Re: [R] R library highcharter function highchart() execute with exception the apparmor read denied for /etc/passwd and /etc/group

Hi Ivan, I'm running the R within docker container. Do you have any idea about it? Thanks! Best Regards! Jay Gu -Original Message- From: Ivan Krylov Sent: Wednesday, August 9, 2023 3:15 AM To: Gu, Jay via R-help Cc: Gu, Jay Subject: Re: [R] R library highcharter function high

[R] R library highcharter function highchart() execute with exception the apparmor read denied for /etc/passwd and /etc/group

like to know if there is any solution to fix it without giving the read access for these two files /etc/passwd and /etc/group in the apparmor profile as I did with ubuntu 18.04 and R 3.6.3. Thanks! Best Regards! Jay Gu [[alternative HTML version deleted]] __

[R] Stats Package Fix

wer even if that timeline is too aggressive. Thank you for your consideration. My contact information is: Jay Spencer Waldron Personal Email (This is the one I am subscribed to R-Help with): gateofti...@gmail.com (385) 335-7879 #---Code paste begins--- > library(readxl) > Growth_Value <-

Re: [R] Change Rcode for a meta-analysis(netmeta) to use a random effects model instead of a mixed effects model

.com/s/j1urqzr99bt76ip/Basics%20excel%20file%20complication%20and%20reoperation%20rate.xlsx?dl=0 Van: Viechtbauer Wolfgang (SP) Verzonden: donderdag 29 juni 2017 19:47 Aan: Jay Zola; r-help@r-project.org Onderwerp: RE: Change Rcode for a meta-analysis(netmeta) to

[R] Change Rcode for a meta-analysis(netmeta) to use a random effects model instead of a mixed effects model

effects model is used? Thank you very much, Jay R code library(meta) library(readxl) All <- read_excel("Basics excel file complication and reoperation rate.xlsx", sheet=1) names(All) <- c("Study_ID","Event_Type","Treatment","Events_

Re: [R] Model studies in one analysis using treatment as a five level moderator in a meta-regression

Dear Vito, Thank you for your reply. I tried to contact the statistics departement numerous times, but did not receive any reply. That is why I started to look on the internet for help. Yours sincerely, Jay Verstuurd vanaf mijn iPhone > Op 26 jun. 2017 om 22:05 heeft Vito Michele Rosa

[R] Model studies in one analysis using treatment as a five level moderator in a meta-regression

meone told me I could best model the data in one analysis using treatment as a five level moderator in a meta-regression. Can some help me with the R code to do this? Your help would be very much appreciated. Thank you, Jay Study| Event Type| Treatment| Number of Events (n)| N| n/N| Kuma

Re: [R] Comparing pooled proportions(complication and reoperation rates) of different treatment modalities

Op 26 jun. 2017 om 15:22 heeft Jay Zola mailto:jayjay.1...@hotmail.nl>> het volgende geschreven: What is the best way to change my R code to be able to compare the pooled proportions(complication and reoperation rates) with the Chi square method? Just adding an adjustment to the links b

Re: [R] Comparing pooled proportions(complication and reoperation rates) of different treatment modalities

people keep coming along >> and sticking things into it." >> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) >> >> >>> On Fri, Jun 23, 2017 at 5:53 AM, Jay Zola wrote: >>> Dear sir/madame, >>> >>> >

Re: [R] Comparing pooled proportions(complication and reoperation rates) of different treatment modalities

treatment modalities separately with the golden standar... Van: David Winsemius Verzonden: vrijdag 23 juni 2017 20:18 Aan: Jay Zola CC: r-help@r-project.org Onderwerp: Re: [R] Comparing pooled proportions(complication and reoperation rates) of different treatment modalities > On Ju

[R] Comparing pooled proportions(complication and reoperation rates) of different treatment modalities

Dear sir/madame, I am currently writing a meta-analysis on the complication and reoperation rates of 5 different treatment modalities after a distal radius fracture. I was able to pool the rates of the 5 different rates using R. Now I have to compare the pooled rates of the 4 treatment modalit

Re: [R] Qvalue package: I am getting back 1, 000 q values when I only want 1 q value.

What you're doing makes no sense. Given p-values p_i, i=1...n, resulting from hypothesis tests t_i, i=1...n, the q-value of p_i is the expected proportion of false positives among all n tests if the significance level of each test is α=p_i. Thus a q-value is only defined for an observed p-value.

Re: [R] t-statistic for independent samples

Dear David, On Wed, Apr 17, 2013 at 6:24 PM, David Arnold wrote: > Hi, [snip] > > D. Before posting to StackExchange, check out the Wikipedia entry for "Behrens-Fisher problem". Cheers, Jay -- G. Jay Kerns, Ph.D. Youngstown State University http://peo

Re: [R] Results from clogit out of range?

I'm not positive of the question you are asking b/c I lost some of initial messages in thread but I think >predict(model, type="expected") gives fitted probabilities Apologies if I answered a question no one asked. On Feb 28, 2013, at 7:45 PM, lisa wrote: > I do appreciate this answer. I hea

[R] First time Rcpp user needs compiler help, I think

I am trying to write a C++ function to be called from R and have never done this before. I have done the following: require(Rcpp) require(inline) src <- 'blahblahblah' fun <- cxxfunction(signature(a="numeric",b="numeric"),src,plugin="Rcpp") That last line generates the error message: Error in co

[R] error msg using na.approx "x and index must have the same length"

I am not sure why I get the error message. Jay [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htm

[R] practical to loop over 2million rows?

ever be able to write efficient enough code to perform a complicated loop over 2 million rows in a reasonable time. Is it useless for me to try to do any complicated loops on 2 million rows, or if I get much better at programming in R will it be manageable even for complicated situa

Re: [R] car::linearHypothesis Sum of Sqaures Error?

: Tuesday, October 09, 2012 4:00 PM To: John Jay Wiley Jr. Cc: r-help@r-project.org Subject: RE: [R] car::linearHypothesis Sum of Sqaures Error? Dear John, > -Original Message- > From: John Jay Wiley Jr. [mailto:jwile...@syr.edu] > Sent: Tuesday, October 09, 2012 3:37 PM > To: J

Re: [R] car::linearHypothesis Sum of Sqaures Error?

variances are similar. Is there another metric I am missing for a continuous covariate? Cheers, John From: John Fox [j...@mcmaster.ca] Sent: Tuesday, October 09, 2012 2:59 PM To: John Jay Wiley Jr. Cc: r-help@r-project.org Subject: RE: [R] car::linearHypo

Re: [R] car::linearHypothesis Sum of Sqaures Error?

el,"cB vs. A&C") linearHypothesis(model,"cA vs. C") #Sum of squares of the individual contrasts do not add to the main effect of c John J. Wiley, Jr. PhD Candidate State University of New York College of Environmental Science and Forestry Department of Environmenta

[R] car::linearHypothesis Sum of Sqaures Error?

I am working with a RCB 2x2x3 ANCOVA, and I have noticed a difference in the calculation of sum of squares in a Type III calculation. Anova output is a follows: > Anova(aov(MSOIL~Forest+Burn*Thin*Moisture+ROCK,data=env3l),type=3) Anova Table (Type III tests) Response: MSOIL

Re: [R] r data structures

quire as to the length of a list, so might, if forced to, admit that lists have one dimension, length. But I do not think it is helpful to think of lists as having dimension. Certainly, lists do not have two dimensions. -- Don MacQueen Lawrence Livermore National Laboratory 7000 East Ave., L-627

Re: [R] r data structures

s.htm - On Aug 16, 2012, at 11:49 AM, Schumacher, Jay S wrote: > > > hi, > i'm trying to understand r data structures. i see that vectors, > matrix, factors and arrays have a "dimension." > there seems to be no

[R] r data structures

hi, i'm trying to understand r data structures. i see that vectors, matrix, factors and arrays have a "dimension." there seems to be no mention of dimensionality anywhere for lists or dataframes. can i consider lists and frames to be of fixed dimension 2?

Re: [R] Memory limit for Windows 64bit build of R

any R analytics under the hood use matrices, so you may not know up front where you could hit a limit. Jay Original message I have a Windows Server 2008 R2 Enterprise machine, with 64bit R installed running on 2 x Quad-core Intel Xeon 5500 processor with 24GB DDR3 1066 Mhz RAM. I am se

Re: [R] bigmemory

ly on both matrix and big.matrix objects. Jay Hi Jay, > > I have a question about your reply. > > You mentioned that "the more serious problem is that you can't expect to > run just any R function on a big.matrix (or on an ff object, if you check > out ff for some nice f

Re: [R] bigmemory

tures). In particular, for large data sets you would likely use up all of RAM (other reasons are more subtle and important, but out of place in this reply). Jay -- John W. Emerson (Jay) Associate Professor of Statistics Department of Statistics Yale University http://www.stat.yale.edu/~jay

Re: [R] R report generator (for Word)?

quot;, such as TODO lists, agendas, capturing-archiving, calendar integration, time tracking,...  These could possibly address some of the other issues you mentioned. Good luck, and Happy New Year.Jay ********* G. Jay Kerns, Ph.D. Mathematics and Statistics Youngstown Stat

[R] bigmemory on Solaris

ear up the other warnings in the logs, though. !-) We should also revisit the possibility of a CRAN BOOST library for use by a small group of packages (like bigmemory) which might make patches to BOOST easier to track and maintain. This might improve things in the long run. Jay -- John W. Em

Re: [R] Foreach (doMC)

n you might try joining the r-sig-...@r-project.org group. Clearly there are far more users of "core" R and hence "mainstream" questions on r-help are likely to be answered more quickly (on average) than specialized questions. Regards, Jay On Thu, Oct 20, 2011 at 4:27 PM, J

Re: [R] Foreach (doMC)

relating to my own packages is something I try to do, but it doesn't always happen. I would like to think foreach is widely used -- it does have a growing list of reverse depends/suggests. And was updated as recently as last May, I just noticed. http://cran.r-project.org/web/packages/foreach/

Re: [R] efficient coding with foreach and bigmemory

her backends do; otherwise, the workers will not be able to properly address the shared-memory or filebacked big.matrix. Some documentation on bigmemory.org may help, and feel free to email us directly. Jay -- John W. Emerson (Jay) Associate Professor of Statistics Department of Stati

Re: [R] On-line machine learning packages?

have a particular algorithm or technique in mind? Does it have a > name? > > How does sequential classification differ form running a one-off > classifier for each run? > > On 09/12/2011 05:24 AM, Jay wrote: > > > > > In my mind this sequential classification t

Re: [R] On-line machine learning packages?

ms in R, please respond. Or will "http://cran.r-project.org Look for 'Task Views'" be my next piece of advice? On Sep 12, 11:31 am, Dennis Murphy wrote: > http://cran.r-project.org/web/views/ > > Look for 'machine learning'. > > Dennis > > >

Re: [R] On-line machine learning packages?

If the answer is so obvious, could somebody please spell it out? On Sep 11, 10:59 pm, Jason Edgecombe wrote: > Try this: > > http://cran.r-project.org/web/views/MachineLearning.html > > On 09/11/2011 12:43 PM, Jay wrote: > > > > > Hi, > > > I used the r

Re: [R] On-line machine learning packages?

what I'm looking for..(?) BR, Jay On Sep 11, 7:15 pm, David Winsemius wrote: > On Sep 11, 2011, at 11:42 AM, Jay wrote: > > > What R packages are available for performing classification tasks? > > That is, when the predictor has done its job on the dataset (based on > &g

[R] On-line machine learning packages?

round. //Jay __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.

Re: [R] rpart: apply tree to new data to get "counts"

I tried that, while I find the documentation a bit short, but the only result I get from this is a probability distribution of my data (I'm building a tree with 2 classes). How do I plot a tree where the counts are show in each step/node? BR, Jay On Aug 29, 9:40 pm, Weidong Gu

[R] rpart: apply tree to new data to get "counts"

Hi, when I have made a decision tree with rpart, is it possible to "apply" this tree to a new set of data in order to find out the distribution of observations? Ideally I would like to plot my original tree, with the counts (at each node) of the new data. Rea

Re: [R] Exception while using NeweyWest function with doMC

. It also doesn't appear that you are making use of shared memory, so I'm unsure what the gains are. However, I don't have any particular insight as to the subsequent problem with NeweyWest (which doesn't seem to be using the big.matrix objects). Jay -- Mess

[R] Decision tree with the group median as response?

As I am only familiar with the basics regarding decision trees I would like to ask, with the risk of sating a silly question: is it possible to perform recursive partitioning with the group median as the response/objective? For example, in stead of rpart focusing on means, could a similar tree be

[R] rpart: plot without scientific notation

While I'm very pleased with the results I get with rpart and rpart.plot, I would like to change the scientific notation of the dependent variable in the plots into integers. Right now all my 5 or more digit numbers are displayed using scientific notation. I managed to find this: http://tolstoy.new

Re: [R] Extracting columns with specific string in their names

hard to be certain. > > Use dput() and head() to give a small cut-and-paste-able example. > > Michael > > > > > > > > > > On Mon, Aug 22, 2011 at 10:33 AM, Jay wrote: > > Hi, > > > Let's say that I have a set of column names

[R] Extracting columns with specific string in their names

Hi, Let's say that I have a set of column names that begin with the string "Xyz". How do I extract these specific columns? I tried to do the following: dataframe1[,grep("Xyz",colnames(dataframe1))] But it does not work. What is wrong with my expression? _

Re: [R] Installation of bigmemory fails

look at it and see what we can do. Please email us if you don't hear back in the next week or so. Thanks, Jay --- Hello All, I tried to intall the bigmemory package from a CRAN mirror site and receive

Re: [R] Rcmdr Plugin error

ectly, the same thing happened to me when my Plugin removed a menu which was used (that is, added to) by some other Plugin (in particular, RcmdrPlugin.IPSUR deleted a menu to which RcmdrPlugin.HH added a submenu.) The solution in my case was "don't do that". Can't really

[R] Count occurances in integers (or strings)

Hi, I have a dataframe column from which I want to calculate the number of 1's in each entry. Some column values could, for example, be "0001001000" and "111". To get the number of occurrences from a string I use this: sum(unlist(strsplit(mydata[,"my_column"], "")) == "1") However, as my

[R] Factor analysis on ordinal & nominal data

Hi, are there readily available R packages that are able to perform FA on ordinal and/or nominal data? If not, what other approaches and helpful packages would you suggest? BR, Jay __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman

Re: [R] How to calculate KMO?

Dear Thibault, On Tue, Apr 12, 2011 at 5:06 PM, Thibault Grava wrote: > Hello Jay, > > I know that an old post but I really need to calculate KMO for my data and > this is the only thread I found on the subject. > > I'm a very newby to R so sorry for the odd questions. &g

[R] ggplot2: "ndensity" and "density" parameters

Hello, if I want to compare the distributions of two datasets using ggplots, how should I choose the density type? More exactly, what assumptions and are behind the "ndensity" and "density" parameters? And when should they be used? See http://had.co.nz/ggplot2/stat_bin.html While I understand th

Re: [R] Kolmogorov-smirnov test

, tsippel wrote: > Is the kolmogorov-smirnov test valid on both continuous and discrete data? > ?I don't think so, and the example below helped me understand why. > > A suggestion on testing the discrete data would be appreciated. > > Thanks, -- John W. Emerson (Jay) Associat

[R] kohonen: "Argument data should be numeric"

hat I want. How did I end up with this data format? What I did: data1 <- read.csv("data1.txt", sep = ";") training <- sample(nrow(data1), 1000) data.train <- data1[training,2:20] I tried to use scan as the import method (read about this somewhere) and unlist,

[R] Fuzzy Discriminant Analysis (DA)

Hello all, as the combination DA and R is rather new to me I would like to know: are there packages that implement a fuzzy version of Discriminant Analysis? Thanks! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLE

Re: [R] lm without intercept

ll data set: if you sent an R command such as: x <- c(x1, x2, ..., xn) y <- c(y1, y2, ..., yn) you might even get some more interesting feedback. One of the many good intro stats textbooks might also be helpful as you get up to speed. Jay - Origina

[R] Shared nearest neighbor (SNN) clustering algorithm implementation?

Hello, is there an implementation available for a shared nearest neighbor (SNN) clustering algorithm? //Jay __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org

Re: [R] A question to get all possible combinations

you store all of those in a data frame A, say, then you can get all possible samples from df1 with something like apply(A, 2, function(x) df1[x])) The good news is that the result will also be a matrix. Each row will be a possible sample of size 6 from df1. Hope this helps, Jay P.S. Note th

Re: [R] [Fwd: adding more columns in big.matrix object of bigmemory package]

For good reasons (having to do with avoiding copies of massive things) we leave such merging to the user: create a new filebacking of the proper size, and fill it (likely a column at a time, assuming you have enough RAM to support that). Jay On Fri, Dec 17, 2010 at 2:16 AM, utkarshsinghal wrote

Re: [R] How to generate multivariate uniform distribution random

On Sat, Nov 6, 2010 at 8:22 PM, michael wrote: > Jay, > >   Yes I'm looking for unif(0,1) and your method works just fine. I > suppose your method should work for dimensions greater than 2, am I right? > > Michael > Yes, but it gets that much more tricky to spe

Re: [R] How to generate multivariate uniform distribution random

) You could also use copulas, but those depend on contributed packages (and you can read more about them on the CRAN Task View for probability distributions). Hope this helps, Jay __ G. Jay Kerns, Ph.D. Youngstown State University http://people.ysu.edu/~gkerns/

Re: [R] big data and lmer

means, and perhaps a few other things. In many cases, it's just a matter of someone deciding to port a tool/analysis of interest to one of these different object types -- we welcome collaborators and would be happy to offer advice if you want to adapt something for bigmemory structures! Jay

Re: [R] merging and working with big data sets

ot;smart" cbind() would be possible simply by manipulating the descriptor file. Again, not something we advise or formally provide, but it wouldn't be hard. Jay -- John W. Emerson (Jay) Associate Professor of Statistics Department of Statistics Yale University http://www.stat.yale.edu/~jay

Re: [R] Is there a regression surface demo?

, from the command line: library(Rcmdr) with(rock, scatter3d(area, peri, shape)) I hope that this helps, Jay __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/post

Re: [R] same random numbers in different sessions

t loading it? I ask because the vignette is built by making a special choice for set.seed, and the workspace that ships with the package might be interacting in an unexpected way. Please let me know if IPSUR is the culprit. Regards, Jay __ R-help@

Re: [R] R-help

like this using R is like shooting a squirrel with a ballistic missile. Not that there's anything wrong with that; I don't like squirrels. Cheers, Jay P.S. Just kidding. On Tue, Oct 5, 2010 at 12:06 PM, Greg Snow wrote: > I would do it like this: > > library(TeachingDemos) >

[R] Prediction plot for logistic regression output

How do I construct a figure showing predicted value plots for the dependent variable as a function of each explanatory variable (separately) using the results of a logistic regression? It would also be helpful to know how to show uncertainty in the prediction (95% CI or SE). Thanks- This emai

Re: [R] bigmemory doubt

accomplish this, yes. Feel free to email us directly for advice. Jay > Message: 153 > Date: Wed, 8 Sep 2010 10:52:19 +0530 (IST) > From: "raje...@cse.iitm.ac.in" > To: r-help > Subject: [R] bigmemory doubt > Message-ID: > <1204692515.13855.1283923339865

Re: [R] choose.dir() gone?

anks, Joh > [snip] Have a look at tk_choose.files in the tcltk package. library(tcltk) ?tk_choose.files Good luck, Jay ******* G. Jay Kerns, Ph.D. Associate Professor Department of Mathematics & Statistics Youngstown State University Youngstown,

[R] DNA sequence Fst

Hi, I want to analyse DNA sequence data (mtDNA) in R as in calculate Fst, Heterozygosity and such summary statistics. Package Adagenet converts the DNA sequence into retaining only retaining the polymorphic sites and then calcuates Fst.. but is there any other way to do this? I mean analyse the DN

Re: [R] Bigmemory: Error Running Example

ize until you get a failure. This sort of exercise is extremely helpful in situations like this. Jay Subject: [R] Bigmemory: Error Running Example Message-ID: > Content-Type: text/plain Hi, I am trying to run the bigmemory example provided on the http://www.bigmemory.org/ The exa

Re: [R] Introductory statistics and introduction to R

lly, it depends on what you mean by 'get through'.) > > Also, do you have other suggestions for texts, manuals, web sites, etc. that > would introduce statistics and R simultaneously? Have you seen this? http://rwiki.sciviews.org/doku.php?id=books:intrstat Good luck, Jay

[R] [R-pkgs] IPSUR-1.0 is on CRAN, plus update to RcmdrPlugin.IPSUR

aming scheme for menus is also updated to be consistent with the other plugins in particular, and naming conventions in general. Cheers, Jay P.S. If you are thinking to print parts of IPSUR yourself then I recommend the publisher-quality PDF linked from the Downloads secti

[R] Error installing tkrplot

Hi, I've been trying to install tkrplot and have been coming across this error. Loading required package: tcltk Loading Tcl/Tk interface ... Error : .onLoad failed in loadNamespace() for 'tcltk', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared library '/L

Re: [R] (help) This is an R workspace memory processing question

You should look at packages like ff, bigmemory, RMySQL, and so on. However, you should really consider moving to a different platform for large-data work (Linux, Mac, or Windows 7 64-bit). Jay - This is an R workspace memory processing question

Re: [R] Parallel computing on Windows (foreach) (Sergey Goriatchev)

ple, doing blocks of tasks in chunks rather than passing each one as an individual job). But more to the point, doSNOW works just fine on an SMP, no problem, it doesn't require a cluster. Jay <> Not only is the sequential foreach much slower than the simple for-loop (as least in this part

[R] RODBC: owerwrite into a named range in Excel

them. Should I use sqlSave() or sqlUpdate()? Using the update I get the error: "cannot update ‘data_001’ without unique column" sqlUpdate(connection_name, my_new_data_frame, "name_of_the_range_in_excel") Let's say that the range in Excel is in E10:

[R] [R-pkgs] bigmemory 4.2.3

visit http://www.bigmemory.org/. Jay Emerson & Mike Kane -- John W. Emerson (Jay) Associate Professor of Statistics Department of Statistics Yale University http://www.stat.yale.edu/~jay ___ R-packages mailing list r-packa...@r-project.org h

[R] [R-pkgs] Bayesian change point" package bcp 2.2.0 available

consider taking advantage of it for tasks that might be computationally intensive and could be easily done in parallel.  Some vignettes are available at http://cran.r-project.org/web/packages/foreach/index.html. Jay Emerson & Chandra Erdman (Apologies, the first version of this announcement was not pl

[R] Lattice: location of key inside a xyplot()

ot;, but surely this must be possible somehow? BR, Jay __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, min

[R] [R-pkgs] "Bayesian change point" package bcp 2.2.0 available

consider taking advantage of it for tasks that might be computationally intensive and could be easily done in parallel. Some vignettes are available at http://cran.r-project.org/web/packages/foreach/index.html. Jay Emerson & Chandra Erdman -- John W. Emerson (Jay) Associate Professor of Stati

[R] nnclust: nnfind() distance metric?

Hello, pardon my ingorance, but what distance metric is used in this function in the nnclust package? The manual only says: "Find the nearest neighbours of points in one data set from another data set. Useful for Mallows-type distance metrics."

Re: [R] bigmemory package woes

ldn't be a problem with the new version. The CRAN update should take place early next week, along with some revised documentation. Regards, Jay --- Message: 125 Date: Fri, 23 Apr 2010 13:51:32 -0800 (PST) From: zerdna To: r-help@r-project.org Subject: [R] bigmemory package woe

Re: [R] Huge data sets and RAM problems

though you can afford 1 (or a few) copies of this, it doesn't leave you much room for the memory overhead of working with such an object. Part of the oringal message below. Jay - Message: 80 Date: Mon, 19 Apr 2010 22:07:03 +02

[R] Check for overdispersion in logit model

A quick question for those that are familiar with the subject, is it OK to check for overdispersion in a logit model using: sum(resid(model, type = "pearson")^2) / df.residual(model) Are tehre other commands? packages? /Jay __ R-help@r-p

[R] xyplot ontop a contourplot (package: lattice)

Hello, I have a contourplot plot that shows the data I want. However, I would like to point a certain amount of points from this plot via a xyplot(). Example: x <- seq(pi/4, 5 * pi, length.out = 100) y <- seq(pi/4, 5 * pi, length.out = 100) r <- as.vector(sqrt(outer(x^2, y^2, "+"))) grid <- expa

[R] Cross-validation for parameter selection (glm/logit)

) What is the correct way to perform this variable selection? And are the readily available packages for this? Similarly, when I have my final parameter set, how should I go about and make the final assessment of the models predictability? CV? What package? Thank you in ad

Re: [R] large dataset

For example, RMySQL supports MySQL databases. At the other end of the spectrum, there are possibilities discussed on a nice page by Dirk Eddelbuettel which you might look at: http://cran.r-project.org/web/views/HighPerformanceComputing.html Jay -- John W. Emerson (Jay) Associate Profess

Re: [R] Mosaic plots

real challenge faced by all of us with these plots, so you should try each version. I'm not sure what you intend to do with a legend, but if you want the ability to customize and hack code, I suggest you look at grid and a modification to vcd's version to suit your purposes. Jay > &g

Re: [R] Gamma parametrization

ave a 'scale' parameter at all. Just be careful, and you should be fine. And IMHO, given that the PDF of the density is shown it is reasonably clear as-is. Best, Jay *** G. Jay Kerns, Ph.D. Associate Professor Department of Mathematic

[R] RMySQL_0.7-4 core dumped on dbWriteTable

/usr/lib64/R/bin/exec/R terminated" How can I fix this? Appreciate your help. Sincerely, Jay James Castino, PE Principal JJCENG.COM, PC www.jjceng.com +1 (541) 633-7990 1560 NE 1st ST. #14 Bend, OR USA 97701 ## partial .RHistory ### >sessionInfo() R version 2.10.1 (2009-

Re: [R] Extract information from S4 object

Tahnk you. But, when I try the command you both suggested I get a NULL as the results. > names(object1 @ x.values) NULL Where did I go wrong? On Feb 22, 4:34 pm, David Winsemius wrote: > On Feb 22, 2010, at 8:05 AM, Jay wrote: > > > > > The function prediction() retur

[R] Extract information from S4 object

The function prediction() returns this: Formal class 'performance' [package "ROCR"] with 6 slots ..@ x.name : chr "Cutoff" ..@ y.name : chr "Accuracy" ..@ alpha.name : chr "none" ..@ x.values:List of 1 .. ..$ : Named num [1:89933] Inf 2.23 2.22 2.17 2.16 ... .. .. ..- at

Re: [R] Checking the assumptions for a proper GLM model

last couple of days. However, their section on using R for validating the assumptions is very lacking. Naturally links like google.com and amazon.com will eventually get me there, but if somebody have other recommendations, I would be very fortunate to get even more help. BR, Jay On Feb 18, 7:

Re: [R] Checking the assumptions for a proper GLM model

ssion. * boxtid--performs power transformation of independent variables and performs nonlinearity test. But, since I'm new to GLM, I owuld greatly appreciate how you/others go about and test the validity of a GLM model. On Feb 18, 1:18 am, Jay wrote: > Hello, > > Are there any

[R] Checking the assumptions for a proper GLM model

Hello, Are there any packages/functions available for testing the assumptions underlying assumptions for a good GLM model? Like linktest in STATA and smilar. If not, could somebody please describe their work process when they check the validity of a logit/probit model? Regards, Jay

[R] Extract values from a predict() result... how?

Hello, silly question I suppose, but somehow I can't manage to extract the probabilities from a glm.predict() result: > str(res) Named num [1:9] 0.00814 0.01877 0.025 0.02941 0.03563 ... - attr(*, "names")= chr [1:9] "1" "2" "3" "4" ... I got from: # A Gamma example, from McCullagh & Nelder (

Re: [R] question about bigmemory: releasing RAM from a big.matrix that isn't used anymore

c(). >>> But it's available for re-use; if you want to be really sure, have a look >>> in /dev/shm to make sure the shared memory segments have been >>> deleted. Thanks, Matt -- John W. Emerson (Jay) Associate Professor of Statistics Department of Statistics Ya

Re: [R] Update problem? Rcmdr disappears, won't re-open

done that because A) it confuses students and B) John went to nonzero trouble to make the "remove" capability functional; I think it's cool. I will think about it some more. Maybe there is a way to reorganize it to not confuse students and simultaneously avoid conflicts with other

Re: [R] Update problem? Rcmdr disappears, won't re-open

I will have to boot into Windows later this evening to investigate, but in the meantime you may want to post your sessionInfo(). I have run RcmdrPlugin.IPSUR on R-2.10.1, Windows XP, as recently as yesterday during class without any problems. Gotta go for now. Jay -- **

Re: [R] xyplot: adjusting the scale (min, max & tick)

Peter Ehlers wrote: > > Have a look at the 'scales' argument. For example: > > # default plot > xyplot(Sepal.Length ~ Petal.Length | Species, data = iris) > > # modified plot > xyplot(Sepal.Length ~ Petal.Length | Species, data = iris, > scales=

[R] xyplot: adjusting the scale (min, max & tick)

Hi, I'm terribly sorry but it seems it cannot figure this one out by myself so, please, if somebody could help I would be very grateful. So, when I plot with xyplot() I get an y-axis that is very ugly... starting from a random number and having so many ticks that it becomes unreadable. How do I t

  1   2   >