[R] displaying percentage in bar plot
Hi, I have a query regarding barplot I have a following data AIS LEvel 1 23 body regionA 10 15 20 B 15 25 15 Now I want to plot a barplot and in each bar (corresponding a body region), I need a percentage of AIS level 1 displayed in the plot. Is there an easy way to do this ? Thanks, Nataraju GM -- No relationship is Static .. You either Step up or Step down [[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] issue building my own package... moving from Apple OS to Windows
Yeah, you have to build a binary package for windows, unless you just want to simply source all the functions into R. 2009/4/24 Daryl Morris dar...@u.washington.edu: Hello, I have written my own very simple package. On an Apple, I was able to run through the R CMD build and R CMD check successfully. I have also installed the package, and successfully loaded the library on my Apple. This package is written entirely in R and requires no compilation. I am trying to move the package to a Windows machine. I (perhaps naively) thought, given that it contains no code requiring compilation, that I should just be able to take the .tar.gz file and directly install it in Windows. This didn't work. Nor did translating' the contents of the .tar.gz file into a .zip file. I was about to provide the errors, but more googling on this issue suggests that maybe what I'm trying to do is impossible. Do I really have to build on a Windows box ... even when the package requires no compilation? Is there no simple translation tool available for this case? thank you, Daryl U. Washington Biostatistics __ 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. -- HUANG Ronggui, Wincent PhD Candidate Dept of Public and Social Administration City University of Hong Kong Home page: http://asrr.r-forge.r-project.org/rghuang.html __ 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 intervals (alpha and beta) for model average estimates from binomial glm and model.avg (library=dRedging)
Hi all, I was wondering if there is a function out there, or someone has written code for making confidence intervals around model averaged predictions (y~á+âx). The model average estimates are from the dRedging library? It seems a common thing but I can't seem to find one via the search engines Examples of the models are: fit1 - glm(y~ dbh, family = binomial, data = data) fit2 - glm(y~ dbh+vegperc, family = binomial, data = data) fit3 - glm(y~ dbh, family = binomial, data = data) and the model averaging model.averaging -model.avg(fit1,fit2,fit3, method=0) and the output (from model.avg) has the following items: Coefficient, Variance, Standard error, adjusted standard error and lower and upper confidence interval for each parameter (and intercept). What I would like to do is make prediction intervals. I know I need to include covariance and variance. Please let me know if anyone has a function or code to get these prediction intervals out of this output. Thanks in advance for your help, and please advise me if you need more information M michelle.ens...@nt.gov.au R version 2.8.1 [[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] Terminology: Multiple Regression versus multivariate Regression
Hello R-Members, can anyone explain the difference between multiple and multivariate regression to me in terms of the terminology and eventually its respect to the mathematical foundation respectively ? Is multiple regression perhaps more related to GLM and multivariate Regression rather applied, if there are no explizit numeric factor levels ? Thanks for elucidations on that topic. Many thanks and best regrads Bjoern Heute schon gefreeMailt? Jetzt kostenlose E-Mail-Adresse sichern! http://email.freenet.de/dienste/emailoffice/produktuebersicht/basic/mail/index.html?pid=6831 __ 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] issue building my own package... moving from Apple OS to Windows
Daryl Morris wrote: Hello, I have written my own very simple package. On an Apple, I was able to run through the R CMD build and R CMD check successfully. I have also installed the package, and successfully loaded the library on my Apple. This package is written entirely in R and requires no compilation. I am trying to move the package to a Windows machine. I (perhaps naively) thought, given that it contains no code requiring compilation, that I should just be able to take the .tar.gz file and directly install it in Windows. This didn't work. Nor did translating' the contents of the .tar.gz file into a .zip file. I was about to provide the errors, but more googling on this issue suggests that maybe what I'm trying to do is impossible. Do I really have to build on a Windows box ... even when the package requires no compilation? Is there no simple translation tool available for this case? You need to INSTALL a source package (that has been build) as on any other platform. How to colect the tools in order to make R CMD INSTALL work under Windows (and other OSs) is described in the R Installation and Administration manual. Best, Uwe Ligges thank you, Daryl U. Washington Biostatistics __ 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] power.t.test formula
Peter Dalgaard: Does anyone of you knows a reference for the formula used in power.t.test function? And also why it uses the Student's distribution instead of Normal. (I know both of them can be used but don't see whether choose one or the other) It is a straightforward first-principles calculation. The t distribution calculation is exact for normally distributed data with the same unknown variance in both groups. I didn’t know about power.t.test. A very nice function, indeed. Is there a similar function that handles unequal number of observations for each group, and unequal variances? The help file mislead me into thinking that power.t.test handles unequal number of observations, and for example ‘power.t.test(c(10,3),1)’ *does* give some output (and not a warning or error), just not the output I was expecting. (It gives two power values, one for sample of size 10 (for each group) and one for samples of size 3 (for each group), while I was expecting the power for a sample size 10 for one group and 3 for the other group). -- Karl Ove Hufthammer __ 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] Terminology: Multiple Regression versus multivariate Reg
On 24-Apr-09 08:14:34, str...@freenet.de wrote: Hello R-Members, can anyone explain the difference between multiple and multivariate regression to me in terms of the terminology and eventually its respect to the mathematical foundation respectively ? Is multiple regression perhaps more related to GLM and multivariate Regression rather applied, if there are no explizit numeric factor levels ? Thanks for elucidations on that topic. Many thanks and best regrads Bjoern This is indeed a question of terminology and usage, and there is a degree of variability in it. As far as I am concerned (and others, though not all), multivariate regression refers to regression where the dependent (outcome) variable is mutltivariate: Y ~ X where each instance of Y is a multivariate observation. For example, suppose G (growth) consists of two pieces of data: height and weight, and A is Age. Then a multivariate regression model would look like G ~ A or (Ht,Wt) ~ Age (two variables on the left, one variable on the right). This allows for correlation between Ht and Wt to be part of the model. What is generally meant by multiple regression is regression of a single variable (on the left) on more than one variable (on the right), for example Wt ~ Ht + Age If you must make a distinction, there is the term simple regression (nowadays rarely used) for when there is only one variable on the right: Wt ~ Age Whether this is a linear model (use lm()) or a generalised linear model (use glm()) has nothing to do with the termonology. There is an unfortunate (in my view) tendency for people to use multivariate regression whden talking about what I call multiple regression above (i.e. more than 1 independent variable). I think this should be reserved for regression where the left-hand side is multivariate. But maybe I'm in a minority ... Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 24-Apr-09 Time: 10:00:23 -- XFMail -- __ 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] displaying percentage in bar plot
I have a following data
AIS LEvel
1 23
body regionA 10 15 20
B 15 25 15
Now I want to plot a barplot and in each bar (corresponding a body
region),
I need a percentage of AIS level 1 displayed in the plot. Is there an
easy
way to do this ?
Try this:
x - matrix(c(10,15,15,25,20,15), ncol=3)
pct - apply(x, 1, function(x) 100*x[1]/sum(x))
custompanelfn - function(...)
{
panel.barchart(...)
panel.text(x=c(5,5), y=c(1,2),paste(format(pct, digits=3),%, sep=))
}
library(lattice)
barchart(x, panel=custompanelfn)
Regards,
Richie.
Mathematical Sciences Unit
HSL
ATTENTION:
This message contains privileged and confidential inform...{{dropped:20}}
__
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] Terminology: Multiple Regression versus multivariate Reg
(Ted Harding) wrote: There is an unfortunate (in my view) tendency for people to use multivariate regression whden talking about what I call multiple regression above (i.e. more than 1 independent variable). I think this should be reserved for regression where the left-hand side is multivariate. But maybe I'm in a minority ... If so, a minority of at least two... Part of the problem is that people will often (for better or worse) screen a set of predictors by univariate regression, which should probably be the rather less catchy single-predictor regression. (As far as I remember, SPSS, canonicalizes the term in its menu system.) -- 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.
Re: [R] Can't install package glmnet
Liang Zhang wrote: Hi, I was trying to install package glmnet in R, but failed and it show such messages: * Installing *source* package glmnet ... This package has only been tested with gfortran. So some checks are needed. R_HOME is /home/username/R/R-2.9.0 Attempting to determine R_ARCH... R_ARCH is Attempting to detect how R was configured for Fortran 90 Unsupported Fortran 90 compiler or Fortran 90 compilers unavailable! Stop! ERROR: configuration failed for package glmnet * Removing /home/username/R/R-2.9.0/library/glmnet The downloaded packages are in /tmp/RtmpwsLWSc/downloaded_packages Updating HTML index of packages in '.Library' Warning message: In install.packages(glmnet) : installation of package 'glmnet' had non-zero exit status It seems that it needs fortran 90 complier. What can I do to solve this problem? (I am not the administrator, only a user in the linux system). Ask for a suitable compiler? Uwe Ligges Thank you very much! Liang [[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] Box-counting dimension and package 'fdim'
Remko Duursma wrote: Dear R-helpers, I am looking for an implementation of the box-counting algorithm to estimate the box dimension of a cloud of points in 3D (aka fractal dimension, or similarity dimension). The package 'fdim' might be doing this, but the documentation is awful and I don't understand what is what there. Does anyone know of an implementation of this algorithm in R, or elsewhere, or uses the fdim package successfully and can help me out? Perhaps ask the author or package maintainer? And if so, you might want to volunteer to improve the help pages and add what you looked for, then both of you can benefit. Best, Uwe Ligges thanks, Remko - Remko Duursma Post-Doctoral Fellow Centre for Plant and Food Science University of Western Sydney Hawkesbury Campus Richmond NSW 2753 Dept of Biological Science Macquarie University North Ryde NSW 2109 Australia Mobile: +61 (0)422 096908 __ 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] suffix convention?
Sebastian P. Luque wrote: Hi, Is there some convention for choosing 'RData' or 'rda' for binary files written by save() or save.image()? I don't think so, I'd prefer RData myself. The docs treat these interchangeably. Thanks. Indeed. Best, Uwe Ligges Cheers, __ 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 see the content of geepack package
Dear list members, I need to see the content of the functions in package geepack. It uses some C functions in the computation they are not available in the package directory. How can I see the content of C functions? Kind Regards, Thank you, Aysun Cetinyurek __ 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] Array
Hi there, Just wondering if anyone has any tips for using arrays? I am trying to convert the following SAS code to R: data A2; set A1; by subject_id; retain BX1-BX10i; array b(1:10) BX1-BX10 ; if first.subject_id then do ; do j=1 to 10; b(j) = .; end; i=1; end; b(i) = BX; i = i+1; if last.subject_id then output; run ; Many thanks in advance, Bronagh [[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] Nonlinear regression help
Taylor Hermes wrote: I seek help with nonlinear regression for my data. I've run intro trouble fitting a model to my data as follows: rate_parameter stable_population 75 1996.1277 100 1623.2979 125 1362.3475 150 1164.6738 175 1014.8227 200 892.0851 225 794.1844 250 710.1489 275 639.6738 300 578.0496 325 525.4965 350 479.4752 375 440.3050 400 402.4397 The rate_parameter here will be my independent variable which affects the stable_population quantity in an agent-based simulation. I can see that the plot of this data seems to fit an exponential decay. I would greatly appreciate if someone could help me out with this task. I've found the following info on this page helpful: https://stat.ethz.ch/pipermail/r-help/2001-December/017330.html yet, still unable to grasp what I need to do. Is this homework? Anyway, I'd go with a simple linear model given your data.frame is called dat: lm(log(stable_population) ~ sqrt(rate_parameter), data = dat) Not sure why you want to apply something nonlinear. Uwe Ligges 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. __ 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 see the content of geepack package
you can download the source code of the package from: http://cran.r-project.org/web/packages/geepack/index.html and inspect it; you probably want to look at the 'src' directory. I hope it helps. Best, Dimitris Cetinyürek Aysun wrote: Dear list members, I need to see the content of the functions in package geepack. It uses some C functions in the computation they are not available in the package directory. How can I see the content of C functions? Kind Regards, Thank you, Aysun Cetinyurek __ 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. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ 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 see the content of geepack package
For example, read Ligges, U. (2006): R Help Desk: Accessing the Sources. R News 6 (4), 43-45. http://cran.r-project.org/doc/Rnews/Rnews_2006-4.pdf Best, Uwe Ligges Cetinyürek Aysun wrote: Dear list members, I need to see the content of the functions in package geepack. It uses some C functions in the computation they are not available in the package directory. How can I see the content of C functions? Kind Regards, Thank you, Aysun Cetinyurek __ 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] Array
Bronagh Grimes wrote: Just wondering if anyone has any tips for using arrays? You're presupposing that R works like SAS. It doesn't. This looks like a job for reshape (either Hadley Wickham's package or the built-in function). I am trying to convert the following SAS code to R: data A2; set A1; by subject_id; retain BX1-BX10i; array b(1:10) BX1-BX10 ; if first.subject_id then do ; do j=1 to 10; b(j) = .; end; i=1; end; b(i) = BX; i = i+1; if last.subject_id then output; run ; -- 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.
Re: [R] Array
Thanks for this, will have a look now. Much appreciated, -Original Message- From: Peter Dalgaard [mailto:p.dalga...@biostat.ku.dk] Sent: 24 April 2009 11:40 To: Bronagh Grimes Cc: r-help@r-project.org Subject: Re: [R] Array Bronagh Grimes wrote: Just wondering if anyone has any tips for using arrays? You're presupposing that R works like SAS. It doesn't. This looks like a job for reshape (either Hadley Wickham's package or the built-in function). I am trying to convert the following SAS code to R: data A2; set A1; by subject_id; retain BX1-BX10i; array b(1:10) BX1-BX10 ; if first.subject_id then do ; do j=1 to 10; b(j) = .; end; i=1; end; b(i) = BX; i = i+1; if last.subject_id then output; run ; -- 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] stata == R - error messages
Dear Sirs, I am just starting with R and I think it is a great system. Now, I want to import Stata datasets (.dta) with read.dta, but receive errormessages like: Error in grep(^(http|ftp|https)://, file) : object Rklein not found Error in read.dta(Rklein) : unable to open file: 'No such file or directory' this happens when I use What is the problem and how can I solve it? Best regards, Rob Bakker, Amsterdam [[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] Failing to print mer object in an RData image
Have you load lme4 before you print the object? Yes, I have. If yes, it may be caused by the change of representation of mer class. That may be so (although the image was saved on 12/19/2008, i.e. AFTER the release data of the lmer version I have now. But maybe I did that on a different computer. Question though: does that mean that the mer object is now inaccessible and the only way to get the data back is to run the analyses again? The changes are not backward compatible?? Thx, RZ 2009/4/23 Robert Zimbardo robertzimba...@gmail.com: Hi all I have problems in accessing a mer object called model.01 from a workspace that was created with R 2.8.1 and saved with save into an .RData file (on Windows XP or Ubuntu 8.10, don't remember anymore). Now I want to open it in R 2.9.0 on Ubuntu 8.10. I use # load workspace load(name.RData) which seems to work: ls() # all objects in there [1] all all.dd model.01 model.sorter It also recognizes the class of model.01: class(model.01) [1] mer attr(,package) [1] lme4 But when I want to print it or look at its structure: print(model.01) Error in slot(value, what) : no slot of name Xst for this object of class mer str(model.01) Error in FUN(c(env, nlmodel, frame, call, flist, X, Xst, : no slot of name Xst for this object of class mer Any idea what to do? R.version platform i486-pc-linux-gnu arch i486 os linux-gnu system i486, linux-gnu status major 2 minor 9.0 year 2009 month 04 day 17 svn rev 48333 language R version.string R version 2.9.0 (2009-04-17) library(help=lme4) Package: lme4 Version: 0.999375-28 Date: 2008-12-13 Thanks, RZ -- HUANG Ronggui, Wincent PhD Candidate Dept of Public and Social Administration City University of Hong Kong Home page: http://asrr.r-forge.r-project.org/rghuang.html __ 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] Generalized 2D list/array/whatever?
Toby wrote: I'm trying to figure out how I can get a generalized 2D list/array/matrix/whatever working. Seems I can't figure out how to make the variables the right type. I always seem to get some sort of error... out of bounds, wrong type, wrong dim, etc. Very confused... :) x[[some label, some other index]] - 3 x[[some other label, something else]] - 4 I don't know the indexes/label ahead of time... they get generated... Any thoughts? What you have there is not legal syntax, but this would be: x[[c(some label, some other index)]] - 3 This assumes that x is a list, and one of its entries is a list named some label. It will not create that entry, but it will create an entry named some other index, so you need if (is.null(x[[some label]])) x[[some label]] - list() first. After executing this line and your first line above, you'll get x $`some label` $`some label`$`some other index` [1] 3 Duncan Murdoch __ 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] Stuck using constrOptim
I'm very interested. If you wouldn't mind I would love to see it. Thank you for the help. dre968 wrote: Trying to use constrOptim to minimize the sum of squared deviations. I put the objective function in as: sum((x %*% Y - Z)^2) so i'm trying to get values for x to minimize the sum of the squared deviations between the product of x and Y and Z. Anyways i have no problem using this when x is a 3x1 test variable. it works great with the constraints and everything. when i actually use it on my data x is 3x900 or so and it wont optimize it just gives me back my initial guessthis is the output i'm getting: $value [1] 22.7438 $counts function gradient 906 NA $convergence [1] 1 $message NULL $outer.iterations [1] 1 $barrier.value [1] 1.381551e-06 this is definitely not the right answer and it is just spitting back my initial guess back. Any ideas? are there limits as to how big the variables can be for this function? -- View this message in context: http://www.nabble.com/Stuck-using-constrOptim-tp23197912p23214410.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] deleting rows provisionally
Hi. Thanks very much for the reply and the good suggestion. It works well. But I don't get why the for loop is not deleting anything or making any assignments? Or I should say, doesn't answer3[-i,] delete entries from answer3 when the if condition is true? Also, in your first solution answer2[-(answer2[,1]==answer2[,2]),] can I say that you are indexing answer2 by answer2[,] and all of the deletion is coming in the first argument and specifically you are deleting every entry in answer2 where the first elements of the first and second columns are the same. So for example, if I wanted instead to switch the elements of the first and second column whenever they are different what would I do? confused. Ben Bolker wrote: onyourmark wrote: I have an object. I think it is a matrix, called 'answer2' str(answer2) int [1:1537, 1:2] 1 399 653 2 3 600 4 5 271 870 ... - attr(*, dimnames)=List of 2 ..$ : chr [1:1537] a4.1 hirschsprung.399 peritoneal.653 abdomen.2 ... ..$ : chr [1:2] row col I want to delete rows that have the same entries. Your for loop didn't make any assignments. How about answer3 - answer2[-(answer2[,1]==answer2[,2]),] or answer3 - answer2[answer2[,1]!=answer2[,2],] (which will be much faster than a loop anyway) ? -- View this message in context: http://www.nabble.com/deleting-rows-provisionally-tp23209365p23214891.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] displaying percentage in bar plot
Hi Jim, Thank you for the help. Along with the bars I wanted to show the respective percentage as well. Is that possible ? Regards, Nataraju GM On Fri, Apr 24, 2009 at 4:38 PM, Jim Lemon j...@bitwrit.com.au wrote: Nattu wrote: Hi, I have a query regarding barplot I have a following data AIS LEvel 1 23 body regionA 10 15 20 B 15 25 15 Now I want to plot a barplot and in each bar (corresponding a body region), I need a percentage of AIS level 1 displayed in the plot. Is there an easy way to do this ? Thanks, Nataraju GM Hi Nataraju, I might not understand exactly what you want, but try this: bardat-matrix(c(10,15,15,25,20,15),nrow=2) barpos-barplot(bardat,beside=TRUE) library(plotrix) boxed.labels(barpos,bardat/2,bardat/(sum(bardat[,1]/100))) Jim -- No relationship is Static .. You either Step up or Step down [[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-help]Remove error data and clustering analysis
Hi, all, I’d like to do the clustering analysis in my dataset. The example data are as follows: Dataset 1: 500, 490, 486, 490, 491, 493, 480, 461, 504, 476, 434, 500, 470, 495, 3116, 3142, 12836, 3062, 3091, 3141, 3177, 3150, 3114, 3149; Dataset 2: 506, 473, 495, 494, 434, 459, 445, 475, 476, 128367, 470, 513, 466, 476,482, 1201, 469, 502; I had so many datasets like that. Basically, every dataset can classify one or two clusters (no more than 2), meanwhile, there have error data points, for example, 12836 is error data point in Dataset 1; and 128367, 1201 is error data points in dataset2. The clustered data is following the normal distribution, the standard deviation was known. That’s mean the one cluster is following the normal distribution when the dataset classified one cluster like dataset2; the two clusters are following the normal distribution respectively when the dataset classified two clusters like dataset1. Error data are far away of the mean. I am wondering is there any mathematic pipeline/function can do the analysis that removing error data, and clustering the dataset in 1 or 2 clusters? Thank you for your reply. __ 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] stata == R - error messages
Rob Bakker wrote: Dear Sirs, I am just starting with R and I think it is a great system. Now, I want to import Stata datasets (.dta) with read.dta, but receive errormessages like: Error in grep(^(http|ftp|https)://, file) : object Rklein not found Error in read.dta(Rklein) : unable to open file: 'No such file or directory' this happens when I use What is the problem and how can I solve it? Hi Rob, Looks like you're on Windows, and you have probably fallen victim to the Microsoft (and Apple) hide-everything-you-can-from-them file manager defaults. Your file Rklein probably has an extension on it (maybe .dta?) and if you can find that by turning off extension hiding, you will probably see the solution immediately. 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] stata == R - error messages
On 24/04/2009 7:42 AM, Peter Dalgaard wrote: Jim Lemon wrote: Rob Bakker wrote: Dear Sirs, I am just starting with R and I think it is a great system. Now, I want to import Stata datasets (.dta) with read.dta, but receive errormessages like: Error in grep(^(http|ftp|https)://, file) : object Rklein not found Error in read.dta(Rklein) : unable to open file: 'No such file or directory' this happens when I use What is the problem and how can I solve it? Hi Rob, Looks like you're on Windows, and you have probably fallen victim to the Microsoft (and Apple) hide-everything-you-can-from-them file manager defaults. Your file Rklein probably has an extension on it (maybe .dta?) and if you can find that by turning off extension hiding, you will probably see the solution immediately. Jim Also, notice the function choose.file() which lets browse your way to The function name is actually file.choose(), which exists on all (?) platforms. There's also a function choose.files(), only on Windows, and mainly used for choosing multiple files (but it has a few other Windows-only differences from file.choose()). Duncan Murdoch the file in the usual Windows style. If used on its own, then it returns the full path to the file, so that you know what to feed to read.dta(). You can short-circuit by using read.dta(choose.file()), but if you do it in a script, then you need to do the browsing every time you run the script. __ 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] iteration limit error in gamm and notExp2
Isidora, What is the actual model structure that you are trying to fit? It's not clear to me that modifying the nonExp2 defaults will help convergence here, but it may be that some slight modifications of the model itself will sort things out, which is why it would be good to know what the model is. One issue with `gamm' is that it is built on PQL estimation, so there is no guarantee that fitting will converge, although it usually does. best, Simon On Thursday 23 April 2009 19:40, isidora k wrote: hi, I am trying to run a mixed effect gam using gamm (mgcv) and I get the following error: Error in lme.formula(y ~ X - 1, random = rand, data = strip.offset(mf), : nlminb problem, convergence error code = 1 message = iteration limit reached without convergence (9) I've read all about 'notExp2' but since I am not an expert I didn't understand that much. I was wondering if anyone has an example of the use of notExp2, or another suggestion on solving this problem. many thanks Isidora [[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. -- Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK +44 1225 386603 www.maths.bath.ac.uk/~sw283 __ 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] Almost ideal demand system with ADL
As anyone knows how to estimate an almost ideal demand system with autoregressive distributed las? Thanks! Marie - Le Bureau federal du Plan fete ses 50 ans en 2009. Het Federaal Planbureau viert zijn 50-ste verjaardag in 2009. The Federal Planning Bureau celebrates its 50-th anniversary in 2009. - Disclaimer: please see www.plan.be/disclaimer.html Please, think before you print... __ 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] Terminology: Multiple Regression versus multivariate Reg
Peter Dalgaard wrote: (Ted Harding) wrote: There is an unfortunate (in my view) tendency for people to use multivariate regression whden talking about what I call multiple regression above (i.e. more than 1 independent variable). I think this should be reserved for regression where the left-hand side is multivariate. But maybe I'm in a minority ... If so, a minority of at least two... Part of the problem is that people will often (for better or worse) screen a set of predictors by univariate regression, which should probably be the rather less catchy single-predictor regression. (As far as I remember, SPSS, canonicalizes the term in its menu system.) Another approach (maybe more correct?) that I have seen in some papers, is to use multivariable regression for more than one predictors, and univariable regression for just a single one. Best, Dimitris -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 __ 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 see the content of geepack package
Cetinyürek Aysun wrote: Dear list members, I need to see the content of the functions in package geepack. It uses some C functions in the computation they are not available in the package directory. How can I see the content of C functions? You need to download the source of the package from CRAN. It's in http://cran.r-project.org/src/contrib/geepack_1.0-16.tar.gz. Duncan Murdoch __ 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] deleting rows provisionally
On Fri, Apr 24, 2009 at 04:50:48AM -0700, onyourmark wrote:
Hi. Thanks very much for the reply and the good suggestion. It works well.
But I don't get why the for loop is not deleting anything or making any
assignments? Or I should say, doesn't answer3[-i,] delete entries from
answer3 when the if condition is true?
Your for loop was:
for(i in 1:1537){if(answer2[i,1]==answer2[i,2]){answer3[-i,]}}
No, answer3[-i] does not remove item i from answer3, it returns an
anonymous temporary object which is identical to (answer3 without item
i). Since that object not saved, it is deleted when the loop enters
the next iteration. To actually *modify* answer3 you can use:
answer3 - answer3[-i]
--
Hans Ekbrand (http://sociologi.cjb.net) h...@sociologi.cjb.net
Q. What is that strange attachment in this mail?
A. My digital signature, see www.gnupg.org for info on how you could
use it to ensure that this mail is from me and has not been
altered on the way to you.
signature.asc
Description: Digital signature
__
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] stata == R - error messages
Jim Lemon wrote: Rob Bakker wrote: Dear Sirs, I am just starting with R and I think it is a great system. Now, I want to import Stata datasets (.dta) with read.dta, but receive errormessages like: Error in grep(^(http|ftp|https)://, file) : object Rklein not found Error in read.dta(Rklein) : unable to open file: 'No such file or directory' this happens when I use What is the problem and how can I solve it? Hi Rob, Looks like you're on Windows, and you have probably fallen victim to the Microsoft (and Apple) hide-everything-you-can-from-them file manager defaults. Your file Rklein probably has an extension on it (maybe .dta?) and if you can find that by turning off extension hiding, you will probably see the solution immediately. Jim Also, notice the function choose.file() which lets browse your way to the file in the usual Windows style. If used on its own, then it returns the full path to the file, so that you know what to feed to read.dta(). You can short-circuit by using read.dta(choose.file()), but if you do it in a script, then you need to do the browsing every time you run the script. -- 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.
Re: [R] stata == R - error messages
Rob Bakker wrote: Dear Peter, Also thank you for your quick reply. I did the following with no positive result: library(foreign) read.dta(choose.file(C:\Rklein)) Error: unexpected input in read.dta(choose.file(C:\ read.dta(choose.file(C:\Rklein)) Error in grep(^(http|ftp|https)://, file) : could not find function choose.file As Duncan points out, it is file.choose(), sorry about that - I don't use Windows regularly. Notice also that you need to run it _without_ any argument. -- 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.
Re: [R] displaying percentage in bar plot
Nattu wrote: Hi, I have a query regarding barplot I have a following data AIS LEvel 1 23 body regionA 10 15 20 B 15 25 15 Now I want to plot a barplot and in each bar (corresponding a body region), I need a percentage of AIS level 1 displayed in the plot. Is there an easy way to do this ? Thanks, Nataraju GM Hi Nataraju, I might not understand exactly what you want, but try this: bardat-matrix(c(10,15,15,25,20,15),nrow=2) barpos-barplot(bardat,beside=TRUE) library(plotrix) boxed.labels(barpos,bardat/2,bardat/(sum(bardat[,1]/100))) 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] deleting rows provisionally
On Apr 24, 2009, at 7:50 AM, onyourmark wrote: Hi. Thanks very much for the reply and the good suggestion. It works well. But I don't get why the for loop is not deleting anything or making any assignments? Or I should say, doesn't answer3[-i,] delete entries from answer3 when the if condition is true? No, it doesn't. It returns a copy of answer3 without the ith row, but it does not touch answer3, because as Ben said before you did no assignment. Also, in your first solution answer2[-(answer2[,1]==answer2[,2]),] can I say that you are indexing answer2 by answer2[,] and all of the deletion is coming in the first argument and specifically you are deleting every entry in answer2 where the first elements of the first and second columns are the same. Actually you are still not deleting. But the rest of you characterization of the process looks correct. So for example, if I wanted instead to switch the elements of the first and second column whenever they are different what would I do? confused. The easiest approach would probably be to swap their names but if you want to swap the entries without touching the names then something like: temp.ans - answer2[,2] answer2[ , 2] - answer2[ , 1] answer2[ , 2] - temp.ans Or possibly answer2[ , c(2,1)] - answer2[ , c(1,2)] but I am not a sufficiently experienced R programmer to know the answer to that without testing. -- David. Ben Bolker wrote: onyourmark wrote: I have an object. I think it is a matrix, called 'answer2' str(answer2) int [1:1537, 1:2] 1 399 653 2 3 600 4 5 271 870 ... - attr(*, dimnames)=List of 2 ..$ : chr [1:1537] a4.1 hirschsprung.399 peritoneal.653 abdomen.2 ... ..$ : chr [1:2] row col I want to delete rows that have the same entries. Your for loop didn't make any assignments. How about answer3 - answer2[-(answer2[,1]==answer2[,2]),] or answer3 - answer2[answer2[,1]!=answer2[,2],] (which will be much faster than a loop anyway) 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.
Re: [R] Generalized 2D list/array/whatever?
On Fri, Apr 24, 2009 at 5:50 AM, Duncan Murdoch murd...@stats.uwo.ca wrote: Toby wrote: I'm trying to figure out how I can get a generalized 2D list/array/matrix/whatever working. Seems I can't figure out how to make the variables the right type. I always seem to get some sort of error... out of bounds, wrong type, wrong dim, etc. Very confused... :) x[[some label, some other index]] - 3 x[[some other label, something else]] - 4 I don't know the indexes/label ahead of time... they get generated... Any thoughts? What you have there is not legal syntax, but this would be: It isn't? a - as.list(1:4) dim(a) - c(2, 2) rownames(a) - c(a, b) colnames(a) - c(c, d) a[[a, d]] Hadley -- http://had.co.nz/ __ 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] prediction intervals (alpha and beta) for model average estimates from binomial glm and model.avg (library=dRedging)
In R, the predict family of functions provides that facility. If you
want the code it will be in the particular function associated with
the model type.
?predict
?predict.glm
# the example illustrates creation of prediction curves on the
response scale for a specific range of data.
# create the desired CI's by appropriate use of the se.fit value
returned from the predict call.
# This is the code inside predict.glm that does the work when se.fit
is set as TRUE in the predict call:
se.fit - pred$se.fit
switch(type, response = {
se.fit - se.fit * abs(family(object)$mu.eta(fit))
fit - family(object)$linkinv(fit)
}, link = , terms = )
--
David Winsemius
On Apr 24, 2009, at 3:03 AM, Michelle Ensbey wrote:
Hi all,
I was wondering if there is a function out there, or someone has
written code for making confidence intervals around model averaged
predictions (y~á+âx). The model average estimates are from the
dRedging library?
It seems a common thing but I can't seem to find one via the search
engines
Examples of the models are:
fit1 - glm(y~ dbh, family = binomial, data = data)
fit2 - glm(y~ dbh+vegperc, family = binomial, data = data)
fit3 - glm(y~ dbh, family = binomial, data = data)
and the model averaging
model.averaging -model.avg(fit1,fit2,fit3, method=0)
and the output (from model.avg) has the following items:
Coefficient, Variance, Standard error, adjusted standard error and
lower and upper confidence interval for each parameter (and
intercept).
What I would like to do is make prediction intervals. I know I
need to include covariance and variance. Please let me know if
anyone has a function or code to get these prediction intervals out
of this output.
Thanks in advance for your help, and please advise me if you need
more information
M
michelle.ens...@nt.gov.au
R version 2.8.1
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] power.t.test formula
Hello, Thank you, but can you understand this result? first I calculate the sd for n = 2 and then n with that sd. It should give me 2 right? FC = 1.5 alfa = 0.01 power = 0.85 sd1 - power.t.test( n = 2, delta = FC, sig.level = alfa, +power = power, type = two.sample, sd = NULL)$sd n1 - round( power.t.test( n = NULL, delta = FC, sig.level = alfa,power = power, type = two.sample, sd = sd1)$n) Error in uniroot(function(n) eval(p.body) - power, c(2, 1e+07)) : f() values at end points not of opposite sign 2009/4/23 Peter Dalgaard p.dalga...@biostat.ku.dk Usuario R wrote: Hi, Does anyone of you knows a reference for the formula used in power.t.test function? And also why it uses the Student's distribution instead of Normal. (I know both of them can be used but don't see whether choose one or the other) It is a straightforward first-principles calculation. The t distribution calculation is exact for normally distributed data with the same unknown variance in both groups. Formulas based on the normal distribution assumes the variance to be known, which overestimates small n. -- 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 [[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] Array
Bronagh Grimes wrote: Hi there, Just wondering if anyone has any tips for using arrays? I am trying to convert the following SAS code to R: You're probably going to get more useful responses in general if, instead of posting code from SAS to be ported to R, you describe what the code is doing (e.g., give some sample input, and describe what you'd like the output to be). That way, you do not limit those who will reply to the set of people who know SAS. Many times, the concepts will be different between the two approaches one would take when programming something in SAS and R. __ 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] Generalized 2D list/array/whatever?
On 24/04/2009 8:48 AM, hadley wickham wrote: On Fri, Apr 24, 2009 at 5:50 AM, Duncan Murdoch murd...@stats.uwo.ca wrote: Toby wrote: I'm trying to figure out how I can get a generalized 2D list/array/matrix/whatever working. Seems I can't figure out how to make the variables the right type. I always seem to get some sort of error... out of bounds, wrong type, wrong dim, etc. Very confused... :) x[[some label, some other index]] - 3 x[[some other label, something else]] - 4 I don't know the indexes/label ahead of time... they get generated... Any thoughts? What you have there is not legal syntax, but this would be: It isn't? You're right, it is. Sorry. However, I think the solution I gave (not to make the list into an array, but rather to use a list of lists) is probably better in a lot of situations where the indices show up unpredictably. Duncan Murdoch a - as.list(1:4) dim(a) - c(2, 2) rownames(a) - c(a, b) colnames(a) - c(c, d) a[[a, d]] Hadley __ 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.t.test formula
Usuario R wrote: Hello, Thank you, but can you understand this result? first I calculate the sd for n = 2 and then n with that sd. It should give me 2 right? FC = 1.5 alfa = 0.01 power = 0.85 sd1 - power.t.test( n = 2, delta = FC, sig.level = alfa, +power = power, type = two.sample, sd = NULL)$sd n1 - round( power.t.test( n = NULL, delta = FC, sig.level = alfa,power = power, type = two.sample, sd = sd1)$n) Error in uniroot(function(n) eval(p.body) - power, c(2, 1e+07)) : f() values at end points not of opposite sign The error message pretty much says it: uniroot is looking for a root between 2 and 1e7 and complains that the root is not properly bracketed. If the root is supposed to be AT 2, then this easily happens due to rounding issues. (This could have better error trapping, but you're really not expected to be planning studies with such low n.) -- 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] plot() - thicker points when pair exist more than 1 time?
Hi to all, is it possible to show in anyway that point 1,1 is existing more than 1one time? f.e.: f- data.frame(x=c(1,3,5,6,1),y=c(1,2,3,4,1)) plot(f) Regards Knut __ 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] plot() - thicker points when pair exist more than 1 time?
On Apr 24, 2009, at 8:09 AM, Knut Krueger wrote: Hi to all, is it possible to show in anyway that point 1,1 is existing more than 1one time? f.e.: f- data.frame(x=c(1,3,5,6,1),y=c(1,2,3,4,1)) plot(f) Regards Knut Several options: # See ?sunflowerplot sunflowerplot(f) # See ?xyTable referenced in the above coords - xyTable(f) plot(coords$x, coords$y, cex = coords$number) or coords - xyTable(f) plot(f, type = n) text(coords$x, coords$y, labels = coords$number) # See ?jitter plot(jitter(f$x), jitter(f$y)) HTH, Marc Schwartz __ 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] plot() - thicker points when pair exist more than 1 time?
on suitable devices, you could consider transparency, plot(f,col=alpha(grey,0.8),pch=19) baptiste On 24 Apr 2009, at 14:09, Knut Krueger wrote: f- data.frame(x=c(1,3,5,6,1),y=c(1,2,3,4,1)) plot(f) __ 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] Interpreting the results of Friedman test
Hello, Peter Dalgaard wrote: Not necessarily, but the first suspicion one gets is that what you're doing with Friedman is not equivalent to what you're doing with ANOVA, could you show us the code and data (or an outline of it)? Please find attached the R script and the data input files. The values in dataForFriedmanTest.dat represent the geometric mean of the values of three repetitions for one observer and one condition. Am I doing something wrong there? Thanks in advance Doerte PS: I'm not sure if it is possible to send the dat-files by mail. Therefore I renamed them to *.txt. Please rename back to *.dat. Original-Nachricht Datum: Fri, 24 Apr 2009 14:52:44 +0200 Von: Peter Dalgaard p.dalga...@biostat.ku.dk An: Doerte doerte.ap...@gmx.de Betreff: Re: [R] Interpreting the results of Friedman test Doerte wrote: Hello, I have problems interpreting the results of a Friedman test. It seems to me that the p-value resulting from a Friedman test and with it the significance has to be interpreted in another way than the p-value resulting from e.g. ANOVA? Let me describe the problem with some detail: I'm testing a lot of different hypotheses in my observer study and only for some the premises for performing an ANOVA are fulfilled (tested with Shapiro Wilk and Bartlett). For the others I perform a Friedman test. To my surprise, the p-value of the Friedman test is 0.05 for all my tested hypotheses. Thus, I tried to compare the results with the results of an ANOVA by performing both test methods (Friedman, ANOVA) to a given set of data. While ANOVA results in p = 0.34445 (-- no significant difference between the groups), the Friedman test results in p = 1.913e-06 (-- significant difference between the groups?). How can this be? Or am I doing something wrong? I have three measured values for each condition. For ANOVA I use them all, for the Friedman test I calculated the geometric mean of the three values, since this test does not work with replicated values. Is this a crude mistake? Not necessarily, but the first suspicion one gets is that what you're doing with Friedman is not equivalent to what you're doing with ANOVA, could you show us the code and data (or an outline of it)? -- 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 -- Observer | Condition | Repetition | AUC 2 | 1 | 2 | 11.6698729267 2 | 1 | 3 | 11.3614841831 2 | 1 | 1 | 11.6320875675 3 | 1 | 3 | 11.3813182648 3 | 1 | 2 | 11.9791654383 3 | 1 | 1 | 11.3193295274 4 | 1 | 3 | 11.6271912743 4 | 1 | 1 | 11.7277539642 4 | 1 | 2 | 11.3073525275 6 | 1 | 2 | 11.5356087785 6 | 1 | 3 | 11.8625252416 6 | 1 | 1 | 11.1631417327 7 | 1 | 1 | 12.0811987417 7 | 1 | 2 | 11.4253889199 7 | 1 | 3 | 11.1438163937 8 | 1 | 2 | 12.3351513361 8 | 1 | 1 | 11.0075952969 8 | 1 | 3 | 11.2701354076 1 | 1 | 2 | 11.9582160341 1 | 1 | 3 | 11.3128071894 1 | 1 | 1 | 11.4041971251 2 | 2 | 2 | 11.1937509173 2 | 2 | 1 | 11.6252278612 2 | 2 | 3 | 11.7113976885 3 | 2 | 3 | 11.1192253767 3 | 2 | 1 | 11.3755159053 3 | 2 | 2 | 12.0029900345 4 | 2 | 3 | 11.6105418939 4 | 2 | 2 | 11.4205387926 4 | 2 | 1 | 11.5200504433 6 | 2 | 2 | 11.3150843227 6 | 2 | 3 | 11.087942451 6 | 2 | 1 | 12.0640315424 7 | 2 | 1 | 11.6605537521 7 | 2 | 3 | 11.6189671844 7 | 2 | 2 | 11.2636316548 8 | 2 | 3 | 11.3865060588 8 | 2 | 2 | 12.1672455368 8 | 2 | 1 | 10.9692943665 1 | 2 | 3 | 11.4617141335 1 | 2 | 1 | 11.5455368466 1 | 2 | 2 | 11.5463396473 2 | 3 | 2 | 11.3473263733 2 | 3 | 1 | 11.7839556008 2 | 3 | 3 | 11.1316960504 3 | 3 | 3 | 11.8686526315 3 | 3 | 2 | 11.0739149317 3 | 3 | 1 | 11.403959013 4 | 3 | 1 | 11.5870552325 4 | 3 | 2 | 11.3401354648 4 | 3 | 3 | 11.3424292954 6 | 3 | 3 | 11.3615420894 6 | 3 | 1 | 11.4887245966 6 | 3 | 2 | 11.3741010608 7 | 3 | 2 | 11.3180993919 7 | 3 | 1 | 11.4960941843 7 | 3 | 3 | 11.454173957 8 | 3 | 3 | 11.2121329748 8 | 3 | 1 | 11.5712149501 8 | 3 | 2 | 11.4525667984 1 | 3 | 3 | 11.1470495671 1 | 3 | 1 | 11.3843720685 1 | 3 | 2 | 11.7803942389 2 | 4 | 1 | 11.7049906947 2 | 4 | 2 | 11.3104231298 2 | 4 | 3 | 11.6789580111 3 | 4 | 2 | 11.9600062087 3 | 4 | 3 | 11.2497720322 3 | 4 | 1 | 11.5070118114 4 | 4 | 3 | 11.6880141384 4 | 4 | 2 | 11.6823046979 4 | 4 | 1 | 11.3789895286 6 | 4 | 1 | 11.2340767853 6 | 4 | 3 | 12.0463303433 6 | 4 | 2 | 11.4281136904 7 | 4 | 2 | 11.9397313286 7 | 4 | 1 | 11.5816813225 7 | 4 | 3 | 11.2157780218 8 | 4 | 3 | 11.3649382115 8 | 4 | 1 | 11.7537482956 8 | 4 | 2 | 11.6151737679 1 | 4 | 2 | 11.8833021895 1 | 4 | 1 | 11.6774568059 1 | 4 | 3 | 11.218661679 1 | 11.5549259143 | 11.5177949943 | 11.4343007933 | 11.5897878773 2 | 11.5536609678 |
[R] Dealing with unix signal
Hi all, I'm wondering if there is any module or function in R can deal with unix signals such as SIGXCPU. In this way, when I get a signal from OS, I like to do something (such as saving current variables or terminating gracefully) by interrupting current execution of R. Thank you for your help in advance. Thanks, Jong __ 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] My surprising experience in trying out REvolution's R
David, thanks for following this through. I do not know how big a matrix needs to be before the multi-core multi-threading will start save time. But it seems useful to build this protection in your distribution so that it will not do multi-core when multi-threading is more likely to do harm. Jason -Original Message- From: David M Smith [mailto:da...@revolution-computing.com] Sent: Thursday, April 23, 2009 6:05 PM To: Jason Liao Cc: r-help@r-project.org Subject: Re: [R] My surprising experience in trying out REvolution's R We've taken a look at this in a bit more detail; it's a very interesting example. Although the code uses several functions that exploit the parallel processing in REvolution R (notably %*% and chol), this was one of those situations where the overheads of threading pretty much balanced any performance gains: the individual matrices for the operations were too small. For some examples where the performance gains do show, see: http://www.revolution-computing.com/products/r-performance.php A more promising avenue for speeding up this code lies in parallelizing the outer for(i in 1:200) loop... # David Smith On Tue, Apr 21, 2009 at 9:26 AM, Jason Liao jl...@hes.hmc.psu.edu wrote: I care a lot about R's speed. So I decided to give REvolution's R (http://revolution-computing.com/) a try, which bills itself as an optimized R. Note that I used the free version. My machine is a Intel core 2 duo under Windows XP professional. The code I run is in the end of this post. First, the regular R 1.9. It takes 2 minutes and 6 seconds, CPU usage 50% Next, REvolution's R. It takes 2 minutes and 10 seconds, CPU usage 100%. In other words, REvolution's R consumes double the CPU with slightly less speed. The above has been replicated a few times (as a statistician of course). Anyone has any insight on this? Anyway, my high hope was dashed. -- David M Smith da...@revolution-computing.com Director of Community, REvolution Computing www.revolution-computing.com Tel: +1 (206) 577-4778 x3203 (San Francisco, USA) Check out our upcoming events schedule at www.revolution-computing.com/events __ 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] RES: How to force axis to have the same range
Thanks to Greg and Deepayan for their answers. *Sebastien Bihorel, PharmD, PhD* PKPD Scientist Cognigen Corp Email: sebastien.biho...@cognigencorp.com mailto:sebastien.biho...@cognigencorp.com Phone: (716) 633-3463 ext. 323 Greg Snow wrote: For variables named my.x and my.y try: plot( my.x, my.y, xlim=range(my.x,my.y), ylim=range(my.x,my.y) ) If all you want is to have the same range of values on both the x and y axes. __ 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] stata == R - error messages
Dear Duncan, Peter and Jim, Thank you very much!! It worked! Best regards, Rob Bakker 2009/4/24 Duncan Murdoch murd...@stats.uwo.ca On 24/04/2009 7:42 AM, Peter Dalgaard wrote: Jim Lemon wrote: Rob Bakker wrote: Dear Sirs, I am just starting with R and I think it is a great system. Now, I want to import Stata datasets (.dta) with read.dta, but receive errormessages like: Error in grep(^(http|ftp|https)://, file) : object Rklein not found Error in read.dta(Rklein) : unable to open file: 'No such file or directory' this happens when I use What is the problem and how can I solve it? Hi Rob, Looks like you're on Windows, and you have probably fallen victim to the Microsoft (and Apple) hide-everything-you-can-from-them file manager defaults. Your file Rklein probably has an extension on it (maybe .dta?) and if you can find that by turning off extension hiding, you will probably see the solution immediately. Jim Also, notice the function choose.file() which lets browse your way to The function name is actually file.choose(), which exists on all (?) platforms. There's also a function choose.files(), only on Windows, and mainly used for choosing multiple files (but it has a few other Windows-only differences from file.choose()). Duncan Murdoch the file in the usual Windows style. If used on its own, then it returns the full path to the file, so that you know what to feed to read.dta(). You can short-circuit by using read.dta(choose.file()), but if you do it in a script, then you need to do the browsing every time you run the script. [[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] stata == R - error messages
Dear Peter, Also thank you for your quick reply. I did the following with no positive result: library(foreign) read.dta(choose.file(C:\Rklein)) Error: unexpected input in read.dta(choose.file(C:\ read.dta(choose.file(C:\Rklein)) Error in grep(^(http|ftp|https)://, file) : could not find function choose.file In addition: Warning messages: 1: '\R' is an unrecognized escape in a character string 2: unrecognized escape removed from C:\Rklein The Rklein file is indeed .dta. So what is the next step I can do? Best regards, Rob Bakker 2009/4/24 Peter Dalgaard p.dalga...@biostat.ku.dk Jim Lemon wrote: Rob Bakker wrote: Dear Sirs, I am just starting with R and I think it is a great system. Now, I want to import Stata datasets (.dta) with read.dta, but receive errormessages like: Error in grep(^(http|ftp|https)://, file) : object Rklein not found Error in read.dta(Rklein) : unable to open file: 'No such file or directory' this happens when I use What is the problem and how can I solve it? Hi Rob, Looks like you're on Windows, and you have probably fallen victim to the Microsoft (and Apple) hide-everything-you-can-from-them file manager defaults. Your file Rklein probably has an extension on it (maybe .dta?) and if you can find that by turning off extension hiding, you will probably see the solution immediately. Jim Also, notice the function choose.file() which lets browse your way to the file in the usual Windows style. If used on its own, then it returns the full path to the file, so that you know what to feed to read.dta(). You can short-circuit by using read.dta(choose.file()), but if you do it in a script, then you need to do the browsing every time you run the script. -- 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 [[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] Interpreting the results of Friedman test
doerte.ap...@gmx.de wrote: Hello, Peter Dalgaard wrote: Not necessarily, but the first suspicion one gets is that what you're doing with Friedman is not equivalent to what you're doing with ANOVA, could you show us the code and data (or an outline of it)? Please find attached the R script and the data input files. The values in dataForFriedmanTest.dat represent the geometric mean of the values of three repetitions for one observer and one condition. Am I doing something wrong there? The .R file came as BIN file to me, so r-help may be missing it. Anyways, Friedman's test is a replacement for a two-way ANOVA and you are comparing it to a one-way analysis, and the latter is likely just wrong. Try anova(lm(AUC~as.factor(Condition)+as.factor(Observer),data=dataForANOVA)) or, maybe better summary(aov(AUC ~ as.factor(Condition) + Error(as.factor(Observer) / as.factor(Condition)), data=dataForANOVA)) Thanks in advance Doerte PS: I'm not sure if it is possible to send the dat-files by mail. Therefore I renamed them to *.txt. Please rename back to *.dat. -- 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.
Re: [R] My surprising experience in trying out REvolution's R
You can always turn the multi-threading off with: setMKLthreads(1) We tested your code with this setting, and it ran in exactly the same time as CRAN R. # David Smith On Fri, Apr 24, 2009 at 7:34 AM, Jason Liao jl...@hes.hmc.psu.edu wrote: David, thanks for following this through. I do not know how big a matrix needs to be before the multi-core multi-threading will start save time. But it seems useful to build this protection in your distribution so that it will not do multi-core when multi-threading is more likely to do harm. Jason -Original Message- From: David M Smith [mailto:da...@revolution-computing.com] Sent: Thursday, April 23, 2009 6:05 PM To: Jason Liao Cc: r-help@r-project.org Subject: Re: [R] My surprising experience in trying out REvolution's R We've taken a look at this in a bit more detail; it's a very interesting example. Although the code uses several functions that exploit the parallel processing in REvolution R (notably %*% and chol), this was one of those situations where the overheads of threading pretty much balanced any performance gains: the individual matrices for the operations were too small. For some examples where the performance gains do show, see: http://www.revolution-computing.com/products/r-performance.php A more promising avenue for speeding up this code lies in parallelizing the outer for(i in 1:200) loop... # David Smith On Tue, Apr 21, 2009 at 9:26 AM, Jason Liao jl...@hes.hmc.psu.edu wrote: I care a lot about R's speed. So I decided to give REvolution's R (http://revolution-computing.com/) a try, which bills itself as an optimized R. Note that I used the free version. My machine is a Intel core 2 duo under Windows XP professional. The code I run is in the end of this post. First, the regular R 1.9. It takes 2 minutes and 6 seconds, CPU usage 50% Next, REvolution's R. It takes 2 minutes and 10 seconds, CPU usage 100%. In other words, REvolution's R consumes double the CPU with slightly less speed. The above has been replicated a few times (as a statistician of course). Anyone has any insight on this? Anyway, my high hope was dashed. -- David M Smith da...@revolution-computing.com Director of Community, REvolution Computing www.revolution-computing.com Tel: +1 (206) 577-4778 x3203 (San Francisco, USA) Check out our upcoming events schedule at www.revolution-computing.com/events -- David M Smith da...@revolution-computing.com Director of Community, REvolution Computing www.revolution-computing.com Tel: +1 (206) 577-4778 x3203 (San Francisco, USA) Check out our upcoming events schedule at www.revolution-computing.com/events __ 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] Interpreting the results of Friedman test
Hello again, it seems, the R script has been filtered from the previous posting. Thus, I include is as text here: dataForANOVA - read.csv(C:/R/dataForANOVA.dat, sep=|, as.is=T, na.strings=., header=TRUE) dataForFriedman - read.csv(C:/R/dataForFriedmanTest.dat, sep=|, as.is=T, na.strings=., header=FALSE) anova1 - lm(AUC~as.factor(Condition),data=dataForANOVA) result_shapiro - shapiro.test(anova1$residuals) result_bartlett - bartlett.test(anova1$residuals~as.factor (Condition),data=dataForANOVA) summaryANOVA1 - summary(anova1) anova1Results - anova(lm(AUC~as.factor(Condition),data=dataForANOVA)) print(anova1Results) friedman.test(as.matrix(dataForFriedman)) __ 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] Text Contrast in a Plot
Hi List,
I would appreciate any suggestion on how can I make a text Ive inserted in
a plot show some contrast? With this I mean that I have a white text on a
plot and I would like to make a tiny border around it in black, so even
being small sized and the entire graphic being small in the text page Ill
insert it. It will be visible.
Well I tried inserting a box() function inside the text() function, R
accepts the command but there is no effect. I even tried to plot a greater
black text and then a smaller white one at the same place, but it doesnt
look good.
Any ideas!
Bellow is my plot code without the above mentioned attempts. Id like to add
this effect at the second text() command.
png('BaseMap.png',width=5.2,height=3.6,pointsize=5,units='in',bg=NA,restoreC
onsole=T,res=1200)
par(mar=c(5,0,0,0))
map('worldHires','brazil',ylim=c(-5.15,-4.55),xlim=c(-37,-36.1),type='n')
rect(-37.1,-5.25,-36,-4.9,density=NULL,angle=45,col='#dbf4ff',border=F)
plot(Batimetria,ylab='',xlab='',border=F,col=Cor$Cor,add=T)
plot(Municipios,ylab='',xlab='',col=rgb(245,232,140,max=255,alpha=255),add=T
,lwd=0.2)
axis(1,xaxp=c(-37,-36.1,5),cex.axis=1.5)
axis(2,yaxp=c(-5.15,-4.55,5),cex.axis=1.5)
text(Prof$Long,Prof$Lat,rownames(Prof),col='black',cex=0.9,srt=-24,font=2)
text(c(-36.96,-36.96,-36.865,-36.54,-36.37,-36.2),c(-4.96,-5.05,-5.11,-5.14,
-5.14,-5.14),c('Areia
Branca','Serra
do Mel','Porto do
Mangue','Macau','Guamaré','Galinhos'),col='Black',cex=1.3,font=2)
rect(-36.20,-4.56,-36.155,-4.565,density=NULL,angle=45,col='black',border='b
lack',lwd=0.1)
rect(-36.155,-4.56,-36.111,-4.565,density=NULL,angle=45,col='white',border='
black',lwd=0.1)
text(c(-36.20,-36.155,-36.111,-36.215),c(-4.573,-4.573,-4.573,-4.562),c('0',
'5','10','km'),col='white',cex=1)
Norte(-36.155,-4.60,0.02)
box(which='plot',lty='solid')
dev.off()
Thanks in advance!
-
MSc. mailto:r.alui...@gmail.com Rodrigo Aluizio
Centro de Estudos do Mar/UFPR
Laboratório de Micropaleontologia
Avenida Beira Mar s/n - CEP 83255-000
Pontal do Paraná - PR Brasil
[[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] stata == R - error messages
On Fri, Apr 24, 2009 at 01:50:04PM +0200, Rob Bakker wrote: Dear Peter, Also thank you for your quick reply. I did the following with no positive result: library(foreign) read.dta(choose.file(C:\Rklein)) a) quote the filename b) include the suffix rklein - read.dta(C:\Rklein.dta) -- Hans Ekbrand (http://sociologi.cjb.net) h...@sociologi.cjb.net GPG Fingerprint: 1408 C8D5 1E7D 4C9C C27E 014F 7C2C 872A 7050 614E signature.asc Description: Digital signature __ 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] use of input in system()
First, it looks like there is bug in the documentation...
According to the documentation for system():
http://stat.ethz.ch/R-manual/R-patched/library/base/html/system.html
input if a character vector is supplied, this is copied one string per
line to a temporary file, and the standard input of command is
redirected to the file
This seems to mean that the standard input of command is redirected *from*
the file. From the file, to the command. Example:
i - 42
system( cat -, input=as.character(i) )
42
I guess the documentation needs to be clarified because I couldn't
understand what it meant.
Second, I'm trying to use a system call to write files with names based on
an integer value in an R variable (in this case the variable is called
i). As above, I can do this (on a GNU/Linux system):
system( cat -, input=sprintf(%04d, i) )
0005
I am running bash, but system calls go to sh. I want to be able to put
that input string (0005) into a variable and do something like this:
system( i=`cat /dev/stdin` ; run_script file${i}.out ,
input=sprintf(%04d, i) )
I think my problem is more with sh than with R, but someone here must have
tried this, so I'm hoping I can get an answer here. Thanks in advance.
Best,
Mike
--
Michael B. Miller, Ph.D.
Minnesota Center for Twin and Family Research
Department of Psychology
University of Minnesota
__
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] stata == R - error messages
On 4/24/2009 10:18 AM, Hans Ekbrand wrote: On Fri, Apr 24, 2009 at 01:50:04PM +0200, Rob Bakker wrote: Dear Peter, Also thank you for your quick reply. I did the following with no positive result: library(foreign) read.dta(choose.file(C:\Rklein)) a) quote the filename b) include the suffix rklein - read.dta(C:\Rklein.dta) c) use forward slashes, or double backslashes: rklein - read.dta(C:/Rklein.dta) Duncan Murdoch __ 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] use of input in system()
On 4/24/2009 10:29 AM, Mike Miller wrote:
First, it looks like there is bug in the documentation...
According to the documentation for system():
http://stat.ethz.ch/R-manual/R-patched/library/base/html/system.html
input if a character vector is supplied, this is copied one string per
line to a temporary file, and the standard input of command is
redirected to the file
This seems to mean that the standard input of command is redirected *from*
the file. From the file, to the command. Example:
The redirection is done *to* the file handle. The fact that input is
read from that handle is a different issue.
Duncan Murdoch
i - 42
system( cat -, input=as.character(i) )
42
I guess the documentation needs to be clarified because I couldn't
understand what it meant.
Second, I'm trying to use a system call to write files with names based on
an integer value in an R variable (in this case the variable is called
i). As above, I can do this (on a GNU/Linux system):
system( cat -, input=sprintf(%04d, i) )
0005
I am running bash, but system calls go to sh. I want to be able to put
that input string (0005) into a variable and do something like this:
system( i=`cat /dev/stdin` ; run_script file${i}.out ,
input=sprintf(%04d, i) )
I think my problem is more with sh than with R, but someone here must have
tried this, so I'm hoping I can get an answer here. Thanks in advance.
Best,
Mike
__
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] Interpreting the results of Friedman test
Anyways, Friedman's test is a replacement for a two-way ANOVA and you are comparing it to a one-way analysis, and the latter is likely just wrong. Okay. Thanks for the hint. Try anova(lm(AUC~as.factor(Condition)+as.factor(Observer),data=dataForANOVA)) This results in p-value = 0.37969. This value is still quite different from p-value = 1.913e-06, which is the result of friedman.test (as.matrix(dataForFriedman)). Is the method friedman.test (version R 2.9.0) working correctly for certain types of data and hypotheses? Which limitations are known? @ Jim: Thanks for the link. Unfortunately, I'm a newbie in statistics, and I'm not sure, which method can be used instead of the Friedman Test. Do you have an eye on a certain R-program from this given website? Doerte __ 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] the puzzle of eigenvector and eigenvalue
Dear all I am so glad the R can provide the efficient calculate about eigenvector and eigenvalue. However, i have some puzzle about the procedure of eigen. Fristly, what kind of procedue does the R utilize such that the eigen are obtained? For example, A=matrix(c(1,2,4,3),2,2) we can define the eigenvalue lamda, such as det | 1-lamda 4| =0 |23-lamda | then we can obtain the lamda=5 and -1 however, i am interesting in that how does the R to obatin lamda? By the way, how does the R also obtain the eigenvector? Basically, i must to know those definition in the R because i have to utilize eigenvalue and eigenvector to develope SVD (single value decomposition) by myself. Furthermore, i want to obtain the bi-plot about my data. Although someone suggest that i can obtain those result by R (base), there are exist some tough problems which is difficult to solve it. My data is too huge to do it. for example, the size of matrix is 40*800. So, i think that i should follow whole steps by myself. Finally, it is also my serious problem in the R, I have three estimators which work for the same data. Moreover, i utilize the biplot to realize those tendency. But i find that the the tendency of third estimator mirror the other two, the figures are linked below http://hopjimmy123.pixnet.net/album/photo/108526615#pictop i believe that the tendency should have the same way with the other estimator and the major problem is about the eigenvalue, i hope that someone can give me some idea or provide me some solution about this problem. Sincerely __ 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] Using JRI and Java 1.6 on MAC OS X
if you wish to use jni with java 1.6 on a mac you have to compile the native code as a 64 bit application (-m64 on a gcc command line) hope this helps [[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] use of input in system()
First, it looks like there is bug in the documentation...
According to the documentation for system():
http://stat.ethz.ch/R-manual/R-patched/library/base/html/system.html
input if a character vector is supplied, this is copied one string per
line to a temporary file, and the standard input of command is
redirected to the file
This seems to mean that the standard input of command is redirected *from*
the file. From the file, to the command. Example:
i - 42
system( cat -, input=as.character(i) )
42
I guess the documentation needs to be clarified because I couldn't
understand what it meant.
Second, I'm trying to use a system call to write files with names based on
an integer value in an R variable (in this case the variable is called
i). As above, I can do this (on a GNU/Linux system):
system( cat -, input=sprintf(%04d, i) )
0005
I am running bash, but system calls go to sh. I want to be able to put
that input string (0005) into a variable and do something like this:
system( i=`cat /dev/stdin` ; run_script file${i}.out ,
input=sprintf(%04d, i) )
I think my problem is more with sh than with R, but someone here must have
tried this, so I'm hoping I can get an answer here. Thanks in advance.
Best,
Mike
--
Michael B. Miller, Ph.D.
Minnesota Center for Twin and Family Research
Department of Psychology
University of Minnesota
__
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] use of input in system()
On Fri, 24 Apr 2009, Mike Miller wrote:
I am running bash, but system calls go to sh. I want to be able to put
that input string (0005) into a variable and do something like this:
system( i=`cat /dev/stdin` ; run_script file${i}.out ,
input=sprintf(%04d, i) )
In sh, both of these commands execute ls:
echo ls | `cat /dev/stdin`
echo ls | `cat -`
In R, both of these simply hang until I hit ctrl-c...
system( `cat /dev/stdin`, input=ls )
system( `cat -`, input=ls )
...but the stdin is getting to the command because both of these return
ls to stdout:
system( cat -, input=ls )
system( cat /dev/stdin, input=ls )
So what am I missing? I don't understand why the backtick method isn't
working. Is there another way to do this?
Mike
__
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] Interpreting the results of Friedman test
Doerte wrote: Anyways, Friedman's test is a replacement for a two-way ANOVA and you are comparing it to a one-way analysis, and the latter is likely just wrong. Okay. Thanks for the hint. Try anova(lm(AUC~as.factor(Condition)+as.factor(Observer),data=dataForANOVA)) This results in p-value = 0.37969. This value is still quite different from p-value = 1.913e-06, which is the result of friedman.test (as.matrix(dataForFriedman)). If you had read ALL that I wrote, then you would have seen this: summary(aov(AUC ~ as.factor(Condition) + Error(as.factor(Observer) / + as.factor(Condition)), data=dataForANOVA)) Error: as.factor(Observer) DfSum Sq Mean Sq F value Pr(F) Residuals 6 0.0066907 0.0011151 Error: as.factor(Observer):as.factor(Condition) Df Sum Sq Mean Sq F valuePr(F) as.factor(Condition) 3 0.275825 0.091942 405.23 2.2e-16 *** Residuals18 0.004084 0.000227 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Error: Within Df Sum Sq Mean Sq F value Pr(F) Residuals 56 6.5337 0.1167 I.e. the thing that is going on is that the Observer:Condition interaction is incredibly small (0.000227) compared to the replication variation (0.1167), or put differently that you seem to have strong negative correlation between replicates. This can happen if you have things like plants growing in the same pot, but you need to consider what could be happening in your case. Looking at the table of means with(dataForANOVA,tapply(AUC,list(Observer,Condition),mean)) 1234 1 11.55841 11.51786 11.43727 11.59314 2 11.55448 11.51013 11.42099 11.56479 3 11.55994 11.49924 11.44884 11.57226 4 11.55410 11.51704 11.42321 11.58310 6 11.52043 11.48902 11.40812 11.56951 7 11.55013 11.51438 11.42279 11.57906 8 11.53763 11.50768 11.41197 11.57795 this is essentially the same as your dataForFriedman and it is pretty clear that the 3rd column is substantially below the others, which is what the Friedman test and also the F value of 405.23 above is picking up on. Is the method friedman.test (version R 2.9.0) working correctly for certain types of data and hypotheses? Which limitations are known? @ Jim: Thanks for the link. Unfortunately, I'm a newbie in statistics, and I'm not sure, which method can be used instead of the Friedman Test. Do you have an eye on a certain R-program from this given website? Doerte __ 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. -- 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] what is this experimental design (mixed-effects model)?
Dear R community, I am wondering what experimental design I am dealing with? I study the effect of daily air temperature on daily body temperature of the overwintering turtles (i.e. sleeping in soil). The model is a cosine wave with the air temperature as a covariate. Objects are 19 overwintering turtles. Data were combined over the three years. Each turtle was studied only once during these years, while 2 turtles were studied during two years (see table below). The study area was the same for these three studied years. Turtles were overwintering in different sites within this area. Is that correct to treat the study years as a random effect? I understand that I should incorporate autocorrelation model to account for daily variations in turtles body temperature. Is there a spatial correlation between the three study years, since the study was done within the same area? Study year turtle# 2005 year 1 2 3 4 5 6 7 2006 year 8 9 0 11 12 2006 year 13 14 15 4 16 17 18 12 19 Thanks for your help, Julia Internet Explorer 8 Now Available. Faster, safer, easier. Download FREE now! _ Rediscover Hotmail®: Now available on your iPhone or BlackBerry Mobile2_042009 [[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] the puzzle of eigenvector and eigenvalue
On 4/24/2009 10:30 AM, Abelian wrote: Dear all I am so glad the R can provide the efficient calculate about eigenvector and eigenvalue. However, i have some puzzle about the procedure of eigen. Fristly, what kind of procedue does the R utilize such that the eigen are obtained? For example, A=matrix(c(1,2,4,3),2,2) we can define the eigenvalue lamda, such as det | 1-lamda 4| =0 |23-lamda | then we can obtain the lamda=5 and -1 however, i am interesting in that how does the R to obatin lamda? By the way, how does the R also obtain the eigenvector? The documentation for eigen says, By default 'eigen' uses the LAPACK routines DSYEVR, DGEEV, ZHEEV and ZGEEV whereas 'eigen(EISPACK=TRUE)' provides an interface to the EISPACK routines 'RS', 'RG', 'CH' and 'CG'. So you would need to consult the documentation for those functions (which is listed in the references) for details. Duncan Murdoch Basically, i must to know those definition in the R because i have to utilize eigenvalue and eigenvector to develope SVD (single value decomposition) by myself. Furthermore, i want to obtain the bi-plot about my data. Although someone suggest that i can obtain those result by R (base), there are exist some tough problems which is difficult to solve it. My data is too huge to do it. for example, the size of matrix is 40*800. So, i think that i should follow whole steps by myself. Finally, it is also my serious problem in the R, I have three estimators which work for the same data. Moreover, i utilize the biplot to realize those tendency. But i find that the the tendency of third estimator mirror the other two, the figures are linked below http://hopjimmy123.pixnet.net/album/photo/108526615#pictop i believe that the tendency should have the same way with the other estimator and the major problem is about the eigenvalue, i hope that someone can give me some idea or provide me some solution about this problem. Sincerely __ 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] lagged variable in a dataframe
Hi! I have the following dataframe which represents a financial variable: revenue firm year revenue id 10.1 500194670 2007 27725 10 10.2 500194670 2006 9717 10 10.3 500194670 2005 125621 10 10.4 500194670 2004 84837 10 12.1 500278725 2007 308532 12 12.2 500278725 2006 493755 12 12.3 500278725 2005 238195 12 12.4 500278725 2004 35472 12 13.1 502616695 2007725 13 13.2 502616695 2006 14392 13 13.3 502616695 2005 32502 13 13.4 502616695 2004 35271 13 And I want to compute the lagged version of it, like this: firm year revenue id 10.1 500194670 2007 9717 10 10.2 500194670 2006 125621 10 10.3 500194670 2005 84837 10 10.4 500194670 2004 NA 10 12.1 500278725 2007 493755 12 12.2 500278725 2006 238195 12 12.3 500278725 2005 35472 12 12.4 500278725 2004 NA 12 13.1 502616695 2007 14392 13 13.2 502616695 2006 32502 13 13.3 502616695 2005 35271 13 13.4 502616695 2004 NA 13 Ive tried lag(revenue,k=1) but I failed. The error message was: Error in attr(x, tsp) - c(1, NROW(x), 1) : invalid time series parameters specified Thank you for your help, Cecília Carmo (Portugal) __ 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] function returns R object with name based on input
I wanted to ask how I can make a for loop or a function return an R
object with a unique name based on either some XX of the for loop or
some input for the function.
For example
if I have a function:
fn-function(data,year){
which does does some stuff
}
How do I return an object from the function called X.year, such that if
I run fn(data,1989), the output is an object called X.1989?
In a separate but related process, I'm also trying to subset data by
year, where there are multiple observations by years, using the subset()
function. For example:
data.1946-subset(data, year==1946)
data.1947-subset(data, year==1947)
data.1948-subset(data, year==1948)
data.1949-subset(data, year==1949)
...
How should I set this up? I was thinking of writing a for loop, but I
have never written a for loop that creates objects based on the loop's
index, for example a loop for(i in 1946:2000) that returns 55 objects
with the object names based on the index.
Thanks for your help!
__
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] function returns R object with name based on input
On Apr 24, 2009, at 11:56 AM, Jennifer Brea wrote:
I wanted to ask how I can make a for loop or a function return an R
object with a unique name based on either some XX of the for loop or
some input for the function.
For example
if I have a function:
fn-function(data,year){
which does does some stuff
}
How do I return an object from the function called X.year, such that
if I run fn(data,1989), the output is an object called X.1989?
Read:
?assign
?paste
#and FAQ 7.21
http://cran.r-project.org/doc/FAQ/R-FAQ.html#How-can-I-turn-a-string-into-a-variable_003f
In a separate but related process, I'm also trying to subset data by
year, where there are multiple observations by years, using the
subset() function. For example:
data.1946-subset(data, year==1946)
data.1947-subset(data, year==1947)
data.1948-subset(data, year==1948)
data.1949-subset(data, year==1949)
...
list.of.subsets - sapply(1946:200, function(x) subset(data,
year==x) ) # with no example ... untested
Using data as a dataframe names is poor R programming practice, since
many functions use data a a parameter name and it is also a function
name.
How should I set this up? I was thinking of writing a for loop, but
I have never written a for loop that creates objects based on the
loop's index, for example a loop for(i in 1946:2000) that returns 55
objects with the object names based on the index.
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] argument 'exclude' in function xtabs
Dear all I was willing to use argument 'exclude' in function xtabs to remove some levels of factors (xtabs help page says 'exclude: a vector of values to be excluded when forming the set of levels of the classifying factors). I tried: mydata - data.frame( treatment = c(B, A, C, C, B, B, C, A, B, B, NA, C), surv = c(YES, NO, YES, YES, NO, NO, NO, YES, YES, NO, NO, NA) ) levels(mydata$treatment) [1] A B C # try to remove level B in variable treatment xtabs(formula = ~ treatment + surv, data = mydata, exclude = B) surv treatment NO YES A 1 1 B 3 2 C 1 2 One alternative is to do: xtabs(formula = ~ treatment + surv, data = mydata[mydata$treatment != B, ], drop.unused.levels = TRUE) surv treatment NO YES A 1 1 C 1 2 But I don't understand why I cannot remove B directly with argument exclude. Any help is welcome Regards Matthieu My version on Windows XP platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 9.0 year 2009 month 04 day17 svn rev48333 language R version.string R version 2.9.0 (2009-04-17) -- Matthieu Lesnoff CIRAD Bamako, Mali E-mail: matthieu.lesn...@cirad.fr [[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] argument 'exclude' in function xtabs
I was willing to use argument 'exclude' in function xtabs to remove some levels of factors (xtabs help page says 'exclude: a vector of values to be excluded when forming the set of levels of the classifying factors). I think I see what's happening, and it's a little confusing to me, too. If your classifying factor to xtabs is not actually a factor, but say, a character vector, it will be converted to a factor while using the exclude argument. However, if it already is a factor, this does not happen. So, for example, contrast: trt.char - c(A,B,C,A,B,C) xtabs(~trt.char, exclude = B) with trt.fac - factor(c(A,B,C,A,B,C)) xtabs(~trt.fac, exclude = B) Hope that helps, Erik Iverson __ 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 custom the tick and type in bwplot
Dear R users I use bwplot to plot some figures. There are two troubles: 1. How to change the dot of the mean to a line, like the style in boxplot 2. How to hide some tick marks. For example, I have seven tick: A, B, C, D, E, F, G, but I want show four marks: A, C, E, G on the x-axis. Thanks! -- Kind Regards, Guanghong [[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] By= levels with the Hmisc summarize function.
Hi, All I have a data frame as follows: attach(mf) names(mf) [1] centre complex appl pool monthalloc_gb I want to summarize this as follows: agg-summarize(alloc_gb,by=llist(centre,complex,appl,month),FUN=sum, na.rm=TRUE) That seems to run fine but there something odd about the output. The first 3 by levels are as expected, for example levels(agg$centre) [1] B G O Q However, month gets messed up somehow: levels(agg$month) NULL The original input data was in yearmon format: class(month) [1] yearmon I was expecting agg$month to have all the various values of mf$month. What am I doing wrong here? Do I have to drop mf$pool somehow? Jim Lane Capacity Planner RBC Financial Group 315 Front St W 6th Floor - H14 Toronto, Ontario CANADA M5V 3A4 416-348-6024 Display of superior knowledge is as great a vulgarity as display of superior wealth - greater indeed, inasmuch as knowledge should tend more definitely than wealth towards discretion and good manners. - H. W. Fowler, Modern English Usage ___ This e-mail may be privileged and/or confidential, and the sender does not waive any related rights and obligations. Any distribution, use or copying of this e-mail or the information it contains by other than an intended recipient is unauthorized. If you received this e-mail in error, please advise me (by return e-mail or otherwise) immediately. Ce courrier électronique est confidentiel et protégé. L'expéditeur ne renonce pas aux droits et obligations qui s'y rapportent. Toute diffusion, utilisation ou copie de ce message ou des renseignements qu'il contient par une personne autre que le (les) destinataire(s) désigné(s) est interdite. Si vous recevez ce courrier électronique par erreur, veuillez m'en aviser immédiatement, par retour de courrier électronique ou par un autre moyen. [[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] what is this experimental design (mixed-effects model)?
J S-19 wrote: I am wondering what experimental design I am dealing with? I study the effect of daily air temperature on daily body temperature of the overwintering turtles (i.e. sleeping in soil). The model is a cosine wave with the air temperature as a covariate. Not sure if I fully got it, but check the estus cycle example in Pinheiro/Bates that looks similar, or the beaver example in 13.5 of MASS (probably less likely). Dieter -- View this message in context: http://www.nabble.com/what-is-this-experimental-design-%28mixed-effects-model%29--tp23218975p23219579.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] Text Contrast in a Plot
Hi Rodrigo,
I would appreciate any suggestion on how can I make a text Ive inserted
in
a plot show some contrast?
There are quite a few approaches, but why not try legend?
Best, Mark.
Rodrigo Aluizio wrote:
Hi List,
I would appreciate any suggestion on how can I make a text Ive inserted
in
a plot show some contrast? With this I mean that I have a white text on a
plot and I would like to make a tiny border around it in black, so even
being small sized and the entire graphic being small in the text page Ill
insert it. It will be visible.
Well I tried inserting a box() function inside the text() function, R
accepts the command but there is no effect. I even tried to plot a greater
black text and then a smaller white one at the same place, but it doesnt
look good.
Any ideas!
Bellow is my plot code without the above mentioned attempts. Id like to
add
this effect at the second text() command.
png('BaseMap.png',width=5.2,height=3.6,pointsize=5,units='in',bg=NA,restoreC
onsole=T,res=1200)
par(mar=c(5,0,0,0))
map('worldHires','brazil',ylim=c(-5.15,-4.55),xlim=c(-37,-36.1),type='n')
rect(-37.1,-5.25,-36,-4.9,density=NULL,angle=45,col='#dbf4ff',border=F)
plot(Batimetria,ylab='',xlab='',border=F,col=Cor$Cor,add=T)
plot(Municipios,ylab='',xlab='',col=rgb(245,232,140,max=255,alpha=255),add=T
,lwd=0.2)
axis(1,xaxp=c(-37,-36.1,5),cex.axis=1.5)
axis(2,yaxp=c(-5.15,-4.55,5),cex.axis=1.5)
text(Prof$Long,Prof$Lat,rownames(Prof),col='black',cex=0.9,srt=-24,font=2)
text(c(-36.96,-36.96,-36.865,-36.54,-36.37,-36.2),c(-4.96,-5.05,-5.11,-5.14,
-5.14,-5.14),c('Areia
Branca','Serra
do Mel','Porto do
Mangue','Macau','Guamaré','Galinhos'),col='Black',cex=1.3,font=2)
rect(-36.20,-4.56,-36.155,-4.565,density=NULL,angle=45,col='black',border='b
lack',lwd=0.1)
rect(-36.155,-4.56,-36.111,-4.565,density=NULL,angle=45,col='white',border='
black',lwd=0.1)
text(c(-36.20,-36.155,-36.111,-36.215),c(-4.573,-4.573,-4.573,-4.562),c('0',
'5','10','km'),col='white',cex=1)
Norte(-36.155,-4.60,0.02)
box(which='plot',lty='solid')
dev.off()
Thanks in advance!
-
MSc. mailto:r.alui...@gmail.com Rodrigo Aluizio
Centro de Estudos do Mar/UFPR
Laboratório de Micropaleontologia
Avenida Beira Mar s/n - CEP 83255-000
Pontal do Paraná - PR Brasil
[[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.
--
View this message in context:
http://www.nabble.com/Text-Contrast-in-a-Plot-tp23217307p23221789.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] omit empty cells in crosstab?
Perhaps this is a common question but I haven't been able to find the answer. I have data with many factors, each taking many values. However, only relatively few combinations appear in the data, ie have nonzero counts, in other words the resulting table is sparse. Say we have 10 factors each with 10 levels. The result of table() would exceed the memory space (on a 32bit machine). Is there any way to produce a table with empty cells omitted? (without first producing the whole table and then removing rows.) Thanks, Steve -- View this message in context: http://www.nabble.com/omit-empty-cells-in-crosstab--tp2363p2363.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] omit empty cells in crosstab?
Hi Steve, The general answer is yes, but the specific will depend on your problem. Could you provide a small reproducible example to illustrate your problem? Hadley On Fri, Apr 24, 2009 at 1:19 PM, sjaffe sja...@riskspan.com wrote: Perhaps this is a common question but I haven't been able to find the answer. I have data with many factors, each taking many values. However, only relatively few combinations appear in the data, ie have nonzero counts, in other words the resulting table is sparse. Say we have 10 factors each with 10 levels. The result of table() would exceed the memory space (on a 32bit machine). Is there any way to produce a table with empty cells omitted? (without first producing the whole table and then removing rows.) Thanks, Steve -- View this message in context: http://www.nabble.com/omit-empty-cells-in-crosstab--tp2363p2363.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. -- http://had.co.nz/ __ 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] use of input in system()
On Fri, 24 Apr 2009, Mike Miller wrote:
On Fri, 24 Apr 2009, Mike Miller wrote:
I am running bash, but system calls go to sh. I want to be able to put
that input string (0005) into a variable and do something like this:
system( i=`cat /dev/stdin` ; run_script file${i}.out ,
input=sprintf(%04d, i) )
In sh, both of these commands execute ls:
echo ls | `cat /dev/stdin`
echo ls | `cat -`
In R, both of these simply hang until I hit ctrl-c...
system( `cat /dev/stdin`, input=ls )
system( `cat -`, input=ls )
...but the stdin is getting to the command because both of these return
ls to stdout:
system( cat -, input=ls )
system( cat /dev/stdin, input=ls )
So what am I missing? I don't understand why the backtick method isn't
working. Is there another way to do this?
I still can't figure that out, but it is OK because I found a better way.
For some reason I was thinking of the system function like this...
system( command )
...when I could have been thinking of it like this:
foo - command
system( foo )
Maybe obvious in retrospect, but that makes it much easier to take values
from R and insert them into system commands. Here is a mini example:
i - 5
foo - ls
bar - paste(touch file, sprintf(%04d, i), .out, sep=)
bar
[1] touch file0005.out
Thus I have placed two system commands into variables foo and bar. The
system commands can be pasted together using ; as a separator...
barfoo - paste(bar, foo, sep= ; )
barfoo
[1] touch file0005.out ; ls
...then executed like so:
system( barfoo )
Mike
Michael B. Miller, Ph.D.
Minnesota Center for Twin and Family Research
Department of Psychology
University of Minnesota
__
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] Problem with greek beta symbol in plot using CairoPDF (Windows)
Dear R-Helpers, I have a problem with displaying the greek beta symbol in PDF files using Cairo library - it displays as an empty box. The same also happens for a dash symbol in subscript. Both symbols are displayed correctly if the plot is produced on screen (outside of CairoPDF). The syntax that I use for it in plot command is: 'xlab=expression(paste(A,beta,)[1-42])'. When I try to select a different font family using 'family' option in the CairoPDF command - it has no effect. I tried 'CairoFonts', but it displays an error: 'Warning message: In CairoFonts() : the R Cairo package was not installed with fontconfig. Please consider installing the cairo graphics engine (www.cairographics.org) with freetype and fontconfig support' I have the most recent GTK+ installed. I don't know where to look for solution. Anyone able to help? Here is my session info: sessionInfo() R version 2.8.1 (2008-12-22) i386-pc-mingw32 locale: LC_COLLATE=Polish_Poland.1250;LC_CTYPE=Polish_Poland.1250;LC_MONETARY=Polish_Poland.1250;LC_NUMERIC=C;LC_TIME=Polish_Poland.1250 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Cairo_1.4-5 -- Michal J. Figurski HUP, Pathology Laboratory Medicine Biomarker Research Laboratory Philadelphia, USA __ 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 custom the tick and type in bwplot
On Apr 24, 2009, at 1:33 PM, Guanghong Zuo wrote: Dear R users I use bwplot to plot some figures. There are two troubles: 1. How to change the dot of the mean to a line, like the style in boxplot Sometimes you need to refer the the help page for panel.type of plot, in this case: ?panel.bwplot ... so the answer is now staring you in the face: bwplot(decrease ~ treatment, OrchardSprays, groups = rowpos, pch=|) 2. How to hide some tick marks. For example, I have seven tick: A, B, C, D, E, F, G, but I want show four marks: A, C, E, G on the x-axis. Using the example in bwplot again, and a fair amount of fruitless experimentation with the theory that one could do anything useful with scales=list(at= list(something)), I finally ended up trying , labels=c( ) per Sarkar's Lattice book, producing this: bwplot(decrease ~ treatment, OrchardSprays, groups = rowpos, scales=list(x=list( labels=c(A,,,D,,F,,) ))) -- 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] font size relative to graphic
I am printing numbers onto horizontal bars in a bar plots, but I am finding it difficult to make the number always the right size. If there are more bars, the bars get narrower and the font is too big. I also find that if I change the size of the graph, the bars will get wider or narrower and the font stays about the same size. The result depends on whether I view the graph in X11 or in postscript. Is there a way to specify font size relative to bar width, or at least specify font size relative to graph coordinates? Here's a bit of what I've been doing: x.bar.plot - barplot(as.matrix(x), horiz=TRUE, beside=TRUE, xlim=c(0,100), xlab=Score, las=1) text(as.matrix(x), x.bar.plot-.07, as.character(as.matrix(round(x))), pos=2, col=black) The -.07 is something I added to make the numbers align well with the bars under one condition, but it doesn't always help. Any tips would be greatly appreciated. Thanks in advance. Mike -- Michael B. Miller, Ph.D. Minnesota Center for Twin and Family Research Department of Psychology University of Minnesota __ 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] Can't install package glmnet
Liang Zhang wrote: I am just wondering how to solve this installation problem. As I said, ask your admin to install suitable compilers. Uwe Thanks, Liang From: Uwe Ligges lig...@statistik.tu-dortmund.de To: Liang Zhang zhangl...@yahoo.com Cc: r-help@r-project.org Sent: Friday, April 24, 2009 2:50:00 AM Subject: Re: [R] Can't install package glmnet Liang Zhang wrote: Hi, I was trying to install package glmnet in R, but failed and it show such messages: * Installing *source* package glmnet ... This package has only been tested with gfortran. So some checks are needed. R_HOME is /home/username/R/R-2.9.0 Attempting to determine R_ARCH... R_ARCH is Attempting to detect how R was configured for Fortran 90 Unsupported Fortran 90 compiler or Fortran 90 compilers unavailable! Stop! ERROR: configuration failed for package glmnet * Removing /home/username/R/R-2.9.0/library/glmnet The downloaded packages are in /tmp/RtmpwsLWSc/downloaded_packages Updating HTML index of packages in '.Library' Warning message: In install.packages(glmnet) : installation of package 'glmnet' had non-zero exit status It seems that it needs fortran 90 complier. What can I do to solve this problem? (I am not the administrator, only a user in the linux system). Ask for a suitable compiler? Uwe Ligges Thank you very much! Liang [[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] font size relative to graphic
On Apr 24, 2009, at 3:14 PM, Mike Miller wrote: I am printing numbers onto horizontal bars in a bar plots, but I am finding it difficult to make the number always the right size. If there are more bars, the bars get narrower and the font is too big. I also find that if I change the size of the graph, the bars will get wider or narrower and the font stays about the same size. The result depends on whether I view the graph in X11 or in postscript. Is there a way to specify font size relative to bar width, or at least specify font size relative to graph coordinates? Here's a bit of what I've been doing: x.bar.plot - barplot(as.matrix(x), horiz=TRUE, beside=TRUE, xlim=c(0,100), xlab=Score, las=1) text(as.matrix(x), x.bar.plot-.07, as.character(as.matrix(round(x))), pos=2, col=black) The -.07 is something I added to make the numbers align well with the bars under one condition, but it doesn't always help. Any tips would be greatly appreciated. Thanks in advance. The values returned from the barplot function are the locations of the bars. Why not call barplot, collect the values, and then use the length of the result to determine your sizes and widths? hh - t(VADeaths)[, 5:1] mybarcol - gray20 mp - barplot(hh, beside = TRUE, col = c(lightblue, mistyrose, lightcyan, lavender), legend = colnames(VADeaths), ylim= c(0,100), main = Death Rates in Virginia, font.main = 4, sub = Faked upper 2*sigma error bars, col.sub = mybarcol, cex.names = 1.5) length(mp) # [1] 20 -- 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.
Re: [R] omit empty cells in crosstab?
sjaffe sjaffe at riskspan.com writes: I have data with many factors, each taking many values. However, only relatively few combinations appear in the data, ie have nonzero counts, in other words the resulting table is sparse. Say we have 10 factors each with 10 levels. The result of table() would exceed the memory space (on a 32bit machine). Is there any way to produce a table with empty cells omitted? (without first producing the whole table and then removing rows.) It would be easier if you had a reproducible base example, but I suggest to create ONE new factor of the pasted levels using unique(), and creating a table of these. Dieter __ 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] Invert Deviance Residuals
I have a vector of deviance residuals, r, a vector of fitted values, yhat and
I need to solve for a vector of actuals, y. The deviance residual formula
is r={2(c ln c - c + 1)}^1/2. c=y/yhat.
Since this can't be solved in closed form, I believe that I should be able
to solve this numerically using a function like optim but I can't get my
head around how to setup the problem and looking at the examples for optim
it hasn't clicked for me. Any help would be appreciated.
I am using this result as part of a funtion to do non-parametric
bootstrapping of a glm to build a range around my parameter errors.
Thanks.
Bill
--
View this message in context:
http://www.nabble.com/Invert-Deviance-Residuals-tp23223703p23223703.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] omit empty cells in crosstab?
Dieter Menne wrote: sjaffe sjaffe at riskspan.com writes: I have data with many factors, each taking many values. However, only relatively few combinations appear in the data, ie have nonzero counts, in other words the resulting table is sparse. Say we have 10 factors each with 10 levels. The result of table() would exceed the memory space (on a 32bit machine). Is there any way to produce a table with empty cells omitted? (without first producing the whole table and then removing rows.) It would be easier if you had a reproducible base example, but I suggest to create ONE new factor of the pasted levels using unique(), and creating a table of these. interaction(..., drop=TRUE) may be a neater way. -- 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.
Re: [R] Can't install package glmnet
I am just wondering how to solve this installation problem. Thanks, Liang From: Uwe Ligges lig...@statistik.tu-dortmund.de Cc: r-help@r-project.org Sent: Friday, April 24, 2009 2:50:00 AM Subject: Re: [R] Can't install package glmnet Liang Zhang wrote: Hi, I was trying to install package glmnet in R, but failed and it show such messages: * Installing *source* package glmnet ... This package has only been tested with gfortran. So some checks are needed. R_HOME is /home/username/R/R-2.9.0 Attempting to determine R_ARCH... R_ARCH is Attempting to detect how R was configured for Fortran 90 Unsupported Fortran 90 compiler or Fortran 90 [[elided Yahoo spam]] ERROR: configuration failed for package glmnet * Removing /home/username/R/R-2.9.0/library/glmnet The downloaded packages are in /tmp/RtmpwsLWSc/downloaded_packages Updating HTML index of packages in '.Library' Warning message: In install.packages(glmnet) : installation of package 'glmnet' had non-zero exit status It seems that it needs fortran 90 complier. What can I do to solve this problem? (I am not the administrator, only a user in the linux system). Ask for a suitable compiler? Uwe Ligges [[elided Yahoo spam]] Liang [[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] saved workspace
I saved the workspace once and now it automatically restore it whenever I open R How can I turn off this? Thank you __ 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] saved workspace
Assuming you are starting R from a terminal window, you can use R --no-restore or change to a different directory first. If you are starting R in some other fashion, it will depend on what you are doing, a piece of information you neglected to provide (along with OS, which could be relevant, and is requested regardless). Sarah On Fri, Apr 24, 2009 at 1:49 PM, bogdanno bodins...@gmail.com wrote: I saved the workspace once and now it automatically restore it whenever I open R How can I turn off this? Thank you -- 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] font size relative to graphic
On Fri, 24 Apr 2009, David Winsemius wrote: On Apr 24, 2009, at 3:14 PM, Mike Miller wrote: I am printing numbers onto horizontal bars in a bar plots, but I am finding it difficult to make the number always the right size. If there are more bars, the bars get narrower and the font is too big. I also find that if I change the size of the graph, the bars will get wider or narrower and the font stays about the same size. The result depends on whether I view the graph in X11 or in postscript. Is there a way to specify font size relative to bar width, or at least specify font size relative to graph coordinates? Here's a bit of what I've been doing: x.bar.plot - barplot(as.matrix(x), horiz=TRUE, beside=TRUE, xlim=c(0,100), xlab=Score, las=1) text(as.matrix(x), x.bar.plot-.07, as.character(as.matrix(round(x))), pos=2, col=black) The -.07 is something I added to make the numbers align well with the bars under one condition, but it doesn't always help. Any tips would be greatly appreciated. Thanks in advance. The values returned from the barplot function are the locations of the bars. Why not call barplot, collect the values, and then use the length of the result to determine your sizes and widths? That is exactly the kind of thing I want to do, but I don't know how the font size can be specified so that it fits. My bars are horizontal and yours (from code below) are vertical. Your barplot output was called mp and mine was called x.bar.plot and here is what they looked like: mp [,1] [,2] [,3] [,4] [,5] [1,] 1.5 6.5 11.5 16.5 21.5 [2,] 2.5 7.5 12.5 17.5 22.5 [3,] 3.5 8.5 13.5 18.5 23.5 [4,] 4.5 9.5 14.5 19.5 24.5 x.bar.plot [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [1,] 1.5 4.5 7.5 10.5 13.5 16.5 19.5 22.5 25.5 28.5 31.5 34.5 [2,] 2.5 5.5 8.5 11.5 14.5 17.5 20.5 23.5 26.5 29.5 32.5 35.5 They are pretty similar numbers. It seems that [1,1] element is always 1.5 and consecutive elements in the same column differ by 1.0, but in the rows we see something different: mine are 3.0 apart and yours are 5.0 apart. So what does this tell me? I think fonts are specified in points which correspond to 1/72 inches, while bars are specified in coordinates that are independent of inches. So I need to know how coordinates correspond to inches before I can get this fixed. Mike hh - t(VADeaths)[, 5:1] mybarcol - gray20 mp - barplot(hh, beside = TRUE, col = c(lightblue, mistyrose, lightcyan, lavender), legend = colnames(VADeaths), ylim= c(0,100), main = Death Rates in Virginia, font.main = 4, sub = Faked upper 2*sigma error bars, col.sub = mybarcol, cex.names = 1.5) length(mp) # [1] 20 __ 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] omit empty cells in crosstab?
small example: a-c(1.1, 2.1, 9.1) b-cut(a,0:10) c-data.frame(b,b) d-table(c) dim(d) ##result: c(10, 10) But only 9 of the 100 cells are non-zero. If there were 10 columns, the table have 10 dimensions each of length 10, so have 10^10 elements, too much even to fit in memory Dieter Menne wrote: sjaffe sjaffe at riskspan.com writes: I have data with many factors, each taking many values. However, only relatively few combinations appear in the data, ie have nonzero counts, in other words the resulting table is sparse. Say we have 10 factors each with 10 levels. The result of table() would exceed the memory space (on a 32bit machine). Is there any way to produce a table with empty cells omitted? (without first producing the whole table and then removing rows.) It would be easier if you had a reproducible base example, but I suggest to create ONE new factor of the pasted levels using unique(), and creating a table of these. Dieter __ 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/omit-empty-cells-in-crosstab--tp2363p23224071.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] update.packages(checkBuilt=TRUE) returns Error: invalid version specification NA in 2.9.0
Just a guess: We had an issues with malformed PACKAGES files in the Windows repositories. Maybe you are affected here. Can you please try in 24 hours from now to do that again using the mirror in Austria. If the problem persists, please let me know. Thank you, Uwe Ligges peter_kel...@fws.gov wrote: I installed R-2.9.0 yesterday, and followed the instructions in the R for Windows FAQ, 2.8 What's the best way to upgrade? It reads run update.packages(checkBuilt=TRUE, ask=FALSE) in the new R and then delete anything left of the old installation. I did this but it returned an error. It's the checkBuilt=TRUE which causes it, though I don't know why: leaving it out or changing it to checkBuilt=FALSE do not return errors. update.packages(checkBuilt=TRUE, ask=FALSE) --- Please select a CRAN mirror for use in this session --- Error: invalid version specification NA update.packages(checkBuilt=TRUE) Error: invalid version specification NA Peter Keller Wildlife Biologist Tetlin National Wildlife Refuge [[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] saved workspace
One could also move the file out of the R search path, or rename it with an extension that prevents R from seeing it.( Some operating systems may not allow you to see it in their default mode, however.) -- David On Apr 24, 2009, at 4:07 PM, Sarah Goslee wrote: Assuming you are starting R from a terminal window, you can use R --no-restore or change to a different directory first. If you are starting R in some other fashion, it will depend on what you are doing, a piece of information you neglected to provide (along with OS, which could be relevant, and is requested regardless). Sarah On Fri, Apr 24, 2009 at 1:49 PM, bogdanno bodins...@gmail.com wrote: I saved the workspace once and now it automatically restore it whenever I open R How can I turn off this? Thank you -- 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. 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.
Re: [R] rounding problem + sprintf
Prof Brian Ripley wrote:
I think your subject line should read 'Excel bug'. From the R help
for round()
Note that for rounding off a 5, the IEC 60559 standard is expected
to be used, '_go to the even digit_'.
In case you did not recognize it, IEC 60559 is an international
standard: Excel is not.
R is Open Source and so you can modify it to emulate the bugs in other
software: that is not one of the aims of its developers so please
don't expect us to do so for you.
It is rare for round() to be called explicitly in R code: rounding is
usually going on inside print routines.
besides noting that r is as much an international standard as excel,
here's an example of how the otherwise buggy sprintf (less so now,
thanks to martin's recent fixes) and other print routines let excel bugs
sneak into r:
(x = c(0.15, 0.25, 0.35, 0.45, 0.55, 0.65))
round(x, 1)
print(x, 1)
sprintf('%.1f', x)
?print and ?sprintf do not say anything about how rounding is done, but
given the above strong statement about standards, one would expect that
the ties-to-even mode is used. apparently, round (the function) and the
print routines (sprintf and print) either operate in different rounding
modes, or read the input (the internal representation of numbers)
differently.
not so surprisingly, sprintf in r reproduces the behaviour of sprintf in
c. but would it be a good idea to blame c for excel bugs in r?
vQ
__
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] font size relative to graphic
On Apr 24, 2009, at 4:10 PM, Mike Miller wrote: On Fri, 24 Apr 2009, David Winsemius wrote: On Apr 24, 2009, at 3:14 PM, Mike Miller wrote: I am printing numbers onto horizontal bars in a bar plots, but I am finding it difficult to make the number always the right size. If there are more bars, the bars get narrower and the font is too big. I also find that if I change the size of the graph, the bars will get wider or narrower and the font stays about the same size. The result depends on whether I view the graph in X11 or in postscript. Is there a way to specify font size relative to bar width, or at least specify font size relative to graph coordinates? Here's a bit of what I've been doing: x.bar.plot - barplot(as.matrix(x), horiz=TRUE, beside=TRUE, xlim=c(0,100), xlab=Score, las=1) text(as.matrix(x), x.bar.plot-.07, as.character(as.matrix(round(x))), pos=2, col=black) The -.07 is something I added to make the numbers align well with the bars under one condition, but it doesn't always help. Any tips would be greatly appreciated. Thanks in advance. The values returned from the barplot function are the locations of the bars. Why not call barplot, collect the values, and then use the length of the result to determine your sizes and widths? That is exactly the kind of thing I want to do, but I don't know how the font size can be specified so that it fits. My bars are horizontal and yours (from code below) are vertical. Your barplot output was called mp and mine was called x.bar.plot and here is what they looked like: mp [,1] [,2] [,3] [,4] [,5] [1,] 1.5 6.5 11.5 16.5 21.5 [2,] 2.5 7.5 12.5 17.5 22.5 [3,] 3.5 8.5 13.5 18.5 23.5 [4,] 4.5 9.5 14.5 19.5 24.5 x.bar.plot [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [1,] 1.5 4.5 7.5 10.5 13.5 16.5 19.5 22.5 25.5 28.5 31.5 34.5 [2,] 2.5 5.5 8.5 11.5 14.5 17.5 20.5 23.5 26.5 29.5 32.5 35.5 They are pretty similar numbers. It seems that [1,1] element is always 1.5 and consecutive elements in the same column differ by 1.0, but in the rows we see something different: mine are 3.0 apart and yours are 5.0 apart. So what does this tell me? I think fonts are specified in points which correspond to 1/72 inches, while bars are specified in coordinates that are independent of inches. So I need to know how coordinates correspond to inches before I can get this fixed. They do not correspond to inches, but the the numeric scale of the values. Here is your plot with the numbers moved so they are to the right of the bar ends: txt - 1.5 4.5 7.5 10.5 13.5 16.5 19.5 22.5 25.5 28.5 31.5 34.5 2.5 5.5 8.5 11.5 14.5 17.5 20.5 23.5 26.5 29.5 32.5 35.5 x - read.table(textConnection(txt), header=FALSE) x.bar.plot - barplot(as.matrix(x), horiz=TRUE, beside=TRUE, xlim=c(0,100), xlab=Score, las=1) text(as.matrix(x+6), x.bar.plot-.07, as.character(as.matrix(round(x))), pos=2, col=black) # the rounding is what makes the dissimilar bars labeled with the same numbers, ... yecch. Haven't figured out what the requirements on sizing really are; but here is an example you might play with: text(as.matrix(x+6), x.bar.plot-.07, as.character(as.matrix(round(x))), pos=2, col=black, cex= 24/length(as.matrix(x))) 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.
Re: [R] How to custom the tick and type in bwplot
On 4/24/09, David Winsemius dwinsem...@comcast.net wrote: On Apr 24, 2009, at 1:33 PM, Guanghong Zuo wrote: Dear R users I use bwplot to plot some figures. There are two troubles: 1. How to change the dot of the mean to a line, like the style in boxplot Sometimes you need to refer the the help page for panel.type of plot, in this case: ?panel.bwplot ... so the answer is now staring you in the face: bwplot(decrease ~ treatment, OrchardSprays, groups = rowpos, pch=|) 2. How to hide some tick marks. For example, I have seven tick: A, B, C, D, E, F, G, but I want show four marks: A, C, E, G on the x-axis. Using the example in bwplot again, and a fair amount of fruitless experimentation with the theory that one could do anything useful with scales=list(at= list(something)), I finally ended up trying , labels=c( ) per Sarkar's Lattice book, producing this: bwplot(decrease ~ treatment, OrchardSprays, groups = rowpos, scales=list(x=list( labels=c(A,,,D,,F,,) ))) or bwplot(decrease ~ treatment, OrchardSprays, groups = rowpos, pch=|, scales = list(x = list(at = c(1, 3, 5, 7), labels = c(A, C, E, G or bwplot(decrease ~ treatment, OrchardSprays, groups = rowpos, pch=|, xlim = c(A, , C, , E, , G)) -Deepayan __ 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.t.test formula
Look at the pwr package, it has functions for 2 samples of different sizes. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Karl Ove Hufthammer Sent: Friday, April 24, 2009 2:41 AM To: r-h...@stat.math.ethz.ch Subject: Re: [R] power.t.test formula Peter Dalgaard: Does anyone of you knows a reference for the formula used in power.t.test function? And also why it uses the Student's distribution instead of Normal. (I know both of them can be used but don't see whether choose one or the other) It is a straightforward first-principles calculation. The t distribution calculation is exact for normally distributed data with the same unknown variance in both groups. I didn’t know about power.t.test. A very nice function, indeed. Is there a similar function that handles unequal number of observations for each group, and unequal variances? The help file mislead me into thinking that power.t.test handles unequal number of observations, and for example ‘power.t.test(c(10,3),1)’ *does* give some output (and not a warning or error), just not the output I was expecting. (It gives two power values, one for sample of size 10 (for each group) and one for samples of size 3 (for each group), while I was expecting the power for a sample size 10 for one group and 3 for the other group). -- Karl Ove Hufthammer __ 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] issue building my own package... moving from Apple OS to Windows
Thanks for the various responses. It was easier than I thought to get all the tools together and setup Windows paths for the build process. I've been successful now on Windows. BUT... how do I make a package which DOES NOT require R CMD INSTALL to install? Obviously, it should not be required for everyone to have Perl on their Windows box to install a package. When I tried to install the .tar.gz file from the GUI, I got the same errors as I did when I used the version I had built on my Apple. Error in gzfile(file,r) : cannot open the connection In addition: Warning messages: 1: In unzip(zipname, exdir=dest) :error 1 in extracting from zip file 2: In gzfile(file,r): cannot open compressed file 'multgeneriskpredperf_1.0.tar.gz/DESCRIPTION', probable reason 'No such file or directory' Thanks, Daryl Uwe Ligges wrote: You need to INSTALL a source package (that has been build) as on any other platform. How to colect the tools in order to make R CMD INSTALL work under Windows (and other OSs) is described in the R Installation and Administration manual. Best, Uwe Ligges __ 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.
