Re: [R] Excel
Ah . . . the hammer analogy. In a conversation like this it's not a question of will somebody drop it, it's when will it be dropped. --Matt Matt Austin Statistician Amgen, Inc. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Greg Snow Sent: Thursday, August 30, 2007 12:14 PM To: Erich Neuwirth; r-help Subject: Re: [R] Excel Earlier this week I was doing some work at our house and since my wife was at the dentist office our 3 year old son was helping me. He really wanted to use the hammer, so I showed him where to tap and he was excited to tap (not doing much good, but also not doing any damage). He liked that so much that he started to look for other things that he could use the hammer on, some were benign, others made me jump in and stop him before he did major damage. What does this have to do with Excel and R? Well I see Excel as being very much like my hammer and different users like the different users of the hammer. There are some carpenters who can use a hammer along with other tools to make things of pure beauty. Simillarly, I expect there are people who can use excel/spreadsheets along with other tools to make useful and beautiful things (I expect that you (Erich) may be one of those). My use of the hammer is far less than that of the experts, I can about 9 times out of 10 survive the use without blood and major bruising, fix or make something that works, but is far from a work of art. My use of spreadsheets is similar, I do use them for some specific purposes (holding the bus schedule on my pda, amortization tables), but I know better than to use them where I would cause more harm than good. I fear that many users of Excel and other spreadsheets are much like my toddler, they have a tool and they want to use it, ignorant of whether they will cause more damage than good. This is part of why I put in the reference to Dr. Burns page, he does not say get rid of spreadsheet altogether, but he points out that there are several cases where other tools work better (It is possible to embed a screw in a piece of wood using a hammer, but a screwdriver generally works better). Erich Neuwirth wrote: -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Erich Neuwirth Sent: Wednesday, August 29, 2007 4:46 PM To: r-help Subject: Re: [R] Excel Greg Snow wrote: Or do you trust all of your clients to know to use R(D)COM as well as how to install and use it? Do you trust your clients to be fluent enough in R to use it? I admitted that I don't trust some of my clients with their own data (I think my record is 9 different sexes), I certainly don't expect them to use R. I trust them to bring their questions and data to me, then I use R (or one of my coworkers uses their favorite stats package) to help them. That way I know that the correct things are being done (on the flip side, they trust me to leave patient care up to them and not try surgery myself, it is much better for the patients that way). For most of my clients, that is not true. For this kind of users, the following strategy works. They have their data in Excel, and I write some macros in Excel which use RExcel to compute results and put them in the sheet. The clients press buttons similar to what they would do with the Analysis toolpack in Excel, but they get the full power of R. Who installs R and sets up R dcom on all these computers? If the above clients want something in addition to what you prepared, do you add additional macros for them? Do they know enough R to write their own Rapply statement? Or do they go looking in the Excel help and use the wrong set of tools? Or do you have them trained enough that they don't ask any additional questions? I have no problem with you using this approach, I just think that if you are going to advocate that others use excel with clients, that you also let them know of the extra work that they may be committing themselves to. The formula =RApply(var,A1:A1000) in an Excel cell for example will use R to compute the variance of the data in column A in Excel. If you change any of the values in the range A1:A1000 will automatically recompute the variance. And what happens when you enter a value in cell A1001? If you use the following formula =RApply(var,DownFrom(A1)) where DownFrom ist he following function defined in VBA Function DownFrom(startcell As Range) As Range Application.Volatile Set DownFrom = Range(startcell, startcell.End(xlDown)) End Function Then writing a value in A1001 will a extend the range to which the function var is applied. So to answer a known inconsistancy in spreadsheets, you are now bringing in a 3rd program/language. At what point is it just simpler to use R directly? (for me it was back a couple of steps). Arguments of worksheet function can be dynamic ranges, but sadly this is a
[R] Unexpected behavior in boxplot
When plotting using the cex.axis argument to boxplot(), the size of the plotting symbols beyond the whiskers of the boxplot are being changes. Example: par(mfrow=c(2,1)) boxplot(c(rnorm(10), 10), horizontal=TRUE, main=Test, las=2, cex.axis=2) boxplot(c(rnorm(10), 10), horizontal=TRUE, main=Test, las=2, cex.axis=1) This is from the following line in bxp() outcex - pcycle(pars$outcex, pars$cex, par(cex)) Where pars$cex is matching pars$cex.axis. This would also effect other parameter specifications. This is a behavior I did not expect; I'm not sure if this is a design feature or something else. --Matt Matt Austin Statistician Amgen, Inc 800 9AMGEN9 x77431 805-447-7431 The purpose of computing is insight, not numbers --Richard Hamming [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Unexpected behavior in boxplot
Apologies for the html mail, my company just upgraded and I forgot to change the default mail behavior. Version information that I also forgot: version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 4.0 year 2006 month 10 day03 svn rev39566 language R version.string R version 2.4.0 (2006-10-03) --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Austin, Matt Sent: Saturday, November 11, 2006 8:15 PM To: r-help@stat.math.ethz.ch Subject: [R] Unexpected behavior in boxplot When plotting using the cex.axis argument to boxplot(), the size of the plotting symbols beyond the whiskers of the boxplot are being changes. Example: par(mfrow=c(2,1)) boxplot(c(rnorm(10), 10), horizontal=TRUE, main=Test, las=2, cex.axis=2) boxplot(c(rnorm(10), 10), horizontal=TRUE, main=Test, las=2, cex.axis=1) This is from the following line in bxp() outcex - pcycle(pars$outcex, pars$cex, par(cex)) Where pars$cex is matching pars$cex.axis. This would also effect other parameter specifications. This is a behavior I did not expect; I'm not sure if this is a design feature or something else. --Matt Matt Austin Statistician Amgen, Inc 800 9AMGEN9 x77431 805-447-7431 The purpose of computing is insight, not numbers --Richard Hamming [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with sample function
I couldn't help but respond to this one, it's not often I see my own name.
Using data from the survival library:
library(survival)
lung[1:10, c('time', 'status')]
Surv(lung$time, lung$status)[1:10]
--Matt
Matt Austin
Statistician
Amgen, Inc
800 9AMGEN9 x77431
805-447-7431
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Matthew Austin
Sent: Wednesday, June 07, 2006 6:57 AM
To: r-help@stat.math.ethz.ch
Subject: [R] Help with sample function
I have generated some some survival times and censoring indicators.
Thus I have an ordered pair for each observation. How do I sample these
ordered paris? I only know how to sample from a vector? I would
appreciate any help I could get.
Thanks
Matt
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Re: [R] Reading SPSS .sav files
I don't use SPSS, so I can't help with the details. That being said, have you looked at the foreign package? --Matt Matt Austin Statistician Amgen, Inc 800 9AMGEN9 x77431 805-447-7431 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of David Kaplan Sent: Sunday, April 16, 2006 1:35 PM To: r-help@stat.math.ethz.ch Subject: [R] Reading SPSS .sav files Greetings, How to I read in SPSS .sav files into R. Thank you. David = David Kaplan, PhD Professor of Education School of Education University of Delaware Newark DE 19716 Voice: 302-831-8696 Fax:302-831-4110 email: mailto:[EMAIL PROTECTED] Homepage: http://www.udel.edu/dkaplan SOE page: http://www.udel.edu/educ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How can I pass a R matrix as parameter to C code?
You need to pass it as a vector and then you can convert to an array
structure in C. Look at carray.c for one way to do this, there are others.
Browse the source code and see how different authors handle your problem.
Matt Austin
Statistician
Amgen, Inc
800 9AMGEN9 x77431
805-447-7431
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of johan Faux
Sent: Monday, March 20, 2006 1:13 PM
To: r-help
Subject: [R] How can I pass a R matrix as parameter to C code?
Hello,
Is it possible to pass R matrix as a parameter to an internal C procedure?
From the documentation I got the impression that only 1-dim vectors can be
passed.
Why the following wont work for me?
a-matrix(1:15,3,5)
.C(pr,as.integer(a))
void pr(int **a){
a[1][1]=100;
}
Thanks,
Johan
-
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Re: [R] How to add two different axis to one plot?
Using traditional graphics you probably want to look at ?lines, ?points, ?text . . . These allow you to add to your plot without calling new axes. For custom axes: plot(1:10, 1:10, axes=FALSE) lines(1:10, 10:1) points(1:10, runif(10, 2, 5), col=1, pch=21, bg=3, cex=3) axis(1, at=1:10) axis(3, at=1:10, lab=10:1) axis(2) box() Look at ?axis for details. --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Michael Sent: Sunday, January 29, 2006 8:49 PM To: [EMAIL PROTECTED] Cc: R-help@stat.math.ethz.ch Subject: Re: [R] How to add two different axis to one plot? No this is not good. When I used par(new=TRUE), it does not adjust axis accordingly... Thus two different axes end up overlap together. For example, if my first plot has x-axis from 0 to 10, with ticks at 1, 3, 5, 7, 9; and my second plot has x-axis from 2 to 12, with ticks at 2, 2.9, 5.5... then the two plots have two different axes with ticks overlap together. The visual appearance is very bad. On 1/29/06, Andrew Robinson [EMAIL PROTECTED] wrote: Use the axis() command to add custom axes. To hold the plot, insert par(new=TRUE) between the plot statements, thus: plot(x1, y1, etc ...) par(new=TRUE) plot(x2, y2, etc ...) Andrew On Mon, January 30, 2006 2:49 pm, Michael said: Hi all, I need to put two different axis to one plot. On the top of the plot, I need to put one axis, with increments from left side to the right side; then at the bottom of the same plot, I need to put another axis, with increments from right side to the left side and showing a different unit. How do I do that? By the way, is there a hold command for plotting? If I first plot a picture, how to add another plot command onto it without erasing it? In matlab, it can be convinient done by hold on and hold off... and can I do it in R? Thanks a lot, Micheal [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Andrew Robinson Senior Lecturer in Statistics Tel: +61-3-8344-9763 Department of Mathematics and StatisticsFax: +61-3-8344 4599 University of Melbourne, VIC 3010 Australia Email: [EMAIL PROTECTED]Website: http://www.ms.unimelb.edu.au [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] question about system command
Something like this.
See ?formatC, ?paste
for (i in 1:100)
{
system(paste(C:\\Progra~1\\DOSPROGRAM\\RUN.exe input,
formatC(i, digits=2, flag='0'),
'.dat',
sep=''))
}
--Matt
Statistician
Amgen, Inc
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Taka Matzmoto
Sent: Wednesday, January 25, 2006 9:31 PM
To: r-help@stat.math.ethz.ch
Subject: [R] question about system command
Hi R Users
I am going to write a very short script for my small pilot simulation study.
I need to call a DOS program with different input data files in the middle
of for loop.
There are 100 input data files (e.g., input001.dat, input002.dat, ,
input100.dat)
for (1 in i :100)
{
system('C:\\Program Files\\DOSPROGRAM\\RUN.exe input001.dat')
}
I like to change the input data file name as for loop runs. How can I do
that ?
Thanks in advance
TM
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Re: [R] multiple lowess line in one plot
Try using the panel.plsmo function in Dr. Harrell's Hmisc package. xyplot(AWGT ~ lipid, groups = var_name, panel=panel.plsmo) --Matt Matt Austin Statistician Amgen, Inc. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Dean Sonneborn Sent: Wednesday, January 04, 2006 8:54 AM To: r-help@stat.math.ethz.ch Subject: [R] multiple lowess line in one plot I'm using this code to plot a smoothed line. These two columns of data really represent 4 groups and I'd like to plot a separate line for each group but have them all in the same plot. The R-Docs for lowess do not seem to indicate some type of GROUPS=var_name option. What would be the syntax for this? plot(AWGT ~ lipid ) lines(lowess(lipid , AWGT, f=.8)) -- Dean Sonneborn, MS Programmer Analyst Department of Public Health Sciences University of California, Davis (530) 754-9516 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] How do I edit the x-axis on a time series plot?
Phil, Does the following do what you want? plot(RecfS, ylab = 'Temperature (deg C)', xlab = 'Year', main = 'Average air temperature (deg C) at Recife, Brazil, in successive months from 1953 to 1962', adj = 0.5, axes=FALSE) axis(1, at=1952:1962, label=paste(Jan, 52:62), las=2) axis(2) box() --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Philip Turk Sent: Tuesday, December 20, 2005 8:37 PM To: r-help@stat.math.ethz.ch Subject: [R] How do I edit the x-axis on a time series plot? I am merely trying to reproduce Figure 1.2 of Chris Chatfield's 6th edition of his The Analysis of Time Series: An Introduction (page 2). The S-PLUS code is on pages 305-306. I am almost there but I am having a heck of a time trying to modify and change the x-axis per the book. The book shows the x-axis with 10 tick marks, correctly positioned, and labeled Jan 53, ..., Jan 62. I have not provided the data for the sake of brevity although it is readily available at http://www.bath.ac.uk/~mascc/Recife.TS Can anyone help? recife - as.vector(t(recife)) RecfS - ts(recife, start = c(1953,1), frequency = 12) plot(RecfS, ylab = Temperature (deg C), xlab = Year, main = Average air temperature (deg C) at Recife, Brazil, in successive months from 1953 to 1962, adj = 0.5) Thanks, Philip Turk __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Impaired boxplot functionality - mean instead of median
Check your syntax on the bwplot call. fa - data.frame(doz=sample(500:2000, size=500), fabp2=rep(1:20, 25)) bwplot(factor(fabp2) ~ doz, data=fa, panel=panel.bpplot) fa.sum - summarize( fa$doz, list( fabp2 = fa$fabp2), smean.sd, stat.name=doz) Dotplot( factor(fabp2) ~ Cbind(doz, doz - SD, doz + SD) , data=fa.sum) You can ignore the warning, I'm sure Dr. Harrell has already fixed that issue. --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Evgeniy Kachalin Sent: Thursday, December 01, 2005 2:43 PM To: Frank E Harrell Jr Cc: r-help@stat.math.ethz.ch Subject: Re: [R] Impaired boxplot functionality - mean instead of median Frank E Harrell Jr пишет: Evgeniy Kachalin wrote: Marc Schwartz (via MN) пишет: Marc Schwartz (via MN) пишет: library(Hmisc) library(lattice) ?panel.bpplot bwplot(, panel=panel.bpplot) By default, panel.bpplot shows the mean (dot) and median (line) plus several quantiles. To bother Martin in a friendly way, I think that means can be useful additions - not that they are so useful by themselves, but that when they differ a lot from the median, non-statisticians gain further information about asymmetry. Also, even though the simple box plot is elegant, I sometimes think it has a high ink to information ratio. I have gained a lot from seeing outer quantiles on the plot, and I don't like to show outer points for fear of someone labeling them outliers. For describing raw data distributions, I never find standard deviations useful, however. = fa doz fabp2 1900 2 4 1500 2 6 1000 2 8750 3 10 750 1 11 1750 2 12 500 3 bwplot(doz~factor(fabp2),data=fa,panel=panel.bpplot) Error in sort(x, partial = unique(c(lo, hi))) : unsupported options for partial sorting That's NOT simple way. I need just one change. Is there any good way? $-( -- Evgeniy __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] floor()
I believe this is a FAQ. Examine: format((5.05-floor(5))*100, nsmall=16) [1] 4.9822 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Werner Bier Sent: Tuesday, November 29, 2005 3:35 PM To: r-help@stat.math.ethz.ch Subject: [R] floor() Dear All, Is this right? floor((5.05-floor(5))*100) [1] 4 I would expect 5, or am I wrong? Thanks and regards, W - [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] rotated ylab with xyplot
Try library(grid) xyplot(y~x,data.frame(x=1:10,y=runif(10)), ylab=textGrob(label=my label, rot=0)) Note in the ?xyplot the xlab/ylab section points to the 'main' parameter where it defines that a list can be used, however string rotation parameters are not in the list. The helpfile notes that a grob object can be used. The reference for lattice and grid is R Graphics by Paul Murrell. --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Viet Nguyen Sent: Monday, November 28, 2005 8:33 PM To: r-help@stat.math.ethz.ch Subject: [R] rotated ylab with xyplot hi all, in R, what's the best way to have a rotated ylab in a graph plotted with either xyplot or xYplot? I tried this but it didn't work. xyplot(y~x,data.frame(x=1:10,y=runif(10)),ylab=list(srt=90,crt =90,rot=90,label=my label)) more generally, how do you output a text at an angle in a lattice graph? what would be a good reference for R lattice graphics? I need more help than the help pages provide. thank you in advance. vn __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] On survival curve scale
In the helpfile, look at the ymin argument to the plot method for survfit. --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Zhaojing Gong Sent: Sunday, November 20, 2005 6:47 PM To: R-help@stat.math.ethz.ch Cc: Zhaojing Gong Subject: [R] On survival curve scale Hello, everyone, I was wondering if you can kindly help me to set the scale in the plot.survfit, whose default range is (0,1). In my case, I need to set at (0.8,1). I have tried plot.window with ylim=(0.8,1) but it did not work. Many thanks in advance. -- Zhaojing Gong Ph D. student in Statistics The Department of Mathematics and Statistics University of Canterbury New Zealand __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] nlme questions
Warning: non-expert thoughts to follow. When passing an object to a predict method, the method looks at (a copy) of the original information from the dataframe that was used in the fit. Your original data contains information on trt1 and trt2, but factor(trt1) and factor(trt2) cannot be found in the original data. If you did the factor conversion in the original data myDat - factor(myDat$trt1) myDat - factor(myDat$trt2) then used myDat as the dataframe in the nlme call, all information would be available for the augPred method. That's why it works when you use trt1 and trt2 instead of factor(trt1) and factor(trt2). There is actually an implicit factor conversion happening in the nlme call if trt1 and trt2 are character variables, however if trt1 and trt2 are defined as numeric (ie 0 1) then it will fit as a numeric. --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Christian Mora Sent: Friday, November 18, 2005 4:01 AM To: Spencer Graves Cc: r-help@stat.math.ethz.ch Subject: Re: [R] nlme questions Spencer; Thanks for your suggestions. I found the problem is in the library nlme. If you define phi1~factor(trt1)+factor(trt2) instead of phi1~trt1+trt2 the augPred function works. A bug? I don't know. Christian Spencer Graves [EMAIL PROTECTED] on 17-11-2005 20:19:32 To:Christian Mora [EMAIL PROTECTED] cc:r-help@stat.math.ethz.ch Subject:Re: [R] nlme questions Both your questions seem too vague to me. You might get more useful replies if you provide a simple example in a few lines of R code that a reader could copy from your email into R and see the result (as suggested in the posting guide! www.R-project.org/posting-guide.html). The process of preparing such a simple example might by itself provide the insight you desire. Alternatively, you might work line by line through the code for the R function you are using. Also, if you don't have Pinheiro and Bates (2000) Mixed-Effects Models in S and S-PLUS (Springer), I suggest you get it; it is excellent for things like this. I'm sorry I couldn't help more. spencer graves Christian Mora wrote: Dear R users; Ive got two questions concerning nlme library 3.1-65 (running on R 2.2.0 / Win XP Pro). The first one is related to augPred function. Ive been working with a nonlinear mixed model with no problems so far. However, when the parameters of the model are specified in terms of some other covariates, say treatment (i.e. phi1~trt1+trt2, etc) the augPred function give me the following error: Error in predict.nlme(object, value[1:(nrow(value)/nL),,drop=FALSE], : Levels 0,1 not allowed for trt1, trt2. The same model specification as well as the augPred function under SPlus 2000 run without problems. The second question has to deal with the time needed for the model to converge. It really takes a lot of time to fit the model on R in relation to the time required to fit the same model on SPlus. I can imagine this is related to the optimization algorithm or something like that, but I would like to have a different opinion on these two issues. Thanks in advance Christian Mora __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html -- Spencer Graves, PhD Senior Development Engineer PDF Solutions, Inc. 333 West San Carlos Street Suite 700 San Jose, CA 95110, USA [EMAIL PROTECTED] www.pdf.com http://www.pdf.com Tel: 408-938-4420 Fax: 408-280-7915 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Using pakage foreign and to import SAS file
If sas isn't in the path, then you might have trouble with sas.get or read.ssd. Assuming you are using windows, go to the Start menu, select run and type sas. If sas fires up it's in your path, if not then that is the reason. --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Rick Bilonick Sent: Monday, November 14, 2005 8:22 PM To: Walter R. Paczkowski Cc: r-help@stat.math.ethz.ch Subject: Re: [R] Using pakage foreign and to import SAS file On Mon, 2005-11-14 at 22:55 +, Walter R. Paczkowski wrote: Hi, I'm struggling with foreign to import a SAS file. The file, for lack of imagination, is d.sas7bdat and is in my root directory (c:\) under Windows XP. When I type read.ssd(c:\\, d) which I think I'm suppose to enter, I get SAS failed. SAS program at C:\DOCUME~1\Owner\LOCALS~1\Temp\Rtmp32758\file19621.sas The log file will be file19621.log in the current directory NULL Warning messages: 1: sas not found 2: SAS return code was -1 in: read.ssd(c:\\, d) I have SAS 9.1 running on my computer so SAS is there. What am I doing wrong? Thanks, Walt I've not used read.ssd but I've had good results with sas.get in Hmisc. Rick B. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] ltext - adding text to each panel from a matrix
Haven't checked it too carefully, but how about:
bwplot(treatment~foo|group, data = dat,
panel=function(x,y,...) {
panel.violin(x,y, ..., col = transparent, varwidth = F)
gt0 - table( x 0, y)
panel.abline(v=0, lty = dotted)
grid.text(as.character(gt0[1,]), unit(1, 'lines'), unit(1:3,
'native'), just='left')
grid.text(as.character(gt0[2,]), unit(1, 'npc') - unit(1,
'lines'), unit(1:3, 'native'), just='left')
},
par.strip.text = list(cex = 0.8), xlim = my.xlim)
--Matt
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Andy Bunn
Sent: Thursday, November 10, 2005 8:19 AM
To: R-Help
Subject: [R] ltext - adding text to each panel from a matrix
Hi all (really probably just Deepayan):
In the plot below I want to add text on either side of each
violin plot that
indicates the number of observations that are either positive
or negative.
I'm trying to do this with ltext() and I've also monkeyed about with
panel.text(). The code below is generally what I want but my calls to
ltext() are wrong and I'm not sure how to fix them. Right now
they replicate
the first column of the matrices obs.pos and obs.neg for each
panel. How do
I tell ltext to advance to the next column when the next
panel is plotted? I
don't see how subscripts can do it, but I bet it's something
along that
line...
Thanks, Andy
rm(list = ls())
set.seed(354)
# make a bimodal dataset with three groups and three treatments
foo - c(rnorm(150,-1,0.5), rnorm(150,1,0.25))
treatment - factor(rep(seq(1,3),100), labels = c(Treatment
1, Treatment
2, Treatment 3))
group - factor(rep(seq(1,3),100), labels = c(Group A,
Group B, Group
C))
group - sample(group)
# corrupt Group A, Treatment 2 for fun.
foo[group==Group A treatment==Treatment 2][1:8] - rnorm(8,1,1)
dat - data.frame(foo,treatment,group)
# set the limits for the plot, which also tells where to put the text
my.xlim - c(-6, 6)
# make a matrix that counts the number of obs greater or less
than zero
obs.pos - tapply(dat[dat[,1] 0,1], dat[dat[,1] 0,-1], length)
obs.neg - tapply(dat[dat[,1] = 0,1], dat[dat[,1] = 0,-1], length)
#write some coordinate data
x.obs.pos - rep(my.xlim[2],dim(obs.pos)[2])
y.obs.pos - 1:dim(obs.pos)[2]
x.obs.neg - rep(my.xlim[1],dim(obs.neg)[2])
y.obs.neg - 1:dim(obs.neg)[2]
bwplot(treatment~foo|group, data = dat,
panel=function(...) {
panel.violin(..., col = transparent, varwidth = F)
panel.abline(v=0, lty = dotted)
ltext(x.obs.pos, y.obs.pos, obs.pos, pos = 2)
ltext(x.obs.neg, y.obs.neg, obs.neg, pos = 4)
},
par.strip.text = list(cex = 0.8), xlim = my.xlim)
obs.pos
obs.neg
# note that the numbers in the plot only match the matrices
for Group A,
# which is the first panel. Alas.
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Re: [R] Use of paste with apply()
The apply function is passing each row of you matrix as a single vector into paste. If paste receives a single vector and collapse is NULL, it will simply coerce the vector into a character vector. However, when you collapse instead of sep test - matrix( as.character(1:4), 2) apply(test, 1, paste, sep=+) [,1] [,2] [1,] 1 2 [2,] 3 4 apply(test, 1, paste, collapse=+) [1] 1+3 2+4 Which may be closer to what you were expecting, but I'm just guessing. --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Kjetil Brinchmann halvorsen Sent: Sunday, November 06, 2005 5:34 AM To: r-help@stat.math.ethz.ch Subject: [R] Use of paste with apply() I was surprised by: test - matrix( as.character(1:4), 2) test [,1] [,2] [1,] 1 3 [2,] 2 4 apply(test, 1, paste, sep=+) [,1] [,2] [1,] 1 2 [2,] 3 4 apply(test, 1, paste, sep=*) [,1] [,2] [1,] 1 2 [2,] 3 4 te - matrix(1:4, 2) te [,1] [,2] [1,]13 [2,]24 apply(te, 1, sum) [1] 4 6 Why doesn't paste behave in apply as sum? Kjetil -- Checked by AVG Free Edition. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Still a bug with NA in sd() or var()?
The behavior is actually documented in the var() help file (?var), although it's not clear that this would be the behavior if you just read ?sd. sd() does call var if you look at the code, so the behavior should not be unexpected. --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Roger Dungan Sent: Monday, October 31, 2005 1:24 PM To: r-help@stat.math.ethz.ch Subject: [R] Still a bug with NA in sd() or var()? Dear R-users, Running R 2.1.1 in WindowsXP, there seems to be a 'bug' in sd() If x-c(1,2,3,NA,5) mean(x) [1] NA But sd(x) Or var(x) give Error in var(x, na.rm = na.rm) : missing observations in cov/cor There are obvious work-rounds, like sd(x, is.na(x)==F) which gives the result (with error message) [1] 1.707825 Warning message: the condition has length 1 and only the first element will be used in: if (na.rm) complete.obs else all.obs or y-subset(x, is.na(x)==F) sd(y) [1] 1.707825 Am I missing something, or is this a problem with sd()? Why does mean(x) give a simple NA, but var(x) requires some additional work? There was some previous discussion in r-help about this for R v 1.6.0, with mention of a fix for 1.6.1. Dr Roger Dungan School of Biological Sciences University of Cantebury Christchurch, New Zealand ph +64 3 366 7001 ext. 4848 fax +64 3 364 2590 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] why does glm.predict give values over 1 ?
If you left the type argument to the predict method then your predictions are on the log-odds scale. Try using the type='response' in the predict method for glm. --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Rohit Singh Sent: Monday, October 31, 2005 2:52 PM To: r-help@stat.math.ethz.ch Subject: [R] why does glm.predict give values over 1 ? Hi, This is a newbie question. I have been using glm to perform some logistic regression. However, if I take the fitted parameters (as part of the glm object) and pass them on the glm.predict function, for some test cases I am getting predicted values that are a little over 1. This is a bit puzzling for me, because my understanding was that these numbers are probabilities and so should be between 0 and 1. Thanks a lot! I'd appreciate any help you could provide. -rohit __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] adding error bars to lattice plots
Have you looked at xYplot and panel.xYplot from Dr. Harrell's Hmisc package?
--Matt
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Mario
Aigner-Torres
Sent: Thursday, October 20, 2005 9:52 AM
To: Berton Gunter; r-help@stat.math.ethz.ch
Subject: Re: [R] adding error bars to lattice plots
Thanks Bert!
I have right now a dataset that looks like this:
tail(partition, 3)
element run logfO2 TC buffer xAn sdXan Di Disigma
416 Al 36 -0.68 1180 AIR 0.734 0.007 2.10 0.02
417 Ca 36 -0.68 1180 AIR 0.734 0.007 1.29 0.02
418 Na 36 -0.68 1180 AIR 0.734 0.007 1.16 0.06
Basicaly I would like to insert error bars into a xyplot like this
xyplot(log10(Di) ~ TC | element.ord, groups=buffer.ord, #pch=16,
+ #subset=no1140,
+ data=partition,
+ auto.key=list(columns=3),
+ )
How could llines, lsegments or perhaps panel.arrows look like?
I appreciate any help on this.
Best regards,
Mario
On 10/19/05, Berton Gunter [EMAIL PROTECTED] wrote:
?llines, lsegments and the like can be used in the panel
functions to draw
any sort of error bar that you can compute from the x,y,...
data of the
panel.
-- Bert Gunter
Genentech Non-Clinical Statistics
South San Francisco, CA
The business of the statistician is to catalyze the
scientific learning
process. - George E. P. Box
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] On Behalf Of Mario
Aigner-Torres
Sent: Wednesday, October 19, 2005 2:34 PM
To: r-help@stat.math.ethz.ch
Subject: [R] adding error bars to lattice plots
Dear R-Users,
how to include error bars within lattice?
How should the panel = function(x,y,...){
looks like?
Does panel.arrows works here as well?
I appreciate any help on this.
Regards,
Mario AT
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Re: [R] what OS
.Platform$OS.type -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Omar Lakkis Sent: Tuesday, September 13, 2005 11:30 AM To: r-help@stat.math.ethz.ch Subject: [R] what OS How can I determine whT OS I am running under? if WINDOWS do this if LINUX do that __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Plot of multiple data sets
The book is out--I received mine a few weeks ago. It is very useful. --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Chris Buddenhagen Sent: Friday, September 09, 2005 6:30 AM To: r-help@stat.math.ethz.ch Subject: Re: [R] Plot of multiple data sets I found a lot of answers at this type of problem website wrt graphics and multiple plots- I bet the book will be useful when it comes out. http://www.stat.auckland.ac.nz/~paul/RGraphics/rgraphics.html Chris Buddenhagen, Botany Department, Charles Darwin Research Station, Santa Cruz,Galapagos. Mail: Charles Darwin Foundation, Casilla 17-01-3891 Avenida 6 de Diciembre N36-109 y Pasaje California Quito, ECUADOR __ EL CONTENIDO DE ESTE MENSAJE ES DE ABSOLUTA RESPONSABILIDAD DEL AUTOR. FUNDACION CHARLES DARWIN WWW.DARWINFOUNDATION.ORG [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] lme How to validate a model with a validation set and a t est set
If you used all 28 animals to find the model out of a group of candidate models, I would have my reservations about this 'validation'. Any confidence intervals you get from the final model are bound to be overly optimistic because you haven't accounted for the degrees of freedom chewed up during the model fitting/finding process. Matt Austin Statistician Amgen One Amgen Center Drive M/S 24-2-C Thousand Oaks CA 93021 (805) 447 - 7431 Today has the fatigue of a Friday and the desperation of a Monday -- S. Pearce 2005 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Laurent Fanchon Sent: Wednesday, May 11, 2005 9:56 AM To: r-help@stat.math.ethz.ch Subject: [R] lme How to validate a model with a validation set and a test set Dear all, I am still trying to fit a model for habituation with lme (Dogs are trotting on a treadmill once a week during 4 consecutive weeks). I have maybe found a good one. In order to validate it, I would like to split my data. I have 28 dogs, I am thinking to build the model with 20 and use the remaining 8 to validate it. Is it a good method to validate the model? How can I do this? I would like to use the data from the first 2 weeks as input and see how good the model is to predict the data from the last 2 weeks. I tried to use predict but this function does not take into account the data from the first 2 weeks. I can only get the results for the population. I would appreciate any suggestions for this Thank for your help Laurent __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Help with MERGE gratefully accepted
dat1 - data.frame(var1=c(140, 151, 167), var2=c(30.1, 11.4, 40)) dat2 - data.frame(var1=c(140, 167), var3=c(5.7, 30.3)) merge(dat1, dat2, all=TRUE) var1 var2 var3 1 140 30.1 5.7 2 151 11.4 NA 3 167 40.0 30.3 Matt Austin Statistician Amgen One Amgen Center Drive M/S 24-2-C Thousand Oaks CA 93021 (805) 447 - 7431 Today has the fatigue of a Friday and the desperation of a Monday -- S. Pearce 2005 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Briggs, Meredith M Sent: Thursday, April 14, 2005 18:26 PM To: r-help@stat.math.ethz.ch Subject: [R] Help with MERGE gratefully accepted Hello How do I use function 'MERGE to combine the FILE A and FILE B below to make FILE C? Thank you FILE A 140151167 30.1 11.4 40 FILE B 140 167 5.7 30.3 FILE C 140151167 30.1 11.4 40 5.7 NA30.3 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] One mixed effects model for two variables
Here are two possibilities, but neither tests simultaneously--others may have those suggestions. 1. If one of the variables in clinically more important than the other, consider a stepdown procedure where the more important is tested first, then if the first is successful the second is tested. Procedures such as this are well documented in the literature. 2. Find a function of the two that has a clinical interpretation and model that response. Body mass index is an example of such a function (kg/m^2), but probably is not an endpoint that would be of interest in a growth study in pediatrics. Matt Austin Statistician Amgen One Amgen Center Drive M/S 24-2-C Thousand Oaks CA 93021 (805) 447 - 7431 Today has the fatigue of a Friday and the desperation of a Monday -- S. Pearce 2005 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Dominik Grathwohl Sent: Monday, March 07, 2005 17:18 PM To: r-help@stat.math.ethz.ch Subject: [R] One mixed effects model for two variables Hello R-help group, I need some suggestions in stating a mixed effects model. I would like to fit one mixed effect model to two or more variables and than investigating treatment effects by applying the multcomp library. I will explain my problem along an example of weight and length measurements on infants. Weight and length are measured at two occasions in time and for two treatment groups, one group got some experimental formula and the other some control formula. It is also reasonable to assume that weight and length are correlated. Aim is to estimate the treatment effect on weight and on length taking multiplicity into account. Below I generated some data of the proposed properties and I applied also two mixed effects models, one model for weight and one for length. Up to now I#8217;m not able to state a model for both variables together, any suggestions? library(nlme) n - 200# n = number of subjects id - rep(1:n, each=2) # id = subject identification number t - rep(0:1, times=n) # two occations in time trt - rep(sample(rep(0:1, times=n/2)), each=2) # two treatment groups b1 - rnorm(n, mean=0, sd=0.5) # b1 = random effect of weight y1 - 3.5 + rep(b1, each=2) + 0.7 * t + 0.01 * trt + 0.1 * t * trt + rnorm(2*n,mean=0, sd=0.09) # y1 = weight measurements, 3.5 kg at baseline, # 0.7 kg more at the second time occation # 0.01 = the treatment effect at baseline, # the treatment effect is 0.1 kg for the # experimental group at at the second time occation. # The whithin subject standard deviation is 0.09. b2 - 0.9 * 3/sd(b1) * b1 + rnorm(length(b1), mean=0, sd=sqrt(1-0.9**2)*3) # b2 = random effect for length with standard deviation = 3 # and correlated with the random effect of weight (b1) by r=0.9 y2 - 49 + rep(b2, each=2) + 2 * t - 0.05 * trt + 0.5 * t * trt + rnorm(2*n,mean=0, sd=1) # y2 = length measurements, 49 cm at baseline, # 2 cm more at the second time occation # 0.05 = the treatment effect at baseline, # the treatment effect is 0.5 cm for the # experimental group at at the second time occation. # The whithin subject standard deviation is 1. # data frame of the data: df - data.frame(var=as.factor(rep(0:1, each=2*n)), id=c(id, id), t=as.factor(c(t, t)), trt=as.factor(c(trt, trt)), y=c(y1, y2)) # grouped data object: gd - groupedData(y ~ t | id, data=df) # mixed effects model on weight: fm1weight - lme(y ~ t * trt, random = ~ 1 | id, data = gd, subset=var==0) summary(fm1weight) # mixed effect model on length: fm1length - lme(y ~ t * trt, random = ~ 1 | id, data = gd, subset=var==1) summary(fm1length) -- DSL Komplett von GMX +++ Supergünstig und stressfrei einsteigen! AKTION Kein Einrichtungspreis nutzen: http://www.gmx.net/de/go/dsl __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Passing colnames to graphics title
If i is 1:20, there are no column names. Make sure you are indexing the
names from your your dataframe.
xx - data.frame(a=c(1:10), b = letters[1:10])
colnames(xx)
[1] a b
for(i in 1:2) print(colnames(xx)[i])
[1] a
[1] b
for(i in colnames(xx)) print(i)
[1] a
[1] b
Matt Austin
Statistician
Amgen
One Amgen Center Drive
M/S 24-2-C
Thousand Oaks CA 93021
(805) 447 - 7431
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Laura Quinn
Sent: Wednesday, February 16, 2005 6:47 AM
To: Uwe Ligges
Cc: r-help@stat.math.ethz.ch
Subject: Re: [R] Passing colnames to graphics title
Obviously I have been trying to use the colnames() function!
However, when I try to subscript ie:
for(i in 1:20){
main=paste(Site:,colnames(i),sep=)
}
this doesn't work! I thought that as.character(colnames(i)) or
substitute(colnames(i)) might work, but to no avail...
Laura Quinn
Institute of Atmospheric Science
School of Earth and Environment
University of Leeds
Leeds
LS2 9JT
tel: +44 113 343 1596
fax: +44 113 343 6716
mail: [EMAIL PROTECTED]
On Wed, 16 Feb 2005, Uwe Ligges wrote:
Laura Quinn wrote:
Hi,
Just a quick query - if I'm creating a function to
produce a number of
histograms per page of output (one per column from a
matrix), how can I
pass the column name of the matrix into the title (or
indeed to form part
of the x-axis label)?
By extracting them using colnames()?
Uwe Ligges
TIA,
Laura
Laura Quinn
Institute of Atmospheric Science
School of Earth and Environment
University of Leeds
Leeds
LS2 9JT
tel: +44 113 343 1596
fax: +44 113 343 6716
mail: [EMAIL PROTECTED]
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RE: [R] no. at risk in survfit()
Have you looked at the times argument to the summary method? --Matt Matt Austin Statistician Amgen One Amgen Center Drive M/S 24-2-C Thousand Oaks CA 93021 (805) 447 - 7431 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of array chip Sent: Friday, February 04, 2005 12:2 PM To: r-help@stat.math.ethz.ch Subject: [R] no. at risk in survfit() Hi, when I generated a survfit() object, I can get number of patients at risk at various time points by using summary(): fit-survfit(Surv(time,status)~class,data=mtdata) summary(fit) class=1 time n.risk n.event survival std.err lower 95% CI upper 95% CI 9.9 78 10.987 0.0127 0.963 1 41.5 77 10.974 0.0179 0.940 1 54.0 76 10.962 0.0218 0.920 1 99.1 38 10.936 0.0328 0.874 1 class=2 time n.risk n.event survival std.err lower 95% CI upper 95% CI 6.9102 10.990 0.00976 0.971 1.000 8.0101 10.980 0.01373 0.954 1.000 14.4100 10.971 0.01673 0.938 1.000 16.1 99 10.961 0.01922 0.924 0.999 16.6 98 10.951 0.02138 0.910 0.994 18.7 97 10.941 0.02330 0.897 0.988 : : : I have many censoring observations in the dataset, and I would like to know the number of patients at risk (n.risk in the above output) for certain time points, for example at 60, 72, etc, which is not available from the above printout for class=1. Is there anyway I can get them? Thanks __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] PBIB datataset
Is it the PBIB dataset in the SASmixed package? I don't have my copy of the text at home. --Matt library(SASmixed) Loading required package: lme4 Attaching package 'lme4': The following object(s) are masked from package:nlme : Alfalfa Assay bdf BodyWeight Cefamandole Dialyzer Earthquake ergoStool Fatigue Gasoline getCovariateFormula getResponseFormula Glucose Glucose2 Gun IGF lmeControl Machines MathAchieve MathAchSchool Meat Milk Muscle Nitrendipene Oats Orthodont Ovary Oxboys Oxide PBG Phenobarb Pixel Quinidine Rail RatPupWeight Relaxin Remifentanil Soybean Spruce Tetracycline1 Tetracycline2 Wafer Wheat Wheat2 Warning message: package 'SASmixed' was built under R version 2.0.1 data(PBIB) PBIB response Treatment Block 1 2.415 1 2 2.5 9 1 3 2.6 1 1 4 2.013 1 5 2.7 5 2 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of [EMAIL PROTECTED] Sent: Sunday, December 19, 2004 11:44 AM To: [EMAIL PROTECTED] Subject: [R] PBIB datataset I'm looking at Pinheiro Bates Mixed-Effects Models in S and S-PLUS at the moment. Several datasets are used, one of which is called PBIB (a partially balanced incomplete block design). All the other datasets can be found somewhere or other in R. However, I cannot locate PBIB, and it does not seem to be mentioned in the latest edition of the R Full Reference Manual. I Have Been Good. I Have Searched The Arcives. There was a similar query back on 16 July 2002 from E. Corda; it seems this got no response (that I could find). So: Is it available? If not, is there a particular reason (e.g. copyright)? If not available on CRAN, is there an alternative source? With thanks, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 [NB: New number!] Date: 19-Dec-04 Time: 19:44:19 -- XFMail -- __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] SAS or R software
One point that is missing in this discussion is ease of review by the statistician at the FDA. As a statistician in clinical trials, you want to make it as easy as possible for your colleague at the FDA to do their job, so you put the programs in a format that they are more likely to find useful. As more reviewing statisticians are familiar with SAS than with other statistical packages/languages, I feel more comfortable sending a submission in SAS. Reviewers do use the programs in a filing that were written for creation of data sets and analysis to check for correct variable definitions and appropriate analyses. If the programs are written in a package/language that the reviewer understands they can get their job done easier. Given this, I have used S-Plus in regulatory work where it was clearly stronger--at some point I hope to use R where it adds a clear benefit. Of course 95% of the statistical analyses that are performed for regulatory submission can probably be done just as well with any of the major statistical package/languages available. $0.02 --Matt Matt Austin Statistician Amgen One Amgen Center Drive M/S 24-2-C Thousand Oaks CA 93021 (805) 447 - 7431 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Marc Schwartz Sent: Friday, December 17, 2004 16:19 PM To: Alexander C Cambon Cc: R-Help; Douglas Bates Subject: Re: [R] SAS or R software On Fri, 2004-12-17 at 17:11 -0500, Alexander C Cambon wrote: I apologize for adding this so late to the SAS or R software thread. This is a question, not a reply, but it seems to me to fit in well with the subject of this thread. I would like to know anyone's experiences in the following two areas below. I should add I have no experience myself in these areas: 1) Migrating from SAS to R in the choice of statistical software used for FDA reporting. You will find that to be a non-issue from the FDA's perspective. This has been discussed here with some frequency. If you search the archives you will find comments from Frank Harrell and others. The FDA does not and cannot endorse a particular software product. Nor does it validate any statistical software for a specific purpose. They do need to be able to reproduce the results, which means they need to know what software product was used, which version and on what platform, etc. The SAS XPORT Transport Format (which is openly defined and documented), has been used for the transfer of data sets and has been available in many statistical products. There have been a variety of activities (CDISC, HL-7, etc) regarding the electronic submission of data to the FDA. Some additional information is here: http://www.fda.gov/cder/regulatory/ersr/default.htm and here: http://www.cdisc.org/news/index.html Any other issues impacting the selection of a particular statistical application are more likely to be political within your working environment and FUD. As you are likely aware, other statistically relevant issues are contained in various ICH guidance documents regarding GCP considerations and principles for clinical trials: http://www.ich.org/[EMAIL PROTECTED]@_TEMPLATE=272 Keep in mind also that one big advantage R has (in my mind) is the use of Sweave for the reproducible generation of reports, which to an extent are self-documenting. (For example, was there more effort involved in areas of documentation, revision tracking, or validation of software codes? Since the FDA's role with computer software and validation has been raised before, the following documents cover many of these areas. The list is not meant to be exhaustive, but should give a flavor in this domain. There are specific guidance documents by the FDA pertaining to software that is contained in a medical device (ie. the firmware in a pacemaker or medical monitoring equipment) or is used to develop a medical device. The current guidance in this case is here: http://www.fda.gov/cdrh/comp/guidance/938.html Other guidance pertains to 21 CFR 11, which addresses data management systems used for clinical trials and covers issues such as electronic signatures, audit trails and the like. A guidance document for that is here: http://www.fda.gov/cder/guidance/5667fnl.htm Keep in mind, from a perspective standpoint, that even MS Excel and Access can be made to be 21 CFR 11 compliant and there are companies whose business is focused on just that task. There is also a general guidance document for computer systems used in clinical trials here: http://www.fda.gov/ora/compliance_ref/bimo/ffinalcct.htm Though it is to be superseded by a draft document here: http://www.fda.gov/cder/guidance/6032dft.htm 2) Migrating from SAS to R in the choice of statistical software used for NIH reporting (or other US or non-US) government agencies) . Same here to
RE: [R] The survival rate at a certain time
You can use the summary method for a survfit object from the package survival as in the following example: library(survival) summary( survfit( Surv(futime, fustat)~rx,data=ovarian), times=500) Call: survfit(formula = Surv(futime, fustat) ~ rx, data = ovarian) rx=1 time n.risk n.event survival std.err lower 95% CI 500.0005.0006.0000.5380.138 0.326 upper 95% CI 0.891 rx=2 time n.risk n.event survival std.err lower 95% CI 500.0007.0004.0000.6580.141 0.433 upper 95% CI 1.000 Matt Austin Statistician Amgen One Amgen Center Drive M/S 24-2-C Thousand Oaks CA 93021 (805) 447 - 7431 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Lisa Wang Sent: Monday, December 06, 2004 8:27 AM To: R-Help Subject: [R] The survival rate at a certain time Hello there, I am doing analysis on survival data. How do I pick out a probability of survival at a chosen landmark time(for example, 3 years, 4 years) from the result of survfit? or any other functions? As I know, the result of 'survfit' only have the probabilities for all event or cencor time. Thank you very much Lisa Wang Princess Margaret Hospital Toronto, Ca tel: 416-946-4501 ext.5201 __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Response Surface
wireframe() is available in the package lattice. --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of [EMAIL PROTECTED] Sent: Thursday, November 25, 2004 20:36 PM To: [EMAIL PROTECTED] Subject: [R] Response Surface Hi. I'm a student at Simon Fraser University in British Columbia, Canada. I can't for the life of me figure out how to plot a 3D surface (A 3D response surface to be more specific) in R. I found your email address on a web board, and saw someone mention wireframe(), but using the help in R yielded no results. Any suggestions? Thanks. Dean Vrecko __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] scatterplot of 100000 points and pdf file format
-Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of [EMAIL PROTECTED] Sent: Wednesday, November 24, 2004 16:37 PM To: R Help Mailing List Subject: RE: [R] scatterplot of 10 points and pdf file format On 24-Nov-04 Prof Brian Ripley wrote: On Wed, 24 Nov 2004 [EMAIL PROTECTED] wrote: 1. Multiply the data by some factor and then round the results to an integer (to avoid problems in step 2). Factor chosen so that the result of (4) below is satisfactory. 2. Eliminate duplicates in the result of (1). 3. Divide by the factor you used in (1). 4. Plot the result; save plot to PDF. As to how to do it in R: the critical step is (2), which with so many points could be very heavy unless done by a well-chosen procedure. I'm not expert enough to advise about that, but no doubt others are. unique will eat that for breakfast x - runif(1e6) system.time(xx - unique(round(x, 4))) [1] 0.55 0.09 0.64 0.00 0.00 length(xx) [1] 10001 'unique' will eat x for breakfast, indeed, but will have some trouble chewing (x,y). xx - data.frame(x=round(runif(100),4), y=round(runif(100),4)) system.time(xx2 - unique(xx)) [1] 14.23 0.06 14.34NANA The time does not seem too bad, depending on how many times it has to be performed. --Matt Matt Austin Statistician Amgen One Amgen Center Drive M/S 24-2-C Thousand Oaks CA 93021 (805) 447 - 7431 I still can't think of a neat way of doing that. Best wishes, Ted. E-Mail: (Ted Harding) [EMAIL PROTECTED] Fax-to-email: +44 (0)870 094 0861 [NB: New number!] Date: 25-Nov-04 Time: 00:37:15 -- XFMail -- __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Error in anova(): objects must inherit from classes
The lme method for anova() checks the inheritance of the object when a single object is supplied, which is why there is no error when you use one object at a time. When two objects are supplied, the method uses the class of the object by invoking the data.class function (which does not list glmmPQL class). If you replace the check of the class with a check of inheritance it should work. Following is a check from the example listed in MASS (Venables and Ripley) library(MASS) library(nlme) x1 - glmmPQL(y ~ I(week 2), random = ~ 1 | ID, + family = binomial, data = bacteria) iteration 1 iteration 2 iteration 3 iteration 4 iteration 5 iteration 6 x2 - glmmPQL(y ~ trt + I(week 2), random = ~ 1 | ID, + family = binomial, data = bacteria) iteration 1 iteration 2 iteration 3 iteration 4 iteration 5 iteration 6 anova(x1) numDF denDF F-value p-value (Intercept) 1 169 35 .0001 I(week 2) 1 169 21 .0001 anova(x2) numDF denDF F-value p-value (Intercept) 1 169 35 .0001 trt 247 20.22 I(week 2) 1 169 20 .0001 anova(x1, x2) Error in anova.lme(x1, x2) : Objects must inherit from classes gls, gnls lm,lmList, lme,nlme,nlsList, or nls After replacement: anovaLME(x1, x2) Model df AIC BIC logLik Test L.Ratio p-value x1 1 4 1107 1121 -550 x2 2 6 1114 1134 -551 1 vs 2 2.60.28 Matt Austin Statistician Amgen One Amgen Center Drive M/S 24-2-C Thousand Oaks CA 93021 (805) 447 - 7431 -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Andrew Criswell Sent: Wednesday, November 24, 2004 18:47 PM To: R-help Subject: [R] Error in anova(): objects must inherit from classes Hello: Let me rephrase my question to attract interest in the problem I'm having. When I appply anova() to two equations estimated using glmmPQL, I get a complaint, anova(fm1, fm2) Error in anova.lme(fm1, fm2) : Objects must inherit from classes gls, gnls lm,lmList, lme,nlme,nlsList, or nls The two equations I estimated are these: fm1 - glmmPQL(choice ~ day + stereotypy, +random = ~ 1 | bear, data = learning, family = binomial) fm2 - glmmPQL(choice ~ day + envir + stereotypy, +random = ~ 1 | bear, data = learning, family = binomial) Individually, I get results from anova(): anova(fm1) numDF denDF F-value p-value (Intercept) 1 2032 7.95709 0.0048 day 1 2032 213.98391 .0001 stereotypy 1 2032 0.42810 0.5130 anova(fm2) numDF denDF F-value p-value (Intercept) 1 2031 5.70343 0.0170 day 1 2031 213.21673 .0001 envir 1 2031 12.50388 0.0004 stereotypy 1 2031 0.27256 0.6017 I did look through the archives but didn't finding anything relevant to my problem. Hope someone can help. ANDREW _ platform i586-mandrake-linux-gnu arch i586 os linux-gnu system i586, linux-gnu status major2 minor0.0 year 2004 month10 day 04 language R -- Andrew R. Criswell, Ph.D. Graduate School, Bangkok University mailto:[EMAIL PROTECTED] http://email.bu.ac.th/src/compose.php?send_to=andrew.c%40bu.ac.th mailto:[EMAIL PROTECTED] http://email.bu.ac.th/src/compose.php?send_to=andrew%40arcris well.com __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] RE: [S] worked in R, but not in S-Plus
The following works, you need to include x=TRUE in the call to coxph.
Passing the time and status variables as additional arguments is a matter of
personal preference.
f.coxph.zph-function(x, timeVar, statusVar)
{
cox.fit - coxph(Surv(timeVar, statusVar) ~ x, na.action =
na.exclude, method = breslow, x=TRUE)
fit.zph-cox.zph(cox.fit)
fit.zph$table[,3]
}
time.cox - ovarian$futime
status.cox - ovarian$fustat
apply(ovarian[,-(1:2)],2, f.coxph.zph, timeVar = time.cox, statusVar =
status.cox)
--Matt
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of array chip
Sent: Tuesday, November 09, 2004 16:50 PM
To: [EMAIL PROTECTED]; [EMAIL PROTECTED]
Subject: [S] worked in R, but not in S-Plus
Hi,
I wrote a function that worked well in R, but not in
S-Plus, can anyone suggest a solution?
f.coxph.zph-function(x)
{
cox.fit - coxph(Surv(time.cox, status.cox) ~ x,
na.action = na.exclude, method = breslow)
fit.zph-cox.zph(cox.fit,transform='log')
fit.zph$table[,3]
}
yyy is my data frame that contains survial time,
censor status and predictor variables.
time.cox-yyy$time
status.cox-yyy$status
apply(yyy[,-(1:2)],2,f.coxph.zph)
When run in S-Plus, it gave the following error
message:
Problem in model.frame.coxph(fit): Object x not
found
If I remove the 2nd and 3rd lines inside the function,
it worked, so definitely something is wrong in passing
the coxph object into the cox.zph().
Thanks
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RE: [R] List seems to drop empty levels of factors when containin g them
I don't get the same result, do you have a package loaded that would change the default behavior (such as Hmisc)? list(grp.1) [[1]] [1] 1 2 Levels: 1 2 list(grp.1[mask]) [[1]] [1] 1 Levels: 1 2 library(Hmisc) snip list(grp.1[mask]) [[1]] [1] 1 Levels: 1 --Matt version _ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major2 minor0.0 year 2004 month10 day 04 language R -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Andrew Robinson Sent: Tuesday, November 09, 2004 19:44 PM To: R-Help Discussion Cc: Andrew Robinson Subject: [R] List seems to drop empty levels of factors when containing them Greetings R community, I am curious about the following behaviour: if I define a factor, and then store a subset of it in a list, the stored version seems to drop levels that were not included in the subset. E.g. .. mask - c(T, F) grp.1 - factor(c(1,2)) list(grp.1) [[1]] [1] 1 2 Levels: 1 2 list(grp.1[mask]) [[1]] [1] 1 Levels: 1 It is as though the list were redefining the factor and dropping empty levels. I would like to keep them (I am using the list for a two-dimensional tapply). Is there any way to avoid this? I'm using R 2.0.0 on FreeBSD 5.2.1. Thanks, Andrew -- Andrew Robinson Ph: 208 885 7115 Department of Forest Resources Fa: 208 885 6226 University of Idaho E : [EMAIL PROTECTED] PO Box 441133W : http://www.uidaho.edu/~andrewr Moscow ID 83843 Or: http://www.biometrics.uidaho.edu No statement above necessarily represents my employer's opinion. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] lag variable addition to data frame question
?diff --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of s viswanath Sent: Friday, October 29, 2004 7:22 AM To: [EMAIL PROTECTED] Subject: [R] lag variable addition to data frame question Hi, I was wondering if there is a more efficient way of handling the following method of creating a lagged value in a data frame without using the recursive 'for(i in 1:n)' loop and without using as.ts #Steps to creating a lag variable in a data frame 'my.dat.fr' # with 275 columns, 2400 rows of numbers and factors . The #variable x is a factor of #with five different levels the way i am creating the variable now is: attach(my.dat.fr) #my.dat.fr contains a variable 'x', i want to create #lagged variables #of this without using as.ts(). Is #there a more effient way of doing this than#below and #without using a recursive loop such as #for( i in 1:obs)x.lag[i]= x[(i-1)] 1.here is the way i am doing the lag now x=c(3,2,3,2,1,1,1,2,1,2,1,3...1) obs=length(x) x.nolag=x[2:obs] x.lag1=x[1:(obs-1)] my.new=cbind(x.nolag,x.lag1) #since my data frame must line up my orginal x values to other columns I also # add the following x.fill= cbind(0,0) # as named the above cell lines up my factor to other factors in my data frame, #since I had chopped off the first x observation to create x above (ie x[2:obs]) #then finally my.dat.fr=rbind(x.fill, my.new) my.dat.fr #Is there a easier way to create a lag variable and install in my data frame? #thankyou in advance, Sri __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Secondary y axis
You could replace your last two lines with the following. You'll need to play with the axes labeling to make it pretty. scaled.c - scale(c) par(new=TRUE) plot(scaled.c, ylim=c(-5, 5), xaxt=n, yaxt=n, col='green', type='l', xlab=, ylab=) axis (4, labels=round(seq(-2, 2, .25)*attr(scaled.c, 'scaled:scale') + attr(scaled.c, 'scaled:center'), 1), at=seq(-2, 2, .25), col=black, tck=-0.01, cex=.5) par(new=FALSE) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of John Robot Sent: Tuesday, October 26, 2004 16:46 PM To: [EMAIL PROTECTED] Subject: [R] Secondary y axis Hi I had a look at the help and previous discussions but I am still unable to solve these issues: 1 I have a set of air pressure data. I would like to plot a and b (both about 980-1000 millibar) and c, the difference (around 0-8 millibar). I use axis (4) to create a new axis (to the right) but I do not know how to assign c to the new axis which currently features the same values as the first axis. So, how do I show a, b and c in the same plot with different scales (one for each y-axis)? 2 I would like the x-axis to be time (h): 04, 05, 06 ... 24, 01, 02 ... (the data is stored in the same table as a and b). How do define where to get data for the a-axis and show for example every 5th value along the axis? When I try plot (a ~ h ... the results are messed up in the plot. 3 Is there a way to define the color within the box in the plot? I pasted my current code here: - # Import a = read.table(pres.txt, header=TRUE) b = read.table(pres.txt, header=TRUE) h = read.table(pres.txt, header=TRUE) a = (a[,2]) b = (b[,3]) c = abs(a-b) h = (h[,1]) f = seq(980, 995, 2.5) ### Plot par (mfrow=c(1,1))# rows, columns par (cex.lab=1, col.axis=black, bg=lightyellow, fg=black, mar=c(4, 4, 2.5, 2))# cex sets font size # Plot 1 plot (a, type=l, xlab=Time (h), ylab=Temperature (°C), ylim=c(980, 995), pch=1, col=red, lwd=2, tck=-0.01) abline (h=f, lwd=1, lty=2) lines(b, pch=3, col=blue, cex=2, type=l, lty=1, lwd=2) # lty controls line type title(Air Pressure (mb), font.main=1, adj=0.5, cex.main=2) axis (4, labels=TRUE, tick=TRUE, col=black, tck=-0.01) lines(c, pch=3, col=green, cex=2, type=l, lty=5, lwd=2) - Best regards, Magnus Nilsson, Sweden __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: ??: [R] R plot problems
The following should work, note I made x.name a factor.
x - data.frame(main.name=AAA,
x.name=factor(rep(c(Apply,Watermelon,Lemon,Banana,
Grape,Pineapply,Cherry,Peach,Orange,Mango,Strawberry),each=5))
,
y.name=(1:55))
plot(x$x.name, x$y.name, axes=FALSE)
axis(1, at=1:length(levels(x$x.name)), lab=FALSE)
axis(2)
box()
text(1:length(levels(x$x.name)), par('usr')[3]-par('cxy')[2]*.5,
levels(x$x.name), offset=1, xpd=TRUE, srt=-45, adj=0)
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Ivy_Li
Sent: Sunday, October 17, 2004 19:27 PM
To: Bobby Corpus
Cc: Henric Nilsson; [EMAIL PROTECTED]
Subject: ??: ??: [R] R plot problems
Yes! You are right ! It is perpendicular to the axis.
Thank you very much!
Could I choose the angle ,such as 45 degree?
Best Regards!
Ivy Li
YMS in Production Testing
Semiconductor Manufactory International(ShangHai) Corporation
#18 ZhangJiang Road, PuDong New Area, Shanghai, China
Tel: 021-5080-2000 *11754
Email: [EMAIL PROTECTED]
--
: Bobby Corpus [mailto:[EMAIL PROTECTED]
: 20041018 10:01
: Ivy_Li
: Henric Nilsson; [EMAIL PROTECTED]
: Re: : [R] R plot problems
Hi Ivy,
How about
x - data.frame(main.name=AAA,
x.name=rep(c(Apply,Watermelon,Lemon,Banana,
Grape,Pineapply,Cherry,Peach,Orange,Mango,Strawberry),each=5),
y.name=(1:55))
par(las=2);
plot(x$x.name, x$y.name)
Bobby
On Mon, 18 Oct 2004 09:36:12 +0800, Ivy_Li [EMAIL PROTECTED] wrote:
Thank you for your help!
I gave you an example, you could run it in R . Maybe you will understand
my meaning clearly.
x - data.frame(main.name=AAA,
x.name=rep(c(Apply,Watermelon,Lemon,Banana,
Grape,Pineapply,Cherry,Peach,Orange,Mango,Strawberry),each=5),
y.name=(1:55))
plot(x$x.name, x$y.name)
I can't find you said package ,whick library should I include in R ?
Best Regards!
Ivy Li
YMS in Production Testing
Semiconductor Manufactory International(ShangHai) Corporation
#18 ZhangJiang Road, PuDong New Area, Shanghai, China
Tel: 021-5080-2000 *11754
Email: [EMAIL PROTECTED]
--
: Henric Nilsson [mailto:[EMAIL PROTECTED]
: 20041015 17:39
: Ivy_Li
: [EMAIL PROTECTED]
: Re: [R] R plot problems
At 16:17 2004-10-15 +0800, you wrote:
[...] I want to rotate the direction of x-coordinates' letter so that it
can show all. But I don't know how to write this option or function .
I'm not sure if I've understood your question correctly. But if you use
base graphics and want e.g. rotated labels, you'll achive this rather
easily using functions in the gridBase package. (Take a look at the
package
vignette for an example that'll get you started.)
Henric
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RE: [R] incomplete function output
I would return the values from the various tests in a list. If you only want
them to print and not for use in other parts of your program you could
explicitly print each test using print().
root - function(var)
{
#---Phillips-Perron
test1 - PP.test(var, lshort = TRUE)
test2 - PP.test(var, lshort = FALSE)
#---Augmented Dickey-Fuller
test3 - adf.test(var, alternative = stationary, k =
test4 - trunc((length(var)-1)^(1/3)))
#---KPSS
test5 - kpss.test(var, null = Level, lshort = TRUE)
test6 - kpss.test(var, null = Trend, lshort = FALSE)
list(test1, test2, test3, test4, test5, test6)
}
--Matt
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of bogdan romocea
Sent: Wednesday, October 13, 2004 10:20 AM
To: [EMAIL PROTECTED]
Subject: [R] incomplete function output
Dear R users,
I have a function (below) which encompasses several tests.
However, when I run it, only the output of the last test is
displayed. How can I ensure that the function root(var)
will run and display the output from all tests, and not
just the last one?
Thank you,
b.
root - function(var)
{
#---Phillips-Perron
PP.test(var, lshort = TRUE)
PP.test(var, lshort = FALSE)
#---Augmented Dickey-Fuller
adf.test(var, alternative = stationary, k =
trunc((length(var)-1)^(1/3)))
#---KPSS
kpss.test(var, null = Level, lshort = TRUE)
kpss.test(var, null = Trend, lshort = FALSE)
}
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RE: [R] covariate selection?
I like Kjetil's suggestion of a shrinkage estimator. Perhaps this would be a good time to experiment with Trevor Hastie's 'lars' package. If you have a lot of correlated inputs I might suggest using Andy Liaw's randomforest package. I have found this technique to be very valuable in this setting. The partial dependency plots are a good way to explore the functional relationships of the variables. --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Kjetil Brinchmann Halvorsen Sent: Tuesday, October 12, 2004 17:16 PM To: Ian Fiske Cc: [EMAIL PROTECTED] Subject: Re: [R] covariate selection? Ian Fiske wrote: Hello, I am hoping someone can help me with the following multivariate issue: I have a model consisting of about 50 covariates. I would like to reduce this to about 5 covariate for the reduced model by combining cofactors that are strongly correlated. Is there a package or function that would help me with this in R? I appreciate any suggestions. Thanks, Ian __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html have a look at package leaps, and also consider ridge regression. -- Kjetil Halvorsen. Peace is the most effective weapon of mass construction. -- Mahdi Elmandjra __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: followup: Re: [R] Issue with predict() for glm models
Could you just use lines(newX, myPred, col=2) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Paul Johnson Sent: Thursday, September 23, 2004 10:3 AM To: r help Subject: followup: Re: [R] Issue with predict() for glm models I have a follow up question that fits with this thread. Can you force an overlaid plot showing predicted values to follow the scaling of the axes of the plot over which it is laid? Here is an example based on linear regression, just for clarity. I have followed the procedure described below to create predictions and now want to plot the predicted values on top of a small section of the x-y scatterplot. x - rnorm(100, 10, 10) e - rnorm(100, 0, 5) y - 5 + 10 *x + e myReg1 - lm (y~x) plot(x,y) newX - seq(1,10,1) myPred - predict(myReg1,data.frame(x=newX)) Now, if I do this, I get 2 graphs overlaid but their axes do not line up. par(new=T) plot(newX,myPred$fit) The problem is that the second one uses the whole width of the graph space, when I'd rather just have it go from the small subset where its x is defined, from 1 to 10. Its stretching the range (1,10) for newX to use the same scale that goes from (-15, 35) where it plots x I know abline() can do this for lm, but for some other kinds of models, no lines() method is provided, and so I am doing this the old fashioned way. pj John Fox wrote: Dear Uwe, -Original Message- From: Uwe Ligges [mailto:[EMAIL PROTECTED] Sent: Thursday, September 23, 2004 8:06 AM To: John Fox Cc: [EMAIL PROTECTED]; [EMAIL PROTECTED] Subject: Re: [R] Issue with predict() for glm models John Fox wrote: Dear Uwe, Unless I've somehow messed this up, as I mentioned yesterday, what you suggest doesn't seem to work when the predictor is a matrix. Here's a simplified example: X - matrix(rnorm(200), 100, 2) y - (X %*% c(1,2) + rnorm(100)) 0 dat - data.frame(y=y, X=X) mod - glm(y ~ X, family=binomial, data=dat) new - data.frame(X = matrix(rnorm(20),2)) predict(mod, new) Dear John, the questioner had a 2 column matrix with 40 and one with 50 observations (not a 100 column matrix with 2 observation) and for those matrices it works ... Indeed, and in my example the matrix predictor X has 2 columns and 100 rows; I did screw up the matrix for the new data to be used for predictions (in the example I sent today but not yesterday), but even when this is done right -- where the new data has 10 rows and 2 columns -- there are 100 (not 10) predicted values: X - matrix(rnorm(200), 100, 2) # original predictor matrix with 100 rows y - (X %*% c(1,2) + rnorm(100)) 0 dat - data.frame(y=y, X=X) mod - glm(y ~ X, family=binomial, data=dat) new - data.frame(X = matrix(rnorm(20),10, 2)) # corrected -- note 10 rows predict(mod, new) # note 100 predicted values 12345 6 5.75238091 0.31874587 -3.00515893 -3.77282121 -1.97511221 0.54712914 789 10 11 12 1.85091226 4.38465524 -0.41028694 -1.53942869 0.57613555 -1.82761518 . . . 91 92 93 94 95 96 0.36210780 1.71358713 -9.63612775 -4.54257576 -5.29740468 2.64363405 97 98 99 100 -4.45478627 -2.44973209 2.51587537 -4.09584837 Actually, I now see the source of the problem: The data frames dat and new don't contain a matrix named X; rather the matrix is split columnwise: names(dat) [1] y X.1 X.2 names(new) [1] X.1 X.2 Consequently, both glm and predict pick up the X in the global environment (since there is none in dat or new), which accounts for why there are 100 predicted values. Using list() rather than data.frame() produces the originally expected behaviour: new - list(X = matrix(rnorm(20),10, 2)) predict(mod, new) 1 2 3 4 5 6 7 5.9373064 0.3687360 -8.3793045 0.7645584 -2.6773842 2.4130547 0.7387318 8 9 10 -0.4347916 8.4678728 -0.8976054 Regards, John Best, Uwe 12345 6 1.81224443 -5.92955128 1.98718051 -10.05331521 2.6506 -2.50635812 789 10 11 12 5.63728698 -0.94845276 -3.61657377 -1.63141320 5.03417372 1.80400271 13 14 15 16 17 18 9.32876273 -5.32723406 5.29373023 -3.90822713 -10.95065186 4.90038016 . . . 97 98 99 100 -6.92509812 0.59357486 -1.17205723 0.04209578 Note that there are 100 rather than 10 predicted values. But with individuals predictors (rather than a matrix), x1 - X[,1] x2 - X[,2] dat.2 - data.frame(y=y, x1=x1, x2=x2) mod.2 - glm(y ~ x1 + x2, family=binomial, data=dat.2)
RE: [R] unable to download
You may need to supply some additional information about your setup. What operating system and version are you using? How are you connecting to the internet? Can you download packages from other sources (such as CRAN)? Exactly what procedure are you using to download the packages? Have you tried to download individual packages and install locally? Asking for help ASAP because you are running late is not considerate to those willing to provide help, because most of us are already behind on our own projects. --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of #AMELIA ANWAR# Sent: Monday, September 20, 2004 19:40 PM To: [EMAIL PROTECTED] Subject: [R] unable to download Hi, I am currently trying to install packages from BioConductor to R. However, I received a error stating: unable to connect to 'www.bioconductor.org' on port 80 May I know what is wrong and how may I correct it?? If possible give a step by step procedures on how can I do it... Thanks alot, Amelia PS: Please reply ASAP as I am currently doing a Final Year Project on microarray analysis and already beyond scheduled. __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] how to take this experiment with R?
My mistake, you can't use the structure I proposed with lm() in combination with step(). If what was suggested earlier by Gabor was not what you wanted, and instead you want the 'best' three variable model, then it may be easier to use the leaps package. library(leaps) x - data.frame(matrix(rnorm(1550),c(50,31))) model - regsubsets(y=x[,1], x=x[,2:31]) m1-summary(model, matrix=TRUE, matrix.logical=TRUE) apply(m1$outmat, 1, which)[3] $3 ( 1 ) X10 X14 X15 9 13 14 lm.fit(x=as.matrix(x[,as.vector(unlist(apply(m1$outmat, 1, which)[3])+1)]), y=x[,1]) $coefficients X10X14X15 -0.2694923 -0.4055546 -0.2692063 --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Gabor Grothendieck Sent: Monday, September 20, 2004 21:57 PM To: [EMAIL PROTECTED]; [EMAIL PROTECTED] Subject: Re: [R] how to take this experiment with R? Suppose you just wanted variables 2,4 and 7 (which are in columns 3, 5 and 8, respectively). Then you could do this: lm(X1 ~ X2 + X4 + X7, x) or lm(X1 ~., x[,c(2,4,7)+1]) Date: Tue, 21 Sep 2004 12:27:38 +0800 From: rongguiwong [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject:Re: [R] how to take this experiment with R? ÔÚ 2004Äê9ÔÂ21ÈÕ ÐÇÆÚ¶þ 12:10£¬Gabor Grothendieck дµÀ£º it works. but i come across anather problem. i just wnat to select 3 of the best indepent variables. but the reslut from step(lm(X1 ~., x)) is : Step: AIC= -37.64 X1 ~ X2 + X3 + X4 + X8 + X10 + X11 + X13 + X14 + X15 + X18 + X21 + X22 + X25 + X26 + X27 + X29 + X30 + X31 Df Sum of Sq RSS AIC none 11.014 -37.642 - X8 1 0.559 11.574 -37.165 - X27 1 0.867 11.881 -35.853 - X2 1 0.971 11.986 -35.416 - X18 1 0.978 11.992 -35.390 - X31 1 1.122 12.136 -34.793 - X10 1 1.400 12.414 -33.659 - X15 1 1.563 12.578 -33.005 - X29 1 1.608 12.622 -32.828 - X13 1 1.805 12.819 -32.055 - X30 1 1.880 12.894 -31.763 - X4 1 2.368 13.382 -29.906 - X14 1 2.495 13.509 -29.433 - X3 1 2.983 13.997 -27.659 - X22 1 2.999 14.013 -27.600 - X21 1 3.377 14.391 -26.271 - X25 1 4.323 15.338 -23.086 - X11 1 6.775 17.789 -15.672 - X26 1 7.232 18.246 -14.403 You can express your model like this: lm(X1 ~., x) ?formula gives some help on formulas although the . notation above does not seem to be referred to there. Date: Tue, 21 Sep 2004 11:52:04 +0800 From: rongguiwong [EMAIL PROTECTED] To: [EMAIL PROTECTED] Subject: [R] how to take this experiment with R? i want to generate 30 independent variables and 1 dependent variable,each has 50 draws from a unit normal distribution. then, searching for the independent variables that together would do the best job for fitting the denpendent variabe. my way to generate the data is. x-data.frame(matrix(rnorm(1550),c(50,31))) but is there more better way to do it? i want to use the followling is to search the model. model-step(lm(X1~X2+X3+X4.)) but i don't know the to express the formula with lm function.i think there is a way the express it efficently. i try ?lm .but on result be found. any help is welcome! __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Printing output on Plot
The following example should get you started.
library(survival)
test1 - list(time= c(4, 3,1,1,2,2,3),
status=c(1,NA,1,0,1,1,0),
x= c(0, 2,1,1,1,0,0),
sex= c(0, 0,0,0,1,1,1))
cpfit - coxph( Surv(time, status) ~ x + strata(sex), test1) #stratified
model
cpfit
pval - paste(P-value: , round(1 -
pchisq((cpfit$coef/sqrt(diag(cpfit$var)))^2, 1), 3))
plot(survfit(cpfit))
text(par('usr')[1], par('usr')[3] +par('cxy')[2], pval, adj=0)
--Matt
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Neil Leonard
Sent: Thursday, September 02, 2004 19:12 PM
To: [EMAIL PROTECTED]
Subject: [R] Printing output on Plot
Hi,
I'm trying to print the p-values from the output of a CPH test onto a
Kaplan Meier plot. Can this be done? I only really want the p-values
from the CPH test to appear but if this can't be done I am willing to
have the entire CPH output.
This is what I am currently trying: (it doesn't print the CPH output)
plot_KM - function(field)
{
library(survival)
y = length(levels(factor(field)))
field.KM - survfit(Surv(age_at_death,death)~field)
field.CPH - coxph(Surv(age_at_death,death)~factor(field))
plot(field.KM,mark.time=FALSE,col=2:
(y+1),lty=1,main=paste(as.character(substitute(field)), Kaplan-Meier
Plot))
text(1000, .3, paste(as.character(field.CPH)), col=red)
legend(1000, .5, levels(factor(field)), col=2:(y+1), lty=1)
}
Thanks,
Neil
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RE: [R] (no subject)
You need to use a device to print to such as postscript(file=/where/to/put/file/filename.ps) ##your plotting code here dev.off() Writing a plot at each iteration of your simulation can impact the runtime greatly. Please read the posting guide at the bottom of the e-mail, it can help you get more helpful . . . help --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Loke Chok Kang Sent: Monday, August 30, 2004 18:42 PM To: [EMAIL PROTECTED] Subject: [R] (no subject) Hi, Sorry, I have a problem that require some help. As I am doing a project with R and this project requires me to do a lot of plotting as I run my simulation, I need R to help me store my plots automatically as the simulation is run. Could anyone advise me on how this can be done? If possible I need all the plots to be written to a file. PS:In all I have over 500 over plots, thus it will not be possible to manually plot all the plots out. From yours faithfully, Chok Kang [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] (no subject)
A correction. You either need to open the plotting device prior to the simulation that includes your plotting commands and close it after the simulation or have the name change dynamically in your simulation so that the runs go in separate files. An example of the first method would be postscript(file=/where/to/put/file/filename.ps) ## your simulation commands dev.off() for the second method more info would be needed to know how you are running your simulation to help with dynamic naming. --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Austin, Matt Sent: Monday, August 30, 2004 18:56 PM To: 'Loke Chok Kang'; [EMAIL PROTECTED] Subject: RE: [R] (no subject) You need to use a device to print to such as postscript(file=/where/to/put/file/filename.ps) ##your plotting code here dev.off() Writing a plot at each iteration of your simulation can impact the runtime greatly. Please read the posting guide at the bottom of the e-mail, it can help you get more helpful . . . help --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Loke Chok Kang Sent: Monday, August 30, 2004 18:42 PM To: [EMAIL PROTECTED] Subject: [R] (no subject) Hi, Sorry, I have a problem that require some help. As I am doing a project with R and this project requires me to do a lot of plotting as I run my simulation, I need R to help me store my plots automatically as the simulation is run. Could anyone advise me on how this can be done? If possible I need all the plots to be written to a file. PS:In all I have over 500 over plots, thus it will not be possible to manually plot all the plots out. From yours faithfully, Chok Kang [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] column names in data.frame
Note that split() creates a list with each component named by the year. When you use the sapply function the names are retained in the attribute names, you can print this out to see or use str() or look at the output from the attribute() function. Your division also maintains the names and then when you coerce av.tl into a dataframe they are translated to row names. Check out the output from row.names(d2). If you want these as part of your dataframe you could so something like data.frame(d2, year=row.names(d2)) or data.frame(av.tl, year=names(av.tl)) Hope this helps, --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Louize Hill Sent: Thursday, August 19, 2004 16:26 PM To: [EMAIL PROTECTED] Subject: [R] column names in data.frame Dear R-help, Please can someone explain how to put a column name on an output data.frame. ##Starting with a data.frame with 3 columns (d$Year, d$NoIndiv, d$wtd_tl) yr_ind - split (d$NoIndiv, d$Year) yr_tl - split (d$wtd_tl, d$Year) ann_ind - sapply (yr_ind, sum) ann_tl - sapply (yr_tl, sum) av_tl - ann_tl/ann_ind d2- data.frame (av_tl) ##This gives me a data.frame with columns, the second of which has a column name (av_tl) I have tried d2- data.frame (year = x, av_tl) d2- data.frame (x=year, av_tl) d2- data.frame (x=year, av_tl, check.names = TRUE) d2- data.frame (year, av_tl) as well as several combinations with cbind, as.matrix, etc... I cannot relate the examples given in ?data.frame with my problem or find a similar problem in the archives. Thanks Louize __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] calibration/validation sets
You could keep a row index vector like in the following example. data(iris) indx - sample(nrow(iris), 20, replace=FALSE) train - iris[indx,] test - iris[-indx,] --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Peyuco Porras Porras . Sent: Saturday, August 14, 2004 17:15 PM To: [EMAIL PROTECTED] Subject: [R] calibration/validation sets Importance: High Hi; Does anyone know how to create a calibration and validation set from a particular dataset? I have a dataframe with nearly 20,000 rows! and I would like to select (randomly) a subset from the original dataset (...I found how to do that) to use as calibration set. However, I don't know how to remove this calibration set from the original dataframe in order to get my validation set.Any hint will be greatly appreciated. TT __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Private methods
.class1 is an 'internal' method in the namespace of the package 'methods'.
It can be accessed with the ::: operator. A good start for documentation
may be Vol 3/1 of R-News.
methods:::.class1
function (x)
class(x)[[1]]
environment: namespace:methods
--Matt
-Original Message-
From: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] Behalf Of Matthew Walker
Sent: Friday, August 13, 2004 17:19 PM
To: [EMAIL PROTECTED]
Subject: [R] Private methods
Hi,
I'm trying to understand R's object oriented abilities.
I have read (in a very recent email to r-help) that R's methods package
does not support private methods. However, I also looked at the source
for the function is:
is
function (object, class2)
{
cl - .class1(object)
if (missing(class2))
return(extends(cl))
if (.identC(cl, class2) || .identC(class2, ANY))
return(TRUE)
...
The first line of the function, the assignment to cl, seems to call a
function called .class1. I was unable to see the source for .class1:
.class1
Error: Object .class1 not found
It seems to me that either (a) I don't understand what I'm doing, or (b)
.class1 is a very private method. The help system finds nothing about
.class1.
Could someone please help me to understand this. Most helpful of all
would be pointers on where I could find more information. (So far I
have found only two documents on R's object oriented abilities: A
guide to using S4 Objects and A draft of the R language definition.)
Thanks,
Matthew
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RE: [R] How to put multiple plots in the same window? (not par(mf row=))
Lattice graphics may be the answer depending on your exact problem. Here is an example of four traditional plots without space: par(mfrow=c(2,2), omi=c(.5, .5, .5, .5)) par(mar=c(0, 2, 2, 0)) plot(rnorm(10), rnorm(10), axes=FALSE) box(); axis(2); axis(3) par(mar=c(0, 0, 2, 2)) plot(rnorm(10), rnorm(10), axes=FALSE) box(); axis(3); axis(4) par(mar=c(2, 2, 0, 0)) plot(rnorm(10), rnorm(10), axes=FALSE) box(); axis(1); axis(2) par(mar=c(2, 0, 0, 2)) plot(rnorm(10), rnorm(10), axes=FALSE); box() box(); axis(1); axis(4) I have generalized this in the past to allow for more (in a for loop I think), but I don't have access to my home computer from here. --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of F Duan Sent: Friday, July 30, 2004 8:42 AM To: [EMAIL PROTECTED] Subject: [R] How to put multiple plots in the same window? (not par(mfrow=)) Dear All, I am sorry if this question has been asked before. Below is my Question: I want to put several plots in the same window, but I don't want the blank space between plots (like par(mfrow=)) --- that makes the plots too small. Could anyone tell me how to do it? Thanks a lot. Frank __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] Problem with bwplot
Try factor(vec2) in your bwplot() call. -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Ernesto Jardim Sent: Friday, July 09, 2004 9:41 AM To: Mailing List R Subject: [R] Problem with bwplot Hi, I'm ploting some box-and-whisker plots with bwplot but I'm not getting any box-and-whiskers ... just dots. I'm using lattice 0.9-16 with R 1.9.1. Try library(lattice) rnorm(60)-vec1 rep(1:3,20)-vec2 rep(LETTERS[1:2],30)-vec3 bwplot(vec1~vec2|vec3) Thanks EJ __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] funny plotting
Try something like plot(x,y) box.dat - boxplot(x=split(counts, dial), plot=FALSE) bxp(box.dat, add=TRUE, at=c(-1, 0, 1), show.names=FALSE) -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Karla Meurk Sent: Tuesday, June 29, 2004 21:46 PM To: [EMAIL PROTECTED] Subject: [R] funny plotting Hi, I just wanted to plot a boxplot with a nice curve going through it, I thought this would be a simple task but for some reason I can't get the two graphs on the same page accurately. Enclosed is the code showing the two plots seperately and together. I would have thought it should work if I could use boxplot() then plot() overlayed but it won't allow the command add=TRUE (which has worked for me in the past). Thanks Carla P.S. please excuse the clumsy code! #Section 2 Data Set particle dial-rbind(-1, -1, 0, 0, 0, 0, 1, 1, 1) counts-rbind(2, 3, 6, 7, 8, 9, 10, 12, 15) particle-as.data.frame(cbind(dial,counts),row.names=NULL) names(particle)-c(dial,counts) attach(particle) pois.particle-glm(counts~dial,family=poisson) x-seq(-2,2,length=20) y-predict(pois.particle,data.frame(dial=x),type=response) #Overlaying plots x11() boxplot(counts~dial,main=Boxplot of counts for dial setting and poisson fit,ylim=c(0,25)) lines(x,y) #The seperate plots x11() boxplot(counts~dial,ylim=c(0,25)) x11() plot(x,y,ylim=c(0,25),type=l) __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] function for running MS-DOS on R
Perhaps you could use the R2WinBugs package? --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:r-help- [EMAIL PROTECTED] Behalf Of bang jeong sook Sent: Thursday, May 20, 2004 19:9 PM To: [EMAIL PROTECTED] Subject: [R] function for running MS-DOS on R I had downloaded the program that runs on MS-DOS. Is it possible for MS-DOS to be run in R such as WinBugs1.4? I wonder whether there is the R function for running MS-DOS from R such as the 'bug.r' function to make Winbugs practicable in R. I had heard Rterm.exe that runs on MS-DOS. However, What I need is to run MS-DOS in R but to run R in MS-DOS. _ MSN Hotmail . http://loginnet.passport.com/login.srf?id=2svc=mailcbid=24325msppjph=1lc =1042 __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting- guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
RE: [R] question
You want to use instead of . --Matt -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Behalf Of Svetlana Eden Sent: Friday, February 27, 2004 7:57 AM To: r-help Subject: [R] question Hi everybody. The question: I get two vectors 'iFalseFalse' and 'i2'. I think they should be the same but they are not. Is it because R does not handle complicated logical expressions in such cases or I do something wrong? z1 = c(NA, , 3, NA, , 3) z2 = c(, , 3, NA, 3, NA) cV = (as.character(z1)==as.character(z2)) cV [1]NA TRUE TRUENA FALSENA iFalse = (c(1:(length(z1[(cV==FALSE)] iNonNA = (c(1:(length(z1[(!(is.na(cV)))] iFalse [1] NA NA 5 NA iNonNA [1] 2 3 5 iFalseFalse = intersect(iFalse, iNonNA) iFalseFalse [1] 5 i2 = (c(1:(length(z1[( (cV==FALSE)(!(is.na(cV))) )] i2 numeric(0) -- Svetlana EdenBiostatistician IISchool of Medicine Department of Biostatistics Vanderbilt University __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
