Displaying 20 results from an estimated 6000 matches similar to: "Gibbs sampler"
2011 Nov 07
3
Correction in error
Hello R community, following is my code and it shows error, can some one
fix this error and explain why this occurs?
gibbs <-function(m,n, theta = 0, lambda = 1){
alpha <- 1.5
beta <- 1.5
gamma <- 1.5
x<- array(0,c(m+1, 3))
x[1,1] <- theta
x[1,2] <- lambda
x[1,3]<- n
for(t in 2:m+1){
x[t,1] <- rbinom(x[t-1,3], 1, x[t-1,1])
2009 Aug 17
1
Bayesian data analysis - help with sampler function
I have downloaded the Umacs (Universal Markov chain sampler) and submitted the following sample code from Kerman and Gelman.
s <-Sampler(
J=8,
sigma.y =c(15,10,16,11,9,11,10,18),
y =c(28, 8,-3,7,-1,1,18,12),
theta =Gibbs(theta.update,theta.init),
V =Gibbs(V.update,mu.init),
mu =Gibbs(mu.update,mu.init),
tau =Gibbs(tau.update,tau.init),
2009 Jan 25
1
Gibbs sampler...did it work?
I am writing a Gibbs sampler. I think it is outputting some of what I want,
in that I am getting vector of several thousand values (but not 10,000) in a
txt file at the end.
My question is, is the error message (see below) telling me that it can't
output 10,000 values (draws) because of a limitation in my memory, file
size, shape etc, or that there is an error in the sampler itself?
>
2006 Jun 26
1
Griddy-Gibbs sampler
Hey everyone,
I have read the paper by Ritter and Tanner(1992) on Griddy-Gibbs sampler and I am trying to implement it in R without much luck. I was wondering if anyone had used this or could point me to any example code.
Thanks,
Liz
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2011 Nov 09
2
Error in drawing
I have got following error in drawing wavelet fitting. can some one help?
> library(faraway)
> data(lidar)
> newlidar<-lidar[c(1:128),]
> library(wavethresh)
> wds <- wd(newlidar$logratio)
> draw(wds)
Error in plot.default(x = x, y = zwr, main = main, sub = sub, xlab = xlab,
:
formal argument "type" matched by multiple actual arguments
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2004 Jul 16
0
for loops in Gibbs sampler
Dear all:
I am using R to do multiple imputation for longitudinal data set. The
Gibbs chain basically requires draw posterior distribution of model
parameters, including the random effects. The multiple imputation requires
several independent Gibbs chains. So my program structure is like:
for (chain in 1:5)
{
# perform Gibbs sampling...
for (row in 1:row.no)
{
b.row=some function # draw
2011 Nov 29
3
Problem in log
Hi all I have a function of log defined by y = log(1- exp(-a)), when
exp(-a) is greater, 1, it produce NaN. How can I remove this in R?
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2004 Apr 16
0
autologistic regression with Gibbs sampler
Hello everyone,
I have some binary, spatially autocorrelated data I would like to run autologistic regression on. I hope to incorporate both ordinary covariates (environmental predictors) and a spatial autocovariate in the model, ideally with a second-order neighbourhood structure. Since my computing skills are limited, I am wondering if anyone has composed an algorithm for this purpose, and
2012 Dec 05
4
Import multiple data frames and combine them using "cbind"
Hi group,
I imported 16 data frames using the function "list.files"
temp <- list.files(path="...........")
myfiles = lapply(temp, read.table,sep = "")
Now I have 16 data set imported in R window.
I want to combine them by row and tried some thing like (Here I am
considering only 20 columns)
for(i in 1:16){
data<- cbind(myfiles[[i]][,1:20])
}
but it
2012 Apr 06
2
Bayesian 95% Credible interval
Hi all,
I have the data from the posterior distribution for some parameter. I want
to find the 95% credible interval. I think "t.test(data)" is only for the
confidence interval. I did not fine function for the Bayesian credible
interval. Could some one suggest me?
Thanks
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2012 Aug 27
3
How to generate a matrix of Beta or Binomial distribution
Hi folks,
I have a question about how to efficiently produce random numbers from Beta
and Binomial distributions.
For Beta distribution, suppose we have two shape vectors shape1 and shape2.
I hope to generate a 10000 x 2 matrix X whose i th rwo is a sample from
reta(2,shape1[i]mshape2[i]). Of course this can be done via loops:
for(i in 1:10000)
{
X[i,]=rbeta(2,shape1[i],shape2[i])
}
However,
2011 Nov 18
3
Permutations
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
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2011 Nov 16
2
Error in random walk Metroplis-hasting
Hi R community,
I have some data set and construct the likelihood as follows
likelihood <- function(alpha,beta){
lh<-1
d<-0
p<-0
k<-NULL
data<-read.table("epidemic.txt",header = TRUE)
attach(data, warn.conflicts = F)
k <-which(inftime==1)
d <- (sqrt((x-x[k])^2+(y-y[k])^2))^(-beta)
p<-1 - exp(-alpha*d)
for(i in 1:100){
2011 Nov 21
1
Sub sets
I'd appreciate it if you'd keep on list for the archives. That said, I
think this function does what you were hoping for.
Michael
powerset <- function(n, items = NULL){
if(!is.null(items)) {
if(n != length(items)) warning("Resetting n in preference to
length(items)")
n = length(items)
}
smat <- do.call(expand.grid, rep(list(c(0,1)), n))
2011 Nov 08
3
GAM
Hi R community!
I am analyzing the data set "motorins" in the package "faraway" by using
the generalized additive model. it shows the following error. Can some one
suggest me the right way?
library(faraway)
data(motorins)
motori <- motorins[motorins$Zone==1,]
library(mgcv)
>amgam <- gam(log(Payment) ~ offset(log(Insured))+
s(as.numeric(Kilometres)) + s(Bonus) + Make +
2008 Sep 17
3
Is there a way to not use an explicit loop?
I have a problem in where i generate m independent draws from a
binomial distribution,
say
draw1 = rbinom( m , size.a, prob.a )
then I need to use each draw to generate a beta distribution. So,
like using a beta prior, binomial likelihood, and obtain beta
posterior, m many times. I have not found out a way to vectorize
draws from a beta distribution, so I have an explicit for loop
2012 Oct 22
1
random forest
Hi all,
Can some one tell me the difference between the following two formulas?
1. epiG.rf <-randomForest(gamma~.,data=data, na.action = na.fail,ntree =
300,xtest = NULL, ytest = NULL,replace = T, proximity =F)
2.epiG.rf <-randomForest(gamma~.,data=data, na.action = na.fail,ntree =
300,xtest = NULL, ytest = NULL,replace = T, proximity =F)
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2011 Nov 18
1
Permutation matrix
Hi all,
I have a set of elements (1, 1, 0,1,1,0,1,0,1,1) with ten elements. I have
to construct the permutation matrix of this set which is of the size 10 by
2^10. Can some one help how is this possible? Is there is a particular
function in R or I need to make function?
Best
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2011 Dec 05
1
Problem in while loop
Hi all,
I have the following code,
When I run the code, it never terminate this is because of the while loop i
am using. In general, if you need a loop for which you don't know in
advance how many iterations there will be, you can use the `while'
statement so here too i don't know the number how many iterations are
there. So Can some one suggest me whats going on?
I am using the
2012 Oct 01
1
Problem with nls regression fit
Hi all,
I got following problem in fitting the data.
Any kind of suggestions are welcome
> beta <- 3.5
> d <- seq(0.1,62.5,0.1)
> y <- exp(-beta*d)
> y1 <- y
> x <- read.table("epidist.txt", header = TRUE)
> data.nls <- as.data.frame(cbind(y1,x))
> #attach(data.nls)
> nls.fit <- nls(y1~dist,data.nls)
Error in cll[[1L]] : object of type