Re: [R] RTisean executable problem in STLperArea

2011-11-30 Thread Prof Brian Ripley
It is one of the rather confusing things about the RTisean package. It does not say what your subject says: it says 'TISEAN executables'. The DESCRIPTION *should* have a SystemRequirements line (and this has been reported), It does say It requires that you have the Tisean-3.0.1 algorithms

Re: [R] Generalized singular value decomposition

2011-11-30 Thread Oana Tomescu
Am 30.11.2011 16:13, schrieb Berend Hasselman: tom wrote I don't think you have to install "something". You have not told us how you are trying to load the dll's. You can use the GSVD function from http://r.789695.n4.nabble.com/problem-with-generalized-singular-value-decomposition-using-LAPAC

Re: [R] Average of Two Matrices

2011-11-30 Thread Joshua Wiley
Well, you're rather stuck writing them all out unless you have them in some other data structure. ## three dimensional array (50 4 x 4 matrices) x <- array(rnorm(16 * 50), dim = c(4, 4, 50)) > apply(x, 1:2, mean) [,1][,2] [,3][,4] [1,] -0.09460574 0.01572077 -0

[R] ordinal data simulation

2011-11-30 Thread yuying shi
Dear all, I am doing an ordinal data simulation. I have a question regarding the cut off values between categories. Suppose I have three categories, if I do regression, there should be two cut off values. I find some simulation code for the ordinal data. However, they usually only generate a

[R] error in ZIGP package and optim

2011-11-30 Thread chenandfuok
Dear all: I am trying to use the response.zigp and est.zigp from the ZIGP package. Firstly, I generated a simple data via response.zigp and then I try to fit them by est.zigp function, this is the code: - > library(ZIGP) > #try-ZIGP-1 > n<-100 > X<-matrix(c(rep(1,n),

Re: [R] Average of Two Matrices

2011-11-30 Thread T.D. Rudolph
What if you have over 50 matrices and you don't want to write them all out one-by-one? I know there's something really quite simple, but I haven't found it yet!... -- View this message in context: http://r.789695.n4.nabble.com/Average-of-Two-Matrices-tp860672p4126615.html Sent from the R help m

[R] R code

2011-11-30 Thread nsaraf
Hi everybody, I am unable to resolve this error using the following for loop. Would appreciate help. The same loop works with for(i in 1:92) strangely. I checked the .raw input file and everything is kosher, even Line 547 mentioned in the error message. I wonder if there is any problem with the p

[R] RTisean executable problem in STLperArea

2011-11-30 Thread lglew
Hi, I’m trying to use the STLperArea function in the ndvits package. I can run the sample data (“SLPSAs_full”) without any problem. However, when I come to run the function on my own data, I get the following message. Waiting to confirm page change... Error in .checkPath(path) : no TISEAN execu

Re: [R] Random Forests in R

2011-11-30 Thread Peter Langfelder
On Wed, Nov 30, 2011 at 7:48 PM, Axel Urbiz wrote: > I understand the original implementation of Random Forest was done in > Fortran code. In the source files of the R implementation there is a note > "C wrapper for random forests:  get input from R and drive  the Fortran > routines.". I'm far fro

Re: [R] R endnote entry

2011-11-30 Thread Luke Miller
I have R entered as a "computer program", and in the Programmer Name field I write it as: R Development Core Team, Notice the comma after Team. That seems to be the key to getting Endnote to treat the whole thing as a surname that doesn't get abbreviated. On Wed, Nov 30, 2011 at 10:56 PM, Matt C

[R] R endnote entry

2011-11-30 Thread Matt Cooper
I know citation() gives the R citation to be used in publications. Has anyone put this into endnote nicely? I'm not very experienced with endnote, and the way I have it at the momeny the 'R Development Core Team' becomes R. D. C. T. etc. Cheers. __ R-he

[R] R logo in eps formt

2011-11-30 Thread Ben Madin
G'day all, Sorry if this message has been posted before, but searching for R is always difficult... I was hoping for a copy of the logo in eps format? Can I do this from R, or is one available for download? cheers Ben __ R-help@r-project.org mailing

[R] Random Forests in R

2011-11-30 Thread Axel Urbiz
I understand the original implementation of Random Forest was done in Fortran code. In the source files of the R implementation there is a note "C wrapper for random forests: get input from R and drive the Fortran routines.". I'm far from an expert on this...does that mean that the implementation

[R] FIML with missing data in sem package

2011-11-30 Thread Dustin Fife
Is there a way to use full information maximum likelihood (FIML) to estimate missing data in the sem package? For example, suppose I have a dataset with complete information on X1-X3, but missing data (MAR) on X4. Is there a way to use FIML in this case? I know lavaan and openmx allow you to do it,

Re: [R] how to call a function for each row

2011-11-30 Thread Florent D.
if you want to store the result in a column of your data.frame: within(df, Y <- 6*X1+7*X2+8*X3) On Wed, Nov 30, 2011 at 9:59 AM, David L Carlson wrote: > Isn't this even easier? > >> X1 <- c(1:3) >> X2 <- c(3, 4, 6) >> X3 <- c(5, 6, 1) >> Y <- 6*X1 + 7*X2 + 8*X3 >> Y > [1] 67 88 68 > > Or if yo

Re: [R] Invalid number of components, ncomp

2011-11-30 Thread R. Michael Weylandt
I'm not familiar with the package and I don't currently have it loaded, but looking at the examples in the documentation here http://www.stat.ucl.ac.be/ISdidactique/Rhelp/library/pls.pcr/html/mvr.html it seems that you need ncomp = 1:6. Saying you want to do multivariate regression on only a sing

Re: [R] forecasting linear regression from lagged variable

2011-11-30 Thread Gabor Grothendieck
On Wed, Nov 30, 2011 at 4:40 PM, AaronB wrote: > I'm currently working with some time series data with the xts package, and > would like to generate a forecast 12 periods into the future. There are > limited observations, so I am unable to use an ARIMA model for the forecast. > Here's the regressi

Re: [R] Bootstrapping for residuals

2011-11-30 Thread David Winsemius
On Nov 30, 2011, at 11:31 AM, bubbles1990 wrote: Hi, Ive been trying to write a program for bootstrapping residuals in R but without much success. A lecturer wants to predict the performance of students in an end-of- year physics exam, y. The lecturer has the students results from a mid-

Re: [R] Problem installing the package tkrplot

2011-11-30 Thread peter dalgaard
On Nov 30, 2011, at 15:31 , Marcos Amaris Gonzalez wrote: > Hello people. My problem is that when I try to install the package > tkrplot, I got the next problem: You seem to be missing the tk.h file. This is, most likely, in a tcl/tk development package that you haven't installed. This is part

Re: [R] forecasting linear regression from lagged variable

2011-11-30 Thread Mark Leeds
hi: that model is what the political scientists called an LDV ( lagged dependent variable model ), the marketing people call a koyck distributed model and the economists call it an ADL(1,0) or ADL(0,1). ( i forget ). You have to be careful about the error term because, if it's not white noise, the

[R] forecasting linear regression from lagged variable

2011-11-30 Thread AaronB
I'm currently working with some time series data with the xts package, and would like to generate a forecast 12 periods into the future. There are limited observations, so I am unable to use an ARIMA model for the forecast. Here's the regression setup, after converting everything from zoo objects t

Re: [R] Bootstrapping for residuals

2011-11-30 Thread bubbles1990
I study a part-time long distance learning course so only really have access to online sources for help, i'm sure ill crack it eventually. I understand how to do it with 2 variables, its just having 3 that is confusing me -- View this message in context: http://r.789695.n4.nabble.com/Bootstrappin

Re: [R] Calculating marginal effects in R

2011-11-30 Thread z-list_economist
The relevant code is contained in the following working paper: http://ideas.repec.org/p/ucn/wpaper/201122.html -- View this message in context: http://r.789695.n4.nabble.com/Calculating-marginal-effects-in-R-tp887488p4124996.html Sent from the R help mailing list archive at Nabble.com.

Re: [R] nls help

2011-11-30 Thread chuck.01
Ah, I see, thank you both. Michael Weylandt wrote > > It's a scaling problem: > > If you do this: > > datum <- datum[order(datum$X),] > > with(datum, plot(Y~X)) > with(datum, lines(X, 3400*exp(-1867*X))) > > you'll see that your initial guess is just so far gone that the nls() > optimizer

[R] Error adding Bigmemory package

2011-11-30 Thread RogerP
I am trying to add the bigmemory packages but I get the following error message: In file included from bigmemory.cpp:14:0: ../inst/include/bigmemory/isna.hpp: In function 'bool neginf(double)': ../inst/include/bigmemory/isna.hpp:22:57: error: 'isinf' was not declared in this scope make: *** [bigme

Re: [R] Package "field" missing from repositories

2011-11-30 Thread David Winsemius
On Nov 30, 2011, at 1:15 PM, joseph.s...@geog.ubc.ca wrote: Hi all; After an overnight Ubuntu upgrade to 10.10, I had to reinstall some R packages. But the "fields" package appears to be missing from my usual repository, and a few of the other repositories I've tested: install.packages('

Re: [R] Bootstrapping for residuals

2011-11-30 Thread David Winsemius
On Nov 30, 2011, at 11:31 AM, bubbles1990 wrote: Hi, Ive been trying to write a program for bootstrapping residuals in R but without much success. A lecturer wants to predict the performance of students in an end-of- year physics exam, y. The lecturer has the students results from a mid-

Re: [R] SAS to R: I would like to replicate a statistical analysis performed in SAS in R.

2011-11-30 Thread Ben Bolker
Marianne Stephan hotmail.com> writes: > A statistician performed an analysis in SAS for me which I would > like to replicate in R. I have however problems in figuring out the > R code to do that. As I understood it was a "covariance regression > model". In the analysis, baseline was used as cov

Re: [R] install "multtest" and "preprocessCore" packages in Bioconductor library

2011-11-30 Thread Dan Tenenbaum
Hi Nguyen, On Wed, Nov 30, 2011 at 12:11 PM, UyenThao Nguyen wrote: > Thank you All for your prompt helps. > > Dear Dan, > > Before I used > source("http://bioconductor.org/biocLite.R";) > biocLite("Biobase") # GET BIOCONDUCTOR PACKAGE FROM SOURCE > > then, I went to "Install packages" in Rgui po

Re: [R] install "multtest" and "preprocessCore" packages in Bioconductor library

2011-11-30 Thread UyenThao Nguyen
Thank you All for your prompt helps. Dear Dan, Before I used source("http://bioconductor.org/biocLite.R";) biocLite("Biobase") # GET BIOCONDUCTOR PACKAGE FROM SOURCE then, I went to "Install packages" in Rgui pointing to BioConductor to load these packages in. That was why I got the error messa

Re: [R] help about fitdistr funtion

2011-11-30 Thread R. Michael Weylandt
I like to use split() to split your data into groups, then run lapply() to use fitdistr on each element of the list. E.g, df <- data.frame(X = rnorm(500), ID = sample(letters[1:5], 500, TRUE)) temp <- split(df$X, df$ID) lapply(temp, fitdistr, "normal") Though it's just as easy with tapply(): t

[R] How can I pick a matrix from a function? (Out Product of Gradient)

2011-11-30 Thread yanghaowang
Hi all, I would like to use optim() to estimate the equation by the log-likelihood function and gradient function which I had written. I try to use OPG(Out Product of Gradient) to calculate the Hessian matrix since sometime Hessian matrix is difficult to calculate. Thus I want to pick the Gradient

Re: [R] nls help

2011-11-30 Thread R. Michael Weylandt
It's a scaling problem: If you do this: datum <- datum[order(datum$X),] with(datum, plot(Y~X)) with(datum, lines(X, 3400*exp(-1867*X))) you'll see that your initial guess is just so far gone that the nls() optimizer can't handle it. If you try a more reasonable initial guess it works fine: fi

[R] Bootstrapping for residuals

2011-11-30 Thread bubbles1990
Hi, Ive been trying to write a program for bootstrapping residuals in R but without much success. A lecturer wants to predict the performance of students in an end-of-year physics exam, y. The lecturer has the students results from a mid-term physics exam, x, and a mid-term biology exam, z. He pr

[R] Problem installing the package tkrplot

2011-11-30 Thread Marcos Amaris Gonzalez
Hello people. My problem is that when I try to install the package tkrplot, I got the next problem: > install.packages("tkrplot") Installing package(s) into ‘/home/marcos/R/i686-pc-linux-gnu-library/2.13’ (as ‘lib’ is unspecified) probando la URL 'http://www.vps.fmvz.usp.br/CRAN/src/contrib/tkrplo

[R] formula for calculating the survival probability for nomogram

2011-11-30 Thread min
Hi, I used Dr. Harrell's rms package to make a nomogram. Below is my code for nomogram and calculate total points and probability *in original data set* used for building the nomogram. *My question is how I get the formula for calculating the survival probability for this nomogram. Then I can use

[R] How can I pick a matrix from a function? (Out Product of Gradient)

2011-11-30 Thread Yanghao Wang
Hi all, I would like to use optim() to estimate the equation by the log-likelihood function and gradient function which I had written. I try to use OPG(Out Product of Gradient) to calculate the Hessian matrix since sometime Hessian matrix is difficult to calculate. Thus I want to pick the Gradient

[R] Nomogram with stratified cph in rms package, how to get failure probability

2011-11-30 Thread min
Hello, I am using Dr. Harrell's rms package to make a nomogram. I was able to make a beautiful one. However, I want to change 5-year survival probability to 5-year failure probability. I couldn’t get hazard rate from Hazard(f1) because I used cph for the model. Here is my code: library(rms) f1

Re: [R] install "multtest" and "preprocessCore" packages in Bioconductor library

2011-11-30 Thread Dan Tenenbaum
Hi Nguyen, > Subject: [R] install "multtest" and "preprocessCore" packages in > Bioconductor library > Date: Wed, 30 Nov 2011 09:57:36 -0800 > From: UyenThao Nguyen > To: r-help > CC: uth.ngu...@ucdavis.edu > > Hi All, > > I've tried to install these "multtest" and "preprocessCore" packages in

[R] Package "field" missing from repositories

2011-11-30 Thread joseph . shea
Hi all; After an overnight Ubuntu upgrade to 10.10, I had to reinstall some R packages. But the "fields" package appears to be missing from my usual repository, and a few of the other repositories I've tested: >install.packages('fields',lib='/usr/local/lib/R/site-library',repos='http://cran.st

[R] help about fitdistr funtion

2011-11-30 Thread Carlos Javier Rincon Rodriguez
Hi, I have a variable X classified in a lot of groups and I need to run the [fitdistr] funtion for each group. I tried with the [by] or the [tapply] funtions because my data is organize in two columns (variable and the groups), but neither of these command work. If somebody have a tip to help me

[R] nls help

2011-11-30 Thread chuck.01
Hello, I have data like the following: datum <- structure(list(Y = c(415.5, 3847.8325, 1942.83325, 1215.223, 950.142857325, 2399.585, 804.75, 579.5, 841.70825, 494.053571425 ), X = c(1.081818182, 0.492727273, 0.756363636, 0.896363636, 1.518181818, 0.49917, 1.35454545

Re: [R] R help

2011-11-30 Thread R. Michael Weylandt
Just throwing this out there: there's no probability distribution in the equation you gave, so there's no context for an MLE: what is the likelihood for m? Knowing a little bit about the NS model, it seems like it makes more sense to use nls() to fit all four parameters to the data at once. Somet

[R] SAS to R: I would like to replicate a statistical analysis performed in SAS in R.

2011-11-30 Thread Marianne Stephan
Hello everybody, A statistician performed an analysis in SAS for me which I would like to replicate in R. I have however problems in figuring out the R code to do that. As I understood it was a "covariance regression model". In the analysis, baseline was used as covariate and autoregressive

Re: [R] Problem in log

2011-11-30 Thread R. Michael Weylandt
You still haven't provided anything reproducible since we can't get to your data file (also you used the-you-really-shouldn't-use-this-function function attach) but here's what I'd guess: Your say the problem occurs when exp(-alpha*d^(-beta)) > 1 Of course, this happens when alpha*d^(-beta) < 0

Re: [R] problem during installing bayesQR package for R 2.14 version

2011-11-30 Thread John C Frain
1. Start R (as administrator i.e. right click on the R icon on your desktop and select run as administrator). 2 Select Packages form menu bar 3 Select Install package(s) from local zip files.. and negotiate to your zip file. When you want to use the package you must enter library(bayesQR) I wo

Re: [R] nls help

2011-11-30 Thread Dieter Menne
chuck.01 wrote > > > datum <- structure(list(Y = c(415.5, 3847.8325, 1942.83325, > 1215.223, > 950.142857325, 2399.585, 804.75, 579.5, 841.70825, 494.053571425 > ), X = c(1.081818182, 0.492727273, 0.756363636, 0.896363636, > 1.518181818, 0.49917, 1.354545455, 1.61,

Re: [R] install "multtest" and "preprocessCore" packages in Bioconductor library

2011-11-30 Thread David Winsemius
On Nov 30, 2011, at 12:57 PM, UyenThao Nguyen wrote: Hi All, I've tried to install these "multtest" and "preprocessCore" packages in Mac, but kept getting error messages. I tried to load the packages using 2 ways: 1. Installed from BioConductor (sources) You should read the directions

Re: [R] install "multtest" and "preprocessCore" packages in Bioconductor library

2011-11-30 Thread R. Michael Weylandt
My apologies: the posting guide doesn't actually suggest updating to the most recent stable version -- though perhaps it would be a good addition to the "before posting" section -- but I still think that's the necessary fix to your problem. Michael On Wed, Nov 30, 2011 at 1:08 PM, R. Michael Weyl

Re: [R] install "multtest" and "preprocessCore" packages in Bioconductor library

2011-11-30 Thread R. Michael Weylandt
As the posting guide strongly suggests, I think the first step is to update to R 2.14: there have been changes in package design and I'm not sure back-compatibility will run that far. Doing so should let you download fresh binaries straight from BioC. I'm not sure why you would get compilation err

[R] install "multtest" and "preprocessCore" packages in Bioconductor library

2011-11-30 Thread UyenThao Nguyen
Hi All, I've tried to install these "multtest" and "preprocessCore" packages in Mac, but kept getting error messages. I tried to load the packages using 2 ways: 1. Installed from BioConductor (sources) 2. And installed from BioConductor (binaries) Both ways, I got these error messages: For pre

Re: [R] "Non-finite finite-difference value" error in eha's aftreg

2011-11-30 Thread Göran Broström
On Wed, Nov 16, 2011 at 3:06 PM, Milan Bouchet-Valat wrote: > Hi list! > > > I'm getting an error message when trying to fit an accelerated failure > time parametric model using the aftreg() function from package eha: > > Error in optim(beta, Fmin, method = "BFGS", control = list(trace = > > as.

Re: [R] Replace columns in a data.frame randomly splitted

2011-11-30 Thread R. Michael Weylandt
Two ways immediately come to mind: 1) Change the values before splitting 2) Use the same seed for the two splits so the rows match exactly and then just do the changes directly Any more automated solution will depend on whether your data has rownames or not. Michael PS - As a general rule, mos

Re: [R] Negative exponential fit

2011-11-30 Thread Ben Bolker
On 11-11-30 11:32 AM, peter dalgaard wrote: > > On Nov 29, 2011, at 23:19 , Ben Bolker wrote: > >> rch4 geneseo.edu> writes: >> >>> >>> We need help >>> >>> We are doing a project for a statistical class in and we are >>> looking at world record times in different running events over >>>

Re: [R] Negative exponential fit

2011-11-30 Thread peter dalgaard
On Nov 29, 2011, at 23:19 , Ben Bolker wrote: > rch4 geneseo.edu> writes: > >> >> We need help >> >> We are doing a project for a statistical class in and we are looking at >> world record times in different running events over time. We are trying to >> fit the data with a negative expone

Re: [R] Parameters setting in functions optimization

2011-11-30 Thread Diane Bailleul
Dear Florent, I know that I'm asking to optim to minimize my values, and that the results with a lower fvalue are best supported than those with a higher fvalue. My comment was just from a data point of view. I'd like the lower ms (second parameter) as possible, as well as the fvalue. So a ms o

Re: [R] All combinations

2011-11-30 Thread David Winsemius
On Nov 30, 2011, at 7:18 AM, R. Michael Weylandt wrote: expand.grid() This one is admittedly rather hard to find... Well, it is linked from the `combn` help page. And it is the likely to be first or second in a search with ??combinations since it is in pkg:base and at least on my interfa

Re: [R] Parameters setting in functions optimization

2011-11-30 Thread John C Nash
optimx does allow you to use bounds. The default is using only methods from optim(), but even though I had a large hand in those methods, and they work quite well, there are other tools available within optimx that should be more appropriate for your problem. For example, the current version of

Re: [R] Generalized singular value decomposition

2011-11-30 Thread Berend Hasselman
tom wrote > > Thank you for your help! > > The GSVD (SVDgen) in PTAk does not perform a generalized singular value > decomposition for 2 matrices, only for 1. I should have mentioned this - > sorry. > Are there maybe other packages? > > I have also found the last 2 links, but I look for a way

Re: [R] SPSS -> R

2011-11-30 Thread John Fox
Dear Michael, The original poster and I ended up pursuing this question off-list and, I think, resolving the issue, discovering in the process that SPSS apparently reports "type-II" tests that are really "type-III" tests. (Yes, one fits a multivariate linear model prior to calling Anova() with the

Re: [R] how to call a function for each row

2011-11-30 Thread David L Carlson
Isn't this even easier? > X1 <- c(1:3) > X2 <- c(3, 4, 6) > X3 <- c(5, 6, 1) > Y <- 6*X1 + 7*X2 + 8*X3 > Y [1] 67 88 68 Or if you really need a function: > MakeY <- function(x, y, z) 6*x + 7*y + 8*z > MakeY(X1, X2, X3) [1] 67 88 68 -- David L Carlson

Re: [R] Negative exponential fit

2011-11-30 Thread Indrajit Sengupta
Thanks Peter, will take a look at this package. Regards, Indrajit From: Peter Ruckdeschel To: r-h...@stat.math.ethz.ch Sent: Wednesday, November 30, 2011 5:03 PM Subject: Re: [R] Negative exponential fit I do not want to shed out any doubt as to the merits

Re: [R] glm step() fkt

2011-11-30 Thread R. Michael Weylandt
Put them in a list: ModelList <- vector("list", 100) ModelList[[i]] <- mod.step <- step(mod, direction="both",trace=T) Then come back and use sapply() to do whatever you want to the set of models to compare/count/etc them Michael On Wed, Nov 30, 2011 at 6:12 AM, Schrabauke wrote: > Hi

Re: [R] how to call a function for each row

2011-11-30 Thread Bert Gunter
Homework. ? I would say that this indiicates that you need to open the R tutorials and start reading. -- Bert On Wed, Nov 30, 2011 at 5:10 AM, arunkumar wrote: > Hi > >  I have  a data-frame which look like this > > X1 X2 X3 > 1   3  5 > 2   4  6 > 3   6  1 > > I want to apply a formula Y=

Re: [R] how to call a function for each row

2011-11-30 Thread jim holtman
will this do it: > x <- read.table(text = "X1 X2 X3 + 1 3 5 + 2 4 6 + 3 6 1", header = TRUE) > x X1 X2 X3 1 1 3 5 2 2 4 6 3 3 6 1 > apply(x, 1, function(a) 6 * a[1] + 7 * a[2] + 8 * a[3]) [1] 67 88 68 > > On Wed, Nov 30, 2011 at 8:10 AM, arunkumar wrote: > Hi > >  I have

Re: [R] how to call a function for each row

2011-11-30 Thread R. Michael Weylandt
Read ?apply This is easiest: df <- matrix(c(1,2,3,3,4,6,5,6,1), 3) apply(df, 1, function(x) 6*x[1]+7*x[2]+8*x[3]) But it's much more efficient to do it with matrix multiplication. In keeping with the best of tradition, this is left as an exercise to the reader. Michael On Wed, Nov 30, 2011 at

Re: [R] Problems with Raster and clim.pact packages with large netcdf files (2.7G) in x64 bit R

2011-11-30 Thread Roger Bivand
Emmanuel Jjunju gmail.com> writes: > > I normally use the raster or clim.pact pckages to read netcdf (.nc) files. > This has always worked out for me until this weekend every time i try to > read a .nc file i get the following error > ... Could you please: 1. Consider moving this thread to R-

[R] Replace columns in a data.frame randomly splitted

2011-11-30 Thread agent dunham
Dear community, I'm working with the data.frame attached ( http://r.789695.n4.nabble.com/file/n4122926/df1.xls df1.xls ), let's call it df1. I typed: df1<- read.xls("C:/... dir .../df1.xls",colNames= TRUE, rowNames= TRUE) Then I splited randomly df1 using splitdf function (http://gettingg

Re: [R] Non parametric, repeated-measures, factorial ANOVA

2011-11-30 Thread RobH2011
Hi Thanks for your reply. The package appears to be for the analysis of longitudinal designs, and requires a time factor to be input on the relevant . My experiment is just a standard repeated-measures design, and I just need a direct, non-parametricc equivalent of the Factorial repeated-measures

[R] how to call a function for each row

2011-11-30 Thread arunkumar1111
Hi I have a data-frame which look like this X1 X2 X3 1 3 5 2 4 6 3 6 1 I want to apply a formula Y=6*X1 + 7*X2 + 8*X3 for every row Thanks in Advance -- View this message in context: http://r.789695.n4.nabble.com/how-to-call-a-function-for-each-row-tp4122906p4122906.html Se

[R] glm step() fkt

2011-11-30 Thread Schrabauke
Hi volks, i have a question about the step() fkt. Is there a possibility to save the last model generated from this method. I have a loop and so i generate 100 different models with the step fkt and i want to know which model is the most common. CODE: ... missStep -> numeric(100) for (j in 1:10

[R] Invito a collegarsi su LinkedIn

2011-11-30 Thread giovanni parrinello
Vorrei aggiungerti alla mia rete professionale su LinkedIn. -giovanni giovanni parrinello Senior Statistical Consultant at University of Brescia Italy Confirm that you know giovanni parrinello: https://www.linkedin.com/e/-92ffr2-gvmdq8pr-1/isd/5085379353/o5O4tnc8/?hs=false&tok=0BYzKxkO2MnB01

Re: [R] Generalized singular value decomposition

2011-11-30 Thread Oana Tomescu
Thank you for your help! The GSVD (SVDgen) in PTAk does not perform a generalized singular value decomposition for 2 matrices, only for 1. I should have mentioned this - sorry. Are there maybe other packages? I have also found the last 2 links, but I look for a way to use LAPACK with Windows

Re: [R] Problem in log

2011-11-30 Thread Gyanendra Pokharel
The loglikelihood() looks ok and gives some value. But I am using this function for the simulated annealing, generating the random samples from uniform proposal density., The codes are as follows epiannea <- function(T0 = 1, N = 500,beta = 0.1,x0 = 0.1, rho = 0.90, eps = 0.1, loglikelihood, data)

Re: [R] Problem in log

2011-11-30 Thread R. Michael Weylandt
I'd suggest you do some leg-work and figure out why you are getting values >1. If your algorithm is motivated by some approximation then a min() or pmin() *might* be the right fix, but if there are no approximations you may need to start debugging properly to see why you are getting an out of bo

Re: [R] Notation

2011-11-30 Thread Paul Hiemstra
Hi Silvano, Your function is not part of the standard R installation. After some googling I found out, but next time: PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. The betareg package provides manua

Re: [R] Generalized singular value decomposition

2011-11-30 Thread Paul Hiemstra
Hi, Googling for "R-help gsvd" leads to a number of interesting entries on the mailing list. It seems that GSVD is present in the lapack version included with R and can be called (see the mailing list entries). https://stat.ethz.ch/pipermail/r-help/2004-August/056713.html http://r.789695.n4.nabbl

Re: [R] All combinations

2011-11-30 Thread R. Michael Weylandt
expand.grid() This one is admittedly rather hard to find... Michael On Nov 30, 2011, at 7:15 AM, Alaios wrote: > Dear all, > I would like something simple to do in R that I do not know how I should > search for it. > > Let's say that I have a list of > a<-c(1,2,3,4,5) > b<-(6,7,8) > and I wa

[R] All combinations

2011-11-30 Thread Alaios
Dear all, I would like something simple to do in R that I do not know how I should search for it. Let's say that I have a list of a<-c(1,2,3,4,5) b<-(6,7,8) and I want to get back all their possible cominations like 1,6 1,7 1,8 2,6 2,7 2,8 3,6 3,7 3,8 and so on. How I can do that? B.R Alex

Re: [R] Storing the linear model object

2011-11-30 Thread R. Michael Weylandt
If you mean storing it within one session, it's just like any other object m <- lm(...) and it can be put in lists, modified, whatever just like any other object. Michael On Nov 30, 2011, at 4:23 AM, Diane Bailleul wrote: > Good morning, > Normally, if you save your R environment, some objec

Re: [R] Replacing a value in a dataframe

2011-11-30 Thread Uwe Ligges
On 30.11.2011 12:26, Bert Gunter wrote: er... Uwe, shouldn't that be, e.g. dataframe$Cheque<- as.integer(dataframe$Cheque) Sure, thanks. ## or building on Rolf's suggestion dataframe<- within(dataframe, Cheque<- as.integer(Cheque)) While I am at it, is there any practical difference in

Re: [R] SPSS -> R

2011-11-30 Thread Michael Dewey
At 16:41 27/11/2011, Kristi Shoemaker wrote: Hi John, Your assumptions are correct and those examples were very helpful, thanks! I think I'm almost there, but I'm screwing up something with the within-subjects factor (the example has two, I only have one). See below. Why am I not seeing my wi

Re: [R] Negative exponential fit

2011-11-30 Thread Peter Ruckdeschel
Am 29.11.2011 07:06, schrieb Indrajit Sengupta: > What have you tried so far - can you explain? "fitdistrplus" package is the > default package for fitting distributions. > > Regards, > Indrajit > > > > > From: rch4 > To: r-help@r-project.org > Sent: Tuesday

Re: [R] Replacing a value in a dataframe

2011-11-30 Thread Bert Gunter
er... Uwe, shouldn't that be, e.g. dataframe$Cheque <- as.integer(dataframe$Cheque) ## or building on Rolf's suggestion dataframe <- within(dataframe, Cheque <- as.integer(Cheque)) While I am at it, is there any practical difference in efficiency between these two approaches? -- Bert 2011/11

Re: [R] Parameters setting in functions optimization

2011-11-30 Thread Florent D.
With optimx(c(30,50),ms=c(0.4,0.5), fn=LogLiketot) where LogLiketot<- function(dist,ms) { res <- NULL for(i in 1:nrow(pop5)) { for(l in 1:nrow(freqvar)) { res <- c(res, pop5[i,l]*log(LikeGi(l,i,dist,ms))) } } return(-sum(res)) } I think it will do something l

[R] Generalized singular value decomposition

2011-11-30 Thread Oana Tomescu
Hello, I would like to perform a generalized singular value decomposition with R. The only possibility I found is "GSVD" that is based on LAPACK/BLAS. Are there other possibilities too? If not, has anybody used LAPACK/BLAS under Windows XP? How can I install them? Following [1] did not help.

[R] Invalid number of components, ncomp

2011-11-30 Thread Vytautas Rakeviius
Error in mvr(Kd_nM ~ qsar, ncomp = 6, data = my, validation = "CV", method = "kernelpls") :   Invalid number of components, ncomp How I can fix this? [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.

Re: [R] Replacing a value in a dataframe

2011-11-30 Thread Uwe Ligges
On 30.11.2011 09:16, arunkumar wrote: hi I have data like this in a dataframe Var Value Cheque X140FALSE X220FALSE X328TRUE I want to replace it FLASE with 0 and TRUE with 1. is there any method by which i can do without using LOOP dataframe$Cheque <- as.int

Re: [R] Hiding message

2011-11-30 Thread Rolf Turner
On 30/11/11 20:22, Jeff Newmiller wrote: "Don't do that." Use $ notation to refer to elements of lists/data frames explicitly. Or use with(). It is truly-ruly handy and effective. cheers, Rolf Turner --- Je

[R] Replacing a value in a dataframe

2011-11-30 Thread arunkumar1111
hi I have data like this in a dataframe Var Value Cheque X140FALSE X220FALSE X328TRUE I want to replace it FLASE with 0 and TRUE with 1. is there any method by which i can do without using LOOP -- View this message in context: http://r.789695.n4.nabble.com/Replacing

Re: [R] Storing the linear model object

2011-11-30 Thread Diane Bailleul
Good morning, Normally, if you save your R environment, some objects, like your lm, must be saved in with. Otherwise, have you tried save() or dput() functions ? Le 11/30/2011 6:10 AM, arunkumar a écrit : Hi Please let me know if we can store the linear model object in the data base an

Re: [R] Parameters setting in functions optimization

2011-11-30 Thread Diane Bailleul
Le 11/30/2011 2:09 AM, Florent D. a écrit : Thanks for your answer ! I also think your last write-up for LogLiketot (using a single argument "par") is the correct approach if you want to feed it to optim(). I'm not dedicated to optim() fonction. I just want to optimise my two parameters and the

Re: [R] Non parametric, repeated-measures, factorial ANOVA

2011-11-30 Thread Jim Lemon
On 11/29/2011 10:31 PM, RobH2011 wrote: Hi I have data from an experiment that used a repeated-measures factorial 2x2 design (i.e. each participant contributed data to both levels of both factors). I need a non-parametric version of the repeated-measures factorial ANOVA to analyse the data. SPSS

Re: [R] Negative exponential fit

2011-11-30 Thread Uwe Ligges
On 30.11.2011 07:25, Indrajit Sengupta wrote: Agreed, nobody has deemed it "default", but is there any other such package that you can think of for this purpose. Not that I know. Suggesting it is perfect. I'd just not call any package a "default" if it does not ship with R. Best, Uwe