search for: mcmc

Deal all, as MCMClogit does not allow for the specification of several chains, I have run my model 3 times with different random number seeds and differently dispersed multivariate normal priors. For example: res1 = MCMClogit(y~x,b0=0,B0=0.001,data=mydat, burnin=500, mcmc=5500, seed=1234, thin=5) res2 = MCMClogit(y~...

...te(theWd,sp,"xy",sep="") + MINPOP=1 + MAXPOP=25 + INITPOP=1 + NITS=500000 + THIN=NITS/1000 + nrun <- 10 + burnin <- 200 + geno<-noquote(read.table(GENO.TABLE)) + coord<-read.table(XY.TABLE) + + ## Loop for multiple runs + + for(irun in 1:nrun) + { + ## define path to MCMC directory + + path.mcmc <- paste(path.sp,irun,"/",sep="") + dir.create(path.mcmc) + MCMC(coordinates=coord, ploidy=2, genotypes=geno, varnpop=T, npopmax=MAXPOP, npopinit=MINPOP, spatial=T, freq.model="Correlated", nit=NITS, thinning=500, rate.max=nrow(geno), delta...

I have an mcmc object and I''m trying to plot the quantiles of the variables - and not as a function of the iterations as in cumuplot. I cannot seem to find the right combination of indexing to access the variables; after which I''m sure I can plot all the statistics I could hope for. Any hints...

Dear List members, I am using R to generate MCMC time series plots. This is the code I use; however, everytime an error message will come out saying could not find function "plot.mcmc." I have coda package and Lattice package installed. Does anyone know what may get wrong here? Thanks so much for your suggestions. Hongli Li *library (...

...for convergence. To do that, I need at least two chains. If I run second chain with different starting values and seed, I could save to the matrix 'samp2'. So, I will have two matrices 10,000x86. I want to use the function gelman.diag(x, confidence = 0.95, transform=FALSE), where x: An 'mcmc.list' object with more than one chain, and with starting values that are overdispersed with respect to the posterior distribution. How do I create mcmc object from these matrices? I need to create an mcmc object with the two chains I have stored in 'samp' and 'samp2'. Thanks for...

Hello, I tryed to use the MCMC pack, particularly the function MCMCirtKd to simulate the posterior distribution in a multidimensional IRT model. The code I used is: posterior1 <- MCMCirtKd(Y, dimensions=2, item.constraints=list("V2"=list(3,0)), burnin = 1000, mcmc = 10000, thin=1, verbose = 1, seed = NA, alph...

...tate University-Iligan Institute Technology (MSU-IIT), Philippines. I am currently working on my master's thesis titled "Comparing the Three Estimation Methods for the Four Parametric Logistic (4PL) Item Response Model". While I am looking for a package about Markov chain Monte Carlo (MCMC) method for 4PL model in this R forum, I found an sirt package of an MCMC method but only for the three parametric normal ogive (3PNO) item response model. However, my study focus on 4PL model. In line with this, I would like to know if there exist a function of MCMC method for 4PL model in R langu...

Dear R-users (and developers), I am looking for an efficient framework to carry out parameter estimations based on MCMC (optionally with specified priors). My goal is as follow: * take ANY R-function returning a likelihood-value (this function may itself call external programmes or other code!) * run a sampler that covers the multidimensional parameter space (thus creating a posterior distribution) * do the above...

Dear all I am now running a MCMC iteration in the R program. But it is always stucked in some loop. This cause big problems for my research. So I want to know whether we can skip the current dataset and move to next simulated data when the iteration is stucked? Alternatively, can the MCMC chain skip the current iteration when it i...

...ata <- simdata(nindiv=200, coord.lim=c(0,1,0,1) , number.nuclei=5 , allele.numbers=rep(10,20), IBD=FALSE, npop=2, give.tess.grid=FALSE) geno <- data$genotypes coord <- t(data$coord.indiv) path.mcmc <- paste(tempdir(),"/",sep="") set.seed(1) mcmcFmodel(coordinates=coord, genotypes=geno, path.mcmc=path.mcmc, rate.max=10, delta.coord=0, npopmin=1, npopinit=5, npopmax=5, nb.nuclei.max=...

...scored as double null alleles, this even though I use the default setting NA in my 'score matrix'. I am therefore trying to enter a matrix of 103 x 9 (103 individual x 9loci) with 0 for real alleles (null or not) and 1 for non scored alleles called upon using the miss.loc function in MCMC, in addition to the 'genotype' and 'coordinate' matrices. However when starting the MCMC, after initialisation of all functions I get this message: list (object) can not be coerced into integer And the MCMC is stopped. I only get this message when entering the 'null all...

...and inconsistencies in my documentation, for which I am very grateful. The only problem I have is with code/documentation mismatches when I have written a method for a generic function, e.g. * checking for code/documentation mismatches ... WARNING Objects with usage in documentation object `plot.mcmc' but missing from code: [1] "plot" Objects with usage in documentation object `summary.mcmc' but missing from code:[1] "summary" Objects with usage in documentation object `time.mcmc' but missing from code: [1] "end" "start" "time"...

I know of no existing functions for estimating the parameters of this model using MCMC or MML. Many years ago, I wrote code to estimate this model using marginal maximum likelihood. I wrote this based on the using nlminb and gauss-hermite quadrature points from statmod. I could not find that code to share with you, but I do have code for estimating the 3PL in this way and you could...

Dear list users, I need to learn about MCMC methods, and since there are several packages in R that deal with this subject, I want to use them. I want to buy a book (or more than one, if necessary) that satisfies the following requirements: - it teaches well MCMC methods; - it is easy to implement numerically the ideas of the book, and n...

Hello, I am doing mcmc=10000 simulations from a posterior distribution of the parameters of a mixture of K=6 normal densities. I have mcmc by K matrices simMeans, simVars and simWeights containing the simulation output: one row for each simulation, one column for each normal component of the mixture. One thing I would l...

Hi Does anyone know of any R coding/functions for MCMC approaches? I am currently using BUGS but I wonder if the bazaar has produced anything? I think I am pushing BUGS to it's limit and possibly past it at the moment. John -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci....

Dear Friends, I am trying to use the gelman-rubin convergence test. I generated a matrix samp[10,000x86] with the gibbs sampler. the test requires the creation of "mcmc" objects. Since I don't know how to define samp as a "mcmc" object, I tried to create one mcmc object by means of the mcmc() function. With this function I tried to create a mcmc object dul from samp but I got the message below. What am I doing wrong? > dim(samp) [1] 10000...

Hello, I am about to move all of my modelling work into R, and I have been investigating the present state of MCMC and Bayesian methods in R. Following a thread on the mailing list in 2000, I have looked at mcmcpack and Hydra. Three years down the line, is there anything new in this area? I have used both MCSim and WinBUGS in the past. The first one seems promising, but is too focused towards toxicology work, a...

Dear R users, I am leaning MCMC sampling, and have a problem while trying to sample exponential r.v.'s via the following code: samp <- MCMCmetrop1R(dexp, theta.init=1, rate=2, mcmc=5000, burnin=500, thin=10, verbose=500, logfun=FALSE) I tried other distribtions such as...

Hi, I have a dataset with the binary outcome Y(0,1) and 4 covariates (X1,X@,X#,X$). I am trying to use MCMClogit to model logistic regression using MCMC. I am getting an error where it doesnt identify the covariates ,although its reading in correctly. The dataset is a sample of actual dataset. Below is my code: > ####################### > > > #retreive data > # considering four covariate...