Re: [R] trouble with Rcmdr

Hello, On 8/18/09, Erin Hodgess erinm.hodg...@gmail.com wrote: I used it on Saturday, and it worked fine. When I used it today, the window did not appear. This is version 2.9.1 on Ubuntu Jaunty Jackalope. Did you make any system updates between Sat and today? Liviu

Re: [R] Plot(x,y)

Hi malcolm, sorry but your post continue with pour quality, because it is not reproducible, it is!? By the way, gavin.simp...@ucl.ac.uk wrote: . You really shouldn't call your data, 'data' as it will get very confusing when you start using modelling functions and using the data argument, or

Re: [R] ggplot 2 semi-transparency error

I really don't know anything much about this but I tried device=pdf (no-quotes) and I got a pdf file with transparent plots. ?device.print gives help with some links to other devices hth rajesh j wrote: Hi, I used the command ggplot as follows...

[R] histogram scaling

Hi, I'm drawing two histograms in the same plot.However, my point of comparison is the difference in their x coordinates.But my problem is one histogram is much taller than the other.How can I get them both to the same height? -- Rajesh.J [[alternative HTML version deleted]]

Re: [R] histogram scaling

Hey, Rajesh I bit light on detail here. Being a mind reader is not an R-help prerequisite. However since I have been working on histograms today and you've just posted a question using ggplot, let me guess that its ggplot you are refering to. Then here is an example, which you can find in my

[R] Why are there small circles in my plot

Dear R-listers, There is my data and my codes to create a plot. I want to know why there are two small circles in the upper right and lower left of the plot respectively. Could you please share your experience or advice with me? # dummy data factor-rep(c(Alice,Jone,Mike),each=100)

[R] Odp: Remove columns

Hi r-help-boun...@r-project.org napsal dne 18.08.2009 10:14:26: Hi Everbody Could somebody help me.? I need to remove the columns where the sum of it components is equal to zero. For example a-matrix(c(0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,0,0,0,1,1,0,0,1,0), ncol=4) a [,1] [,2]

Re: [R] moving color key in heatmap

Booboo Qu wrote: I have a question on moving color keys when side color bars are added to a heatmap. The R code below produces the color key in the upper left corner. Notice I have added side bars to the heatmap, but how could I move the color key below the image? Thanks for the

Re: [R] ggplot 2 semi-transparency error

rajesh j wrote: I used the command ggplot as follows... p-ggplot(a,aes(x=a$V1,colour=a$V2,fill=a$V2)) p + geom_density(alpha = 0.2,xlim=c(-10,10),ylim=c(0,0.5)) when I say, dev.print(device=postscript,file=/alpha/dct.pdf) I get Warning message: In grid.Call.graphics(L_polygon,

Re: [R] Why are there small circles in my plot

Hi, Mao Jianfeng schrieb: plot(c(min(myda$traits),max(myda$traits)),c(-0.03,0.5), xlab='State', ylab='ylab') Here, you are plotting two data points: (min(myda$traits),-0.03) and (max(myda$traits),0.5). Try this: plot(c(min(myda$traits),max(myda$traits)),c(-0.03,0.5), xlab='State',

Re: [R] Polygon function

Cetinyürek Aysun wrote: Dear all, I would like to plot credible interval for a function estimate in R. I would like to plot the credible intervals as shaded region using polygon function. Does anyone ever used that? I tried several times but I could not obtain the right figure.

[R] Performance measure for probabilistic predictions

Hello, I'm using an SVM for predicting a model, but I'm most interested in the probability output. This is easy enough to calculate. My challenge is how to measure the relative performance of the SVM for different settings/parameters/etc. An AUC curve comes to mind, but I'm NOT interested

[R] how to fill the area under the density line with semitransparent colors

Dear R-listers, I have created a plot to display the density lines for the same variable by different entities. Now, I want to fill the area under the density lines with semitransparent colors. Though I have checked that in web-searching and book-reading, I still do not perform that. Could

[R] Move legend text to the left legend box border

Hi, in legend I'am coloring my text rather than using symbols or lines: legend(bottomleft, txt, text.col=col, cex=0.7) However, between the left legend box border and the text in txt is a large empty space. Can I somehow move the text more to the left and get also a smaller legend box? Thanx

Re: [R] ggplot 2 semi-transparency error

ggplot2 has it's own build in wrapper-function to store plots: ggsave. p - ggplot(a,aes(x=V1,colour=V2,fill=V2)) + geom_density(alpha = 0.2,xlim=c(-10,10),ylim=c(0,0.5)) ggsave(p, filename = /alpha/dtc.pdf) HTH, Thierry

Re: [R] Move legend text to the left legend box border

On Wed, 19 Aug 2009 10:20:03 +0200 Sigbert Klinke sigb...@wiwi.hu-berlin.de wrote: SK in legend I'am coloring my text rather than using symbols or lines: SK SK legend(bottomleft, txt, text.col=col, cex=0.7) SK SK However, between the left legend box border and the text in txt is a SK large

[R] ggplot2 transparent pdf

Hi, I plotted a histogram using ggplot2 and saved it as a pdf.However, the portions outside the histogram dont appear transparent when I use a non-white bg colour in my latex document.What can I do to make them transparent? -- Rajesh.J [[alternative HTML version deleted]]

Re: [R] ggplot2 transparent pdf

Try this, print(p+ opts(plot.background= theme_rect(fill=NA))) HTH, baptiste 2009/8/19 rajesh j akshay.raj...@gmail.com: Hi, I plotted a histogram using ggplot2 and saved it as a pdf.However, the portions outside the histogram dont appear transparent when I use a non-white bg colour in my

Re: [R] lmer with random slopes for 2 or more first-level factors?

Dear Jason, Both models have a correct syntax. Although I would write the last model rather as lmer(DV ~ IV1 + IV2 + (1|Subject) + (IV1 - 1| Subject) + (IV2 - 1| Subject)) The only difference is indeed the correlation between the random effects. The random effects in the model I wrote are all

[R] Package read large file

Dear R-Users, I am looking for packages that could read large files in R? any suggestions are welcome. Regards, ML __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] how to fill the area under the density line with semitransparent colors

Hi, One way using ggplot2, library(ggplot2) ggplot(data=myda, mapping=aes(x=traits, y=..density..)) + stat_density(aes(fill=factor), alpha=0.5, col=NA, position = 'identity') + stat_density(aes(colour = factor), geom=path, position = 'identity', size=2) HTH, baptiste 2009/8/19 Mao Jianfeng

Re: [R] how to Transpose a dataset

rajclinasia ha scritto: Hi everyone, How to a transpose a R dataset with a specified variable. If possible send the code. it will be very helpful for us. Thanks in Advance. A written code of your problem would be useful for us to help you. If you have a dataframe you may want to take a

Re: [R] Move legend text to the left legend box border

I believe you want x.intersp, txt - c(Setosa Petals, Versicolor Sepals) plot(1,1,t=n) legend(top, txt, text.col=1:2, cex=0.7, inset=c(0,1/3)) legend(center, txt, text.col=1:2, cex=0.7, x.intersp = -0.5) HTH, baptiste 2009/8/19 Stefan Grosse singularit...@gmx.net: On Wed, 19 Aug 2009

Re: [R] radial.plot() in plotrix module

Jon Case wrote: Hello, Is it possible to plot differently colored points with the radial.plot() function in the plotrix package? For example, the code: radial.plot( c(.5,.6, .7), c(1,2,3), rp.type = s, point.col=c(red, green, blue) ) produces a plot whose three points are all red, instead of

Re: [R] Why are there small circles in my plot

Mao Jianfeng jianfeng@gmail.com 19/08/2009 08:10:54 There is my data and my codes to create a plot. I want to know why there are two small circles in the upper right and lower left of the plot respectively. Because your first plot() command put them there. add type=n to the first plot

Re: [R] Embedding lists in matrices and matrices in lists

Unfortunately the matrix(list(),x,y) way seems to have some limitations. I want to continue working with the matrices which are saved in the database matrix. But for example the following doesn't work: tetrahedron=matrix(c( 0,1,1,1, 1,0,1,1, 1,1,0,1, 1,1,1,0 ),nrow=4, byrow=TRUE) # an example

[R] Fitting a logistic regression

Hello, I have this data: Time AMP 0 0.200 10 0.1958350 20 0.2914560 40 0.6763628 60 0.8494534 90 0.9874526 120 1.0477692 where AMP is the concentration of this metabolite with time. If you plot the data, you can see that it could be fitted using a logistic

[R] font size on graphics

Dear R users, My question is about finding the proper font size for graphics. For this i had written a code that creats 4 diferent graphics and saves them as a png file. From these PNG.graphics , i select one of the proper size and past it to a word document. I have experimented with lots of

Re: [R] how to fill the area under the density line with semitransparent colors

On Aug 19, 2009, at 4:05 AM, Mao Jianfeng wrote: Dear R-listers, I have created a plot to display the density lines for the same variable by different entities. Now, I want to fill the area under the density lines with semitransparent colors. Though I have checked that in web-searching and

Re: [R] Embedding lists in matrices and matrices in lists

Strange, it doesn't work for me: Error in database[4, 4][[1]][1, ] : incorrect number of dimensions Execution halted R version 2.9.0 (2009-04-17) on Arch Linux, no additional packages installed. David Winsemius schrieb: On Aug 19, 2009, at 6:02 AM, Michael Kogan wrote: Unfortunately the

Re: [R] R function for Probabilities for the (standard) normal distribution

Dear All, I need to write an R function which computes values of Probabilities for the (standard) normal distribution, ¦µ(z) for z 0 by summing this power series. (We should accumulate terms until the sum doesn't change). I also need to make the function work for vector of values z. The

[R] font size on graphics question (correction in example,sorry)

Dear R users, My question is about finding the proper font size for graphics. For this i had written a code that creats 4 diferent graphics and saves them as a png file. From these PNG.graphics , i select one of the proper size and past it to a word document. I have experimented with lots of

Re: [R] R function for Probabilities for the (standard) normal distribution

On Aug 19, 2009, at 7:04 AM, Rene wrote: Dear All, I need to write an R function which computes values of Probabilities for the (standard) normal distribution, ¦µ(z) for z 0 by summing this power series. (We should accumulate terms until the sum doesn't change). I also need to make

Re: [R] three dimensions barchart

Thanks David and Berton, But I am so sorry for my mistake. I have just found what I want is a three dimension *histogram*. So correct problem is: I draw the Relative Distribution graph, it looks like histogram(X,Y plot), but I have ten(year) Relative Distribution graphs, have any command can

[R] Gam (mgcv) function

Dear all, I have obtained a model for my data set using gam function in mgcv library. The model is as follows: Family: Binomial Link function : Logit RU ~ s(time, by = Status, bs = ps) + Region*Status+ Gender*Status I have obtained the results. While presenting the results for Region

Re: [R] Embedding lists in matrices and matrices in lists

Try this: database[[4,4]] - tetrahedron database[[4,4]][1,] [1] 0 1 1 1 On Wed, Aug 19, 2009 at 6:02 AM, Michael Koganmichael.ko...@gmx.net wrote: Unfortunately the  matrix(list(),x,y) way seems to have some limitations. I want to continue working with the matrices which are saved in the

[R] Canonical link for the GLM gamma model

Hello! When I estimate a glm gamma model using the canonical link (inverse), I get the opposite signs on almost all coefficients compared to the same model (i.e. with the same linear predictor) estimated using other suitable links (log, logit). What confuses me is that most of sources quote

Re: [R] Odd results with Chi-square test. (Not an R problem, but general statistics, I think.)

Anybody any ideas? Any help would be appreciated! Cheers, Mika -- View this message in context: http://www.nabble.com/Odd-results-with-Chi-square-test.-%28Not-an-R-problem%2C-but-general-statistics%2C-I-think.%29-tp25026167p25041900.html Sent from the R help mailing list archive at

[R] mild and extreme outliers in boxplot

dear all, could somebody tell me how I can plot mild outliers as a circle(°) and extreme outliers as an asterisk(*) in a box-whisker plot? Thanks very much in advance -- View this message in context: http://www.nabble.com/mild-and-extreme-outliers-in-boxplot-tp25040545p25040545.html Sent from

Re: [R] ggplot2 legend problem

On Tue, Aug 18, 2009 at 11:10 PM, Chris Friedlcfrieda...@gmail.com wrote: Still struggling with this. A further example using a slightly different organisation of the data. The factors A and B are included in the dataframe in an attempt to get ggplot to generate a legend automatically. x -

Re: [R] Performance measure for probabilistic predictions

Noah Silverman wrote: Hello, I'm using an SVM for predicting a model, but I'm most interested in the probability output. This is easy enough to calculate. My challenge is how to measure the relative performance of the SVM for different settings/parameters/etc. An AUC curve comes to mind,

[R] scale or not to scale that is the question - prcomp

Dear all here is my data called rglp structure(list(vzorek = structure(1:17, .Label = c(179/1/1, 179/2/1, 180/1, 181/1, 182/1, 183/1, 184/1, 185/1, 186/1, 187/1, 188/1, 189/1, 190/1, 191/1, 192/1, R310, R610L), class = factor), iep = c(7.51, 7.79, 5.14, 6.35, 5.82, 7.13, 5.95, 7.27, 6.29,

Re: [R] Embedding lists in matrices and matrices in lists

This works, but then I can only save a single matrix in each database[x,y] while I need to save a list of matrices. Gabor Grothendieck schrieb: Try this: database[[4,4]] - tetrahedron database[[4,4]][1,] [1] 0 1 1 1 On Wed, Aug 19, 2009 at 6:02 AM, Michael

Re: [R] Embedding lists in matrices and matrices in lists

Hi r-help-boun...@r-project.org napsal dne 19.08.2009 13:04:39: Strange, it doesn't work for me: Error in database[4, 4][[1]][1, ] : incorrect number of dimensions Execution halted R version 2.9.0 (2009-04-17) on Arch Linux, no additional packages installed. database[4,4][[1]][,1]

Re: [R] scale or not to scale that is the question - prcomp

On 19/08/2009 8:31 AM, Petr PIKAL wrote: Dear all here is my data called rglp structure(list(vzorek = structure(1:17, .Label = c(179/1/1, 179/2/1, 180/1, 181/1, 182/1, 183/1, 184/1, 185/1, 186/1, 187/1, 188/1, 189/1, 190/1, 191/1, 192/1, R310, R610L), class = factor), iep = c(7.51, 7.79,

Re: [R] Package read large file

A little more detail would be appropriate. How large is large? What is the format of the file? What do you wnat to do with the data? Do you have to have it all in memory at once? Does it exist in a data base already? What type of system are you running on? How much memory do you have?

Re: [R] scale or not to scale that is the question - prcomp

Thank you Duncan Murdoch murd...@stats.uwo.ca napsal dne 19.08.2009 14:49:52: On 19/08/2009 8:31 AM, Petr PIKAL wrote: Dear all snip I would say the answer depends on the meaning of the variables. In the unusual case that they are measured in dimensionless units, it might make

Re: [R] ggplot2 legend problem

Dear Chris, First of all I would go for the density plot. The 'extra' info from the histogram is just noise. So I guess you are not interessed in it. ggplot(xy, aes(x=value, colour=case, group=case)) + geom_density() But is you want to stick with a histogram then I would use one of the two

Re: [R] three dimensions barchart

On Aug 19, 2009, at 7:44 AM, Yichih Hsieh wrote: Thanks David and Berton, But I am so sorry for my mistake. I have just found what I want is a three dimension histogram. So correct problem is: I draw the Relative Distribution graph, it looks like histogram(X,Y plot), but I have

Re: [R] graph label greek symbol failure

On 18/08/2009, Gavin Simpson gavin.simp...@ucl.ac.uk wrote: On Tue, 2009-08-18 at 13:06 +0100, e-letter wrote: On 17/08/2009, Michael Knudsen micknud...@gmail.com wrote: On Mon, Aug 17, 2009 at 12:51 PM, e-letter inp...@gmail.com wrote: I have tried to add the delta (δ) symbol to the y

Re: [R] scale or not to scale that is the question - prcomp

On 19/08/2009 9:02 AM, Petr PIKAL wrote: Thank you Duncan Murdoch murd...@stats.uwo.ca napsal dne 19.08.2009 14:49:52: On 19/08/2009 8:31 AM, Petr PIKAL wrote: Dear all snip I would say the answer depends on the meaning of the variables. In the unusual case that they are measured in

Re: [R] graph label greek symbol failure

plot(1:10,ylab=expression(temperature *delta*t)) 2009/8/19 e-letter inp...@gmail.com: On 18/08/2009, Gavin Simpson gavin.simp...@ucl.ac.uk wrote: On Tue, 2009-08-18 at 13:06 +0100, e-letter wrote: On 17/08/2009, Michael Knudsen micknud...@gmail.com wrote: On Mon, Aug 17, 2009 at 12:51 PM,

[R] how to specify two variance effects in gls

Hello everybody, I have a dataset where each row has number of subjects and that gives me natural weights for the variance function. Additionally I see that variance increases with Age, which is a regressor. So using gls I have weights=varFixed(~1/n) but don't know how to include the extra

[R] Confidence interval on parameters from optim function

Hi everyone, I have two questions: I would like to get confidence intervals on the coefficients derived from the optim() function. I apply optim() to a given function f res - optim(c(0.08,0.04,1.),f,NULL,method=L-BFGS-B,lower=c(0.,0.,0.)) And I would like to get the p-value and confidence

Re: [R] Help understanding lrm function of Design library

On Tue, Aug 18, 2009 at 8:13 AM, Frank E Harrell Jrf.harr...@vanderbilt.edu wrote: Noah Silverman wrote: Hi, I'm developing an experiment with logistic regression. I've come across the lrm function in the Design  library. While I understand and can use the basic functionality, there are a

Re: [R] RGoogleDocs/RCurl through proxy

Hi Remko There is a new version (1.1-0) of the RCurl package (on which RGoogleDocs depends) (no binary for Windows at this point). This version allows one to specify default curl options that are used each time a new curl handle/object is created. You set these defaults in R's own options()

Re: [R] scale or not to scale that is the question - prcomp

Duncan Murdoch murd...@stats.uwo.ca napsal dne 19.08.2009 15:25:00: On 19/08/2009 9:02 AM, Petr PIKAL wrote: Thank you Duncan Murdoch murd...@stats.uwo.ca napsal dne 19.08.2009 14:49:52: On 19/08/2009 8:31 AM, Petr PIKAL wrote: Dear all snip I would say the answer

Re: [R] lm.fit algo

Thank you, Steve! 2009/8/18 Steve Lianoglou mailinglist.honey...@gmail.com: Hi, On Aug 17, 2009, at 5:09 PM, Pavlo Kononenko wrote: Hi, everyone, This is a little silly, but I cant figure out the algorithm behind lm.fit function used in the context of promax rotation algorithm: The

Re: [R] need help for t.test using by

any one 1Rnwb wrote: I am trying to do ttest for each plate which has equal number of disease and controls. by searching this forum I found one posting suggesting OP to use by(eo,PlateID, function(.sub) t.test(IL1Ra~Group,data=.sub)). when i modified this for my use I used to get the

Re: [R] Confidence interval on parameters from optim function

Hi Emmanuel, You can obtain standard error estimate from the Hessian matrix evaluated at the optimum as: sqrt(diag(solve(ans$hessian))), where `ans' is the object returned by `optim'. However, `optim' does not return the Hessian matrix by default. So, you need to specify `hessian = TRUE' when

Re: [R] Fitting a logistic regression

with my limited understanding, I am not surprised to see this data fitting nicely at the end just by eyeballing at it. the reaction at the early time point is not completed as the time passes which is close to 20 units the reaction generates more metabolite to be measured reliably your t=0 and

[R] ridge regression

Dear all, I considered an ordinary ridge regression problem. I followed three different ways: 1. estimate beta without any standardization 2. estimate standardized beta (standardizing X and y) and then again convert back 3. estimate beta using lm.ridge() function

Re: [R] Confidence interval on parameters from optim function

Emmanuel, I didn't answer your second question. You can use the `try' function to capture errors and keep proceeding through simulations without crashing out: ?try If `L-BFGS-B' does not work well, you could try the `spg' function in the BB package. Ravi. -Original Message- From:

Re: [R] Problem with predict.coxph

In examining the predict.coxph functions for the library I have with 2.7.1 versus the library with 2.9.1 I find a major rewrite of the function. A number of internal survival functions are no longer present so much of the code has changed. This makes identifying the specific problem beyond my

Re: [R] scale or not to scale that is the question - prcomp

On 8/19/2009 10:14 AM, Petr PIKAL wrote: Duncan Murdoch murd...@stats.uwo.ca napsal dne 19.08.2009 15:25:00: On 19/08/2009 9:02 AM, Petr PIKAL wrote: Thank you Duncan Murdoch murd...@stats.uwo.ca napsal dne 19.08.2009 14:49:52: On 19/08/2009 8:31 AM, Petr PIKAL wrote: Dear all

Re: [R] ridge regression

If you didn't post anonymously I would have made a suggestion. Full names and affiliations should be given. Frank spime wrote: Dear all, I considered an ordinary ridge regression problem. I followed three different ways: 1. estimate beta without any standardization 2. estimate standardized

Re: [R] need help for t.test using by

On Aug 19, 2009, at 9:00 AM, 1Rnwb wrote: any one I looked at your posting yesterday and could not figure out what your statistical question was, nor could I figure out how the t.test formula related to the column names in the data.frame. I saw no Group or IL1Ra variables in your

Re: [R] Fitting a logistic regression

I would suggest a model with a baseline level, something like nls(AMP~E0+(Emax-E0)*Time**gamma/(EC50**gamma+Time**gamma),data=your data, start=list(EC50=50,gamma=2,E0=0.2,Emax=1.2))-mod.test AIC(mod.test) does improve. Hope this helps. Jun On Wed, Aug 19, 2009 at 5:04 AM, Dani Valverde

Re: [R] Package read large file

On Wed, Aug 19, 2009 at 10:51 AM, Mohamed Lajnefmohamed.laj...@inserm.fr wrote: I am looking for packages that could read large files in R? any suggestions are welcome. As already pointed out by Jim, your question is not very specific. My wild guess is that you probably have some memory issues

Re: [R] mild and extreme outliers in boxplot

Rnewbie ha scritto: dear all, could somebody tell me how I can plot mild outliers as a circle(°) and extreme outliers as an asterisk(*) in a box-whisker plot? Thanks very much in advance ?boxplot or help(bxp) __ R-help@r-project.org mailing

Re: [R] Embedding lists in matrices and matrices in lists

Thanks, that was the solution! But in fact I didn't want to have this list of lists layer at all. And now I'm having trouble writing matrices into the database. It's really really strange... If I write a matrix into the database manually everything works, but if I create a function which adds

[R] Hist kernel density estimates

Dear All, Attached are the codes of a histogram a kernel density estimate and the output they produced. In fact the variable q is a vector of 1000 simulated values; that is I generated 1000 samples from the pareto distribution, from each sample I calculated the value of q ( a certain fn in

Re: [R] Hist kernel density estimates

Hi, I think I've not received the attachment. Please check. Thanks and Regards. - Indranil Basu, Bangalore, India On Wed, Aug 19, 2009 at 9:01 PM, maram salem marammagdysa...@yahoo.comwrote: Dear All, Attached are the codes of a histogram a kernel density estimate and the output they

Re: [R] scale or not to scale that is the question - prcomp

Ok Thank you for your time. Best regards Petr Pikal Duncan Murdoch murd...@stats.uwo.ca napsal dne 19.08.2009 16:29:07: On 8/19/2009 10:14 AM, Petr PIKAL wrote: Duncan Murdoch murd...@stats.uwo.ca napsal dne 19.08.2009 15:25:00: On 19/08/2009 9:02 AM, Petr PIKAL wrote: Thank you

Re: [R] edit.row.names taking row names from the edited dataframe

Erik Iverson ha scritto: This really has nothing to do with the row names issue you mention, as far as I can tell. It has to do with this: http://stackoverflow.com/questions/1195826/dropping-factor-levels-in-a-subsetted-data-frame-in-r Best, Erik Iverson Perhaps you may also take a

Re: [R] graph label greek symbol failure

On Wed, 2009-08-19 at 14:20 +0100, e-letter wrote: On 18/08/2009, Gavin Simpson gavin.simp...@ucl.ac.uk wrote: On Tue, 2009-08-18 at 13:06 +0100, e-letter wrote: On 17/08/2009, Michael Knudsen micknud...@gmail.com wrote: On Mon, Aug 17, 2009 at 12:51 PM, e-letter inp...@gmail.com wrote:

Re: [R] Hist kernel density estimates

On Aug 19, 2009, at 11:34 AM, indranil basu wrote: Hi, I think I've not received the attachment. Please check. In all likelihood the OP did not read and follow the instructions regarding attachments that are to be found in the Posting Guide. Thanks and Regards. - Indranil Basu,

Re: [R] visualizzazione colonne

sabrina.michie...@alice.it ha scritto: ciao, ho aperto un file in R di classe data frame di 15000 righe e 29 colonne. Nella console però sono visualizzate solo la prima e l'ultima colonna e le ultime 8000 righe circa. E' possibile una visualizzazione completa? Grazie Sabrina Hi Sabrina,

Re: [R] Confidence interval on parameters from optim function

Regrading your second question, I guess somehow you get undefined value like logarithm of zero of your target function for some unfortunate parameter values in the parameter space. Devred, Emmanuel wrote: Hi everyone, I have two questions: I would like to get confidence intervals on

Re: [R] how to compute other columns without a column for sample name

sandsky ha scritto: Data has the first row for variable name and the first column for sample name. I want to take Log for all data, but how to compute without the first column for sample name. log.raw_data=log(raw_data,base=2) Error in Math.data.frame(list(sample_id = c(1L, 2L, 3L, 4L,

Re: [R] Problem with predict.coxph

-- begin included message --- We occasionally utilize the coxph function in the survival library to fit multinomial logit models. (The breslow method produces the same likelihood function as the multinomial logit). We then utilize the predict function to create summary results for various

[R] Fw: Hist kernel density estimates

For the hist estimate par(mex=1.3) dens-density(q) options(scipen=4) ylim-range(dens$y) h-hist(q,breaks=scott,freq=FALSE,probability=TRUE, +  right=FALSE,xlim=c(9000,16000),ylim=ylim,main=Histogram of q(scott)) lines(dens) box()   For the kernel estimateoptions(scipen=4) d - density(q, bw =

Re: [R] graph label greek symbol failure

On 19/08/2009, Gavin Simpson gavin.simp...@ucl.ac.uk wrote: On Wed, 2009-08-19 at 14:20 +0100, e-letter wrote: On 18/08/2009, Gavin Simpson gavin.simp...@ucl.ac.uk wrote: On Tue, 2009-08-18 at 13:06 +0100, e-letter wrote: On 17/08/2009, Michael Knudsen micknud...@gmail.com wrote: On Mon,

Re: [R] scale or not to scale that is the question - prcomp

scaling changes the metric, ie which things are close to each other. there is no reason to expect the picture to look the same when you change the metric. On the other hand, your two pictures don't look so different to me. It appears that the scaled plot is similar to the unscaled plot, with the

Re: [R] scale or not to scale that is the question - prcomp

If you mentally rotate the second biplot by 90 degrees, the plots are not so different. This just indicates that the 2nd and 3rd principal components have switched roles. Kevin Wright On Wed, Aug 19, 2009 at 10:09 AM, Petr PIKAL petr.pi...@precheza.cz wrote: Ok Thank you for your time.

Re: [R] graph label greek symbol failure

On Wed, 2009-08-19 at 17:06 +0100, e-letter wrote: snip / Being familiar with latex, I interpret your description of the tilde (~) as non-breaking space, therefore I used the command: plot(1:10,ylab=expression(temperature~delta*t)) to give me the result I wanted; in other words the space

[R] BUGS

I am running a BUGS function with following   schools.sim -bugs(data,inits, parameters, model.file=schools.txt, n.chains=3, n.iter=1000,

Re: [R] Is there a construct for conditional comment?

I believe that #if lines for C++ programs is handled by the preprocessor, not the compiler. So if you want the same functionality for R programs, it would make sense to just preprocess the R file. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare

Re: [R] BUGS

Naively it seems that there is no school.txt file in your specified directory. Stephen Sefick On Wed, Aug 19, 2009 at 12:05 PM, James Lenihanjamesleni...@sbcglobal.net wrote: I am running a BUGS function with following schools.sim -bugs(data,inits, parameters,  

[R] Best performance measure?

Hello, I working on a model to predict probabilities. I don't really care about binary prediction accuracy. I do really care about the accuracy of my probability predictions. Frank was nice enough to point me to the val.prob function from the Design library. It looks very promising for my

[R] Erros with RVM and LSSVM from kernlab library

Hello, In my ongoing quest to develop a best model, I'm testing various forms of SVM to see which is best for my application. I have been using the SVM from the e1071 library without problem for several weeks. Now, I'm interested in RVM and LSSVM to see if I get better performance. When

Re: [R] BUGS

stephen sefick wrote: Naively it seems that there is no school.txt file in your specified directory. Stephen Sefick On Wed, Aug 19, 2009 at 12:05 PM, James Lenihanjamesleni...@sbcglobal.net wrote: I am running a BUGS function with following schools.sim -bugs(data,inits,

Re: [R] Best performance measure?

Noah Silverman wrote: Hello, I working on a model to predict probabilities. I don't really care about binary prediction accuracy. I do really care about the accuracy of my probability predictions. Frank was nice enough to point me to the val.prob function from the Design library. It looks

[R] a bug in the offset parameter syntax in the geepack package?

Dear R-users, I was doing some Poisson regression using the geepack package and I found a strange behaviour of the geeglm command when defining an offset. Maybe it's my limited knowledge of R syntax, or maybe it's something else. Let's make an example. After loading the geepack library, you may

[R] Urgent Help

Dear Sir, I am using RClimDex. I get following error. Error in scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : scan() expected 'a real', got 'T' I have done copy paste of climate data from excel file to notepad and tried to upload. I do not have any

Re: [R] Error with acf/pacf functions

Ok strangely both acf and pacf work with the xts object as long as the xts package hasn't been loaded. As soon as I load the package, I get the error again. tmakino wrote: I'm trying to apply a acf/pacf function to a xts object and get the following error: Error in if (frequency 1

[R] Ridge regression [Repost]

Dear all, For an ordinary ridge regression problem, I followed three different approaches: 1. estimate beta without any standardization 2. estimate standardized beta (standardizing X and y) and then again convert back 3. estimate beta using lm.ridge() function

Re: [R] lmer with random slopes for 2 or more first-level factors?

Since nobody has answered yet, let me try. I'm not 100% sure. (So why bother? To check my own understanding.) On 08/18/09 20:47, Jason R. Finley wrote: I have data from a design in which items are completely nested within subjects. Subject is the only second-level factor, but I have

Re: [R] double precision

Roger Bivand wrote: On Tue, 5 Dec 2006, Yoni Schamroth wrote: Hi, I am attempting to query a data frame from a mysql database. One of the variables is a unique identification number (numeric) 18 digits long. I am struggling to retrieve this variable exactly without any rounding.

Re: [R] Urgent Help

On Wed, 19 Aug 2009 10:01:19 -0700 (PDT) Bin1aya bpasakh...@gmail.com wrote: B I have done copy paste of climate data from excel file to notepad B and tried to upload. I do not have any knowledge about programming B languages. Please help me. There are better ways of importing data from Excel.

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