Displaying 20 results from an estimated 64 matches for "dunif".
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runif
2011 Nov 07
2
Dunif and Punif
Hi,
I am trying to use dunif and runif
however, I have two problems:
if I do
dunif(1:10, min=1, max=10)
I get 10 values, which summed give me 1.1111
I understand that the probability is computed as f(x) = 1 / (max-min)
but in this case it looks wrong: I have 10 values, each one
equiprobable, and the probability for each one...
2008 Dec 15
3
R2winbugs : vectorization
...censored regressions, the first
is essentially a copy of code in Gelman+Hill):
===================== model 1 : 4 separate a's
model{
for (i in 1:n){
z.lo[i]<- C * equals(y[i],C)
z[i]~dnorm(z.hat[i],tau.y)I(z.lo[i],)
z.hat[i]<-a1*x[i,1]+a2*x[i,2]+a3*x[i,3]+a4*x[i,4]
}
a1~dunif(0,100)
a2~dunif(0,100)
a3~dunif(0,100)
a4~dunif(0,100)
tau.y<-pow(sigma.y,-2)
sigma.y~dunif(0,100)
}
============== model 2 : vector of a's
model{
for (i in 1:n){
z.lo[i]<- C * equals(y[i],C)
z[i]~dnorm(z.hat[i],tau.y)I(z.lo[i],)
z.hat[i]<-inprod(a[],x[i,])
}
for (j...
2008 Jul 23
1
R2WinBUGS problem
...t wishes
Troels
cat("
model {
for (i in 1:126) {
dep[i] ~ dnorm(mu.dep[i],tau.dep)
mu.dep[i] <- alpha[ID[i]]*NAK.cor[i]+beta[ID[i]]*TBW.cor[i]
fit[i] <- mu.dep[i]+CONST[i]
}
tau.dep <- pow(sigma_dep,-2)
sigma_dep ~ dunif(0,100)
for (j in 1:16) {
alpha[lev[j]] <- AB[lev[j],1]
beta[lev[j]] <- AB[lev[j],2]
AB[lev[j],1:2] ~ dmnorm(AB.hat[lev[j],],tau.AB[,])I(lower[],
upper[])
AB.hat[lev[j],1] <- mu.alpha
AB.hat[lev[j],2] <- mu.beta
}...
2010 Oct 15
1
Problem using BRugs
...])<- rho_o * woy[i] + rho_d * wdy[i] + rho_w * wwy[i] + beta[1] +
beta[2] * cap2[i] + beta[3] * pol2[i] + beta[4] * cap1[i] + beta[5] *
pol1[i] + beta[6] * g[i]+ e[i]
}
# Priors
for (j in 1:6) {
beta[1:6] ~ dmnorm(mu[1:6], tau[1:6, 1:6])
}
rho_o ~ dunif(-1,1)
rho_d ~ dunif(-1,1)
rho_w ~ dunif(-1,1)
for (i in 1:676) {
e[i] ~ dnorm(0, 1)
}
}
[[alternative HTML version deleted]]
2010 May 06
1
BRugs dwwinn.exe error
...end. If I use a simple model with data and
initial values bugs() works fine. So, I have to assume that there is
something in my model which is not compatible with bugs().
The model is:
-------------------------------------
model generateStartingValues
{
for (s in 1:Datasets) {
lambda[s]~dunif(0.1,0.9)
for (i in 1:K){
eltheta[s,i]~dunif(0.1,0.3)
q[s,i]~dunif(0.1,0.4)
}
}
}
-------------------------------------
DATA
list(K=19,Datasets=500)
As I said this works fine with openBUGS and WinBUGS.
I start BUGS from R-Console with
----...
2010 Aug 10
0
Error in R2Bugs
...s.plt[s] ~ dnorm(0.0, tau.plt)}
for(k in 1:n.sp){eps.sp[k] ~ dnorm(0.0, tau.sp)}
b.lev~dnorm(0, 0.01)
b.light~dnorm(0, 0.01)
b.con~dnorm(0,0.01)
b.s1~dnorm(0, 0.01)
b.s2~dnorm(0, 0.01)
b.s3~dnorm(0, 0.01)
b.dcon~dnorm(0, 0.01)
tau.ind~dunif(0,100)
sigma.ind<-1/sqrt(tau.ind)
tau.plt ~ dunif(0,100)
sigma.plt<-1/sqrt(tau.plt)
tau.sp ~ dunif(0,100)
sigma.sp<-1/sqrt(tau.sp)
tau ~ dunif(0,100)
sigma.sppl<-1/sqrt(tau) #sd of species x plot random effect
}
-----------------------------------------
Jo...
2009 Jul 16
1
Error with r2winbugs
.../sus.bug"
model {
for (i in 1:n){
y[i] ~ dpois(lamdba[i])
log(lambda[i]) <- mu+bmale[male[i]]+bschn[schn[i]]+epsilon[i] #
epsilon[i] ~ dnorm(0,tau.epsilon)
}
mu ~ dnorm(0,.0001)
bmale ~ dnorm(0,.0001)
tau.epsilon <- pow(sigma.epsilon, -2)
sigma.epsilon ~ dunif(0,100)
for (j in 1:n.schn){
bschn[j] ~ dnorm(0,tau.schn)
}
tau.schn <- pow(sigma.schn, -2)
sigma.schn ~ dunif(0,100)
}
I am running the following syntax:
enroll.wide.m <- na.omit(enroll.wide)
n <- nrow(enroll.wide.m)
y <- enroll.wide.m$sus.5
sch <- as.vector(enroll...
2009 Mar 14
0
[multi-level model] set up categorical variable/indicator?
...bugs as:
model{
for (i in 1:n){
y[i] ~ dnorm(y.hat[i], tau.y)
y.hat[i] <- alpha[region[i]] + beta[county[i]]*bsmt[i]
}
for (j in 1:J){
alpha[j] ~ dnorm(mu.alpha[j], tau.alpha)
}
for (k in 1:K){
beta[k] ~ dnorm(mu.beta[k], tau.beta)
}
mu.y ~ dnorm(0, .0001)
tau.y <- pow(sigma.y, -2)
sigma.y ~ dunif(0, 100)
mu.alpha ~ dnorm(0, .0001)
mu.beta ~ dnorm(0, .0001)
tau.alpha <- pow(sigma.alpha, -2)
sigma.alpha ~ dunif (0, 100)
tau.beta <- pow(sigma.beta, -2)
sigma.beta ~ dunif(0, 100)
}
but my Bugs crashed because it couldn't read "region" data, and as I checked
out my "reg...
2009 Aug 15
1
Filling in a uniform dist plot
Hi all,
Apologies in advance if this is really too simple, but I have given a
good shot at this. I'm generating a standard uniform distibution
y <- dunif(x)
plot(x,y,type="l")
This will draw a horizontal line at y = 1. I want to fill the area from
x=(0,1) with a color. I've tried the polygon command to create a
polygon of the same shape, but can't seem to set the parameters to fill
the figure from x=(0,1). I'm sure there...
2017 Jun 04
0
Hlep in analysis in RWinBugs
...*S1*m1
a21[i]<-sm[i]*S1*(1-m1)*S2*m2
a31[i]<-sm[i]*S1*(1-m1)*S2*(1-m2)*S3
sum[i]<-a11[i]+a21[i]+a31[i]
}
#priors
#priors are dbeta(0.5,0.5), uniform is dbeta(1,1)
S1~dbeta(1,1)#I(0,0.2) #
S2~dbeta(1,1)#I(0.15,0.5) #
S3~dbeta(1,1)#I(0.3,1)
m1~dbeta(1,1)#I(0.01,1)
m2~dbeta(1,1)#I(0,1)
sd ~ dunif(0,100)
sd1 ~ dunif(0,100)
sd2 ~ dunif(0,100)
tau <- 1/(sd*sd)
tau1 <- 1/(sd1*sd1)
tau2 <- 1/(sd2*sd2)
}
model.file <- Model
file.show(model.file)
#The Data
list(N = 4,
sm=c(9309,3253,5292,1361),
a1=c(16,3,4,2),
a2=c(96,31,42,3),
a3=c(47,5,18,1))
inits <- function(){
list(sd = 1000,...
2017 Jun 04
0
Help in analysis in RWinBugs
...*S1*m1
a21[i]<-sm[i]*S1*(1-m1)*S2*m2
a31[i]<-sm[i]*S1*(1-m1)*S2*(1-m2)*S3
sum[i]<-a11[i]+a21[i]+a31[i]
}
#priors
#priors are dbeta(0.5,0.5), uniform is dbeta(1,1)
S1~dbeta(1,1)#I(0,0.2) #
S2~dbeta(1,1)#I(0.15,0.5) #
S3~dbeta(1,1)#I(0.3,1)
m1~dbeta(1,1)#I(0.01,1)
m2~dbeta(1,1)#I(0,1)
sd ~ dunif(0,100)
sd1 ~ dunif(0,100)
sd2 ~ dunif(0,100)
tau <- 1/(sd*sd)
tau1 <- 1/(sd1*sd1)
tau2 <- 1/(sd2*sd2)
}
model.file <- Model
file.show(model.file)
#The Data
list(N = 4,
sm=c(9309,3253,5292,1361),
a1=c(16,3,4,2),
a2=c(96,31,42,3),
a3=c(47,5,18,1))
inits <- function(){
list(sd = 1000,...
2012 Oct 26
1
Openbugs- Array Index
...ects for each functional group
for(i in 1:g){ # number of functional group
for(j in 1:2){ # number of habitat
type
mu.h[i,j] ~ dnorm(0,0.0001) I(-2,2) # filling mu.h with values based
on a random distribution
sigma.h[i,j] ~ dunif(0,6)
tau.h[i,j] <- 1/(sigma.h[i,j]*sigma.h[i,j])
}
}
# detectability
mu.r ~ dnorm(0,0.0001) I(-3,3)
sigma.r ~ dunif(0,6)
tau.r <- 1/(sigma.r*sigma.r)
psi ~ dunif(0,1)# inclusion rate that generates wi
# proportion of number of species among groups
for(i in 1:g){
prop[i] ~ dgamma(1,1)
prob[...
2010 Aug 02
2
Including a text file (JAGS model) in an R package
Hello,
I can`t figure out how to include a text file for use in an example in the .Rd help files of an R package I am writing.
I want the examples section of one help file to look like this:
\examples{
# Load the JAGS model
mod <- jags.model("model.txt")
}
The function jags.model tries to read in the file model.txt. So far every time I run R CMD check, I get an error message:
2008 Aug 21
1
pnmath compilation failure; dylib issue?
...fined
dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/
lib -o pnmath.so bd0.o beta.o chebyshev.o choose.o d1mach.o dbeta.o
dbinom.o dcauchy.o dchisq.o dexp.o df.o dgamma.o dgeom.o dhyper.o
dlnorm.o dlogis.o dnbeta.o dnbinom.o dnchisq.o dnf.o dnorm.o dnt.o
dpois.o dt.o dunif.o dweibull.o fmax2.o fmin2.o ftrunc.o gamma.o
gamma_cody.o i1mach.o imax2.o imin2.o lbeta.o lgamma.o lgammacor.o
mlutils.o pbeta.o pbinom.o pcauchy.o pchisq.o pexp.o pf.o pgamma.o
pgeom.o phyper.o plnorm.o plogis.o pnbeta.o pnbinom.o pnchisq.o pnf.o
pnmath.o pnorm.o pnt.o polygamma.o ppois....
2013 Mar 28
3
problem with plots with short example.
...#
### code chunk number 5: exchange
###################################################
hier.mod <- "model{
for(i in 1:N){
y[i] ~ dnorm(mu[numstate[i]], tau[numstate[i]])
}
for(j in 1:J){
mu[j] ~ dnorm(theta,nu)
tau[j] ~ dgamma(a,b)
}
theta ~ dnorm(0,.01)
nu ~ dgamma(.1,.1)
a ~ dunif(0,1000)
b ~ dunif(0,1000)
}"
hier.out <- run.jags(hier.mod,
data=dat, burnin=10000, sample=100000,
thin=10, monitor=c("mu", "tau", "theta", "nu", "a", "b"),
monitor.deviance=T, monitor.pd=T,
silent.jags=T)
##############...
2012 May 23
1
how a latent state matrix is updated using package R2WinBUGS
...0 0 0 0 1
[9,] 0 0 0 0 0
[10,] 0 0 0 0 0
model {
# Priors and constraints
for (i in 1:nind){
for (t in f[i]:(n.occasions-1)){
phi[i,t] <- mean.phi
p[i,t] <- mean.p
} #t
} #i
mean.phi ~ dunif(0, 1) # Prior for mean survival
mean.p ~ dunif(0, 1) # Prior for mean recapture
# Likelihood
for (i in 1:nind){
# Define latent state at first capture
z[i,f[i]] <- 1
for (t in (f[i]+1):n.occasions){
# State process
z[i,t] ~ dbern(mu1[i...
2009 Dec 03
2
Help R2WinBUGS
...beta.x*x[i] + beta.eco[2]*D.eco2[i] +
beta.eco[3]*D.eco3[i]
}
#
beta.eco[1] <- 0
# priors
beta.0 ~ dnorm (0, 0.0001)
beta.x ~ dnorm (0, 0.0001)
for (j in 2:J){
beta.eco[j] ~ dnorm (0, 0.0001)
}
tau.y <- pow(sigma.y, -2)
sigma.y ~ dunif (0, 100)
}
DATA
list(N=18, J=3,
x = c(0.2, 1.1, 1, 2.2, 2.5, 2.9, 2.9, 3.6, 3.8, 0.6, 1, 2, 2.4, 2.6, 2.8,
3.2, 3.9, 3.5),
y = c(0.5, 1.3, 0.1, 0.7, -0.4, 0.5, -0.9, -0.3, -0.3, 0.6, 0.4, 0.9, -0.1,
-0.4, -0.5, -0.2, 0.3, -1.5),
eco = c(1, 3, 1, 2, 1, 2, 1, 1, 2, 1, 1, 3, 2, 3, 2, 2,...
2012 Jul 13
3
Help with R2 OpenBUGs
...ork/PTY Project/Waterhole
Correction/ungulate.txt")
cat("
model{
# hyperparameters
# habitat effects for each functional group
g <- length(table(G))
for(i in 1:g){ # number of functional group
for(j in 1:3){ # number of habitat type
mu.h[i,j] ~ dnorm(0,0.0001) I(-5,5)
sigma.h[i,j] ~ dunif(0,5)
tau.h[i,j] <- 1/(sigma.h[i,j]*sigma.h[i,j])
}
}
# detectability
mu.r ~ dnorm(0,0.0001) I(-5,5)
sigma.r ~ dunif(0,5)
tau.r <- 1/(sigma.r*sigma.r)
psi ~ dunif(0,1) # inclusion rate that generates wi
# proportion of number of species among groups
for(i in 1:g){
prop[i] ~ dgamma(1,1)...
2008 Oct 19
0
Kullback Leibler Divergence
Hi there,
I'm trying to find the KL divergence measure between a prior and it's
posterior distributions, and I'm using the KLdiv method in the flexmix
package. plese see the example below:
require(flexmix)
x=seq(-4,4,length=100)
d1=dnorm(x,0,1)
d2=dunif(x,-3,3)
y=cbind(d1,d2)
kl=KLdiv(y)
but let say,
x1=seq(-5,5,length=100)
d3=dunif(x1,-3,3)
y1=cbind(d1,d3)
kl1=KLdiv(y1)
Notice that kl1 and kl are not the same. the documentation for the package
doesn't mention to evaluate the densities at the same points. which one is
correct? do I need to...
2007 May 14
1
Hierarchical models in R
Is there a way to do hierarchical (bayesian) logistic regression in R, the
way we do it in BUGS? For example in BUGS we can have this model:
model
{for(i in 1:N) {
y[i] ~ dbin(p[i],n[i])
logit(p[i]) <- beta0+beta1*x1[i]+beta2*x2[i]+beta3*x3[i]
}
sd ~ dunif(0,10)
tau <- pow(sd, -2)
beta0 ~ dnorm(0,0.1)
beta1 ~ dnorm(0,tau)
beta2 ~ dnorm(0,tau)
beta3 ~ dnorm(0,tau)
}
where we put a prior on the parameters betas, but the sd of the priors is
determined along with the parameters in a full bayesian model. I know that
there are...