similar to: need help EM algorithm to find MLE of coeff in mixed effects model

I have a general question about coefficients estimation of the mixed model. I simulated a very basic model: Y|b=X*\beta+Z*b +\sigma^2* diag(ni); b follows N(0,\psi) #i.e. bivariate normal where b is the latent variable, Z and X are ni*2 design matrices, sigma is the error variance, Y are longitudinal data, i.e. there are ni

Dear All, A library (PHYLOGR) that passed the usual tests in R-1.1.1 gives errors with R-devel; my (mis?)understanding of scoping rules is that it should have worked in both. The problems seem related to using the name of the data frame for extracting weights or subsets within a function call. The problems can be reproduced as follows: ********************** datai <- data.frame( y =

In my code below tempa and tempb are numeric vectors that I combined into a dataframe along with the deciles of tempa. I have an lapply statement that goes through the dataframe and does ten plots according to the appropriate decile. The code is below and it works fine. There are no bugs so I figure there was no need to include structure statements on the data. Also, I don't want to use coplot

Hi : I think I need to use sapply but I can't figure this out. Suppose I have two vectors : tempa ( 4, 6,10 ) and tempb ( 11,23 ,39 ) I want a function that returns 4:11,6:23 and 10:39 as vectors. I tried : sapply(1:length(tempa) function (z) seq(tempa[z],tempb[z]) but i got 3 really strange vectors back in the sense that the numbers in them did not make no sense to me. obviously, i

in my previous post in which i asked about creating sequences from two vectors of numbers, all suggestions worked. tradevectors<-mapply(seq,from=tempa,to=tempb) or tradevectors<-sapply(1:length(tempa),function(x) seq(tempa[x],tempb[x]) >both return a list with 3 components. the problem is that i want to take these 3 sequences and use them as the indices of two other vectors, X and

can someone show me how to convert a table to a data.frame or a matrix ? I tried below and as.data.frame rearranges the columns similarly to a melt from reshape and as.matrix didn't change it. I actually would prefer to change it to a dataframe but if someone can show me how to convert it to a matrix, then as.data.frame will work on that. I was thinking about just changing the class to

Greetings all, I am calculating two t-test values for each of many files then save it to file calculate another set and append, repeat. But I can't figure out how to write it to file and then append subsequent t-tests. (maybe too tired ;} ) I have tried to use "dump" and "file.append" to no avial. ttest_results = tempfile() two_sample_ttest <- t.test (tempA, tempB,

OK. About the error it’s a long story, so it’s probably better to pin some source code here. Below is a piece of code related to my problem, clipped from lib/Transforms/Utils/ValueMapper.cpp. I was wondering what “materialized” means here. Value *Mapper::mapBlockAddress(const BlockAddress &BA) { Function *F = cast<Function>(mapValue(BA.getFunction())); // F may not have

Dear R-users, I have longitudinal data and would like to fit a model where both the variance-covariance matrix of the random effects and the residual variance are conditional on a (binary) grouping variable. I guess the model would have the following form (in hierarchical notation) Yi|bi,k ~ N(XiB+Zibi, sigmak*Ident) bi|k ~ N(0, Dk) K~Bernoulli(p) I can obtain different sigmas (sigma0 and

Hello, I call a function via .Call passing to it a raw vector(D) and an integer(I) The vector is a series K1,KData1, V1,VData1, K2, KData2, ... where the integer K1 is the length of Data1 and similarly for Ki (wrt Datai)(similarly for V*) There 2*I such pairs( (Ki,KDatai), (Vi,VDatai)) The numbers Ki(and Vi) are written in network order. I am returning a list of I elements each element a

While I don't know anything about Box's M test, I googled around and found a Matlab M-file that computes it. Below is my straight-forward translation of the code, without knowing Matlab or the formula (and done in a few minutes). I hope this demonstrates one of Prof. Ripley's point: If you really want to shoot yourself in the foot, you can probably program R to do that for you. [BTW:

Hi all, I''ve got the error below in my backgroundrb_debug.log. I''ve tried to reproduce the error in the development environment, but the only way I can get the same thing is by calling ask_work with a bogus worker name. Calling it with the production code causes no error. Here''s an example of what the code calls: MiddleMan.ask_work(:worker => :agronomy_worker,

Hello all, I have searched and have not yet identified a solution so now I am sending this message. In short, I need to split my data into training, validation, and testing subsets that keep all observations from the same sites together ? preferably as part of a cross validation procedure. Now for the longer version. And I must confess that although my R skills are improving, they are not so

Dear R experts, Might be very simple question to ask but would be insightful. As the same story of nested "for loops". following is the code that I am using to get the autocorrelation function of the sample data. I have tried to get rid of for loops but since I am touching R after such a long time that I need to practice more but I need help to revive my skills. I know that apply() or

Hello all, I've installed samba on pretty basic install on centos 4.4. I'm running a P4 2.8Ghz, 1G Ram, Raid 5 SATA-2 disks running on both a 3ware and Highpoint Rocket raid (this is going to get swapped out for a 3ware card soon). When users copy files from a mac os x client I'm seeing the cpu load avg (in top) get up to 7. These copies included 150+Gigs of lots of smaller

Hi, There's something weird happening to my CentOS VMs, cannot switch back to GUI. Black screen with a single underscore character at top left of the screen. Ok so I have ESXI 5.1 host, with 3 VM all running CentOS. I rebooted the esxi host yesterday for a power maintenance. All went well... until I switched console on the vms. I was able to login using the GUI, then I pressed Alt F5, then

The 'systemfit' function in systemfit 0.7-3 CRAN package seems to have a problem with formulas that contain transformed (eg. log) variables. If I have my data in a data frame, apparently systemfit doesn't "pass" the information of where the variables should be taken to the transforming function. I'm not entirely sure if this is a bug or just a limitation, I was just

Marc and many other people ( whose names escape me ) have been very helpful in explaining the use of lapply to me. In his last response, Marc explained that if tradevectors is a list of vectors of different lengths ( excuse my terminology ) then lapply(tradevectors,function(x) G[x]*B[x] ) will go through each component of the list as if it was a vector and apply the element by element

I'm using plot to make a simple plot but I want to control where the tick marks go on bot axes. The graphical parameters xaxp and yaxp seem to be ignored by the plot function so I tried setting them using op <- par(no.readonly=T) par(xaxp=c(-2.4,-2.2,5), yaxp=c(-2500,10000,6)) plot(...) par(op) but they are still ignored. Next I tried to use the axis function as follows op <-

[I am really sorry if it is double posted, I doubt me previous post could not reach forum due to some problem with net] Suppose I have a matrix : a = matrix(1:9, 3) >From this matrix, I construct 9 additional matrices : i = 1:9 bi = a * i Now combining all those 9 new matrices, I construct a final metrix as : c = b1 b4 b7 b2 b5 b8 b3 b6 b8 I want to automate this procedure for any