[R] R, Coda, and OpenBUGS
Hi All, I am trying to figure out how to use R-Coda with the output from OpenBugs. I have installed and loaded the packages BRugs and R2WinBUGS. I have successfully run a simple Bayes model in WinBUGS using R2WinBUGS' bugs and have used read.bugs to build the coda object. I can successfully switch to OpenBugs and run the same model and get the basic summary back. However, I cannot build the coda object. From what I have read read.openbugs should do the trick. However, I have discovered the current version of OpenBUGS (v 3.03) doesn't write any output files in spite of setting codaPkg=TRUE in the bugs call. Str(openbugs.object) reveals a large collection of elements, one of which is an array that contains the MCMC chains. Is there a function to build the coda object? Thanks in advance for any suggestions, Bill Halteman __ 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] rpois formula
Hi all, It's been a while since i've used R and I can't remember how to do the following: i have a = rpois (10, x) b = rpois (10, y) what is the code to show that ab, ba and a=b to show just the number of occurances? at the moment when I type ab I get a nice long list of true or false. so i'm hoping to have the following ab 35000 ba 25000 a=b 4 thanks in advance -- View this message in context: http://www.nabble.com/rpois-formula-tp25774389p25774389.html Sent from the R help mailing list archive at Nabble.com. __ 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] power?
Hi, I have used multiple linear regression on a data set and one if the regressor was significant with a p-value =0.01 I need to calculate the power for a multiple linear regression. i.e. do I have enough power to believe the above p-value? -- View this message in context: http://www.nabble.com/power--tp25776305p25776305.html Sent from the R help mailing list archive at Nabble.com. __ 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] power?
The short answer is Yes. If you reject the null hypothesis based on that p-value, then by definition you had enough power to do that. This is because there is a precise inverse relationship between the p-value and the observed power, once you fix the effect size and the sample size. In other words, your post-hoc power analysis would be a simple re-statement of the p-value. There is no extra information that can be gained from such an analysis. See: The American Statistician, February 2001, Vol. 55, No. 1, pp 19-24 Don't bother with your power analysis, unless you are planning a new experiment. Simon. On Tue, 2009-10-06 at 13:49 -0700, SNN wrote: Hi, I have used multiple linear regression on a data set and one if the regressor was significant with a p-value =0.01 I need to calculate the power for a multiple linear regression. i.e. do I have enough power to believe the above p-value? -- Simon Blomberg, BSc (Hons), PhD, MAppStat. Lecturer and Consultant Statistician School of Biological Sciences The University of Queensland St. Lucia Queensland 4072 Australia Room 320 Goddard Building (8) T: +61 7 3365 2506 http://www.uq.edu.au/~uqsblomb email: S.Blomberg1_at_uq.edu.au Policies: 1. I will NOT analyse your data for you. 2. Your deadline is your problem. Statistics is the grammar of science - Karl Pearson __ 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] gnu ODBC driver for ORACLE in WinXP platform?
On Tue, 6 Oct 2009, Kenneth Roy Cabrera Torres wrote: Hi R users and Dr. Uwe Ligges: I read on the ROracle pre-compiled binary README file that: Hmm, that is from the CRAN README on Windows pre-compiled binary packages: there is no 'ROracle pre-compiled binary' (for Windows or Mac OS X) on CRAN. Although the package ROracle passes make check, it seems to be dangerous to distribute it: I do not have the software available this package depends on. Why it is dangerous to use ROracle for windows? What software does ROracle depends on in windows platform? Oracle (just like every other platform)! I believe the statement is out-of-date: ROracle seems not to build with current versions of R. But the main issues were (a) It needs to link against Oracle's client software, and that depends on the particular version of Oracle. Bitter experience suggests that you need to build such packages from the sources against the client software installed on your machine to get reliable service from them. (b) The package does no actual tests in its examples. It may appear to build but not work in practice, since nothing is tested in the build process. Is there a GNU solution for an ODBC driver on windows XP platform for ORACLE for use it with RODBC? What does GNU have to do with this? RODBC works with Oracle with Oracle's own Windows drivers, and a test suite for Oracle is in the sources. Now, that has been tested against only a couple of versions of Oracle, but ODBC is a well-documented API and Oracle's ODBC driver writers should always be complying with it. If perchance by 'GNU' you meant 'GPL' or 'Open Source' then - Oracle is proprietary, although there are 'free as in beer' versions. - the most open you can be is to communicate with it via an open API, and ODBC is such (and I think the only one supported by Oracle). Thank you for your help. It does seem churlish to be asking why the hard-working volunteers have *not* provided you with a binary version of a package, and such queries are more common than thanks for those that *are* provided (something like 20x as many). Kenneth -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ 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] RExcel
Hello- I am a Graduate Assistant for an instructor who has written programs for statistics calculations such as binomial distributions and regressions. The programs had worked with no problem in Excel 2003. Now we are trying to use it with Excel 2007, and we are having some trouble. I have downloaded RandFriends and have ran the binomial distribution process in 2007 Excel and have received an error that says: Compile error in hidden module: UFDBinomial However, ther are two demo excel files in the RExcel file called RdemoDens. When I open the first RDemoDens excel file, I can run the processes and they work fine. When I run the second RDemoDens excel file, or a blank excel 2007 file, the processes do not work and I get the error message. I am trying to figure out what is different about the first RDemoDens excel file that allows the calculations to process correctly. I am thinking that something in the macro library in the demo must be different than what is in a blank excel document. I just cannot seem to figure out what it is. One thing that I did notice is that there are two different RExcel files in the RExcel folder. One is labled RExcel and one is labed RExcel 2007. What are the difference between these two RExcel files? I am not sure if this has anything to do with the problem, but perhaps the excel demo in which our calculations work uses the correct RExcel file while a regular excel 2007 document does not call the correct one. If anyone has an idea about what might be happening here, or who else I could ask about the situation, I would appreciate any input. Thanks, Ben Ward [[alternative HTML version deleted]] __ 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] R-beta: adjusting y-axis scale with multiple lines in plot
__ 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] Saving tkrplot/Clearing contents on frames/tkProgressBar
1) How do i save tkrplots?do the Jpeg,png commands used for saving plots of RGui work for tkrplots? 2)How do I embed tkProgressBar onto a frame.I do not want that to appear in separate window? 3)Is it possible to insert a StatusBar at the bottom of the window.(My window has three frames)? 4)My window has three frames.There is a button 'RUN' on the first frame .when I run, a table and a plot are displayed in the second frame.I change some parameters and 'RUN' again..then the new table and plot get appended in the second frame.I do not want this to happen.I want the older results to be overwritten by the new results.How or which command do I use ? I am new to R and experimenting with RTcltk package.Please advise ! -- View this message in context: http://www.nabble.com/Saving-tkrplot-Clearing-contents-on-frames-tkProgressBar-tp25781456p25781456.html Sent from the R help mailing list archive at Nabble.com. __ 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] gnu ODBC driver for ORACLE in WinXP platform?
Prof Brian Ripley wrote: On Tue, 6 Oct 2009, Kenneth Roy Cabrera Torres wrote: Hi R users and Dr. Uwe Ligges: I read on the ROracle pre-compiled binary README file that: Hmm, that is from the CRAN README on Windows pre-compiled binary packages: there is no 'ROracle pre-compiled binary' (for Windows or Mac OS X) on CRAN. Although the package ROracle passes make check, it seems to be dangerous to distribute it: I do not have the software available this package depends on. Why it is dangerous to use ROracle for windows? What software does ROracle depends on in windows platform? Oracle (just like every other platform)! I believe the statement is out-of-date: ROracle seems not to build with current versions of R. But the main issues were Indeed, the statement is out of date. I haven't tried to build it for years now. Will change that part of the ReadMe. Thanks to Brian for the comprehensive answer. Best, Uwe Ligges (a) It needs to link against Oracle's client software, and that depends on the particular version of Oracle. Bitter experience suggests that you need to build such packages from the sources against the client software installed on your machine to get reliable service from them. (b) The package does no actual tests in its examples. It may appear to build but not work in practice, since nothing is tested in the build process. Is there a GNU solution for an ODBC driver on windows XP platform for ORACLE for use it with RODBC? What does GNU have to do with this? RODBC works with Oracle with Oracle's own Windows drivers, and a test suite for Oracle is in the sources. Now, that has been tested against only a couple of versions of Oracle, but ODBC is a well-documented API and Oracle's ODBC driver writers should always be complying with it. If perchance by 'GNU' you meant 'GPL' or 'Open Source' then - Oracle is proprietary, although there are 'free as in beer' versions. - the most open you can be is to communicate with it via an open API, and ODBC is such (and I think the only one supported by Oracle). Thank you for your help. It does seem churlish to be asking why the hard-working volunteers have *not* provided you with a binary version of a package, and such queries are more common than thanks for those that *are* provided (something like 20x as many). Kenneth __ 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] how to output profile plots for groups using lattice package
see below George Kalema wrote: Dear R users, I am trying to have an xyplot of a data set which has the following variables: case (n=10,20,30) parameter (parm=a,b) group (grp=g1,g2) y (y values) x (x=2,4,8) My plot should be parameter by case such that I have 2 rows (each row= each parameter) and 3 columns (each column=each case). My R-code is as follows but I am not able to get what I want to: tp1.sim - xyplot(y~ x | case + parm , group=group, data = data, lty = 1:4 , pch = 1:4) print(tp1.sim) How can I have two lines (for g1 and g2) in each plot (each box)? include the type=b argument How do I label the x-axis with only values 2, 4, 8? include the scales= argument or make x a factor How do I label each column with the corresponding case number? make 'case' a factor The following should do what you want: xyplot(y ~ x | factor(case) + parm, group=group, data=data, type='b', lty=1:2, pch=1:2, scales=list(x=list(at=c(2,4,8))) ) I don't understand why you want 4 line types/point chars. -Peter Ehlers My hypothetical data set is as follows: parm x case y group a 2 10 0.03 g1 b 2 10 0.02 g1 a 4 10 0.03 g1 b 4 10 0.02 g1 a 8 10 0.03 g1 b 8 10 0.02 g1 a 2 20 0.03 g1 b 2 20 0.02 g1 a 4 20 0.03 g1 b 4 20 0.02 g1 a 8 20 0.03 g1 b 8 20 0.02 g1 a 2 30 0.03 g1 b 2 30 0.02 g1 a 4 30 0.03 g1 b 4 30 0.02 g1 a 8 30 0.03 g1 b 8 30 0.02 g1 a 2 10 0.13 g2 b 2 10 0.12 g2 a 4 10 0.13 g2 b 4 10 0.12 g2 a 8 10 0.13 g2 b 8 10 0.12 g2 a 2 20 0.13 g2 b 2 20 0.12 g2 a 4 20 0.13 g2 b 4 20 0.12 g2 a 8 20 0.13 g2 b 8 20 0.12 g2 a 2 30 0.13 g2 b 2 30 0.12 g2 a 4 30 0.13 g2 b 4 30 0.12 g2 a 8 30 0.13 g2 b 8 30 0.12 g2 Many thanks in advance for your response. George [[alternative HTML version deleted]] __ 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.
Re: [R] Is there a recent book on Q-Q plot and data visualization in general?
Hi,
See page 335 for a qq plot in the third edition of the book.
cheers,
Paul
Peng Yu wrote:
Hi,
I checked the 3rd edition of this book. But I don't find Q-Q plot.
Would you please take a look of the table of content below and let me
know if the same section is available in the 3rd edition?
http://www.amazon.com/Plane-Answers-Complex-Questions-Theory/dp/0387953612/ref=sr_1_1?ie=UTF8s=booksqid=1254856526sr=8-1#reader
Regards,
Peng
On Tue, Oct 6, 2009 at 9:50 AM, Paul Hiemstra p.hiems...@geo.uu.nl wrote:
Hi Peng Yu,
Chapter 13 of the following book provides a good description of the
assumption done when using regression and other techniques. It also
discusses the QQplot.
@BOOK{Christensen1996,
title = {Plane Answers to Complex Questions: The Theory of Linear Models},
publisher = {Springer, New York},
year = {1996},
author = {Ronald Christensen},
edition = {Second},
note = {496p},
}
cheers,
Paul
Peng Yu wrote:
Hi,
I want to look for some detailed explanation on the properties of Q-Q
plot and how the properties are derived.
In R, there is the following reference.
Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) The New S
Language. Wadsworth Brooks/Cole.
Somebody also mentioned the following book chapter to me.
Chambers et al., Graphical methods for Data Analysis, Ch.6.
But both books are old. I'm wondering if there is any more recent
(therefore, maybe better) books for Q-Q plot, and data visualization
in general.
Regards,
Peng
__
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--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone: +3130 274 3113 Mon-Tue
Phone: +3130 253 5773 Wed-Fri
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and provide commented, minimal, self-contained, reproducible code.
--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone: +3130 274 3113 Mon-Tue
Phone: +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul
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Re: [R] plot an arrow / add arrow to a line
For nicer arrows, there are also the p.arrows() function in pkg:sfsmisc and the Arrows() function in pkg:IDPmisc. -Peter Ehlers Sarah Goslee wrote: How about arrows() ? On Tue, Oct 6, 2009 at 4:25 PM, Martin Batholdy batho...@googlemail.com wrote: hi, is it possible to end a line plotted with lines() with an arrow? Or are there any other functions to add an arrow to plot? thanks! __ 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] 'persp' query
Certainly, you will want to set zlab=. mtext() is quite flexible; you can control distance to the axis with line=1.5, say. But remember that mtext() is a 2-dim graphics function - it looks at your plot as a 2-d plot. That's why I made the comment about your z-axis having to be fairly close to vertical on the page. Try the first example in ?persp and follow the call with mtext(my z label, side=2). Because of the tilt of the z-axis, this looks a bit strange (to me). -Peter Ehlers Geoffrey William Heard wrote: Much thanks David and Peter I thought about mtext, but didn't try it, as was unsure what the appropriate 'side' value would be. Any thoughts? Cheers Geoff -Original Message- From: Peter Ehlers [mailto:ehl...@ucalgary.ca] Sent: Wednesday, 7 October 2009 1:43 AM To: David Winsemius Cc: Geoffrey William Heard; r-help@r-project.org Subject: Re: [R] 'persp' query David Winsemius wrote: On Oct 6, 2009, at 4:46 AM, Geoffrey William Heard wrote: Hi All I'm creating some 3-D plots using the function 'persp', and have a query regarding the ability to make changes to the label of the z-axis. There are two things I would like to do. First, the default setting places the label a little close to the axis for my liking. Is there any way of moving the label? I've tried adjustments with 'mgp' in 'par', but without success. The second is to change the direction of the label. Currently it reads top to bottom, whereas I would like it to read bottom to top, as per a y-axis on a standard plot. Is there anyway of doing so? ?mtext # and use the adj argument Good idea. This works well if your z-axis is fairly vertical on you plot. -Peter Ehlers __ 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] RExcel
Please post this kind of questions to the rcom mailing list. You can subscribe at rcom.univie.ac.at __ 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] Question about mirroring CRAN
Hi this might be the wrong mailing list, but it also does not fit the dev list. As we are planning to setup a mirror of CRAN, we would like to know the approximate size of the mirror and the necessary bandwidth requirements to keep it updated. Thanks a lot in advance, Rainer -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Cell: +27 - (0)83 9479 042 Fax:+27 - (0)86 516 2782 Fax:+49 - (0)721 151 334 888 email: rai...@krugs.de Skype: RMkrug Google: r.m.k...@gmail.com [[alternative HTML version deleted]] __ 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] two plots on the same axis
Good morning. I wish to plot two data on the same axis. I tried plot(x,y, type = l) for the first and tried to use lines or points(x,y, lty = 2, col = 4) to add or plot the second data on alongside the first. However, what I got was not encouraging. I have attached the two data and would be pleased if anybody could be of help. Thank you Best regards Ogbos 05 1 1 3974.8 05 1 2 3967.2 05 1 3 3817.7 05 1 4 3789.4 05 1 5 3803.6 05 1 6 3831.4 05 1 7 3878.6 05 1 8 3861.5 05 1 9 3850.4 05 1 10 3855.0 05 1 11 3900.9 05 1 12 3952.2 05 1 13 3954.7 05 1 14 3942.9 05 1 15 3955.0 05 1 16 3934.1 05 1 17 3859.2 05 1 18 3530.9 05 1 19 3299.9 05 1 20 3398.1 05 1 21 3305.5 05 1 22 3457.7 05 1 23 3753.8 05 1 24 3846.8 05 1 25 3896.9 05 1 26 3914.3 05 1 27 3917.9 05 1 28 3910.1 05 1 29 3938.0 05 1 30 3975.7 05 1 31 3945.0 05 2 1 3952.3 05 2 2 3948.1 05 2 3 3946.7 05 2 4 3957.1 05 2 5 3968.9 05 2 6 3990.2 05 2 7 3980.0 05 2 8 3965.8 05 2 9 3952.8 05 2 10 3942.0 05 2 11 3938.9 05 2 12 3967.6 05 2 13 3986.9 05 2 14 3992.8 05 2 15 3982.8 05 2 16 3986.3 05 2 17 3972.5 05 2 18 3951.4 05 2 19 3929.4 05 2 20 3928.5 05 2 21 3939.6 05 2 22 3951.5 05 2 23 3950.2 05 2 24 3956.3 05 2 25 3970.4 05 2 26 3981.4 05 2 27 3994.2 05 2 28 3988.9 05 3 1 3997.1 05 3 2 4003.9 05 3 3 4011.0 05 3 4 4017.0 05 3 5 4003.2 05 3 6 3993.1 05 3 7 3996.8 05 3 8 3999.1 05 3 9 3988.6 05 3 10 4002.2 05 3 11 3997.9 05 3 12 3981.5 05 3 13 3996.8 05 3 14 4026.5 05 3 15 4025.5 05 3 16 4021.8 05 3 17 4016.5 05 3 18 4011.7 05 3 19 3975.9 05 3 20 3981.0 05 3 21 3961.2 05 3 22 3965.2 05 3 23 3981.5 05 3 24 3996.4 05 3 25 3981.9 05 3 26 3979.0 05 3 27 3976.5 05 3 28 3973.7 05 3 29 3959.5 05 3 30 3974.0 05 3 31 3980.2 05 4 1 3972.3 05 4 2 3982.2 05 4 3 4008.9 05 4 4 4007.0 05 4 5 4009.1 05 4 6 3990.5 05 4 7 4002.5 05 4 8 4027.3 05 4 9 4047.8 05 4 10 4039.4 05 4 11 4025.0 05 4 12 4025.3 05 4 13 4006.2 05 4 14 4013.0 05 4 15 4018.7 05 4 16 4031.2 05 4 17 4037.3 05 4 18 4053.2 05 4 19 4065.3 05 4 20 4065.5 05 4 21 4042.3 05 4 22 4004.8 05 4 23 3974.9 05 4 24 3995.5 05 4 25 4007.9 05 4 26 4005.5 05 4 27 4019.7 05 4 28 4030.3 05 4 29 4045.4 05 4 30 4031.4 05 5 1 3995.6 05 5 2 3978.2 05 5 3 3993.3 05 5 4 4018.4 05 5 5 4027.6 05 5 6 4006.0 05 5 7 3985.5 05 5 8 3993.1 05 5 9 3817.5 05 5 10 3849.4 05 5 11 3880.4 05 5 12 3896.8 05 5 13 3911.0 05 5 14 3922.4 05 5 15 3703.7 05 5 16 3703.8 05 5 17 3783.5 05 5 18 3809.5 05 5 19 3805.4 05 5 20 3837.9 05 5 21 3876.8 05 5 22 3898.2 05 5 23 3925.6 05 5 24 3954.2 05 5 25 3980.9 05 5 26 4007.8 05 5 27 4033.5 05 5 28 4035.3 05 5 29 3957.9 05 5 30 3948.2 05 5 31 3958.8 05 6 1 3973.1 05 6 2 3984.0 05 6 3 4010.9 05 6 4 4027.2 05 6 5 4040.0 05 6 6 4049.8 05 6 7 4027.3 05 6 8 4023.0 05 6 9 4033.8 05 6 10 4051.4 05 6 11 4063.6 05 6 12 4023.0 05 6 13 3998.4 05 6 14 3996.8 05 6 15 3962.9 05 6 16 3922.2 05 6 17 3919.3 05 6 18 3953.7 05 6 19 3994.4 05 6 20 4004.1 05 6 21 3999.8 05 6 22 3981.9 05 6 23 4058.7 05 6 24 4030.6 05 6 25 3999.0 05 6 26 4012.5 05 6 27 4034.3 05 6 28 4044.1 05 6 29 4042.9 05 6 30 4050.3 05 7 1 4049.5 05 7 2 4042.0 05 7 3 4055.2 05 7 4 4059.7 05 7 5 4075.2 05 7 6 4087.6 05 7 7 4083.7 05 7 8 4071.0 05 7 9 4098.5 05 7 10 4024.6 05 7 11 3967.0 05 7 12 3957.2 05 7 13 3896.8 05 7 14 3913.0 05 7 15 3928.0 05 7 16 3888.0 05 7 17 3684.0 05 7 18 3713.6 05 7 19 3820.1 05 7 20 3915.7 05 7 21 4011.0 05 7 22 4004.8 05 7 23 4003.7 05 7 24 3993.1 05 8 2 3927.9 05 8 3 3916.7 05 8 4 3950.6 05 8 5 3936.2 05 8 6 3900.1 05 8 7 3814.6 05 8 8 3861.2 05 8 9 3913.0 05 8 10 3925.0 05 8 11 3907.4 05 8 12 3943.5 05 8 13 3934.6 05 8 14 3938.9 05 8 15 3952.2 05 8 16 3956.1 05 8 17 3976.6 05 8 18 3998.5 05 8 19 4009.5 05 8 20 4007.0 05 8 21 3994.8 05 8 22 4009.2 05 8 23 4042.2 05 8 24 3942.1 05 8 25 3842.2 05 8 26 3907.3 05 8 27 3954.9 05 8 28 3967.2 05 8 29 4014.9 05 8 30 4013.2 05 8 31 3999.4 05 9 1 4007.0 05 9 2 3988.5 05 9 3 3947.2 05 9 4 3946.2 05 9 5 3945.7 05 9 6 3956.0 05 9 7 3980.1 05 9 8 4003.5 05 9 9 3975.5 05 9 10 3903.8 05 9 11 3544.0 05 9 12 3509.6 05 9 13 3463.4 05 9 14 3533.4 05 9 15 3523.9 05 9 16 3567.0 05 9 17 3657.8 05 9 18 3763.7 05 9 19 3805.4 05 9 20 3848.3 05 9 21 3874.8 05 9 22 3901.1 05 9 23 3911.2 05 9 24 3946.8 05 9 25 3927.6 05 9 26 3938.6 05 9 27 3960.8 05 9 28 3961.2 05 9 29 3981.9 05 9 30 3991.5 05 10 1 3987.1 05 10 2 4003.5 05 10 3 4026.8 05 10 4 4044.3 05 10 5 4050.2 05 10 6 4062.4 05 10 7 4069.4 05 10 8 4049.9
[R] Second y-axis --- alternative to par(new=
Hi is there an alternative to par(new), for ading data to a plot for a different y-axis? My problem with par(new=TRUE) is, that it re-defines all axis and labels (as in example 1) and one has to use xlim=... to fix the x-axis. I am looking for something, which simply resets the y-axis, so that a new plot() (or points()/lines()) keeps the x-axis, but re-defines the y-axis. Is there something available? I could re-scale the y-data to fit the existing y-axis, but that would mean to define all the labels and tickmarks for axis 4 manually. HEre is an example about what I mean: x1 - 1:10 y1 - runif(10) x2 - 1:11 y2 - c(y1*100, 0) ## (1) Does not plot points where (x-axis) they should be plot(x1, y1, type=l) par(new=TRUE) plot(x2, y2, type=p) axis(4) ## (2) Does plot points where (x-axis) they should be xlim - range(x1) plot(x1, y1, type=l, xlim=xlim) par(new=TRUE) plot(x2, y2, type=p, xlim=xlim) axis(4) Cheers, Rainer -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Cell: +27 - (0)83 9479 042 Fax:+27 - (0)86 516 2782 Fax:+49 - (0)721 151 334 888 email: rai...@krugs.de Skype: RMkrug Google: r.m.k...@gmail.com [[alternative HTML version deleted]] __ 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] Odp: two plots on the same axis
Hi You did not provide enough information of what and how you want to do the plot summary(temp) V1 V2 V3 V4 Min. :5 Min. : 1.000 Min. : 1.00 Min. :3300 1st Qu.:5 1st Qu.: 3.000 1st Qu.: 8.00 1st Qu.:3947 Median :5 Median : 6.000 Median :15.00 Median :3996 Mean :5 Mean : 6.513 Mean :15.52 Mean :3976 3rd Qu.:5 3rd Qu.:10.000 3rd Qu.:23.00 3rd Qu.:4053 Max. :5 Max. :12.000 Max. :31.00 Max. :4137 temp2-read.table(2006.txt) summary(temp2) V1 V2 V3 V4 Min. :6 Min. : 1.000 Min. : 1.00 Min. :4010 1st Qu.:6 1st Qu.: 3.000 1st Qu.: 9.00 1st Qu.:4190 Median :6 Median : 5.500 Median :16.00 Median :4225 Mean :6 Mean : 5.725 Mean :16.04 Mean :4213 3rd Qu.:6 3rd Qu.: 8.000 3rd Qu.:23.00 3rd Qu.:4248 Max. :6 Max. :11.000 Max. :31.00 Max. :4312 From summaries of your data you have 2 files with year no in first, month in second, day in third and some value in fourth column. The value from year 2006 is greater than the value in 2005. For accommodating all 4.column data you need to set correct range by ylim. And if you use lines on non sorted values it can result in clump of lines. You could maybe consult ?aggregate and or ?supsmu However only you know what you want as an x values and as an y values. Regards Petr r-help-boun...@r-project.org napsal dne 07.10.2009 10:12:24: Good morning. I wish to plot two data on the same axis. I tried plot(x,y, type = l) for the first and tried to use lines or points(x,y, lty = 2, col = 4) to add or plot the second data on alongside the first. However, what I got was not encouraging. I have attached the two data and would be pleased if anybody could be of help. Thank you Best regards Ogbos [příloha 2005.txt odstraněna uživatelem Petr PIKAL/CTCAP] [příloha 2006.txt odstraněna uživatelem Petr PIKAL/CTCAP] __ 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.
Re: [R] two plots on the same axis
Hi,
Your two data sets have a different year so I'm not sure what you want
to do with the x axis.
The code below plots both data sets on the same graph, with a range of
two years,
d1 - read.table(~/Downloads/2005.txt)
d2 - read.table(~/Downloads/2006.txt)
cleanup - function(d){
names(d) - c(year, month, day, value)
transform(d, date=as.Date(paste(0, year, month, day, sep=), %y%m%d))
}
d1 - cleanup(d1)
d2 - cleanup(d2)
d - rbind(d1, d2)
d - transform(d, year=factor(year))
with(d, plot(date,value))
# prettier with ggplot2
library(ggplot2)
qplot(date, value, data=d, colour=year)
HTH,
baptiste
2009/10/7 ogbos okike ogbos.ok...@gmail.com:
Good morning. I wish to plot two data on the same axis. I tried plot(x,y,
type = l) for the first and tried to use lines or points(x,y, lty = 2, col
= 4) to add or plot the second data on alongside the first. However, what I
got was not encouraging.
I have attached the two data and would be pleased if anybody could be of
help.
Thank you
Best regards
Ogbos
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[R] communication of R Programs
Dear All I am very beginner in R I need to communicate between R programs. I have one R program for writing data in XML File. suppose I can execute same program in different R section for writing different XML files but another R program need to read these data after i wrote in XML file. Could you please suggest which is the best method for this type of communication in R Environment. Thanks in advance! Kind Regard W. Mathew -- Wesley C Mathew [[alternative HTML version deleted]] __ 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] 1st R Conferences in Spain!!
Hi all, I would like to announce that the firsts *R Conferences for the Spanish R community* will be taken place in University of Murcia on 26 and 27th of November. You can have all the information in the web page: http://www.ereros.org/where you can also subscribe and send your talk proposals to this direction: comunicaciones2...@ereros.org If you need more information about the *R Conf 2009 in Spain*, you can subscribe to the *R-help-es* mailing list: * https://stat.ethz.ch/mailman/listinfo/r-help-es* or directly write to me. Best regards!!! [[alternative HTML version deleted]] __ 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 with regexps
Hello everybody I'd like to match exactly numbers from 1 to 27. I've tried a character class like [1-27], but it matches 1,2 and 7. How to tell R (pcre) to interpret 27 correctly? Have been fastly looking throughout pcre man pages, without success. Many thanks Luca __ 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] Odp: Second y-axis --- alternative to par(new=
Hi Try ?twoord.plot from plotrix package. Regards Petr r-help-boun...@r-project.org napsal dne 07.10.2009 10:29:53: Hi is there an alternative to par(new), for ading data to a plot for a different y-axis? My problem with par(new=TRUE) is, that it re-defines all axis and labels (as in example 1) and one has to use xlim=... to fix the x-axis. I am looking for something, which simply resets the y-axis, so that a new plot() (or points()/lines()) keeps the x-axis, but re-defines the y-axis. Is there something available? I could re-scale the y-data to fit the existing y-axis, but that would mean to define all the labels and tickmarks for axis 4 manually. HEre is an example about what I mean: x1 - 1:10 y1 - runif(10) x2 - 1:11 y2 - c(y1*100, 0) ## (1) Does not plot points where (x-axis) they should be plot(x1, y1, type=l) par(new=TRUE) plot(x2, y2, type=p) axis(4) ## (2) Does plot points where (x-axis) they should be xlim - range(x1) plot(x1, y1, type=l, xlim=xlim) par(new=TRUE) plot(x2, y2, type=p, xlim=xlim) axis(4) Cheers, Rainer -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Cell: +27 - (0)83 9479 042 Fax:+27 - (0)86 516 2782 Fax:+49 - (0)721 151 334 888 email: rai...@krugs.de Skype: RMkrug Google: r.m.k...@gmail.com [[alternative HTML version deleted]] __ 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.
Re: [R] 1st R Conferences in Spain!!
Hi all, I am sending you again the links for the R Conferences in Spain, I think in the previous message they where not correct: Web page: www.ereros.org Email to send talk proposals: comunicaciones2...@ereros.org Information of the Spanish R community: https://stat.ethz.ch/mailman/listinfo/r-help-es Best regards!! 2009/10/7 Usuario R r.user.sp...@gmail.com Hi all, I would like to announce that the firsts *R Conferences for the Spanish R community* will be taken place in University of Murcia on 26 and 27th of November. You can have all the information in the web page: http://www.ereros.org/where you can also subscribe and send your talk proposals to this direction: comunicaciones2...@ereros.org If you need more information about the *R Conf 2009 in Spain*, you can subscribe to the *R-help-es* mailing list: * https://stat.ethz.ch/mailman/listinfo/r-help-es* or directly write to me. Best regards!!! [[alternative HTML version deleted]] __ 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] previous.best in metaMDS
On Tue, 2009-10-06 at 11:03 +0200, Kim Vanselow wrote: Dear R-community, dear Jari Oksanen! I use metaMDS (package vegan) to calculate NMDS. In a lot of papers I read that it is recommended to use previous best solutions as a new starting configuration to get better results and to avoid local minima. On the help page I found that a previous.best-command is already implemented in metaMDS: metaMDS(comm, distance = bray, ...,plot = FALSE, previous.best,...) But unfortunately I did not manage to use it properly. When I run metaMDS without command previous.best I certainly get a result. I run it again with command previous.best and I get this message: Fehler in metaMDS(data... : object previous.best not found My question: How can I save the best solution and use it in the next NMDS. I also tried to type in the command: previous.best = TRUE Then I get the message: Starting from a previous solution Fehler in s0$stress : $ operator is invalid for atomic vectors Could you please help me? Thank you very much, Kim That argument allows you to pass metaMDS the results of a previous call to metaMDS, such that the function compares the new set of random starts to the previously achieved best solution. For example; require(vegan) data(dune) set.seed(123) sol - metaMDS(dune) sol - metaMDS(dune, previous.best = sol) For this example, the first call to metaMDS converges to the same solution twice within 5 iterations. The second call to metaMDS tells it to compare with the solution found from the first call. A single iteration is required to find a solution that is effectively the same as the solution from the first call. Note how this feature is used; we save the results of the metaMDS function in object 'sol'. We then supply this object to the argument 'previous.best' on our subsequent call to metaMDS. Does that help? The example in ?metaMDS is quite terse and only covers the basic usage. I'll see about adding some further examples to it for future versions. G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ 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] Second y-axis --- alternative to par(new=
On Wed, Oct 7, 2009 at 11:28 AM, Petr PIKAL petr.pi...@precheza.cz wrote: Hi Try ?twoord.plot from plotrix package. Thanks Petr - I was not aeware of this command. But I would prefer a more general solution. An example on where I am using is, to plot a histogram overlayed by its density estimate (easier to digest for others then only a density estimate). And a newY() (or par(newY=TRUE) command would enable exactly this. Regards, Rainer Regards Petr r-help-boun...@r-project.org napsal dne 07.10.2009 10:29:53: Hi is there an alternative to par(new), for ading data to a plot for a different y-axis? My problem with par(new=TRUE) is, that it re-defines all axis and labels (as in example 1) and one has to use xlim=... to fix the x-axis. I am looking for something, which simply resets the y-axis, so that a new plot() (or points()/lines()) keeps the x-axis, but re-defines the y-axis. Is there something available? I could re-scale the y-data to fit the existing y-axis, but that would mean to define all the labels and tickmarks for axis 4 manually. HEre is an example about what I mean: x1 - 1:10 y1 - runif(10) x2 - 1:11 y2 - c(y1*100, 0) ## (1) Does not plot points where (x-axis) they should be plot(x1, y1, type=l) par(new=TRUE) plot(x2, y2, type=p) axis(4) ## (2) Does plot points where (x-axis) they should be xlim - range(x1) plot(x1, y1, type=l, xlim=xlim) par(new=TRUE) plot(x2, y2, type=p, xlim=xlim) axis(4) Cheers, Rainer -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Cell: +27 - (0)83 9479 042 Fax:+27 - (0)86 516 2782 Fax:+49 - (0)721 151 334 888 email: rai...@krugs.de Skype: RMkrug Google: r.m.k...@gmail.com [[alternative HTML version deleted]] __ 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. -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Cell: +27 - (0)83 9479 042 Fax:+27 - (0)86 516 2782 Fax:+49 - (0)721 151 334 888 email: rai...@krugs.de Skype: RMkrug Google: r.m.k...@gmail.com [[alternative HTML version deleted]] __ 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] Second y-axis --- alternative to par(new=
r-help-boun...@r-project.org napsal dne 07.10.2009 11:37:22: On Wed, Oct 7, 2009 at 11:28 AM, Petr PIKAL petr.pi...@precheza.cz wrote: Hi Try ?twoord.plot from plotrix package. Thanks Petr - I was not aeware of this command. But I would prefer a more general solution. An example on where I am using is, to plot a histogram overlayed by its density estimate (easier to digest for others then only a density estimate). That is quite different from your example. I believe overlay of density curve over histogram was discussed several times e.g. http://tolstoy.newcastle.edu.au/R/e4/help/08/06/14198.html And a newY() (or par(newY=TRUE) command would enable exactly this. This is something beyond my knowledge and it could be that this need some deep redefining in base R graphics. Regards Petr Regards, Rainer Regards Petr r-help-boun...@r-project.org napsal dne 07.10.2009 10:29:53: Hi is there an alternative to par(new), for ading data to a plot for a different y-axis? My problem with par(new=TRUE) is, that it re-defines all axis and labels (as in example 1) and one has to use xlim=... to fix the x-axis. I am looking for something, which simply resets the y-axis, so that a new plot() (or points()/lines()) keeps the x-axis, but re-defines the y-axis. Is there something available? I could re-scale the y-data to fit the existing y-axis, but that would mean to define all the labels and tickmarks for axis 4 manually. HEre is an example about what I mean: x1 - 1:10 y1 - runif(10) x2 - 1:11 y2 - c(y1*100, 0) ## (1) Does not plot points where (x-axis) they should be plot(x1, y1, type=l) par(new=TRUE) plot(x2, y2, type=p) axis(4) ## (2) Does plot points where (x-axis) they should be xlim - range(x1) plot(x1, y1, type=l, xlim=xlim) par(new=TRUE) plot(x2, y2, type=p, xlim=xlim) axis(4) Cheers, Rainer -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Cell: +27 - (0)83 9479 042 Fax:+27 - (0)86 516 2782 Fax:+49 - (0)721 151 334 888 email: rai...@krugs.de Skype: RMkrug Google: r.m.k...@gmail.com [[alternative HTML version deleted]] __ 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. -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Cell: +27 - (0)83 9479 042 Fax:+27 - (0)86 516 2782 Fax:+49 - (0)721 151 334 888 email: rai...@krugs.de Skype: RMkrug Google: r.m.k...@gmail.com [[alternative HTML version deleted]] __ 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.
Re: [R] Second y-axis --- alternative to par(new=
On Wed, Oct 7, 2009 at 11:53 AM, Petr PIKAL petr.pi...@precheza.cz wrote: r-help-boun...@r-project.org napsal dne 07.10.2009 11:37:22: On Wed, Oct 7, 2009 at 11:28 AM, Petr PIKAL petr.pi...@precheza.cz wrote: Hi Try ?twoord.plot from plotrix package. Thanks Petr - I was not aeware of this command. But I would prefer a more general solution. An example on where I am using is, to plot a histogram overlayed by its density estimate (easier to digest for others then only a density estimate). That is quite different from your example. Well - in both cases, I want to overlay two graphs - in my example, it is a line and a point plot, in the other a histogram and a density estimate. I believe overlay of density curve over histogram was discussed several times e.g. http://tolstoy.newcastle.edu.au/R/e4/help/08/06/14198.html Thanks - but if I want to have the histogram with counts (freq=TRUE), then I have exactly the situation I was talking about - sorry for not being clear: x - rnorm(200) hist(x, col = blue, freq = TRUE) lines(density(x), col = red, lwd = 2) i.e. left y-axis (histogram): count right y-axis (density estimate): probability density And a newY() (or par(newY=TRUE) command would enable exactly this. This is something beyond my knowledge and it could be that this need some deep redefining in base R graphics. That's what I guess as well - let's see. Rainer Regards Petr Regards, Rainer Regards Petr r-help-boun...@r-project.org napsal dne 07.10.2009 10:29:53: Hi is there an alternative to par(new), for ading data to a plot for a different y-axis? My problem with par(new=TRUE) is, that it re-defines all axis and labels (as in example 1) and one has to use xlim=... to fix the x-axis. I am looking for something, which simply resets the y-axis, so that a new plot() (or points()/lines()) keeps the x-axis, but re-defines the y-axis. Is there something available? I could re-scale the y-data to fit the existing y-axis, but that would mean to define all the labels and tickmarks for axis 4 manually. HEre is an example about what I mean: x1 - 1:10 y1 - runif(10) x2 - 1:11 y2 - c(y1*100, 0) ## (1) Does not plot points where (x-axis) they should be plot(x1, y1, type=l) par(new=TRUE) plot(x2, y2, type=p) axis(4) ## (2) Does plot points where (x-axis) they should be xlim - range(x1) plot(x1, y1, type=l, xlim=xlim) par(new=TRUE) plot(x2, y2, type=p, xlim=xlim) axis(4) Cheers, Rainer -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Cell: +27 - (0)83 9479 042 Fax:+27 - (0)86 516 2782 Fax:+49 - (0)721 151 334 888 email: rai...@krugs.de Skype: RMkrug Google: r.m.k...@gmail.com [[alternative HTML version deleted]] __ 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. -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Cell: +27 - (0)83 9479 042 Fax:+27 - (0)86 516 2782 Fax:+49 - (0)721 151 334 888 email: rai...@krugs.de Skype: RMkrug Google: r.m.k...@gmail.com [[alternative HTML version deleted]] __ 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. -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Cell: +27 - (0)83 9479 042 Fax:+27 - (0)86 516 2782 Fax:+49 - (0)721 151 334 888 email: rai...@krugs.de Skype: RMkrug Google: r.m.k...@gmail.com [[alternative HTML version deleted]] __
Re: [R] Plot
On 10/07/2009 01:05 AM, Ashta wrote: Days- matrix(c(Monday, Tuesday, Wed, Thu, Fri, Sat, Sun),7,1) Hum-matrix(c(56,57,60,75,62,67,70), Temp-matrix(c(76,77,81,95,82,77,83), Hi Ashta, Are you looking for something like this: dht-data.frame( Days=c(Mon,Tue,Wed,Thu,Fri,Sat,Sun), Hum=c(56,57,60,75,62,67,70), Temp=c(76,77,81,95,82,77,83)) plot(dht$Hum,main=Temperature x Humidity plot, xlab=Day of week,ylab=Humidity,xaxt=n,type=n) text(1:7,dht$Hum,dht$Temp) axis(1,at=1:7,labels=dht$Days) Jim __ 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] Second y-axis --- alternative to par(new=
Hi Rainer M Krug r.m.k...@gmail.com napsal dne 07.10.2009 12:09:21: On Wed, Oct 7, 2009 at 11:53 AM, Petr PIKAL petr.pi...@precheza.cz wrote: r-help-boun...@r-project.org napsal dne 07.10.2009 11:37:22: On Wed, Oct 7, 2009 at 11:28 AM, Petr PIKAL petr.pi...@precheza.cz wrote: Hi Try ?twoord.plot from plotrix package. Thanks Petr - I was not aeware of this command. But I would prefer a more general solution. An example on where I am using is, to plot a histogram overlayed by its density estimate (easier to digest for others then only a density estimate). That is quite different from your example. Well - in both cases, I want to overlay two graphs - in my example, it is a line and a point plot, in the other a histogram and a density estimate. I believe overlay of density curve over histogram was discussed several times e.g. http://tolstoy.newcastle.edu.au/R/e4/help/08/06/14198.html Thanks - but if I want to have the histogram with counts (freq=TRUE), then I have exactly the situation I was talking about - sorry for not being clear: x - rnorm(200) hist(x, col = blue, freq = TRUE) lines(density(x), col = red, lwd = 2) i.e. left y-axis (histogram): count right y-axis (density estimate): probability density And a newY() (or par(newY=TRUE) command would enable exactly this. This is something beyond my knowledge and it could be that this need some deep redefining in base R graphics. That's what I guess as well - let's see. In the meantime, what about x - rnorm(200) hist(x, col = blue, freq = TRUE) ddd-density(x) lines(ddd$x, ddd$y*100, col = red, lwd = 2) and then add suitable y axis. axis(4, at=pretty(ddd$y*100), labels=pretty(ddd$y), col=2) Regards Petr Rainer Regards Petr Regards, Rainer Regards Petr r-help-boun...@r-project.org napsal dne 07.10.2009 10:29:53: Hi is there an alternative to par(new), for ading data to a plot for a different y-axis? My problem with par(new=TRUE) is, that it re-defines all axis and labels (as in example 1) and one has to use xlim=... to fix the x-axis. I am looking for something, which simply resets the y-axis, so that a new plot() (or points()/lines()) keeps the x-axis, but re-defines the y-axis. Is there something available? I could re-scale the y-data to fit the existing y-axis, but that would mean to define all the labels and tickmarks for axis 4 manually. HEre is an example about what I mean: x1 - 1:10 y1 - runif(10) x2 - 1:11 y2 - c(y1*100, 0) ## (1) Does not plot points where (x-axis) they should be plot(x1, y1, type=l) par(new=TRUE) plot(x2, y2, type=p) axis(4) ## (2) Does plot points where (x-axis) they should be xlim - range(x1) plot(x1, y1, type=l, xlim=xlim) par(new=TRUE) plot(x2, y2, type=p, xlim=xlim) axis(4) Cheers, Rainer -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Cell: +27 - (0)83 9479 042 Fax:+27 - (0)86 516 2782 Fax:+49 - (0)721 151 334 888 email: rai...@krugs.de Skype: RMkrug Google: r.m.k...@gmail.com [[alternative HTML version deleted]] __ 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. -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Cell: +27 - (0)83 9479 042 Fax:+27 - (0)86 516 2782 Fax:+49 - (0)721 151 334 888 email: rai...@krugs.de Skype: RMkrug Google: r.m.k...@gmail.com [[alternative HTML version deleted]] __ 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. -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch
Re: [R] rpois formula
nedmt60 wrote: Hi all, It's been a while since i've used R and I can't remember how to do the following: i have a = rpois (10, x) b = rpois (10, y) what is the code to show that ab, ba and a=b to show just the number of occurances? at the moment when I type ab I get a nice long list of true or false. so i'm hoping to have the following a = rpois (10, 2) b = rpois (10, 3) table(sign(a-b)) -1 0 1 58712 16550 24738 Duncan Murdoch ab 35000 ba 25000 a=b 4 thanks in advance __ 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] Second y-axis --- alternative to par(new=
On Wed, Oct 7, 2009 at 12:26 PM, Petr PIKAL petr.pi...@precheza.cz wrote: Hi Rainer M Krug r.m.k...@gmail.com napsal dne 07.10.2009 12:09:21: On Wed, Oct 7, 2009 at 11:53 AM, Petr PIKAL petr.pi...@precheza.cz wrote: r-help-boun...@r-project.org napsal dne 07.10.2009 11:37:22: On Wed, Oct 7, 2009 at 11:28 AM, Petr PIKAL petr.pi...@precheza.cz wrote: Hi Try ?twoord.plot from plotrix package. Thanks Petr - I was not aeware of this command. But I would prefer a more general solution. An example on where I am using is, to plot a histogram overlayed by its density estimate (easier to digest for others then only a density estimate). That is quite different from your example. Well - in both cases, I want to overlay two graphs - in my example, it is a line and a point plot, in the other a histogram and a density estimate. I believe overlay of density curve over histogram was discussed several times e.g. http://tolstoy.newcastle.edu.au/R/e4/help/08/06/14198.html Thanks - but if I want to have the histogram with counts (freq=TRUE), then I have exactly the situation I was talking about - sorry for not being clear: x - rnorm(200) hist(x, col = blue, freq = TRUE) lines(density(x), col = red, lwd = 2) i.e. left y-axis (histogram): count right y-axis (density estimate): probability density And a newY() (or par(newY=TRUE) command would enable exactly this. This is something beyond my knowledge and it could be that this need some deep redefining in base R graphics. That's what I guess as well - let's see. In the meantime, what about x - rnorm(200) hist(x, col = blue, freq = TRUE) ddd-density(x) lines(ddd$x, ddd$y*100, col = red, lwd = 2) and then add suitable y axis. axis(4, at=pretty(ddd$y*100), labels=pretty(ddd$y), col=2) Yes - that definitely works. I usually use the following approach: determine the xlims in advance, and then set them manually for each plot: x - rnorm(200) xlim - trunc(range(x)) + c(-1, +1) hist(x, col = blue, freq = TRUE, xlim=xlim) par(new=TRUE) plot(density(x), xlim=xlim, ann=FALSE, axes=FALSE) axis(4) But it is sometimes tricky to get the xlims for the plot. Regards Petr Rainer Regards Petr Regards, Rainer Regards Petr r-help-boun...@r-project.org napsal dne 07.10.2009 10:29:53: Hi is there an alternative to par(new), for ading data to a plot for a different y-axis? My problem with par(new=TRUE) is, that it re-defines all axis and labels (as in example 1) and one has to use xlim=... to fix the x-axis. I am looking for something, which simply resets the y-axis, so that a new plot() (or points()/lines()) keeps the x-axis, but re-defines the y-axis. Is there something available? I could re-scale the y-data to fit the existing y-axis, but that would mean to define all the labels and tickmarks for axis 4 manually. HEre is an example about what I mean: x1 - 1:10 y1 - runif(10) x2 - 1:11 y2 - c(y1*100, 0) ## (1) Does not plot points where (x-axis) they should be plot(x1, y1, type=l) par(new=TRUE) plot(x2, y2, type=p) axis(4) ## (2) Does plot points where (x-axis) they should be xlim - range(x1) plot(x1, y1, type=l, xlim=xlim) par(new=TRUE) plot(x2, y2, type=p, xlim=xlim) axis(4) Cheers, Rainer -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Cell: +27 - (0)83 9479 042 Fax:+27 - (0)86 516 2782 Fax:+49 - (0)721 151 334 888 email: rai...@krugs.de Skype: RMkrug Google: r.m.k...@gmail.com [[alternative HTML version deleted]] __ 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. -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Cell: +27 - (0)83 9479 042 Fax:+27 - (0)86 516 2782 Fax:+49 - (0)721 151 334 888 email: rai...@krugs.de Skype:
Re: [R] two plots on the same axis
On 10/07/2009 07:12 PM, ogbos okike wrote: Good morning. I wish to plot two data on the same axis. I tried plot(x,y, type = l) for the first and tried to use lines or points(x,y, lty = 2, col = 4) to add or plot the second data on alongside the first. However, what I got was not encouraging. I have attached the two data and would be pleased if anybody could be of help. Hi Ogbos, Try this: plot(oo1$daymon,oo1[,4], main=Two years of something,type=l,col=blue, ylim=c(3300,4400)) lines(oo2$daymon,oo2[,4],col=red) legend(oo1$daymon[100],3600,c(2005,2006), col=c(4,2),lty=1) Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Second y-axis --- alternative to par(new=
Hi Rainer M Krug r.m.k...@gmail.com napsal dne 07.10.2009 12:40:39: On Wed, Oct 7, 2009 at 12:26 PM, Petr PIKAL petr.pi...@precheza.cz wrote: Hi Rainer M Krug r.m.k...@gmail.com napsal dne 07.10.2009 12:09:21: snip In the meantime, what about x - rnorm(200) hist(x, col = blue, freq = TRUE) ddd-density(x) lines(ddd$x, ddd$y*100, col = red, lwd = 2) and then add suitable y axis. axis(4, at=pretty(ddd$y*100), labels=pretty(ddd$y), col=2) Yes - that definitely works. I usually use the following approach: determine the xlims in advance, and then set them manually for each plot: x - rnorm(200) xlim - trunc(range(x)) + c(-1, +1) hist(x, col = blue, freq = TRUE, xlim=xlim) hhh - hist(x, col = blue, freq = TRUE) gives you object from which you can extract limits for plotting maybe better then from original data and you do not need to call par(new=TRUE) Regards Petr plot(density(x), xlim=xlim, ann=FALSE, axes=FALSE) axis(4) But it is sometimes tricky to get the xlims for the plot. Regards Petr __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Grid on persp plot
Hello, I have a persp plot that I am generating which shows a growth trend toward the 'rear' of the displayed box. I would like to have grid lines visible on the plot to give a reference to the amount the values are increasing. I have tried rotating the plot 180 degrees to put the growth in the 'front' of the box but then the underside of the mesh is shown and hides much of the other data. I have also tried using grid() but that only placed the lines on what would be the 2d space and didnt correspond to the displayed graph at all. Is there a way to show grid lines within a persp plot? For reference, these are the commands: x - unique(data$X) y - unique(data$Y) theta - 23 phi - 10 expand - 0.5 col - lightblue shade - 0.75 ticktype - detailed # ... persp (x,y,m.avg,theta=theta,phi=phi, expand=expand,col=col,shade=shade,ticktype=ticktype) Thanks in advance, jb __ 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] Formatting outputs:(chronological object)
Hello everyone, I have a data generated in a way similar to the following library(chron);library(zoo) date- seq(as.Date(1990-01-01),, as.Date(2000-12-31), by = 1) obs- zoo(rnorm(length(date), mean = 10, sd = 2.5), order.by = date) monthly- function(date) as.Date(as.yearmon(Date)) result- data.frame ( Date = obs = aggregate(obs, monthly, sum)) Now, I want to get the result data in the following format instead of the continuous table Observation for year 1990, 1990-01-01 314.7547 1990-02-01 266.0105 1990-03-01 353.7275 1990-04-01 273.8321 1990-05-01 325.3691 1990-06-01 253.1501 1990-07-01 318.1684 1990-08-01 291.2097 1990-09-01 298.6409 1990-10-01 304.0167 1990-11-01 279.4668 1990-12-01 286.9456 Total for year 1990 = xxx Observation for year 1991 1991-01-01 313.1515 1991-02-01 297.9274 1991-03-01 315.2565 1991-04-01 290.9797 1991-05-01 327.0480 1991-06-01 281.5030 1991-07-01 316.7332 1991-08-01 289.9122 1991-09-01 296.9334 1991-10-01 280.2053 1991-11-01 295.6098 1991-12-01 321.6451 Total for year 1991 = xxx Any help would be highly appreciated Thanks -- Acharya, Subodh [[alternative HTML version deleted]] __ 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] Second y-axis --- alternative to par(new=
On Wed, Oct 7, 2009 at 1:48 PM, Petr PIKAL petr.pi...@precheza.cz wrote: Hi Rainer M Krug r.m.k...@gmail.com napsal dne 07.10.2009 12:40:39: On Wed, Oct 7, 2009 at 12:26 PM, Petr PIKAL petr.pi...@precheza.cz wrote: Hi Rainer M Krug r.m.k...@gmail.com napsal dne 07.10.2009 12:09:21: snip In the meantime, what about x - rnorm(200) hist(x, col = blue, freq = TRUE) ddd-density(x) lines(ddd$x, ddd$y*100, col = red, lwd = 2) and then add suitable y axis. axis(4, at=pretty(ddd$y*100), labels=pretty(ddd$y), col=2) Yes - that definitely works. I usually use the following approach: determine the xlims in advance, and then set them manually for each plot: x - rnorm(200) xlim - trunc(range(x)) + c(-1, +1) hist(x, col = blue, freq = TRUE, xlim=xlim) hhh - hist(x, col = blue, freq = TRUE) gives you object from which you can extract limits for plotting maybe better then from original data and you do not need to call par(new=TRUE) True. Thanks a lot, Rainer Regards Petr plot(density(x), xlim=xlim, ann=FALSE, axes=FALSE) axis(4) But it is sometimes tricky to get the xlims for the plot. Regards Petr -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Natural Sciences Building Office Suite 2039 Stellenbosch University Main Campus, Merriman Avenue Stellenbosch South Africa Cell: +27 - (0)83 9479 042 Fax:+27 - (0)86 516 2782 Fax:+49 - (0)721 151 334 888 email: rai...@krugs.de Skype: RMkrug Google: r.m.k...@gmail.com [[alternative HTML version deleted]] __ 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] Save plot to text file
See ?recordPlot On Wed, Oct 7, 2009 at 5:09 AM, Pradeep Raje raje.prad...@gmail.com wrote: Dear all:I am sorry if I have missed a solution posted earlier. My collaborator (sitting in a different time zone and not on R) wants to re-plot the charts that I have obtained after some complex processing. There are thirty charts in all, of different types, and some are multi-plots (plot(new=T)). Is there a way to 'save' or 'dump just the x-y coordinates to a text/ASCII file, like x,y1,y2,y3 or even (x,y1), append (x,y2), append (x,y3)... Any help will be gratefully acknowledged. Thanks warm regards, pradeep [[alternative HTML version deleted]] __ 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. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O __ 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] help with regexps
Luca Braglia-2 wrote: I'd like to match exactly numbers from 1 to 27. If you feel in masochistic mode, you can do it: b = c(32,3,17,27,28,57,a13) a = c(^([0-9]|[0-1][0-9]|2[0-7])$) grep(a,b,value=TRUE) A much more flexible way would be to isolate the numeric part first, and test for the range in a seconde step. Dieter -- View this message in context: http://www.nabble.com/help-with-regexps-tp25783202p25783948.html Sent from the R help mailing list archive at Nabble.com. __ 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] Parameters of Beta distribution
Supose I have a data pertaining to credit loss as amounts - c(46839.50,31177.12,35696.69,21192.57,29200.91,42049.64,42422.19, 44976.18, 32135.36,47936.57,27322.91,37359.09,43179.60, 48381.02, 45872.38, 28057.30,44643.83,36156.33,16037.62, 45432.28) I am trying to fit Beta distribution (two parameters distribution but where lower bound and upper bounds are NOT 0 and 1 respectively). For this I need to estimate the two parameters of Beta distribution. I found some code in VGAM pacakge but it deals with standard Beta distribution i.e. lower bound (say A) = 0 and upper bound (say B) = 1. How do I estimate the parameters of the Beta distribution for above data where A and B are not 0's? Please guide. Thanking you in advance Maithili Add whatever you love to the Yahoo! India homepage. Try now! http://in.yahoo.com/trynew [[alternative HTML version deleted]] __ 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] communication of R Programs
wesley mathew wrote: I have one R program for writing data in XML File. suppose I can execute same program in different R section for writing different XML files but another R program need to read these data after i wrote in XML file. It is a bit unclear for me what you mean with 'R section, but the simplest way out would be to generate a shell batch file to run one program (Under windows) rterm.exe --no-save writexml.r rterm.exe --no-save thereport.r If you need to pass parameters to the report writer, you could use Sys.setenv Sys.getenv Dieter -- View this message in context: http://www.nabble.com/communication-of-R-Programs-tp25783067p25783954.html Sent from the R help mailing list archive at Nabble.com. __ 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] rpois formula
David Winsemius wrote: Or: a = rpois (10, 0.1) b = rpois (10, 0.15) table(ab, a==b, ba) table(sign(b-a)) comes to mind too (and table(a,b) is illuminative). -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ 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] [R-pkgs] Updates to rms package
The rms package, a replacement for the Design package, has been updated on CRAN. The most major change is the addition of smooth calibration curves for externally (val.surv function) or internally (calibrate.cph, calibrate.psm) validating a survival model with right-censored data. The polspline package is used to estimate the survival probability at a fixed time point as a function of the predicted survival probability. Some user-requested plotting features have been added to bplot and plot.Predict. Changes in version 2.1-0 * Made Predict not return invisibly if predictors not specified * New option nlines for plot.Predict for getting line plots with 2 categorical predictors * Added rename option to rbind.Predict to handle case where predictor name has changed between models * Added ties=mean to approx( ) calls that did not have ties= specified * Added nlevels argument to bplot to pass to contour * Added par argument to iLegend - list to pass to par(). * Redirected ... argument to iLegend to image( ). * Fixed groupkm - was printing warning messages wrongly * Added new semiparametric survival prediction calibration curve method in val.surv for external validation; this is the first implementation of smooth calibration curves for survival probability validation with right-censored data * Fixed calibrate confidence limits from groupkm * Added smooth calibration curve using hare (polspline package) for calibrate.cph and calibrate.psm * Added display of predicted risks for cph and psm models even for the stratified KM method (old default) -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ 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] R, Coda, and OpenBUGS
Have you tried the rjags package which uses the jags system? It is much more integrated into R and works quite well. It uses the same modeling language as BUGS. It is also better supported than OpenBUGS. Frank Bill Halteman wrote: Hi All, I am trying to figure out how to use R-Coda with the output from OpenBugs. I have installed and loaded the packages BRugs and R2WinBUGS. I have successfully run a simple Bayes model in WinBUGS using R2WinBUGS' bugs and have used read.bugs to build the coda object. I can successfully switch to OpenBugs and run the same model and get the basic summary back. However, I cannot build the coda object. From what I have read read.openbugs should do the trick. However, I have discovered the current version of OpenBUGS (v 3.03) doesn't write any output files in spite of setting codaPkg=TRUE in the bugs call. Str(openbugs.object) reveals a large collection of elements, one of which is an array that contains the MCMC chains. Is there a function to build the coda object? Thanks in advance for any suggestions, Bill Halteman -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ 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] Formatting outputs:(chronological object)
try this -- the example you provided did not work, so I had to hack
together an example:
library(chron);library(zoo)
date- seq(as.Date(1990-01-01), as.Date(2000-12-31), by = 1)
obs-rnorm(length(date), mean = 10, sd = 2.5)
monthly- function(date) as.Date(as.yearmon(date))
obs - tapply(obs, monthly(date), sum)
obs.yr - split(obs, substring(names(obs), 1, 4))
for (i in names(obs.yr)){
cat(Observations for Year, i, '\n')
print(cbind(obs.yr[[i]]))
cat(Total for Year, i, sum(obs.yr[[i]]), '\n\n')
}
Observations for Year 1990
[,1]
1990-01-01 336.1179
1990-02-01 279.0572
1990-03-01 314.8671
1990-04-01 281.0801
1990-05-01 288.1853
1990-06-01 325.3545
1990-07-01 334.3680
1990-08-01 314.9724
1990-09-01 300.5801
1990-10-01 324.7640
1990-11-01 307.5808
1990-12-01 300.1142
Total for Year 1990 3707.042
Observations for Year 1991
[,1]
1991-01-01 314.4718
1991-02-01 269.0690
1991-03-01 309.8057
1991-04-01 287.8462
1991-05-01 337.0155
1991-06-01 299.6412
1991-07-01 310.2771
1991-08-01 271.6742
1991-09-01 293.7720
1991-10-01 301.3979
1991-11-01 294.1190
1991-12-01 310.4470
Total for Year 1991 3599.537
On Wed, Oct 7, 2009 at 8:11 AM, Subodh Acharya shoeb...@gmail.com wrote:
Hello everyone,
I have a data generated in a way similar to the following
library(chron);library(zoo)
date- seq(as.Date(1990-01-01),, as.Date(2000-12-31), by = 1)
obs- zoo(rnorm(length(date), mean = 10, sd = 2.5), order.by = date)
monthly- function(date) as.Date(as.yearmon(Date))
result- data.frame ( Date = obs = aggregate(obs, monthly, sum))
Now,
I want to get the result data in the following format instead of the
continuous table
Observation for year 1990,
1990-01-01 314.7547
1990-02-01 266.0105
1990-03-01 353.7275
1990-04-01 273.8321
1990-05-01 325.3691
1990-06-01 253.1501
1990-07-01 318.1684
1990-08-01 291.2097
1990-09-01 298.6409
1990-10-01 304.0167
1990-11-01 279.4668
1990-12-01 286.9456
Total for year 1990 = xxx
Observation for year 1991
1991-01-01 313.1515
1991-02-01 297.9274
1991-03-01 315.2565
1991-04-01 290.9797
1991-05-01 327.0480
1991-06-01 281.5030
1991-07-01 316.7332
1991-08-01 289.9122
1991-09-01 296.9334
1991-10-01 280.2053
1991-11-01 295.6098
1991-12-01 321.6451
Total for year 1991 = xxx
Any help would be highly appreciated
Thanks
--
Acharya, Subodh
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R, Coda, and OpenBUGS
Bill Halteman wrote: Hi All, I am trying to figure out how to use R-Coda with the output from OpenBugs. I have installed and loaded the packages BRugs and R2WinBUGS. I have successfully run a simple Bayes model in WinBUGS using R2WinBUGS' bugs and have used read.bugs to build the coda object. I can successfully switch to OpenBugs and run the same model and get the basic summary back. However, I cannot build the coda object. From what I have read read.openbugs should do the trick. However, I have discovered the current version of OpenBUGS (v 3.03) doesn't write any output files in spite of setting codaPkg=TRUE in the bugs call. Str(openbugs.object) reveals a large collection of elements, one of which is an array that contains the MCMC chains. Is there a function to build the coda object? For BRugs: Sure, the function is called buildMCMC(). From the examples of ?BRugs: library(BRugs) # loading BRugs ## Now setting the working directory to the examples' one: oldwd - getwd() setwd(system.file(OpenBUGS, Examples, package=BRugs)) ## some usual steps (like clicking in WinBUGS): modelCheck(ratsmodel.txt) # check model file modelData(ratsdata.txt)# read data file modelCompile(numChains=2)# compile model with 2 chains modelInits(rep(ratsinits.txt, 2)) # read init data file modelUpdate(1000)# burn in samplesSet(c(alpha0, alpha)) # alpha0 and alpha should be monitored modelUpdate(1000)# 1000 more iterations ## now let's construct a coda object ## (of class mcmc.list, to be precise) ## for BUGS node alpha: alpha - buildMCMC(alpha) Best, Uwe Ligges Thanks in advance for any suggestions, Bill Halteman __ 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.
Re: [R] Parameters of Beta distribution
Rescale your data x to (x-A)/(B-A). Maithili Shiva maithili_sh...@yahoo.com Sent by: r-help-boun...@r-project.org 10/07/2009 08:39 AM To r-help@r-project.org cc Subject [R] Parameters of Beta distribution Supose I have a data pertaining to credit loss as amounts - c(46839.50,31177.12,35696.69,21192.57,29200.91,42049.64,42422.19, 44976.18, 32135.36,47936.57,27322.91,37359.09,43179.60, 48381.02, 45872.38, 28057.30,44643.83,36156.33,16037.62, 45432.28) I am trying to fit Beta distribution (two parameters distribution but where lower bound and upper bounds are NOT 0 and 1 respectively). For this I need to estimate the two parameters of Beta distribution. I found some code in VGAM pacakge but it deals with standard Beta distribution i.e. lower bound (say A) = 0 and upper bound (say B) = 1. How do I estimate the parameters of the Beta distribution for above data where A and B are not 0's? Please guide. Thanking you in advance Maithili Add whatever you love to the Yahoo! India homepage. Try now! http://in.yahoo.com/trynew [[alternative HTML version deleted]] __ 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. [[alternative HTML version deleted]] __ 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] Prediction from BMA
Dear colleagues, I am doing a little bit of work using the BMA package to examine predictive models for types of pain - the outcome variable is a binary (Yes/No) for the type of pain experienced by a patient. Our observation is that BMA makes a lot of sense in this application, as the data suggests that there are several well-fitting possible logistic models, each with posterior probabilities close to 0.1, as well as a straggle of somewhat less likely models. I am unsure how best to produce predictions from the BMA output - i.e. the posterior means of model coefficients. There isn't a predict.BMA or similar, that I can see. What's the recommended way to produce predictions (i.e. fitted values, or estimates from new data) from these BMA models? Best wishes, Anthony Staines -- Anthony Staines, Professor of Health Systems Research, School of Nursing, Dublin City University, Dublin 9,Ireland. Tel:- +353 1 700 7807. Mobile:- +353 86 606 9713 __ 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] Emacs + ESS + R installer
Dear list, I and some students built an Emacs + ESS + R installer, which allows users to download and install the newest version of Emacs, ESS, and R with little pain.The size of the installer is about 8Mb. http://sourceforge.net/projects/emacs-for-r/ Please feel free to give me comments and suggestions. Thank you. Frank Liu -- Frank C.S. Liu Assistant Professor, Graduate Institute of Political ScienceE-mail: frankcs...@gmail.com National Sun Yat-Sen UniversityOffice:+886.7.525.2000 # 804 Kaohsiung, Taiwan, R.O.C. FAX:+886.7.525.5540 __ 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] how to extract the second table from the factanal functions result's loadings part?
Hi All, Can someone help me?The way to do this may be very easy but i do not know. *Question1:* factanal() function produces the results in this way:-- *RESULTS:--* *fact1- factanal(data_withNA,factors=1,rotation=none) fact1$loadings* Loadings: Factor1 i1 0.784 i2 0.874 i3 0.786 i4 0.839 i5 0.778 i6 0.859 i7 0.850 i8 0.763 i9 0.810 i10 0.575 i11 0.745 i12 0.777 i13 0.674 i14 0.644 i15 0.796 * Factor1 SS loadings 8.995 Proportion Var 0.600* *How to access the second table* i.e the table other than the Loadings table? *Question2:---* How to calculate the* initial communalities*?Is there any function in R? I am getting Extraction communalities. Results as generated by SPSS. CommunalitiesInitial Extraction i1 .654 .614 i2 .781 .764 i3 .645 .617 i4 .695 .704 i5 .681 .605 i6 .747 .738 i7 .758 .722 i8 .607 .583 i9 .661 .657 i10 .409 .330 i11 .579 .554 i12 .668 .604 i13 .595 .454 i14 .521 .415 i15 .682 .634 -- Thanks Moumita [[alternative HTML version deleted]] __ 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] communication of R Programs
I don't understand the context of the question. Since the data is already in R, you should use it from within R. What is the reason for translating it to XML and then back? You take the risk of two levels of distortion. I am guessing that you want continuity of your work over multiple login sessions. One technique for continuity is to save your workspace at the end of each login. Do that by saying yes to the save question when you type q(). The next time you start R from the same directory, the saved workspace will be re-loaded. See ?q and ?save for details. Rich __ 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] R, Coda, and OpenBUGS - Thanks!!
Worked perfectly. Thanks very Much Uwe Ligges wrote: Bill Halteman wrote: Hi All, I am trying to figure out how to use R-Coda with the output from OpenBugs. I have installed and loaded the packages BRugs and R2WinBUGS. I have successfully run a simple Bayes model in WinBUGS using R2WinBUGS' bugs and have used read.bugs to build the coda object. I can successfully switch to OpenBugs and run the same model and get the basic summary back. However, I cannot build the coda object. From what I have read read.openbugs should do the trick. However, I have discovered the current version of OpenBUGS (v 3.03) doesn't write any output files in spite of setting codaPkg=TRUE in the bugs call. Str(openbugs.object) reveals a large collection of elements, one of which is an array that contains the MCMC chains. Is there a function to build the coda object? For BRugs: Sure, the function is called buildMCMC(). From the examples of ?BRugs: library(BRugs) # loading BRugs ## Now setting the working directory to the examples' one: oldwd - getwd() setwd(system.file(OpenBUGS, Examples, package=BRugs)) ## some usual steps (like clicking in WinBUGS): modelCheck(ratsmodel.txt) # check model file modelData(ratsdata.txt)# read data file modelCompile(numChains=2)# compile model with 2 chains modelInits(rep(ratsinits.txt, 2)) # read init data file modelUpdate(1000)# burn in samplesSet(c(alpha0, alpha)) # alpha0 and alpha should be monitored modelUpdate(1000)# 1000 more iterations ## now let's construct a coda object ## (of class mcmc.list, to be precise) ## for BUGS node alpha: alpha - buildMCMC(alpha) Best, Uwe Ligges Thanks in advance for any suggestions, Bill Halteman __ 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.
[R] merging dataframes with an unequal number of variables
Hallo Everyone I have the kind of problem that one should never have because one must always plan well and communicate with your team. But now I haven't so here is my problem. I have data coming in on a daily basis from surveys in 10 towns. The questionnaire has 62 variables but some of the regions have used older versions of the questionnaire that have a few variables less. I want to combine everything a single dataframe on a daily basis. The problem is now that i cannot rbind() the data because the number of variables do not correspond. I have found that i can first subset all datasets to keep just the variables that they all have in common but that is very unsatisfactory. What I want to do is to use a complete list of variable names and look at each data frame and create variable names where they are missing and fill it with NAs. At least then I can merge the data and use the data that I have short example # Make a data frame with 4 variables var1=c(1,2,3,4,5,6) var2=c(a,b,a,b,a,a) var3=c(1,NA,NA,2,3,NA) var4=c(100,200,300,100,200,300) df1=data.frame(cbind(var1,var2,var3,var4)) # Data frame 2 and three has two of the 4 variables and 4 has eveything df2=df1[,c(1,2,4)] df3=df1[,c(2,3,4)] df4=df1 # I wanted to do this but it produces an error because the number of variable differ df=data.frame(rbind(df1,df2,df3,df4)) #I have figured out how to print the names of variable that do match the 'master' list (in this case df1): # example with df3 names(df3[,na.omit(match(names(df1),names(df3)))]) #What I need is the name of the variable that each specific data frame does NOT contain # Something like this, but this gives an error names(df1[-names(df3[,na.omit(match(names(df1),names(df3)))])]) thanks in advance Christiaan [[alternative HTML version deleted]] __ 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] [ESS] Emacs + ESS + R installer
Frank Liu frankcs...@gmail.com wrote: I and some students built an Emacs + ESS + R installer, which allows users to download and install the newest version of Emacs, ESS, and R with little pain.The size of the installer is about 8Mb. http://sourceforge.net/projects/emacs-for-r/ Please feel free to give me comments and suggestions. Thank you. sounds like a great idea - anything to reduce the barrier! How does it overlap/complement with what Vincent kindly provides: http://vgoulet.act.ulaval.ca/en/ressources/emacs/ Installing that + R should get to the same position. Vincent is providing a great resource for win (and mac) users, and if there is anyway of building on what he has done, it wuold be great. Stephen __ 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] merging dataframes with an unequal number of variables
See ?rbind.fill in the plyr package. On Wed, Oct 7, 2009 at 9:32 AM, christiaan pauw cjp...@gmail.com wrote: Hallo Everyone I have the kind of problem that one should never have because one must always plan well and communicate with your team. But now I haven't so here is my problem. I have data coming in on a daily basis from surveys in 10 towns. The questionnaire has 62 variables but some of the regions have used older versions of the questionnaire that have a few variables less. I want to combine everything a single dataframe on a daily basis. The problem is now that i cannot rbind() the data because the number of variables do not correspond. I have found that i can first subset all datasets to keep just the variables that they all have in common but that is very unsatisfactory. What I want to do is to use a complete list of variable names and look at each data frame and create variable names where they are missing and fill it with NAs. At least then I can merge the data and use the data that I have short example # Make a data frame with 4 variables var1=c(1,2,3,4,5,6) var2=c(a,b,a,b,a,a) var3=c(1,NA,NA,2,3,NA) var4=c(100,200,300,100,200,300) df1=data.frame(cbind(var1,var2,var3,var4)) # Data frame 2 and three has two of the 4 variables and 4 has eveything df2=df1[,c(1,2,4)] df3=df1[,c(2,3,4)] df4=df1 # I wanted to do this but it produces an error because the number of variable differ df=data.frame(rbind(df1,df2,df3,df4)) #I have figured out how to print the names of variable that do match the 'master' list (in this case df1): # example with df3 names(df3[,na.omit(match(names(df1),names(df3)))]) #What I need is the name of the variable that each specific data frame does NOT contain # Something like this, but this gives an error names(df1[-names(df3[,na.omit(match(names(df1),names(df3)))])]) thanks in advance Christiaan [[alternative HTML version deleted]] __ 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.
[R] windows system file aux
Hi all, I just would like to notice a small problem of R on windows (XP at least). If you execute the following lines x - rexp(1000) write.csv(x, file=aux.csv) the R GUI just loops for ever... this is due to the fact on windows, users can create a file or directory with the name aux or aux.*. If you try to create a text file on windows aux.txt, it says you could not do it. Is it possible for the R GUI to catch this message? or just raise an error? Thanks in advance Christophe -- Christophe DUTANG Ph. D. student at ISFA [[alternative HTML version deleted]] __ 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] Unable to load rjags
I am trying to install rjags. Although I can install the library, I cannot load the package. See below. Here is my session sessionInfo() R version 2.9.2 (2009-08-24) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] coda_0.13-4 lattice_0.17-26 loaded via a namespace (and not attached): [1] grid_2.9.2 tools_2.9.2 Here I install the rjags package utils:::menuInstallPkgs() trying URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/2.9/rjags_1.0.3-10.zip' Content type 'application/zip' length 308968 bytes (301 Kb) opened URL downloaded 301 Kb package 'rjags' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Documents and Settings\jlucke\Local Settings\Temp\RtmpRAkMZy\downloaded_packages updating HTML package descriptions BUT, library(rjags) Error in fun(...) : Failed to locate JAGS 1.0.3 installation Error : .onLoad failed in 'loadNamespace' for 'rjags' Error: package/namespace load failed for 'rjags' Any advice? Joe [[alternative HTML version deleted]] __ 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] Second y-axis --- alternative to par(new=
Rainer M Krug-6 wrote:
Thanks - but if I want to have the histogram with counts (freq=TRUE), then
I have exactly the situation I was talking about - sorry for not being
clear:
x - rnorm(200)
hist(x, col = blue, freq = TRUE)
lines(density(x), col = red, lwd = 2)
i.e.
left y-axis (histogram): count
right y-axis (density estimate): probability density
When adding a second y-axis, I always rescale the plot with a call to
plot.window() rather than par(new=T). This rescales the plotting area while
still allowing low-level plotting functions like lines and points to be
executed:
x - rnorm(200)
hist(x, col = blue, freq = TRUE)
# recovering par('xaxp') uses the original x limits.
plot.window( xlim = range( par('xaxp')[1:2] ), ylim = range( density(x)$y ))
lines(density(x), col = red, lwd = 2)
Hope this helps!
-Charlie
-
Charlie Sharpsteen
Undergraduate
Environmental Resources Engineering
Humboldt State University
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[R] neural network arguments
hi everyone! my inquiry with neural network is rather basic. i am just learning neural network, particularly the VR bundle. i read the documentations for the said bundle but still is struggling on understanding some arguments - x is the matrix or data frame of x values for example does this mean data frame for training? - y is the matrix or data frame of target values for example does this mean data frame for testing? - would fitting the single-hidden-layer NN train and test my data? what does fitting really do? i know these are very basic questions but i just started exploring NN packages. thanks in advance for your help! -- View this message in context: http://www.nabble.com/neural-network-arguments-tp25787734p25787734.html Sent from the R help mailing list archive at Nabble.com. __ 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] Second y-axis --- alternative to par(new=
cls59 wrote:
# recovering par('xaxp') uses the original x limits.
plot.window( xlim = range( par('xaxp')[1:2] ), ylim = range( density(x)$y
))
Actually, I misspoke. I believe the following is the voodoo you want for
exactly recovering the original xlimit:
plot.window( xlim = range( par('usr')[1:2] ), xaxs = 'i', ylim = range(
density(x)$y ))
Basically, par('xaxp')[1:2] only returns the extreme values of the tick
marks on the original x-axis-- using these can still cause points not to
line up. par('usr')[1:2] returns the coordinates of the left and right edges
of the plot screen. setting xaxs to 'i' causes R to use the xlimit exactly
as given and not to pad it by 4% in an attempt to make it pretty.
Good luck!
-Charlie
-
Charlie Sharpsteen
Undergraduate
Environmental Resources Engineering
Humboldt State University
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Re: [R] Unable to load rjags
jlu...@ria.buffalo.edu wrote: I am trying to install rjags. Although I can install the library, I cannot load the package. See below. Here is my session sessionInfo() R version 2.9.2 (2009-08-24) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] coda_0.13-4 lattice_0.17-26 loaded via a namespace (and not attached): [1] grid_2.9.2 tools_2.9.2 Here I install the rjags package utils:::menuInstallPkgs() trying URL 'http://lib.stat.cmu.edu/R/CRAN/bin/windows/contrib/2.9/rjags_1.0.3-10.zip' Content type 'application/zip' length 308968 bytes (301 Kb) opened URL downloaded 301 Kb package 'rjags' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Documents and Settings\jlucke\Local Settings\Temp\RtmpRAkMZy\downloaded_packages updating HTML package descriptions BUT, library(rjags) Error in fun(...) : Failed to locate JAGS 1.0.3 installation Error : .onLoad failed in 'loadNamespace' for 'rjags' Error: package/namespace load failed for 'rjags' Any advice? You need to install jags separately. The package contains rhe interface only. Uwe Ligges Joe [[alternative HTML version deleted]] __ 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.
[R] princomp data input format
I am trying do to a PCA analysis using princomp. I get a result, but I wonder if I have the data in the correct format. My data contains many stations where fish were sampled as well as environmental information for each station (lat, lon, depth, temp and year). the format is like this: species 1| species 2 | species 3|...|lat | lon | depth | temp| year 1 3132 42 70 200 2 1988 4 34 0 43 54 4001 1988 200 65 4 42 70 200 2 1989 1 32343 54 4000 1989 with nearly 14,000 stations, each in its own row. the result of running princomp(data,cor=T) is just a mess. How do I 'tell' r what columns are species and what are environmental factors? [[alternative HTML version deleted]] __ 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] sinusoidal relationship
Hi, Suppose x and y are vectors whose elements are known. I know that there is a sinusoidal relation between them. In other words, y=a*sin(bx) where b is probably a function of pi. How do I find a and b in R? Hakan [[alternative HTML version deleted]] __ 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] Parameters of Beta distribution
Are A and B known? That is, are there known upper and lower bounds for this credit loss data? If not, you need to think about how to estimate those bounds. Why do you believe the data have a beta distribution? albyn On Wed, Oct 07, 2009 at 09:03:31AM -0400, jlu...@ria.buffalo.edu wrote: Rescale your data x to (x-A)/(B-A). Maithili Shiva maithili_sh...@yahoo.com Sent by: r-help-boun...@r-project.org 10/07/2009 08:39 AM To r-help@r-project.org cc Subject [R] Parameters of Beta distribution Supose I have a data pertaining to credit loss as amounts - c(46839.50,31177.12,35696.69,21192.57,29200.91,42049.64,42422.19, 44976.18, 32135.36,47936.57,27322.91,37359.09,43179.60, 48381.02, 45872.38, 28057.30,44643.83,36156.33,16037.62, 45432.28) I am trying to fit Beta distribution (two parameters distribution but where lower bound and upper bounds are NOT 0 and 1 respectively). For this I need to estimate the two parameters of Beta distribution. I found some code in VGAM pacakge but it deals with standard Beta distribution i.e. lower bound (say A) = 0 and upper bound (say B) = 1. How do I estimate the parameters of the Beta distribution for above data where A and B are not 0's? Please guide. Thanking you in advance Maithili Add whatever you love to the Yahoo! India homepage. Try now! http://in.yahoo.com/trynew [[alternative HTML version deleted]] __ 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. [[alternative HTML version deleted]] __ 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.
Re: [R] sinusoidal relationship
I assume that you are trying to fit the sinusoidal model, with an error term, to data: y = a * sin(b*x) + error Here you can use the `nls' function for non-linear least-squares. ?nls Here is an example: a - 0.5 b - 0.2 x - seq(0, 10, length=100) eps - rnorm(length(x), sd=0.1) y - a*sin(b*x) + eps plot(x, y, type=p) nls(y ~ a * sin(b*x), start=list(a=0.1, b=0.1)) Note that `nls' will fail to converge without the error term. Best, Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: rvarad...@jhmi.edu Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.h tml -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of HAKAN DEMIRTAS Sent: Wednesday, October 07, 2009 11:28 AM To: r-help@r-project.org Subject: [R] sinusoidal relationship Hi, Suppose x and y are vectors whose elements are known. I know that there is a sinusoidal relation between them. In other words, y=a*sin(bx) where b is probably a function of pi. How do I find a and b in R? Hakan [[alternative HTML version deleted]] __ 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.
Re: [R] [ESS] Emacs + ESS + R installer
Le mer. 7 oct. à 09:41, Stephen Eglen a écrit : Frank Liu frankcs...@gmail.com wrote: I and some students built an Emacs + ESS + R installer, which allows users to download and install the newest version of Emacs, ESS, and R with little pain.The size of the installer is about 8Mb. http://sourceforge.net/projects/emacs-for-r/ Please feel free to give me comments and suggestions. Thank you. sounds like a great idea - anything to reduce the barrier! How does it overlap/complement with what Vincent kindly provides: http://vgoulet.act.ulaval.ca/en/ressources/emacs/ Installing that + R should get to the same position. Vincent is providing a great resource for win (and mac) users, and if there is anyway of building on what he has done, it wuold be great. Stephen Ah, but I also have AUCTeX! ;-) Will definitely have a look at Frank et al.'s offer. Vincent Goulet, Full Professor École d'actuariat Université Laval, Québec vincent.gou...@act.ulaval.ca http://vgoulet.act.ulaval.ca __ 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] Plotting 1 covariate, 3 factors
I'm interested in plotting a y with an x factor as the combination of 2
factors and colour with respect to a third, which the code below does with
interaction.plot(). However, this is because I redefine the x to be 1
factor. Is there a way of getting it to plot without redefining it, and
ideally to not join up the lines BETWEEN levels a and b, but just join those
between after and before for one level of f3. I figure this could be done
by manually drawing over blank lines using ?lines but am not sure what the
coordinates would be and figured there is probably an easier way where
someone has dealt with this before. Any thoughts greatly appreciated,
Paul
#
y-rnorm(36)
f1-rep(c(after,before), 18)
f2-rep(1:3,12)
f3-rep(1:2, each=18)
## Define new factor to be f1 and f3 for x axis - clumsy code, but gets its
done;
ff-numeric(length(y))
for (i in 1:length(y))
{if (f1[i]==a f3[i]==1) ff[i]-1, a
else if(f1[i]==a f3[i]==2) ff[i]-2, a
else if(f1[i]==b f3[i]==1) ff[i]-1, b
else ff[i]-2, b}
## Plot of interest;
interaction.plot(ff,f2,y)
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Re: [R] plot an arrow / add arrow to a line
RSearch is your friend! (Do we need an LMRSTFY.org?) Had the OP used the RSearch facilities restricting the search to only functions, he would have found an astonishingly large number of functions (219) that mention arrows: http://search.r-project.org/cgi-bin/namazu.cgi?query=arrowsmax=100result=normalsort=scoreidxname=functions On Oct 7, 2009, at 3:33 AM, Peter Ehlers wrote: For nicer arrows, there are also the p.arrows() function in pkg:sfsmisc and the Arrows() function in pkg:IDPmisc. -Peter Ehlers Sarah Goslee wrote: How about arrows() ? On Tue, Oct 6, 2009 at 4:25 PM, Martin Batholdy batho...@googlemail.com wrote: hi, is it possible to end a line plotted with lines() with an arrow? Or are there any other functions to add an arrow to plot? thanks! David Winsemius, MD Heritage Laboratories West Hartford, CT __ 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] MCMClogit: normal intercept priors don't work
Dear R users, I think that the question I posted yesterday was not specific enough. Apologies for this. The question should have been: why does MCMClogit stop working if I a) set a normal prior for the intercept and b) remove all variables except for the intercept as explanatory? Example code: simulatedCase - rbinom(100,1,0.5) simDf - data.frame(CASE = simulatedCase) posterior_m0 - MCMClogit(CASE ~ 1, data = simDf, b0 = 0, B0 = 1) It should easily be possible to fit this model with the intercept part around -0.2 or so, and, in fact, when I use flat priors with posterior_m0 - MCMClogit(CASE ~ 1, data = simDf) this works -- and -0.2 is easily allowed by a N(0,1) prior on the intercept, so why doesn't this work any more? It this a bug, or am I simply overlooking the most obvious error? Best wishes, Alexander Düdo -- View this message in context: http://www.nabble.com/MCMClogit%3A-normal-intercept-priors-don%27t-work-tp25789993p25789993.html Sent from the R help mailing list archive at Nabble.com. __ 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] 2 questions about mle() /optim() function in stats4
Dear All,
There are two things about mle() that I wasn't so sure.
1) can mle() handle vector based parameter? say
ll-function(theta=rep(1,20)){..}
I tried such function, it worked for optim but not for mle.
2) is there a general suggestion for the maximum number of parameters
allowed to use in mle() or optim()?
Thank you.
Regards,
MJO
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[R] Power for Multiple regression?
Hi All, I came across this problem which is more a statistical question, I am hoping that some one can clarify this for me Is there a rule of thumb to determine how large your sample size should be before you perform multiple regression. I have search the web and I found some online tools where you provide the Alpha level, number of predictors, the effect size and the desired power. I have googled the effect size and I found that the effect size= R2/(1-R2) Where R2 is the coefficient of determination. I do not understand how to provide the effect size before doing the regression and what it means? From my understanding, the power of a test is the probability of rejecting a false null hypothesis. In this case what is the hypothesis we are testing? Would the null be testing All the BETA coefficients are ZERO simultaneously? Is it possible to look at the power to test for each BETA separately? i.e H0: B=0 vr Ha: B not equal to 0 I appreciate your help -- View this message in context: http://www.nabble.com/Power-for-Multiple-regression--tp25787420p25787420.html Sent from the R help mailing list archive at Nabble.com. __ 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] power?
Thanks Simon for the help. Simon Blomberg-4 wrote: The short answer is Yes. If you reject the null hypothesis based on that p-value, then by definition you had enough power to do that. This is because there is a precise inverse relationship between the p-value and the observed power, once you fix the effect size and the sample size. In other words, your post-hoc power analysis would be a simple re-statement of the p-value. There is no extra information that can be gained from such an analysis. See: The American Statistician, February 2001, Vol. 55, No. 1, pp 19-24 Don't bother with your power analysis, unless you are planning a new experiment. Simon. On Tue, 2009-10-06 at 13:49 -0700, SNN wrote: Hi, I have used multiple linear regression on a data set and one if the regressor was significant with a p-value =0.01 I need to calculate the power for a multiple linear regression. i.e. do I have enough power to believe the above p-value? -- Simon Blomberg, BSc (Hons), PhD, MAppStat. Lecturer and Consultant Statistician School of Biological Sciences The University of Queensland St. Lucia Queensland 4072 Australia Room 320 Goddard Building (8) T: +61 7 3365 2506 http://www.uq.edu.au/~uqsblomb email: S.Blomberg1_at_uq.edu.au Policies: 1. I will NOT analyse your data for you. 2. Your deadline is your problem. Statistics is the grammar of science - Karl Pearson __ 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. -- View this message in context: http://www.nabble.com/power--tp25776305p25787766.html Sent from the R help mailing list archive at Nabble.com. __ 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] Simulate negative skewed, fat-tailed distribution
Hi guys Is there a way in R to simulate/generate random numbers from a negative skewed and fat tailed distribution ? I would like to simulate a set of (discrete) data. Regards, Carlos Carlos http://www.nabble.com/file/p25783889/graph.png graph.png -- View this message in context: http://www.nabble.com/Simulate-negative-skewed%2C-fat-tailed-distribution-tp25783889p25783889.html Sent from the R help mailing list archive at Nabble.com. __ 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 with pchisq function
I have some data in my C code, I want to execute chi-square test on those data. I tried implementing pchisq() function making use of header files R.h, Rhead.H and Rinternals.h, but it neither gave me the result nor threw any errors. It just returned 0 or 1. Could you please help me how can I implement those functions ? I am attaching the test-code herewith. ( For test purposes, I have been inputting the data here). http://www.nabble.com/file/p25788093/CforR.c CforR.c -- View this message in context: http://www.nabble.com/Help-with-pchisq-function-tp25788093p25788093.html Sent from the R help mailing list archive at Nabble.com. __ 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] cforest regressions - mean of squared residuals
Hi there, I haven't been able to locate a way to get at this information in the manual or tutorial. Does anybody know how to retrieve it? Or amount of variance explained? Thanks, Annie -- View this message in context: http://www.nabble.com/cforest-regressions---mean-of-squared-residuals-tp25783906p25783906.html Sent from the R help mailing list archive at Nabble.com. __ 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] choose.files limit?
Howdy, When I use the choose.files command to read files a large number of file names to a character vector inside a function, used to access these files one after the other, there appears to be a limit. I do not know whether it is arbitrary, but in this case the limit was 991 files. The file names are long. Does that matter? The error message that appears says that it cannot find file #992 (giving the file name), although it is certainly there (I tried changing which file is #992 and it did not matter). Suggestions? - Gunnar --- Dr. Gunnar W. Schade Assistant Professor Texas AM University Department of Atmospheric Sciences 1104 Eller OM Building 3150 TAMU College Station, TX 77843-3150 USA ph.: 979 845 0633 Fax: 979 862 4466 __ 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] 2 questions about mle() /optim() function in stats4
Muhtar Osman wrote:
Dear All,
There are two things about mle() that I wasn't so sure.
1) can mle() handle vector based parameter? say
ll-function(theta=rep(1,20)){..}
I tried such function, it worked for optim but not for mle.
No. mle2, in the bbmle package, can (sort of) handle these
kinds of functions.
2) is there a general suggestion for the maximum number of parameters
allowed to use in mle() or optim()?
Thank you.
Regards,
MJO
It depends, but I would generally say that using this kind of
general-purpose
optimization with more than 10-20 (20-50?) parameters is likely to be
slow ... on the other hand, my data sets are rarely big enough to support
models like that.
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and provide commented, minimal, self-contained, reproducible code.
[R] Which JAGS interface to use?
Frank (or anyone else), can you offer any comments comparing runjags, R2jags, rjags ? I couldn't find any vignettes, nothing except a brief mention on Task Views. Kevin On Wed, Oct 7, 2009 at 7:48 AM, Frank E Harrell Jr f.harr...@vanderbilt.edu wrote: Have you tried the rjags package which uses the jags system? It is much more integrated into R and works quite well. It uses the same modeling language as BUGS. It is also better supported than OpenBUGS. Frank Bill Halteman wrote: Hi All, I am trying to figure out how to use R-Coda with the output from OpenBugs. I have installed and loaded the packages BRugs and R2WinBUGS. I have successfully run a simple Bayes model in WinBUGS using R2WinBUGS' bugs and have used read.bugs to build the coda object. I can successfully switch to OpenBugs and run the same model and get the basic summary back. However, I cannot build the coda object. From what I have read read.openbugs should do the trick. However, I have discovered the current version of OpenBUGS (v 3.03) doesn't write any output files in spite of setting codaPkg=TRUE in the bugs call. Str(openbugs.object) reveals a large collection of elements, one of which is an array that contains the MCMC chains. Is there a function to build the coda object? Thanks in advance for any suggestions, Bill Halteman -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ 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. [[alternative HTML version deleted]] __ 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] Plotting 1 covariate, 3 factors
## Paul ## I think you are looking for interaction2wt y - rnorm(36) f1 - rep(c(after, before), 18) f2 - rep(1:3, 12) f3 - rep(1:2, each=18) ## your definition of ff was faulty. It gave a constant. f3.f1 - interaction(f3, f1) interaction.plot(f3.f1, f2, y) f2 - factor(f2) f3 - factor(f3) ## lattice would be better xyplot(y ~ f2 | f3, groups=f2) ## if you don't have HH, you will need to install it and its dependencies ## install.packages(HH) ## You may need to close R and restart R require(HH) interaction2wt(y ~ f1 + f2 + f3) position(f1) - c(1.5, 2.5) position(f3) - c(1.5, 2.5) interaction2wt(y ~ f1 + f2 + f3, box.ratio=.6) ## Rich __ 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] Simulate negative skewed, fat-tailed distribution
Take a look at the `rstable' function in the stable package to simulate random deviates from a stable distribution. Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, The Center on Aging and Health Division of Geriatric Medicine and Gerontology Johns Hopkins University Ph: (410) 502-2619 Fax: (410) 614-9625 Email: rvarad...@jhmi.edu Webpage: http://www.jhsph.edu/agingandhealth/People/Faculty_personal_pages/Varadhan.h tml -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of inquil Sent: Wednesday, October 07, 2009 6:56 AM To: r-help@r-project.org Subject: [R] Simulate negative skewed, fat-tailed distribution Hi guys Is there a way in R to simulate/generate random numbers from a negative skewed and fat tailed distribution ? I would like to simulate a set of (discrete) data. Regards, Carlos Carlos http://www.nabble.com/file/p25783889/graph.png graph.png -- View this message in context: http://www.nabble.com/Simulate-negative-skewed%2C-fat-tailed-distribution-tp 25783889p25783889.html Sent from the R help mailing list archive at Nabble.com. __ 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.
Re: [R] Plotting 1 covariate, 3 factors
I'm not sure if this is exactly what you are looking for but I would
generally create an interaction plot using the lattice 'dotplot' with
type = c(p,a) so I get both the original data and the lines
joining the averages for the different factor levels. I also prefer
the horizontal orientation to the vertical orientation. Combining all
these variations produces something like
dotplot(f2 ~ y | f1, groups = f3, aspect = 0.2, layout = c(1,2), type
= c(p,a), pch = 21, strip = FALSE, strip.left = TRUE, auto.key =
list(columns = 2, lines = TRUE))
On Wed, Oct 7, 2009 at 11:00 AM, Paul Chatfield p.s.chatfi...@rdg.ac.uk wrote:
I'm interested in plotting a y with an x factor as the combination of 2
factors and colour with respect to a third, which the code below does with
interaction.plot(). However, this is because I redefine the x to be 1
factor. Is there a way of getting it to plot without redefining it, and
ideally to not join up the lines BETWEEN levels a and b, but just join those
between after and before for one level of f3. I figure this could be done
by manually drawing over blank lines using ?lines but am not sure what the
coordinates would be and figured there is probably an easier way where
someone has dealt with this before. Any thoughts greatly appreciated,
Paul
#
y-rnorm(36)
f1-rep(c(after,before), 18)
f2-rep(1:3,12)
f3-rep(1:2, each=18)
## Define new factor to be f1 and f3 for x axis - clumsy code, but gets its
done;
ff-numeric(length(y))
for (i in 1:length(y))
{if (f1[i]==a f3[i]==1) ff[i]-1, a
else if(f1[i]==a f3[i]==2) ff[i]-2, a
else if(f1[i]==b f3[i]==1) ff[i]-1, b
else ff[i]-2, b}
## Plot of interest;
interaction.plot(ff,f2,y)
--
View this message in context:
http://www.nabble.com/Plotting-1-covariate%2C-3-factors-tp25789442p25789442.html
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Re: [R] power? -- Wait a minute!
Whoa -- wait a minute here! The poster said that one of the regressors had a P-value of .01, and asked if this was believable. One of how many? -- 3? 300? What about multiplicity? How was the regression model selected -- P Values are essentially meaningless when computed **after** model selection. And what does the design look like? -- is the regressor highly correlated with others? So I would say the short answer is that the .01 P value is meaningless without further information. The longer answer is a rant on the misuse and (ir?)relevance of P values hypothesis tests, and the like in scientific work, which I will spare you all from. However, for those who may wonder about such ravings, have a look at: http://www.philosophynow.org/issue74/74pigliucci.htm Cheers, Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of SNN Sent: Wednesday, October 07, 2009 7:31 AM To: r-help@r-project.org Subject: Re: [R] power? Thanks Simon for the help. Simon Blomberg-4 wrote: The short answer is Yes. If you reject the null hypothesis based on that p-value, then by definition you had enough power to do that. This is because there is a precise inverse relationship between the p-value and the observed power, once you fix the effect size and the sample size. In other words, your post-hoc power analysis would be a simple re-statement of the p-value. There is no extra information that can be gained from such an analysis. See: The American Statistician, February 2001, Vol. 55, No. 1, pp 19-24 Don't bother with your power analysis, unless you are planning a new experiment. Simon. On Tue, 2009-10-06 at 13:49 -0700, SNN wrote: Hi, I have used multiple linear regression on a data set and one if the regressor was significant with a p-value =0.01 I need to calculate the power for a multiple linear regression. i.e. do I have enough power to believe the above p-value? -- Simon Blomberg, BSc (Hons), PhD, MAppStat. Lecturer and Consultant Statistician School of Biological Sciences The University of Queensland St. Lucia Queensland 4072 Australia Room 320 Goddard Building (8) T: +61 7 3365 2506 http://www.uq.edu.au/~uqsblomb email: S.Blomberg1_at_uq.edu.au Policies: 1. I will NOT analyse your data for you. 2. Your deadline is your problem. Statistics is the grammar of science - Karl Pearson __ 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. -- View this message in context: http://www.nabble.com/power--tp25776305p25787766.html Sent from the R help mailing list archive at Nabble.com. __ 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.
Re: [R] Problem using with panel.average in Lattice package
On Sun, Oct 4, 2009 at 3:20 PM, Peter Ehlers ehl...@ucalgary.ca wrote:
Deepayan,
Is something similar needed in the last example in ?xyplot? I don't
see panel.linejoin producing any lines.
You are right (I never noticed because that example doesn't get run).
I'll hard-code the type=l in panel.average/linejoin.
-Deepayan
Regards,
Peter Ehlers
Deepayan Sarkar wrote:
On Fri, Oct 2, 2009 at 8:03 PM, Mark Dalphin mark.dalp...@peblnz.com
wrote:
Hi,
I'm having a problem getting the panel.average function to work as I
expect it to in a lattice plot. I wish to draw lines between the
averages of groups of y-values at specific x-values. I have created a
dataset below which is similar to my real data. I also show an example
of using panel.loess in place of panel.average; it performs in a
manner similar to what I want panel.average to do except it shows a
loess line rather than a straight line connecting the means of the
groups.
Please see my coded examples, below.
Regards,
Mark Dalphin
=
My system information:
library(lattice)
print(sessionInfo())
R version 2.9.1 (2009-06-26) i686-pc-linux-gnu
locale:
LC_CTYPE=en_NZ.UTF-8;LC_NUMERIC=C;LC_TIME=en_NZ.UTF-8;LC_COLLATE=en_NZ.UTF-8;
LC_MONETARY=C;LC_MESSAGES=en_NZ.UTF-8;LC_PAPER=en_NZ.UTF-8;LC_NAME=C;
LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_NZ.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lattice_0.17-25
loaded via a namespace (and not attached):
[1] grid_2.9.1 tools_2.9.1
##--
## This dataset is too complicated, but it does show the type of plot I
want.
##
## Create a fake qPCR dataset: Eight 96-well plates over 4 days (2 per
day),
## 2 genes per plate (multiplexed), and 4 Hi positive control and
## 4 Lo positive controls per plate.
## Create the experimental data; by rights it is all identical, expect
for
## experimental errors with in days and between days.
## For this simulation, each gene will be given a base value.
## In qPCR the higher the Ct value, the lower the concentration.
library(lattice) # Add for ease of cut-n-paste of this code
date - c('2009-09-07', '2009-09-08', '2009-09-10', '2009-09-14')
probe - c('Gene.A1', 'Gene.A2', 'Gene.B1', 'Gene.B2')
conc - c('Lo', 'Hi')
base.lo - c(Gene.A1=29, Gene.A2=25, Gene.B1=28, Gene.B2=31)
base.hi - base.lo - 8
day.err - c(Day.1=0, Day.2=1, Day.3=1.5, Day.4=1.0)
d - data.frame()
for(i in seq(along=date)) {
for(j in seq(along=probe)) {
for(k in seq(along=conc)) {
d - rbind(d, data.frame(Date=rep(date[i], length=4),
Probe=rep(probe[j], length=4),
Conc=rep(conc[k], length=4),
Ct=rnorm(4, sd=0.5) + (k-1)*8 +
base.hi[j] + day.err[i]
))
}
}
}
d$Date - as.POSIXct(d$Date)
##--
## Example 1
## Print with LOESS line showing the 'means' for the groups.
## This is close, but I don't want a loess line; I want straight lines
## between mean values.
print(xyplot(Ct ~ Date|Probe, group=Conc, data=d,
panel=panel.superpose,
panel.groups=function(x, y, ...) {
panel.loess(x, y, ...)
panel.xyplot(x, y, ...)
},
auto.key=TRUE))
##--
## Example 2
## Parallel construction to the loess example, above.
## Note the loss of the lines. The 'horizontal' default
## is different between 'panel.loess' and 'panel.average'.
print(xyplot(Ct ~ Date|Probe, group=Conc, data=d,
panel=panel.superpose,
panel.groups=function(x, y, ...) {
panel.average(x, y, horizontal=FALSE, ...)
panel.xyplot(x, y, ...)
},
auto.key=TRUE))
Unfortunately, the implicit type=p argument in panel.superpose is
overriding the type=l in panel.average (may be it should be
unmodifiable). So, you need
print(xyplot(Ct ~ Date|Probe, group=Conc, data=d,
panel=panel.superpose,
panel.groups=function(x, y, ..., type) {
panel.average(x, y, ..., type = l, horizontal = FALSE)
panel.xyplot(x, y, ..., type = type)
},
auto.key=TRUE))
It's more common to use the syntactic sugar provided by panel.xyplot:
print(xyplot(Ct ~ Date|Probe, group=Conc, data=d,
type = c(p, a),
auto.key=TRUE))
##--
## Example 3
## Don't pass along the '...' to the panel.average. Now I
## get lines, but not matching colours to the points.
print(xyplot(Ct ~ Date|Probe, group=Conc, data=d,
panel=panel.superpose,
[R] error using predict() / fRegression-package
Hello! I'm puzzled by the following problem. It occurs while trying to predict responses in a test-dataset using a linear model fitted with regFit from the rMetrics fRegression-package. All goes well when I call predict using the training dataset. However, a call using the test-dataset retuns an error message - telling me that the latter dataset provides variables of different type than the training set. But inspection of the structure of both dataframes shows, that the variables are still all of the type numeric. (See attached session protocol.) Does anyone have an idea how to fix this? Any help would greatly be appreciated! Kind regards, Gero str(regdata) 'data.frame':89 obs. of 7 variables: $ ret1 : num 0.0275 -0.01013 0.00569 -0.01582 0.0226 ... $ lag(ret1): num NA 0.0275 -0.01013 0.00569 -0.01582 ... $ lag(ret2): num NA 0.04072 -0.00509 0.02055 -0.01548 ... $ lag(ret3): num NA 0.05393 0.00299 0.02432 0.02251 ... $ (lag(ret1)*lag(ret2)): num NA 1.12e-03 5.16e-05 1.17e-04 2.45e-04 ... $ (lag(ret1)*lag(ret3)): num NA 1.48e-03 -3.03e-05 1.38e-04 -3.56e-04 ... $ (lag(ret2)*lag(ret3)): num NA 2.20e-03 -1.52e-05 5.00e-04 -3.48e-04 ... str(regdata.test) 'data.frame':23 obs. of 6 variables: $ lag(ret1): num NA 0.01554 0.01458 0.00333 0.01674 ... $ lag(ret2): num NA 0.01373 0 0.01331 0.00686 ... $ lag(ret3): num NA 0.0278 0.0152 0.0211 -0.0104 ... $ (lag(ret1)*lag(ret2)): num NA 2.13e-04 0.00 4.43e-05 1.15e-04 ... $ (lag(ret1)*lag(ret3)): num NA 4.32e-04 2.21e-04 7.03e-05 -1.75e-04 ... $ (lag(ret2)*lag(ret3)): num NA 3.82e-04 0.00 2.81e-04 -7.16e-05 ... ar1.xpred.fitted - regFit(ar1.xpred.model, data = regdata, use = lm) ar1.xpred.train.pred - predict(ar1.xpred.fitted, regdata, se.fit = FALSE) ar1.xpred.test.pred - predict(ar1.xpred.fitted, regdata.test, se.fit = FALSE) Fehler: variable 'lag(ret1)' was fitted with type numeric but type nmatrix.1 was supplied Zusätzlich: Warnmeldung: 'newdata' had 23 rows but variable(s) found have 89 rows __ 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] Which JAGS interface to use?
We use it on Linux - here's our how-to: http://biostat.mc.vanderbilt.edu/JAGSInstallExample Frank Kevin Wright wrote: Frank (or anyone else), can you offer any comments comparing runjags, R2jags, rjags ? I couldn't find any vignettes, nothing except a brief mention on Task Views. Kevin On Wed, Oct 7, 2009 at 7:48 AM, Frank E Harrell Jr f.harr...@vanderbilt.edu mailto:f.harr...@vanderbilt.edu wrote: Have you tried the rjags package which uses the jags system? It is much more integrated into R and works quite well. It uses the same modeling language as BUGS. It is also better supported than OpenBUGS. Frank Bill Halteman wrote: Hi All, I am trying to figure out how to use R-Coda with the output from OpenBugs. I have installed and loaded the packages BRugs and R2WinBUGS. I have successfully run a simple Bayes model in WinBUGS using R2WinBUGS' bugs and have used read.bugs to build the coda object. I can successfully switch to OpenBugs and run the same model and get the basic summary back. However, I cannot build the coda object. From what I have read read.openbugs should do the trick. However, I have discovered the current version of OpenBUGS (v 3.03) doesn't write any output files in spite of setting codaPkg=TRUE in the bugs call. Str(openbugs.object) reveals a large collection of elements, one of which is an array that contains the MCMC chains. Is there a function to build the coda object? Thanks in advance for any suggestions, Bill Halteman -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@r-project.org mailto: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. -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ 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] Need a vectorized way to avoid two nested FOR loops
Hi Friends, I have a data frame d. Let vars be the column indices for a subset of the columns in d (e.g., vars - c(1,3,4,8)) For each row r in d, I want to collect all the other rows in d that match the values in row r for just the columns in vars. The naive way to do this is to have a for loop stepping through each row in d, and within the loop have another loop going through all the rows again, checking for equality. This is quadratic in the number of rows and takes way too long. Is there a better, vectorized way to do this? Thanks in advance! Rama Ramakrishnan __ 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] graphics
Dear Sir,
I am using the following cos which creates a 3 panel figure on one image.
However the legend function i am using only allows the legend to be placed
within the axes of one of the graphs.
The plots however do not allow for a logend to be places within the axes do to
the location of points on the graph. I can add the legend later using imaging
software such as paint but i lose resolution by doing this.
Is it possible to place the legend out side of figure axes on the white area
around all three panels?
Any help would be greatly appreciated.
Thank you
Grant
single-read.table(C:\\Grant\\hatchfirstonly.txt,header=T)
attach(single)
names(single)
par(mfrow=c(1,3))
maleage- factor(maleage, labels = c(Old,Young))
colors - c('gray', navyblue)
shapes - c(17,19)
proportion-(eggs1-unhatch1)/eggs1
plot(proportion~maleage, xlab= Age of Male , ylab = Proportion of Eggs
Hatched)
plot(proportion~femweight, pch=shapes[maleage], col=colors[maleage],bg=gray,
xlab= Female Weight (grams) , ylab = Proportion of Eggs Hatched)
abline(lm(proportion~femweight))
plot(proportion~copdurationsecs, pch=shapes[maleage],
col=colors[maleage],bg=gray, xlab= Copulation Duration (minutes) , ylab =
Proportion of Eggs Hatched)
abline(lm(proportion~copdurationsecs))
legend(locator(1), as.character(levels(factor(maleage))),pch=shapes[maleage],
col=colors[maleage])(levels(factor(maleage)))
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Re: [R] is that possible to graph 4 dimention plot
Suppose there are 4 variables d is a function of a , b and c I want to know how a, b and c change will make d change It will be straightforward to see it if we can graph the d surface if d is only a function of a and b, I can use 'persp' to see the surface of d. I can easily see at what values of a and b, d will get the maxium or minium or multiple modes, etc But for 4 dimention graph, is there a way to show the surface of d Will use color help Thanks a lot Not sure what your data looks like, but you might also consider looking at a 2 dimensional version. See ?coplot for example: coplot(lat ~ long | depth * mag, data = quakes) Or you can make 2 or 3-dimensional plots using the lattice package conditioning on some of the variables - e.g. d ~ a | b * c, etc. If a, b, and c are continuous, you can use equal.count. Here is an uninteresting example, considering a, b, and c as points along a grid: a - b - c - seq(1:10) dat - data.frame(expand.grid(a, b, c)) names(dat) - letters[1:3] dat$d - with(dat, -(a-5)^2 - (b-5)^2 - (c-5)^2) library(lattice) # 2-d: xyplot(d ~ a | equal.count(b)*equal.count(c), data=dat, type=l) # etc. # 3-d: contourplot(d ~ a * b | equal.count(c), data=dat) wireframe(d ~ a * b | equal.count(c), data=dat) __ 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] graphics
On Oct 7, 2009, at 2:01 PM, McDonald, Grant wrote:
Dear Sir,
I am using the following cos which creates a 3 panel figure on one
image. However the legend function i am using only allows the
legend to be placed within the axes of one of the graphs.
The plots however do not allow for a logend to be places within the
axes do to the location of points on the graph. I can add the
legend later using imaging software such as paint but i lose
resolution by doing this.
Is it possible to place the legend out side of figure axes on the
white area around all three panels?
Any help would be greatly appreciated.
Doesn't mtext let you do what you want?
perhaps:
mtext(Desired Text, outer=TRUE)
single-read.table(C:\\Grant\\hatchfirstonly.txt,header=T)
attach(single)
names(single)
par(mfrow=c(1,3))
maleage- factor(maleage, labels = c(Old,Young))
colors - c('gray', navyblue)
shapes - c(17,19)
proportion-(eggs1-unhatch1)/eggs1
plot(proportion~maleage, xlab= Age of Male , ylab = Proportion of
Eggs Hatched)
plot(proportion~femweight, pch=shapes[maleage],
col=colors[maleage],bg=gray, xlab= Female Weight (grams) , ylab
= Proportion of Eggs Hatched)
abline(lm(proportion~femweight))
plot(proportion~copdurationsecs, pch=shapes[maleage],
col=colors[maleage],bg=gray, xlab= Copulation Duration (minutes)
, ylab = Proportion of Eggs Hatched)
abline(lm(proportion~copdurationsecs))
legend(locator(1),
as.character(levels(factor(maleage))),pch=shapes[maleage],
col=colors[maleage])(levels(factor(maleage)))
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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Re: [R] graphics
Hello, On Wed, Oct 7, 2009 at 2:01 PM, McDonald, Grant grant.mcdonal...@imperial.ac.uk wrote: Dear Sir, Well, I'm not a sir but perhaps I can help anyway. Is it possible to place the legend out side of figure axes on the white area around all three panels? Any help would be greatly appreciated. Like this: plot(1:10, 1:10) par(xpd=NA) legend(locator(), nothing, pch=1) Or instead of locator(), a function that lets you use a mouse click to select a point, you can use par(usr) to learn the current coordinate system, and select a value outside of that range. Sarah -- Sarah Goslee http://www.functionaldiversity.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] graphics
Here is another way of creating the legend using layout
layout(cbind(1,2), width=c(7,1))
plot(1:10,1:10)
# now create legend
old.par - par(mar=c(3, 0, 3, 0))
plot.new()
legend('left', legend=c('line 1', 'line 2'))
par(old.par)
On Wed, Oct 7, 2009 at 2:01 PM, McDonald, Grant
grant.mcdonal...@imperial.ac.uk wrote:
Dear Sir,
I am using the following cos which creates a 3 panel figure on one image.
However the legend function i am using only allows the legend to be placed
within the axes of one of the graphs.
The plots however do not allow for a logend to be places within the axes do
to the location of points on the graph. I can add the legend later using
imaging software such as paint but i lose resolution by doing this.
Is it possible to place the legend out side of figure axes on the white area
around all three panels?
Any help would be greatly appreciated.
Thank you
Grant
single-read.table(C:\\Grant\\hatchfirstonly.txt,header=T)
attach(single)
names(single)
par(mfrow=c(1,3))
maleage- factor(maleage, labels = c(Old,Young))
colors - c('gray', navyblue)
shapes - c(17,19)
proportion-(eggs1-unhatch1)/eggs1
plot(proportion~maleage, xlab= Age of Male , ylab = Proportion of Eggs
Hatched)
plot(proportion~femweight, pch=shapes[maleage],
col=colors[maleage],bg=gray, xlab= Female Weight (grams) , ylab =
Proportion of Eggs Hatched)
abline(lm(proportion~femweight))
plot(proportion~copdurationsecs, pch=shapes[maleage],
col=colors[maleage],bg=gray, xlab= Copulation Duration (minutes) , ylab =
Proportion of Eggs Hatched)
abline(lm(proportion~copdurationsecs))
legend(locator(1), as.character(levels(factor(maleage))),pch=shapes[maleage],
col=colors[maleage])(levels(factor(maleage)))
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Re: [R] Installing R on Suse 11.1 , cannot figure it out
see below: Robert Wilkins wrote: Can't figure out how the install works, it is certainly not automatic. Also , the Install option on the R web site for Suse 11.1 does not work. And the install software native to Suse, cannot figure out. Does Suse have more problems installing software than Fedora or Ubuntu? Did you try installing the RPMS listed under your favorite CRAN mirror? (note, I didn't use the install links for the Readme file, I think you could grab these using 'wget' http://streaming.stat.iastate.edu/CRAN/bin/linux/suse/11.1/RPMS/i586/R-base-2.9.0-2.1.i586.rpm -and devel- http://streaming.stat.iastate.edu/CRAN/bin/linux/suse/11.1/RPMS/i586/R-base-devel-2.9.0-2.1.i586.rpm You may also have to compile R from source... Or is this a hassle for any Linux distro? And Windows? My windows installs have been relatively hassle-free (5 workstations). I just finished setting up a small cluster (3) of ubuntu R instances in under 30 minutes. So, your mileage may vary. I've found Ubuntu to be rather simple to install R instances. Hope this helps c = *Cedrick W. Johnson* aolim) cedrickjcvgr www.cedrickjohnson.com *New York - Chicago* __ 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.
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Re: [R] Installing R on Suse 11.1 , cannot figure it out
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