Re: [R] automatic exploration of all possible loglinear models?

Christopher W. Ryan binghamton.edu> writes: > > Is there a way to automate fitting and assessing loglinear models for > several nominal variables . . . something akin to step or drop1 or add1 > for linear or logistic regression? Not strictly for loglinear, but glm works with stepAIC. Make sure

Re: [R] Functions in lists or arrays?

> t <- list() > t[[1]] <- function(b) b*2 ### NOTE, [[ not [ > t [[1]] function (b) b * 2 > Bill Venables http://www.cmis.csiro.au/bill.venables/ -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Toby Sent: Tuesday, 21 April 20

[R] Functions in lists or arrays?

I have a problem where I need to have a "driver" style R program that will extend itself, given more 'source("extra.R")' style lines. IE: easy to modify by other people. The problem becomes when I would like to create an array or list of functions. Each function, possibly hundreds of them, are

Re: [R] n-dimensional vector operations

Peter, Thank you for your array() hint for multi-dimensional matrices. Actually, my final answer should be of dimension 5,3,2 because my funcp(a,b,c) will be reduced to one number when I set a to a column of x, b to a column of y, and c to a column of z. I did make some useful observations, tho

Re: [R] bladder1 dataset in survival library

On Apr 20, 2009, at 9:43 PM, Marc Schwartz wrote: On Apr 20, 2009, at 8:14 PM, David Winsemius wrote: On Apr 20, 2009, at 6:06 PM, Petra Buzkova wrote: Hello, In package survival should be a dataset bladder1. http://stat.ethz.ch/R-manual/R-devel/library/survival/html/bladder.html I can n

Re: [R] bladder1 dataset in survival library

On Apr 20, 2009, at 8:14 PM, David Winsemius wrote: On Apr 20, 2009, at 6:06 PM, Petra Buzkova wrote: Hello, In package survival should be a dataset bladder1. http://stat.ethz.ch/R-manual/R-devel/library/survival/html/bladder.html I can not open it (not found). In the documentation for my

Re: [R] factanal error

Dear william, There must be at least one perfect collinearity (within the numerical accuracy of the computation) among the variables in mydataN; this is not surprising given that there are apparently 923 variables for 982 observations. Do you really want to do an exploratory factor analysis for 92

[R] [R-pkgs] [ANN] ggplot2 version 0.8.3

ggplot2 ggplot2 is a plotting system for R, based on the grammar of graphics, which tries to take the good parts of base and lattice graphics and avoid bad parts. It takes care of many of the fiddly details that make plotting a hassle (l

Re: [R] n-dimensional vector operations

Tena koe Ken I may be misunderstanding you, but it seems to me you have a four dimensional array. If so: ken <- array(rnorm(5*3*2*10), dim=c(5,3,2,10)) ken[,1,1,] ken[1,,1,] may be sufficient to get you going. HTH Peter Alspach > -Original Message- > From: r-help-boun...@r-proj

Re: [R] bladder1 dataset in survival library

On Apr 20, 2009, at 6:06 PM, Petra Buzkova wrote: Hello, In package survival should be a dataset bladder1. http://stat.ethz.ch/R-manual/R-devel/library/survival/html/ bladder.html I can not open it (not found). In the documentation for my installation of survival, version 2.34-1, the h

[R] Vizualization of points within sets

Hi all, I have a visualization question regarding sets. My problem is as follows: I have several sets, each having some members (or 'points'). I would like to connect the points, while keeping the sets. For example, if I have 3 sets (Set 1 contains points A, B, C): Set 1: -- A, B, C Set 2:

[R] n-dimensional vector operations

Let's start with a concrete case of n=3 dimensions. Along dimension x, I have a matrix of 5 vectors (each with ten rows) Along dimension y, I have a matrix of 3 vectors (each with ten rows) Along dimension z, I have a matrix of 2 vectors (each with ten rows) I am trying to write a: function(..

Re: [R] Append to a csv file

Try writing to a connection so that the file stays opens. On Mon, Apr 20, 2009 at 5:39 PM, kayj wrote: > > I am looping over a data set and at each loop I am creating a dataframe > “mydata” > That I wanted to be saves in a .csv file, but I want all the results to be > saved in the same file and t

Re: [R] Append to a csv file

On Apr 20, 2009, at 5:39 PM, kayj wrote: I am looping over a data set and at each loop I am creating a dataframe “mydata” That I wanted to be saves in a .csv file, but I want all the results to be saved in the same file and this is the way I do it write.csv(mydata, file= “data.csv”=F, a

Re: [R] create objects in a loop and adding sqlQuery content to them

On Apr 20, 2009, at 8:04 PM, Katharina May wrote: Hi there, I've got a database or rather spreadsheet with several columns and rows. For one column named sites I want to loop through all possible values and retrieve all data out of the database where site = x and write it into an object

Re: [R] Fitting linear models

Try: model1<-lm(PBW~SO4+NO3+NH4) Does it work? Dimitri On Mon, Apr 20, 2009 at 7:26 PM, Vemuri, Aparna wrote: > I am not sure if this is an R-users question, but since most of you here > are statisticians, I decided to give it a shot. > > I am using the lm() function in R to fit a dependent varia

Re: [R] Fitting linear models

On Apr 20, 2009, at 7:26 PM, Vemuri, Aparna wrote: I am not sure if this is an R-users question, but since most of you here are statisticians, I decided to give it a shot. You can omit the unnecessary preambles. I am using the lm() function in R to fit a dependent variable to a set of 3

Re: [R] create objects in a loop and adding sqlQuery content to them

> > > > > #Here my first try [error message on the line within the loop, saying > > something like: > > # 'recursive indexing on level 2 failed'] > > sites_object_list <- vector("list",99) > > If there's a site number larger than 99 this will be problematic. Sorry, this isn't correct - R will

Re: [R] create objects in a loop and adding sqlQuery content to them

Hello > -Original Message- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] > On Behalf Of Katharina May > Sent: Monday, April 20, 2009 5:05 PM > To: r-help@r-project.org > Subject: [R] create objects in a loop and adding sqlQuery content to them > > Hi there

[R] create objects in a loop and adding sqlQuery content to them

Hi there, I've got a database or rather spreadsheet with several columns and rows. For one column named sites I want to loop through all possible values and retrieve all data out of the database where site = x and write it into an object named 'sitex_data'. Somehow I'm really missing someth

[R] bladder1 dataset in survival library

Hello, In package survival should be a dataset bladder1. http://stat.ethz.ch/R-manual/R-devel/library/survival/html/bladder.html I can not open it (not found). Both bladder and bladder2 are there. Thanks, Petra __ R-help@r-project.org mailing list ht

[R] Append to a csv file

I am looping over a data set and at each loop I am creating a dataframe “mydata” That I wanted to be saves in a .csv file, but I want all the results to be saved in the same file and this is the way I do it write.csv(mydata, file= “data.csv”=F, append=T) . the csv file looks fine but I always get

[R] factanal error

Hi. I tried running the following code. I don't understand the error. mydata <- read.table("C:/dataForR/radiology/wordFrequencies.csv", header=TRUE, sep=",") > dim(mydata) [1] 982 924 mydataN<-mydata[,-923] > dim(mydataN) [1] 982 923 cor(mydataN) factanal(mydataN, factors=3) Error in solve.d

Re: [R] The assign(paste(...,i),...) idiom

On Mon, 20 Apr 2009, Stavros Macrakis wrote: Judging from the traffic on this mailing list, a lot of R beginners are trying to write things like assign( paste( "myvar", i), ...) where they really should probably be writing myvar[i] <- ... Do we have any idea where this bizarre habi

Re: [R] Fitting linear models

Is this homework? If so, you need to read the text and/or class notes more carefully. -- Bert Gunter -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Vemuri, Aparna Sent: Monday, April 20, 2009 4:26 PM To: r-help@r-project.org Subje

[R] Fitting linear models

I am not sure if this is an R-users question, but since most of you here are statisticians, I decided to give it a shot. I am using the lm() function in R to fit a dependent variable to a set of 3 to 5 independent variables. For this, I used the following commands: >model1<-lm(function=PBW~SO4+N

Re: [R] The assign(paste(...,i),...) idiom

Perhaps a good R WIKI topic, though there's no assurance that info there would be consulted, of course... Bert Gunter Genentech Nonclinical Biostatistics 650-467-7374 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of baptiste auguie

Re: [R] what is R best for; what should one learn in addition to R

What do folks think about the c/gsl/Apophenia combination as one of the other stat packages? http://modelingwithdata.org/ http://apophenia.sourceforge.net/ Tom Greg Snow-2 wrote: > > > I also recommend that people doing statistics know at least the basics of > 3 different stats packages

[R] [R-pkgs] New versions for the distr-family of packages

--- New versions released for the distr family of package --- We would like to announce the availability on CRAN (with possibly a minor delay unti

Re: [R] R 2.9.0 MASS package

I learned something good today (MASS is in R by default). Thanks. Tom Peter Dalgaard wrote: Tom La Bone wrote: In Windows Xp Pro: R2.8.1 USA(CA1) repository markerSearchPower MASS(VR) MasterBayes R2.9.0 USA(CA1) repository markerSearchPower MasterBayes MASS is not where it used to be. I

Re: [R] The assign(paste(...,i),...) idiom

I vaguely recall thinking with such convoluted constructs when switching from Matlab to R. The lack of generic data structures such as lists makes you define variable names that you can identify and manipulate. There are structures in Matlab, but I think they are much less used than lists i

Re: [R] R 2.9.0 MASS package

Tom La Bone wrote: In Windows Xp Pro: R2.8.1 USA(CA1) repository markerSearchPower MASS(VR) MasterBayes R2.9.0 USA(CA1) repository markerSearchPower MasterBayes MASS is not where it used to be. I checked a couple of other repositories in the US and got similar results. Tom But it's in R

[R] The assign(paste(...,i),...) idiom

Judging from the traffic on this mailing list, a lot of R beginners are trying to write things like assign( paste( "myvar", i), ...) where they really should probably be writing myvar[i] <- ... Do we have any idea where this bizarre habit comes from? -s _

Re: [R] Multiple Hexbinplots in 2 columns with a Single Categorical Variable

On Thu, Apr 9, 2009 at 4:18 AM, Stuart Reece wrote: > Dear Ladies and Gentlemen, > >  I have a fairly large database (N=13,000) and a single main categorical > discriminator between the groups. > >  I want to look at the time course of a number of continuous biochemical > variables over chronolo

Re: [R] graph with 15 combinations

Le lundi 20 avril 2009 à 21:04 +0200, Penner, Johannes a écrit : > Dear R helpers, > > I have a data set with 4 types (W, C, E & S). Now I have values for all > types plus all possible combinations (the order is unimportant): W, C, > WC, E, WE, CE, WCE, S, WS, CS, WCS, ES, WES, CES & WCES. Ideally

[R] Cross-Correlation function (CCF) issues

Dear all, I have two series of returns and I want to find the cross-correlations between these two series. I know of the ccf, but it does not work as I'd like if i type ccf(x,y,lag.max=20,type="correlation",plot=FALSE) i got the error message Error in na.fail.default(ts.intersect(as.ts(x), as.t

Re: [R] R 2.9.0 MASS package

In Windows Xp Pro: R2.8.1 USA(CA1) repository markerSearchPower MASS(VR) MasterBayes R2.9.0 USA(CA1) repository markerSearchPower MasterBayes MASS is not where it used to be. I checked a couple of other repositories in the US and got similar results. Tom Peter Dalgaard wrote: > > Tom

Re: [R] R 2.9.0 MASS package

Tom La Bone wrote: I can't seem to find MASS for the latest version of R. Is it coming or has the name of the package changed? Tom Where did you look? It is in the sources (as part of VR), and also in my (SUSE) test builds. -- O__ Peter Dalgaard Øster Farimagsgade 5, Ent

[R] R 2.9.0 MASS package

I can't seem to find MASS for the latest version of R. Is it coming or has the name of the package changed? Tom -- View this message in context: http://www.nabble.com/R-2.9.0-MASS-package-tp23144198p23144198.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] R-Squared with biglm?

On Mon, 20 Apr 2009, Bryan Lim wrote: I've been working with a rather large data set (~10M rows), and while biglm works beautifully for generating coefficients, it does not report an r-squared. It does report RSS. Any idea on how one could coax an R-squared out of biglm? Hmm. I don't ever us

Re: [R] graph with 15 combinations

Thanks a lot! That is exactly what I was looking for! Best wishes Johannes -- Project Coordinator BIOTA West Amphibians Museum of Natural History Dep. of Research (Herpetology) Invalidenstrasse 43 D-10115 Berlin Tel: +49 (0)30 2093 8708 Fax: +49 (0)30 2093 8565 http://www.biota-africa.org http:

Re: [R] generic genotype calling algorithm?

Hi Nigel -- ask on the Bioconductor mailing list. http://bioconductor.org/docs/mailList.html Look at their package descriptions. http://bioconductor.org/packages/release/Software.html Martin Nigel Birney wrote: Hi, I have Agilent and Illumina SNP data. That's the only thing I know abou

Re: [R] bug when subtracting decimals?

Hi, Gavin Simpson wrote: I bemoan the apparent inability of those asking such questions to use the resources provided to solve these problems for themselves... Looking at all the people who quite obviously do NOT "read the posting guide and provide commented, minimal, self-contained, reprod

Re: [R] graph with 15 combinations

http://en.wikipedia.org/wiki/Venn_Diagram#Extensions_to_higher_numbers_of_sets shows a couple of solutions, not in R, but the ideas could be implemented in R. Hope this helps, -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center Intermountain Healthcare greg.s...@imail.org 801.408.8111 > -

[R] Is latest R faster?

Hi Folks, I just upgraded R to the latest R version 2.9.0 (2009-04-17) (from the Debian Etch repository). It seems to me that it at least starts up much faster than it used to and, though I don't have comparative timing data for long jobs, also that it does its work faster. Is that just an impressi

Re: [R] SEM package

Dear Tijana, I'm afraid that I can't entirely read the messages, but the problem doesn't look like it's peculiar to the sem package. It appears as if the package may have been properly installed but you didn't have permission to update HTML help links. If that's the case, then you can still load a

Re: [R] what is R best for; what should one learn in addition to R

What things you should learn in addition to R depends on what types of things you want to do. But here are some of the programs that I recommend people take a look at: gnuplot ggobi Imagemagick LaTeX xfig Make Emacs (or other programming editor) SQL Perl (or other scripting language) Tk (actual

Re: [R] bug when subtracting decimals?

Dieter Menne wrote: wolfgang.siewert gmail.com> writes: There is a way around: round(0.7-0.3,1)==0.4 (TRUE) Obviously there is a problem with some combinations of decimal subtractions, that - we have the feeling - shouldt be solved. Oh no, not that one again! This was lecture two in my fir

Re: [R] Calling objects in a loop

Hi Brendan, If you really, really want to work with the for() loop, then for(i in 1:10){ assign(paste("theta1_",i,sep=""),data.frame(scale(rnorm(250 assign(paste("theta2_",i,sep=""),data.frame(scale(rnorm(250 assign(paste("theta3_",i,sep=""), get(paste("

[R] Matrix package,solve() errors and crashes

Hello All, I am working on graph object using IGRAPH package wanted to do Bonacich Power. This is my graph object. The file 'Graph.RData' (4.2 MB) is available for download at http://dropbox.unl.edu/uploads/20090424/cfe4fcb854bb17f2/Graph.RData Graph size Vertices: 20984 Edges: 326033 Direct

[R] graph with 15 combinations

Dear R helpers, I have a data set with 4 types (W, C, E & S). Now I have values for all types plus all possible combinations (the order is unimportant): W, C, WC, E, WE, CE, WCE, S, WS, CS, WCS, ES, WES, CES & WCES. Ideally I would like to represent everything in one graph and as concise as possib

Re: [R] Calling objects in a loop

Brendan, I think you should create objects outside of the "for" loop. You can't create objects instide the loop. You can try this: metalist1<-list() for(i in 1:10) {metalist1[[i]]<-assign(paste("theta1_",i,sep=""),data.frame(scale(rnorm(250} lapply(metalist1,function(x){print(dim(x))}) # Che

Re: [R] Calling objects in a loop

On 4/20/2009 2:35 PM, Brendan Morse wrote: Hi everyone, I am trying to calculate a particular variable (vector) from some previously defined variables in a loop but I am having trouble figuring out how to get the loop to recognize that it should index for the previously defined objects. Here is a

[R] R Golf?

Hello, This is probably off-topic but have the R community ever organized R Golf contents similar to Perl Golf: http://perlgolf.sourceforge.net/ ? It would be nice to see how R gurus solve problems in many different ways (although you see it at this list every day :-)). Regards, -L _

[R] Random Forests: Predictor importance for Regression Trees

Hello! I think I am relatively clear on how predictor importance (the first one) is calculated by Random Forests for a Classification tree: Importance of predictor P1 when the response variable is categorical: 1. For out-of-bag (oob) cases, randomly permute their values on predictor P1 and then

[R] Calling objects in a loop

Hi everyone, I am trying to calculate a particular variable (vector) from some previously defined variables in a loop but I am having trouble figuring out how to get the loop to recognize that it should index for the previously defined objects. Here is a simplified version of what I am trying to do

Re: [R] R graph into MS Word: which format to use?

They may stipulate word files for the manuscript, but during submission, journals usually request EPS or PDF formats. In fact, all I've dealt with stipulate NEVER include graphcis into a Word document. May be worth checking again! Mark 2009/4/20 jjh21 : > > Hello, > > The journal I am publishing

Re: [R] SEM package

Nina, did you try to install this package using some other mirror? Dimitri On Mon, Apr 20, 2009 at 1:35 PM, Tijana Gonja wrote: > Hi > > I tried to install the sem package and it was succsessful but I keep getting > the following message > > Paket 'sem' erfolgreich ausgepackt und MD5 Summen abgeg

Re: [R] what is R best for; what should one learn in addition to R

On Mon, Apr 20, 2009 at 10:37 AM, Stefan Grosse wrote: > I know of people doing optimization stuff which needs a > lot of computational power. They use Matlab since it is easy for them > to use multiple processors (+multiple pc's). R at the moment only uses > one processor and also does not yet (t

Re: [R] what is R best for; what should one learn in addition to R

You might also try looking in to Python. It has lots of mathematical and computational libraries (numpy and scipy are particularly useful), as well some to deal with concurrency (e.g. Parallel Python), and can interact with R (rpy and rpy2). Josh Stumpf On Mon, Apr 20, 2009 at 8:49 AM, Juliet Ha

[R] RES: How to force axis to have the same range

Hi Sebastien, take a look at the par(pty='s') argument. Maybe its can solve your issue. Best wishes. Rodrigo. -Mensagem original- De: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Em nome de Sebastien Bihorel Enviada em: segunda-feira, 20 de abril de 2009 12:26 Para:

[R] SEM package

Hi I tried to install the sem package and it was succsessful but I keep getting the following message Paket 'sem' erfolgreich ausgepackt und MD5 Summen abgeglichen Die heruntergeladenen Pakete sind in C:\Users\Dean\AppData\Local\Temp\RtmpVRxlLZ\downloaded_packages aktualisiere HTML Pak

[R] generic genotype calling algorithm?

Hi, I have Agilent and Illumina SNP data. That's the only thing I know about the files - there seem to be no version specification in any of them. Is there a generic genotype calling algorithm that I could try to use on these datasets? thanks, N. -- View this message in context: http://www

Re: [R] Re : PCA and automatic determination of the number of components

Thanks to all for the suggestions. Are you aware of a convenient implementation of AIC/BIC for the problem of selecting the number of factors? Nick William Revelle wrote: > > > At 12:08 PM + 4/20/09, Jari Oksanen wrote: >>justin bem yahoo.fr> writes: >> >>> >>> See ade4 or mva package

[R] Sweave and executive summaries - WORK AROUND

__ 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] Random Forests: Question about R^2

I would like to summarize. Would you please confirm that my summary is correct? Thank you very much! Determining R^2 in Random Forests (for a Regression Forest): 1. For each individual case, record a mean prediction on the dependent variable y across all trees for which the case is OOB (Out-of-Ba

Re: [R] what is R best for; what should one learn in addition to R

On Mon, 20 Apr 2009 11:49:29 -0400 Juliet Hannah wrote: JH> I've been working with R for a couple of years, and I've JH> been able to get most of the things done that I needed (sometimes in JH> a roundabout way). A few experienced statisticians told me that JH> R is best for interactive data anal

Re: [R] how can I run to multinomial PLS regression in R?

There are functions in the caret package to do classification with pls and spls, if that is what you mean. They are plsda and splsda. -- Max __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting g

[R] automatic exploration of all possible loglinear models?

Is there a way to automate fitting and assessing loglinear models for several nominal variables . . . something akin to step or drop1 or add1 for linear or logistic regression? Thanks. --Chris -- Christopher W. Ryan, MD SUNY Upstate Medical University Clinical Campus at Binghamton 40 Arch Street

Re: [R] Re : PCA and automatic determination of the number of components

ade4 has the 'testdim' function which implements a recent method for estimating the number of dimension for PCA on correlation matrix. Paper describing the approach is available at http://pbil.univ-lyon1.fr/members/dray/articles/SD805.php William Revelle wrote: At 12:08 PM + 4/20/09,

Re: [R] drawing data structures

I am not sure that I fully understand what you want, but look at the TkListView function in the TeachingDemos package for one possible solution. If that is not what you meant, then a better problem description will help us to help you. -- Gregory (Greg) L. Snow Ph.D. Statistical Data Center In

Re: [R] bug when subtracting decimals?

wolfgang.siewert gmail.com> writes: > There is a way around: > round(0.7-0.3,1)==0.4 > (TRUE) > > Obviously there is a problem with some combinations of decimal subtractions, > that - we have the feeling - shouldt be solved. Oh no, not that one again! This was lecture two in my first computer

Re: [R] How to force axis to have the same range

On Apr 20, 2009, at 12:18 PM, Dieter Menne wrote: Sebastien Bihorel cognigencorp.com> writes: I am trying to produce (standard and trellis) scatterplots which use the same range of the x and y axes. In addition, I would like the plots to be physically square. Is there one or more specific

Re: [R] doing zero inflated glmm for count data with fmr

Thank you very much Ben. I took you advice and run the lmer model with family="quasipoisson" and got sigma~10. I guess this means that the data has overdispertion but not too high (>15) for me to must use zero inflated model. Am I right? I will also post to the r-sig-mixed-models specialty list..

Re: [R] Re : PCA and automatic determination of the number of components

At 12:08 PM + 4/20/09, Jari Oksanen wrote: justin bem yahoo.fr> writes: See ade4 or mva package. Justin BEM BP 1917 Yaoundé I guess the problem was not to find PCA (which is easy to find), but finding an automatic method of selecting ("determining" sounds like that selection would

Re: [R] How to force axis to have the same range

Sebastien Bihorel cognigencorp.com> writes: > I am trying to produce (standard and trellis) scatterplots which use the > same range of the x and y axes. In addition, I would like the plots to > be physically square. Is there one or more specific argument(s) to plot > and xyplot what would do t

[R] How to force axis to have the same range

Dear R-users, I am trying to produce (standard and trellis) scatterplots which use the same range of the x and y axes. In addition, I would like the plots to be physically square. Is there one or more specific argument(s) to plot and xyplot what would do that? I have looked at various combinat

Re: [R] data$ID -> I always get a NULL

Now everything is clear for me. Thanks David! :) David Winsemius wrote: > > > On Apr 20, 2009, at 4:33 AM, Grześ wrote: > >> >> This is my result: >> >>> class(data) >> [1] "data.frame" >> >>> str(data) >> 'data.frame':2193 obs. of 83 variables: >> $ X.ID.

Re: [R] Constraining equality between parameters of multinomial logit regression using VGAM)

Hello, I am using the VGAM library to perform a multinomial logistic regression with 3 outcome categories and a binary independant factor. How can I constraint the 2 beta parameters to be equal. I intend to do that in order to obtain a Log-Likelihood to test against the model with 2 different beta

[R] Constraining equality between parameters of multinomial logit regression using VGAM)

Hello, I am using the VGAM library to perform a multinomial logistic regression with 3 outcome categories and a binary independant factor. How can I contraint the beta [[alternative HTML version deleted]] __ R-help@r-project.org mailing list htt

[R] what is R best for; what should one learn in addition to R

Hi, I've been working with R for a couple of years, and I've been able to get most of the things done that I needed (sometimes in a roundabout way). A few experienced statisticians told me that R is best for interactive data analysis, but for large-scale computations, one needs something else. I

[R] importing spreadsheet data - linera regression - panel data

Dear Cecilia, just adding some examples to Stefan's post, which says everything already. I've recently gone mad with reshaping, so I assume it is a little tricky. Or maybe what I tell you is obvious, then just skip it. **import** Your files are spreadsheets, so the best way to import is to save

Re: [R] setting levels in contourplot()

On Apr 20, 2009, at 11:22 AM, Dieter Menne wrote: Cable, Samuel B hanscom.af.mil> writes: Does the contourplot() routine have an argument analogous to the "levels" argument in the contour() routine? More generally, is there a way for the user to fix the contour levels in contourplot()?

Re: [R] R graph into MS Word: which format to use?

Uwe Ligges statistik.tu-dortmund.de> writes: > > The journal I am publishing in requires MS Word files. What is my best > > option for getting a high quality image of a graph done in R into Word? > > JPEG? Postscript? > > Windows metafile, if you are under Windows anyway. But make sure that cli

Re: [R] setting levels in contourplot()

Cable, Samuel B hanscom.af.mil> writes: > Does the contourplot() routine have an argument analogous to the > "levels" argument in the contour() routine? More generally, is there a > way for the user to fix the contour levels in contourplot()? Thanks. Assuming lattice: cuts Dieter __

Re: [R] doing zero inflated glmm for count data with fmr

levyofi wrote: > > Hello R users, > Doing My PhD I collected count data which I believe is zero inflated. I > have run a statistical model with lmer and family=poisson and got > summary(model)@sigma=1 so I believe there is no overdispertion. > You have been misled. sigma is set to 1 by def

Re: [R] setting levels in contourplot()

On Apr 20, 2009, at 10:30 AM, Cable, Samuel B Civ USAF AFMC AFRL/RVBXI wrote: Does the contourplot() routine have an argument analogous to the "levels" argument in the contour() routine? More generally, is there a way for the user to fix the contour levels in contourplot()? Thanks. --S

Re: [R] Two or more dimensional root (Zero) finding

Ravi Varadhan wrote: > That is not a good approach, i.e. finding the zero, x*, of F(x), such that > F(x*) = 0, as a minimum of ||F(x)|| is NOT a good approach. Any root of > F(x) is indeed a global minimum of ||F(x)||, or for that matter, the global > minimum of any f(F(x)), where f(.) is a mappi

[R] setting levels in contourplot()

Does the contourplot() routine have an argument analogous to the "levels" argument in the contour() routine? More generally, is there a way for the user to fix the contour levels in contourplot()? Thanks. --Sam Cable __ R-help@r-project.org mailing li

[R] How estimate VAR(p)-model robustly?

Hello, Does anyone know about robust estimation of vector autoregressive models (VAR(p)) in R? Or in Matlab? Currently I am using the function ar(). The problem is, that the variances of my data change a lot with time, and we also have some outliers in the data. That is why, I presume, that w

Re: [R] explicit documentation

ronggui wrote: It is always unfair to complain about volunteer work, and what you should do is to make contributions. I only half agree with this: I think that it's fair to complain, as long as you make contributions. With documentation, if you don't think it's clear, as part of your com

[R] how to access file backed big matrix (package bigmemory)

__ 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] Paired test for 2-way ANOVA

Paired (aka. Repeated measures, aka. within-Ss) tests can be achieved by using aov() and specifying the within-Ss effect in the error term: my_aov = aov( dependent_variable~between_Ss_variable*within_Ss_variable + Error(Ss_id/(within_Ss_variable))) summary(my_aov) On Mon, Apr 20, 2009 at 10:25 A

Re: [R] Two or more dimensional root (Zero) finding

Ben, That is not a good approach, i.e. finding the zero, x*, of F(x), such that F(x*) = 0, as a minimum of ||F(x)|| is NOT a good approach. Any root of F(x) is indeed a global minimum of ||F(x)||, or for that matter, the global minimum of any f(F(x)), where f(.) is a mapping from R^p to R, such t

Re: [R] bug when subtracting decimals?

this is a (very) Frequently Asked Question; check: http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-doesn_0027t-R-think-these-numbers-are-equal_003f Best, Dimitris wolfgang.siewert wrote: Try this: 0.7-0.3==0.4 (We get FALSE) 0.7-0.3<0.4 (We get TRUE) but 0.8-0.3==0.5 (TRUE) 0.8-0.3<0.5 (F

Re: [R] bug when subtracting decimals?

This is a FAQ. Try this: all.equal(0.7-0.3, 0.4) On Mon, Apr 20, 2009 at 10:07 AM, wolfgang.siewert < wolfgang.siew...@gmail.com> wrote: > > Try this: > > 0.7-0.3==0.4 > (We get FALSE) > 0.7-0.3<0.4 > (We get TRUE) > > but > 0.8-0.3==0.5 > (TRUE) > 0.8-0.3<0.5 > (FALSE) > > Funny, he? > > There

[R] doing zero inflated glmm for count data with fmr

Hello R users, Doing My PhD I collected count data which I believe is zero inflated. I have run a statistical model with lmer and family=poisson and got summary(model)@sigma=1 so I believe there is no overdispertion. I would like to use the fmr function from the 'gnlm' library but I just cannot f

Re: [R] problem with new version

Roslina Zakaria wrote: > > > Hi R-users, > > I just change to the new version of R.  I just wonder why everytime I run > my function I will get this message: > >> source(.trPaths[4], echo=TRUE, max.deparse.length=1) > > Are you by any chance using Tinn-R? Could be a glitch in the in

[R] bug when subtracting decimals?

Try this: 0.7-0.3==0.4 (We get FALSE) 0.7-0.3<0.4 (We get TRUE) but 0.8-0.3==0.5 (TRUE) 0.8-0.3<0.5 (FALSE) Funny, he? There is a way around: round(0.7-0.3,1)==0.4 (TRUE) Obviously there is a problem with some combinations of decimal subtractions, that - we have the feeling - shouldt be solv

[R] Paired test for 2-way ANOVA

Hi, I have an experimental data with 2 factors: visit and treatment. Each subject has 2 visits and on each visit they get a treatment. We take samples before and after treatment. I can easily to do the 2-way ANOVA in R with visit and treatment as factors. anova( lm(data ~ visit*treatment) )

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