Re: [R] see the example and help me

Hi Jonathan, On a side note, my predicted values are consistently about $50,000 higher than the ones you got from what were using. Since I don't know what exactly your tool is doing, I can't tell you why that is). If you want to take into account the fact that it's actually a time series, R has p

Re: [R] nice log-log plots

On 03/15/2010 03:12 AM, ElManuelito wrote: I'm open to any suggestions and improvements... ... #plot.loglog(f,S,type="o",col=4,pch="",xaxs="i",yaxs="i"); Hi ElManuelito, The first improvement would be to send toy data so that we could play with your functions. The second improvement would b

Re: [R] barplot with a probability density curve

On 03/15/2010 08:32 AM, Olga Lyashevska wrote: Dear all, I am making a barplot as following: barplot(c(1,2,3,5,2,3,1),names.arg=c("100","200","300","400","500","600","700"),xlab="diameter",ylab="flow",main="some title",space=0.1) I am also trying to add a probability density curve, however us

Re: [R] likelihood ratio test between glmer and glm

Davnah Urbach dartmouth.edu> writes: > Thanks for this answer but does that mean that working > with the deviances is better? Or how else could I > evaluate the importance of my random terms? You should probably (a) search the archives of the r-sig-mixed-models mailing list and (b) ask this

Re: [R] barplot with a probability density curve

On 15/03/2010, at 3:37 PM, S Ellison wrote: > I begin to think that R needs a _mis_fortunes package... I am tempted to nominate *that* as a fortune! :-) cheers, Rolf Turner ## Attention:\ This e-mail m

Re: [R] Error--memory could not be "read"

On 15/03/2010, at 4:01 PM, rusers.sh wrote: > Hi, > I wrote my own function to finish my work. One strange thing happened. If > i set the number of simulations to be "10", it goes correctly. But if i set > the number of simulations into "100", then errors appeared. > Error information: The instr

[R] Error--memory could not be "read"

Hi, I wrote my own function to finish my work. One strange thing happened. If i set the number of simulations to be "10", it goes correctly. But if i set the number of simulations into "100", then errors appeared. Error information: The instruction at "0x6abf12cf" referenced memory at "0x0286fff

Re: [R] likelihood ratio test between glmer and glm

> Thanks for this answer but does that mean that working with the deviances is better? Or how else could I evaluate the importance of my random terms? Many thanks, Davnah > On Mar 14, 2010, at 8:12 PM, hadley wickham wrote: > >>> Based on a discussion found on the R mailing list but dating

Re: [R] barplot with a probability density curve

I begin to think that R needs a _mis_fortunes package... Steve E >>> Rolf Turner 03/15/10 2:21 AM >>> On 15/03/2010, at 3:07 PM, S Ellison wrote (in response to a very confused question about superimposing density curves on barplots): > So the bad news is that not a lot of what you'

Re: [R] Why doesn't vec[-real.number] give an error or warning? Kids do the darndest things!

>>> Bryan Hanson 03/14/10 2:39 AM >>> >Under what circumstances would the documented behavior be valuable? It would be useful in all the circumstances in which it would be sensible to use a real number as a vector index. Not that I can think of any. Somebody else might, though. And it is pos

Re: [R] barplot with a probability density curve

On 15/03/2010, at 3:07 PM, S Ellison wrote (in response to a very confused question about superimposing density curves on barplots): > So the bad news is that not a lot of what you're doing is right. Sounds like a fortune to me! :-) cheers, Rolf Tur

Re: [R] special symbols into a text string

See ?plotmath, especially the examples. S >>> Gerard Smits 03/14/10 3:38 PM >>> All, I am trying to put a few special symbols into a string to place on a graph (e.g., >= and superscript 2). This clearly works, but does not look good: text<-c("x2", "A>=B") I tried pasting in the >= symbol

Re: [R] barplot with a probability density curve

You have three problems: i) Barplot's plot locations are not at 100-700 in your picture. ii) density applied to your bar hights will produce the density as if those are x locations, not heights. iii) density's height is scaled to unit area and not the height of your bars. And a statistical issue:

[R] the problem about sample size

Hi all: I am a user of "JM" package. Here's the problem of "sample size". The warning is: Error in jointModel(fitLME, fitSURV_death, timeVar = "time", method = "piecewise-PH-GH") : sample sizes in the longitudinal and event processes differ. According to the suggestion of "missing data",

Re: [R] barplot with a probability density curve

Hi Olga, may be you can work around with the suggestions below, while other provide the best solution for your: barplot(c(1,2,3,5,2,3,1),names.arg=c("100","200","300","400","500","600","700"), xlab="diameter",ylab="flow",main="some title",space=0.1) lines(lowess(c(1,2,3,5,2,3,1),f=1), type="b",

Re: [R] Form using R

Tal Galili gmail.com> writes: > > Hi Nilza, > I just wrote a more detailed answer to your question in the following post: > Google spreadsheets + google forms + R = Easily collecting and importing > data for analysis

Re: [R] likelihood ratio test between glmer and glm

> Based on a discussion found on the R mailing list but dating back to 2008, I > have compared the log-likelihoods of the glm model and of the glmer model as > follows: > > lrt <- function (obj1, obj2){ > L0 <- logLik(obj1) > L1 <- logLik(obj2) > L01 <- as.vector(- 2 * (L0 - L1)) > df <- attr(L1,

[R] CRAN (and crantastic) updates this week

CRAN (and crantastic) updates this week New packages * apcluster (1.0.1) Ulrich Bodenhofer http://crantastic.org/packages/apcluster The apcluster package implements Frey's and Dueck's Affinity Propagation clustering in R. The algorithms are analogous to the Matlab code pub

[R] likelihood ratio test between glmer and glm

I am currently running a generalized linear mixed effect model using glmer and I want to estimate how much of the variance is explained by my random factor. summary(glmer(cbind(female,male)~date+(1|dam),family=binomial,data= liz3")) Generalized linear mixed model fit by the Laplace approximatio

Re: [R] Create vectors from a vector

Thanks a lot. It is exactly what I was looking for. I found though and another way (worse) to do it, so I just post in case someone find it useful sk<-nz*e*(vnk[c(i:0)]%*%vro[c(0:i)]) for(i in 0:200){ sk[i]<-nz*e*(vnk[c(i:0)]%*%vro[c(0:i)]) } -- View this message in context: http://n4.nabble.

Re: [R] R on Linux - a primer

Just to make this thoroughly confusing, I will say that I am very happy with Fedora, which is the bleeding-edge version of RedHat, which I used starting around 1996. Tom "Spot" Callaway pays close attention to the R RPM, and several of the R packages are also available as RPMs (but I don't use tho

Re: [R] R on Linux - a primer

On Sun, Mar 14, 2010 at 3:04 PM, Axel Urbiz wrote: > Hi, > > I'm looking to move from Windows into a 64-bit Linux environment. Which is > the best Linux Flavor to use within R? To install R on this environment, do > I need to do any compiling? > > Thanks all! > > Axel. > Do NOT pick your Linux en

Re: [R] R on Linux - a primer

Dne Ne 14. března 2010 23:04:02 Axel Urbiz napsal(a): > Hi, > > I'm looking to move from Windows into a 64-bit Linux environment. Which is > the best Linux Flavor to use within R? To install R on this environment, do > I need to do any compiling? IMHO distributions like Ubuntu, openSUSE or Mandri

Re: [R] R on Linux - a primer

I am up and running on ubuntu. I have not had to compile anything, but If I did apt-get build-dep r-base and everything would work fine. Maybe I am understating this. You can add some repositories that are not the main ones to always have an up to date R on your system. hth, Stephen On Sun, Mar

[R] R on Linux - a primer

Hi, I'm looking to move from Windows into a 64-bit Linux environment. Which is the best Linux Flavor to use within R? To install R on this environment, do I need to do any compiling? Thanks all! Axel. [[alternative HTML version deleted]] __ R

[R] barplot with a probability density curve

Dear all, I am making a barplot as following: barplot(c(1,2,3,5,2,3,1),names.arg=c("100","200","300","400","500","600","700"),xlab="diameter",ylab="flow",main="some title",space=0.1) I am also trying to add a probability density curve, however using lines(density(c(1,2,3,5,2,3,1))) does not gi

Re: [R] passing a function as an argument using lazy loading

Try this: > foo2 <- function(x=2*y, y=x/2) eval(substitute(cat(x,y,"\n"))) > foo2(x = 1, y = x/3) 1 0.333 > foo2(x = y/2, y = 10) 5 10 On Wed, Mar 10, 2010 at 7:26 AM, Mark Heckmann wrote: > I have the following function that makes use of lazy loading. > > foo <- function(x=2*y, y=x/2) cat(x

Re: [R] passing a function as an argument using lazy loading

On 14/03/2010 4:33 PM, Mark Heckmann wrote: Yes. I meant lazy evaluation :) I will try to clarify what I mean. I have a function foo and in its arguments use a reference to another argument, like: foo <- function(x=y, y=x) I would like to specify the function in a way it is possible to chang

Re: [R] the error in DoSimulateRF function

Hello all, Thanks for the help. I was able to run the code by removing random seed statement and putting set.seed(1) Sincerely, Maddy -- View this message in context: http://n4.nabble.com/the-error-in-DoSimulateRF-function-tp1592572p1592709.html Sent from the R help mailing list archive at Nab

Re: [R] for() loop

Hi Martin, it is slightly unclear to me what you are trying to achieve... are you trying to tabulate how often each value appears in datjan[,4]? Then table(datjan[,4]) may be what you want. HTH Stephan Schmidt Martin schrieb: Hello I'm working with R since a few month and have still many

Re: [R] Error in object$tables[[v]] : subscript out of bounds

On 14.03.2010 19:12, Amy Hessen wrote: Hi Uwe, Thanks for your reply. I did not understand what you mean and I still receive the error message. OK, so which version of R and which version of e1071 is this? Do you have any objects in your workspace? I do not get an error message, just a

Re: [R] Error in object$tables[[v]] : subscript out of bounds

On 14.03.2010 20:17, Amy Hessen wrote: Hi Uwe, Thank you so much for your reply. I still receive the error message. These are the details of R: 1)R version 2.9.1 2)package 'e1071' was built under R version 2.9.2 this is the whole code- I don’t use any other code: library(e1071) data(iris

Re: [R] Error in object$tables[[v]] : subscript out of bounds

Hi Uwe, Thank you so much for your reply. I still receive the error message. These are the details of R: 1)R version 2.9.1 2)package 'e1071' was built under R version 2.9.2 this is the whole code- I don’t use any other code: library(e1071) data(iris) attach(iris) class_label <- names(iri

Re: [R] the error in DoSimulateRF function

Hello Sir, Thanks for reply. The SessionInfo() gives the following output, R version 2.10.1 (2009-12-14) i386-pc-mingw32 locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C

[R] Joining nodes on a minimum spanning tree

Hi, I am new to R and I am trying to plot a minimum spanning tree from a distance matrix. The following code will plot the minimum spanning tree for me, however, genomes that have a distance of 0 between them in the distance matrix are plotted as two separate nodes on the minimum spanning tree i.e.

Re: [R] Direction and scaling of cumulative distribution in ecdfplot

Jeff Stevens googlemail.com> writes: > I have two questions regarding the ecdfplot function in the > latticeExtra package. > 1. How can I plot the fraction of values >= x rather than <=x, like > the what = "1-F" argument in the Ecdf function in the Hmisc package? > > 2. When I try to log-transfor

[R] for() loop

Hello I'm working with R since a few month and have still many trivial questions - I guess! Here is what I want: I have this matrix: dim(datjan) [1] 899 4 The first 10 rows looks as follows: datjan[1:10,] V1 V2 V3 V4 1 1961 1 1 24 2 1961 1 2 24 3 1961 1 3 24 4 1961 1 4

Re: [R] passing a function as an argument using lazy loading

Yes. I meant lazy evaluation :) I will try to clarify what I mean. I have a function foo and in its arguments use a reference to another argument, like: foo <- function(x=y, y=x) I would like to specify the function in a way it is possible to change the way the argument y is evaluated. e.g.:

Re: [R] the error in DoSimulateRF function

maddy gmail.com> writes: > > > Hello, > > I did not understand what you mean by updating the system. I am new > user of R and I downloaded R a few days ago. Also I installed the > required packages for my program(geoR, randomFields), there was just > one version I could see for the packages. >

[R] Direction and scaling of cumulative distribution in ecdfplot

I have two questions regarding the ecdfplot function in the latticeExtra package. 1. How can I plot the fraction of values >= x rather than <=x, like the what = "1-F" argument in the Ecdf function in the Hmisc package? 2. When I try to log-transform the y-axis, I get a warning that it can't have

Re: [R] the error in DoSimulateRF function

Hello, I did not understand what you mean by updating the system. I am new user of R and I downloaded R a few days ago. Also I installed the required packages for my program(geoR, randomFields), there was just one version I could see for the packages. The code I am using is as follows .Random.se

[R] the error in DoSimulateRF function

Hello, I am a graduate student of University of Florida. I am trying to run a process variation model and I am facing the following error. - Analysis of geostatistical data For an Introduction to geoR go to http://www.leg.ufpr.br/geoR g

Re: [R] the error in DoSimulateRF function

maddy wrote: > > I did not understand what you mean by updating the system. I am new > user of R and I downloaded R a few days ago. Also I installed the > required packages for my program(geoR, randomFields), there was just > one version I could see for the packages. > The code I am using is as

Re: [R] the error in DoSimulateRF function

maddy wrote: > > Error in DoSimulateRF(n = n, reg = register, paired = paired) : > .Random.seed is not an integer vector but of type 'double' > > I tried to trace back the source of the error but installations seem > correct to me. > rm(.Random.seed) does not work in my case. > > You told us

Re: [R] Error in object$tables[[v]] : subscript out of bounds

Hi Uwe, Thanks for your reply. I did not understand what you mean and I still receive the error message. Do you mean that something is wrong in computing FORMULA? I want to use formula in Naïve instead of using the class label, could you please tell me where is the wrong? Cheers, Amy

Re: [R] Improve lattice XYPLOT graphic

## Sorry, typo in my last email. "frac" is the correct spelling, not "fraction" ## RIch tmp <- data.frame(trat=letters[1:3], y=rnorm(3), x=1:3) xyplot(y ~ x | trat, data=tmp) strip.levelnames <- c(expression(H[2]*O), expression(x^2+y^2), expression(frac(x^3, 1+x^3))) xyplot(y ~ x | trat, data=

Re: [R] Improve lattice XYPLOT graphic

## It looks like something like this will meet your needs ## Rich tmp <- data.frame(trat=letters[1:3], y=rnorm(3), x=1:3) xyplot(y ~ x | trat, data=tmp) strip.levelnames <- c(expression(H[2]*O), expression(x^2+y^2), expression(fraction(x^3, 1+x^3))) xyplot(y ~ x | trat, data=tmp, stri

Re: [R] create picture (k -the nearest neighbours)

On 09.03.2010 14:01, Grzesiek wrote: Hi I want to create a nice picture about my result of k -the nearest neighbours algorithm. Here is my easy code: # library(klaR) library(ipred) library(mlbench) data(PimaIndiansDiabetes2) dane=na.omit(PimaIndiansDiabetes2)[,

Re: [R] nice log-log plots

Here's what I do, I'm open to any suggestions and improvements... seq.log=function(x1,x2="1"){ if(length(x1)==2){x2=x1[2];x1=x1[1];} n1=floor(log(x1)/log(10)) n2=floor(log(x2)/log(10)) suff=NULL; if(x1==1000){n1=n1+1;} if(x2==1000){suff=1000;}

Re: [R] Error loading R Commander with version 2.10.1 on MacOS 10.5 or 10.6

Dear Dwight, I've never observed this problem myself, and many people apparently run the tcltk and Rcmdr packages with R 2.10.1 under Mac OS 10.6 without difficulty. You can confirm that the problem is with tcltk by trying to load that package independently of the Rcmdr: i.e., library(tcltk). Si

Re: [R] confidence intervals for non-linear regression

In the paste I had provided one possible solution to this, see http://n4.nabble.com/Confidence-intervals-nls-td1556487.html#a1556702 Walmes. - ..ooo0 ... ..()... 0ooo...

Re: [R] Create vectors from a vector

On Mar 14, 2010, at 8:11 AM, Dimitris Kapetanakis wrote: Dear all, I would like to create a number of vectors which contain the the first n elements of an existing vector. For example I have the vectors vnk (200x1) and vro(200x1) and I want to create 200 vectors that contain the 1st till

Re: [R] special symbols into a text string

See ?plotmath Example: plot(1:10); text(4:5, 5:4, c(expression(A >= B), expression(x^2))) Uwe Ligges On 14.03.2010 16:38, Gerard Smits wrote: All, I am trying to put a few special symbols into a string to place on a graph (e.g.,>= and superscript 2). This clearly works, but does not look

[R] Error loading R Commander with version 2.10.1 on MacOS 10.5 or 10.6

Dear R Commander experts, I have now had multiple failures in loading R Commander with R version 2.10.1 (most recent one on the CRAN site) on a Mac running OS 10.5 or 10.6. The installation of R Commander seems to proceed normally, but when I try to start up R Commander, it never loads. It appe

[R] confidence intervals for non-linear regression

Dear all, I am interested to calculate confidence interval for fitted values in general for non-linear regressions. Lets say we have y=f(x1,x2,..xN) where f() is a non-linear regression. I would like to calculate a confidence interval for new prediction f(a1,..,aN). I am aware of techniques fo

[R] special symbols into a text string

All, I am trying to put a few special symbols into a string to place on a graph (e.g., >= and superscript 2). This clearly works, but does not look good: text<-c("x2", "A>=B") I tried pasting in the >= symbol, but just comes out as an =. I have tried expression() with no luck: text<-c("x2

Re: [R] dmvnorm masked by emdbook

Tobias Verbeke gmail.com> writes: > > Hi Dan, > > For this to work, the copula package should > explicitly import dmvnorm from the mvtnorm > package by including > > importFrom(mvtnorm, dmvnorm) > > in their NAMESPACE file. > > You can do the same thing and rebuild + reinstall > the package

Re: [R] passing a function as an argument using lazy loading

On 10.03.2010 13:26, Mark Heckmann wrote: I have the following function that makes use of lazy loading. I guess you mean *lazy evaluation* rather than *lazy loading* (as used in loading functions or data from the package databases). foo <- function(x=2*y, y=x/2) cat(x,y) Now I want to

Re: [R] formula and class label

On 14.03.2010 07:44, Amy Hessen wrote: Hi, Could you please tell me whether there is a difference in the result of svm when using formula instead of class label? Well, a factor object (where you have class labels in) is not sufficient, you also need explaining variables. The formula

Re: [R] Error in object$tables[[v]] : subscript out of bounds

On 14.03.2010 11:55, Amy Hessen wrote: Hi, Could you please tell me how I correct the following error message? “Error in object$tables[[v]] : subscript out of bounds” This is the code: library(e1071) data(iris) attach(iris) class_label<- names(iris)[1] This is not the name for the class

[R] Inline text labels in Lattice barchart

Dear all, I'm trying to create a very simple stacked barchart where the percentages are displayed inside the bar. Apparently, this is not as simple as I thought because I can only create the chart, not the labels: barchart(prop.table(umgang.bpa,margin=1),xlab="Proportion",auto.key=list(adj =1),co

Re: [R] Why doesn't vec[-real.number] give an error or warning? Kids do the darndest things!

I had a case yesterday where indexing with a real number was "close enough". I had about 4000 data point that I was plotting with just: plot(x) which would lay them out sequentially on the x-axis. As a point of reference, I want to put on the x-axis about 20 equally spaced tick marks with the n

Re: [R] R and R commander

Dear John, These instructions appear to come from your instructor, and you might try asking him or her what to do. Duncan Murdoch has already suggested that you might not have permission to edit a file in Program Files, and explained an alternative. You could also try running Notepad as administr

Re: [R] R and R commander

On 14/03/2010 1:23 AM, john_j_carr...@mail.com wrote: Hi, I am a student studying Biostatistics at University. We have been advised to install R and R commander. I managed to do this successfully, except I wasn't able to complete the final step - which would enable both R and R commander to laun

Re: [R] Why doesn't vec[-real.number] give an error or warning? Kids do the darndest things!

On 14/03/2010 10:09 AM, Bryan Hanson wrote: Jim, I completely agree with everything you said. I am curious about the cases where one would use a real number as an index and anticipate that R would do the as.integer for you, rather than turning it into an integer yourself. Indices are very freq

Re: [R] Why doesn't vec[-real.number] give an error or warning? Kids do the darndest things!

Jim, I completely agree with everything you said. I am curious about the cases where one would use a real number as an index and anticipate that R would do the as.integer for you, rather than turning it into an integer yourself. If anyone has a simple example or situation where this arises, I'd l

[R] Improve lattice XYPLOT graphic

Hi, How I could improve this graphic? http://www.divshare.com/download/10754700-f81 I would like to write groups labels in each panel and override the labels from object. I am try this code: xyplot(percentagem.mortos~tempo|trat, data=bio.ens, type="a",       auto.key=list(points=FALSE, lines=T

[R] Create vectors from a vector

Dear all, I would like to create a number of vectors which contain the the first n elements of an existing vector. For example I have the vectors vnk (200x1) and vro(200x1) and I want to create 200 vectors that contain the 1st till the n_th element of the vectors and thus be able to create a vec

[R] error message when using mice: missing observations in cov/cor

Hi there, I am trying to do multiple imputations with the mice package. My dataset consists of 132 variables and 92 data rows. I specified the predictor matrix using quickpred, which resulted in about 30 predictors per variable. I am using norm as imputation method for continuous variables and

[R] Error in object$tables[[v]] : subscript out of bounds

Hi, Could you please tell me how I correct the following error message? “Error in object$tables[[v]] : subscript out of bounds” This is the code: library(e1071) data(iris) attach(iris) class_label <- names(iris)[1] myformula <- formula(paste(class_label,"~ .")) mymodel<-naiveBayes(myform

Re: [R] Creating images without X11

On Sun, Mar 14, 2010 at 5:14 AM, Sharpie wrote: > I had this exact same problem last summer when attempting to set up an > automated process involving image generation on a remote server.  Since I > didn't have admin rights to the server, I ended up switching to the Cairo > package for image gene

Re: [R] R and R commander

On 3/14/10, john_j_carr...@mail.com wrote: > I would appreciate any assistance as soon as possible (so I don't get too > far behind in my studies). > I am not sure what the exact issue is, but you can always start Rcmdr manually after the R start-up. Simply issue a require(Rcmdr) to load Rcmdr.

Re: [R] Creating images without X11

Is it possible the problem is another? I cannot generate png images when R runs on a machine without *installed* X11 Here is the error message when I submit a simple png() plot on a computing node of my cluster. Error in X11(paste("png::", filename, sep = ""), width, height, pointsize, :

[R] R and R commander

Hi, I am a student studying Biostatistics at University. We have been advised to install R and R commander. I managed to do this successfully, except I wasn't able to complete the final step - which would enable both R and R commander to launch when I open the R icon on my desktop. However,