Re: [R] array complexity for the MH test

Thanks for your answer. The answer advertises your VCD package, which by the way is a very nice package that I use and recommend for everyone doing such kind of data analysis. However if you really examine the answer you gave me, it does not really or specifically answer my question. -- View this

[R] array complexity for the MH test

If we take the matel-haenszel test on these data of five 2x2 tables stratified along Penicillin.Levels array(c(0, 0, 6, 5, 3, 0, 3, 6, 6, 2, 0, 4, 5, 6, 1, 0, 2, 5, 0, 0), dim = c(2, 2, 5), dimnames = list( Delay = c(None, 1.5h),

[R] R as a shared library only

Hello, I know how to embed R in other applications by linking my applications to the R.dll shared library. For example I can use R from within a Lisp program by having the foreign function interface in lisp connect directly to R.dll lib. However I still need all R (the other libs and supporting

[R] Cumulative density (kernel smoothing)

Hi, in R there is the function density which computes kernel density estimates. Is there a cumulative version of it? Something like they have in Matlab: http://www.mathworks.nl/help/toolbox/stats/ksdensity.html I know there is ecdf, but I'm not sure it's based on kernel density smoothing. Thanks

[R] KS test and theoretical distribution

x - runif(100) y - runif(100) ks.test(x,y) Two-sample Kolmogorov-Smirnov test data: x and y D = 0.11, p-value = 0.5806 alternative hypothesis: two-sided ok I expected that, but: ks.test(runif(100), runif) One-sample Kolmogorov-Smirnov test data: runif(100) D = 0.9106,

[R] 3D plot RGL

Hi, anyone has experience with 3D plot (ex: in package RGL) I have a question, I draw a 3D plot of country, year and sales in z axis but when the type is h then it's ok but when I want to link the points and type is 'l' lines it's a mess Is there a way to link the points only in one direction? For

[R] bootstrap/boot unknown distribution

Hi, this is a question about bootstrapping, it relates more to the concept than to the R package boot. But I wonder below if boot can help me. I have the below to calculate a certain point estimate: estimate= (0.9 * 0.03 * 70 * (((77 * (76 / 76.0)) / 83107) - ((174 * (154 / 154.0)) /

[R] anova of glm output

Hi, this is more related to understanding some statistics while using R; I've see such output in a paper: out - glm(response~Var1+Var2+Var3..,family=binomial,data=mydata) summary(out) stepAIC(out) anova(out, test='Chisq') I understand that stepAIC is used to select the model with the lowest AIC

[R] GLM outputs in condensed versus expanded table

Hi I'm having different outputs from GLM when using a condensed table V1 V2 V3 Present Absent 0 0 0 3 12 0 0 1 0 0 0 1 0 0 0 0 1 1 1 0 1 0 0 7 20 1 0

[R] R-help IRC chat?

Just throwing the idea around: Maybe it would be a good to have an IRC chat forum for R on Freenode? There are several devoted to programming (c, c++, lisp etc). It would be a good addition to a mailing list. -- View this message in context:

[R] fisher.test CIs

The reason I had asked how and what method was used to calculated the confidence intervals of the odds ratio in the fisher.test is because I don't think it's the exact method based on permutations. It seems that the exact method is not implemented in R or anywhere else: In a tactic originally

[R] Confidence Limits for a Cross-Product Ratio

Data from Fisher's paper: Confidence Limits for a Cross-Product Ratio. y col1 col2 [1,] 103 [2,]2 15 fisher.test(y) Fisher's Exact Test for Count Data data: y p-value = 0.0005367 alternative hypothesis: true odds ratio is not equal to 1 95 percent confidence

[R] User defined GLM?

Hello, I have this generalized linear formula: log(x[i]/n[i])=log(sum(x)/sum(n)) + beta[i] where the the x[i] and the n[i] are known. Is there a way to program the GLM procedure to input the formula above and get the beta[i] estimates? If not the GLM is there another procedure to do that? The aim

Re: [R] User defined GLM?

Emmanuel Charpentier wrote: I do not understand the problem as stated. if x[i] and n[i] are known, and unless sum(n)=0, your dataset reduces to a set of nrow(dataset) independent linear equations with nrow(dataset) unknowns (the beta[i]), whose solution is trivially

[R] R code compiled, assembled or interpreted?

Hi all, do you know if an R program is compiled to machine language when executed? And also is there any way to disassemble an R code/program: to see how it is generating the machine instructions for the processor? Thanks -- View this message in context:

[R] Where to find old R packages?

What happens to old R packages? Is there a place where they are stored like an archive? I'm looking for a package called ScanoR that doesn't exist anymore on CRAN, the author doesn't exist anymore... I had made copies of all packages (fearing that some might be taken off the air but unfortuantely

[R] Calling LISP programs in R

I have written some programs in Common Lisp and I have been using SAS to pipe those programs to my lisp compiler in batch mode by using the %xlog and %xlst SAS commands. I wonder if there is in R a similar way to pipe commands to LISP so that all my work would be concentrated in R even when I

[R] Similarity matching with probabilities

Hello, It's just a strange coincidence that someone posted just very recently a question about matching. I know there are several match function in the base package (such as match, pmatch, charmatch, and the gsub etc) but I can't seem to use them wisely to be able to get what I need. suppose I

[R] Binning groups

Hi, this is probably quite simple but I can't seem to do it correctly. I have a data frame of counts of infections in different ages; something like: count=c(1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 4, 4, 4, 4, 4, 7, 8, 8, 9, 9, 10, 11, 15, 17, 17, 17, 17, 19, 19, 19, 19, 20, 20, 20, 21, 21, 21, 22, 22,

[R] Symbolic Integration in R

This may be a question to R-development but I'm not sure. Symbolic differentiation is implemented in R (maybe not for extremely complex expressions), but it proves that it can be done. I know that in C++ it can be done (symbolic c++), do you think in R it can be programmed just using the R

Re: [R] help me to debug this part of code?

jinjin wrote: I am trying to solve the integration equation, for different values of K from 4 to 25, the integration is with respect to u, Here is the equation:gamma(k/2) / ( sqrt(k-1)*gamma((k-1)/2) ) * integrate(f= (1+u^2/k-1)^(-k/2), lower=0, upper= sqrt(a^2*k/(k+1-a^2)) ) = the

[R] Permanent change to the working directory

Dear helpers, I've looked in the help files (maybe not very thoroughly but I looked) and I couldn't find a straightforward way to permanently set the working directory (where I save and read files). Each time I startup R the working dir is automatically C:/R/bin [using:getwd()], and I know I can

Re: [R] help me to debug this part of code?

There are a lot of syntax errors such as unclosed parentheses, missing commas etc; Example: exp@(@lgamma((k+1)/2)-lgamma(k/2)*1/sqrt(k), where the parenthesis between the @s is not closed. I suggest you get an editor such as Tinn that can highlight those for you. In addition I notice that you use

[R] pairwise.t.test for paired data

Dear R-help, I have a question about pairwise.t.test and adjustment for multiple comparisons for paired data points. I have the following data: n=c(x, x, x, x, x, x, x, x, x, x, y, y, y, y, y, y, y, y, y, y, z, z, z, z, z, z, z, z, z, z) and d=c(3.38501220258169, 0.732526675324789,

Re: [R] pairwise.t.test for paired data

francogrex wrote: snipped... I have no indication that the test is taking into account that the data are paired! Is it possible to do a pairwise t test with adjustement for multiple comparisons using pairwise.t.test? If not any other function for that? Thanks. Dear all, Peter Dalgaard

[R] Compile R code into exe

*I did some search before, I saw in the Nabbles forum one question about it but without replies*. I have a program written in R. For regulatory purposes I need to make exe program of it and distribute to some users (the reason they don't want that I provide the raw R code and that users run it

[R] Solving equations with optim

Hello, optim searches for min (or max) of a function, but is it possible to solve for a specific value? I mean, I want to find the value of a and b that give the function value closest to ZERO (and not min or max) in the below. is it possible? thanks test=function(x){ a=x[1] b=x[2] if

[R] Re peated Measures (lme?)

Hello, I have a general data analysis question. I recently visited a lab where they are testing a new treatment and they had done the experiment several times on different dates. They repeated the experiment 3-5 times per day. And then for practical reasons they repeated the whole procedure

Re: [R] Interesting remarks about R back in 1999

Hi, yes it's true Mathematica is too expensive (I think one of the most expensive out there), but yacas has a lng way to go before becoming mathematica. I agree mathematica is not really for data analysis but I think it's to help researchers and inventors invent new ideas, understand concepts

[R] Interesting remarks about R back in 1999

Hi, this is not an R-help post, but I found this extract below that was written by a leading mathematician back in 1999 when he was talking about statistics and computing. I found it interesting to share and I ask your opinion do you think this still holds today or things have changed? Thanks.

[R] rJava error (assistance needed)

I have a problem I cannot run rJava properly, I have a winXP, below is the error log I hope someone can help me because I need rJava to run other programs like RLadayBug that I need for my research. Mr Hohle was kind enough to assist me but I think the problem is with my PC not being able to run

Re: [R] Modelling disease spread

Thanks Marcel, In addition to your program and the reference to simecol, someone had replied to my private email pointing out RLadyBug: An R package for stochastic epidemic models which is on CRAN and which seems one of the most relevant. I write it here as a reference for users doing a future

[R] Modelling disease spread

I was at a lecture the other day and I saw a presentation of very neat (short) animation modeling epidemic disease spread over a map region. When I ask what software they used they mentioned SAS. Do you know if there are equivalent resources in R to model the spread of disease with animation

[R] Ryacas behaving weird

There is either something wrong with either me or is Yacas/Ryacas doing odd things. See below I ask to simpify an expression and the there's output! If this is a simplification.. well.. Do you think there is something set wrong somewhere. Thanks. library(Ryacas) Loading required package: XML

[R] Analytical Optimization (Stat question)

Dear Experts, this is more a general stat question, I tried to ask in other places but had no luck with answers (expect one that suggested numerical instead of analytical optimization): The likelihood below is a mixture of two negative binomial distributions: P*f(n;x1,x2,E) + (1-P)*f(n;x3,x4,E)

[R] data.frame manipulation: Unbinding strings in a row

Hi all, I have a data.frame I received with data that look like this (comma separated strings in last row): ID ShopItems ID1 A1 item1, item2, item3 ID2 A2 item4, item5 ID3 A1 item1, item3, item4 But I would like to unbind the strings in col(2) items so that

[R] Bayesian Integration (stat question)

This may be far-fetched: In Bayesian analysis to find the marginal posterior distribution of a parameter it requires integration out of the so-called nuisance parameters. Is there in R (like an equivalent to the deriv function) but to find the expression of the integration (or an

Re: [R] Bayesian Integration (stat question)

Yacas and Ryacas does exactly what I want. Actually I had asked previously a question about algebra (not integration precisely) and guys here have pointed out package Ryacas. Sorry to disturb. francogrex wrote: This may be far-fetched: In Bayesian analysis to find the marginal posterior

[R] How can I change the language back to english?

I have reset my windows and re-installed R (I explicitly asked for english) and although the windows XP version is in english I am having R display in french. like: R est un logiciel libre livré sans AUCUNE GARANTIE. Vous pouvez le redistribuer sous certaines conditions. Tapez 'license()' ou

[R] expand.grid overflows?

cbn-as.matrix(expand.grid( rep( list(0:1), 50))) Error in rep.int(rep.int(seq_len(nx), rep.int(rep.fac, nx)), orep) : invalid 'times' value In addition: Warning message: In rep.int(rep.int(seq_len(nx), rep.int(rep.fac, nx)), orep) : NAs introduced by coercion But I'm only interested in

Re: [R] Generating these matrices going backwards

Hi, thanks but the way you are doing it is to assign the values of N in the x matrix, knowing from the example I have given where they are supposed to be. While the assumption is, you ONLY have values of N and R and do NOT know where they would be placed in the x and y matrix a-priori, but their

[R] Where to ask general stats questions?

I see that some people ask general statistics questions here sometimes. As I understand this list is only for technical help with R-related issues. But does anyone know of a list/forum where we can ask help/questions regarding general statistics problems (and where solutions are offered possibly

[R] EM algorithm on a mixture of two negative binomials?

Dear R stat experts, I am looking for an R function/code that can perform the EM algorithm to estimate the parameters of a mixture of two negative binomial distributions. I know that there are functions written that use the EM to estimate a mixture of normal distributions and also within the

Re: [R] Errors in R-2-6-0?

Uwe Ligges wrote: The recent version of BRugs works for me. The file \buffer.txt is required for some inetraction between OpenBUGS and R and is in R's temporary directory. No idea why it does not work for you. That's because I was using the older version of BRugs which was ok on

[R] Errors in R-2-6-0?

I was happy today to install the new version of R 2-6-0 But I ran into problems I did not have before: setwd(C:/R/DATA/BRugs) library(BRugs) modelCheck(rcapturemodel.txt) Error in file(con, r) : unable to open connection In addition: Warning message: In file(con, r) : cannot open file

Re: [R] Errors in R-2-6-0?

I re-installed version 2-5-0 and it works well. I believe this problem is due to an incompatibility of BRugs with R-2-6-0 francogrex wrote: I was happy today to install the new version of R 2-6-0 But I ran into problems I did not have before: setwd(C:/R/DATA/BRugs) library(BRugs