Re: [R] Install package of "BRugs"?

2010-03-30 Thread Uwe Ligges
On 31.03.2010 08:36, Dieter Menne wrote: Hua Li wrote: I'm trying to install the package "BRugs" and could not find it on the install package list. Then I tried the suggestion to run the following command in R install.packages("BRugs") Use R2WinBUGS instead http://cran.at.r-project.or

Re: [R] Install package of "BRugs"?

2010-03-30 Thread Uwe Ligges
On 30.03.2010 22:01, David Winsemius wrote: On Mar 30, 2010, at 3:42 PM, Hua Li wrote: Hi All, I'm trying to install the package "BRugs" and could not find it on the install package list. Then I tried the suggestion to run the following command in R install.packages("BRugs") but get the f

Re: [R] Install package of "BRugs"?

2010-03-30 Thread Dieter Menne
Hua Li wrote: > > I'm trying to install the package "BRugs" and could not find it on the > install package list. Then I tried the suggestion to run the following > command in R > > install.packages("BRugs") > > Use R2WinBUGS instead http://cran.at.r-project.org/web/packages/R2WinBUGS/index.

Re: [R] nlsList{nlme} control of min and max parameter bounds?

2010-03-30 Thread Dieter Menne
Steve Oswald wrote: > > I'm analysing growth rates using a gompertz (logistic) curve and am > attempting > to fit parameters for all of my study birds using nlsList. > > I've been looking for an option in nlsList to set min and max limits for > parameter values during estimation, although I hav

[R] Predict function in ARIMA/GARCH- Real time forecastinng

2010-03-30 Thread RAGHAVENDRA PRASAD
Hi, I m working on time series forecasting.I was checking ARIMA and GARCH model for forecasting.Is there any possibility that we can include test data as input for predict function.I am working on real time forecasting where i would be getting real time feeds using which i need forecas

Re: [R] creating a variable using concatenation

2010-03-30 Thread David Winsemius
On Mar 30, 2010, at 11:15 PM, Steve Chen wrote: You can try this: library(tutoR) That's an interesting set of goals: "Package to mask common functions so that inputs in error are explained and able to be corrected, prior to execution. 'assist' offers step-by-step assistance to correctly

Re: [R] GUI /IDE

2010-03-30 Thread Philippe Grosjean
Not really *named* regions, but an easy way to run portions of code quickly in SciViews-K (http://www.sciviews.org/SciViews-K): * R -> Run marked block (or Ctrl+Shift+M) runs code between two bookmarks, * R -> Run function (or Ctrl+Shift+F) runs the code of the whole current function (you may pr

Re: [R] How to calculate fold change and its confidence interval

2010-03-30 Thread Steve Lianoglou
Hi, Firstly, you should bring your bioinformatics related questions over to the bioconductor mailing list. Please sign up and post that portion there, see: http://www.bioconductor.org/docs/mailList.html But, getting to your last question: >> fc.perSample <- cbind(tb[,1]/tb[,3], tb[,2]/tb[,4]) >

[R] (no subject)

2010-03-30 Thread Roslina Zakaria
Hi r-users,   I would like to display my legend with fill box and line symbol.  The first color will be in the box and the second colour will just be a line.   legend("topright", c("observed","gamma sum fit"), col= c("greenyellow","red"),pch=c(15, NA),lty = c(0,1),lwd=2)   Is it possible?  

[R] How to calculate fold change and its confidence interval

2010-03-30 Thread xyang2
Dear all, I am reading the book "statistic analysis of gene expression microarray data" by Terry Speed . On page16-17, there is an example that I can not repeat. The content can be found using below linkage: http://books.google.com/books?id=MBzcRjez9ccC&pg=PA16&lpg=PA16&dq=confidence+interval+

Re: [R] creating a variable using concatenation

2010-03-30 Thread Steve Chen
You can try this: library(tutoR) plot(eval.string(toplot)) Steve Chen On 2010/3/31 上午 09:24, zubin wrote: > A general problem i run into, i know there must be a simple solution. > > I like to create a variable by appending a 1 for example, (i need to > loop later on from 1 to X, thus the reaso

[R] nlsList{nlme} control of min and max parameter bounds?

2010-03-30 Thread Steve Oswald
Hi All I'm analysing growth rates using a gompertz (logistic) curve and am attempting to fit parameters for all of my study birds using nlsList. I've been looking for an option in nlsList to set min and max limits for parameter values during estimation, although I have failed to find any u

Re: [R] Choosing and preserving a random duplicate

2010-03-30 Thread Jorge Ivan Velez
Hi Jeff, Here is a suggestion using aggregate(): # some data set.seed(123) genes <- sample(c("UNC93A", "CLEC2B", "KCTD12", "CDKN3", "DAB2"), 20, replace = TRUE) pfake <- runif(20, 0, 10e-21) gd10df <- data.frame(genes, pfake) gd10df gd10df[order(gd10df$genes),] # selecting one p-value ra

[R] nlsList{nlme} control of min and max parameter bounds?

2010-03-30 Thread Steve Oswald
Hi All I'm analysing growth rates using a gompertz (logistic) curve and am attempting to fit parameters for all of my study birds using nlsList. I've been looking for an option in nlsList to set min and max limits for parameter values during estimation, although I have failed to find any unde

Re: [R] creating a variable using concatenation

2010-03-30 Thread zubin
Perfect - this works!! -zubin Peter Alspach wrote: > Tena koe Zubin > > Would this work for your application: > > toPlot <- paste("X",i,sep="") > plot(x[, toPlot]) > > HTH > > Peter Alspach > > >> -Original Message- >> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- >

Re: [R] creating a variable using concatenation

2010-03-30 Thread David Winsemius
On Mar 30, 2010, at 9:24 PM, zubin wrote: A general problem i run into, i know there must be a simple solution. I like to create a variable by appending a 1 for example, (i need to loop later on from 1 to X, thus the reason for this). So i assign the variable vplot with this value, however

Re: [R] Value-at-Risk Portfolio(both equity and option)

2010-03-30 Thread Cedrick Johnson
It would help if I included the link: http://n4.nabble.com/VaR-for-path-dependent-option-portfolio-td1676787.html -c On 3/30/10, Cedrick Johnson wrote: > Check out this discussion on r-sig-finance regarding VaR for options. > Quite informative and should be a good starting point. > > -c > > On

Re: [R] creating a variable using concatenation

2010-03-30 Thread Peter Alspach
Tena koe Zubin Would this work for your application: toPlot <- paste("X",i,sep="") plot(x[, toPlot]) HTH Peter Alspach > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- > project.org] On Behalf Of zubin > Sent: Wednesday, 31 March 2010 2:25 p.m. >

Re: [R] Value-at-Risk Portfolio(both equity and option)

2010-03-30 Thread Cedrick Johnson
Check out this discussion on r-sig-finance regarding VaR for options. Quite informative and should be a good starting point. -c On 3/30/10, zhang wrote: > > Hello All, > > I am working on the risk measures for a portfolio, which contain both equity > futures, equity options and currency options.

[R] creating a variable using concatenation

2010-03-30 Thread zubin
A general problem i run into, i know there must be a simple solution. I like to create a variable by appending a 1 for example, (i need to loop later on from 1 to X, thus the reason for this). So i assign the variable vplot with this value, however it has quotes and when i use it in a barplot,

Re: [R] question on creating zoo object from indexed time series: re-arranges dates

2010-03-30 Thread Christina Karamperidou
great, I used the global option, and set the cut.off to 10, so now it understands all years from 1913 to 2005 without a problem and, as per your instructions in other threads, I got all the daily, monthly, yearly averages in the proper way. thank you so much! Christina K. ck4...@gmail.com P Ple

Re: [R] question on creating zoo object from indexed time series: re-arranges dates

2010-03-30 Thread Gabor Grothendieck
Here is one more solution. chron has a global option, chron.year.expand, that can be set to a function that will do the 2 year to 4 year translation. We can use it to change the cut.off to 20 (instead of 30). (Its important to set the option after the library(chron) call since that call resets t

Re: [R] Choosing and preserving a random duplicate

2010-03-30 Thread Peter Alspach
Tena koe Jeff If I understand you correctly, one approach would be to randomly order your dataframe, remove the duplicates, and then reorder the resulting dataframe back into the original order: g10dfA <- g10df[sample(nrow(g10df)),] g10dfA <- g10dfA[!duplicated(g10dfA$GENE),] g10dfA <- g10dfA[ord

Re: [R] about the possible errors in Rgraphviz Package

2010-03-30 Thread HU,ZHENGJUN
Hi Martin, I am 100% sure that I set my 'PATH' environment variable correctly because all other packages can loaded correctly as well as because R can be run correctly under both MS DOS and MS Windows XP. Also, I can create some simple R packages correctly. Thanks. Howard On Tue Mar 30

Re: [R] about the possible errors in Rgraphviz Package

2010-03-30 Thread HU,ZHENGJUN
Hi All, Sorry that it is unclear in the last email (see below), and I should say that: I got the following error messages when I loaded the package through library("Rgraphviz") or library(Rgraphviz): "Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library

[R] Choosing and preserving a random duplicate

2010-03-30 Thread jeff.m.ewers
Dear R-Helpers, I have a dataframe (g10df) formatted like this: GENE PVAL 1 KCTD12 4.06904e-22 2 UNC93A 9.91852e-22 3 CDKN3 1.24695e-21 4 CLEC2B 4.71759e-21 5 DAB2 1.12062e-20 The rows are ranked in ascending order by PVAL, and I need to end up with t

[R] "is" and the story of a typo

2010-03-30 Thread Jim Lemon
Hi all, The gurus may pour scorn on me for not knowing this, but I happened to mistype "if" as "is" in the heat of debugging a function. As I scanned the debugged function with some satisfaction, I noticed the error. How could this have worked? I assume that "is" is a generic function that cal

Re: [R] S3 vs S4

2010-03-30 Thread Steve Lianoglou
Hi, On Tue, Mar 30, 2010 at 5:57 AM, Ivan Calandra wrote: > Dear R users, > > I'm still a beginner and I'm wondering whether S3 or S4 methods really > differ for my use. > > I understand more or less the distinction between the 2 classes from the > documentation I've read but the big question is:

Re: [R] jpeg() saving blank files?

2010-03-30 Thread Sarah Berke
Phil and Jim-- Ah, thank you so much! I had read all the help files on jpeg() and dev.off(), but I had not caught on to the fact that image.plot() comes *between* jpeg() and dev.off(), not before them! (though I guess it's supposed to be obvious from the example code). Again, thanks! --Sarah

Re: [R] use logical in cor.test

2010-03-30 Thread pgseye
Many thanks Peter, This did indeed work. Regards, Paul -- View this message in context: http://n4.nabble.com/use-logical-in-cor-test-tp1744701p1746008.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing li

Re: [R] question on creating zoo object from indexed time series: re-arranges dates

2010-03-30 Thread Christina Karamperidou
thanks a million for solving this problem for me! I really appreciate it. best, Christina K. ck4...@gmail.com P Please consider the environment - Do you really need to print this email? On Mar 30, 2010, at 5:44 PM, Gabor Grothendieck wrote: > The problem is that chron uses 30 as the cutoff yea

Re: [R] Using the get() function on an object within a list

2010-03-30 Thread David Winsemius
On Mar 30, 2010, at 5:23 PM, klc wrote: Hi- I am trying use the get function to return the value of an object within a list. As an abbreviated example: "original" represents a list of several objects, one of which is "a. 1". original<-vector('list',5) names(original) <- c("a.1","a.

[R] predict.kohonen for SOM returns NA?

2010-03-30 Thread Tidal Wave
All, The kohonen predict function is returning NA for SOM predictions regardless of data used... even the package example for a SOM using wine data is returning NA's Does anyone have a working example SOM. Also, what is the purpose of trainY, what would be the dependent data for an unsupervised SO

Re: [R] question on creating zoo object from indexed time series: re-arranges dates

2010-03-30 Thread Gabor Grothendieck
The problem is that chron uses 30 as the cutoff year for two digit years. If the year is prior to 30 it adds 2000 to the two digit year to get the 4 digit year and if the 2 digit year is 30 or more it adds 1900 to the two digit year to get the 4 digit year. In the line marked # we convert

Re: [R] GUI /IDE

2010-03-30 Thread Peter
Emacs allows you run regions. Not sure about naming them Peter ManInMoon wrote: Does anyone know of a gui for R that has "regions" i.e areas of code in a script that can be named and hopefully run as a section? @region Init library(whatever) myprint<-function(...){print(...)} @endregion

Re: [R] Multivariate hypergeometric distribution version of phyper()

2010-03-30 Thread Charles C. Berry
On Tue, 30 Mar 2010, Karl Brand wrote: Peter, Chuck, Big thanks for your input. I will be following up each and every of your suggestions on the morrow. Something of note though that you may have further thoughts on- phyper() was *specifically* recommneded by BioC responders for my applicati

[R] Using the get() function on an object within a list

2010-03-30 Thread klc
Hi- I am trying use the get function to return the value of an object within a list. As an abbreviated example: "original" represents a list of several objects, one of which is "a.1". original<-vector('list',5) names(original) <- c("a.1","a.2","a.3","b.1","b.2") original$a.1 <- c(4,3)

Re: [R] jpeg() saving blank files?

2010-03-30 Thread jim holtman
?dev.off On Tue, Mar 30, 2010 at 4:53 PM, Sarah Berke wrote: > Hi, > > I am having trouble saving graphics from R. jpeg() saves a file with > the correct name to the correct directory, but it consists of a blank > (white) jpeg with the specified dimensions--the image itself is not > being saved

Re: [R] question on creating zoo object from indexed time series: re-arranges dates

2010-03-30 Thread Christina Karamperidou
true, sorry, I posted a few minutes ago the code for going from 1929 to 1930, and it is not working on my computer. so, when I use the full record, z goes from 1930 to 2005, and then jumps to what it perceives to be 2013 and takes it all the way to 2029 (when in reality it is 1913 to 1929) Line

Re: [R] about the possible errors in Rgraphviz Package

2010-03-30 Thread Gabor Grothendieck
I have also installed numerous different versions of Rgraphviz/graphviz in an attempt to get it to work and so far have been unsuccessful in getting it to install as well. Some time ago I used it successfully but have had no luck with recent versions. Its too bad there are so many installation p

Re: [R] question on creating zoo object from indexed time series: re-arranges dates

2010-03-30 Thread Gabor Grothendieck
What is the problem? The code in your post seems to work fine: > Lines <- "Date Time Value + 12/31/99 22:00:00 1.8 + 12/31/99 23:00:00 1.9 + 01/01/00 00:00:00 1.8 + 01/01/00 01:00:00 1.7 + 01/01/00 02:00:00 1.6 + 01/01/00 03:00:00 1.5 + 01/01/00 04:00:00 1.4 + 01/01/00 05:00:00

[R] update.packages() and install.packages() does not work more because of "Error in read.dcf"

2010-03-30 Thread R P Herrold
On Tue, 30 Mar 2010, Prof Brian Ripley wrote: A hint: I have seen this exact error message with a build configured to use the system's zlib 1.2.4 (which has been out for about 2 weeks), and this incompatibility is noted in the current R 2.11.0 alpha's manuals. We do recommend *not* using the

Re: [R] about the possible errors in Rgraphviz Package

2010-03-30 Thread Martin Morgan
On 03/30/2010 01:13 PM, HU,ZHENGJUN wrote: > Hi Martin, > > I uninstalled graphviz-2.26.3.msi and then installed > graphviz-2.20.3.1.msi. Then installed the > Rgraphviz package again. As expected, I got the same error messages as > before: > > "Error in inDL(x, as.logical(local), as.logical(now)

Re: [R] about the possible errors in Rgraphviz Package

2010-03-30 Thread Prof Brian Ripley
Let me add that not only do you need to match binary versions, even if you install from the sources, Rgraphviz does not work with graphviz-2.26.3.msi which is built with an incompatible compiler. You need to follow the instructions exactly: they are in the Rgraphviz source package. Idealy Rg

[R] GEE for a timeseries of count (one cluster)

2010-03-30 Thread miriza
Hi! I was wondering if there were any packages that would allow me to fit a GEE to a single timeseries of counts so that I could account for autocorrelation in the data. I tried gee, geepack and yags packages, but I do not get standard errors for the parameters when using a single cluster. Any

Re: [R] question on creating zoo object from indexed time series: re-arranges dates

2010-03-30 Thread Christina Karamperidou
I was wrong before not to check the turn of 1929 to 1930. So, here is what happens: Lines <- "Date Time Value 149014 12/31/29 21:00:00 1.4 149015 12/31/29 22:00:00 1.4 149016 12/31/29 23:00:00 1.5 149017 01/01/30 00:00:00 1.6 149018 01/01/30 01:00:00 1.7 149019 01/01/30 02:00:00

Re: [R] about the possible errors in Rgraphviz Package

2010-03-30 Thread HU,ZHENGJUN
Hi All, Before installing the Rgraphviz package successfully [e.g., source("http://bioconductor.org/biocLite.R";); biocLite("Rgraphviz")], (1) I downloaded graphviz-2.20.3.1.msi (also tried graphviz-2.26.3.msi) for MS Windows (XP) and installed it successfully and (2) I also installed the pa

[R] jpeg() saving blank files?

2010-03-30 Thread Sarah Berke
Hi, I am having trouble saving graphics from R. jpeg() saves a file with the correct name to the correct directory, but it consists of a blank (white) jpeg with the specified dimensions--the image itself is not being saved. My code is jpeg(filename="myfile.jpg", height = 2.5, wi

Re: [R] about the possible errors in Rgraphviz Package

2010-03-30 Thread HU,ZHENGJUN
Hi Martin, I uninstalled graphviz-2.26.3.msi and then installed graphviz-2.20.3.1.msi. Then installed the Rgraphviz package again. As expected, I got the same error messages as before: "Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/PROGRA~1/R

[R] GUI /IDE

2010-03-30 Thread ManInMoon
Does anyone know of a gui for R that has "regions" i.e areas of code in a script that can be named and hopefully run as a section? @region Init library(whatever) myprint<-function(...){print(...)} @endregion -- View this message in context: http://n4.nabble.com/GUI-IDE-tp1745858p1745858.ht

Re: [R] Confusing concept of vector and matrix in R

2010-03-30 Thread lith
> Reframe the problem. Rethink why you need to keep dimensions. I never ever > had to use drop. The problem is that the type of the return value changes if you happen to forget to use drop = FALSE, which can easily turn into a nightmare: m <- matrix(1:20, ncol=4) for (i in seq(3, 1, -1)) { p

Re: [R] update.packages() and install.packages() does not work more because of "Error in read.dcf"

2010-03-30 Thread Prof Brian Ripley
A hint: I have seen this exact error message with a build configured to use the system's zlib 1.2.4 (which has been out for about 2 weeks), and this incompatibility is noted in the current R 2.11.0 alpha's manuals. We do recommend *not* using the system zlib, but if you do insist on doing so

Re: [R] question on creating zoo object from indexed time series: re-arranges dates

2010-03-30 Thread Christina Karamperidou
Truly sorry about before. So, it works perfectly fine when I do it at the turn of the century, but still when I try it on my full record, I get the same problem. Maybe it is reading in the table in a wrong way. I just read it in as DF <- read.table("myfile.dat", header = TRUE, as.is = TRUE) m

Re: [R] Error when checking a package.

2010-03-30 Thread Jim Lemon
On 03/30/2010 09:53 PM, Duncan Murdoch wrote: ... That test has been around at least since 2003: it applies in package testing, not to people typing in the console. Duncan Murdoch It just takes longer for us old codgers to make changes in our habits. It's called the Seven Year Switch. Jim

Re: [R] about the possible errors in Rgraphviz Package

2010-03-30 Thread Duncan Murdoch
On 30/03/2010 3:58 PM, HU,ZHENGJUN wrote: Hi Martin, Thank you for the reply and help. I don't think that this is the version problem of Graphviz. All the R packages are installed under 'C:/PROGRA~1/R/R-2.10.1/library' instead of 'C:/PROGRA~1/R/R-210~1.1/library', whereas the error messages

Re: [R] about the possible errors in Rgraphviz Package

2010-03-30 Thread HU,ZHENGJUN
Hi Martin, Thank you for the reply and help. I don't think that this is the version problem of Graphviz. All the R packages are installed under 'C:/PROGRA~1/R/R-2.10.1/library' instead of 'C:/PROGRA~1/R/R-210~1.1/library', whereas the error messages are: "Error in inDL(x, as.logical(local),

Re: [R] Multivariate hypergeometric distribution version of phyper()

2010-03-30 Thread Karl Brand
Peter, Chuck, Big thanks for your input. I will be following up each and every of your suggestions on the morrow. Something of note though that you may have further thoughts on- phyper() was *specifically* recommneded by BioC responders for my application in spite of the fact i originally tho

Re: [R] Install package of "BRugs"?

2010-03-30 Thread David Winsemius
On Mar 30, 2010, at 3:42 PM, Hua Li wrote: Hi All, I'm trying to install the package "BRugs" and could not find it on the install package list. Then I tried the suggestion to run the following command in R install.packages("BRugs") but get the following error message: Loading required

Re: [R] Problem comparing hazard ratios

2010-03-30 Thread David Winsemius
On Mar 30, 2010, at 3:45 PM, Michal Figurski wrote: Dear R-Helpers, I am a novice in survival analysis. I have the following code: for (i in 3:12) print(coxph(Surv(time, status)~a[,i], data=a)) I used it to fit the Cox Proportional Hazard models separately for every available parameter (col

Re: [R] Problem comparing hazard ratios

2010-03-30 Thread Frank E Harrell Jr
Michal Figurski wrote: Dear R-Helpers, I am a novice in survival analysis. I have the following code: for (i in 3:12) print(coxph(Surv(time, status)~a[,i], data=a)) I used it to fit the Cox Proportional Hazard models separately for every available parameter (columns 3:12) in my data set - with

[R] Fw: Install package of "BRugs"?

2010-03-30 Thread Hua Li
Sorry, I think I miscopied the error messages. Here they are. install.packages("BRugs") Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.8 Warning message: package ‘BRugs’ is not available > require(BRugs) Loading required package: BRugs W

Re: [R] question on creating zoo object from indexed time series: re-arranges dates

2010-03-30 Thread Gabor Grothendieck
Not for me. Please provide your data and code in reproducible form as per last line of every r-help message and the posting guide. > Lines <- "Date Time Value + 01/01/13 00:00:00 1.6 + 01/01/13 01:00:00 1.6 + 01/01/13 02:00:00 1.6 + 01/01/13 03:00:00 1.6 + 01/01/13 04:00:00 1.6 + 01

Re: [R] Confusing concept of vector and matrix in R

2010-03-30 Thread Rolf Turner
On 30/03/2010, at 10:04 PM, Barry Rowlingson wrote: > On Tue, Mar 30, 2010 at 2:42 AM, Rolf Turner wrote: > >> Well then, why don't you go away and design and build your own statistics and >> data analysis language/package to replace R? You can then make whatever >> design decisions you like,

[R] Problem comparing hazard ratios

2010-03-30 Thread Michal Figurski
Dear R-Helpers, I am a novice in survival analysis. I have the following code: for (i in 3:12) print(coxph(Surv(time, status)~a[,i], data=a)) I used it to fit the Cox Proportional Hazard models separately for every available parameter (columns 3:12) in my data set - with intention to compare t

[R] Install package of "BRugs"?

2010-03-30 Thread Hua Li
Hi All, I'm trying to install the package "BRugs" and could not find it on the install package list. Then I tried the suggestion to run the following command in R install.packages("BRugs") but get the following error message: Loading required package: BRugs Warning message: In library(package,

Re: [R] list index rules evaluation behavior

2010-03-30 Thread David Winsemius
On Mar 30, 2010, at 1:41 PM, Dgnn wrote: Sorry for not supplying some example code for the above example. Here's an example list 'a' with histogram elements A, B, and C which are also lists. That is not code. That is output. It is not clear how "a" was created a $A $breaks If you

[R] question on creating zoo object from indexed time series: re-arranges dates

2010-03-30 Thread Christina Karamperidou
Dear all, I have a time series of daily measurements that starts like this: KWhourly[1:10,] Date Time Value 01/01/13 00:00:00 1.6 01/01/13 01:00:00 1.6 01/01/13 02:00:00 1.6 01/01/13 03:00:00 1.6 01/01/13 04:00:00 1.6 01/01/13 05:00:00 1.6 01/01/13 06:00:00 1.6 01/01/13 0

[R] Inflection point on a curve

2010-03-30 Thread FMH
Dear All, I have been trying to find an inflection point from a nonparametric model, for instance on  a series of Economics, Financial, Environmental data, which was fitted via sm.regression package, but have difficulty to find the derivative of the model. The following are the data and the cod

Re: [R] about the possible errors in Rgraphviz Package

2010-03-30 Thread Martin Morgan
On 03/30/2010 10:24 AM, HU,ZHENGJUN wrote: > Hi Duncan, > >> (They are pretty hard to find, but I think you can find them on the >> Bioconductor site.) It is > not enough to install the Rgraphviz >> package, you also need to install Graphviz. > > Yes I did. Before installing the Rgraphviz packa

Re: [R] Error "grid must have equal distances in each direction"

2010-03-30 Thread maddy
Hello All, Can anyone please help me on this error? Error in FUN(X[[1L]], ...) : different grid distances detected, but the grid must have equal distances in each direction -- try gridtriple=TRUE that avoids numerical errors. The program that I am trying to run posted in the previous post of

[R] Lord-, Weir-, and Median test

2010-03-30 Thread Burny
Dear R community, I am looking for small n (<20) alternatives for t-, Welch- and U-tests, i.e. the Lord, Weir, and Median 2-sample tests. Does anybody have an idea (R package, commands?) where to find these tests? Thanks inadvance, Burny -- View this message in context: http://n4.nabble.com/Lo

Re: [R] list index rules evaluation behavior

2010-03-30 Thread Dgnn
Sorry for not supplying some example code for the above example. Here's an example list 'a' with histogram elements A, B, and C which are also lists. >a $A $breaks [1] -80 -70 -60 -50 -40 -30 -20 -10 0 10 20 30 40 50 60 $counts [1] 1 0 0 2 29 120 301 433 421 265 93 43 9

Re: [R] about the possible errors in Rgraphviz Package

2010-03-30 Thread HU,ZHENGJUN
Hi Duncan, (They are pretty hard to find, but I think you can find them on the Bioconductor site.) It is > not enough to install the Rgraphviz package, you also need to install Graphviz. Yes I did. Before installing the Rgraphviz package successfully, (1) I downloaded graphviz-2.26.3.msi f

[R] list index rules evaluation behavior

2010-03-30 Thread sharkbrainpdx
Hi David, Thanks for taking the time to respond to my post. Sorry for not putting an example in the original, which I've replied to with some code and a more explicit question. Jason __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/li

Re: [R] dataframe in loop

2010-03-30 Thread Rob Forler
Wait so basically you want to merge the two data sets on some key value? On Tue, Mar 30, 2010 at 12:30 PM, Muting Zhang wrote: > hello all: > > I would like to thank those who helped me out of the string problem..but > now I got another problem. > I used R to query from SQL and got a list of cr

Re: [R] library(): load library from a specified location

2010-03-30 Thread Barry Rowlingson
On Tue, Mar 30, 2010 at 7:58 PM, Rolf Turner wrote: > But ***please*** say ``load *package*'', not ``load library''.  The > *location* (collection of packages) from which you wish to load the > given package is the ``library''. Anyone vote for deprecating the library() function and renaming it

Re: [R] library(): load library from a specified location

2010-03-30 Thread Rolf Turner
On 31/03/2010, at 1:10 AM, Jannis wrote: > Sorry folks! > > My way worked already! I was just too blind to realize. > Treat this post as solved. Anybody trying to achieve the same as me is > adviced to try the way I described in my earlier post! > > And thanks a lot for the advice I already rec

Re: [R] for loop; lm() regressions; list of vectors

2010-03-30 Thread David Winsemius
On Mar 30, 2010, at 12:42 PM, Driss Agramelal wrote: ## Hello everyone, ## ## I am trying to execute 150 times a lm regression using the 'for' loop, with 150 vectors for y, ## ## and always the same vector for x. ## ## I have an object with 150 elements named "a", ## ## and a vector of

Re: [R] open help files in browser

2010-03-30 Thread Duncan Murdoch
On 30/03/2010 2:19 PM, Martin Batholdy wrote: Hi, I am working on Mac OS X 10.6. R-version: 2.9.0. > the Mac GUI will intercept the call and do HTML display in the internal browser With internal browser you mean a built-in browser of R? Is there also a way to invoke Safari to display the hel

Re: [R] open help files in browser

2010-03-30 Thread Martin Batholdy
Hi, I am working on Mac OS X 10.6. R-version: 2.9.0. > the Mac GUI will intercept the call and do HTML display in the internal > browser With internal browser you mean a built-in browser of R? Is there also a way to invoke Safari to display the help-file (with the common help-functions)? W

Re: [R] open help files in browser

2010-03-30 Thread Duncan Murdoch
On 30/03/2010 1:46 PM, Martin Batholdy wrote: Hi, Is there a way to open help files in the default web browser instead of a new R-window when I use the help-functions (like ?, help.search() etc.)? You don't say what platform you're using. Generally the way to do this is to run options(help_t

Re: [R] update.packages() and install.packages() does not work more because of "Error in read.dcf"

2010-03-30 Thread Uwe Ligges
On 30.03.2010 16:55, Juergen Rose wrote: Hi, on all my systems update.packages() and install.packages() fails now. I get the following message: r...@orca:/root(28)# R R version 2.10.1 (2009-12-14) Copyright (C) 2009 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free sof

Re: [R] MySQL and RODBC - limitations

2010-03-30 Thread Uwe Ligges
On 30.03.2010 19:43, Duncan Murdoch wrote: On 30/03/2010 1:35 PM, jorgusch wrote: I found the solution. The problem was indeed R. Their is a simple way to solve the problem, but it just needs a bit more time. If you download large integers from a database, convert it "on the fly" with SELECT

Re: [R] open help files in browser

2010-03-30 Thread Henrik Bengtsson
If you're not already using R v2.10.0 or newer, try that first. My $.02 /Henrik On Tue, Mar 30, 2010 at 7:46 PM, Martin Batholdy wrote: > Hi, > > > Is there a way to open help files in the default web browser instead of a new > R-window > when I use the help-functions (like ?, help.search() et

Re: [R] Code is too slow: mean-centering variables in a data frame bysubgroup

2010-03-30 Thread Bert Gunter
?scale Bert Gunter Genentech Nonclinical Biostatistics -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Dimitri Liakhovitski Sent: Tuesday, March 30, 2010 8:05 AM To: r-help Subject: [R] Code is too slow: mean-centering variables

Re: [R] Error "singular gradient matrix at initial parameterestimates" in nls

2010-03-30 Thread Bert Gunter
Your model is almost certainly over-parameterized (given the data that you have to fit it), and the asymptotic correlation matrix of the parameters that you should get from the solutions that converged will probably have some large off diagonal elements. In other words, your model is essentially no

[R] open help files in browser

2010-03-30 Thread Martin Batholdy
Hi, Is there a way to open help files in the default web browser instead of a new R-window when I use the help-functions (like ?, help.search() etc.)? thanks! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE

Re: [R] MySQL and RODBC - limitations

2010-03-30 Thread Duncan Murdoch
On 30/03/2010 1:35 PM, jorgusch wrote: I found the solution. The problem was indeed R. Their is a simple way to solve the problem, but it just needs a bit more time. If you download large integers from a database, convert it "on the fly" with SELECT CONVERT(yourcolumn,char) That is it. Thi

[R] dataframe in loop

2010-03-30 Thread Muting Zhang
hello all: I would like to thank those who helped me out of the string problem..but now I got another problem. I used R to query from SQL and got a list of crsp_fundno of G-style mutual funds which is still alive. I use the following codes and got what I want: library(RODBC) channel<-odbcConn

Re: [R] MySQL and RODBC - limitations

2010-03-30 Thread jorgusch
I found the solution. The problem was indeed R. Their is a simple way to solve the problem, but it just needs a bit more time. If you download large integers from a database, convert it "on the fly" with SELECT CONVERT(yourcolumn,char) That is it. This is nor problem, as long you do NO compar

Re: [R] about the possible errors in Rgraphviz Package

2010-03-30 Thread Duncan Murdoch
On 30/03/2010 1:24 PM, HU,ZHENGJUN wrote: Hi Duncan, > (They are pretty hard to find, but I think you can find them on > the Bioconductor site.) It is > not enough to install the > Rgraphviz package, you also need to install Graphviz. Yes I did. Before installing the Rgraphviz package suc

Re: [R] Multivariate hypergeometric distribution version of phyper()

2010-03-30 Thread Peter Ehlers
Karl, I strongly support Chuck's recommendations. If you do still want to compute such probabilities 'by hand', you could consider the lchoose() function which does work for your example. -Peter Ehlers On 2010-03-30 9:55, Charles C. Berry wrote: On Tue, 30 Mar 2010, Karl Brand wrote: Dear R

[R] for loop; lm() regressions; list of vectors

2010-03-30 Thread Driss Agramelal
## Hello everyone, ## ## I am trying to execute 150 times a lm regression using the 'for' loop, with 150 vectors for y, ## ## and always the same vector for x. ## ## I have an object with 150 elements named "a", ## ## and a vector of 60 values named "b". ## ## Each element in "a" has 60 value

Re: [R] weighted.median function from package R.basic

2010-03-30 Thread Brian S Cade
While perhaps not the solution you were looking for, you might consider estimating weighted medians with linear quantile regression (just specify an intercept for single sample analysis, tau=0.50, and weights = your weights) in the quantreg package. Quantile regression does not require sorting

Re: [R] From THE R BOOK -> Warning: In eval(expr, envir, enclos) : non-integer #successes in a binomial glm!

2010-03-30 Thread Robert A LaBudde
At 12:08 PM 3/30/2010, David Winsemius wrote: I don't understand this perspective. You bought Crowley's book so he is in some minor sense in debt to you. Why should you think it is more appropriate to send your message out to thousands of readers of r- help around the world (some of whom have

Re: [R] large dataset

2010-03-30 Thread Thomas Lumley
KeithC, If you're arguing that there should be more documentation and examples explaining how to use very large data sets with R, then I agree. Feel free to write some. I've been giving tutorials on this for years now. I wrote the first netCDF interface package for R because I needed to use

Re: [R] From THE R BOOK -> Warning: In eval(expr, envir, enclos) : non-integer #successes in a binomial glm!

2010-03-30 Thread Graham Smith
Corrado > I am afraid not the paragraph's title is a bit of a give away: > > Proportion Data and Binomial Errors > > The sentence reads: > " are dealt with by using a generalised linear model with a binomial > error structure". > > with the example: > > glm(y~x,family=binomial) > > You

Re: [R] From THE R BOOK -> Warning: In eval(expr, envir, enclos) : non-integer #successes in a binomial glm!

2010-03-30 Thread Berwin A Turlach
G'day all, On Tue, 30 Mar 2010 16:19:46 +0100 Corrado wrote: > David Winsemius wrote: > > A) It is not an error, only a warning. Wouldn't it seem reasonable > > to issue such a warning if you have data that violates the > > distributional assumptions? > I am not questioning the approach. I am on

Re: [R] list index rules evaluation behavior

2010-03-30 Thread David Winsemius
On Mar 30, 2010, at 11:47 AM, Dgnn wrote: I have what may be a simple/foolish question, but I've done the due diligence and looked through pages of posts here as well as several of the PDFs on the CRAN site, but haven't been able find what I'm after. I am working with a list of say 3 his

Re: [R] about the possible errors in Rgraphviz Package

2010-03-30 Thread Duncan Murdoch
On 30/03/2010 10:44 AM, HU,ZHENGJUN wrote: Hi All, I tried to install the package of Rgraphviz in the following two ways successfully: source("http://bioconductor.org/biocLite.R";) biocLite("Rgraphviz") install.packages(pkgs="C:/Progra~1/R/lib_download/Rgraphviz_1.24.0.zip", lib="C:/Progr

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