Re: [R] replace double backslash with singel backslash

2011-11-09 Thread Kay Cecil Cichini
Thanks, that helped! Yours, Kay Zitat von Gene Leynes gleyne...@gmail.com: I think that people are afraid to say You can't do that in R... But I think the real answer is: you can't do that in R. Although, it is helpful to understand Jeff's reply. I hadn't fully realized why this particular

[R] Min Frequency in findFreqTerms

2011-11-09 Thread vioravis
I am using 'tm' package for text mining. I use the function findFreqTerms to obtain the frequent words based on their frequency in the term document matrix. The following is the example given in the help page of this function: library(tm) data(crude) tdm - TermDocumentMatrix(crude)

Re: [R] Opening excel CSV file in R

2011-11-09 Thread Uwe Ligges
On 09.11.2011 04:42, Dan Zhou wrote: Hi, So I have everything written out. I used R-studio (same as R console but with an IDE) and I had no trouble calling upon and opening the csv file for computation. However, when I try to run my code in plain old R, it says that the file could not be

[R] Are there equivalents to xblocks or rect that can be used with plot.xts?

2011-11-09 Thread thierrydb
I would like to add vertical shaded blocks in plot.xts graphs (like recession periods in FRED graphs) The reason I use plot.xts instead of plot.zoo is that I like the fact that the grid is automatically aligned with major ticks in plot.xts. xblocks() and rect() do not seem to work with plot.xts

Re: [R] VAR and VECM in multivariate time series

2011-11-09 Thread Setlhare Lekgatlhamang
Hi, Please read Time series Econometrics books and you will find out that acf and pacf are not to be used to determine whether or not a series is stationary. The question of nonstationarity or stationarity of a series is answered using the formal tests comprising ADF, PP, KPSS, etc. I will let

[R] Installing binaries from R-Forge

2011-11-09 Thread Downey, Patrick
Hello, I'm attempting to install the splm package from R-Forge. https://r-forge.r-project.org/R/?group_id=352 The page says, In order to successfully install the packages provided on R-Forge, you have to switch to the most recent version of R... It later says To install this package directly

Re: [R] Are there equivalents to xblocks or rect that can be used with plot.xts?

2011-11-09 Thread Gabor Grothendieck
On Wed, Nov 9, 2011 at 4:33 AM, thierrydb thierr...@gmail.com wrote: I would like to add vertical shaded blocks in plot.xts graphs (like recession periods in FRED graphs) The reason I use plot.xts instead of plot.zoo is that I like the fact that the grid is automatically aligned with major

[R] Problem with simple random slope in gam and bam (mgcv package)

2011-11-09 Thread Martijn Wieling
Dear useRs, This is the first time I post to this list and I would appreciate any help available. I've used the excellent mgcv package for a while now to investigate geographical patterns of language variation, and it has has always worked without any problems for me. The problem below occurs

Re: [R] GAM

2011-11-09 Thread Simon Wood
Kilometres has only 5 unique values, while Bonus has only 7, but the default smoothing basis dimension for the s terms is 10, so there is a problem. Solution is to reduce the basis dimension. e.g. amgam - gam(log(Payment) ~ offset(log(Insured))+ + s(as.numeric(Kilometres),k=5) + s(Bonus,k=7) +

Re: [R] GAM

2011-11-09 Thread Patrick Breheny
On 11/08/2011 11:57 AM, Gyanendra Pokharel wrote: Hi R community! I am analyzing the data set motorins in the package faraway by using the generalized additive model. it shows the following error. Can some one suggest me the right way? library(faraway) data(motorins) motori-

Re: [R] Problem with simple random slope in gam and bam (mgcv package)

2011-11-09 Thread Simon Wood
Martijn, Thanks for this. It's a bug. The p-value computation involves model matrices for each `smooth' term (in your case actually a random effect). When the data set is large, then random sub-sampling of the data is used to keep the computational cost of these model matrices down. This is

Re: [R] Installing binaries from R-Forge

2011-11-09 Thread Uwe Ligges
The Windows binary seems not to be there. Since this is a development platform and there may be various reasons a binary does currently not exist, you could install the package from source, just add the argument type=source in your call to install.packages(). How to prepare your environment

Re: [R] window?

2011-11-09 Thread rkevinburton
Thank you. I am glad I asked. It wasn't giving answers that I expected and now I know why. Rather than pull in another package just for this functionality, I will just reassign the frequency by generating a new time series like: dswin - window(ds, start=..., end=...) dswin - ts(dswin,

Re: [R] Installing binaries from R-Forge

2011-11-09 Thread Downey, Patrick
Hi Uwe, Thanks for your response. I tried your suggestion and got the following error message: install.packages(splm, repos=http://R-Forge.R-project.org,type=source;) Warning message: In getDependencies(pkgs, dependencies, available, lib) : package 'splm' is not available I have downloaded

Re: [R] Installing binaries from R-Forge

2011-11-09 Thread Uwe Ligges
On 09.11.2011 15:15, Downey, Patrick wrote: Hi Uwe, Thanks for your response. I tried your suggestion and got the following error message: install.packages(splm, repos=http://R-Forge.R-project.org,type=source;) Warning message: In getDependencies(pkgs, dependencies, available, lib) :

Re: [R] Installing binaries from R-Forge

2011-11-09 Thread Downey, Patrick
I'm sorry. I made a mistake. I accidentally had 2 versions of R open and got that error message from R-2.10. When I correctly enter the commands you suggest into R-2.14 I get the same as you. However, my installation is filled with errors. I assume the following means that I should install each

[R] reorder data.frame

2011-11-09 Thread Johannes Radinger
Hello, I very general question but probably usefull to others as well: Is there any prebuild function that reorders a dataframe from: x1x2 1 100 200 2 101 201 3 102 202 4 103 203 5 104 204 6 105 205 to 1 100 x1 2 101 x1 3 102 x1 4 103 x1 5 104 x1 6 105 x1

Re: [R] window?

2011-11-09 Thread R. Michael Weylandt
Yes, that will definitely create a time series with the desired frequency, though the actual time index won't correspond to the original so you may need to exercise a little bit of caution in interpreting the outputs of ets(). Glad this could help, Michael On Wed, Nov 9, 2011 at 9:15 AM,

Re: [R] reorder data.frame

2011-11-09 Thread R. Michael Weylandt
df = data.frame(x1 = 100:105, x2 = 200:205) library(reshape2) melt(df) Michael On Wed, Nov 9, 2011 at 10:14 AM, Johannes Radinger jradin...@gmx.at wrote: Hello, I very general question but probably usefull to others as well: Is there any prebuild function that reorders a dataframe from:  

Re: [R] reorder data.frame

2011-11-09 Thread David Winsemius
On Nov 9, 2011, at 10:14 AM, Johannes Radinger wrote: Hello, I very general question but probably usefull to others as well: Is there any prebuild function that reorders a dataframe from: x1x2 1 100 200 2 101 201 3 102 202 4 103 203 5 104 204 6 105 205 to 1 100

Re: [R] Intervals in function cut

2011-11-09 Thread JulioSergio
jim holtman jholtman at gmail.com writes: ... Thanks Jim, very useful your information, Sergio. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

[R] algorithm that iteratively drops columns of a data-frame

2011-11-09 Thread Martin Batholdy
Dear R-Users, I have a problem with an algorithm that iteratively goes over a data.frame and exclude n-columns each step based on a statistical criterion. So that the 'column-space' gets smaller and smaller with each iteration (like when you do stepwise regression). The problem is that in

[R] Invalid 'yscale' in viewport

2011-11-09 Thread Erin Jonaitis
I tried Googling for help on this problem, but what I saw only increased my puzzlement. I found a lovely bit of code called esplot() that makes scatterplots with associated histograms and rug plots. I have been trying to use it on my own data, but the viewport routine on which it depends (I

Re: [R] algorithm that iteratively drops columns of a data-frame

2011-11-09 Thread R. Michael Weylandt
Perhaps attach placeholder names to your columns and use those rather than indices? Michael On Wed, Nov 9, 2011 at 10:36 AM, Martin Batholdy batho...@googlemail.com wrote: Dear R-Users, I have a problem with an algorithm that iteratively goes over a data.frame and exclude n-columns each

Re: [R] Installing binaries from R-Forge

2011-11-09 Thread Jeff Newmiller
As Uwe said, you need to read the fine manual and set up your system to be able to compile source packages. On Windows that essentially means installing Rtools and Miktek, and configuring some environment variables. --- Jeff

Re: [R] Installing binaries from R-Forge

2011-11-09 Thread Gabor Grothendieck
On Wed, Nov 9, 2011 at 11:08 AM, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: As Uwe said, you need to read the fine manual and set up your system to be able to compile source packages. On Windows that essentially means installing Rtools and Miktek, and configuring some environment

Re: [R] algorithm that iteratively drops columns of a data-frame

2011-11-09 Thread Jeff Newmiller
Try data[,!names(data) %in% names(col_means)] On Wed, 9 Nov 2011, Martin Batholdy wrote: Dear R-Users, I have a problem with an algorithm that iteratively goes over a data.frame and exclude n-columns each step based on a statistical criterion. So that the 'column-space' gets smaller and

[R] Interpreting Multiple Linear Regression Summary

2011-11-09 Thread Rich Shepard
I would appreciate pointers on what I should read to understand this output: summary(lm(TDS ~ Cond + Ca + Cl + Mg + Na + SO4)) Call: lm(formula = TDS ~ Cond + Ca + Cl + Mg + Na + SO4) Residuals: ALL 1 residuals are 0: no residual degrees of freedom! Coefficients: (6 not defined because of

Re: [R] Interpreting Multiple Linear Regression Summary

2011-11-09 Thread B77S
Please see ?dput use dput(your data) and paste the output into a reply, thanks. This way we know what you are working with. Rich Shepard wrote: I would appreciate pointers on what I should read to understand this output: summary(lm(TDS ~ Cond + Ca + Cl + Mg + Na + SO4)) Call:

Re: [R] Interpreting Multiple Linear Regression Summary

2011-11-09 Thread David Winsemius
On Nov 9, 2011, at 12:04 PM, Rich Shepard wrote: I would appreciate pointers on what I should read to understand this output: summary(lm(TDS ~ Cond + Ca + Cl + Mg + Na + SO4)) I don't see a data= argument specified, so you are telling lm() that your workspace has individual vectors by

[R] path.diagram in SEM--display covariances without variances

2011-11-09 Thread Dustin Fife
Forgive me if I'm posting to the wrong placeIt's my first time posting. Here's the situation: I'm using the sem package and making path diagrams using path.diagrams. Suppose I have the following code: #install.packages(ggm) require(ggm) cor = rcorr(7) nm = c(SOF, IWF, PWF, FSC, FSF, EF, GPA)

Re: [R] Interpreting Multiple Linear Regression Summary

2011-11-09 Thread Rich Shepard
On Wed, 9 Nov 2011, David Winsemius wrote: I don't see a data= argument specified, so you are telling lm() that your workspace has individual vectors by those names in the formula. That is not what is implied by hte rest of your message. David, That's because I attached the data frame

[R] Creating 3D plot

2011-11-09 Thread Michal Zimmermann
Hi to all, i have a data set of international airports with latitude, longitude and altitude. I was thinking of creating a 3D plot out of them, but haven't succeeded yet. With plot3d(x=seq(min(traffic$lon),max(traffic$lon)),y=seq(min(traffic$lat),max(traffic$lat)),z=traffic$alt) all i get is

[R] Help with tryCatch with a for loop

2011-11-09 Thread Spencer S
Hello all, I'm a beginner in R working on a script that will produce a set of models (linear, polynomial and logistic) for each location in a dataset. However, the self-starting logistic model often fails - if this happens I would like to just skip to the next iteration of the loop using

Re: [R] Interpreting Multiple Linear Regression Summary

2011-11-09 Thread Daniel Nordlund
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Rich Shepard Sent: Wednesday, November 09, 2011 9:05 AM To: r-help@r-project.org Subject: [R] Interpreting Multiple Linear Regression Summary I would appreciate pointers

Re: [R] Creating 3D plot

2011-11-09 Thread Sarah Goslee
Hi, On Wed, Nov 9, 2011 at 11:56 AM, Michal Zimmermann zimm...@gmail.com wrote: Hi to all, i have a data set of international airports with latitude, longitude and altitude. I was thinking of creating a 3D plot out of them, but haven't succeeded yet. With

Re: [R] Interpreting Multiple Linear Regression Summary

2011-11-09 Thread Daniel Nordlund
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Rich Shepard Sent: Wednesday, November 09, 2011 9:42 AM To: r-help@r-project.org Subject: Re: [R] Interpreting Multiple Linear Regression Summary On Wed, 9 Nov 2011, David

Re: [R] Invalid 'yscale' in viewport

2011-11-09 Thread R. Michael Weylandt
Two things: 1) It sounds like you are right in thinking there's something funny about your particular data: could you provide it to us? The easiest way to do so is to use dput() to get a plain text representation ready for copy and paste. 2) What is esplot()? It's not in base R, but I imagine

Re: [R] path.diagram in SEM--display covariances without variances

2011-11-09 Thread John Fox
Dear Dustin, -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Dustin Fife Sent: November-09-11 10:57 AM To: r-help@r-project.org Subject: [R] path.diagram in SEM--display covariances without variances Forgive me if I'm

Re: [R] path.diagram in SEM--display covariances without variances

2011-11-09 Thread Dustin Fife
Thanks for the quick response...I've never edited someone else's package before. How do I go about doing that? On Wed, Nov 9, 2011 at 12:47 PM, John Fox j...@mcmaster.ca wrote: Dear Dustin, -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org]

Re: [R] Interpreting Multiple Linear Regression Summary

2011-11-09 Thread Rich Shepard
On Wed, 9 Nov 2011, Daniel Nordlund wrote: I would guess that there is something problematic with the how the data frame is structured relative to what lm() is expecting. Dan, I was not comfortable with my explanation, but the formula (and data frame) was equivalent to those of the other 8

Re: [R] Interpreting Multiple Linear Regression Summary

2011-11-09 Thread Marc Schwartz
On Nov 9, 2011, at 1:17 PM, Rich Shepard wrote: On Wed, 9 Nov 2011, Daniel Nordlund wrote: I would guess that there is something problematic with the how the data frame is structured relative to what lm() is expecting. Dan, I was not comfortable with my explanation, but the formula

[R] raking weighting

2011-11-09 Thread Sebastián Daza
Hi everyone, Does anyone know if there is a package to compute raking weights using R? What I need is to create a variable with weights base in some demographic variables (e.g. sexo, age group, area) using the raking procedure. Thank you in advance! -- Sebastián Daza

[R] Error in drawing

2011-11-09 Thread Gyanendra Pokharel
I have got following error in drawing wavelet fitting. can some one help? library(faraway) data(lidar) newlidar-lidar[c(1:128),] library(wavethresh) wds - wd(newlidar$logratio) draw(wds) Error in plot.default(x = x, y = zwr, main = main, sub = sub, xlab = xlab, : formal argument type

Re: [R] Interpreting Multiple Linear Regression Summary

2011-11-09 Thread David Winsemius
On Nov 9, 2011, at 2:17 PM, Rich Shepard wrote: On Wed, 9 Nov 2011, Daniel Nordlund wrote: I would guess that there is something problematic with the how the data frame is structured relative to what lm() is expecting. Dan, I was not comfortable with my explanation, but the formula

Re: [R] Interpreting Multiple Linear Regression Summary

2011-11-09 Thread John C Frain
As far as I know if there is an NA in any variable in an observation the default is to drop the entire observation. Thus there are no observations in your calculation Best Regards John On 9 November 2011 19:17, Rich Shepard rshep...@appl-ecosys.com wrote: On Wed, 9 Nov 2011, Daniel Nordlund

[R] Compare clustering solutions to a correct one

2011-11-09 Thread Massimo Lole
Hello everyone, I have a set of data, J healthy subjects, K diseased subjects, N features for each person. I would like to clusterize my data. Since I know that subjects are from two populations ideally I would prefer an algorithm that first is able to discriminate them, in order to see how it

Re: [R] Interpreting Multiple Linear Regression Summary

2011-11-09 Thread Rich Shepard
On Wed, 9 Nov 2011, Marc Schwartz wrote: # 'DF' is the result of copying your data above from the # clipboard on OSX DF - read.table(pipe(pbpaste), header = TRUE) Marc, Oh? I don't do Apple so there's no OSX here. After removing incomplete records (any records with NA values) which is

Re: [R] Interpreting Multiple Linear Regression Summary

2011-11-09 Thread Rich Shepard
On Wed, 9 Nov 2011, John C Frain wrote: As far as I know if there is an NA in any variable in an observation the default is to drop the entire observation. Thus there are no observations in your calculation John, Hadn't realized that. I know there are NA's in other data frames that yield

Re: [R] raking weighting

2011-11-09 Thread David Winsemius
On Nov 9, 2011, at 2:27 PM, Sebastián Daza wrote: Hi everyone, Does anyone know if there is a package to compute raking weights using R? What I need is to create a variable with weights base in some demographic variables (e.g. sexo, age group, area) using the raking procedure. There is a

Re: [R] Interpreting Multiple Linear Regression Summary

2011-11-09 Thread Ted Harding
On 09-Nov-11 19:39:54, Rich Shepard wrote: On Wed, 9 Nov 2011, John C Frain wrote: As far as I know if there is an NA in any variable in an observation the default is to drop the entire observation. Thus there are no observations in your calculation John, Hadn't realized that. I know

[R] ggplot stat_summary (mean_cl_boot)

2011-11-09 Thread Nathan Miller
Hello, This is a pretty simple question, but after spending quite a bit of time looking at Hmisc and using Google, I can't find the answer. If I use stat_summary(fun.data=mean_cl_boot) in ggplot to generate 95% confidence intervals, how many bootstrap iterations are preformed by default? Can

Re: [R] raking weighting

2011-11-09 Thread Sebastián Daza
I did. However, I am not sure that I can create a weight variable in my database with the rake function you mention. That is why I am asking. El día 9 de noviembre de 2011 13:44, David Winsemius dwinsem...@comcast.net escribió: On Nov 9, 2011, at 2:27 PM, Sebastián Daza wrote: Hi everyone,

Re: [R] Compare clustering solutions to a correct one

2011-11-09 Thread Andrew Ziem
It sounds like you want to do supervised classification, so maybe a supervised classification algorithm would be more appropriate? Consider logistic regression, rpart, ctree, earth, etc. Andrew -Original Message- From: r-help-boun...@r-project.org

Re: [R] raking weighting

2011-11-09 Thread David Winsemius
On Nov 9, 2011, at 3:07 PM, Sebastián Daza wrote: I did. However, I am not sure that I can create a weight variable in my database with the rake function you mention. That is why I am asking. Since you have provided absolutely no information about the data you have or the problem you are

Re: [R] Invalid 'yscale' in viewport

2011-11-09 Thread Erin McMullen Jonaitis
Never mind, I found it -- I had some NA values I didn't know about! I will infer that viewport doesn't handle NA values gracefully! (If I'm wrong about that and I've just missed something key, please correct me.) Erin -Original Message- From: R. Michael Weylandt

Re: [R] Invalid 'yscale' in viewport

2011-11-09 Thread Erin McMullen Jonaitis
Thanks for your quick response, Michael. That is indeed the script I was talking about -- I didn't see it in a standard package, so I just copied it and ran it as a standalone thing. I'm afraid the data are proprietary (human subjects, health data) and so I can't share them. I was able to

Re: [R] Interpreting Multiple Linear Regression Summary

2011-11-09 Thread B77S
There is only one row with a complete set of observations; I think lm() is throwing out the rest. Rich Shepard wrote: On Wed, 9 Nov 2011, John C Frain wrote: As far as I know if there is an NA in any variable in an observation the default is to drop the entire observation. Thus there are

Re: [R] Interpreting Multiple Linear Regression Summary

2011-11-09 Thread B77S
This is the output of dput(your data) structure(list(Ca = c(NA, NA, 24.4, NA, 21.4, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 28, 32, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 34.7, NA, 42.5, NA, 26, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 0.6, 21.4, NA, 48.3,

Re: [R] ggplot stat_summary (mean_cl_boot)

2011-11-09 Thread David Winsemius
On Nov 9, 2011, at 2:59 PM, Nathan Miller wrote: Hello, This is a pretty simple question, but after spending quite a bit of time looking at Hmisc and using Google, I can't find the answer. If I use stat_summary(fun.data=mean_cl_boot) in ggplot to generate 95% confidence intervals, how

Re: [R] ggplot stat_summary(mean_cl_boot)

2011-11-09 Thread Ben Bolker
David Winsemius dwinsemius at comcast.net writes: On Nov 9, 2011, at 2:59 PM, Nathan Miller wrote: Hello, This is a pretty simple question, but after spending quite a bit of time looking at Hmisc and using Google, I can't find the answer. If I use

Re: [R] ggplot stat_summary (mean_cl_boot)

2011-11-09 Thread David Winsemius
On Nov 9, 2011, at 4:10 PM, David Winsemius wrote: mean_cl_boot OK. Things do change. Hadley has written a wrapper for some of the Hmisc functions and you appear to be looking for smean.cl.boot() (Note that Hadley's functions use _'s and Harrells use .'s. And this could be found by

Re: [R] ggplot stat_summary (mean_cl_boot)

2011-11-09 Thread Nathan Miller
Sorry, I didn't realize I was being so obscure. Within ggplot it is possible to use stat_summary() to generate confidence intervals about a mean. One method for generating these CI assumes normality. The other uses bootstrapping to generate the CI. I am using the second method which requires code

Re: [R] Help with tryCatch with a for loop

2011-11-09 Thread Jeff Newmiller
Without a sample data set that fails the first pass and succeeds on the second pass this is a pain to test. Don't forget to read the posting guide... Reproducible sample code isn't too reproducible without some specified data or autogenerated data.

[R] Stack trace?

2011-11-09 Thread rkevinburton
Currently I have a for loop executing functions and at the end I get a message like: There were 50 or more warnings (use warnings() to see the first 50) If I do what it says and type warnings(), I get 50 messages like: 2: In !is.na(x) !is.na(rowSums(xreg)) : longer object length is not a

[R] installing java on ubuntu 11.10 installation

2011-11-09 Thread ravi
Dear list members, I am starting to get acquainted with linux on a ubuntu 11.10 installation on an external hard disk. I have just installed R and all the packages available in the r-cran-* list. Now, I would like to get on with the installation of packages like Deducer and Acinonyx. The former

Re: [R] Stack trace?

2011-11-09 Thread Thomas Lumley
On Thu, Nov 10, 2011 at 10:35 AM, rkevinbur...@charter.net wrote: Currently I have a for loop executing functions and at the end I get a message like: There were 50 or more warnings (use warnings() to see the first 50) If I do what it says and type warnings(), I get 50 messages like: 2:

Re: [R] ggplot stat_summary (mean_cl_boot)

2011-11-09 Thread Nathan Miller
Ok, I got it. smean.cl.boot(x, conf.int=.95, B=1000, na.rm=TRUE, reps=FALSE) Looks like its 1000. Cool. Thanks for the help, Nate On Wed, Nov 9, 2011 at 1:35 PM, Nathan Miller natemille...@gmail.comwrote: Sorry, I didn't realize I was being so obscure. Within ggplot it is possible to use

Re: [R] raking weighting

2011-11-09 Thread Thomas Lumley
2011/11/10 Sebastián Daza sebastian.d...@gmail.com: I did. However, I am not sure that I can create a weight variable in my database with the rake function you mention. That is why I am asking. Yes, you can. -thomas -- Thomas Lumley Professor of Biostatistics University of Auckland

[R] Kmeans with hamming distance?

2011-11-09 Thread Rui Esteves
Hello, I need to do kmeans clustering with hamming distance instead of the euclidean. The kmeans function only uses euclidean. How can I do it? Thank you Rui [[alternative HTML version deleted]] __ R-help@r-project.org mailing list

Re: [R] ggplot stat_summary (mean_cl_boot)

2011-11-09 Thread David Winsemius
On Nov 9, 2011, at 4:35 PM, Nathan Miller wrote: Sorry, I didn't realize I was being so obscure. Within ggplot it is possible to use stat_summary() to generate confidence intervals about a mean. One method for generating these CI assumes normality. The other uses bootstrapping to generate

Re: [R] ggplot stat_summary(mean_cl_boot)

2011-11-09 Thread David Winsemius
On Nov 9, 2011, at 4:30 PM, Ben Bolker wrote: David Winsemius dwinsemius at comcast.net writes: On Nov 9, 2011, at 2:59 PM, Nathan Miller wrote: Hello, This is a pretty simple question, but after spending quite a bit of time looking at Hmisc and using Google, I can't find the answer. If

[R] latent class models

2011-11-09 Thread Frank Lawrence
I would like to extract the information criteria from an hlme object (lcmm package). Would you please advise me on how to extract just the BIC (AIC)? On another topic, when I apply hlme (lcmm) and flexmix (flexmix package) to the same data set, I get BIC values that suggest two different latent

[R] R to automate scatter plots

2011-11-09 Thread Cynthia Lee Page
Hi R people! I have a directory of .csv files I would like to make into objects then scatter plots. I have been having varying degrees of progress. I was able make an object of all files, loop through it, and make a pdf of the last file I looped through. I kept renaming the pdf so instead

Re: [R] path.diagram in SEM--display covariances without variances

2011-11-09 Thread John Fox
Dear Dustin, -Original Message- From: Dustin Fife [mailto:fife.dus...@gmail.com] Sent: November-09-11 2:12 PM To: John Fox Cc: r-help@r-project.org Subject: Re: [R] path.diagram in SEM--display covariances without variances Thanks for the quick response...I've never edited

Re: [R] R to automate scatter plots

2011-11-09 Thread David Winsemius
On Nov 9, 2011, at 4:22 PM, Cynthia Lee Page wrote: Hi R people! I have a directory of .csv files I would like to make into objects then scatter plots. I have been having varying degrees of progress. I was able make an object of all files, loop through it, and make a pdf of the last

[R] Web based R-help not a list

2011-11-09 Thread Cem Girit
Hello, Is there a web version of this R-Help user group (such as the ones under Google Groups) such that 1. I can do a search on any topic over thousands of posts on R easily and effectively 2. My mailbox do not overflow with emails so that I do not need to

[R] [ reached getOption(max.print) -- omitted 8178 rows ]]

2011-11-09 Thread Sean Robert McGuffee
Hi, I have a weird thing I don¹t understand. Here¹s what I did: I read some data: data=read.table(fileName²) then I printed the data to the screen: data But it didn¹t finish: lot¹s of data was written out, but not all of it... Then it interrupted and said: [ reached getOption(max.print) -- omitted

Re: [R] Help with tryCatch with a for loop

2011-11-09 Thread Spencer S
My apologies for not including some test data. Attached is a sample dataset that fails with the first stateroute and works with the second. http://r.789695.n4.nabble.com/file/n4021696/testdata.csv testdata.csv -- View this message in context:

Re: [R] Web based R-help not a list

2011-11-09 Thread David Winsemius
On Nov 9, 2011, at 5:38 PM, Cem Girit wrote: Hello, Is there a web version of this R-Help user group (such as the ones under Google Groups) such that There is Nabble. It's not going to make you any friends unless you learn to post in plain text AND to include context

Re: [R] Stack trace?

2011-11-09 Thread William Dunlap
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Thomas Lumley Sent: Wednesday, November 09, 2011 1:53 PM To: rkevinbur...@charter.net Cc: r-help Subject: Re: [R] Stack trace? On Thu, Nov 10, 2011 at 10:35 AM,

Re: [R] Web based R-help not a list

2011-11-09 Thread Jeff Newmiller
Such a resource would no longer be R-help. You might like stackoverflow. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go...

Re: [R] Stack trace?

2011-11-09 Thread Bert Gunter
To Bill's suggestion for a stack trace on warnings: Question: What would this do in situations where one might get, e.g. 100 warnings? -- Bert On Wed, Nov 9, 2011 at 3:08 PM, William Dunlap wdun...@tibco.com wrote: -Original Message- From: r-help-boun...@r-project.org

Re: [R] path.diagram in SEM--display covariances without variances

2011-11-09 Thread Dustin Fife
Perfect! Thanks for the help. On Wed, Nov 9, 2011 at 4:27 PM, John Fox j...@mcmaster.ca wrote: Dear Dustin, -Original Message- From: Dustin Fife [mailto:fife.dus...@gmail.com] Sent: November-09-11 2:12 PM To: John Fox Cc: r-help@r-project.org Subject: Re: [R] path.diagram in

Re: [R] Help with tryCatch with a for loop

2011-11-09 Thread William Dunlap
If your loop is of the form for(i in 1:n) { doSomethingSafe() x - doSomethingThatFailsSometimes() doSomethingWithX(x) # cannot do this if previous line fails doSomethingElseSafe() } and you want it to somehow recover when doSomethingThatFailsSometimes() throws an error, then change

Re: [R] Web based R-help not a list

2011-11-09 Thread Clint Bowman
Cem, Thanks for your comments. 1. http://cran.r-project.org/ and select Search in the left-hand panel. 2. Use a filter to funnel r-help into it's own area and review as desired. 3. I find that there are many posts that have been quite educational and have helped me with analyses. 4.

Re: [R] Web based R-help not a list

2011-11-09 Thread Hasan Diwan
On 9 November 2011 15:24, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: Such a resource would no longer be R-help. You might like stackoverflow. Perhaps our man was looking for a searchable mail archive? If no one has one, I can set one up pretty quickly. Just let me know... Thanks in advance!

Re: [R] Stack trace?

2011-11-09 Thread William Dunlap
It will call recover() for each warning. When you exit recover() the code continues on. This is handy if you expect the first warning or two but are curious about the third. I'd expect that you could reset options(warning.expression=NULL) when in recover() so that recover() would not be called

Re: [R] path.diagram in SEM--display covariances without variances

2011-11-09 Thread Dustin Fife
For those who have the same question laterafter following John's steps of extracting the function, I just replaced the line of code that says: if ((!ignore.double) || (heads[par] == 1)) with if (((!ignore.double) || (heads[par] == 1)) variables[from[par]] != variables[to[par]]) That

Re: [R] Stack trace?

2011-11-09 Thread William Dunlap
Bert, At the end of my previous message I mentioned tryCatch(). I should have said withCallingHandlers(). E.g., f - function() { + warning(Hmmm) + retval - c(1,2) + c(5,6,7) # warns about incompatible lengths in + + warning(Really?) + retval + }

Re: [R] algorithm that iteratively drops columns of a data-frame

2011-11-09 Thread Martin Batholdy
great, thank you both! On 09.11.2011, at 17:27, Jeff Newmiller wrote: Try data[,!names(data) %in% names(col_means)] On Wed, 9 Nov 2011, Martin Batholdy wrote: Dear R-Users, I have a problem with an algorithm that iteratively goes over a data.frame and exclude n-columns each

Re: [R] ggplot stat_summary (mean_cl_boot)

2011-11-09 Thread Nathan Miller
For all those that are interested. To adjust the number of reps in the stat_summary() mean_cl_boot function simply specify B to the number of bootstrap resamples. I set B to 2000 resamplings below. stat_summary(fun.data=mean_cl_boot, geom=errorbar,width=0.1,colour = red, B=2000 ) If you run

Re: [R] Web based R-help not a list

2011-11-09 Thread Marc Schwartz
On Nov 9, 2011, at 5:40 PM, Hasan Diwan wrote: On 9 November 2011 15:24, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: Such a resource would no longer be R-help. You might like stackoverflow. Perhaps our man was looking for a searchable mail archive? If no one has one, I can set one up

Re: [R] Stack trace?

2011-11-09 Thread R. Michael Weylandt
Very nifty tricks re: getting recover on warnings. Thanks, Michael On Wed, Nov 9, 2011 at 7:11 PM, William Dunlap wdun...@tibco.com wrote: Bert, At the end of my previous message I mentioned tryCatch(). I should have said withCallingHandlers().  E.g., f - function() { +     warning(Hmmm)

Re: [R] [ reached getOption(max.print) -- omitted 8178 rows ]]

2011-11-09 Thread R. Michael Weylandt
? options options(max.print = Inf) Michael On Wed, Nov 9, 2011 at 4:48 PM, Sean Robert McGuffee sean.mcguf...@gmail.com wrote: Hi, I have a weird thing I don¹t understand. Here¹s what I did: I read some data: data=read.table(fileName²) then I printed the data to the screen: data But it

Re: [R] Help with SEM package: Error message

2011-11-09 Thread John Fox
Dear Lisa, Here's a little CFA simulation of my own. I used the development version 2.1-0 of the sem package (on R-Forge) to allow equation-style specification of the model, but you should get the same results with version 2.0-0: --- snip library(MASS) # for mvrnorm()

Re: [R] R to automate scatter plots

2011-11-09 Thread R. Michael Weylandt
It sounds like something is going wrong in your data read -- the warnings indicate that R probably isn't data to the plotting commands. My totally off the wall guess is that if your data is coming by way of excel, the commas are leading to your data becoming characters and hence not plotting

Re: [R] R to automate scatter plots

2011-11-09 Thread R. Michael Weylandt
Sorry for the rambling answer: On Wed, Nov 9, 2011 at 8:28 PM, R. Michael Weylandt michael.weyla...@gmail.com wrote: It sounds like something is going wrong in your data read -- the warnings indicate that R probably isn't data** meant to say: getting numerical data. to the plotting

Re: [R] Error in drawing

2011-11-09 Thread R. Michael Weylandt
Your code is not reproducible. Where is the lidar data coming from? Michael On Wed, Nov 9, 2011 at 2:29 PM, Gyanendra Pokharel gyanendra.pokha...@gmail.com wrote:  I have got following error in drawing wavelet fitting. can some one help? library(faraway) data(lidar)

Re: [R] How to handle empty arguments

2011-11-09 Thread R. Michael Weylandt
Perhaps the missing() command will help in regards to suggestion a. I'd caution against b for obvious reasons, though I think options(error = ) can get you that behavior (you'll have to figure out what XXX is, I have never tried to lessen my error messages...) Michael On Tue, Nov 8, 2011 at

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