similar to: Fitting binomial lmer-model, high deviance and low logLik

Ok...I made the leap. Compiled a copy of 1.2b4 (very pleasant compile BTW - almost no warnings, nice code Timo!)...tweaked a config...had a few false starts... 1.2b4 seems to working quite nicely. Now...for my next magical trick... I would like to migrate from maildir to dbox. I've tried using the convert plugin, but it kept failing during the conversion. I should mention my paths:

>On Wed, 3 Aug 2005, Bernd Weiss wrote: > >> I am trying to replicate some multilevel models with binary outcomes >> using R's "lmer" and "glmmPQL" and Stata's gllmm, respectively. > >That's not going to happen as they are not using the same criteria. the glmmPQL and lmer both use the PQL method to do it ,so can we get the same result by

Hi, I have a problem with R, after an update: this piece of code: cat("creating resolver data frame\n"); dfG<-cbind(dfG,2^(RGN$G)) dfR<-cbind(dfR,2^(RGN$R)) suddenly, creates values to inf. Is the syntax changed for the ^ symbol in the latest R downloadable version? Kind regards, wilfred -- Dr. Ir. Wilfred Van IJcken Labmanager Genomics Erasmus Center for Biomics,

Full_Name: Chanseok Park Version: 1.8.1 OS: linux-gnu Submission from: (NULL) (130.127.112.183) digamma with any negative value does not give a right answer. It gives -1.797693e+308 for any negative arguments. For example, digamma(-1.1) gives -1.797693e+308. The right answer should be 10.15416 This bug can be easily fixed by using the following digamma identity. digamma(x) = digamma(1-x) -

The Intel compiled version also fails the below test: > ###------------ Very big and very small > umach <- unlist(.Machine)[paste("double.x", c("min","max"), sep='')] > xmin <- umach[1] > xmax <- umach[2] > tx <- unique(outer(-1:1,c(.1,1e-3,1e-7)))# 7 values (out of 9) > tx <- unique(sort(c(outer(umach,1+tx))))# 11 values

R-1.7.0 built on NetBSD 1.6, but the validation test suite failed: Machinetype: Intel Pentium III (600 MHz); NetBSD 1.6 (GENERIC) Remote gcc version: gcc (GCC) 3.2.2 Remote g++ version: g++ (GCC) 3.2.2 Configure environment: CC=gcc CXX=g++ LDFLAGS=-Wl,-rpath,/usr/local/lib make[5]: Entering directory `/local/build/R-1.7.0/src/library' >>> Building/Updating

Hi all, why factorial(150) shows the error out of range in 'gammafn'? I have to calculate the number of subset formed by 150 samples taking 10 at a time. How is this possible? best [[alternative HTML version deleted]]

I am experiencing some difficulties with vorbis on my LX164 alpha. Specifically, in bark_noise (psy.c) I see the following behaviour on the first pass through the function: val=-3.4e38 del=1 noise[0]+=val*del noise[1]-=val*del norm[0]+=del norm[1]-=del del=1 noise[1]-=val*del <== here is the problem At this point, noise[1]==3.4e38. We are trying to add another 3.4e38 to it and this is

Hi All, I am using DNAcopy package in R for copy number analysis of 500K chip. The final output which I get from DNA copy is too big to be printed in a file. So I am getting an error as "reached getOption("max.print") -- omitted 475569 rows " Can somebody please provide me the pointers with how to increase the limit for max.print . Thanks, Pooja DISCLAIMER\

Hello all, Here's my query: Running R 1.6.2 on FreeBSD 5.0, and on WinXP, and I find that the following hangs the process: dchisq(alpha=0.01, df=1, ncp=295) but it does work for ncp < 294.92. Is this general? Best wishes to all, Andrew Andrew Robinson Ph: 208 885 7115 Department of Forest Resources Fa: 208 885 6226 University of Idaho E : andrewr at uidaho.edu PO

Dear List, I'm new in R. I'm trying to solve a simple constrained optimization problem. Essentially, let's say I have a matrix as in the object 'mm' inside the function below. My objective function should have a matrix of parameters, one parameter for each element 'mm' (4 in this case). The problem is to select the value of the parameters to maximize the function

Hi, I'm getting some strange behaviour when trying to use the power operator (a^b) when a is large and b is less than one: big <- .Machine$double.xmax big big^0.5 sqrt(big) > big <- 1.797693134862315708384e+308 > big^0.5 [1] Inf > sqrt(big) [1] 1.340781e+154 I'm guessing that this behaviour is not expected, or am I missing something about ^? Cheers Martyn >

Hi, I'm trying to calculate p-value to findout definitely expressed genes compare A to B situation. I got this data(this is a part of data) from whole organism , and each number means each expression values (that means, we could think 'a' gene is 13 in A situation, and it turns 30 in B situation) To findout probability, I'm going to use Audic - Claverie Method. ( The significance

Hello R-users, When I didn't know about the internal 'choose' function, I made such function, 'my.choose' below. But when I used them instead of choose(6000,20), they didn't give me any answer. What is the difference between 'choose', 'my.choose1', and 'my.choose2' below? That is, what is behind 'choose' function and what's the problem

Update (for me): * On HPUX (cc/f77/make), make check passes the Examples but fails in arith-true.R because is.infinite(.Machine$double.base ^ .Machine$double.max.exp) gives FALSE. Interestingly > .Machine$double.base [1] 2 > .Machine$double.max.exp [1] 1024 > 2 ^ 1024 [1] 1.797693e+308 > 2 ^ 1025 [1] 1.797693e+308 > 2 ^ 2024 [1] 1.797693e+308 so I guess we need help here. *

The current situation is as follows. AIX: * I still need f77 for linking. Using ld with the suggested flags gives a binary with `exec format error'. The problem seems to be with an unreferenced __start. * The floating point (finite|isnan) stuff is strange, but under control, I think. Plain cc works, gcc has a problem and seems to need having prototypes turned off for IEEE fp.

Merry Xmas to all, I am writing a function and curiously this runs sometimes on one data set and fails on another and i cannot figure out why. Any help much appreciated. If i run the code below with data <- iris[ ,1:4] The code runs fine, but if i run on a large dataset i get the following error (showing data structures as matrix is large) > str(cluster.data) num [1:9985, 1:811] 0 0 0 0

Hello: The development version of Ecdat on R-Forge contains a vignette in which optim(?, method=?L-BFGS-B?) stops with an error message while violating the lower bound. To see all the details, try the following: install.packages("Ecdat", repos="http://R-Forge.R-project.org") Then do "help(pac=Ecdat)" -> "User guides, package

Hello! I am trying to create an R optimization routine for a task that's currently being done using Excel (lots of tables, formulas, and Solver). However, otpim seems to be finding a local minimum. Example data, functions, and comparison with the solution found in Excel are below. I am not experienced in optimizations so thanks a lot for your advice! Dimitri ### 2 Inputs:

I am trying to install R-0.63.3 on a Digital Alpha running OSF V4.0D, and having some difficulties. Can anyone help? Also, I found some "oddities" in the installation process. I expect that this message is read by the developers, maybe some of my suggestions can be incorporated into future releases. Please reply to me directly (as well as possibly also to this mailing list): I am not a