Re: [R] installing the package Rcplex

2012-02-22 Thread zheng wei
I suspect one possible reason is that while I unzip the file .tar.gz, it destroys the structure between files as the manual indicated. But there seems no unix-like environment. I tried the cmd command, but it does not recognize tar command. Section 6.3 of the manual said that install.packages ca

[R] creating a loop for multiple file

2012-02-22 Thread Kawthar Alajmi
Hi all, need help very urgently I did stepwise logistic regression for 35 covariates and added one SNP out of (50) to get the best model for each model As my professor asked me using this command, outfiles <- paste(colnames(snps), ".txt", sep="") # list of output files for the best models f

Re: [R] How do I save the current session?

2012-02-22 Thread Petr PIKAL
Hi > > [R] How do I save the current session? > > savehistory() gives me the option of saving the executable lines only. I'd > like to save everything. Using save is not enough? Regards Petr >[[alternative HTML version deleted]] > > __ > R-hel

Re: [R] why is generating the same graph???

2012-02-22 Thread Petr PIKAL
Hi > > > Hi, > why my script iss always generating the same graph?when I change the > parameters and the name of text file? > library(MASS) > dados<-read.table("inverno.txt",header=FALSE) > vento50<-fitdistr(dados[[1]],densfun="weibull") > png(filename="invernoRG.png",width=800,height=600) > his

Re: [R] inserting a dataframe into the table

2012-02-22 Thread arunkumar1111
Yes the table already exist and it contains data ant to insert two data frame into that separately - Thanks in Advance Arun -- View this message in context: http://r.789695.n4.nabble.com/inserting-a-dataframe-into-the-table-tp4409756p4412667.html Sent from the R help mailing list arch

Re: [R] Good and modern Kernel Regression package in R with auto-bandwidth?

2012-02-22 Thread Michael
Is "np" an okay package to use? I am worried about the "multi-start" thing... and also it's very slow... On Wed, Feb 22, 2012 at 8:35 PM, Liaw, Andy wrote: > Bert's question aside (I was going to ask about laundry, but that's much > harder than taxes...), my understanding of the situation is th

Re: [R] Good and modern Kernel Regression package in R with auto-bandwidth?

2012-02-22 Thread Michael
Imeant its very slow when I use "cv.aic"... On Wed, Feb 22, 2012 at 11:24 PM, Michael wrote: > Is "np" an okay package to use? > > I am worried about the "multi-start" thing... and also it's very slow... > > > On Wed, Feb 22, 2012 at 8:35 PM, Liaw, Andy wrote: > >> Bert's question aside (I wa

Re: [R] Lattice and horizontally stacked density plots

2012-02-22 Thread Manish Nag
> With lattice alone you can easily get all curves on the same level: > densityplot(~ val | factor(id2), groups=factor(id1),data=a_df,pch='|') > I just tried the method above. Unfortunately it just makes plots with different colored lines that overlap one another. Can anyone point me to an example

Re: [R] Median In Survival

2012-02-22 Thread Marc Schwartz
On Feb 22, 2012, at 7:47 PM, David Winsemius wrote: > > On Feb 22, 2012, at 6:59 PM, niloo javan wrote: > >> hi >> I have a problem with Median in Survival. >> when I use >> S1=survfit(Surv(Time,Status)) >> the result shows the median but I cannot use it as numeric! >> S1$median in Null > > Th

Re: [R] convert zoo object to "standard" R object so I can plot and output to csv file

2012-02-22 Thread Gabor Grothendieck
On Wed, Feb 22, 2012 at 9:54 PM, Henry wrote: > Gabor, > Thanks very much. > I have all the zoo functions to get 1 minute aggregation and 15 min. means > working and now able to write out to a file/etc. > > One question on the 15 min. mean results. > > m1 <- times("00:01:00") > g <- seq(trunc(star

Re: [R] Lattice and horizontally stacked density plots

2012-02-22 Thread ilai
The plot you referred to depends on packages flowViz and flowCore from R-bioconductor. With lattice alone you can easily get all curves on the same level: densityplot(~ val | factor(id2), groups=factor(id1),data=a_df,pch='|') But if that doesn't do it for you, you could write your own panel functi

[R] Improving performance of split-apply problem

2012-02-22 Thread Martin
Hello, I'm very new to R so my apologies if I'm making an obvious mistake. I have a data frame with ~170k rows and 14 numeric variables. The first 2 of those variables (let's call them group1 and group2) are used to define groups: each unique pair of (group1,group2) is a group. There are roughly 5

Re: [R] convert zoo object to "standard" R object so I can plot and output to csv file

2012-02-22 Thread Henry
Gabor, Thanks very much. I have all the zoo functions to get 1 minute aggregation and 15 min. means working and now able to write out to a file/etc. One question on the 15 min. mean results. m1 <- times("00:01:00") g <- seq(trunc(start(z),m1),end(z),by = m1) z1<-na.approx(z,xout = g) m15 <- times

Re: [R] Good and modern Kernel Regression package in R with auto-bandwidth?

2012-02-22 Thread Liaw, Andy
Bert's question aside (I was going to ask about laundry, but that's much harder than taxes...), my understanding of the situation is that "optimal" is in the eye of the beholder. There were at least two schools of thought on which is the better way of automatically selecting bandwidth, using pl

Re: [R] sqlite create new unique id

2012-02-22 Thread Jadhav, Alok
Thanks for the information. In my case I know that the rows will never be deleted so logically I could use max(rowid), but I am going to stick to my original solution of using a table to get the max id. But there is no in built table to maintain this, I will have to create a new table and maintain

Re: [R] why is generating the same graph???

2012-02-22 Thread David Winsemius
On Feb 22, 2012, at 7:08 PM, Vanúcia Schumacher wrote: Hi, why my script iss always generating the same graph?when I change the parameters and the name of text file? library(MASS) dados<-read.table("inverno.txt",header=FALSE) vento50<-fitdistr(dados[[1]],densfun="weibull") png(filename="inv

Re: [R] Median In Survival

2012-02-22 Thread David Winsemius
On Feb 22, 2012, at 6:59 PM, niloo javan wrote: hi I have a problem with Median in Survival. when I use S1=survfit(Surv(Time,Status)) the result shows the median but I cannot use it as numeric! S1$median in Null That does not look like a formula. Furthermore I do not think there is an elem

[R] how to make gwaa.data

2012-02-22 Thread Kyoto 812
How to make the gwaa.data file I have the genotype data in plink format As binary and as text file Can anyone assist me ? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLE

[R] Issue with RODBC

2012-02-22 Thread Jadhav, Alok
Hi team, My RODBC connection times out after certain period (while creating a new channel). Is there a way to set a different value for timeout property? I looked into RODBC document and I didn't find any such property. I am trying to connect to a Sybase database. Maybe I can use something els

[R] best R command to assess SNP-covariates logistic regression

2012-02-22 Thread Kyoto 812
Good morning In case control study I do have 35 covariates (personal and environmental details about the patients) and genotype data for 50 SNPs I need to apply all the covariates and one SNP at a time in the logistic regression model How can i do this in R ? I have the Covariate file and

[R] why is generating the same graph???

2012-02-22 Thread Vanúcia Schumacher
Hi, why my script iss always generating the same graph?when I change the parameters and the name of text file? library(MASS) dados<-read.table("inverno.txt",header=FALSE) vento50<-fitdistr(dados[[1]],densfun="weibull") png(filename="invernoRG.png",width=800,height=600) hist(dados[[1]], seq(0, 18,

[R] Median In Survival

2012-02-22 Thread niloo javan
hi I have a problem with  Median in Survival. when I use S1=survfit(Surv(Time,Status)) the result shows the median but I cannot use it as numeric! S1$median in Null   Could u pleas help me. Many Many Tank You. Niloofar. [[alternative HTML version deleted]]

[R] How can I save plot()/points() using SHP files into KML format?

2012-02-22 Thread gztourek
Hi, I am new to R and am a very basic user. I'm importing SHP files, adding plots of random locations within my polygon (these files have GPS data), and then want to save these plots (intact with added points) as KML files to look at in GoogleEarth (or possibly as SHP files which I can then conve

[R] Using R to read Nortek Aquadopp Profiler

2012-02-22 Thread Vinny Moriarty
Hello, I have current data from a nortek ADP, which is basically current speed and direction data in a 3 dimensional X Y Z format http://www.nortekusa.com/usa/products/current-profilers/aquadopp-profiler-1 The instrument logs data in a complex way and I was wondering if anyone has had any exp

Re: [R] how to merge commands

2012-02-22 Thread MacQueen, Don
Are you absolutely certain that the data must be stored in Excel? In the long run I believe you will find it easier if the data is stored in an external database, or some other data repository that does not require you to read so many separate files. Probably the best you can hope for as it is no

Re: [R] R package built with Fortran code

2012-02-22 Thread MacQueen, Don
As far as I know, you must convert your main program into a subroutine. In my experience, this consist mostly if not entirely of converting user input from prompts to subroutine arguments. -Don -- Don MacQueen Lawrence Livermore National Laboratory 7000 East Ave., L-627 Livermore, CA 94550 925

[R] Lattice and horizontally stacked density plots

2012-02-22 Thread Manish Nag
Hello, I am try to make a density plot where plots are stacked like the one found here: http://dsarkar.fhcrc.org/lattice/book/images/Figure_14_03_stdBW.png I am facing problems, however. Using the code example below, I'd like to generate a separate panel for each val of id2. Within each panel, I

[R] LSA package: problem with textmatrix()

2012-02-22 Thread Ashton, Triss
I have a problem with the textmatrix() function of the LSA package whenever I specify 'removeNumbers=TRUE'. The data for the function are stored in a directory LSAwork which consists of a series of files that houses the text in column form. As long as removeNumbers = FALSE or it is not present

Re: [R] Repeated cross-validation for a lm object

2012-02-22 Thread samuel-rosa
Dear Max Thank you for your attention. The train function in the caret package realy does what I need. Best regards, - Bc.Sc.Agri. Alessandro Samuel-Rosa Postgraduate Program in Soil Science Federal University of Santa Maria Av. Roraima, nº 1000, Bairro Camobi, CEP 97105-970 Santa Maria, Rio

Re: [R] Good and modern Kernel Regression package in R with auto-bandwidth?

2012-02-22 Thread Bert Gunter
Would you like it to do your your taxes for you too? :-) Bert Sent from my iPhone -- please excuse typos. On Feb 22, 2012, at 11:46 AM, Michael wrote: > Hi all, > > I am looking for a good and modern Kernel Regression package in R, which > has the following features: > > 1) It has cross-vali

Re: [R] tapply for enormous (>2^31 row) matrices

2012-02-22 Thread ilai
On Tue, Feb 21, 2012 at 4:04 PM, Matthew Keller wrote: > X <- read.big.matrix("file.loc.X",sep=" ",type="double") > hap.indices <- bigsplit(X,1:2) #this runs for too long to be useful on > these matrices > #I was then going to use foreach loop to sum across the splits > identified by bigsplit Ho

[R] Writting to global variable in using doSNOW on multiple cores?

2012-02-22 Thread Michael
Hi all, Is there a problem when accessing/writing to global variable in using doSNOW package on multiple cores? In the below program, each of the MyCalculations(ii) writes to the ii-th column of the matrix "globalVariable"... Do you think the result will be correct? Will there be hidden catches?

[R] xtable prcomp

2012-02-22 Thread Riccardo Romoli
Hi, I need to export to LaTex the summary of a PCA. So: myPCA <- prcomp(myDF) mySummary <- summary(myPCA) # print(xtable(mySummary)) How can I export to LaTeX not all the summary but only the first nPCs?? Best Riccardo __ R-help@r-project.org mailing

Re: [R] Multiple lines for each record: how do I handle that

2012-02-22 Thread Luca Meyer
Hi Jorge, The method you suggest is indeed working fine on the small sample data set. When I apply to a larger dataset (714 rows by 160 columns) it transforms some variables from "factor" to "list", how can I change it back to their original class in an automatic way? Thanks, Luca Il giorno 2

[R] Generate a Weibull regression data

2012-02-22 Thread FU-WEN LIANG
Hi all, I'm trying to generate a Weibull distribution including four covariates in the model. Here is the code I used: # Generate survival time T = rweibull(200, shape=1.3, scale=0.004*exp(-(-2.5*b1+2.5*b2+0.9*x1-1.3*x2)/1.3)) C = rweibull(n, shape=1.5, scale=0.008) #censoring time time = pmin

Re: [R] rank with uniform count for each rank

2012-02-22 Thread Ben quant
Thank you everyone! We already use the Hmisc package so I'll likely use cut2. Ben On Wed, Feb 22, 2012 at 2:22 PM, David Winsemius wrote: > > On Feb 22, 2012, at 4:01 PM, Ben quant wrote: > > Hello, >> >> What is the best way to get ranks for a vector of values, limit the range >> of rank value

Re: [R] rank with uniform count for each rank

2012-02-22 Thread David Winsemius
On Feb 22, 2012, at 4:01 PM, Ben quant wrote: Hello, What is the best way to get ranks for a vector of values, limit the range of rank values and create equal count in each group? I call this uniform ranking...uniform count/number in each group. Here is an example using three groups: Sa

Re: [R] rank with uniform count for each rank

2012-02-22 Thread Sarah Goslee
Hi, On Wed, Feb 22, 2012 at 4:01 PM, Ben quant wrote: > Hello, > > What is the best way to get ranks for a vector of values, limit the range > of rank values and create equal count in each group? I call this uniform > ranking...uniform count/number in each group. > > Here is an example using thre

[R] rank with uniform count for each rank

2012-02-22 Thread Ben quant
Hello, What is the best way to get ranks for a vector of values, limit the range of rank values and create equal count in each group? I call this uniform ranking...uniform count/number in each group. Here is an example using three groups: Say I have values: x = c(3, 2, -3, 1, 0, 5, 10, 30, -1, 4

Re: [R] installing the package Rcplex

2012-02-22 Thread zheng wei
Based on my understanding of the manual, I moved upziped the file and put the folder of Rcplex under the directory of c:/temp Then I use cmd under windows to go to the director of C:\Program Files\R\R-2.13.0\bin, where my R is installed and typed R CMD INSTALL "c:/temp/Rcplex" I got the error of c

[R] How do I save the current session?

2012-02-22 Thread Ajay Askoolum
savehistory() gives me the option of saving the executable lines only. I'd like to save everything. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

Re: [R] Multiple lines for each record: how do I handle that

2012-02-22 Thread Jorge I Velez
Hi Luca, Thank you for the example. Here is one way of doing what you want (of course there are many of them!): # data d0 <- structure(list(id = c(1, 1, 2, 2, 2, 3), v1 = c(NA, 1, NA, 1, NA, 1), v2 = structure(c(3L, 1L, 2L, 1L, 1L, 3L), .Label = c("", "no", "yes"), class = "factor"), v3 = struct

Re: [R] Multiple lines for each record: how do I handle that

2012-02-22 Thread Luca Meyer
Sure, I am sorry I have not done that in the first place. The datasets I have looks like: id <- c(1,1,2,2,2,3) v1 <- c(NA,1,NA,1,NA,1) v2 <- as.character(c("yes","","no","","","yes")) v3 <- as.factor(c(NA,1,NA,NA,3,2)) d0 <- data.frame(id,v1,v2,v3) d0 What I would need is to derive a dataset tha

[R] Good and modern Kernel Regression package in R with auto-bandwidth?

2012-02-22 Thread Michael
Hi all, I am looking for a good and modern Kernel Regression package in R, which has the following features: 1) It has cross-validation 2) It can automatically choose the "optimal" bandwidth 3) It doesn't have random effect - i.e. if I run the function at different times on the same data-set, the

Re: [R] Installing rgl

2012-02-22 Thread Milan Bouchet-Valat
Le mercredi 22 février 2012 à 14:00 -0500, R. Michael Weylandt a écrit : > I haven't been following this thread so I may be off base, but are you > sure you don't mean plot(ca(table))? > > ca is a function from the ca package -- you want to plot the output of > the function, not the function itsel

Re: [R] removing particular row from matrix

2012-02-22 Thread Sarah Goslee
Is this not what you want: a[a[,2] != -999.99,] I didn't see the earlier message so I'm not sure how rowSums was involved. Sarah On Wed, Feb 22, 2012 at 1:50 PM, uday wrote: > Hi Petr, > Thanks for reply > > sorry for late message there was typo error the both values are -999.99 >  a[rowSums(a

Re: [R] Multiple lines for each record: how do I handle that

2012-02-22 Thread Sarah Goslee
If you provide a small reproducible example of your data format and expected output, I'm sure someone here can offer a useful solution. Without knowing what your data look like, not so easy. Sarah On Wed, Feb 22, 2012 at 2:22 PM, Luca Meyer wrote: > Hi Folks, > > I just discovered that my datas

[R] Multiple lines for each record: how do I handle that

2012-02-22 Thread Luca Meyer
Hi Folks, I just discovered that my dataset (coming from QuestionPro platform) has got multiple lines for each respondent id, but what I would really need is a "regular" data matrix where each respondent's data is shown on a single line. Does anyone has already develop a procedure that automati

Re: [R] removing particular row from matrix

2012-02-22 Thread R. Michael Weylandt
all you need is rowSums(a == -999.99) -- this will check for -999.99 in *any* spot. If you do only want to check a certain column/row, add drop=FALSE to your subscripting. Michael On Wed, Feb 22, 2012 at 1:50 PM, uday wrote: > Hi Petr, > Thanks for reply > > sorry for late message there was typo

Re: [R] line width in legend of interaction.plot

2012-02-22 Thread ilai
On Wed, Feb 22, 2012 at 11:37 AM, Matthias Gondan wrote: > Dear R developers, > > The following command produces an interaction plot with lwd=2. > > interaction.plot(c(1, 2, 1, 2), c(1, 1, 2, 2), 1:4, lwd=2) > > In the legend, however, lwd seems to be 1, which does not seem > to be intended behavi

[R] Gamm and post comparison

2012-02-22 Thread RHam
My data set consist of number of calls (lcin) across Day. I am looking for activity differences between three features (4 sites per feature). I am also looking for peaks of activity across time (Day). I am using a gamm since I believe these are nonlinear trends with nested data. gammdata<-gamm(lci

Re: [R] removing particular row from matrix

2012-02-22 Thread uday
Hi Petr, Thanks for reply sorry for late message there was typo error the both values are -999.99 a[rowSums(a == -999.99) == 0, ], this solution works only if we have to remove certain value from matrix. but if a<-matrix(c(1,2,3,5,-999.99,5,-999.99,6,1,5,9,1),nrow=4) a [,1][,2]

Re: [R] Repeated cross-validation for a lm object

2012-02-22 Thread samuel-rosa
Dear Max and Greg Thank you for your help. Unfortunately I was not able in getting what I need using the functions you suggested. I believe it can be a result of my inexperience with the packages caret and rms. Therefore, I provide more information about my problem and wish you can again provide m

Re: [R] Installing rgl

2012-02-22 Thread ilai
On Wed, Feb 22, 2012 at 3:23 AM, aoife wrote: > Hey guys,I'm working with R version 2.14.1 (2011-12-22) on a unix machine You may be missing some openGL libraries (mesa ? ) On Ubuntu, this solved my problem of installing rgl: sudo apt-get build-dep r-cran-rgl Can't vouch for any future complicat

Re: [R] Installing rgl

2012-02-22 Thread R. Michael Weylandt
I haven't been following this thread so I may be off base, but are you sure you don't mean plot(ca(table))? ca is a function from the ca package -- you want to plot the output of the function, not the function itself. Sorry if this is unhelpful, Michael On Wed, Feb 22, 2012 at 10:02 AM, aoife

[R] line width in legend of interaction.plot

2012-02-22 Thread Matthias Gondan
Dear R developers, The following command produces an interaction plot with lwd=2. interaction.plot(c(1, 2, 1, 2), c(1, 1, 2, 2), 1:4, lwd=2) In the legend, however, lwd seems to be 1, which does not seem to be intended behavior. Probably the lwd is not correctly forwarded to legend: from the i

Re: [R] Several densityplots in single figure

2012-02-22 Thread ilai
On Wed, Feb 22, 2012 at 8:49 AM, David Winsemius wrote: > > After going back and constructing a proper dataset, you should be passing > 'groups' into the panel function and picking it up inside panel.abline. Close, but unfortunately things get more complicated when using groups in densityplot. A

Re: [R] Huge difference btw system time and elapsed time

2012-02-22 Thread Libo Sun
Thanks. I also did some parallel computing. Here are some time I spent by using 'snowfall' package on intel centrino 2 laptop (2 cores) on windows 7. user system elapsed 0.240.05 2442.77 Libo On Wed, Feb 22, 2012 at 12:53 AM, Martin Maechler < maech...@stat.math.ethz.ch> wrote: > >>

[R] Optim() maximum number of parameters

2012-02-22 Thread Rainer Haidinger
Hello, I'm trying to maximize a likelihood function for a HMM with the optim() function using the Nelder-Mead Method. The LLF has 20 Parameters which are to be estimated. We found out that R changes some variables but not all of them, especially the last 2 parameters aren't changed. I already

Re: [R] counts

2012-02-22 Thread Rui Barradas
Hello, Just look at your second 'apply': the 'function(x)' is not using the 'x' (!) Solution: function(x) hist(x, breaks=0:nrow(test), plot=FALSE)$counts) Note that instead of 'nrow' you could also use 'length(x)'. Hope this helps, Rui Barradas -- View this message in context: http://r.789

Re: [R] barplot with both color and shading

2012-02-22 Thread Shi, Tao
Thank you both, Michael and Jim, for the answers! - Original Message - > From: Michael Bibo > To: r-h...@stat.math.ethz.ch > Cc: > Sent: Wednesday, February 22, 2012 12:46 AM > Subject: Re: [R] barplot with both color and shading > > Shi, Tao yahoo.com> writes: > >> >> Hi list, >

Re: [R] how to make hash?& append element, if i want following condition

2012-02-22 Thread slre
sagarnikam123 wrote > > i did it, but using hash package ,i got error like > >>hash1 <- new.env() >> hash1$A <- c(1.2, 3.4, 4.5) >> hash1$A > [1] 1.2 3.4 4.5 > >> h<-hash(keys=c("A","B"),values=c(hash1$A,hash1$A) ) > Error in .set(h, ...) : Keys of length 2 do not match values of length 6 >

Re: [R] Installing rgl

2012-02-22 Thread aoife
Thank you for the reply, my problem is that i don't understand the error that plot(ca) is giving me: > plot(ca) Error in matrix(as.matrix(obj), nrow = I, ncol = J) : non-numeric matrix extent so just to put this in context: my workscreen looks like this: > table A B C G1 1 34.0

Re: [R] how to make hash?& append element, if i want following condition

2012-02-22 Thread sagarnikam123
i did it, but using hash package ,i got error like >hash1 <- new.env() > hash1$A <- c(1.2, 3.4, 4.5) > hash1$A [1] 1.2 3.4 4.5 > h<-hash(keys=c("A","B"),values=c(hash1$A,hash1$A) ) Error in .set(h, ...) : Keys of length 2 do not match values of length 6 how should i proceed -- View this me

Re: [R] Using earth.dist function

2012-02-22 Thread cmartin
Thanks so much for the good advice. I was able to get the function to work. Cloe -- View this message in context: http://r.789695.n4.nabble.com/Using-earth-dist-function-tp4407892p4410920.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] Loop

2012-02-22 Thread Eik Vettorazzi
Hi Florian, 'yet that doesn't work' is an improper question on this list, see the posting guide. Besides that, something like set<-vector(mode = "list", length = 10) for (i in 1:10){ set[[i]] <- complete(imp,i)} or saving some typing set<-lapply(1:10,function(i)complete(imp,i)) should work.

Re: [R] Week number from a date

2012-02-22 Thread Gabor Grothendieck
On Wed, Feb 22, 2012 at 8:09 AM, arunkumar wrote: > Hi > > My data looks like this > > startDate="2008-06-01" > > dateRange =c( "2008-10-01","2008-12-01") > Is there any method to find the week number from the startDate range > Is the question how many weeks are from the startDate to each of

Re: [R] Week number from a date

2012-02-22 Thread Jan van der Laan
The suggestion below gives you week numbers with week 1 being the week containing the first monday of the year and weeks going from monday to sunday. There are other conventions. The ISO convention is that week 1 is the first week containing at least 4 days in the new year (week 1 of 2012

Re: [R] Several densityplots in single figure

2012-02-22 Thread David Winsemius
On Feb 22, 2012, at 9:13 AM, josh rosen wrote: thank you very much David! Can I follow up with a slight complication of this? A 2 by 2 case, where the abline is different in each plot. A relevant input code would be thedataA1 <- data.frame(x1=rnorm(100,1,1),x2=rnorm(100,3,1)) #create data

Re: [R] Query: list within a list

2012-02-22 Thread R. Michael Weylandt
It's certainly possible and I don't think you get any grueling inefficiencies. along the way. Another way that might or might not make sense for you is to use a nifty trick I saw Gabor and Duncan M use a few weeks ago: you can give dimensionality to a list and then subset it in the "normal" ways:

Re: [R] Query: list within a list

2012-02-22 Thread Milan Bouchet-Valat
Le mercredi 22 février 2012 à 16:17 +0100, Stefano Sofia a écrit : > Dear R users, > I have difficulty to create a list within a list. > Example: with > > > A <- vector(mode="list", 4) > > I create a list of 4 elements: > > A > [[1]] > NULL > > [[2]] > NULL > > [[3]] > NULL > > [[4]] > NULL >

[R] Query: list within a list

2012-02-22 Thread Stefano Sofia
Dear R users, I have difficulty to create a list within a list. Example: with > A <- vector(mode="list", 4) I create a list of 4 elements: > A [[1]] NULL [[2]] NULL [[3]] NULL [[4]] NULL In each element of this list I can store, for example, a matrix: A[[1]] <- matrix ... I need each element

Re: [R] how to make hash?& append element, if i want following condition

2012-02-22 Thread R. Michael Weylandt
The easiest way to get a hash structure is to use environments. hash1 <- new.env() hash1$A <- c(1.2, 3.4, 4.5) # etc. If I remember right there is a package on CRAN that abstracts some of this interface away (it's not the most intuitive) but this would likely be the core of it. Michael On Wed,

Re: [R] Several densityplots in single figure

2012-02-22 Thread josh rosen
thank you very much David! Can I follow up with a slight complication of this? A 2 by 2 case, where the abline is different in each plot. A relevant input code would be thedataA1 <- data.frame(x1=rnorm(100,1,1),x2=rnorm(100,3,1)) #create data thedataB1 <- data.frame(x1=rnorm(100,2,1),x2=rnorm(100

Re: [R] Loop

2012-02-22 Thread Florian Weiler
Thanks a lot all of you! @ Berend, your code works fine, thanks. @ Milan, you have a point there, makes sense to create 1 instead of 10 objects! -- View this message in context: http://r.789695.n4.nabble.com/Loop-tp4409865p4410444.html Sent from the R help mailing list archive at Nabble.com. _

Re: [R] "CV" for log normal data

2012-02-22 Thread Terry Therneau
If a variable y has (approximately) constant CV, then log(y) has (approximately) constant variance. So, use the standard deviation of the data. begin included message --- Hi, I have a microarray dataset from Agilent chips. The data were really log ratio between test samples and a universal r

Re: [R] Package 'fCalendar'

2012-02-22 Thread R. Michael Weylandt
I believe fCalendar was replaced by timeDate which does have a namespace and can be acquired from CRAN. Michael On Wed, Feb 22, 2012 at 5:41 AM, Britt Grt wrote: > > Dear, > > I'm a master student mathematics at university Gent, who's writing a thesis > about vines and copula's. > I'm in troubl

Re: [R] variance explained in a cox ph model

2012-02-22 Thread Federico Calboli
On 22 Feb 2012, at 14:01, Terry Therneau wrote: > --- begin included message --- > I have a left truncated, right censored cox model: > > coxph(Surv(start, stop, censor) ~ x + y, mydata) > > I would like to know how much of the observed variance (as a number > between 0 and 1) is explained by ea

Re: [R] variance explained in a cox ph model

2012-02-22 Thread Terry Therneau
--- begin included message --- I have a left truncated, right censored cox model: coxph(Surv(start, stop, censor) ~ x + y, mydata) I would like to know how much of the observed variance (as a number between 0 and 1) is explained by each variable. How could I do that? Adding terms sequentially an

Re: [R] inserting a dataframe into the table

2012-02-22 Thread Sarah Goslee
Hi, On Wed, Feb 22, 2012 at 4:47 AM, arunkumar wrote: > Hi, > > I have a dataset > >        X         Y > A=   10      15 >        20      30 >        40      50 > > B =   X     Z >        10   30 >        20     50 > > I have a table   containing X Y Z columns A table, or is this another da

Re: [R] Logistic population growth and deSolve

2012-02-22 Thread Thomas Petzoldt
Hi Thomas, I've been out of office for a time, but maybe you are still waiting ... As far as I see your model is a correctly implemented ODE (!!!) system and I don't understand what you mean with "unexpected results". Would it be possible that your original intention was not a *continuous* O

Re: [R] Week number from a date

2012-02-22 Thread Patrick Breheny
To give a little more detail, you can convert your character strings into POSIX objects, then extract from it virtually anything you would want using strftime. In particular, %W is how you get the week number: > dateRange <- c("2008-10-01","2008-12-01") > x <- as.POSIXlt(dateRange) > strftime(

Re: [R] Several densityplots in single figure

2012-02-22 Thread David Winsemius
On Feb 22, 2012, at 5:28 AM, josh rosen wrote: Hi, I have created two separate overlapping density plots- see example code below. What I wish now to do is combine them into one figure where they sit side by side. Any help would be great! many thanks in advance, josh. ##

Re: [R] Loop

2012-02-22 Thread Milan Bouchet-Valat
Le mercredi 22 février 2012 à 05:40 -0800, Florian Weiler a écrit : > Thanks for the answer, and sorry if I was not clear. > > So I run the data imputation using mice with 10 chains and then I get a > mids-object. From that object I can then extract 10 data sets using the > complete(imp, n) comman

Re: [R] Installing rgl

2012-02-22 Thread Milan Bouchet-Valat
Le mercredi 22 février 2012 à 04:51 -0800, aoife a écrit : > Because for example I've done this: > > I made a simple table: > > A B C > G11 34 231 > G2231 1 0.1 > G312 0.0223 > > > and ran a correspondance analysis on it using the ca p

Re: [R] Loop

2012-02-22 Thread Berend Hasselman
On 22-02-2012, at 14:40, Florian Weiler wrote: > Thanks for the answer, and sorry if I was not clear. > > So I run the data imputation using mice with 10 chains and then I get a > mids-object. From that object I can then extract 10 data sets using the > complete(imp, n) command (with n=c(1:10)).

Re: [R] Loop

2012-02-22 Thread Florian Weiler
Thanks for the answer, and sorry if I was not clear. So I run the data imputation using mice with 10 chains and then I get a mids-object. From that object I can then extract 10 data sets using the complete(imp, n) command (with n=c(1:10)). Now I can type this out 10 times: set1 <- complete(imp, 1

Re: [R] Week number from a date

2012-02-22 Thread Ingmar Visser
?strptime is a good place to start hth, Ingmar On Wed, Feb 22, 2012 at 2:09 PM, arunkumar wrote: > Hi > > My data looks like this > > startDate="2008-06-01" > > dateRange =c( "2008-10-01","2008-12-01") > Is there any method to find the week number from the startDate range > > - > Thanks

[R] Several densityplots in single figure

2012-02-22 Thread josh rosen
Hi, I have created two separate overlapping density plots- see example code below. What I wish now to do is combine them into one figure where they sit side by side. Any help would be great! many thanks in advance, josh. # thedataA <- data.frame(x1=rnorm(100,1,1),x2=rnorm(100

Re: [R] stepwise selection for conditional logistic regression

2012-02-22 Thread Frank Harrell
Stepwise variable selection is an invalid statistical method. Who or which book recommended it? Frank Subha P. T. wrote > >  Hi, > > Is there any function available to do stepwise selection of variables in > Conditional(matched) logistic regression( clogit)? step, stepwise  etc are > failing in

Re: [R] stepwise selection for conditional logistic regression

2012-02-22 Thread David Winsemius
On Feb 22, 2012, at 12:03 AM, Subha P. T. wrote: Hi David My data set has about 20 significant variables and step function with logistic regression is working fine( in R-commander). I tried to get conditional logistic by introducing the stratum variable and clogit. The clogit is not conv

[R] Week number from a date

2012-02-22 Thread arunkumar1111
Hi My data looks like this startDate="2008-06-01" dateRange =c( "2008-10-01","2008-12-01") Is there any method to find the week number from the startDate range - Thanks in Advance Arun -- View this message in context: http://r.789695.n4.nabble.com/Week-number-from-a-date-tp4410223

Re: [R] sqlite create new unique id

2012-02-22 Thread Chris Campbell
Hi Alok Yes, last_insert_rowid() will always look for the last row inserted in this connection, so you will always get 0 before inserting a new row in a new connection. Maintaining the connection may cause other problems as the last inserted rowid might not be relevant to your query. Getting m

Re: [R] Installing rgl

2012-02-22 Thread aoife
Because for example I've done this: I made a simple table: A B C G1 1 34 231 G2 231 1 0.1 G3 12 0.0223 and ran a correspondance analysis on it using the ca package: > library(ca) Loading required package: rgl Warning messages: 1:

Re: [R] Challenge

2012-02-22 Thread Berend Hasselman
On 22-02-2012, at 13:49, Silvano wrote: > Hi, > > I have the following equation: > > x1 + x2 + x3 - 2(x4 + x5 + x6) + 3(x7) = N > > each x_i can take any value: 1, 2, 3, 5, 6, 10, 15 or 30 and > each one is different from each other. > > Which combination of values ??in the formula which lead

Re: [R] Loop

2012-02-22 Thread Helios de Rosario
-- Helios de Rosario Martínez Researcher >>> El día 22/02/2012 a las 11:32, Florian Weiler escribió: > Dear all, > > I have a (probably very basic) question. I am imputing data with the mice > package, using 10 chains. I can then write out the 10 final values of the > chains simply by > >

[R] Challenge

2012-02-22 Thread Silvano
Hi, I have the following equation: x1 + x2 + x3 - 2(x4 + x5 + x6) + 3(x7) = N each x_i can take any value: 1, 2, 3, 5, 6, 10, 15 or 30 and each one is different from each other. Which combination of values ??in the formula which leads to the smallest value of N? How can I program this situa

[R] Package 'fCalendar'

2012-02-22 Thread Britt Grt
Dear, I'm a master student mathematics at university Gent, who's writing a thesis about vines and copula's. I'm in trouble with the package 'fCalendar' which I need for running 'QRMlib'. The problem is that 'fCalendar' doesn't have a namespace. I need to use R.2.14.1 because I also need the pa

Re: [R] Installing rgl

2012-02-22 Thread aoife
Hey guys,I'm working with R version 2.14.1 (2011-12-22) on a unix machine and I'm having a similar problem. I have a matrix and i want to do a simple correspondance analysis. I tried to install the ca package i get this error: > library(ca) Loading required package: rgl Warning messages: 1: In rgl

[R] inserting a dataframe into the table

2012-02-22 Thread arunkumar1111
Hi, I have a dataset X Y A= 10 15 20 30 40 50 B = X Z 10 30 20 50 I have a table containing X Y Z columns How to insert a data frame into the table without using for loop ? now currently i'm using the for loop with

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