Re: [R] how to explain the interaction terms regarding treatmentcontrast of lm model
Thank you all for your help. Daniel, I want to know if I really understand your answer. I calculated each group mean and sub mean as below: tapply(val,group,mean) group1 group2 group3 4.215670 5.664411 7.210819 tapply(val,sub,mean) abcd 4.856927 5.199305 6.183979 6.547655 and intercept (group=1 and sub=a) is: 3.506216 (see original post table) average difference between group2 and group1 is: 5.664411 - 4.215670=1.448741 average difference between sub b and sub a is: 5.199305-4.856972=0.342333 therefore, if I understand this right, the reference level for interaction between sub=b and group=2 should be the sum of the above numbers, which is: 3.506216+1.448741+0.342333=5.29729 Am I right? Thank you vey much. On Fri, Aug 28, 2009 at 7:02 PM, Daniel Malter dan...@umd.edu wrote: The intercept is group=1, sub=a, The interaction between sub=b and group=2 implies that both sub=b and group=2 direct effects are included. That is, with the direct effects only you are now at: intercept+group2+subb, which means the intercept (group1 and sub=a) + the average difference between group=2 and group=1 + the average difference between sub=b and sub=a. This is the reference level for the interaction effect between group=2 and sub=b. This is not one-specific group in your experiment but rather a generic average group (average group=2, average sub=b). Your interaction effect now asks the question how much does group=2 with sub=b stand out from the average in its group and in its sub. To clarify your confusion, you may want to write out the model formula. Daniel - cuncta stricte discussurus - -Ursprüngliche Nachricht- Von: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Im Auftrag von zrl Gesendet: Friday, August 28, 2009 6:49 PM An: r-help Betreff: [R] how to explain the interaction terms regarding treatmentcontrast of lm model Dear list, I am confused on how to explain the interaction term in the context of treatment contrast. for example, I have an data frame as below: sub group val 1a group1 3.685625 2a group1 3.407445 3a group1 4.040920 4a group1 2.890875 5b group1 3.853280 6b group1 4.113585 7b group1 3.043250 8b group1 3.800920 9c group1 5.394305 10 c group1 5.004290 11 c group1 4.651435 12 c group1 4.286650 13 d group1 4.773440 14 d group1 3.982200 15 d group1 5.718690 16 d group1 4.803815 . 45 d group3 8.021240 46 d group3 7.641685 47 d group3 7.519445 48 d group3 9.514580 then: tapply(val,list(group,sub),mean) abcd group1 3.506216 3.702759 4.834170 4.819536 group2 4.831503 5.246833 5.930116 6.649191 group3 6.233062 6.648325 7.787651 8.174238 summary(lm(val~group*sub)) Call: lm(formula = val ~ group * sub) Residuals: Min 1Q Median 3Q Max -1.24378 -0.50184 -0.03726 0.51748 1.34034 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept)3.5062 0.3278 10.696 9.98e-13 *** groupgroup21.3253 0.4636 2.859 0.00703 ** groupgroup32.7268 0.4636 5.882 9.98e-07 *** subb 0.1965 0.4636 0.424 0.67411 subc 1.3280 0.4636 2.865 0.00693 ** subd 1.3133 0.4636 2.833 0.00751 ** groupgroup2:subb 0.2188 0.6556 0.334 0.74052 groupgroup3:subb 0.2187 0.6556 0.334 0.74060 groupgroup2:subc -0.2293 0.6556 -0.350 0.72851 groupgroup3:subc 0.2266 0.6556 0.346 0.73158 groupgroup2:subd 0.5044 0.6556 0.769 0.44671 groupgroup3:subd 0.6279 0.6556 0.958 0.34460 --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 Residual standard error: 0.6556 on 36 degrees of freedom Multiple R-squared: 0.8607, Adjusted R-squared: 0.8182 F-statistic: 20.22 on 11 and 36 DF, p-value: 3.296e-12 My question is: with treatment contrast in R, Coefficients, groupgroup2,groupgroup3, subb, subc,subd are the difference from Intercept 3.5062 (reference level for intercepts). But what is the reference level for the interaction terms? such as groupgroup2:subb,groupgroup3:subb,and etc. Thanks. [[alternative HTML version deleted]] [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] unix like commands in R?
Thank you Ted.
I did try page(file,method=print), it did behave as less.
I will try the code to modify the profile as well to see how it goes. Thank
you very much.
On Mon, Aug 24, 2009 at 5:32 PM, Ted Harding
ted.hard...@manchester.ac.ukwrote:
On 24-Aug-09 21:56:06, zrl wrote:
Dear List:
I am trying to find a command in R which is like the unix command
less or more to show the data in a object of R.
did anyone can help me on this?
Is there a collection of such unix-like commands in R?
Thanks.
-ZRL
There is a page() command in R -- see '?page'. From your query I take
it you are in fact using either Linux or Unix (or possible a Mac BSD
type OS).
Have a look at options(pager) to see what is currently uses.
I have modified my R setup so that it uses 'less' (on Linux) as
the pager program.
I did this in my .Rprofile (in home directory) by putting in the
lines:
.xthelp - function() {
tdir - tempdir()
pgr - paste(tdir, /pgr, sep=)
con - file(pgr, w)
cat(#! /bin/bash\n, file=con)
cat(export HLPFIL=`mktemp , tdir, /R_hlp.XX`\n,
sep=, file=con)
cat(cat $HLPFIL\nxterm -e less $HLPFIL \n, file=con)
close(con)
system(paste(chmod 755 , pgr, sep=))
options(pager=pgr)
}
.xthelp()
rm(.xthelp)
This opens anything which might be paged in a separate xterm,
so thatfor instance, all responses to ?. come up in a new
xterm being paged by 'less'. Likewise, if you page a large object
(such as a matrix M with 500 rows), using 'page(M), you will
again see the result paged in 'less' in a separate window.
This code was suggested by Roger Bivand in response to a query
of mine back in 2003. The URL is
http://finzi.psych.upenn.edu/R/Rhelp02/archive/21642.html
This was an improvement on a previous solution of my own, which
is also quoted in the above URL.
Hoping this helps,
Ted.
E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 24-Aug-09 Time: 23:32:18
-- XFMail --
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Annotation database
Hi, I have 15 CEL files of Affymetrix platform from GEO. Title of experiment is : Ecoli_ASv2 Affymetrix E. coli Antisense Genome Array. I am looking for the package available in R for this array for annotation. I have already tried doing annotation from packages like org.EcK12.eg.db but I don't got the success. Is any other package in the form of database available for E.coli for Annotation? By Sukhbir Singh Rattan [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Annotation database
On Aug 29, 2009, at 2:43 AM, Sukhbir Rattan wrote: Hi, I have 15 CEL files of Affymetrix platform from GEO. Title of experiment is : Ecoli_ASv2 Affymetrix E. coli Antisense Genome Array. I am looking for the package available in R for this array for annotation. I have already tried doing annotation from packages like org.EcK12.eg.db but I don't got the success. Is any other package in the form of database available for E.coli for Annotation? You're probably on the wrong mailing list, but see if these help: http://article.gmane.org/gmane.science.biology.informatics.conductor/20614 http://www.bioconductor.org/data/cdfenvs/repos/html/ecoliasv2cdfv1.4.3.html -- David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Rcmdr installalation under Viata gives a warning. Do I need to do anything?
On Fri, 28 Aug 2009 21:39:41 -0400 John Sorkin jsor...@grecc.umaryland.edu wrote: JS Windows Vista JS R 2.9.1 JS JS When trying to install Rcmdr I get the message shown below. What JS does it mean, do I need to do anything? JS JS The downloaded packages are in JS C:\Users\John JS Sorkin\AppData\Local\Temp\RtmpRCLbhe\downloaded_packages updating JS HTML package descriptions Warning message: JS In file.create(f.tg) : JS cannot create file JS 'C:\PROGRA~1\R\R-29~1.1/doc/html/packages.html', reason 'Permission JS denied' Vista does not allow normal Users to write into the program folder. So either you run R with admin rights (right click, then run as administrator) or you circumvent this by installing R into your User directory like into C:\Users\John Sorkin\R hth Stefan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] CHAID in R
On Fri, 28 Aug 2009, Arup wrote: Hi..I am trying to run CHAID in R..I have installed the sofyware Party and trying to use the function ctree() to carry out the analysis. but I am getting the following message Error in terms.default(formula, data = data) : no terms component Without a simple reproducible example (as the posting guide tells you) it's hard to say what went wrong for you. . I am having some Likert scale variable where I have variables like Overall satisfaction(Dependent Variable),Product quality, Brand image,Warranty(Independent variable) etc.. ctree() can handle this situation appropriately, see vignette(party, package = party) for more details and worked examples. Now can anyone tell me how to run CHAID in this case..what would be the formula? Thanks in Advance.. CTree is similar in spirit to CHAID but not the same. However, there is the CHAID package on R-Forge (as pointed out previously, thanks to Max). CTree is more flexible and can deal with more types of variables, e.g., it would be possible to use linear-by-linear type tests instead of plain Chi-squared tests for ordinal variables. hth, Z -- View this message in context: http://www.nabble.com/CHAID-in-R-tp25188573p25188573.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Numeric, 2 ??? as a result of marix???
Strange things are going on in R, if you reshape a matrix in R: g=gretldata[1:2,] g Empfang Versand Transit Inland AuslandSumS 1 787844.0 1307176.6 223395.4 1474726 16199.1 3809341 2 421473.1 306445.4 448801.2 1779402 14445.6 2970567 dim(g) [1] 2 6 as.vector(g) Empfang Versand Transit Inland AuslandSumS 1 787844.0 1307176.6 223395.4 1474726 16199.1 3809341 2 421473.1 306445.4 448801.2 1779402 14445.6 2970567 gg=matrix(as.vector(g),nrow=1,byrow=TRUE) gg [,1] [,2] [,3] [,4] [,5] [,6] [1,] Numeric,2 Numeric,2 Numeric,2 Numeric,2 Numeric,2 Numeric,2 Help please,the docu on thids is lousy!!!. Wolfgang [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] script navigation in Vista
Why is the option last changed not working if I open a script from R under Vista? Wolfgang [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Resolved: Problem in local ~/.fonts.conf broke symbol font in pdf device (Was: Re: Plotmath, sweave and lattice graphics interaction problem)
On Sat, 2009-08-29 at 09:04 +1000, Duncan Mackay wrote:
Hi Gavin
I am running on windows and have no problem
Thanks for confirming that this appears to be peculiar to my system,
Duncan. I've narrowed this down to just the PDF device so nothing to do
with Sweave and / or lattice as the characters are missing with base
graphics also.
I suspect a font issue somewhere on my system. In fact I've just found
the source of the problem now. Under earlier versions of Fedora (9 and
10) I had to use the following ~/.fonts.conf
alias binding=same
familyZapfDingbats/family
acceptfamilyDingbats/family/accept
familySymbol/family
acceptfamilyStandard Symbols L/family/accept
/alias
The definition for Symbol is what is breaking this font for me on the
pdf device. The suggestion for ~/.fonts.conf in ?pdf,
alias binding=same
familyZapfDingbats/family
acceptfamilyDingbats/family/accept
/alias
solves the problem with the symbol font on Fedora 11 for me but still
fixes the pch = 1 issue.
All the best,
Gavin
R version 2.9.2 (2009-08-24)
i386-pc-mingw32
locale:
LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
attached base packages:
[1] datasets utils stats graphics grDevices
grid methods base
other attached packages:
[1] Hmisc_3.6-1 R.oo_1.4.8R.methodsS3_1.0.3
foreign_0.8-37chron_2.3-30 MASS_7.2-48 lattice_0.17-25
loaded via a namespace (and not attached):
[1] cluster_1.12.0
Can forward you my sweave file et al if required
Regards
Duncan Mackay
Department of Agronomy and Soil Science
University of New England
ARMIDALE NSW 2351
Email home: mac...@northnet.com.au
At 03:10 29/08/2009, you wrote:
Dear List,
I have hit this problem with using a plotmath expression in an axis
label on a lattice plot I'm including in a Sweave document. The actual
document is far too long and boring (unless you are interested in the
hydrochemistry of upland lakes) to include here, but the following
minimal example reproduces the problem; basically, the PDF produced by
Sweave has missing characters in the plotmath label whilst the eps file
doesn't.
Here is the minimal Rnw document:
\documentclass[a4paper,12pt]{article}
\usepackage{graphicx,xspace}
\usepackage[utf8]{inputenc}
\usepackage[left=1.5cm,top=2cm,bottom=2cm,right=1.5cm]{geometry}
\usepackage{/home/gavin/R/2.9-patched/build/share/texmf/Sweave}
\setkeys{Gin}{width=1\textwidth}
\begin{document}
\title{FOO}
\author{Gavin Simpson}
\maketitle
fig=true=
require(lattice)
dat - data.frame(A = runif(10), B = runif(10))
print(xyplot(A ~ B, data = dat,
ylab = expression(H^+ ~ (mu*eq ~ L^-1
@
\end{document}
Note the ylab expression:
ylab = expression(H^+ ~ (mu*eq ~ L^-1))
this produces a ylab like H+ (mueq L-1) when run interactively and on
the eps file, but the pdf file is missing the parentheses and the mu
(micro) symbol.
R session info:
sessionInfo()
R version 2.9.1 Patched (2009-08-07 r49104)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] tools stats graphics grDevices utils datasets
methods
[8] base
other attached packages:
[1] lattice_0.17-25
loaded via a namespace (and not attached):
[1] grid_2.9.1
So I'm running this in a UTF-8 locale. Is it this that is causing the
problem? Any suggestions as to how to proceed?
Thanks in advance,
G
--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk
Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/
UK. WC1E 6BT. [w] http://www.freshwaters.org.uk
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%
Dr. Gavin Simpson [t] +44 (0)20 7679 0522
ECRC, UCL Geography, [f] +44 (0)20 7679 0565
Re: [R] setting par(srt) according to plot aspect ratio
Levi Waldron wrote: For posterity's sake, here is the solution I figured out. Putting the following lines after the plot(f) command seems to set the angle correctly: myasp - (par(fin)[2]-par(mai)[1]-par(mai)[3])/(par(fin)[1]-par(mai)[2]-par(mai)[4]) (f_angle - atan(myasp)*180/pi) (g_angle - atan(2*myasp)*180/pi) Hi Levi, Why not just: plotpin-par(pin) myasp-plotpin[2]/plotpin[1] Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Numeric, 2 ??? as a result of marix???
Wolfgang Polasek wrote: Strange things are going on in R, if you reshape a matrix in R: g=gretldata[1:2,] g Empfang Versand Transit Inland AuslandSumS 1 787844.0 1307176.6 223395.4 1474726 16199.1 3809341 2 421473.1 306445.4 448801.2 1779402 14445.6 2970567 dim(g) [1] 2 6 as.vector(g) Empfang Versand Transit Inland AuslandSumS 1 787844.0 1307176.6 223395.4 1474726 16199.1 3809341 2 421473.1 306445.4 448801.2 1779402 14445.6 2970567 gg=matrix(as.vector(g),nrow=1,byrow=TRUE) gg [,1] [,2] [,3] [,4] [,5] [,6] [1,] Numeric,2 Numeric,2 Numeric,2 Numeric,2 Numeric,2 Numeric,2 Help please,the docu on thids is lousy!!!. If you don't like the documentation, then improve it. You don't make friends by insulting people who provide you with something for free. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] script navigation in Vista
On Sat, 29 Aug 2009 00:07:44 +0200 Wolfgang Polasek wolfgang.pola...@gmail.com wrote: WP Why is the option last changed not working if I open a script WP from R under Vista? Because it remembers the changes only of a current session? You should be a bit more descriptive: which editor? which R? What do you mean with last changes etc. hth Stefan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Numeric, 2 ??? as a result of marix???
On Sat, 29 Aug 2009 00:15:45 +0200 Wolfgang Polasek wolfgang.pola...@gmail.com wrote: WP g=gretldata[1:2,] WP g WPEmpfang Versand Transit Inland AuslandSumS WP 1 787844.0 1307176.6 223395.4 1474726 16199.1 3809341 WP 2 421473.1 306445.4 448801.2 1779402 14445.6 2970567 WP dim(g) WP [1] 2 6 WP as.vector(g) WPEmpfang Versand Transit Inland AuslandSumS WP 1 787844.0 1307176.6 223395.4 1474726 16199.1 3809341 WP 2 421473.1 306445.4 448801.2 1779402 14445.6 2970567 WP gg=matrix(as.vector(g),nrow=1,byrow=TRUE) WP gg WP [,1] [,2] [,3] [,4] [,5] [,6] WP [1,] Numeric,2 Numeric,2 Numeric,2 Numeric,2 Numeric,2 Numeric,2 WP WP Help please,the docu on thids is lousy!!!. Depending on what you want which is not really clear again, you can use ?reshape or maybe also ?stack to reshape a data-frame which gretldata supposedly is. Note that with your as.vector(g) you dont create a vector as: dat1-data.frame(x=1:3, y=5:7) v1-as.vector(dat1) str(v1) resp. is.vector(v1) clearly shows. So you were also not debugging your problem. And you clearly did not have a look at the lousy documentation as this is shown in the example in ?as.vector, so don't blame others! Cheers Stefan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Numeric, 2 ??? as a result of marix???
g does not appear to be a matrix, as described. Its more likely a data frame. If that is the case then as.matrix(g) will create a matrix from it. Also depending on what you want to do ?unlist, ?t or ?c may be of help. Also try str(g) and dput(g) to see internals of object as they seem not to be what you believe them to be. On Fri, Aug 28, 2009 at 6:15 PM, Wolfgang Polasekwolfgang.pola...@gmail.com wrote: Strange things are going on in R, if you reshape a matrix in R: g=gretldata[1:2,] g Empfang Versand Transit Inland Ausland SumS 1 787844.0 1307176.6 223395.4 1474726 16199.1 3809341 2 421473.1 306445.4 448801.2 1779402 14445.6 2970567 dim(g) [1] 2 6 as.vector(g) Empfang Versand Transit Inland Ausland SumS 1 787844.0 1307176.6 223395.4 1474726 16199.1 3809341 2 421473.1 306445.4 448801.2 1779402 14445.6 2970567 gg=matrix(as.vector(g),nrow=1,byrow=TRUE) gg [,1] [,2] [,3] [,4] [,5] [,6] [1,] Numeric,2 Numeric,2 Numeric,2 Numeric,2 Numeric,2 Numeric,2 Help please,the docu on thids is lousy!!!. Wolfgang [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] linear model with interaction / segments
Dear R-help, Suppose I have the following data: df=data.frame(x=1:10, y=c(1,2,3,4,5,12,14,16,18,20)) plot(y~x, df, t=b) How can I fit a model which estimates the slopes between x = 1-5, 5-6, and 6-10? Adding the factor f: df$f - gl(2,5) Allows me to fit a linear model with interaction lm(y ~ x:f, data=df) which gives me the slope of 1 and 2 between 1-5, and 6-10 respectively, however it can not cope with the change from 5 to 6. I would appreciate if someone could point me into the right direction. Many thanks Markus __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Google's R Style Guide
Duncan Murdoch wrote: On 8/28/2009 8:59 AM, Esmail wrote: Perhaps most of you have already seen this? http://google-styleguide.googlecode.com/svn/trunk/google-r-style.html Comments/Critiques? The rules are mostly reasonable, though they aren't the ones followed in the R source. One bad rule is the one on curly braces: An opening curly brace should never go on its own line; a closing curly brace should always go on its own line. The problem is the second part. If the closing brace is followed by an else clause, the else should go on the same line as the brace, or things will parse differently when pasted than they do in a function. F Excellent point, thanks, this has caused me some problems in the past too. Esmail __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Google's R Style Guide
(Ted Harding) wrote: On 28-Aug-09 12:59:24, Esmail wrote: Perhaps most of you have already seen this? http://google-styleguide.googlecode.com/svn/trunk/google-r-style.html Comments/Critiques? I think it is grossly over-prescriptive. For example: function names have initial capital letters and no dots is violated throughout R itself. Thanks Ted, the way I look at these is as recommendations that I can choose to follow .. if something strikes me as silly I will happily ignore it ;-) Best, Esmail __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Google's R Style Guide
Kingsford Jones wrote: A few thoughts: ... -- It's nice that people have made these guides available Agreed .. it helps those relatively new to the language (and possible other language biases) get their orientation. Cheers, Esmail __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Google's R Style Guide
Barry Rowlingson wrote: On Fri, Aug 28, 2009 at 5:11 PM, hadley wickhamh.wick...@gmail.com wrote: In my view, that's the purpose of indenting - you see scope from indenting. *cough* python *cough* :-) (my favorite language at the moment) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Kolmogorov-Smirnov statistic
Hi, More of a statistical question, I'm trying to understand the formulation of the one-sample two-sided Kolmogorov-Smirnov statistic in stats::ks.test(), testing against a uniform distribution. Basically, it boils down to: x - rnorm(100) n - length(x) z - punif(sort(x)) - (0:(n - 1)) / n max(z, 1 / n - z) which is equivalent to the textbook definition n - length(x) z - punif(sort(x)) Dplus - max(sapply(1:n, function(i) i / n - z[i])) Dminus - max(sapply(1:n, function(i) z[i] - (i - 1) / n)) max(Dplus, Dminus) (See, e.g., http://www.itl.nist.gov/div898/handbook/eda/section3/eda35g.htm, and Durbin (1971) ``Distribution theory for tests based on the sample distribution function'', p. 6) Why does the definition of Dminus have an i-1 in the numerator instead of i? I have a hunch it's got to do with right-continuity of the ecdf, but perhaps someone can shed some light on it. Thanks, Gad -- Gad Abraham MEng Student, Dept. CSSE and NICTA The University of Melbourne Parkville 3010, Victoria, Australia email: gabra...@csse.unimelb.edu.au web: http://www.csse.unimelb.edu.au/~gabraham __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] RFE: vectorize URLdecode
In R 2.9.2, URLdecode(c(a%20b, b%20c)) [1] a b Warning message: In charToRaw(URL) : argument should be a character vector of length 1 all but the first element will be ignored Could URLdecode be modified to actually process all elements of the vector, not just the first? Thanks in advance __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RFE: vectorize URLdecode
Here is a workaround URLdecode.vec - Vectorize(URLdecode) # test it out x - c(a%20b, b%20c) URLdecode.vec(x) On Sat, Aug 29, 2009 at 10:31 AM, Jack Tanneri...@hotmail.com wrote: In R 2.9.2, URLdecode(c(a%20b, b%20c)) [1] a b Warning message: In charToRaw(URL) : argument should be a character vector of length 1 all but the first element will be ignored Could URLdecode be modified to actually process all elements of the vector, not just the first? Thanks in advance __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Best R text editors?
Emacs + ESS On Thu, Aug 27, 2009 at 12:43 PM, Jonathan Greenberggreenb...@ucdavis.edu wrote: Quick informal poll: what is everyone's favorite text editor for working with R? I'd like to hear from people who are using editors that have some level of direct R interface (e.g. Tinn-R, Komodo+SciViews). Thanks! --j -- Jonathan A. Greenberg, PhD Postdoctoral Scholar Center for Spatial Technologies and Remote Sensing (CSTARS) University of California, Davis One Shields Avenue The Barn, Room 250N Davis, CA 95616 Cell: 415-794-5043 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Google's R Style Guide
Perhaps this is obvious, but Ive never understood why this is the
general convention:
An opening curly brace should never go on its own line;
I tend to do this:
f - function()
{
if (TRUE)
{
cat(TRUE!!\n)
} else {
cat(FALSE!!\n)
}
}
(I don't usually put one-liners in if/else blocks; here I would have
used ifelse)
I haven't seen many others format code in this way. Is there an
objective reason for this (such as the rule for the trailing }) or
is this just aesthetics?
Thanks,
Max
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Anderson-Darling (one sample)
Hi, I would like to compute a goodness-of-fit statistic for one data series against a t-distribution, and obtain the quantiles of the distribution of the statistic with given degrees of freedom. I wonder if this is implemented in a package. I know that the critical values have to be computed for every distribution, and this requires numerical integration typically. I would prefer if I could get script or code implementing this rather than published critical values. Thanks, __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Anderson-Darling (one sample)
Do you know how to calculate what you want? Why not write a function- to do it and contribute to CRAN. On Sat, Aug 29, 2009 at 10:07 AM, tzygmund mcfarlanetzygm...@googlemail.com wrote: Hi, I would like to compute a goodness-of-fit statistic for one data series against a t-distribution, and obtain the quantiles of the distribution of the statistic with given degrees of freedom. I wonder if this is implemented in a package. I know that the critical values have to be computed for every distribution, and this requires numerical integration typically. I would prefer if I could get script or code implementing this rather than published critical values. Thanks, __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Stephen Sefick Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Google's R Style Guide
An opening curly brace should never go on its own line;
I tend to do this:
f - function()
{
if (TRUE)
{
cat(TRUE!!\n)
} else {
cat(FALSE!!\n)
}
}
(I don't usually put one-liners in if/else blocks; here I would have
used ifelse)
I haven't seen many others format code in this way. Is there an
objective reason for this (such as the rule for the trailing }) or
is this just aesthetics?
It's probably just aesthetics. I don't like it because it increases
the number of lines without much real benefit - indenting already
gives you all the hints you need.
Hadley
--
http://had.co.nz/
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Google's R Style Guide
Max Kuhn wrote:
Perhaps this is obvious, but Ive never understood why this is the
general convention:
An opening curly brace should never go on its own line;
I tend to do this:
f - function()
{
if (TRUE)
{
cat(TRUE!!\n)
} else {
cat(FALSE!!\n)
}
}
(I don't usually put one-liners in if/else blocks; here I would have
used ifelse)
... where you certainly know that ifelse evaluates both cases (if and
else) and hence might be less efficient for scalar valued problems?
Uwe Ligges
I haven't seen many others format code in this way. Is there an
objective reason for this (such as the rule for the trailing }) or
is this just aesthetics?
Thanks,
Max
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Google's R Style Guide
I do not understand why one should use a S3 preferentially on a S4 class, if
S4 is more rigorous.
(The premiss is I am a newbie with OO programming in R, and would like to
understand what is the proper way to OO program in R )
Regards
On Saturday 29 August 2009 16:23:39 hadley wickham wrote:
An opening curly brace should never go on its own line;
I tend to do this:
f - function()
{
if (TRUE)
{
cat(TRUE!!\n)
} else {
cat(FALSE!!\n)
}
}
(I don't usually put one-liners in if/else blocks; here I would have
used ifelse)
I haven't seen many others format code in this way. Is there an
objective reason for this (such as the rule for the trailing }) or
is this just aesthetics?
It's probably just aesthetics. I don't like it because it increases
the number of lines without much real benefit - indenting already
gives you all the hints you need.
Hadley
--
Corrado Topi
Global Climate Change Biodiversity Indicators
Area 18,Department of Biology
University of York, York, YO10 5YW, UK
Phone: + 44 (0) 1904 328645, E-mail: ct...@york.ac.uk
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to index a list with a string?
Peter Alspach wrote: Tena koe Try either L[foo()] or L[[foo()]] These return subtly (or not so subtly depending on your point of view) different results. which is quite important, hence read the documentation. [] returns a list of length 1 (or a vector of length 1 of type list) where [[]] returns the value of the corresponding list element. This also means that mutpiple indices are interpreted recursively in [[]] but will select the corresponding list elements in []. Best, Uwe Ligges HTH Peter Alspach -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Ning Ma Sent: Thursday, 27 August 2009 3:35 p.m. To: r-help@r-project.org Subject: [R] how to index a list with a string? Hi, everybody. I have a list obj L, sth like $`aaa` [1] 5753 if the string 'aaa' is a returned value of a function foo(). what is the right syntax form of L$foo() I'm new to R, thanks in advance. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Google's R Style Guide
Max Kuhn wrote:
Perhaps this is obvious, but Ive never understood why this is the
general convention:
An opening curly brace should never go on its own line;
I tend to do this:
f - function()
{
if (TRUE)
{
cat(TRUE!!\n)
} else {
cat(FALSE!!\n)
}
}
(I don't usually put one-liners in if/else blocks; here I would have
used ifelse)
I haven't seen many others format code in this way. Is there an
objective reason for this (such as the rule for the trailing }) or
is this just aesthetics?
I think the problem is not much putting the opening brace after
function(), or after if (...), like you do. The problem is putting the
else at a new line like in:
if (TRUE) {
cat(TRUE!!\n)
}
else
{
cat(FALSE!!\n)
}
When you source this code, the first part until the first closing brace
is considered complete by the R parser, and then, 'else' is considered
as the begining of a new command, which is a syntax error:
if (TRUE) {
+ cat(TRUE!!\n)
+ }
TRUE!!
else
Error: syntax error
{
+ cat(FALSE!!\n)
+ }
FALSE!!
If you put the same code in a function, you got the expected behaviour:
f - function () {
+ if (TRUE) {
+ cat(TRUE!!\n)
+ }
+ else
+ {
+ cat(FALSE!!\n)
+ }
+ }
f() # No syntax error!
TRUE!!
Thus, this is technical reason for NOT putting else on another line.
For the rest, I share Hadley's feeling that you consumes too much
lines and I tend to prefer the regular R syntax you got when you
source your code.
Best,
Philippe
Thanks,
Max
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] linear model with interaction / segments
On Aug 29, 2009, at 7:56 AM, Markus Gesmann wrote: Dear R-help, Suppose I have the following data: df=data.frame(x=1:10, y=c(1,2,3,4,5,12,14,16,18,20)) plot(y~x, df, t=b) How can I fit a model which estimates the slopes between x = 1-5, 5-6, and 6-10? Adding the factor f: df$f - gl(2,5) Allows me to fit a linear model with interaction lm(y ~ x:f, data=df) which gives me the slope of 1 and 2 between 1-5, and 6-10 respectively, however it can not cope with the change from 5 to 6. Can you be a bit more mathematically precise, ... and less anthropomorphic, in explaining what you mean by cannot cope? When I look at the plot of fitted values I fail to see any coping deficiencies, at least with my understanding regarding what you were expecting about which I am very much guessing at this point. Did you want only two regression lines that share a joinpoint at x=5.5? I would appreciate if someone could point me into the right direction. Many thanks Markus David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] cannot upgrade to R 2.9.1 in Ubuntu
Luis, I missed this email earlier. Consider using r-sig-debian for Debian / Ubuntu question (but you need to subscribe before you can post). On 7 August 2009 at 13:27, Luis Ridao Cruz wrote: | R-help, | | At the moment the R version installed on my machine is 2.8.1. (Ubuntu 9.04) | I wish to upgrade to R 2.9.1. | | I did: | $ sudo apt-get upgrade | | ..but R is not upgraded although the sources.list file is updated with: | | deb http://cran.ii.uib.no/bin/linux/ubuntu jaunty/ By force of habit, I usually do 'apt-get update; apt-get dist-upgrade'. I can never remember where upgrade and dist-upgrade differ. Make sure you run 'apt-get update' first though. One useful check is 'apt-cache policy r-base-core' where apt will tell you which versions from which repos it knows to be available and how it ranks them (equally by default; you can change that with 'pinning'). Hth, Dirk | | When I run from the terminal I still get: | | $ R | R version 2.8.1 (2008-12-22) | Copyright (C) 2008 The R Foundation for Statistical Computing | ISBN 3-900051-07-0 | | R is free software and comes with ABSOLUTELY NO WARRANTY. | You are welcome to redistribute it under certain conditions. | Type 'license()' or 'licence()' for distribution details. | | Natural language support but running in an English locale | .. | .. | | | Thanks in advance | | __ | R-help@r-project.org mailing list | https://stat.ethz.ch/mailman/listinfo/r-help | PLEASE do read the posting guide http://www.R-project.org/posting-guide.html | and provide commented, minimal, self-contained, reproducible code. -- Three out of two people have difficulties with fractions. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] linear model with interaction / segments
On Sat, 2009-08-29 at 12:56 +0100, Markus Gesmann wrote: Dear R-help, Suppose I have the following data: df=data.frame(x=1:10, y=c(1,2,3,4,5,12,14,16,18,20)) plot(y~x, df, t=b) How can I fit a model which estimates the slopes between x = 1-5, 5-6, and 6-10? Does the segmented package do what you want? G Adding the factor f: df$f - gl(2,5) Allows me to fit a linear model with interaction lm(y ~ x:f, data=df) which gives me the slope of 1 and 2 between 1-5, and 6-10 respectively, however it can not cope with the change from 5 to 6. I would appreciate if someone could point me into the right direction. Many thanks Markus __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Google's R Style Guide
S3 is very easy to change; S4 is very difficult. This provides
advantages and disadvantages for both. Some people swear by one and
curse the other -- from both sides.
S4 is newer, and I have had problems in the past finding out what
S4 methods are available and finding acceptable documentation more
generally. The methods function quickly identifies all installed S3
methods for an object of a particular class and all classes for which a
given generic function has S3 methods. The help page for methods now
says, See Also: ... For S4, 'showMethods', 'Methods'. I very much
appreciate the work of whomever added this See Also, because the next
time I want to find S4 methods, it will make it easier for me to do so.
Chambers (1998) Programming with Data (Springer) described many things
that did not work in any version of S to which I've had access.
Chambers (2008) Software for Data Analysis (Springer) is better but
still includes many things that I could not get to work without writing
the author.
I use S3 routinely, and I've tried multiple times to learn more
about S4 methods without yet achieving a critical mass that would allow
me to use them. S-Plus and R have been my primary tool for well over 15
years.
Hope this helps.
Spencer
Corrado wrote:
I do not understand why one should use a S3 preferentially on a S4 class, if
S4 is more rigorous.
(The premiss is I am a newbie with OO programming in R, and would like to
understand what is the proper way to OO program in R )
Regards
On Saturday 29 August 2009 16:23:39 hadley wickham wrote:
An opening curly brace should never go on its own line;
I tend to do this:
f - function()
{
if (TRUE)
{
cat(TRUE!!\n)
} else {
cat(FALSE!!\n)
}
}
(I don't usually put one-liners in if/else blocks; here I would have
used ifelse)
I haven't seen many others format code in this way. Is there an
objective reason for this (such as the rule for the trailing }) or
is this just aesthetics?
It's probably just aesthetics. I don't like it because it increases
the number of lines without much real benefit - indenting already
gives you all the hints you need.
Hadley
--
Spencer Graves, PE, PhD
President and Chief Operating Officer
Structure Inspection and Monitoring, Inc.
751 Emerson Ct.
San José, CA 95126
ph: 408-655-4567
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] adding factor scores back to an incomplete dataset...
Hi David, Phil,
Phil Spector wrote:
David -
Here's the easiest way I've been able to come up with.
Easiest? You are making unnecessary work for yourselves and seem not to
understand the purpose of ?naresid (i.e. na.action = na.exclude). Why not
take the simple route that I gave, which really is R's + factanal's route.
Using Phil's data as example:
##
dat = data.frame(matrix(rnorm(100),20,5))
dat[3,4] = NA
dat[12,3] = NA
scrs - factanal(~X1+X2+X3+X4+X5, data=dat,factors=2,scores='regression',
na.action=na.exclude)$scores
TrueDat - merge(dat,scrs,by=0,all.x=TRUE,sort=FALSE)
TrueDat
Regards, Mark.
David G. Tully wrote:
Thanks, Prof Spector. Your first solution works well for me.
Phil Spector wrote:
David -
Here's the easiest way I've been able to come up with. I'll provide
some sample data to make things clearer (hint, hint):
dat = data.frame(matrix(rnorm(100),20,5))
dat[3,4] = NA
dat[12,3] = NA
scrs = factanal(na.omit(dat),factors=2,scores='regression')$scores
rownames(scrs) = rownames(na.omit(dat))
newdat = merge(dat,scrs,by=0,all.x=TRUE,sort=FALSE)
This will result in the observations with missing values being
at the end of the data frame. If you want the original order
(assuming default row names), you could use
newdat[order(as.numeric(newdat$Row.names)),]
A somewhat more complicated approach is, in some sense, more direct:
dat$Factor1 = NA
dat$Factor2 = NA
dat[rownames(na.omit(dat[,-c(6,7)])),c('Factor1','Factor2')] =
+
factanal(na.omit(dat[,-c(6,7)]),factors=2,scores='regression')$scores
The order of the data is preserved.
- Phil Spector
Statistical Computing Facility
Department of Statistics
UC Berkeley
spec...@stat.berkeley.edu
On Tue, 25 Aug 2009, David G. Tully wrote:
I am sure there is a simple way to do the following, but i haven't
been able to find it. I am hoping a merciful soul on R-help could
point me in the right direction.
I am doing a factor analysis on survey data with missing values. to
do this, I run:
FA1-factanal(na.omit(DATA), factors = X, rotation = 'oblimin',
scores = 'regression')
Now that I have my factors and factor scores, I want to add those
scores back to my original dataset so I can plot factor scores by
demographics. However, when I try to add the scores back to the
original data frame, the variables are of different lengths.
Is there a way to subset from my original data set that will work
with factanal() and preserve the original rows or that will allow me
to append the factor scores back onto the original dataset with the
proper rows and NAs where there could be no data?
Again, I apologize if I am missing something basic. I am a self
taught R user and couldn't find an answer to this question.
Thanks in advance,
David
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
View this message in context:
http://www.nabble.com/adding-factor-scores-back-to-an-incomplete-dataset...-tp25140959p25204698.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Numeric, 2 ??? as a result of marix???
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Wolfgang Polasek Sent: Friday, August 28, 2009 3:16 PM To: r-help@r-project.org Subject: [R] Numeric, 2 ??? as a result of marix??? Strange things are going on in R, if you reshape a matrix in R: g=gretldata[1:2,] g Empfang Versand Transit Inland AuslandSumS 1 787844.0 1307176.6 223395.4 1474726 16199.1 3809341 2 421473.1 306445.4 448801.2 1779402 14445.6 2970567 dim(g) [1] 2 6 as.vector(g) Empfang Versand Transit Inland AuslandSumS 1 787844.0 1307176.6 223395.4 1474726 16199.1 3809341 2 421473.1 306445.4 448801.2 1779402 14445.6 2970567 gg=matrix(as.vector(g),nrow=1,byrow=TRUE) gg [,1] [,2] [,3] [,4] [,5] [,6] [1,] Numeric,2 Numeric,2 Numeric,2 Numeric,2 Numeric,2 Numeric,2 This last printout is how R prints a matrix whose contents are a list. Rouughly, if a list element has length 1 its value is printed; otherwise its type and, usually, length are printed. E.g., z-matrix(list(one=1, two=exp(0:1), three=c(i,ii,iii), four=quote(log(x))), nrow=2) z [,1] [,2] [1,] 1 Character,3 [2,] Numeric,2 Expression When you see a printout that you cannot interepret, try using the str() function to print the object and you may be able to make sense of it. str(z) List of 4 $ : num 1 $ : num [1:2] 1 2.72 $ : chr [1:3] i ii iii $ : language log(x) - attr(*, dim)= int [1:2] 2 2 matrix(data.frame(...)) strips the attributes from the data.frame, making it a list, then attaches dimensions to the list, making an object like 'z' above. as.matrix(data.frame()) makes a matrix that is roughly equivalent to the data.frame input. Bill Dunlap TIBCO Software Inc - Spotfire Division wdunlap tibco.com Help please,the docu on thids is lousy!!!. Wolfgang [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Google's R Style Guide
Max Kuhn wrote:
Perhaps this is obvious, but Ive never understood why this is the
general convention:
An opening curly brace should never go on its own line;
I tend to do this:
f - function()
{
if (TRUE)
{
cat(TRUE!!\n)
} else {
cat(FALSE!!\n)
}
}
I favor your approach. BUT I add one more level of indentation. Your
function would look like:
f - function()
{
if (TRUE)
{
cat(TRUE!!\n)
} else {
cat(FALSE!!\n)
}
}
This way I quickly identify the beginning of the function, which is the one
line at the top of the expression AND sticking to the left margin.
In your code you use this same indentation in the if/else construct. I find
it also useful for the function itself.
-
~~
Diego Mazzeo
Actuarial Science Student
Facultad de Ciencias Económicas
Universidad de Buenos Aires
Buenos Aires, Argentina
--
View this message in context:
http://www.nabble.com/Google%27s-R-Style-Guide-tp25189544p25204937.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Within factor random factor
Let's say that location defined a group, and observations may be more similar in a group. You could account for this similarity with the following model. model1 -lme(X~CorP,random=~1|location,data=mydata,method=ML) This fits a random intercept model grouped by location. This would assume that the slope of the regression of X on CorP is the same by group, but the group means differ. CorP defines the fixed part of the model. random= ~1 defines the random part (in this case just an intercept). The last part specifies the estimation method. I would recommend reading through Pinheiro and Bates. Brady West's Linear Mixed Models also has nice examples. It is difficult (for me) to assess your analysis. For example, I can see how location and subject would be random if you had repeated measures on subjects within location. These concepts take some time to understand. I would recommend working on this problem with someone experienced in this. In your studying, if you come across specific questions about nlme or lme4, there is a mixed model mailing list that is very helpful. One more note, your response takes values between 0 and 1, so you would have to make sure the residuals are behaving ok (read up on diagnostics). Best, Juliet 2009/8/26 細田弘吉 khos...@med.kobe-u.ac.jp: Hi, I am quite new to R and trying to analyze the following data. I have 28 controls and 25 patients. I measured X values of 4 different locations (A,B,C,D) in the brain image of each subject. And X ranges from 0 to 1. I think control or patient is a between subject factor and location is a within subject factor. So, controls: 28 patients: 25 (unbalanced data set) respone measure: X values (ranging 0 to 1) fixed factor: control vs. patient (between subject factor) random factor: location (level: A,B,C,D ;no order) (within subject factor) random factor: subjectID 1-53 My data looks like this; CorPX locationsubjectID control 0.708 A 1 control 0.648 A 2 patient 0.638 C 3 control 0.547 D 4 patient 0.632 B 5 control 0.723 C 6 ... I want to know (a) if there is a significant difference between controls and patients in X values. (b) where (A,B,C,D?) the difference is between controls and patients in X values. (There may be an interaction) I constructed linear mixed model with lme as followings; (1) model1 - lme(X ~ CorP*location, random= ~ 1| subjectID, mydata) (2) model2 - lme(X ~ CorP*location, random= ~ location| subjectID, mydata) I am not familiar with lme syntax. I'm just wondering which formula [(1) or (2)] is appropriate for my model to know answers of (a) and (b) questions. Or may be both of the formulas are wrong. I would appreciate it very much if somebody could help me. Sincerely, Kohkichi Hosoda __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Google's R Style Guide
On 29-Aug-09 17:51:54, diegol wrote:
Max Kuhn wrote:
Perhaps this is obvious, but Ive never understood why this is the
general convention:
An opening curly brace should never go on its own line;
I tend to do this:
f - function()
{
if (TRUE)
{
cat(TRUE!!\n)
} else {
cat(FALSE!!\n)
}
}
I favor your approach. BUT I add one more level of indentation.
Your function would look like:
f - function()
{
if (TRUE)
{
cat(TRUE!!\n)
} else {
cat(FALSE!!\n)
}
}
This way I quickly identify the beginning of the function, which is
the one line at the top of the expression AND sticking to the left
margin.
In your code you use this same indentation in the if/else construct.
I find it also useful for the function itself.
When I want to rely on indentation and vertical alignments to keep
track of program structure, I would tend to write the above like
f -
function()
{ if (TRUE)
{
cat(TRUE!!\n)
} else
{
cat(FALSE!!\n)
}
}
so that an opening { is aligned with the keyword it is associated
with, and then at the end of the block so also is the closing }.
However, in this case (if I keep all the {...} for the sake of
structure) I would also tend to save on lines with
f -
function()
{ if (TRUE)
{ cat(TRUE!!\n) } else
{ cat(FALSE!!\n) }
}
which is still clear enough for me. This probably breaks most
guidelines! But in practice it depends on what it is, and on
how readily I find I can read it.
Ted.
E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk
Fax-to-email: +44 (0)870 094 0861
Date: 29-Aug-09 Time: 19:26:51
-- XFMail --
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] RODBC: how to set the data-source?
Dumblauskas, Jerry jerry.dumblauskas at credit-suisse.com writes: OK Is your PostGres server on the same Linux box you are running R on? Sample values Server = 169.49.30.69 (localhost host means you are on the same box) Port= 2700 (make sure your port is correct) Also, I am not seeing your id and password I use the signature CONNREAD - odbcConnect(READDBID, uid = READDBUSER, pwd = READDBPWD, believeNRows=FALSE) So for you this would be channel - odbcConnect(rtestdb, uid=rtest, pwd=???, believeNRows=FALSE) As I do all stuff locally I have not configures for necessity of login username/passwd. So i assume I can omit it. With psql I don't need one. ??? means my password I assume... Well, I have configured it, so I maybe need it? With psql not, but I have set it. I think it will not be checked from the db. Why did you make uid=rtest? rtest is the name of the database. I use oliver as db-login-name. The alloc error means you are close... Make sure you can connect to your DB outside of R as well With psql I can login. And I need no passwd. Maybe it's different for the R-connection, instead of starting psql from the shell? But I don't think so. Ciao, Oliver __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RODBC: how to set the data-source?
Dumblauskas, Jerry jerry.dumblauskas at credit-suisse.com writes: [...] The alloc error means you are close... [...] Ah, ok, I see... ...then you are right that Driver has to be the path to the shared library. :-) Oliver __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Sequence generation
Hey guys, I was wondering how to create this sequence: 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3... with the '1, 2, 3' repeated over 10 times. Also, is there a simple method to generate 1, 1, 1, 2, 2, 2, 3, 3, 3? Anyways, any help with be greatly appreciated! -- View this message in context: http://www.nabble.com/Sequence-generation-tp25205593p25205593.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sequence generation
I think should work rep(c(1,2,3),10) Alfredo On Sat Aug 29 15:14:15 EDT 2009, njhuang86 njhuan...@yahoo.com wrote: Hey guys, I was wondering how to create this sequence: 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3... with the '1, 2, 3' repeated over 10 times. Also, is there a simple method to generate 1, 1, 1, 2, 2, 2, 3, 3, 3? Anyways, any help with be greatly appreciated! -- View this message in context: http://www.nabble.com/Sequence-generation-tp25205593p25205593.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- RIOS,ALFREDO ARTURO __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] memisc/mtable: show only estimates (one line)
Hello! mtable from memisc package shows estimates and standard error by default. I wanted to show only the estimates. Therefore, I created a new template: setCoefTemplate(simple=c(est=($est:#)($p:*))) But this leads to the following error when used: mtable(berk0,berk1,berk2, coef.style=simple) Error in dim(ans) - newdims : dims [product 1] do not match the length of object [2] Did I make a mistake? Or is it not possible to show only estimates (or, rather, have only one element in a template) with memisc? Thanks, Frederik 8 library(memisc) # Models from mtable example berkeley - aggregate(Table(Admit,Freq)~.,data=UCBAdmissions) berk0 - glm(cbind(Admitted,Rejected)~1,data=berkeley,family=binomial) berk1 - glm(cbind(Admitted,Rejected)~Gender,data=berkeley,family=binomial) berk2 - glm(cbind(Admitted,Rejected)~Gender +Dept,data=berkeley,family=binomial) # Create one-line style setCoefTemplate(simple=c(est=($est:#)($p:*))) mtable(berk0,berk1,berk2, coef.style=simple) 8 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sequence generation
On Aug 29, 2009, at 3:14 PM, njhuang86 wrote: Hey guys, I was wondering how to create this sequence: 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3... with the '1, 2, 3' repeated over 10 times. As noted earlier rep(1:3, 10) Also, is there a simple method to generate 1, 1, 1, 2, 2, 2, 3, 3, 3? ?gl the gl function will return a factor and it can be converted to a vector: gl(10, 3) [1] 1 1 1 2 2 2 3 3 3 4 4 4 5 5 5 6 6 6 7 7 7 8 8 8 9 9 9 10 10 10 Levels: 1 2 3 4 5 6 7 8 9 10 as.numeric(gl(10,3)) [1] 1 1 1 2 2 2 3 3 3 4 4 4 5 5 5 6 6 6 7 7 7 8 8 8 9 9 9 10 10 10 Or you can cobble something together like: floor(1 + 0:29 / 3) [1] 1 1 1 2 2 2 3 3 3 4 4 4 5 5 5 6 6 6 7 7 7 8 8 8 9 9 9 10 10 10 which depends on the higher precedence of the : operator over infix-+ and /. ?Syntax -- David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sequence generation
On Sat, Aug 29, 2009 at 8:14 PM, njhuang86njhuan...@yahoo.com wrote: Hey guys, I was wondering how to create this sequence: 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3... with the '1, 2, 3' repeated over 10 times. rep(1:3,10) # rep repeats its first argument according to the number in its second argument Also, is there a simple method to generate 1, 1, 1, 2, 2, 2, 3, 3, 3? The second argument can be a vector, so what you want here is: rep(1:3,c(3,3,3)) but you can create the second vector here also using rep! Hence: rep(1:3,rep(3,3)) Barry __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] RODBC: missing files? (Re: RODBC: how to set the data-source?)
Hello,
I stracet the R session when trying to connect to the database.
Strange, that /etc/odbc.ini first should be opened with Append-mode:
open(/etc/odbc.ini, O_WRONLY|O_CREAT|O_APPEND, 0666) = -1 EACCES (Permission
denied)
open(/etc/odbc.ini, O_RDONLY) = 3
fstat(3, {st_mode=S_IFREG|0644, st_size=259, ...}) = 0
mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0) =
0x7f305ae91000
read(3, [rtestdb]\nDescription = rtest..., 4096) = 259
also strange: the file will be read many, many times.
I did not pasted it here, but /etc/odbc.ini and /etc/passwd
are read very often.
I assume for each entry in /etc/passwd until the one that os looked for,
/etc/odbc.ini is opened once...
...maybe I should test this hypothesis... looks strange.
The next stuff also looks strange: as if there is a problem because of a missing
locale-stuff?
mprotect(0x7f30565eb000, 4096, PROT_READ) = 0
open(/usr/share/locale/de_DE.UTF-8/LC_MESSAGES/libc.mo, O_RDONLY) = -1 ENOENT
(No such file or directory)
open(/usr/share/locale/de_DE.utf8/LC_MESSAGES/libc.mo, O_RDONLY) = -1 ENOENT
(No such file or directory)
open(/usr/share/locale/de_DE/LC_MESSAGES/libc.mo, O_RDONLY) = -1 ENOENT (No
such file or directory)
open(/usr/share/locale/de.UTF-8/LC_MESSAGES/libc.mo, O_RDONLY) = -1 ENOENT (No
such file or directory)
open(/usr/share/locale/de.utf8/LC_MESSAGES/libc.mo, O_RDONLY) = -1 ENOENT (No
such file or directory)
open(/usr/share/locale/de/LC_MESSAGES/libc.mo, O_RDONLY) = -1 ENOENT (No such
file or directory)
open(/usr/share/locale-langpack/de_DE.UTF-8/LC_MESSAGES/libc.mo, O_RDONLY) =
-1 ENOENT (No such file or directory)
open(/usr/share/locale-langpack/de_DE.utf8/LC_MESSAGES/libc.mo, O_RDONLY) = -1
ENOENT (No such file or directory)
open(/usr/share/locale-langpack/de_DE/LC_MESSAGES/libc.mo, O_RDONLY) = -1
ENOENT (No such file or directory)
open(/usr/share/locale-langpack/de.UTF-8/LC_MESSAGES/libc.mo, O_RDONLY) = -1
ENOENT (No such file or directory)
open(/usr/share/locale-langpack/de.utf8/LC_MESSAGES/libc.mo, O_RDONLY) = -1
ENOENT (No such file or directory)
open(/usr/share/locale-langpack/de/LC_MESSAGES/libc.mo, O_RDONLY) = -1 ENOENT
(No such file or directory)
open(/usr/share/locale/de_DE.UTF-8/LC_MESSAGES/RODBC.mo, O_RDONLY) = -1 ENOENT
(No such file or directory)
open(/usr/share/locale/de_DE.utf8/LC_MESSAGES/RODBC.mo, O_RDONLY) = -1 ENOENT
(No such file or directory)
open(/usr/share/locale/de_DE/LC_MESSAGES/RODBC.mo, O_RDONLY) = -1 ENOENT (No
such file or directory)
open(/usr/share/locale/de.UTF-8/LC_MESSAGES/RODBC.mo, O_RDONLY) = -1 ENOENT
(No such file or directory)
open(/usr/share/locale/de.utf8/LC_MESSAGES/RODBC.mo, O_RDONLY) = -1 ENOENT (No
such file or directory)
open(/usr/share/locale/de/LC_MESSAGES/RODBC.mo, O_RDONLY) = -1 ENOENT (No such
file or directory)
open(/usr/share/locale-langpack/de_DE.UTF-8/LC_MESSAGES/RODBC.mo, O_RDONLY) =
-1 ENOENT (No such file or directory)
open(/usr/share/locale-langpack/de_DE.utf8/LC_MESSAGES/RODBC.mo, O_RDONLY) =
-1 ENOENT (No such file or directory)
open(/usr/share/locale-langpack/de_DE/LC_MESSAGES/RODBC.mo, O_RDONLY) = -1
ENOENT (No such file or directory)
open(/usr/share/locale-langpack/de.UTF-8/LC_MESSAGES/RODBC.mo, O_RDONLY) = -1
ENOENT (No such file or directory)
open(/usr/share/locale-langpack/de.utf8/LC_MESSAGES/RODBC.mo, O_RDONLY) = -1
ENOENT (No such file or directory)
open(/usr/share/locale-langpack/de/LC_MESSAGES/RODBC.mo, O_RDONLY) = -1 ENOENT
(No such file or directory)
semop(294920, 0x7fff62e9c110, 2)= 0
semop(294920, 0x7fff62e9c130, 1)= 0
open(/usr/share/locale/de_DE.UTF-8/LC_MESSAGES/R-RODBC.mo, O_RDONLY) = -1
ENOENT (No such file or directory)
open(/usr/share/locale/de_DE.utf8/LC_MESSAGES/R-RODBC.mo, O_RDONLY) = -1
ENOENT (No such file or directory)
open(/usr/share/locale/de_DE/LC_MESSAGES/R-RODBC.mo, O_RDONLY) = -1 ENOENT (No
such file or directory)
open(/usr/share/locale/de.UTF-8/LC_MESSAGES/R-RODBC.mo, O_RDONLY) = -1 ENOENT
(No such file or directory)
open(/usr/share/locale/de.utf8/LC_MESSAGES/R-RODBC.mo, O_RDONLY) = -1 ENOENT
(No such file or directory)
open(/usr/share/locale/de/LC_MESSAGES/R-RODBC.mo, O_RDONLY) = -1 ENOENT (No
such file or directory)
open(/usr/share/locale-langpack/de_DE.UTF-8/LC_MESSAGES/R-RODBC.mo, O_RDONLY)
= -1 ENOENT (No such file or directory)
open(/usr/share/locale-langpack/de_DE.utf8/LC_MESSAGES/R-RODBC.mo, O_RDONLY) =
-1 ENOENT (No such file or directory)
open(/usr/share/locale-langpack/de_DE/LC_MESSAGES/R-RODBC.mo, O_RDONLY) = -1
ENOENT (No such file or directory)
open(/usr/share/locale-langpack/de.UTF-8/LC_MESSAGES/R-RODBC.mo, O_RDONLY) =
-1 ENOENT (No such file or directory)
open(/usr/share/locale-langpack/de.utf8/LC_MESSAGES/R-RODBC.mo, O_RDONLY) = -1
ENOENT (No such file or directory)
open(/usr/share/locale-langpack/de/LC_MESSAGES/R-RODBC.mo, O_RDONLY) = -1
ENOENT (No such file or directory)
open(/usr/share/locale-langpack/de_DE.UTF-8/LC_MESSAGES/R.mo, O_RDONLY) = -1
ENOENT (No such file
Re: [R] RODBC: missing files? (Re: RODBC: how to set the data-source?)
Oliver Bandel oliver at first.in-berlin.de writes: [...] I assume for each entry in /etc/passwd until the one that os looked for, /etc/odbc.ini is opened once... ...maybe I should test this hypothesis... looks strange. [...] No, my loginname is in line 31 of /etc/passwd. oli...@siouxsie:~$ grep -n etc\/odbc.ini LOG 4006:open(/etc/odbc.ini, O_WRONLY|O_CREAT|O_APPEND, 0666) = -1 EACCES (Permission denied) 4024:open(/etc/odbc.ini, O_WRONLY|O_CREAT|O_APPEND, 0666) = -1 EACCES (Permission denied) 4042:open(/etc/odbc.ini, O_WRONLY|O_CREAT|O_APPEND, 0666) = -1 EACCES (Permission denied) 4310:open(/etc/odbc.ini, O_WRONLY|O_CREAT|O_APPEND, 0666) = -1 EACCES (Permission denied) 4311:open(/etc/odbc.ini, O_RDONLY) = 3 4326:open(/etc/odbc.ini, O_WRONLY|O_CREAT|O_APPEND, 0666) = -1 EACCES (Permission denied) 4327:open(/etc/odbc.ini, O_RDONLY) = 3 4342:open(/etc/odbc.ini, O_WRONLY|O_CREAT|O_APPEND, 0666) = -1 EACCES (Permission denied) 4343:open(/etc/odbc.ini, O_RDONLY) = 3 4358:open(/etc/odbc.ini, O_WRONLY|O_CREAT|O_APPEND, 0666) = -1 EACCES (Permission denied) 4359:open(/etc/odbc.ini, O_RDONLY) = 3 4374:open(/etc/odbc.ini, O_WRONLY|O_CREAT|O_APPEND, 0666) = -1 EACCES (Permission denied) 4375:open(/etc/odbc.ini, O_RDONLY) = 3 4390:open(/etc/odbc.ini, O_WRONLY|O_CREAT|O_APPEND, 0666) = -1 EACCES (Permission denied) 4391:open(/etc/odbc.ini, O_RDONLY) = 3 4406:open(/etc/odbc.ini, O_WRONLY|O_CREAT|O_APPEND, 0666) = -1 EACCES (Permission denied) 4407:open(/etc/odbc.ini, O_RDONLY) = 3 oli...@siouxsie:~$ grep -c etc\/odbc.ini LOG 17 Looks nevertheless quite strange. Ciao, Oliver __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Google's R Style Guide
On 29/08/2009 12:03 PM, Corrado wrote:
I do not understand why one should use a S3 preferentially on a S4 class, if
S4 is more rigorous.
As Spencer said, most people use either one or the other. I think it's
generally a bad idea to mix them (there are strange semantics if you do
that), so using just one is a good idea.
Which do you use? If you're a programmer working in a group, whatever
the rest of the group uses. It appears from the style guide that at
Google that's S3. That would be my choice too, but there are lots of
people who are very successful with S4.
Now I'm tempted to try to guess what character traits would make someone
prefer S4, but I think I'd only get into trouble ;-).
Duncan Murdoch
(The premiss is I am a newbie with OO programming in R, and would like to
understand what is the proper way to OO program in R )
Regards
On Saturday 29 August 2009 16:23:39 hadley wickham wrote:
An opening curly brace should never go on its own line;
I tend to do this:
f - function()
{
if (TRUE)
{
cat(TRUE!!\n)
} else {
cat(FALSE!!\n)
}
}
(I don't usually put one-liners in if/else blocks; here I would have
used ifelse)
I haven't seen many others format code in this way. Is there an
objective reason for this (such as the rule for the trailing }) or
is this just aesthetics?
It's probably just aesthetics. I don't like it because it increases
the number of lines without much real benefit - indenting already
gives you all the hints you need.
Hadley
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Best R text editors?
Great question to put up here :) My preferences: 1) notepad++ with NPPToR 2) tinn-R (was leading for a long time, but recently I decided to go with notepad++ ) 3) JGR / RCMDR (although RCMDR can be connected with the previous ones - and I wish it would get more developed) With the rest I didn't have experience in. Jedit - I am still waiting for Romain (from http://romainfrancois.blog.free.fr/) to release his connection of R to Jedit (What he showed me in useR 2009, was better then anything else I have seen until then) Best, Tal Galili On Thu, Aug 27, 2009 at 10:43 PM, Jonathan Greenberg greenb...@ucdavis.eduwrote: Quick informal poll: what is everyone's favorite text editor for working with R? I'd like to hear from people who are using editors that have some level of direct R interface (e.g. Tinn-R, Komodo+SciViews). Thanks! --j -- Jonathan A. Greenberg, PhD Postdoctoral Scholar Center for Spatial Technologies and Remote Sensing (CSTARS) University of California, Davis One Shields Avenue The Barn, Room 250N Davis, CA 95616 Cell: 415-794-5043 AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- -- My contact information: Tal Galili Phone number: 972-50-3373767 FaceBook: Tal Galili My Blogs: http://www.r-statistics.com/ http://www.talgalili.com http://www.biostatistics.co.il [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Google's R Style Guide
For my money, and perspective as one who has written a compiler, this reflects
a failing of the R parser. Both
if (TRUE) {
cat(TRUE!!\n)
}
else
{
cat(FALSE!!\n)
}
and
if (TRUE)
{
cat(TRUE!!\n)
}
else
{
cat(FALSE!!\n)
}
are easy to read, and should be accepted as a valid if . . . . else statement.
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Philippe Grosjean phgrosj...@sciviews.org 8/29/2009 12:12 PM
Max Kuhn wrote:
Perhaps this is obvious, but Ive never understood why this is the
general convention:
An opening curly brace should never go on its own line;
I tend to do this:
f - function()
{
if (TRUE)
{
cat(TRUE!!\n)
} else {
cat(FALSE!!\n)
}
}
(I don't usually put one-liners in if/else blocks; here I would have
used ifelse)
I haven't seen many others format code in this way. Is there an
objective reason for this (such as the rule for the trailing }) or
is this just aesthetics?
I think the problem is not much putting the opening brace after
function(), or after if (...), like you do. The problem is putting the
else at a new line like in:
if (TRUE) {
cat(TRUE!!\n)
}
else
{
cat(FALSE!!\n)
}
When you source this code, the first part until the first closing brace
is considered complete by the R parser, and then, 'else' is considered
as the begining of a new command, which is a syntax error:
if (TRUE) {
+ cat(TRUE!!\n)
+ }
TRUE!!
else
Error: syntax error
{
+ cat(FALSE!!\n)
+ }
FALSE!!
If you put the same code in a function, you got the expected behaviour:
f - function () {
+ if (TRUE) {
+ cat(TRUE!!\n)
+ }
+ else
+ {
+ cat(FALSE!!\n)
+ }
+ }
f() # No syntax error!
TRUE!!
Thus, this is technical reason for NOT putting else on another line.
For the rest, I share Hadley's feeling that you consumes too much
lines and I tend to prefer the regular R syntax you got when you
source your code.
Best,
Philippe
Thanks,
Max
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Confidentiality Statement:
This email message, including any attachments, is for th...{{dropped:6}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Google's R Style Guide
But in interactive use the R parser is constrained to work a line at a
time (unless it could predict what you were going to type next ;)
Hadley
On Sat, Aug 29, 2009 at 5:05 PM, John Sorkinjsor...@grecc.umaryland.edu wrote:
For my money, and perspective as one who has written a compiler, this
reflects a failing of the R parser. Both
if (TRUE) {
cat(TRUE!!\n)
}
else
{
cat(FALSE!!\n)
}
and
if (TRUE)
{
cat(TRUE!!\n)
}
else
{
cat(FALSE!!\n)
}
are easy to read, and should be accepted as a valid if . . . . else statement.
John
John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)
Philippe Grosjean phgrosj...@sciviews.org 8/29/2009 12:12 PM
Max Kuhn wrote:
Perhaps this is obvious, but Ive never understood why this is the
general convention:
An opening curly brace should never go on its own line;
I tend to do this:
f - function()
{
if (TRUE)
{
cat(TRUE!!\n)
} else {
cat(FALSE!!\n)
}
}
(I don't usually put one-liners in if/else blocks; here I would have
used ifelse)
I haven't seen many others format code in this way. Is there an
objective reason for this (such as the rule for the trailing }) or
is this just aesthetics?
I think the problem is not much putting the opening brace after
function(), or after if (...), like you do. The problem is putting the
else at a new line like in:
if (TRUE) {
cat(TRUE!!\n)
}
else
{
cat(FALSE!!\n)
}
When you source this code, the first part until the first closing brace
is considered complete by the R parser, and then, 'else' is considered
as the begining of a new command, which is a syntax error:
if (TRUE) {
+ cat(TRUE!!\n)
+ }
TRUE!!
else
Error: syntax error
{
+ cat(FALSE!!\n)
+ }
FALSE!!
If you put the same code in a function, you got the expected behaviour:
f - function () {
+ if (TRUE) {
+ cat(TRUE!!\n)
+ }
+ else
+ {
+ cat(FALSE!!\n)
+ }
+ }
f() # No syntax error!
TRUE!!
Thus, this is technical reason for NOT putting else on another line.
For the rest, I share Hadley's feeling that you consumes too much
lines and I tend to prefer the regular R syntax you got when you
source your code.
Best,
Philippe
Thanks,
Max
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Confidentiality Statement:
This email message, including any attachments, is for ...{{dropped:15}}
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Google's R Style Guide
On 29/08/2009 6:05 PM, John Sorkin wrote:
For my money, and perspective as one who has written a compiler, this reflects
a failing of the R parser. Both
if (TRUE) {
cat(TRUE!!\n)
}
else
{
cat(FALSE!!\n)
}
and
if (TRUE)
{
cat(TRUE!!\n)
}
else
{
cat(FALSE!!\n)
}
are easy to read, and should be accepted as a valid if . . . . else statement.
And if you enter
if (FALSE) {
cat(TRUE!!\n)
}
at the console, how long should it wait before it decides the else isn't
coming?
Duncan Murdoch
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to generate a random correlation matrix with restrictions
Thanks Ravi -- with my limited linear algebra skills I was assuming
invertible symmetric was sufficient (rather than just necessary) for
positive definiteness. So, the open challenge is to generate a pd
matrix of dimension 100 with r_ij = 1 if i=j else -1 r_ij 1, with
about 10% of the elements .9.
I tried for a bit without luck, but I can offer another way to
generate a pd matrix:
ev - runif(100) # choose some positive eigenvalues
U - svd(matrix(runif(1), nc=100))$u # an orthogonal matrix
pdM - U %*% diag(ev) %*% t(U)
Kingsford
On Fri, Aug 28, 2009 at 9:41 PM, Ravi Varadhanrvarad...@jhmi.edu wrote:
Hi Kingsford,
There is more structure to a correlation matrix than that meets the eye!
Your method will produce a matrix R that looks like a correlation matrix,
but beware - it is an impostor!
You can obtain a valid correlation matrix, Q, from the impostor R by using
the `nearPD' function in the Matrix package, which finds the positive
definite matrix Q that is nearest to R. However, note that when R is far
from a positive-definite matrix, this step may give a Q that does not have
the desired property.
require(Matrix)
R - matrix(runif(16), ncol=4)
R - (R * lower.tri(R)) + t(R * lower.tri(R))
diag(R) - 1
eigen(R)$val
Q - nearPD(R, posd.tol=1.e-04)$mat
eigen(Q)$val
max(abs(Q - R)) # maximum discrepancy between R and Q
Another easy way to produce a valid correlation matrix is:
R - matrix(runif(36), ncol=6)
RtR - R %*% t(R)
Q - cov2cor(RtR)
But this does not have the property that the correlations are uniformly
distributed.
Hope this helps,
Ravi.
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology
School of Medicine
Johns Hopkins University
Ph. (410) 502-2619
email: rvarad...@jhmi.edu
- Original Message -
From: Kingsford Jones kingsfordjo...@gmail.com
Date: Friday, August 28, 2009 10:12 pm
Subject: Re: [R] how to generate a random correlation matrix with
restrictions
To: Ning Ma pnin...@gmail.com
Cc: r-help@r-project.org
Ahh -- Mark Leeds just pointed out off-list that it was supposed to be
a correlation matrix.
Perhaps
R - matrix(runif(1), ncol=100)
R - (R * lower.tri(R)) + t(R * lower.tri(R))
diag(R) - 1
These are of course uniformly distributed positive correlations.
Kingsford
On Fri, Aug 28, 2009 at 7:36 PM, Kingsford
Joneskingsfordjo...@gmail.com wrote:
R - matrix(runif(1), ncol=100)
hth,
Kingsford Jones
On Fri, Aug 28, 2009 at 7:26 PM, Ning Mapnin...@gmail.com wrote:
Hi,
How can I generate a random 100x100 correlation matrix, R={r_ij},
where about 10% of r_ij are greater than 0.9
Thanks in advance.
__
R-help@r-project.org mailing list
PLEASE do read the posting guide
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
PLEASE do read the posting guide
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sequence generation
Or just use the 'each' argument to seq. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- project.org] On Behalf Of Barry Rowlingson Sent: Saturday, August 29, 2009 1:50 PM To: njhuang86 Cc: r-help@r-project.org Subject: Re: [R] Sequence generation On Sat, Aug 29, 2009 at 8:14 PM, njhuang86njhuan...@yahoo.com wrote: Hey guys, I was wondering how to create this sequence: 1, 2, 3, 1, 2, 3, 1, 2, 3, 1, 2, 3... with the '1, 2, 3' repeated over 10 times. rep(1:3,10) # rep repeats its first argument according to the number in its second argument Also, is there a simple method to generate 1, 1, 1, 2, 2, 2, 3, 3, 3? The second argument can be a vector, so what you want here is: rep(1:3,c(3,3,3)) but you can create the second vector here also using rep! Hence: rep(1:3,rep(3,3)) Barry __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] lrm in Design
Hello everybody, I am trying to do a logistic regression model with lrm() from the design package. I am comparing to groups with different medical outcome which can either be good or bad. In the help file it says that lrm codes al responses to 0,1,2,3, etc. internally and does so in alphabetical order. I would guess this means bad=0 and good=1. My question: I am trying to figure out the connection between my factors and my response. Which probability is being calculated that of good or bad (1 or 0, respectively). I'm not sure whether I made clear what I was trying to say but will be very grateful for all help. -- View this message in context: http://www.nabble.com/lrm-in-Design-tp25206737p25206737.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] std.error
Mcdonald, Grant wrote: dear sir, i am trying to calculate the standard error of my data (x), i have tried se(x, na.rm=TRUE) and std.error(x) neither have worked and i cannot find an alternative Hi Grant, There is a convenience function std.error that calculates the conventional standard error of the mean in the plotrix package. Make sure that it does the calculation that you want. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] std.error
Standard error usually means the estimated standard deviation of a parameter estimate, e.g. the sample mean. Perhaps you mean the estimated standard deviation of the data. If so sdev - sd(x, na.rm = TRUE) If you want the standard error of the mean there are several ways of doing it. Perhaps the simplest is seMean - sd(x, na.rm=TRUE)/sqrt(length(na.omit(x))) missing values complicate the issue just a little. Bill Venables. From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of Mcdonald, Grant [grant.mcdonal...@imperial.ac.uk] Sent: 29 August 2009 04:50 To: r-help@R-project.org Subject: [R] std.error dear sir, i am trying to calculate the standard error of my data (x), i have tried se(x, na.rm=TRUE) and std.error(x) neither have worked and i cannot find an alternative sorry to bother with such a basic problem __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] how to generate a random correlation matrix with restrictions
Yes, Kingsford. This problem does not appear to be trival. I am not sure if
there is any literature on this. I have seen a paper by Davies and Higham (BIT
2000) on Stable generation of correlation matrices. There is also a paper by
Harry Joe on generating correlation matrices with given partial correlation
structure. I am not sure if these papers would be helpful for this problem.
Of course, one can readily cook up an ad-hoc, trial-error procedure to generate
the type of matrices that Ning wants.
By the way, the easiest way to generate a PD matrix is:
N - 10
amat - matrix(rnorm(N*N), N, N)
A - amat %*% t(amat) # A is PD
Best,
Ravi
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology
School of Medicine
Johns Hopkins University
Ph. (410) 502-2619
email: rvarad...@jhmi.edu
- Original Message -
From: Kingsford Jones kingsfordjo...@gmail.com
Date: Saturday, August 29, 2009 7:43 pm
Subject: Re: [R] how to generate a random correlation matrix with restrictions
To: Ravi Varadhan rvarad...@jhmi.edu
Cc: Ning Ma pnin...@gmail.com, r-help@r-project.org
Thanks Ravi -- with my limited linear algebra skills I was assuming
invertible symmetric was sufficient (rather than just necessary) for
positive definiteness. So, the open challenge is to generate a pd
matrix of dimension 100 with r_ij = 1 if i=j else -1 r_ij 1, with
about 10% of the elements .9.
I tried for a bit without luck, but I can offer another way to
generate a pd matrix:
ev - runif(100) # choose some positive eigenvalues
U - svd(matrix(runif(1), nc=100))$u # an orthogonal matrix
pdM - U %*% diag(ev) %*% t(U)
Kingsford
On Fri, Aug 28, 2009 at 9:41 PM, Ravi Varadhanrvarad...@jhmi.edu wrote:
Hi Kingsford,
There is more structure to a correlation matrix than that meets the
eye! Your method will produce a matrix R that looks like a
correlation matrix, but beware - it is an impostor!
You can obtain a valid correlation matrix, Q, from the impostor R
by using the `nearPD' function in the Matrix package, which finds
the positive definite matrix Q that is nearest to R. However, note
that when R is far from a positive-definite matrix, this step may give
a Q that does not have the desired property.
require(Matrix)
R - matrix(runif(16), ncol=4)
R - (R * lower.tri(R)) + t(R * lower.tri(R))
diag(R) - 1
eigen(R)$val
Q - nearPD(R, posd.tol=1.e-04)$mat
eigen(Q)$val
max(abs(Q - R)) # maximum discrepancy between R and Q
Another easy way to produce a valid correlation matrix is:
R - matrix(runif(36), ncol=6)
RtR - R %*% t(R)
Q - cov2cor(RtR)
But this does not have the property that the correlations are
uniformly distributed.
Hope this helps,
Ravi.
Ravi Varadhan, Ph.D.
Assistant Professor,
Division of Geriatric Medicine and Gerontology
School of Medicine
Johns Hopkins University
Ph. (410) 502-2619
email: rvarad...@jhmi.edu
- Original Message -
From: Kingsford Jones kingsfordjo...@gmail.com
Date: Friday, August 28, 2009 10:12 pm
Subject: Re: [R] how to generate a random correlation matrix with
restrictions
To: Ning Ma pnin...@gmail.com
Cc: r-help@r-project.org
Ahh -- Mark Leeds just pointed out off-list that it was supposed
to be
a correlation matrix.
Perhaps
R - matrix(runif(1), ncol=100)
R - (R * lower.tri(R)) + t(R * lower.tri(R))
diag(R) - 1
These are of course uniformly distributed positive correlations.
Kingsford
On Fri, Aug 28, 2009 at 7:36 PM, Kingsford
Joneskingsfordjo...@gmail.com wrote:
R - matrix(runif(1), ncol=100)
hth,
Kingsford Jones
On Fri, Aug 28, 2009 at 7:26 PM, Ning Mapnin...@gmail.com wrote:
Hi,
How can I generate a random 100x100 correlation matrix, R={r_ij},
where about 10% of r_ij are greater than 0.9
Thanks in advance.
__
R-help@r-project.org mailing list
PLEASE do read the posting guide
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
PLEASE do read the posting guide
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] lrm in Design
See: https://stat.ethz.ch/pipermail/r-help/2009-July/204192.html and also other posts in that thread. On Sat, Aug 29, 2009 at 6:02 PM, loch1l...@gmx.li wrote: Hello everybody, I am trying to do a logistic regression model with lrm() from the design package. I am comparing to groups with different medical outcome which can either be good or bad. In the help file it says that lrm codes al responses to 0,1,2,3, etc. internally and does so in alphabetical order. I would guess this means bad=0 and good=1. My question: I am trying to figure out the connection between my factors and my response. Which probability is being calculated that of good or bad (1 or 0, respectively). I'm not sure whether I made clear what I was trying to say but will be very grateful for all help. -- View this message in context: http://www.nabble.com/lrm-in-Design-tp25206737p25206737.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Infinite != NaN?
Greetings. I somehow had the impression that an infinite number, as obtained by dividing by zero, for instance, would be flagged as both missing (NA) and not a number (NaN). It appears that I was wrong on both counts, although the is.finite function correctly returns FALSE in such a case. Please see the appended for some details. I guess that the bottom line is that R works the way it works, but if you can add anything that will further instruct me, I'd appreciate it. Thanks. -- Mike y - 2/0 y [1] Inf is.na(y) [1] FALSE is.nan(y) [1] FALSE is.finite(y) [1] FALSE z - log(-1) Warning message: In log(-1) : NaNs produced z [1] NaN is.nan(z) [1] TRUE is.na(z) [1] TRUE - R version 2.9.2 (2009-08-24) Copyright (C) 2009 The R Foundation for Statistical Computing ISBN 3-900051-07-0 - $ uname -a Linux xxx.localdomain 2.6.29.6-217.2.16.fc11.x86_64 #1 SMP Mon Aug 24 17:17:40 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Infinite != NaN?
It is not clear that you have read the help page that arise with: ?Inf Note: In R, basically all mathematical functions (including basic Arithmetic), are supposed to work properly with +/- Inf and NaN as input or output. The basic rule should be that calls and relations with Infs really are statements with a proper mathematical limit. Also: Inf+Inf [1] Inf Inf-Inf [1] NaN -2/0 [1] -Inf Inf*Inf [1] Inf Inf*(-Inf) [1] -Inf On Aug 29, 2009, at 9:58 PM, Michael Hannon wrote: Greetings. I somehow had the impression that an infinite number, as obtained by dividing by zero, for instance, would be flagged as both missing (NA) and not a number (NaN). It appears that I was wrong on both counts, although the is.finite function correctly returns FALSE in such a case. Please see the appended for some details. I guess that the bottom line is that R works the way it works, but if you can add anything that will further instruct me, I'd appreciate it. So I suppose the obvious further instruction is to read the help pages. Thanks. -- Mike y - 2/0 y [1] Inf is.na(y) [1] FALSE is.nan(y) [1] FALSE is.finite(y) [1] FALSE z - log(-1) Warning message: In log(-1) : NaNs produced z [1] NaN is.nan(z) [1] TRUE is.na(z) [1] TRUE - David Winsemius, MD Heritage Laboratories West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RFE: vectorize URLdecode
Not sure if your context is rapache, but if so urlEncode() and urlDecode() are available to you and are vectorized: http://biostat.mc.vanderbilt.edu/rapache/manual.html#urlEncode Best, Jeff -Original Message- From: r-help-boun...@r-project.org on behalf of Jack Tanner Sent: Sat 8/29/2009 9:31 AM To: r-h...@stat.math.ethz.ch Subject: [R] RFE: vectorize URLdecode In R 2.9.2, URLdecode(c(a%20b, b%20c)) [1] a b Warning message: In charToRaw(URL) : argument should be a character vector of length 1 all but the first element will be ignored Could URLdecode be modified to actually process all elements of the vector, not just the first? Thanks in advance __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] aggregating irregular time series
Hi, I have a couple of aggregation operations that I don't know how to accomplish. Let me give an example. I have the following irregular time series time x 10:00:00.02120 10:00:00.22420 10:00:01.00219 10:00:02:94820 1) For each entry time, I'd like to get sum of x for the next 2 seconds (excluding itself). Using the above example, the output should be timesumx 10:00:00.02139 10:00:00.22419 10:00:01.44220 10:00:02:948 0 2) For each i-th of x in the series, what's the first passage time to x[i]-1. I.e. the output should be time firstPassgeTime 10:00:00.0210.981 10:00:00.2240.778 10:00:01.442NA 10:00:02:948NA Is there any shortcut function that allows me to do the above? Thank you. adschai __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] POSIX time conversion doesn't display digit
Hi, I have the following string that I converted to a POSIXct: a - 2009-08-24 10:00:00.213 a.p - strptime(a,%Y-%m-%d %H:%M:%OS) as.double(as.POSIXct(a.p)) [1] 1251122400 I can't seem to get the decimal fraction of .213 out by casting to double or numeric. Is there anyway to make sure that POSIXct spits that out? Thank you. adschai __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
