Save to File?
Duncan Murdoch wrote: On 9/11/2006 3:57 PM, Michael Prager wrote: R 2.3.1 on Windows XP Professional. I am writing some scripts to generate examples. The Rgui menu item File, Save to File is helpful. Is there perhaps an equivalent R function that can be incorporated into a script? I think sink() is the closest you can get: set R to write to a file before generating whatever output you want to save. The menu item writes out the GUI text buffer; the R core doesn't know what's in that buffer. Other front ends don't have a buffer at all. [...] Thanks, Duncan, for the helpful response. Unless I have overlooked something (quite possible), sink() saves only the output, not the input as well. I'll continue using the menu system -- which I am delighted to have. Mike Mike Prager Southeast Fisheries Science Center, NOAA Beaufort, North Carolina USA __ R-help@stat.math.ethz.ch 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] Command equivalent of rgui File, Save to File?
R 2.3.1 on Windows XP Professional. I am writing some scripts to generate examples. The Rgui menu item File, Save to File is helpful. Is there perhaps an equivalent R function that can be incorporated into a script? Mike Prager Southeast Fisheries Science Center, NOAA Beaufort, North Carolina USA __ R-help@stat.math.ethz.ch 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] Successive Graphs
[EMAIL PROTECTED] wrote: Hello! I have written an R script on a Windows platform where I calculate eight result matrices I plot using matplot. I would like to display the resulting plots successively, rather than simultaneously, and I was wondering if anyone could point me in the right direction as to how to do this. The graphs pop up in this manner by default when I run my script in S-PLUS, with tabs separating them so I can view each graph at my leisure. However when I run my script in R, each graph pops up only for a moment before it is replaced by the next until I am left with only the plot of the eighth matrix at the end of the script. Thanks in advance for your help! Others have pointed out the R plot history mechanism, which is very nice. A few additions. If you are re-running the script often and want to get rid of old windows, you can put near the top of your script graphics.off() You can open a graphics window -- with history enabled -- with windows(record=TRUE) Plot history is saved. If desired, you can clear the old history before making new plots with .SavedPlots - NULL Mike Prager Southeast Fisheries Science Center, NOAA Beaufort, North Carolina USA __ R-help@stat.math.ethz.ch 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] macro facility in R
Here is one user's perspective on this, with no pretense of being definitive. In the S (R) world, the expression computing on the language is used to encompass what I would call the tasks of macro programming. This involves uses of various S (R) expressions that convert between names of objects and the object themselves; pasting together expressions out of fixed and variable text; and executing them. I for one have been able to do everything I could do in the SAS macro language, but it has taken trial and error. To get started, you might consult section 3.5 of S Programming by Venables and Ripley. MHP John Sorkin wrote on 7/3/2006 7:39 AM: R 2.2 on windows XP I have a dataset with multiple columns. Some of the columns represent independent variables, some represent dependent variables. I would like to run the same analyses on a fixed set of independent variables, changing only the dependent variable, e.g. y1-y2=x1+x2+x3 y3-y4=x1+x2+x3 y5-y6=x1+x2+x3, etc. I know I can write a function to perform the analyses, however in order to make the analyses easy to do, I really need a macro scripting language that will allow preprocessing of the function and substitution of macro variables with parameters passed to the macro, i.e. I need someting akin to the macro facility in SAS. Is there a macro facility that I can use with R? I have tried help.search(macro) and did not have any success. Thanks, John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics Baltimore VA Medical Center GRECC, University of Maryland School of Medicine Claude D. Pepper OAIC, University of Maryland Clinical Nutrition Research Unit, and Baltimore VA Center Stroke of Excellence University of Maryland School of Medicine Division of Gerontology Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR) Baltimore, MD 21201-1524 410-605-7119 [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Michael H. Prager, Ph.D. Population Dynamics Team NOAA Center for Coastal Habitat and Fisheries Research NMFS Southeast Fisheries Science Center Beaufort, North Carolina 28516 USA http://shrimp.ccfhrb.noaa.gov/~mprager/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] warning messages
You might consider passing the output file name to the function as an argument. Matthew Bridgman wrote on 6/25/2006 10:49 AM: I want to put warning messages into some of my functions to remind myself to change the output file names each time I run them. Is there a way to do this that will allow me to respond to the warning message (i.e. continue function or cancel)? Thanks, Matt __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Michael H. Prager, Ph.D. Population Dynamics Team NOAA Center for Coastal Habitat and Fisheries Research NMFS Southeast Fisheries Science Center Beaufort, North Carolina 28516 USA http://shrimp.ccfhrb.noaa.gov/~mprager/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] how to make a series with decimal increment
Gavin Simpson wrote on 6/14/2006 12:44 PM:
On Tue, 2006-06-13 at 05:24 +, anil kumar rohilla wrote:
Hi List,
I am new to this Rsoftware, i want to make a sereis for example
which is having values like this, s- 0,0.1,0.2,0.3,0.4,1
[...]
Hi Anil,
see ?seq for the solution, which is:
s - seq(0, 1, by = 0.1)
for(i in s) {
print(i)
}
I don't know if R avoids this somehow, but in many languages, generated
noninteger sequences are sometimes one item shorter than expected,
because of rounding errors. For that reason, I would prefer to generate
an integer sequence and then form a noninteger one from it. For example:
s - (1:10) / 10
Another option in R would be using the argument length.out, as in
s = seq(from = 0.1, to = 1, length.out = 10)
...Mike
--
Michael H. Prager, Ph.D.
Population Dynamics Team
NOAA Center for Coastal Habitat and Fisheries Research
NMFS Southeast Fisheries Science Center
Beaufort, North Carolina 28516 USA
http://shrimp.ccfhrb.noaa.gov/~mprager/
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[R] Variable number of arguments to function
Dear R List,
I have used ... to pass a varying number of arguments to a function.
The function takes parts of specialized data objects (they happen to be
lists) and makes comparative graphs and analyses. The code shell looks
like this:
models.compare - function(...) {
## Get the data objects passed
models - list(...)
nmodels - length(models)
## Get names of models:
modelnames - as.character(substitute(c(...))[-1])
# much code omitted here #
}
Now I would like to pass a few named arguments to the function as well,
to control how it prints, plots, makes files. I am seeking advice on
the simplest way to do this (along with the varying number of data
arguments).
Mike
--
Michael H. Prager
Population Dynamics Team
NOAA Center for Coastal Habitat and Fisheries Research
Beaufort, North Carolina 28516 USA
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PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Contour plot overlayed with line plot
It seems you have figured out a solution; for another example, you could look here: http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=90 Mike Jonathan Greenberg wrote on 5/10/2006 7:46 PM: I apologize for what may be a newbie question: I have two sets of data, one is X,Y,Z data that I'd like to make a contour plot of (Z defining the contours), and a second set of X,Y data (Y as a function of X) which I would like made into a line plot OVERLAYED on the contour plot (X and Y from both plots are in the same units and will have overlapping values). Any suggestions on how to do this in R? Thanks! --j -- Michael H. Prager, Ph.D. Population Dynamics Team NOAA Center for Coastal Habitat and Fisheries Research NMFS Southeast Fisheries Science Center Beaufort, North Carolina 28516 USA http://shrimp.ccfhrb.noaa.gov/~mprager/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] GUI font size
Erin, I was able to set it larger by making the change manually in the Rconsole file. For details of Rgui (Windows) configuration, try ?Rconsole from the prompt. MHP Erin Hodgess wrote on 4/24/2006 6:44 PM: Dear R People: On the Edit menu, there is a GUI preference tab. On the Font option, the highest value is 18. Has anyone ever had the font size set larger than that will any success, please? Thanks, Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: [EMAIL PROTECTED] PS Windows, R 2-2-1 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Michael H. Prager, Ph.D. Population Dynamics Team NOAA Center for Coastal Habitat and Fisheries Research NMFS Southeast Fisheries Science Center Beaufort, North Carolina 28516 USA http://shrimp.ccfhrb.noaa.gov/~mprager/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] is there a formatted output in R? [User functions]
There is a slightly easier way to make your own functions available.
1. Set up a directory for your R configuration. I use d:\r\mhp. Copy
.Rprofile, Rconsole, Rdevga there.
2. Set up a Windows environment variable R_USER pointing to that
directory. For example: R_USER=d:\r\mhp
The point of the preceding is to set R to load the same .Rprofile each
time it starts.
3. Set up a separate directory for your own functions. I use
d:\r\mhp\mhpmisc.
4. Put your own functions in the directory from step 3. Open R there.
Source the functions. Save the workspace as .Rdata.
5. In your .Rprofile file, add a line like this:
attach(d:/R/MHP/MHPmisc/.RData)
Now your functions will be available from every instance of R you start
up. If you have many functions, I have written an R script that
searches the current directory for all of them, clears the workspace,
sources them all, and saves the workspace. Reply to me by email if you
want a copy.
I have been told by Gurus that my method is too complicated, but I find
it a lot simpler than creating a package.
...MHP
Michael wrote on 3/11/2006 1:33 PM:
Thank you for your reminder!
I think you don't have to tell me to read the document.
I have done that many times already.
My feeling after reading the creating package manual is that my god, this
job needs a Computer Science degree to do it. It is way too complicated.
There should be simpler ways.
Perhaps I don't need a package.
I just need to be able to call my clearscreen function from all of my
other scripts...
Where do I put my clearscreen function?
Is there a command similar to include in C++?
Is there a path management that I can call clearscreen function from
anywhere as long as its in path?
On 3/11/06, Gavin Simpson [EMAIL PROTECTED] wrote:
On Fri, 2006-03-10 at 22:50 -0800, Michael wrote:
Great! It worked! Thank you so much!
Now since it worked greatly, how can I put this function into my own
library
or package, so later on I can call this function from my other scripts?
Thanks a lot!
Michael,
Read the two manuals that cover writing functions and preparing
*packages* of code, which come with R or get them here:
http://cran.r-project.org/manuals.html
An Introduction to R and Writing R Extensions,
After reading and digesting, if you still have questions then post them
to the list. People here provide their time for free and it is not much
to expect posters to try to help themselves out first - especially as
the developers have gone to such great lengths to produce quality
documentation that explains all of this.
HTH
G
On 3/10/06, jim holtman [EMAIL PROTECTED] wrote:
The archives had the following in it:
[R] how to clear screen in R-console?
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*From*: Gabor Grothendieck
ggrothendieckggrothendieck?Subject=Re:%20[R]%20how%20to%20clear%20screen%20in%20R-console?
*Date*: Fri, 17 Feb 2006 12:36:51 -0500
Here is a version that uses rcom instead of RDCOMClient.
This has the advantage that rcom is on CRAN.
cls - function() {
require(rcom)
wsh - comCreateObject(Wscript.Shell)
comInvoke(wsh, SendKeys, \014)
invisible(wsh)
}
cls() # test
On 2/17/06, Gabor Grothendieck ggrothendieck at gmail.com wrote:
* Here is a translation of Norm Olsen's vbscript code into pure R. *
* This is intended for use with the Windows Rgui interface. *
On 3/10/06, Michael [EMAIL PROTECTED] wrote:
something like sprintf in C?
so I can do:
print(sprintf(the correct result is %3.4f\n, myresult));
---
Also, I am desperately looking for a clear console screen function
in
R...
thanks a lot!
[[alternative HTML version deleted]]
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PLEASE do read the posting guide!
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http://www.r-project.org/posting-guide.html
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390 (Cell)
+1 513 247 0281 (Home)
What the problem you are trying to solve?
[[alternative HTML version deleted]]
Re: [R] 2nd R console?
On Windows, I often have more than one R console (instance of Rgui.exe) open at the same time. Unless by mistake, each instance is open on a unique working directory. MHP mark garey wrote on 3/9/2006 8:05 PM: hello all, i'm forwarding this question for a colleague. Is it possible to open a 2nd R Console? regards, mark+ -- mark garey ucsf department of epidemiology and biostatistics division of biostatistics 185 berry street, suite 5700 san francisco, ca. 94107-1739 415.514.8147 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Michael H. Prager, Ph.D. Population Dynamics Team NOAA Center for Coastal Habitat and Fisheries Research NMFS Southeast Fisheries Science Center Beaufort, North Carolina 28516 USA http://shrimp.ccfhrb.noaa.gov/~mprager/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Optimal platform for R
[EMAIL PROTECTED] wrote on 3/9/2006 4:47 PM: I'm looking to buy a new desktop which will primarily be used for analyses of large datasets (100s of MB). I've seen postings from several years back re the 'optimal' platform for running R, but nothing more recently. Specifically, I want to know: 1) if I run R under Windows, does having a dual-processor machine help speed things up? And 2) is it still true that R performs about as well under Windows as Linux? Duncan Murdoch has already answered your questions about operating systems. I would like to add that if there is significant I/O in what you are doing, fast SCSI disks are a worthwhile investment. The speed increase over ATA or SATA disks has been, in my experience, quite noticeable. -- Michael H. Prager, Ph.D. Population Dynamics Team NOAA Center for Coastal Habitat and Fisheries Research NMFS Southeast Fisheries Science Center Beaufort, North Carolina 28516 USA http://shrimp.ccfhrb.noaa.gov/~mprager/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] R and Power Point
Erin, From an Rgui graphics window (windows() device), Ctrl-W will save the current graph to the clipboard as a metafile; Ctrl-C will save as a bitmap. In PPt, Ctrl-V will paste either into a blank spot on a slide. The metafile is a Windows vector spec that will be sharper and smaller. However, I have had trouble when viewing them on different PCs with different fonts installed. Bitmaps will get around that but have all the usual limitations of ... bitmaps. MHP Erin Hodgess wrote on 2/14/2006 1:46 AM: Dear R People: I'm using R in a time series class. This class is being broadcast live to 2 remote sites via closed circuit TV. My people at the remote sites are having a terrible time seeing the computer screen as it is broadcast(resolution issues). I have decided to put together Power Point slides for the teaching. I am currently saving the R screen as WMF files and inserting them into PowerPoint. While this works, it seems that there might be a simpler method. Does anyone have any suggestions for the Power Point, please? Thanks so much! R Version 2.2.1 Windows Sincerely, Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: [EMAIL PROTECTED] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Michael H. Prager, Ph.D. Population Dynamics Team NOAA Center for Coastal Habitat and Fisheries Research NMFS Southeast Fisheries Science Center Beaufort, North Carolina 28516 USA http://shrimp.ccfhrb.noaa.gov/~mprager/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Plotting contour filled.contour in one graph
Besides the answers you already have, you might look at my 4D graph example (with code) on the R Graphics Gallery: http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=90 I think it does exactly what you are asking, and therefore it might fit your needs with only slight code modification. Mike Prager Abd Rahman Kassim wrote on 2/12/2006 11:12 PM: Dear All, I have a question on overlaying a filled.contour (e.g. on soil properties data) and contour (by elevation) in one graph. Both have the same z matrix dimension. I'm able to overlay both graph, but the plots dimension did not overlap well on the same plots. How can I have both filled.contour and contour on the same graph? The commands that I have written are as follows: filled.contour(0:15,0:10,t(matrix(Total.C,nrow=11,ncol=16))) contour(0:15,0:10,as.matrix(elev),add=T) Thanks for anay assistance. Regards. Abd Rahman Kassim Forest Research Institute Malaysia Kepong 52109 Selangor, MALAYSIA * * [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Michael H. Prager, Ph.D. Population Dynamics Team NOAA Center for Coastal Habitat and Fisheries Research NMFS Southeast Fisheries Science Center Beaufort, North Carolina 28516 USA http://shrimp.ccfhrb.noaa.gov/~mprager/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Plotting contour filled.contour in one graph
GG Yes, gladly. It is an idealized example of the following data situation: There are two control or independent variables. They are represented here as x and y, on the horizontal and vertical axes respectively. There are two different responses or dependent variables plotted as different types of contours. The filled contours show response z. The heavy lines show response zz. Thus such a plot displays two different responses from a two-dimensional range of conditions. As an example, in fishery biology, x might be the age at which fish are first subject to capture, y might be the fishing mortality rate (intensity) applied, z might be the resulting yield per fish, and zz might be the resulting spawning per fish. There is usually a trade-off between yield and spawning potential, and such a graph (if done with real data) allows one to look at that trade-off. The OP seemed to be seeking a way of contouring two responses against two independent variables, and that's what this graph does. Is that clearer? Would the graph would be better if I used real data? MHP Gabor Grothendieck wrote on 2/12/2006 11:31 AM: Could you walk us through, in detail, what that graph is showing? On 2/12/06, Michael Prager [EMAIL PROTECTED] wrote: Besides the answers you already have, you might look at my 4D graph example (with code) on the R Graphics Gallery: http://addictedtor.free.fr/graphiques/RGraphGallery.php?graph=90 I think it does exactly what you are asking, and therefore it might fit your needs with only slight code modification. Mike Prager Abd Rahman Kassim wrote on 2/12/2006 11:12 PM: Dear All, I have a question on overlaying a filled.contour (e.g. on soil properties data) and contour (by elevation) in one graph. Both have the same z matrix dimension. I'm able to overlay both graph, but the plots dimension did not overlap well on the same plots. How can I have both filled.contour and contour on the same graph? The commands that I have written are as follows: filled.contour(0:15,0:10,t(matrix(Total.C,nrow=11,ncol=16))) contour(0:15,0:10,as.matrix(elev),add=T) Thanks for anay assistance. Regards. Abd Rahman Kassim Forest Research Institute Malaysia Kepong 52109 Selangor, MALAYSIA * * [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Michael H. Prager, Ph.D. Population Dynamics Team NOAA Center for Coastal Habitat and Fisheries Research NMFS Southeast Fisheries Science Center Beaufort, North Carolina 28516 USA http://shrimp.ccfhrb.noaa.gov/~mprager/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Michael H. Prager, Ph.D. Population Dynamics Team NOAA Center for Coastal Habitat and Fisheries Research NMFS Southeast Fisheries Science Center Beaufort, North Carolina 28516 USA http://shrimp.ccfhrb.noaa.gov/~mprager/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] A comment about R: (sort.data.frame)
Gabor Grothendieck wrote on 1/3/2006 2:37 PM: Looking at the first few queries, see how easy it is to take the top few in Stata whereas in R one would have a complex use of order. Its not hard in R to write a function that would make it just as easy but its not available off the top of one's head though RSiteSearch(sort.data.frame) will find one if one knew what to search for. Yes, R has a few peculiar gaps. As to sort.data.frame(), it should be added to R base, in my opinion. It is silly to make people download code for such a basic operation. MHP __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] copy contributed packages from R 2.2.0 to 2.2.1
When I asked this question, I got some good answers. Based on them, I
wrote a pair of functions to accomplish this. I have tested them in
exactly ONE installation, and they worked.
Of course these are not needed by R gurus, but I attach them (with many
more comment lines than actual source) for the use of anyone else who
would like to use them.
MHP
Helmut Kudrnovsky wrote on 12/23/2005 9:43 AM:
hi R-users,
a few days ago R 2.2.1 came out. on my win xp i'installed R 2.2.0. along the
time i've installed a lot of contributed packages. my internet-connection is
not very fast.
so my question: is it possible after installing R 2.2.1 to do copy/paste the
contributed packages from the C:\Programme\R221 to the C:\Programme\R2.2.1-
location in the files system?
or have i to download and install the packages new?
##
# Functions to (1) save names of installed package from an R
installation to#
# a file and (2) install the same packages on a new R
installation. #
##
# HOW TO MOVE PACKAGES FROM ONE R INSTALLATION TO
ANOTHER: #
# Put this file in your R working directory. Source it. Run
SaveMyPackages() #
# under the old installation. Save your workspace and exit. Open the
new #
# installation on the same directory. Run InstallMyPackages(). The
packages #
# will be installed. You may now rm(SaveMyPackages,InstallMyPackages)
if you #
# like. Also, you may delete the file pkg.list in the working
directory. #
##
# M. H. Prager
[EMAIL PROTECTED]#
# with much from posted code of U. Ligges, H. Nilsson, B. Ripley
#
# December,
2005#
##
SaveMyPackages - function(filename = pkg.list, savepkg = TRUE)
{ # Saves a character vector with names of non-default
# packages installed. Writes it to a dput ASCII file.
# --- Run this from old installation. ---
# Arguments:
# filename --Character, name of file to write.
# savepkg -- Logical, if TRUE save the file; if not, return
#the vector of package names instead.
foo - installed.packages()
foo - as.vector(foo[is.na(foo[, Priority]), 1])
if (savepkg) dput(foo, file = filename) else return(foo)
}
InstallMyPackages - function(x = dget(file = filename), filename =
pkg.list,
install = TRUE)
{ # Install or print list of packages .
# --- Run this from new installation. ---
# Arguments:
# x-- character, contains names of packages to
install; default is
# vector read from argument filename.
# filename-- character, name of file containing vector (in
dput format);
# default is pkg.list as in SaveMyPackages.
# install-- logical, should actual installation be done? If
not,
# the vector of package names in x is returned instead
# of being installed.
if (install) install.packages(x) else return(x)
}
##
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Re: [R] Writing a list to a file !
Here is a function I use to send lists to ASCII files.
list2ascii - function(x,file=paste(deparse(substitute(x)),.txt,sep=))
{
# MHP July 7, 2004
# R or S function to write an R list to an ASCII file.
# This can be used to create files for those who want to use
# a spreadsheet or other program on the data.
#
tmp.wid = getOption(width) # save current width
options(width=1) # increase output width
sink(file)# redirect output to file
print(x) # print the object
sink()# cancel redirection
options(width=tmp.wid)# restore linewidth
return(invisible(NULL)) # return (nothing) from function
}
I hope it's helpful.
To write it to a file that can be read by R, I would suggest using
dput instead.
Regards,
Mike Prager
A Ezhil wrote:
Hi All,
This may be trivial in R but I have been trying with
out any success. I have a list of 100 elements each
having a sub list of different length. I would like to
write the list to a ASCII file. I tried with
write.table(), after converting my list to a matrix.
Now it looks like
Robert c(90, 50, 30)
Johnc(91, 20, 25, 45)
How can I get rid off c(, ..)? In my file, I would
like to have
Robert 90, 50, 30
John91, 20, 25, 45
Thanks in advance.
Regards,
Ezhil
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[R] Tip: Working directory in titlebar
I hope others may find this useful. I use R in many different
directories. By adding the following line to the .Rprofile file:
utils:::setWindowTitle(paste(-,getwd()))
the titlebar of each R instance shows the directory from which it was
started. I have tested this with rterm.exe and rgui.exe under Windows
and with RECENT versions of R only.
-
For changing directories during a session, I use the following function,
a slight modification of Andy Liaw's cd() function that also changes the
titlebar:
cd - function(dir = tclvalue(tkchooseDirectory()), saveOld=NA,
loadNew=TRUE) {
# From Andy Liaw ... additions by MHP
# Change the working directory during an R session
#
# First check that the tcl-tk package is available:
stopifnot(require(tcltk))
# Print any error message from trying to load:
if (.Platform$OS.type==windows) flush.console() ## MHP
# Warn user if saving existing workspace was not chosen: (MHP)
if (is.na(saveOld)) {
tmp = tclvalue(tkmessageBox(message=Save current workspace image?,
type=yesnocancel,title=Changing directories,icon=question))
saveOld = switch(tmp, yes=TRUE, no=FALSE,
cancel=return(invisible(NULL)))
}
# Save old workspace:
if (saveOld) save.image(compress=TRUE)
# Change directory:
# Note: the need to evaluate dir on the next line causes the
tclvalue call
#in the function definition (first line) to take place now:
if (dir==) return(invisible(NULL)) # Fail gracefully if CANCEL
chosen from TK dialog (MHP)
setwd(dir)
# Remove all the data from the old working directory:
rm(list=ls(all=TRUE, envir=.GlobalEnv), envir=.GlobalEnv)
# Change the window title:
setWindowTitle(paste(-,dir))
# Load the new data:
if (loadNew) {
if (file.exists(.RData)) {
loaded - load(.RData, envir=.GlobalEnv)
return(invisible(loaded))
}
else {
cat(Warning: .RData not found in new directory\n)
return(invisible(FALSE))
}
}
}
-
Although both these bits of code have been used, they may have errors.
Comments and corrections welcome.
--
Michael H. Prager, Ph.D.
Population Dynamics Team
NOAA Center for Coastal Habitat and Fisheries Research
NMFS Southeast Fisheries Science Center
Beaufort, North Carolina 28516 USA
http://shrimp.ccfhrb.noaa.gov/~mprager/
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Re: [R] Calling R from fortran
Simon, An hour's worth of contour plots (12) should be able to be saved in far less than 1 Gb, depending on the detail desired. Here is one way to do your task. There are other, and probably better, ones. At each time step (5 mins), you could have the Fortran program write a data file and then write and execute a script file. The script file would call R as a batch process to make a contour graph and save it (as PNG perhaps), and then the script would delete the data file. You might want to have the generated script files omit the delete step once per hour, just in case the R step should fail when you are not around to observe the failure. I don't know if R can easily read Fortran unformatted (sometimes called binary) data, or how. That would speed up the Fortran I/O and possibly reduce file size. If you go with formatted output, consider limiting the number of decimal places you write to save disk space. In most applications, you won't need great precision for simply making graphs. Also, for writing large amounts of data, test various block sizes on the Fortran OPEN statement to get best I/O speed. Another possibility would be to use a Fortran library (like the free or inexpensive DISLIN) that can make the contour plots directly, without using R. ...Mike simon wrote on 7/12/2005 4:02 PM: Hi, The following may sound stupid so please forgive my stupidness. I have a question which I don't know how to name it so I have to start from the beginning. In an attempt to gain better understand how a photochemical air qaulity model works, I plotted hourly ozone concentration contour from the model's standard output to observe the changes in simulation. Because the model actually peroform simulation in time steps of 5 minutes, it will give a better resoultion if I can plot the ozone concentration with time resolution close to the model. However, if I modify the model to output data at every time step, it will be impossible for the computer to store this much information( the hourly standard output is close to 1gb). I was wondering if it is possible to modify fortran to call R or something, which can just plot a contour at every time step rather than put it as data. I am not sure about how to call this act. Also, if this is possible, will output of a contour give a smaller file size than data? Thanks in advance, simon -- Michael H. Prager, Ph.D. Population Dynamics Team NOAA Center for Coastal Habitat and Fisheries Research NMFS Southeast Fisheries Science Center Beaufort, North Carolina 28516 USA http://shrimp.ccfhrb.noaa.gov/~mprager/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] inserting R code in a latex document
Thibaut Jombart wrote: I'm trying to insert R source code (functions) in an appendix of a latex document. I guess the easiest way to do so is to use the package Sweaved (file : Sweaved.sty) I have had very good results with the LaTeX package listings. It is easy to use, and it does the job. -- Michael H. Prager, Ph.D. Population Dynamics Team NOAA Center for Coastal Habitat and Fisheries Research Beaufort, North Carolina 28516 USA __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Graphics file to disk
If you want to write directly to file, ?Devices will get you more information Guy Forrester wrote on 5/11/2005 7:08 PM: Dear All, I have some code that works in S-Plus for writing saving a graphics file to disk :- [...] -- Michael H. Prager, Ph.D. Population Dynamics Team NOAA Center for Coastal Habitat and Fisheries Research NMFS Southeast Fisheries Science Center Beaufort, North Carolina 28516 USA http://shrimp.ccfhrb.noaa.gov/~mprager/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Producing Editable Graphs for PowerPoint
Paul-- It is hard to fight the tide, even when it contains sewage, but (you probably agree) this is an idiotic requirement. Not only does this journal want to change your work (which journals do much too much), they also want you to help them use of low-class tools to do so. You could try asking the journal to tell you what changes they feel are needed promising to make them yourself. That's what I would do, but there's no guarantee it will succeed. An alternative would be to make EPS files from R and send them to them. The XP version (and presumably above) of MSPP can import and edit EPS files. If the journal doesn't like the *way* it edits them, well, what can you do? Maybe that will allow you to gently suggest that their requirement is all wet. We need somehow to restore the roles of authors and journals. Authors are supposed to write the stuff, and journals figure how to get it into print. Somewhere along the line, journals have taken on all the prerogatives of collaborators. It seems to me that is a conflict of interest. Good luck! Regards, ...Mike Paul Hewson wrote: Hello, (apologies, I'm not entirely sure whether this question is about R or my limitations with PowerPoint). I've submitted a paper (which has been accepted) but the journal now require me to submit graphs that are editable in PowerPoint. I would be grateful for suggestions as to how I should do this. The best route seems to be to copy-and-paste the figures from the windows() device as a metafile. However, on converting the graphs to an editable format and ungrouping them, it appears that every line, tickmark, dot and dash is treated as a separate entity by PowerPoint (for example even the horizontal and vertical parts of + are separated). Alternatively, reading in the files from a saved metafile is even more problematic: having used par(new = TRUE) I have a set of layered graphs and all but the last one dissapear once I open the graphic for editing. Is this normal for a figure editable by PowerPoint or am I doing something horribly wrong somewhere? Many thanks Paul -- Michael H. Prager, Ph.D. Population Dynamics Team NOAA Center for Coastal Habitat and Fisheries Research NMFS Southeast Fisheries Science Center Beaufort, North Carolina 28516 USA http://shrimp.ccfhrb.noaa.gov/~mprager/ __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
