[R] ggplot2: how to label lines?

Hi, all, Let's say I have some time series data--10 subjects measured 20 times--that I plot as follows: library(ggplot2) dat - data.frame(subject=as.factor(rep(1:10, each=20)), time=rep(1:20, 10), measure=as.vector(replicate(10, rnorm(20, mean=runif(1, 0, 15), sd=runif(1, 1, 3) p -

[R] problem with arima() function

Hi I posted this problem yesterday but didn't get a reply so I try again today. I hope someone can help me with this. thank you very much for the help cheers Benedikt I would like to use arima () to find the best arima model for a time series. The default in arima

[R] Odp: Panel regression

Hi did you look at help page of lme? r-help-boun...@r-project.org napsal dne 25.10.2010 22:59:40: Hi, I am trying to run a panel regression where I have a matrix of observations and a matrix of independant variables - examples would trying to predict countries's GDP with their data

Re: [R] Conditional looping over a set of variables in R

Hi r-help-boun...@r-project.org napsal dne 25.10.2010 20:41:55: Adrienne, there's one glitch when I implement your solution below. When the loop encounters a case with no data at all (that is, all 140 item responses are missing), it aborts and prints this error message: ERROR: argument

[R] runtime on ising model

So I'm in a stochastic simulations class and I having issues with the amount of time it takes to run the Ising model. I usually don't like to attach the code I'm running, since it will probably make me look like a fool, but I figure its the best way I can find any bits I can speed up run time.

[R] (no subject)

hello. how are you? my name is arsalan. I'm from iran. i want to write the program that done random walk(one variable and two variable). please help me. thank you __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help

Re: [R] ggplot2: how to label lines?

Hi, Have a look at the directlabels package; it does just that for lattice and ggplot2. HTH, baptiste On 26 October 2010 08:02, Jeffrey Spies jsp...@virginia.edu wrote: Hi, all, Let's say I have some time series data--10 subjects measured 20 times--that I plot as follows:

Re: [R] Extract table from a webpage

Maybe you should take a look at the view all button. From there you can guess the next link: http://www.etintelligence.com/etig/et500/et500Ranking.jsp?param=1msg=1year=2010rslt=500 this should give you the whole list Bart -- View this message in context:

Re: [R] Help saving multiple graphics

I have many emails such as the one below, where someone gives thanks for being helped but the help or answer that was given is excluded. I believe, perhaps I am wrong, that emails such as this should not be copied to the list. Such emails only fill up our mail boxes and we DO NOT gain anything

Re: [R] Artifacts in filled.contour+pdf

Thanks David! Indeed the printout is perfect. But this image (produced with higher resolution) should appear in a publication. I will ask to the author to check her copy of the manuscript, if it is acceptable. Anyway, thanks for the pointer to pdf doc.

Re: [R] Artifacts in filled.contour+pdf

Thanks Baptiste! the problem with lattice (or more likely with my ignorance) is that it does not accept NA values. Ciao! mario On 26-Oct-10 07:38, baptiste auguie wrote: Hi, As an alternative, maybe you could use lattice::panel.levelplot.raster which I think doesn't have

Re: [R] Help saving multiple graphics

Hi I agree with this statement especially more complicated problems with longer history of answers could be quite confusing when the history itself is missing in some email. Besides reading help list questions and answers is convenient and quick way to learn R. I do it myself even after

[R] Mahalanobis distance

Hi everyone, Can you please help me on how to estimate the Mahalanobis distance in a large matrix Thanks Ivone [[alternative HTML version deleted]] __ R-help@r-project.org mailing list

Re: [R] rgdal intallation mac ox x

Hi Dr. Vilchis, On Mon, Oct 25, 2010 at 7:11 PM, L. Ignacio Vilchis livilc...@ucdavis.edu wrote: Hi all, Could anybody who has successfully installed the rgdal package on r64 on a mac help me out.  I have downloaded all o the needed frameworks(gdal, proj, etc), I am just having trouble

[R] Markov Switching with TVTP - problems with convergence

Greetings fellow R entusiasts! We have some problems converting a computer routine written initially for Gauss to estimate a Markov Regime Switching analysis with Time Varying Transition Probability. The source code in Gauss is here:

Re: [R] calculate area between intersecting polygons

Thanks for your reply, My main issue is that I don't have any equations to generate the data, just a bunch of points, each corresponding to a polygon. I was looking in package sp and there is a function to calculate areas ( areapl()), but not for intersecting polygons. Is there any other package

[R] lattice key subtitle

Hello everybody, Is there a way to add a subtitle to a lattice key? It is important form me that the subtitle must be linked to the key because those graphs are produced on a daily temporal scale, and the numbers of rectangles from the key may be different from day to day. Thank you, Alexandru

[R] datetime objects

I am trying to create an array of date time objects using the strptime function. The first entry is in the form 1/1/1981 0:00 and U use; strptime(datetime, %m/%d/%Y %H:%M) which gives 1981-01-01 EST. How do I alter this to give me 1981-01-01 0:00 EST? Thanks in advance, Doug -- View this

Re: [R] runtime on ising model

On 10/26/2010 04:50 PM, Michael D wrote: So I'm in a stochastic simulations class and I having issues with the amount of time it takes to run the Ising model. I usually don't like to attach the code I'm running, since it will probably make me look like a fool, but I figure its the best way I

[R] Odp: Mahalanobis distance

Hi r-help-boun...@r-project.org napsal dne 26.10.2010 10:55:57: Hi everyone, Can you please help me on how to estimate the Mahalanobis distance in a large matrix did you by chance tried ?mahalanobis Regards Petr Thanks Ivone

[R] Setting constraints in the glm package

Hi, I would like to set a constraint on the fixed effect estimates in a GLM model, such as b1=b2. Is this possible in the glm package? Similarly I would like to set some to equal zero too. I have tried searching the information with this package, but I can't find anything for this. Thanks in

Re: [R] calculate area between intersecting polygons

jonas garcia garcia.jonas80 at googlemail.com writes: Thanks for your reply, My main issue is that I don't have any equations to generate the data, just a bunch of points, each corresponding to a polygon. I was looking in package sp and there is a function to calculate areas (

[R] Fitting GLM with BFGS algorithm

Dear all, By default the glm function in the stats package use IWLS. How can I fit a glm model using BFGS algorithm ? Justin BEM BP 1917 Yaoundé Tél (237) 76043774 [[alternative HTML version deleted]] __ R-help@r-project.org mailing

Re: [R] Fitting GLM with BFGS algorithm

for instance, for logistic regression you can do something like this: # simulate some data x - cbind(1, runif(100, -3, 3), rbinom(100, 1, 0.5)) y - rbinom(100, 1, plogis(c( x%*% c(-2, 1, 0.3 # BFGS from optim() fn - function (betas, y, x) { -sum(dbinom(y, 1, plogis(c(x %*% betas)), log =

Re: [R] Time series data with dropouts/gaps

On 10/25/2010 09:37 PM, Gabor Grothendieck wrote: On Tue, Oct 26, 2010 at 12:28 AM, Bob Cunninghamflym...@gmail.com wrote: I have time-series data from a pair of inexpensive self-logging 3-axis accelerometers (http://www.gcdataconcepts.com/xlr8r-1.html). Since I'm not sure of the

Re: [R] Time series data with dropouts/gaps

From: ggrothendi...@gmail.com Date: Tue, 26 Oct 2010 00:37:05 -0400 To: flym...@gmail.com CC: r-help@r-project.org Subject: Re: [R] Time series data with dropouts/gaps On Tue, Oct 26, 2010 at 12:28 AM, Bob Cunningham wrote: I have

Re: [R] calculate area between intersecting polygons

Here is a different solution: library(gpclib) p1 - as(poly1, gpc.poly) p2 - as(poly2, gpc.poly) area.poly(p2) + area.poly(p1) - area.poly(union(p1,p2)) I.e., take areas of both polygons and subtract the union (check plot(union(p1,p2)) ) to get the area of the intersection. greetings, Remko

Re: [R] datetime objects

like this: format(strptime(datetime, %m/%d/%Y %H:%M), %m/%d/%Y %H:%M %Z) remko -- View this message in context: http://r.789695.n4.nabble.com/datetime-objects-tp3013417p3013604.html Sent from the R help mailing list archive at Nabble.com. __

Re: [R] calculate area between intersecting polygons

Dear Jonas, I already had to deal with such an issue. Your can use the joinPolys function from the package PBSmapping, with INT as operation. The maptools package has functions SpatialPolygons2PolySet and PolySet2SpatialPolygons to switch between formats suitable for sp or PBSmapping. Hope this

[R] Dispersion ( Plot error bars ) help

Dear List, I am looking to plot error bars on a line using dispersion. I have values for the upper value and for the lower values, however i am unsure how to plot different values for the upper CI and the lower CI? I have been using dispersion(1:35,sim,simCI,col=red) Where there are 35

[R] Reading in a tab delimitated file

Hi all, I have a total newbie question, but I could really use some help. I need to read in this file: SampleIDDisease E-CBIL-28-raw-cel-1435145228.cel1 E-CBIL-28-raw-cel-1435145451.cel2 E-CBIL-28-raw-cel-1435145479.cel2

[R] overall p-value for LASSO model resulting from glmnet

Dear experts, I am using the LASSO method (a shrinkage and selection method for linear regression) to create regression models. I am using the package glmnet My aim is to calculate an overall p-value for a certain regression model with a certain lambda. I would like to do this with a

Re: [R] Reading in a tab delimitated file

2010/10/26 amindlessbrain jillianrowe91...@gmail.com (I'm not sure why the disease column isn't showing up as a tab here, but it is sep by \t in my file. You've got a double tab space, I don't know is there a prettier way, but paste this: pd-read.delim(new_treat.txt,sep=) --

Re: [R] ggplot2: how to label lines?

baptiste auguie baptiste.auguie at googlemail.com writes: Hi, Have a look at the directlabels package; it does just that for lattice and ggplot2. Note that this package is on r-forge, not CRAN http://directlabels.r-forge.r-project.org/ [very nice examples]

Re: [R] calculate area between intersecting polygons

Remko Duursma remkoduursma at gmail.com writes: Here is a different solution: library(gpclib) p1 - as(poly1, gpc.poly) p2 - as(poly2, gpc.poly) area.poly(p2) + area.poly(p1) - area.poly(union(p1,p2)) I.e., take areas of both polygons and subtract the union (check plot(union(p1,p2))

Re: [R] Mahalanobis distance

Hi In that case you have to wait if some more capable people will try to answer you. Besides there are some clustering methods which maybe you can use directly. ??cluster Regards Petr Ivone Figueiredo ivone...@ipimar.pt napsal dne 26.10.2010 12:36:20: Hi Yes we tried but this function

Re: [R] (no subject)

On Oct 25, 2010, at 11:17 PM, Arsalan Fathi wrote: hello. how are you? my name is arsalan. I'm from iran. i want to write the program that done random walk(one variable and two variable). please help me. You should learn to use a search engine that is specific to R. Here's an example:

[R] stripping #s in a text file prior to reading into table or dataframe

I'm importing a lot of text tables of data (from Latent Gold) that includes hashes in some of the column names (Cluster#1, Cluster#2, etc.). Is there an easy way to strip the offending hashes out before pushing the text into a table or data frame? I thought I'd use gsub, e.g., but can't figure

Re: [R] (no subject)

On Tue, Oct 26, 2010 at 10:27 AM, David Winsemius dwinsem...@comcast.net wrote: On Oct 25, 2010, at 11:17 PM, Arsalan Fathi wrote: hello. how are you? my name is arsalan. I'm from iran. i want to write the program that done random walk(one variable and two variable). please help me. You

Re: [R] Reading in a tab delimitated file

A call to read.table(..., sep = , ...) reads in any length of whitespace as the delimiter. On your sample text it read in a 2 column dataframe. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304)

[R] to determine the variable importance in svm

hii everyone!! i have two questions: 1) How to obtain a variable (attribute) importance using e1071:SVM (or other svm methods)? 2) how to validate the results of svm? currently i am using the following code to determine the error. library(ipred) for(i in 1:20) error.model1[i]-

Re: [R] Markov Switching with TVTP - problems with convergence

I've looked at the Kim/Nelson gauss code before, and I applaud your effort to convert it to R. I'm happy to have a look at it for you if you are willing to share your example. -Whit On Tue, Oct 26, 2010 at 4:13 AM, Houge jb.ho...@gmail.com wrote: Greetings fellow R entusiasts! We have some

[R] R on 32-bit ubuntu with PAE enabled

morning, all right now, I have R installed on a 32-bit ubuntu with PAE enabled. And I can see more than 4-g memory available in system monitor. my question is: might this 32-bit R take advantage of the extra memory and handle large data? thank you so much! wensui

Re: [R] stripping #s in a text file prior to reading into table or dataframe

On 26/10/2010 10:33 AM, Donald Braman wrote: I'm importing a lot of text tables of data (from Latent Gold) that includes hashes in some of the column names (Cluster#1, Cluster#2, etc.). Is there an easy way to strip the offending hashes out before pushing the text into a table or data frame? I

Re: [R] Setting constraints in the glm package

The constraint b1=b2 in a model such as b0 + b1 x1 + b2 x2 + b3 x3 implies that b0 + b1 (x1 + x2) + b3 x3, so just add x1 and x2 (call this x12) and fit the model b0 + b1 x12 + b3 x3 and you have imposed the constraint that b1=b2. To impose the constraint that b3=0, just fit the model without

Re: [R] Conditional looping over a set of variables in R

Thank you - I will try this solution as well. Sent via DROID X -Original message- From: Petr PIKAL petr.pi...@precheza.cz To: David Herzberg dav...@wpspublish.com Cc: Adrienne Wootten amwoo...@ncsu.edu, r-help@r-project.org r-help@r-project.org Sent: Tue, Oct 26, 2010 06:43:09

[R] approximation for sum of lognormal random variables

I am looking for approximation for sum of two lognormal variables. I found some papers suggesting power lognormal or Pearson type-IV, but I wonder if there is anything ready in R? Best regards, Ryszard -- Confidentiality

[R] Calculating confidence intervals on subset of bootstrap sample statistics

I have a vector of monthly log asset price returns. I would like use the boot package to sample one-year returns, and then calculate confidence intervals on the loss distribution only. More concretely, I would like to say something like 99% of LOSSES (not RETURNS) are above cutoff X. If the

[R] Multiple, multiple regressions...

Caveats and disclaimers: I am quite happy to undertake self-teaching if directed to a relevant prior posting and welcome such direction. I have programming and statistical training/experience which I would characterize as Masters level. Thank you for reading and replying to this post. It is very

Re: [R] Reading in a tab delimitated file

A call to read.table(..., sep = , ...) reads in any length of whitespace as the delimiter. On your sample text it read in a 2 column dataframe. Thanks! That works for the file, but when I enter in my next line of code it doesn't work. I'm not sure if this is the problem, or if the next line is

Re: [R] Reading in a tab delimitated file

If I try that I get this: Error in scan(file, what = , sep = sep, quote = quote, nlines = 1, quiet = TRUE, : invalid 'sep' value: must be one byte ? -- View this message in context: http://r.789695.n4.nabble.com/Reading-in-a-tab-delimitated-file-tp3013620p3013771.html Sent from the R

Re: [R] Reading in a tab delimitated file

Try this: Lines - SampleIDDisease E-CBIL-28-raw-cel-1435145228.cel1 E-CBIL-28-raw-cel-1435145451.cel2 E-CBIL-28-raw-cel-1435145479.cel2 E-CBIL-28-raw-cel-1435145132.cel3 E-CBIL-28-raw-cel-1435145417.cel3 E-CBIL-28-raw-cel-1435145301.cel2

[R] Forcing results from lm into datframe

Hi I need some help getting results from multiple linear models into a dataframe. Let me explain the problem. I have a dataframe with ejection fraction results measured over a number of quartiles and grouped by base_study. My dataframe (800 different base_studies) looks like afvtprelvefs

Re: [R] Reading in a tab delimitated file

Right, I forgot to mention to use header = T. -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself have purpose? Or do

Re: [R] stripping #s in a text file prior to reading into table or dataframe

That's one of the things I tried, but which didn't work. I get the following error when I do that: Error in read.table(file = don.5.clusters.txt, header = TRUE, comment.char = , : more columns than column names If I remove the hashes by other means, I don't get that error. On Tue, Oct 26,

Re: [R] Setting constraints in the glm package

On Oct 26, 2010, at 7:50 AM, Viechtbauer Wolfgang (STAT) wrote: The constraint b1=b2 in a model such as b0 + b1 x1 + b2 x2 + b3 x3 implies that b0 + b1 (x1 + x2) + b3 x3, so just add x1 and x2 (call this x12) and fit the model b0 + b1 x12 + b3 x3 and you have imposed the constraint that

[R] mixed effects regression with weights using lme (lme4)

Hello! I am sorry if it's a naive/wrong question. But can one run a regression with weights using lme? Thank you! -- Dimitri Liakhovitski Ninah Consulting www.ninah.com __ R-help@r-project.org mailing list

[R] Zoom in in a plot

in a simple plot. When i do plot is it possible to zoom in or out or this is not possible at all? Best Regards Alex [[alternative HTML version deleted]] __ R-help@r-project.org mailing list

Re: [R] Forcing results from lm into datframe

On Oct 26, 2010, at 8:08 AM, Small Sandy (NHS Greater Glasgow Clyde) wrote: Hi I need some help getting results from multiple linear models into a dataframe. Let me explain the problem. I have a dataframe with ejection fraction results measured over a number of quartiles and grouped

Re: [R] Zoom in in a plot

Hi Alex, After you have created the plot I do not know of a way to zoom (in base graphics), but you can always use the xlim and ylim arguments to focus on a particular area (or effectively zoom) when you are create the plot. For instance, plot(x = 1:10, y = 1:10) plot(x = 1:10, y = 1:10, xlim

Re: [R] Zoom in in a plot

I think that this would be possible if you save the graph to a scalable format. Try looking into: ?postscript ?xfig ?pdf -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a

Re: [R] mixed effects regression with weights using lme (lme4)

Hi Dimitri, The lme function is not in the lme4 package, so there is some confusion there. But you can use weights with the lmer function in lme4. ?lmer tells you that weights are specified the same way as in the lm function, and refers you to ?lm for details. HTH, Ista On Tue, Oct 26, 2010 at

Re: [R] Zoom in in a plot

On Oct 26, 2010, at 8:30 AM, Alaios wrote: in a simple plot. When i do plot is it possible to zoom in or out or this is not possible at all? Zoom? Do you mean restrict the region plotted to specific ranges? xlim and ylim arguments provide that facility. -- David. Best Regards Alex

Re: [R] Zoom in in a plot

On Tue, Oct 26, 2010 at 8:38 AM, Jonathan P Daily jda...@usgs.gov wrote: I think that this would be possible if you save the graph to a scalable format. This is true to an extent. I have not checked on postscript or xfig, but at least for PDF, even though you can zoom/blow the picture up, you

Re: [R] stripping #s in a text file prior to reading into table or dataframe

Try this: read.table('don.5.clusters.txt', header = TRUE, comment.char = '', quote = '') On Tue, Oct 26, 2010 at 1:15 PM, Donald Braman dbra...@law.gwu.edu wrote: That's one of the things I tried, but which didn't work. I get the following error when I do that: Error in read.table(file =

[R] Which version control system to learn for managing R projects?

Hello all, I wish to learn a version control system for managing my R (data analysis) projects. I know of SVN and github, and wonder if there is any reason for which I should prefer the one over the other (or any other platform). An example for a reason could be if it will make it easier for me

Re: [R] Zoom in in a plot

On 26/10/2010 11:30 AM, Alaios wrote: in a simple plot. When i do plot is it possible to zoom in or out or this is not possible at all? There's no general support for that, but you could conceivably write it yourself using getGraphicsEvent. The example code there adjusts xlim and ylim

Re: [R] Which version control system to learn for managing R projects?

On 26/10/2010 12:16 PM, Tal Galili wrote: Hello all, I wish to learn a version control system for managing my R (data analysis) projects. I know of SVN and github, and wonder if there is any reason for which I should prefer the one over the other (or any other platform). An example for a

Re: [R] Conditional looping over a set of variables in R

I would still recommend vector_of_column_number - apply(yourdata, 1, match, x=1) as the simplest way if you only want the number of the column that has the first 1 or 1 (the call works as is for both numeric and character data). Rows which have no 1s will return a value of NA. Anything wrong

Re: [R] Setting constraints in the glm package

Many thanks for the help. I assumed that I would need to account for the variables in the model, even though I wish to assign a zero coefficient to them. I've looked at the offset function, but does this not just assign the value 1 to the variables? How would I specify a zero coefficient to more

Re: [R] mixed effects regression with weights using lme (lme4)

Thanks a lot - it's very helpful. On Tue, Oct 26, 2010 at 11:37 AM, Ista Zahn iz...@psych.rochester.edu wrote: Hi Dimitri, The lme function is not in the lme4 package, so there is some confusion there. But you can use weights with the lmer function in lme4. ?lmer tells you that weights are

Re: [R] Setting constraints in the glm package

We can further generalize this: Suppose we want to constrain parameters such that : b2 = a * b1 b3 = a * b1 We can do the following: fit.a - glm( y ~ I(x1 + a* x2 + a * x3), data= , ... ) For a fixed value of `a', we compute the log-likelihood of `fit.a'. This is the profile

Re: [R] Zoom in in a plot

For a quick exploration of the plot you can use the zoomplot function in the TeachingDemos package. But for production graphs it is better to explicitly set the xlim and ylim parameters in creating the plot up front. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain

Re: [R] to determine the variable importance in svm

The caret package has answers to all your questions. -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Neeti Sent: Tuesday, October 26, 2010 10:42 AM To: r-help@r-project.org Subject: [R] to determine the variable importance

Re: [R] Chron object in time series plot

Thanks for your help Gabor. That would be exactly what I am looking for. If I use your code I get the nice representation I am looking for. However, when I try to apply the code in the same fashion to my case, it does not produce the x-axis. I believe the problem hinges on the following warning

Re: [R] Chron object in time series plot

On Tue, Oct 26, 2010 at 12:56 PM, Manta mantin...@libero.it wrote: Thanks for your help Gabor. That would be exactly what I am looking for. If I use your code I get the nice representation I am looking for. However, when I try to apply the code in the same fashion to my case, it does not

Re: [R] Which version control system to learn for managing R projects?

On Oct 26, 2010, at 11:22 AM, Duncan Murdoch wrote: On 26/10/2010 12:16 PM, Tal Galili wrote: Hello all, I wish to learn a version control system for managing my R (data analysis) projects. I know of SVN and github, and wonder if there is any reason for which I should prefer the one

Re: [R] Forcing results from lm into datframe

Thanks David That's great As a matter of interest, to get a data frame by studies why do you have to do fitsdf - as.data.frame(t(as.data.frame(fits))) Why doesn't fitsdf - as.data.frame(t(fits)) work? Sandy Small From: David Winsemius

[R] lme vs. lmer results

Hello, and sorry for asking a question without the data - hope it can still be answered: I've run two things on the same data: # Using lme: mix.lme - lme(DV ~a+b+c+d+e+f+h+i, random = random = ~ e+f+h+i| group, data = mydata) # Using lmer mix.lmer - lmer(DV

Re: [R] Setting constraints in the glm package

On Oct 26, 2010, at 9:27 AM, David Smith wrote: Many thanks for the help. You could express your thanks by including context the next time you present a follow-up (as requested in the Posting Guide). Only a minority of readers view this list on Nabble, so we don't see the web

Re: [R] Forcing results from lm into datframe

On Oct 26, 2010, at 10:22 AM, Small Sandy (NHS Greater Glasgow Clyde) wrote: Thanks David That's great As a matter of interest, to get a data frame by studies why do you have to do fitsdf - as.data.frame(t(as.data.frame(fits))) The apply family of functions often return results

Re: [R] Which version control system to learn for managing R projects?

Marc is exactly right about people having strong opinions. R-forge is really the _only_ reason to consider using svn. git is where the world is headed. This video is a little old: http://www.youtube.com/watch?v=4XpnKHJAok8, but does a good job getting the point across. Hg is a good

Re: [R] Forcing results from lm into datframe

Try this: sapply(by(x, x$basestudy, lm, formula = ef ~ quartile), coef) On Tue, Oct 26, 2010 at 1:08 PM, Small Sandy (NHS Greater Glasgow Clyde) sandy.sm...@nhs.net wrote: Hi I need some help getting results from multiple linear models into a dataframe. Let me explain the problem. I

[R] ncdf4 package installation in R

Hello all, I could use some help installing the ncdf4 package in R (under CentOS 5.4). I've installed R-2.12.0, zlib-1.2.5, hdf5-1.8.4-patch1 and NetCDF4.1.1 from source. Make check reports all tests have passed for all of these programs. When I issue an 'install.packages(c('ncdf4')) in R,

Re: [R] superscript characters in title with '+'

On Fri, 2010-10-22 at 15:39 +0200, Claudia Beleites wrote: On 10/22/2010 03:15 PM, DrCJones wrote: snip / Being a chemist, it seemed natural to me to put the i after the concentration brackets into a subscript - though you didn't say you want that. A more correct expression would be:

Re: [R] ncdf4 package installation in R

shaticus wrote: Hello all, I could use some help installing the ncdf4 package in R (under CentOS 5.4). ... When I issue an 'install.packages(c('ncdf4')) in R, compilation succeeds but I receive the following error during the loading phase of installation: ** building package indices ...

Re: [R] (no subject)

On Fri, 2010-10-22 at 05:54 -0700, Penny Adversario wrote: I am doing cluster analysis on 8768 respondents on 5 lifestyle variables and am having difficulty constructing a dissimilarity matrix which I will use for PAM. I always get an error: “cannot allocate vector of size 293.3 Mb” even if

[R] chfactor.c, line 130 ERROR

Hi all, I have a problem with this code... as it generates an error in R. z-predict(dat.fit, newdata=grd) I saw a post on R forum about this [chfactor.c, line 130: singular matrix in function LDLfactor() ] error and tried pretty much anything I could read about it and still haven

[R] anomalies with the loess() function

Hello Masters, I run the loess() function to obtain local weighted regressions, given lowess() can't handle NAs, but I don't improve significantly my situation.., actually loess() performance leave me much puzzled I attach my easy experiment below

[R] Cox Proportional Models and Haplotypes

Hello, I was wondering if anyone knew of a function that fits haplotype data into a cox proportional hazard model. I have computed my Haplotype frequencies using the haplo.stats package. I have also been using the haplo.glm function but this is a linear regression and is not quite what I am

Re: [R] runtime on ising model

I have an update on where the issue is coming from. I commented out the code for pos[k+1] - M[i,j] and the if statement for time = 10^4, 10^5, 10^6, 10^7 and the storage and everything ran fast(er). Next I added back in the pos statements and still runtimes were good (around 20 minutes). So I'm

Re: [R] Forcing results from lm into datframe

Hi: When it comes to split, apply, combine, think plyr. library(plyr) ldply(split(afvtprelvefs, afvtprelvefs$basestudy), function(x) coef(lm (ef ~ quartile, data=x, weights=1/ef_std))) .id (Intercept) quartile 1 CBP090802020.92140 3.38546887 2 CBP090802129.31632

Re: [R] Which version control system to learn for managing R projects?

git is where the world is headed.  This video is a little old: http://www.youtube.com/watch?v=4XpnKHJAok8, but does a good job getting the point across. And lots of R users are using github already: http://github.com/languages/R/created Hadley -- Assistant Professor / Dobelman Family Junior

Re: [R] superscript characters in title with '+'

On Oct 26, 2010, at 11:15 AM, Gavin Simpson wrote: On Fri, 2010-10-22 at 15:39 +0200, Claudia Beleites wrote: On 10/22/2010 03:15 PM, DrCJones wrote: snip / Being a chemist, it seemed natural to me to put the i after the concentration brackets into a subscript - though you didn't say

Re: [R] anomalies with the loess() function

?loess use this instead: fit - loess(b~a) lines(a, predict(fit)) -- Jonathan P. Daily Technician - USGS Leetown Science Center 11649 Leetown Road Kearneysville WV, 25430 (304) 724-4480 Is the room still a room when its empty? Does the room, the thing itself

Re: [R] Cox Proportional Models and Haplotypes

On Oct 26, 2010, at 8:57 AM, sr500 wrote: Hello, I was wondering if anyone knew of a function that fits haplotype data into a cox proportional hazard model. I have computed my Haplotype frequencies using the haplo.stats package. I have also been using the haplo.glm function but this is

Re: [R] Forcing results from lm into datframe

On Tue, Oct 26, 2010 at 11:55 AM, Dennis Murphy djmu...@gmail.com wrote: Hi: When it comes to split, apply, combine, think plyr. library(plyr) ldply(split(afvtprelvefs, afvtprelvefs$basestudy),         function(x) coef(lm (ef ~ quartile, data=x, weights=1/ef_std))) Or do it in two steps:

[R] specify strata in survfit

Is it possible to get survfit to produce the survival line for a single strata like preddow - survfit(modall,newdata=newdat,se.fit=F,strata=2) # the strata argument is being ignored in the call above Or even get a more economical/faster calculation of the hazard directly from the coxph

[R] sbrier in ipred

Hello I am trying to use sbrier in ipred but got an error message (see below). Can someone help? --- I. function() { library(ipred) library(survival) set.seed(12345) age - rnorm(30, 50, 10) stime - rexp(30) cens - runif(30,.5,2) sevent - as.numeric(stime = cens) stime - pmin(stime, cens)

Re: [R] lme vs. lmer results

On Tue, Oct 26, 2010 at 12:27 PM, Dimitri Liakhovitski dimitri.liakhovit...@gmail.com wrote: Hello, and sorry for asking a question without the data - hope it can still be answered: I've run two things on the same data: # Using lme: mix.lme - lme(DV ~a+b+c+d+e+f+h+i, random = random = ~

  1   2   >