Re: [R] Installation of R in Redhat Linux (64 bit)
On Sat, 6 Jun 2009, Zeljko Vrba wrote: On Fri, Jun 05, 2009 at 08:27:45PM -0700, Santosh wrote: When I run the following: nm /usr/lib64/R/library/stats/libs/stats.so | grep _gfortran_copy_string You probably need to install libraries related to gfortran. Yes, specifically libgfortran. Look at rpm -qa | grep libgfortran to see what versions are installed (if any). But how was R installed? If this was installed from an RPM it should have satisfied such dependencies (and R-sig-fedora would be a more appropriate list). I think the issue relates to the version of libgfortran, and I've seen it using binaries compiled on an older version of Fedora. Maybe that symbol is used by gfortran 4.1.x and not by 4.3.x, so is in libgfortran.so.1 but not in libgfortran.so.3. If this were Fedora, I would be sugggesting installing the compat-libgfortran-41 RPM. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] alternative to built-in data editor
On Thu, May 28, 2009 at 8:52 AM, Dieter Mennedieter.me...@menne-biomed.de wrote: I have never seen the data editor. It's fix(), very similar to View(), but not crashing. Although showData() in relimp (the same used by Rcmdr) is often enough for viewing data, fix() is somewhat rudimentary. Isn't there any other (cross-platform) alternative to fixing data in a spreadsheet-style environment in R (those on Windows can try RExcel)? Perhaps built on other toolkits? Liviu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] S4: When is validObject issued? (or why S4 is killing me:( ..
setMethod(initialize,test2,
function(.Object,...){
.Object-callNextMethod(.Object,...)
validity is checked in the preceeding line
.obj...@b-.obj...@a ## here b is initialized ##
.Object
})
new(test2)
Error in if (obj...@a != obj...@b) print(values must be equal!!)
else TRUE : argument is of length zero
This could mean only one thing, validity of test2 is checked before
it gets to point when b is initialized (i.e. in callNextMethod). But
this is absurd (at leas from my point): callNextMethod constructs
object of type test and should have nothing to do with validity of
test2. Shouldn't validity be checked only after the object is
created?
The class of .Object is test2, and initialize should return a (valid)
instance of test2, right? So the validity check on test2 has to have
been performed before returning from callNextMethod.
Oh yes, that is indeed meaningful. So it's default coercion method from test1 to test2 which is called.
Second my slot a is initialized in test1's constructor and b
must be assigned only after the callNextMethod as in above
code. Seemingly unsolvable paradox? How to be?
My own solution would avoid using initialize (because as you're
discovering the contract is hard to satisfy in general) and instead
use constructors
I am sure this contract and all this
initialization/coercion/creation-sequence stuff must be documented somewhere. Though all
what I can find is a collection of your responses in R-help archive. Could you please
suggest something to read (except R-core code)?
For now I am pretty much clarified. Thanks a lot!
test2 - function(a=runif(1), b=a, ...) new(test2, a=a, b=b, ...)
or similar, which I think helps to provide a bit of an interface
between the class and it's implementation.
One could think of additional solutions (creating a new 'test' inside
'test2', and not using callNextMethod(), for instance) but this is
unlikely to be robust (e.g., when derived classes are relying on
initialize,ANY-method to fill in slots with supplied arguments).
Martin
Many thanks.
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Re: [R] alternative to built-in data editor
On 6/6/09, Liviu Andronic landronim...@gmail.com wrote: (cross-platform) alternative to fixing data in a spreadsheet-style environment in R (those on Windows can try RExcel)? Perhaps built on other toolkits? Oh, there is one, in JGR. Issue object.browser() to browse all workspace objects, and double-click data frames to access a much less rudimentary spreadsheet-like environment that allows to view the data, edit individual cells, insert/remove rows, insert/remove/rename columns, sort by columns and export all modifications to an R object. Individual variables in data frames, and other objects such as matrices can be edited in a similar fashion. Liviu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] time series, longitudinal data or trajectories
Thanks for yours answers. So if I understand: - Trajectories are continuous, the other are discrete. - The difference between time series and longitudinal is that time series are made at regular time whereas longitudinal are not ? - Repeated measures are over a short period of time. So if I measure the weight of my patient daily during one week, it will be repeated measure ; if I measure it once a week during one year, it will time series ; if I measure it once a week during one year but with some missing week, it will longitudinal data ? Well I guess it is not as simple at that, but is it the idea ? Christophe At 04:02 PM 6/5/2009, Christophe Genolini wrote: Hi the list Strictly speaking, this is not a R question, but I need the information for the creation of a package. My question is about vocabulary: What is the difference between time series, longitudinal data and trajectories? Sincerely Christophe Longitudinal data are measurements over long periods of time, often at irregular periods, but consistent across subjects. Repeated measures data are replicates at the same point in time, or over a short period of time (e.g., laboratory experiments). Time series typically have constant increments of time and typically a stochastic character, although this term might be considered all-encompassing for all measurements at different times. Trajectory implies a continuous curve in time, as opposed to discrete times. Trajectory also implies an underlying causal model, as it is a term from kinematics. I hope this helps. Robert A. LaBudde, PhD, PAS, Dpl. ACAFS e-mail: r...@lcfltd.com Least Cost Formulations, Ltd.URL: http://lcfltd.com/ 824 Timberlake Drive Tel: 757-467-0954 Virginia Beach, VA 23464-3239Fax: 757-467-2947 Vere scire est per causas scire __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Need suggestion to present migration flow data
Hi group, I am looking at migration data of very sick children to see if they move because of easier access to tertiary care. In particular, I am investigating the change of their socioeconomic status before the move (5 levels, highest implies best status) and after. Can anyone suggest some kind of graphical display that best represents this kind of flow? In terms of modelling, I can only think of a count data problem like a 5X5 matrix. Has anyone tried another approach? Thanks in advance. Kelvin -- Knowledge is meant to draw people closer to God __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] loglikelihood and AIC
Hi,
I tried fitting loglinear model using the glm(catspec). The data used is
FHtab. . An independence model was fitted. Here summary() and fitmacro( ) give
different values for AIC.
I understand that fitmacro( ) takes the likelilhood ratio L2(deviance) to
calculate AIC and uses the formula AIC= L2- d.f(deviance)*2 and this AIC is
used for comparison of nested models. (Am I right?)
The value given by loglik( ) is used by summary() to calculate AIC in the
formula
AIC= -2 logL + K* e.d.f. Can anybody tell me how this log L is calculated?
It is not logL=Sum(ni* log (pi)), where pi= fitted frequency / total no. of
observations. The help available at extract AIC( ) also is not giving the
answer.
Please help
Thanks
Subha
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[[alternative HTML version deleted]]
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Re: [R] (no subject)
Christophe Genolini cgeno...@u-paris10.fr wrote Thanks for yours answers. So if I understand: - Trajectories are continuous, the other are discrete. - The difference between time series and longitudinal is that time series are made at regular time whereas longitudinal are not ? - Repeated measures are over a short period of time. So if I measure the weight of my patient daily during one week, it will be repeated measure ; if I measure it once a week during one year, it will time series ; if I measure it once a week during one year but with some missing week, it will longitudinal data ? This is not my understanding of the terms. To me, both time series and longitudinal data can be regular or irregular, but time series data typically have a lot more measurement points (20 at a minimum) and often has only one or a few subjects - e.g. trends in the stock market. Logitudinal data are often collected at fewer time points, but with many subject (e.g. measuring people repeatedly to see if something about them changes over time, and changes differently in different people). Peter Peter L. Flom, PhD Statistical Consultant www DOT peterflomconsulting DOT 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] how to make the dynamically creted string work inside if as a condition
Hi,
How to make an if condition work, if the condition inside if() is created
dynamically ,and that is a string .If i type teh dynamically created string
the if works fine but when dynamically created,it is a string and going
inside the if() ,an error is thrown saying : rgument is not logical ..I even
tried changing teh mode of the string to logical,but it doesn't work
Say my dynamically created string is :--
str- name=='tom' || name=='harry' || name=='tina'
where the names are diffrent for diffrent DBs.
if(name=='tom' || name=='harry' || name=='tina' )
{
some code
}
If i do this
if(str)
{
some code
}
It doesn't work:(
--
Thanks
Moumita
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Re: [R] how to make the dynamically creted string work inside if as a condition
Moumita Das wrote:
Hi,
How to make an if condition work, if the condition inside if() is created
dynamically ,and that is a string .If i type teh dynamically created string
the if works fine but when dynamically created,it is a string and going
inside the if() ,an error is thrown saying : rgument is not logical ..I even
tried changing teh mode of the string to logical,but it doesn't work
Say my dynamically created string is :--
str- name=='tom' || name=='harry' || name=='tina'
where the names are diffrent for diffrent DBs.
That's not a string, it will be evaluated to a logical TRUE or FALSE value.
if(name=='tom' || name=='harry' || name=='tina' )
{
some code
}
If i do this
if(str)
{
some code
}
It doesn't work:(
Those should be equivalent. I think you need to simplify your example
and post real code for us to see the problem.
Duncan Murdoch
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[R] SMACOF joint configuration plot with bread data?
Dear R-helpers, I have dist class objects for 10 individuals rating the dissimilarities (on a 100-point scale) of the same 10 faces (analogous to the bread data). I would like to get an individual differences scaling jointly for the individual judges and the faces, and plot them on the same axes. This is the example: library(smacof) data(breakfast) res.rect-smacofRect(breakfast, itmax = 1000) plot(res.rect, joint = TRUE, xlim = c(-10, 10)) However, smacofIndDiff() doesn't produce the desired form of output. This is the bread example, which has data in roughly the same form as mine: data(bread) res.uc - smacofIndDiff(bread, itmax = 1000) Thanks, _ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box 400400Charlottesville, VA 22904-4400 Parcels:Room 102Gilmer Hall McCormick RoadCharlottesville, VA 22903 Office:B011+1-434-982-4729 Lab:B019+1-434-982-4751 Fax:+1-434-982-4766 WWW:http://www.people.virginia.edu/~mk9y/ [[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] No --no-latex?
Hi, Having finally gotten around to installing R-2.9.0, I find that while the docs still say I can invoke the --no-latex option, R CMD INSTALL has decided that I can't. Nor is there any notice of this that I can find in the 2.9 series news. Is this just a trifling oversight that will be repaired? 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] No --no-latex?
Jim Lemon wrote: Hi, Having finally gotten around to installing R-2.9.0, I find that while the docs still say I can invoke the --no-latex option, R CMD INSTALL has decided that I can't. Nor is there any notice of this that I can find in the 2.9 series news. Is this just a trifling oversight that will be repaired? Jim Looks like it was an oversight. I'll fix it. Thanks for the report... 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] Rpad - avoid removal of manually created html-tags in R chunk
Martin Gartner wrote:
Dear Rpad-users,
currently I am setting up a web page using Rpad (www.rpad.org). But I
have a problem with generating dynamic html-output in the Rpad chunk.
Here an example of my problem:
I have the following index.html file:
html
head
titleexample/title
meta http-equiv=Content-Type content=text/html; charset=utf-8
script type=text/javascript src=gui/Rpad.js/script
/head
body
pre dojoType=Rpad rpadRun=init rpadOutput=html
rpadHideSource=true
x -
tabletrthA/ththB/th/trtda/tdtdb/td/table
/pre
/body
/html
If I run Rpad(index.html) in the local server mode and when I turn
to my Rgui, then the object x looks like ABab, i.e. all my
html-tags are removed within the R-chunk.
I know that I can avoid this with nested HtmlTrees, e.g.
H(table, H(tr, H(th, A), H(th, B)), H(tr, H(td, a),
H(td, b)))
but as I have to produce html-output of a large dataframe (100 rows
and 6 colums), the nesting takes too much time (because every cell
element might have conditional formatting and I have to check each
element) and I think it would be faster with pasting all html-code
manually into a character-object and printing this object as html. But
trying this I have the above mentioned problem.
Can anybody help me? If anybody knows a solution, how I can avoid,
that the html-tags are removed from my x (see example above), I
think, I can produce my output very fast.
Thanks and best regards,
Martin
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Hi everybody,
I already got the solution. I have to use the encoded characters for the tags ...
html
head
titleGUI Examples/title
script type=text/javascript
rpadConfig = {
gui: alternate,
rpadHideSource: true
};
/script
script type=text/javascript src=gui/Rpad.js/script
/head
body
#60 #62
pre dojoType=Rpad rpadRun=init rpadOutput=html rpadHideSource=true
x - #60table
border='1'#62#60tr#62#60th#62A#60#47th#62#60th#62B#60#47th#62#60#47tr#62#60td#62A#60#47td#62#60td#62B#60#47td#62#60#47table#62
cat(x)
/body
/html
Best regards,
Martin
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Re: [R] No --no-latex?
Jim Lemon wrote: Hi, Having finally gotten around to installing R-2.9.0, I find that while the docs still say I can invoke the --no-latex option, R CMD INSTALL has decided that I can't. Nor is there any notice of this that I can find in the 2.9 series news. Is this just a trifling oversight that will be repaired? Jim Looks like the corresponding else if clause got omitted in tools:::.install_packages() and before that in share/R/RINSTALL. -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Install RCurl in Linux
Hi If you are getting exactly the same errors, then it is probable that your installation of curl-7.19.2 is not taking effect and the configuration script is still finding the older version. So you may want to check the output of curl-config --version in the same shell as you issue R CMD INSTALL. If the new libcurl header files are being used, I doubt you will get the same errors. So we need to see those also to be able to assist. D. heyi xiao wrote: Thanks Prof. Ripley, I installed the current version curl-7.19.2, still got the same problem. I am installing RCurl_0.97-3 and my system is x86_64/CentOS 5. Looking forward to more suggestions/ideas. --- On *Fri, 6/5/09, Prof Brian Ripley /rip...@stats.ox.ac.uk/* wrote: From: Prof Brian Ripley rip...@stats.ox.ac.uk Subject: Re: [R] Install RCurl in Linux To: heyi xiao xiaohey...@yahoo.com Cc: r-help@r-project.org, dun...@wald.ucdavis.edu Date: Friday, June 5, 2009, 1:50 AM It seems you need a later curl -- 7.15 is rather old (and I think incomplete as a version number) and 7.19.5 is current. It is helpful to tell us what version of packages (here RCurl) you are trying to use, as well as your precise OS. On Thu, 4 Jun 2009, heyi xiao wrote: Hello all, I had both curl and curl-devel (both 7.15) installed on my x86_64/CentOS machine. However, I still got problem when I do R CMD INSTALL RCurl ?? Error message below, since library and/or include path is missing. I tried R CMD INSTALL RCurl --configure-args='--libdir=/usr/lib64/?? --includedir=/usr/include/' That should be part of the default paths. Same result. Any hint/suggestion would be appreciated. ... No CURLOPT_NOPROXY enumeration value. No CURLINFO_CONDITION_UNMET enumeration value. No CURLINFO_REDIRECT_URL enumeration value. No CURLINFO_CERTINFO enumeration value. No CURLINFO_PRIMARY_IP enumeration value. No CURLINFO_APPCONNECT_TIME enumeration value. No CURLOPT_KEYPASSWD enumeration value. No CURLOPT_DIRLISTONLY enumeration value. No CURLOPT_APPEND enumeration value. No CURLOPT_KRBLEVEL enumeration value. ... Version has CURLOPT_PROTOCOLS Version has CURLOPT_REDIR_PROTOCOLS configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -std=gnu99 -I/usr/local/lib64/R/include?? -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -I/usr/local/include?? -fpic?? -g -O2 -c enums.c -o enums.o In file included from CurlOptEnums.h:10, from enums.c:79: CURLOptTable.h:145: error: ??CURLOPT_SOCKOPTFUNCTION?? undeclared here (not in a function) CURLOptTable.h:146: error: ??CURLOPT_SOCKOPTDATA?? undeclared here (not in a function) CURLOptTable.h:147: error: ??CURLOPT_SSL_SESSIONID_CACHE?? undeclared here (not in a function) CURLOptTable.h:148: error: ??CURLOPT_SSH_AUTH_TYPES?? undeclared here (not in a function) CURLOptTable.h:149: error: ??CURLOPT_SSH_PUBLIC_KEYFILE?? undeclared here (not in a function) CURLOptTable.h:150: error: ??CURLOPT_SSH_PRIVATE_KEYFILE?? undeclared here (not in a function) CURLOptTable.h:151: error: ??CURLOPT_FTP_SSL_CCC?? undeclared here (not in a function) make: *** [enums.o] Error 1 ERROR: compilation failed for package ??RCurl?? * Removing ??/usr/local/lib64/R/library/RCurl?? [[alternative HTML version deleted]] -- Brian D. Ripley, rip...@stats.ox.ac.uk /mc/compose?to=rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ http://www.stats.ox.ac.uk/%7Eripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] time series, longitudinal data or trajectories
At 04:54 AM 6/6/2009, Christophe Genolini wrote: Thanks for yours answers. So if I understand: - Trajectories are continuous, the other are discrete. - The difference between time series and longitudinal is that time series are made at regular time whereas longitudinal are not ? - Repeated measures are over a short period of time. So if I measure the weight of my patient daily during one week, it will be repeated measure ; if I measure it once a week during one year, it will time series ; if I measure it once a week during one year but with some missing week, it will longitudinal data ? Well I guess it is not as simple at that, but is it the idea ? snip Not exactly. If you measure weight daily for a week, that is a time series (equally spaced time measurements over an arbitrary period) and repeated measurements (multiple measurements on the same subject, whether on time or at random or in some other way). If you measure weight weekly for each week in a year this is a time series (equally spaced time measurements) and would generally be called a longitudinal study (measurements over a lengthy enough time period that time-related changes are expected). Missing data are common in repeated measures or longitudinal studies. In longitudinal studies, an additional problem of dropouts is present, which may be correlated with the unobserved measurement (i.e., missing, not at random or non-ignorable, non-random). Also, the long time period of a longitudinal study may create issues of measurement bias (due to drift in technique or clinicians over time) and change in the subject baseline state. Time series is typically used in my experience for measurements that have a great degree of regularity (equally-spaced times, few or no missing data). Trajectory is a term for continuous time curve. Examples: Study to measure blood pressure measurement fluctuations: N subjects measured by M operators every 8 hr during a week. Note there is a general expectation of a constant mean value for each subject during the period, with probably short-time fluctuations. This would be called a repeated measure study, Although it could also be called a time series study, the expectation of no total time period effect and the possibility of missing measurements would argue against that term. On the other hand, if a posteriori there were little or no missing data, and regular time-dependent patterns were observed, its name might be shifted to a time series study. Cohort study to measure blood pressure changes over a ten year time frame for treated and untreated subjects: There will be significant amounts of missing data, dropouts from the study and a long time period of observation. This would almost universally be known as a longitudinal study. Controlled experiment to measure rates of gelation of batches of different gelatins: N lots of gelatin, each measured in solution at the same M time periods for viscosity. A continuous underlying viscosity vs. time curve is expected (the trajectory) for each lot. Time periods are equal, and there are few missing data. The goal is to compare gelation trajectories. This is a repeated measure study, and might more particularly be characterized as a time series study. When the subjects are living entities, usually the terms repeated measures or longitudinal are used. If measurements are taken at a single point in time, the term cross-sectional study is used. If there is a single response across time, the term time series is used. If there are multiple responses all measured at the same times for the subjects, the term panel data is used. For controlled experiments, the terms repeated measures and time series are common. Longitudinal could be used, but generally is not. Robert A. LaBudde, PhD, PAS, Dpl. ACAFS e-mail: r...@lcfltd.com Least Cost Formulations, Ltd.URL: http://lcfltd.com/ 824 Timberlake Drive Tel: 757-467-0954 Virginia Beach, VA 23464-3239Fax: 757-467-2947 Vere scire est per causas scire __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Finding a folder at the root level of an unknown drive
Colleagues, R 2.9.0 Windows XP Task is as follows: A folder FOLDERNAME exists at the root level of some drive, e.g., E: \FOLDERNAME I want to search all possible drives to find the location of this folder but I don't know what drives exist or are mounted. The command: dir(path=C:/, pattern=FOLDERNAME) happens to be successful. However, the command: dir(path=C:/, pattern=FOLDERNAME) results is a pop-up message: There is no disk in the drive. Please insert a disk into drive D: Can I avoid the pop-up message? i.e., can I execute a command that silently reports only successes? Thanks in advance. Dennis Dennis Fisher MD P (The P Less Than Company) Phone: 1-866-PLessThan (1-866-753-7784) Fax: 1-415-564-2220 www.PLessThan.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] correct line types in lattice legends
Hallo R-users, I do not understand how to specify the correct line and symbol types in the legends of a lattice xyplot. This is what I tried, but the line types and symbol in the graph are not seen in the legend. Any help is appreciated. Thanks, Gerrit. library(lattice) s-rep(1:3,len=10) x- 1:10 y- x+s+rnorm(10) d-data.frame(s,x,y) xyplot(y~x, groups=s,data=d, type=b, pch=1:3,lty=1:3, auto.key=list(text=c(A,B,C),points=FALSE,lines=TRUE, type=b,lty=1:3,divide=1,pch=1:3,columns=3)) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Finding a folder at the root level of an unknown drive
On 06/06/2009 9:19 AM, Dennis Fisher wrote: Colleagues, R 2.9.0 Windows XP Task is as follows: A folder FOLDERNAME exists at the root level of some drive, e.g., E: \FOLDERNAME I want to search all possible drives to find the location of this folder but I don't know what drives exist or are mounted. The command: dir(path=C:/, pattern=FOLDERNAME) happens to be successful. However, the command: dir(path=C:/, pattern=FOLDERNAME) results is a pop-up message: There is no disk in the drive. Please insert a disk into drive D: Can I avoid the pop-up message? i.e., can I execute a command that silently reports only successes? I think that's quite hard, because the action on failure depends on the drive type. It's coming from the device driver, not from R. I'd guess your drive D: is a CD drive, for example. If you do the same with Z:/ (assuming you don't have a drive Z: defined), you won't get the popup, but you'll get a warning from R because Z:/ is not readable. So to do this, you'd need code to recognize what kind of drive you had, what sort of problems there could be, and avoid triggering them. 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] S4: When is validObject issued? (or why S4 is killing me:( ..
Vitalie S. wrote:
setMethod(initialize,test2,
function(.Object,...){
.Object-callNextMethod(.Object,...)
validity is checked in the preceeding line
.obj...@b-.obj...@a ## here b is initialized ##
.Object
})
new(test2)
Error in if (obj...@a != obj...@b) print(values must be equal!!)
else TRUE : argument is of length zero
This could mean only one thing, validity of test2 is checked before
it gets to point when b is initialized (i.e. in callNextMethod). But
this is absurd (at leas from my point): callNextMethod constructs
object of type test and should have nothing to do with validity of
test2. Shouldn't validity be checked only after the object is
created?
The class of .Object is test2, and initialize should return a (valid)
instance of test2, right? So the validity check on test2 has to have
been performed before returning from callNextMethod.
Oh yes, that is indeed meaningful. So it's default coercion method from
test1 to test2 which is called.
Second my slot a is initialized in test1's constructor and b
must be assigned only after the callNextMethod as in above
code. Seemingly unsolvable paradox? How to be?
My own solution would avoid using initialize (because as you're
discovering the contract is hard to satisfy in general) and instead
use constructors
I am sure this contract and all this
initialization/coercion/creation-sequence stuff must be documented
somewhere. Though all what I can find is a collection of your responses
in R-help archive. Could you please suggest something to read (except
R-core code)?
?Methods and its 'References' and 'See also' section. Also, please take
my explanations with a grain of salt -- it represents my understanding,
not the way things are intended to be. Martin
For now I am pretty much clarified. Thanks a lot!
test2 - function(a=runif(1), b=a, ...) new(test2, a=a, b=b, ...)
or similar, which I think helps to provide a bit of an interface
between the class and it's implementation.
One could think of additional solutions (creating a new 'test' inside
'test2', and not using callNextMethod(), for instance) but this is
unlikely to be robust (e.g., when derived classes are relying on
initialize,ANY-method to fill in slots with supplied arguments).
Martin
Many thanks.
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Re: [R] Installation of R in Redhat Linux (64 bit)
Thanks for your responses! I guess R was installed using the enterprise version (not fedora) rpm package. The version of libgfortran is libgfortran43-4.3.2-7.el5 and I have libgfortran.so.3. From your email, I understand that libgfortran.so.1 is different from libgfortran.so.3, and that _gfortran_copy_string is not used in the libgfortran.so.3. Is that correct? I see the libgfortran.so.1 is available for Fedora. would it work on RHEL5? If not, where can I download libgfortran.so.1 for RHEL5? Thanks much in advance. Santosh On Fri, Jun 5, 2009 at 11:49 PM, Prof Brian Ripley rip...@stats.ox.ac.ukwrote: On Sat, 6 Jun 2009, Zeljko Vrba wrote: On Fri, Jun 05, 2009 at 08:27:45PM -0700, Santosh wrote: When I run the following: nm /usr/lib64/R/library/stats/libs/stats.so | grep _gfortran_copy_string You probably need to install libraries related to gfortran. Yes, specifically libgfortran. Look at rpm -qa | grep libgfortran to see what versions are installed (if any). But how was R installed? If this was installed from an RPM it should have satisfied such dependencies (and R-sig-fedora would be a more appropriate list). I think the issue relates to the version of libgfortran, and I've seen it using binaries compiled on an older version of Fedora. Maybe that symbol is used by gfortran 4.1.x and not by 4.3.x, so is in libgfortran.so.1 but not in libgfortran.so.3. If this were Fedora, I would be sugggesting installing the compat-libgfortran-41 RPM. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/http://www.stats.ox.ac.uk/%7Eripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 [[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] Fitting with Beta-prime
Hi, I need to fit my data with beta-prim distribution. I found the function in the package VGAM: betaprime and betaff. I don't know how can I make it work. I know that i need to calculate the parameters that describe this function on my distribution. But for exemple I don't understand the link function. And then How can I plot my data fitted? Can you help me out with this? Thanks a lot! Alessandra -- View this message in context: http://www.nabble.com/Fitting-with-Beta-prime-tp23903506p23903506.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] Truncated R output in Sweave
Dear Colleagues: In producing a book or a handout I sometimes cut out a large part of the printed output of an R function, substituting ... for that chunk. Deleting non-essential output saves paper. It would be nice to have a capability in Sweave to allow the user to specify a starting and an ending regular expression that would identify consecutive lines of output to replace with ..., without showing the extra code required to do this to the user. I would want the LaTeX output, other than the omission, to appear the same as if the section were not omitted. Does anyone have an idea of how to do this elegantly? By the way I just discovered the SweaveListingUtils package by Peter Ruckdeschel (on CRAN), which produces beautifully printed R code in Sweave code chunks. I put some info about it at http://biostat.mc.vanderbilt.edu/SweaveTemplate which has our Sweave template for statistical reports. Thanks Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] large numbers of observations using ME() of spdep
Dear All, We aim to remove the spatial structure of our data using Moran Eigen Vectors and spdep package . Our data has 3694 samples and 13 variables. The computer stop working after almost 4 days of processing (we found it emitting a sharp sound and with all colors on the screen. No wories, it was restared without problem!). And we are left with nothing: no result file was produced since the calculations were interrumpted! Consequently, I am looking for a way to accelerate calculations with ME() of spdep and to save the results step by step (for each eigen value). I came accross several promissing ideas: 1)make a compiled program in C and call it in R with the command system(); 2)use muliR. However, I do not know how to use these tools. I do not understand exactely why the calculations are so slow and I do know know how to write a program in C... I am using Ubuntu 9.04 and R version 2.8.1 . The code in R is a fallows: taimin.xy = taimin[c(dy, dx)]; coordinates(taimin.xy) - ~dy+dx; #dy, dx, name of the respective coordinate columns coords-coordinates(taimin.xy); library(spdep); TaiminGabrielGraph-gabrielneigh(coords, nnmult = 12); tai.gab.nb-graph2nb(TaiminGabrielGraph,sym=TRUE); nbtaim_distsg - nbdists(tai.gab.nb, coords); nbtaim_simsg - lapply(nbtaim_distsg, function(x) (1-((x/(4*50))^2)) ); MEtaig.listw - nb2listw(tai.gab.nb, glist=nbtaim_simsg, style=B); sevmtaig - ME(Presabs ~Age+Curv+Zon2005+ZoneMeiji+Wi+Sol+Slope+Seadist+Elev+Basin,data=taimin, family=binomial,listw=MEtaig.listw) Any help is welcome! Thanks Lucero Mariani, Yokohama National University, Japan. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Fwd: correct line types in lattice legends
[Forgot to CC r-help] -- Forwarded message -- From: Deepayan Sarkar deepayan.sar...@gmail.com To: Gerrit Draisma g.drai...@erasmusmc.nl On 6/6/09, Gerrit Draisma g.drai...@erasmusmc.nl wrote: Hallo R-users, I do not understand how to specify the correct line and symbol types in the legends of a lattice xyplot. This is what I tried, but the line types and symbol in the graph are not seen in the legend. Any help is appreciated. Thanks, Gerrit. library(lattice) s-rep(1:3,len=10) x- 1:10 y- x+s+rnorm(10) d-data.frame(s,x,y) xyplot(y~x, groups=s,data=d, type=b, Instead of pch=1:3,lty=1:3, try par.settings = simpleTheme(pch=1:3,lty=1:3), auto.key=list(text=c(A,B,C),points=FALSE,lines=TRUE, type=b,lty=1:3,divide=1,pch=1:3,columns=3)) The lty and pch in auto.key are not used. Alternatively, you could use the classic approach using key, where you need specify all parameters again in the key. You are already pretty close to that: xyplot(y~x, groups=s,data=d, type=b, pch=1:3,lty=1:3, key=list(text=list(c(A,B,C)), lines=list(lty=1:3, pch=1:3, type=b), divide=1, columns=3)) You'll need to add matching colors as well. -Deepayan __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Journal Articles that Have Used R
Is there a way to get a reference list of journal articles that have used R? I am just looking for some examples of R graphs and presentation of results where R was used to generate the results. Thanks for any feedback and insights. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Journal Articles that Have Used R
Jason Rupert wrote: Is there a way to get a reference list of journal articles that have used R? I am just looking for some examples of R graphs and presentation of results where R was used to generate the results. Did you try Google Scholar: http://scholar.google.com.br/scholar?q=R%3A+A+Language+and+Environment+for+Statistical+Computing It has cited by links. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Journal Articles that Have Used R
Most of the papers in the Journal of Statistical Software use R so that would give you many examples of such papers. http://www.jstatsoft.org On Sat, Jun 6, 2009 at 2:03 PM, Jason Rupertjasonkrup...@yahoo.com wrote: Is there a way to get a reference list of journal articles that have used R? I am just looking for some examples of R graphs and presentation of results where R was used to generate the results. Thanks for any feedback and insights. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Journal Articles that Have Used R
On 06-Jun-09 18:34:21, Jakson Alves de Aquino wrote: Jason Rupert wrote: Is there a way to get a reference list of journal articles that have used R? I am just looking for some examples of R graphs and presentation of results where R was used to generate the results. Did you try Google Scholar: http://scholar.google.com.br/scholar?q=R%3A+A+Language+and+Environment+f or+Statistical+Computing It has cited by links. A very good suggestion! An even better oone [:)] is to take out the .br: http://scholar.google.com/scholar?q=R%3A+A+Language+and+Environment+ for+Statistical+Computing (158,000 hits of which, on briefly scanning through the first 40, about half seem to be hournal articles; draw you own conclusions). Ted. E-Mail: (Ted Harding) ted.hard...@manchester.ac.uk Fax-to-email: +44 (0)870 094 0861 Date: 06-Jun-09 Time: 19:50:57 -- 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] Truncated R output in Sweave
Frank E Harrell Jr wrote:
Dear Colleagues:
In producing a book or a handout I sometimes cut out a large part of
the printed output of an R function, substituting ... for that chunk.
Deleting non-essential output saves paper. It would be nice to have a
capability in Sweave to allow the user to specify a starting and an
ending regular expression that would identify consecutive lines of
output to replace with ..., without showing the extra code required to
do this to the user. I would want the LaTeX output, other than the
omission, to appear the same as if the section were not omitted. Does
anyone have an idea of how to do this elegantly?
Hello,
You could use the same trick that is sometimes used to embed lattice
calls into print calls (see the grid vignette for example)
\documentclass[a4paper]{article}
\begin{document}
aa,eval=FALSE,echo=T=
rnorm( 200 )
echo=F=
txt - capture.output( {
aa
} )
if( length(txt) 10 ){
txt - c( txt[1:10], ... )
}
cat( txt, sep = \n )
@
\end{document}
By the way I just discovered the SweaveListingUtils package by Peter
Ruckdeschel (on CRAN), which produces beautifully printed R code in
Sweave code chunks. I put some info about it at
http://biostat.mc.vanderbilt.edu/SweaveTemplate which has our Sweave
template for statistical reports.
You might also be interested by the driver that comes with the highlight
package (not yet on cran though, but the r-forge version is stable enough).
install.packages(highlight, repos=http://R-Forge.R-project.org;)
require( highlight )
Sweave( file, driver = HighlightWeaveLatex() )
*||*
Thanks
Frank
--
Romain Francois
Independent R Consultant
+33(0) 6 28 91 30 30
http://romainfrancois.blog.free.fr
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Re: [R] Truncated R output in Sweave
Romain Francois wrote:
Frank E Harrell Jr wrote:
Dear Colleagues:
In producing a book or a handout I sometimes cut out a large part of
the printed output of an R function, substituting ... for that chunk.
Deleting non-essential output saves paper. It would be nice to have a
capability in Sweave to allow the user to specify a starting and an
ending regular expression that would identify consecutive lines of
output to replace with ..., without showing the extra code required to
do this to the user. I would want the LaTeX output, other than the
omission, to appear the same as if the section were not omitted. Does
anyone have an idea of how to do this elegantly?
Hello,
You could use the same trick that is sometimes used to embed lattice
calls into print calls (see the grid vignette for example)
\documentclass[a4paper]{article}
\begin{document}
aa,eval=FALSE,echo=T=
rnorm( 200 )
echo=F=
txt - capture.output( {
aa
} )
if( length(txt) 10 ){
txt - c( txt[1:10], ... )
}
cat( txt, sep = \n )
@
\end{document}
Thank you Romain - I did not know of that construct.
By the way I just discovered the SweaveListingUtils package by Peter
Ruckdeschel (on CRAN), which produces beautifully printed R code in
Sweave code chunks. I put some info about it at
http://biostat.mc.vanderbilt.edu/SweaveTemplate which has our Sweave
template for statistical reports.
You might also be interested by the driver that comes with the highlight
package (not yet on cran though, but the r-forge version is stable enough).
install.packages(highlight, repos=http://R-Forge.R-project.org;)
require( highlight )
Sweave( file, driver = HighlightWeaveLatex() )
Interesting. What would be the corresponding batch file command to
achieve this? I like to run R CMD Sweave my.Rnw. And would you mind
giving a very brief comparison of the two highlighting approaches
regarding the LaTeX output?
Thanks!
Frank
*||*
Thanks
Frank
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
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Re: [R] Excel Export in a beauty way
Hi,
Here's a function to export dataframes to an excel-file with the RDCOMClient
package. It makes bold headers and fits the column widths automatically. If
more than one dataframe is provided to the function, the dataframes are
saved to seperate spreadheets within file.
export.xls - function (..., colnames = TRUE, rownames = FALSE) {
require(RDCOMClient, quietly = TRUE)
y - COMCreate(Excel.Application)
wbs - y$Workbooks()
wb -wbs$add()
shs - wb$Worksheets()
export - function(df, sheetname, sheetnr, colnames = colnames,
rownames = rownames) {
if (!is.data.frame(df)) {
df - as.data.frame(df)
if (ncol(df) == 1) names(df) - sheetname}
cl - sapply(df, function(x) class(x)[1])
dates - which(cl == 'Date')
for (i in dates) df[, i] - format(df[,i], '%Y.%m.%d')
datetimes - which(cl %in% c('POSIXt', 'POSIXct', 'POSIXlt'))
for (i in datetimes) df[, i] - format(df[,i], '%Y.%m.%d %H:%M')
numerics - cl == 'numeric'
for (i in which(!numerics)) df[, i] - as.character(df[, i])
nas - sapply(df, function(x) any(is.na(x)))
missings - which(!numerics nas)
for (i in missings) df[is.na(df[, i]), i] - ''
sh - shs$Item(sheetnr)
sh[['Name']] - sheetname
nr - nrow(df) + colnames
nc - ncol(df) + rownames
cn - dimnames(df)[[2]]
rn - dimnames(df)[[1]]
startstop - function(x) {
l - length(x)
stops - starts - rep(NA, l)
if (x[1] == TRUE) starts[1] - 1
for (i in seq_along(x)[-1]) {
if (x[i] == TRUE x[i-1] == FALSE) starts[i] - i
if (x[i] == FALSE x[i-1] == TRUE) stops[i] - i-1
}
if (x[l] == TRUE) stops[l] - l
rbind(starts = starts[!is.na(starts)], stops = stops[!is.na(stops)])
}
startrow - 1+colnames
startcol - 1+rownames
num - startstop(numerics)
num2 - num + rownames
for (i in seq_len(ncol(num))) {
x - sh$Range(sh$Cells(startrow,num2[1,i]), sh$Cells(nr, num2[2,i]))
x[['Value']] - asCOMArray(df[, num[1,i]:num[2,i]])
}
notnum - startstop(!numerics)
notnum2 - notnum + rownames
for (i in seq_len(ncol(notnum))) {
x - sh$Range(sh$Cells(startrow, notnum2[1, i]), sh$Cells(nr,
notnum2[2, i]))
x[['Value']] - asCOMArray(df[,notnum[1,i]:notnum[2,i]])
}
missings - which(numerics nas) + rownames
for (i in missings) {
na - startstop(is.na(df[,i-rownames])) + colnames
for (k in seq_len(ncol(na))) {
x - sh$Range(sh$Cells(na[1, k] , i), sh$Cells(na[2, k], i))
x[['Value']] - ''
}
}
for (i in (1+rownames):nc) {
x - sh$Cells(1,i)
if (colnames) {
x[['Value']]-cn[i-rownames]
Font - x$Font()
Font[['Bold']] - TRUE
}
EntCol -x$EntireColumn()
if (i %in% dates) EntCol[['NumberFormat']] - '.MM.TT'
if (i %in% datetimes) EntCol[['NumberFormat']] - '.MM.TT hh:mm'
EntCol$AutoFit()
}
if (rownames) {
x - sh$Range(sh$Cells(startrow,1),sh$Cells(nr,1))
x[['Value']] - asCOMArray(rn)
EntCol -x$EntireColumn()
Font - x$Font()
Font[['Bold']] - TRUE
}
}
dfn - deparse(substitute(list(...)))
df - list(...)
dfn - gsub('^list\\(', '', dfn)
dfn - gsub('\\)$', '', dfn)
dfn - gsub('[ ]', '', dfn)
dfn - strsplit(dfn, split = ',')[[1]]
dfn - make.names(dfn, unique = TRUE)
if (length(df) 2) for (i in seq_len(length(df) - 2)) shs$Add()
for (i in seq_len(length(df))) export(df[[i]], sheetname = dfn[i],
sheetnr = i, colnames = colnames, rownames = rownames)
y[[Visible]] - TRUE
}
#example:
export.xls(iris, mtcars, trees)
If you are willing to do the work RDCOMClient or rcom packages
give you complete control. See example here:
https://stat.ethz.ch/pipermail/r-help/2005-July/075877.html
This assumes your platform is Windows and that you have R and Excel
on the same machine so that R can control Excel.
On Wed, Jun 3, 2009 at 8:29 AM, koj jens.koch at gmx.li wrote:
Hallo all,
I`ve read a lot of things in this forum about an Excel export via R. It is
no problem to export my data frames via write.table or write.xls (xls or
csv), but some things are not very convenient for me: I always have to
adjust the column with to see all the numbers or the text and there is no
frame between the cells. And I missing the possibility to make some headers
bold or coloured. I`ve see the output from a Perl-Export and this is a very
nice thing, so my question: Is there really no possibility to produce a xls
or a xlsx - File with this nice features.
Thank you very much in advance,
Jens.
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Re: [R] large numbers of observations using ME() of spdep
Le dimanche 07 juin 2009 à 02:50 +0900, lucero mariani a écrit : Dear All, We aim to remove the spatial structure of our data using Moran Eigen Vectors and spdep package . Our data has 3694 samples and 13 variables. The computer stop working after almost 4 days of processing (we found it emitting a sharp sound and with all colors on the screen. No wories, it was restared without problem!). Cool ! Farm it out to a night club (and get a real computer with the proceedings). Sorry. Couldn't resist ! And twice sorry to be unable to help with your *real* problem... Emmanuel Charpentier And we are left with nothing: no result file was produced since the calculations were interrumpted! Consequently, I am looking for a way to accelerate calculations with ME() of spdep and to save the results step by step (for each eigen value). I came accross several promissing ideas: 1)make a compiled program in C and call it in R with the command system(); 2)use muliR. However, I do not know how to use these tools. I do not understand exactely why the calculations are so slow and I do know know how to write a program in C... I am using Ubuntu 9.04 and R version 2.8.1 . The code in R is a fallows: taimin.xy = taimin[c(dy, dx)]; coordinates(taimin.xy) - ~dy+dx; #dy, dx, name of the respective coordinate columns coords-coordinates(taimin.xy); library(spdep); TaiminGabrielGraph-gabrielneigh(coords, nnmult = 12); tai.gab.nb-graph2nb(TaiminGabrielGraph,sym=TRUE); nbtaim_distsg - nbdists(tai.gab.nb, coords); nbtaim_simsg - lapply(nbtaim_distsg, function(x) (1-((x/(4*50))^2)) ); MEtaig.listw - nb2listw(tai.gab.nb, glist=nbtaim_simsg, style=B); sevmtaig - ME(Presabs ~Age+Curv+Zon2005+ZoneMeiji+Wi+Sol+Slope+Seadist+Elev+Basin,data=taimin, family=binomial,listw=MEtaig.listw) Any help is welcome! Thanks Lucero Mariani, Yokohama National University, Japan. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] A very frustrating read.table error message
On Sat, Jun 6, 2009 at 5:02 PM, Adam D. I. Kramera...@ilovebacon.org wrote: Dear Colleagues, Occasionally I deal with computer-generated (i.e., websurvey) data files that haven't quite worked correctly. When I try to read the data into R, I get something like this: Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 26 did not have 648 elements ...is there any way to get R to tell me how many elements line 26 *did* have? That information would take this error message from frustrating to useful. :) ?count.fields 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] A very frustrating read.table error message
On 06/06/09 15:02, Adam D. I. Kramer wrote: Dear Colleagues, Occasionally I deal with computer-generated (i.e., websurvey) data files that haven't quite worked correctly. When I try to read the data into R, I get something like this: Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : line 26 did not have 648 elements ...is there any way to get R to tell me how many elements line 26 *did* have? That information would take this error message from frustrating to useful. :) count.fields() More generally, you might be interested in our approach to integrating data collection on the Web, using JavaScript, with R. See http://promberger.info/ (which says private but Google finds it pretty fast) http://finzi.psych.upenn.edu/~baron/ex/template.htm http://finzi.psych.upenn.edu/~baron/ex/template.html http://finzi.psych.upenn.edu/~baron/R/template.R http://finzi.psych.upenn.edu/~baron/R/TRIM.R The last makes a nice data file out of the JavaScript output (which is designed more to be readable at the moment than to be useful). It uses count.fields as a check. None of this stuff is ready for prime time. In my case, there is a 14-year history, with various baggage left over from earlier travels. Jon -- Jonathan Baron, Professor of Psychology, University of Pennsylvania Home page: http://www.sas.upenn.edu/~baron __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Journal Articles that Have Used R
Jason Rupert wrote: Is there a way to get a reference list of journal articles that have used R? Ooodles ... as others have pointed out. Another source is the ISI web of science citation index, which reportedly shows up over 5000 citations of R LANG ENV STAT COMP or LANG ENV STAT COMP (I can't easily check from outside the Uni). I am just looking for some examples of R graphs and presentation of results where R was used to generate the results. Thanks for any feedback and insights. A recent and relatively high-profile paper is this one http://www3.interscience.wiley.com/cgi-bin/fulltext/122313738/HTMLSTART (This paper hit the mainstream press because of the connection to H1N1 Swine flu) -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] EBImage not loading
Hello all I've just spent a few joyless hours trying to get EBImage to install in R. I'm running Ubuntu (Hardy Heron), fully updated (including R and Imagemagick). EBImage installation seems to work, but when I 'library(EBImage)' I get the following: - - - - Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/home/qilin/R/i486-pc-linux- gnu-library/2.6/EBImage/libs/EBImage.so': /usr/lib/libgomp.so.1: cannot allocate memory in static TLS block Error: package/namespace load failed for 'EBImage' - - - - Which is meaningless to me. Any help would be enormously appreciated, thanks. Quin * Quin Wills * * DPhil candidate * * * * Department of Statistics University of Oxford 1 South Parks road Oxford OX1 3TG +44 (0)1865 285 394 * [[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] p-values from VGAM function vglm
On Jun 6, 2009, at 4:13 AM, Emmanuel Charpentier wrote: Dear David, Le vendredi 05 juin 2009 à 16:18 -0400, David Winsemius a écrit : On Jun 5, 2009, at 3:15 PM, Steven Matthew Anderson wrote: Anyone know how to get p-values for the t-values from the coefficients produced in vglm? Attached is the code and output — see comment added to output to show where I need p-values + print(paste(** Using VGAM function gamma2 **)) + modl2- vglm(MidPoint~Count,gamma2,data=modl.subset,trace=TRUE,crit=c) + print(coef(modl2,matrix=TRUE)) + print(summary(modl2)) [1] ** Using VGAM function gamma2 ** VGLMlinear loop 1 : coefficients = 0.408464609241, 3.255887520104, -0.000220585671 VGLMlinear loop 2 : coefficients = 2.34723239e-01, 1.28969691e+00, -4.52393778e-05 VGLMlinear loop 3 : coefficients = 2.19500481e-01, 1.92534895e+00, -3.02160949e-05 VGLMlinear loop 4 : coefficients = 2.19383151e-01, 2.26845910e+00, -3.00838664e-05 VGLMlinear loop 5 : coefficients = 2.19383045e-01, 2.34645688e+00, -3.00836087e-05 VGLMlinear loop 6 : coefficients = 2.19383045e-01, 2.34977070e+00, -3.00836082e-05 VGLMlinear loop 7 : coefficients = 2.19383045e-01, 2.34977637e+00, -3.00836082e-05 VGLMlinear loop 8 : coefficients = 2.19383045e-01, 2.34977637e+00, -3.00836082e-05 log(mu) log(shape) (Intercept) 2.193830e-01 2.349776 Count -3.008361e-05 0.00 Call: vglm(formula = MidPoint ~ Count, family = gamma2, data = modl.subset, trace = TRUE, crit = c) Pearson Residuals: Min 1Q Median 3Q Max log(mu)-1.7037 -0.82997 0.072275 0.78520 1.72834 log(shape) -2.5152 -0.32448 0.254698 0.58772 0.70678 # NEED P-VALUES HERE # Perhaps: dt(summary( modl2 )@coef3[ , 3], 1) ??? 1) dt() is the density. didn't you mean pt() ? Quite right. 2) I'd rather quote 2*min(pt(), 1-pt()) (bilateral tests, y'know...) 3) The real hitch here is : what are the right DoF ? I do not think there is an easy answer to *this* one... Which may be the reason that the summary method was not designed that way? Emmanuel Charpentier Coefficients: Value Std. Error t value (Intercept):1 2.1938e-01 5.2679e-02 4.16455 (Intercept):2 2.3498e+00 1.7541e-01 13.39574 Count -3.0084e-05 8.9484e-05 -0.33619 Number of linear predictors: 2 Names of linear predictors: log(mu), log(shape) Dispersion Parameter for gamma2 family: 1 Log-likelihood: -26.39268 on 123 degrees of freedom Number of Iterations: 8 Steven Matthew Anderson Anderson Research, LLC Statistical Programming and Analysis SAS (R) Certified Professional adastr...@mac.com 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] No --no-latex?
10:08 Looks like it was an oversight. I'll fix it. 10:35 Looks like the corresponding else if clause got omitted in tools:::.install_packages() and before that in share/R/RINSTALL. 12:34 Brian Ripley got there first, so it's fixed now in R-devel and R-patched. I thank you all, and am amazed at the speed of response. 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.
[R] Survreg function for loglogistic hazard estimation
I am trying to use R to do loglogistic hazard estimation. My plan is to
generate a loglogistic hazard sample data and then use survreg to estimate
it. If everything is correct, survreg should return the parameters I have
used to generate the sample data.
I have written the following code to do a time invariant hazard estimation.
The output of summary(modloglog) shows the factor loading of dfico is -0.002
instead of 0.005. Also I can not find the survreg's output of alpha and
beta of loglogistic regression. Any comments? Thanks a lot,
Jiakai Chen
Code:
BEGIN==
# A time invariant loglogistic estimation
library(survival)
# Clear the workspace
rm(list = ls(all = TRUE))
# Totally 100K samples which may die during 100 periods
timeline = 100
samplesize = 10
dfico - rnorm(samplesize, mean = 0, sd = 25)
dficoeff - 0.005
# Baseline loglogistic hazard function stored in bhaz
a- 20
b - 4
time - 1:timeline
bhaz - ((b/a) * (time /a) ^ (b-1))/(1+(time/a)^b)
# Event time stored in endtime. Baseline hazard function is controlled by
# dfico value with factor loading dficoeff
endtime - numeric(samplesize)
for ( i in 1:samplesize) {
rnos - runif(timeline)
endtime[i] - which(rnos = bhaz * exp(dfico[i]*dficoeff))[1]
}
# Construct data frame
raw - data.frame(end = endtime, status = 1, fico_demean = dfico)
# Adding censorship
for( i in 1:samplesize) {
if(is.na(raw$end[i])) {raw$status[i] - 0}
}
for( i in 1:samplesize) {
if(is.na(raw$end[i])) {raw$end[i] - timeline }
}
# Output the factory
factory - factor(raw$end)
plot(factory)
# Use survreg to estimate the coefficents of loglogistic distribution
modloglog - survreg(Surv(end, status) ~ fico_demean, data = raw, model =
TRUE, dist = 'loglogistic')
summary(modloglog)
END==
--
View this message in context:
http://www.nabble.com/Survreg-function-for-loglogistic-hazard-estimation-tp23907598p23907598.html
Sent from the R help mailing list archive at Nabble.com.
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Re: [R] RPostgreSQL segfault with LEFT JOIN
Dylan Beaudette wrote:
After some further investigation, I see that the query works fine if I *do not
use column aliases* :
Looks like *any* query using a column alias will segfault unless the
alias exactly matches the column name (in which case why bother). The
code starting at line 423 in RS-PostgreSQL.c looks like:
8---
if(PQftablecol(my_result,j) !=0) {
/* Code to find whether a row can be nullable or not */
sprintf(buff,
select attnotnull from pg_attribute
where attrelid=%d and attname='%s',
PQftable(my_result,j),(char*)PQfname(my_result,j));
res = PQexec (conn, buff );
if(strcmp(PQgetvalue(res,0,0),f)==0) {
8---
The crash occurs at line 430 (the strcmp()) because PQgetvalue(res,0,0)
returns NULL.
PQfname() will return the column alias, not the actual column name,
therefore the PQexec() here returns no results. At the very least,
PQresultStatus(res) or perhaps PQntuples(res) should be used immediately
after PQexec() to ensure you have a good result before trying to use it
in strcmp().
In any case, I think the simple fix (untested) is something like:
8---
if(PQftablecol(my_result,j) !=0) {
/* Code to find whether a row can be nullable or not */
sprintf(buff,
select attnotnull from pg_attribute
where attrelid=%d and attnum=%d,
PQftable(my_result,j),PQftablecol(my_result,j));
8---
i.e. use the table column number and pg_attribute.attnum field.
This is beyond what is appropriate for r-help, so I suggest any further
discussion go off-list (or is there somewhere more appropriate, e.g.
r-devel?)
HTH,
Joe
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