Running rJAGS when the likelihood is a custom density - r

I am trying to figure out how to sample from a custom density in rJAGS but am running into issues. having searched the site, I saw that there is a zeroes (or ones) trick that can be employed based on BUGS code but am having a hard time with its implementation in rJAGS. I think I am doing it correctly but keep getting the following error:
Error in jags.model(model1.spec, data = list(x = x, N = N), n.chains = 4, :
Error in node dpois(lambda)
Length mismatch in Node::setValue
Here is my rJAGS code for reproducibility:
library(rjags)
set.seed(4)
N = 100
x = rexp(N, 3)
L = quantile(x, prob = 1) # Censoring point
censor = ifelse(x <= L, 1, 0) # Censoring indicator
x[censor == 1] <- L
model1.string <-"
model {
for (i in 1:N){
x[i] ~ dpois(lambda)
lambda <- -N*log(1-exp(-(1/mu)))
}
mu ~ dlnorm(mup, taup)
mup <- log(.0001)
taup <- 1/49
R <- 1 - exp(-(1/mu) * .0001)
}
"
model1.spec<-textConnection(model1.string)
jags <- jags.model(model1.spec,
data = list('x' = x,
'N' = N),
n.chains=4,
n.adapt=100)
Here, my negative log likelihood of the density I am interested in is -N*log(1-exp(-(1/mu))). Is there an obvious mistake in the code?

Using the zeros trick, the variable on the left-hand side of the dpois() relationship has to be an N-length vector of zeros. The variable x should show up in the likelihood somewhere. Here is an example using the normal distribution.
set.seed(519)
N <- 100
x <- rnorm(100, mean=3)
z <- rep(0, N)
C <- 10
pi <- pi
model1.string <-"
model {
for (i in 1:N){
lambda[i] <- pow(2*pi*sig2, -0.5) * exp(-.5*pow(x[i]-mu, 2)/sig2)
loglam[i] <- log(lambda[i]) + C
z[i] ~ dpois(loglam[i])
}
mu ~ dnorm(0,.1)
tau ~ dgamma(1,.1)
sig2 <- pow(tau, -1)
sumLL <- sum(log(lambda[]))
}
"
model1.spec<-textConnection(model1.string)
set.seed(519)
jags <- jags.model(model1.spec,
data = list('x' = x,
'z' = z,
'N' = N,
'C' = C,
'pi' = pi),
inits = function()list(tau = 1, mu = 3),
n.chains=4,
n.adapt=100)
samps1 <- coda.samples(jags, c("mu", "sig2"), n.iter=1000)
summary(samps1)
Iterations = 101:1100
Thinning interval = 1
Number of chains = 4
Sample size per chain = 1000
1. Empirical mean and standard deviation for each variable,
plus standard error of the mean:
Mean SD Naive SE Time-series SE
mu 4.493 2.1566 0.034100 0.1821
sig2 1.490 0.5635 0.008909 0.1144
2. Quantiles for each variable:
2.5% 25% 50% 75% 97.5%
mu 0.6709 3.541 5.218 5.993 7.197
sig2 0.7909 0.999 1.357 1.850 2.779

Related

How to simulate data in R, such that p-value of regressor is exactly 0.05?

I have written a small function that simulates data from a normal distribution, how it is usual in linear models. My question is how to get a model with a pvalue of sim[, 1] == 0.05. I want to show that if I add a random variable even it is normal distributed around zero with small variance N(0,0.0023) , that pvalue of sim[,1] changes. The code below shows the true model.
set.seed(37) # seed for reproducability
simulation <- function(b_0, b_1,n,min_x_1 ,max_x_1,sd_e){
mat <- NA
x_1 <- runif(n = n, min = min_x_1, max =max_x_1)
error <- rnorm(mean = 0,sd = sd_e, n = n )
y <- b_0 + b_1*x_1 + error
mat <- matrix(cbind(x_1,y), ncol = 2)
return(mat)
#plot(mat[,1],mat[,2])
}
sim <- simulation(10,-2,10000,-10,70,0.003)
summary(lm(sim[,2] ~ sim[,1] ))

Linear regression gradient descent algorithms in R produce varying results

I am trying to implement a linear regression in R from scratch without using any packages or libraries using the following data:
UCI Machine Learning Repository, Bike-Sharing-Dataset
The linear regression was easy enough, here is the code:
data <- read.csv("Bike-Sharing-Dataset/hour.csv")
# Select the useable features
data1 <- data[, c("season", "mnth", "hr", "holiday", "weekday", "workingday", "weathersit", "temp", "atemp", "hum", "windspeed", "cnt")]
# Split the data
trainingObs<-sample(nrow(data1),0.70*nrow(data1),replace=FALSE)
# Create the training dataset
trainingDS<-data1[trainingObs,]
# Create the test dataset
testDS<-data1[-trainingObs,]
x0 <- rep(1, nrow(trainingDS)) # column of 1's
x1 <- trainingDS[, c("season", "mnth", "hr", "holiday", "weekday", "workingday", "weathersit", "temp", "atemp", "hum", "windspeed")]
# create the x- matrix of explanatory variables
x <- as.matrix(cbind(x0,x1))
# create the y-matrix of dependent variables
y <- as.matrix(trainingDS$cnt)
m <- nrow(y)
solve(t(x)%*%x)%*%t(x)%*%y
The next step is to implement the batch update gradient descent and here is where I am running into problems. I dont know where the errors are coming from or how to fix them, but the code works. The problem is that the values being produced are radically different from the results of the regression and I am unsure of why.
The two versions of the batch update gradient descent that I have implemented are as follows (the results of both algorithms differ from one another and from the results of the regression):
# Gradient descent 1
gradientDesc <- function(x, y, learn_rate, conv_threshold, n, max_iter) {
plot(x, y, col = "blue", pch = 20)
m <- runif(1, 0, 1)
c <- runif(1, 0, 1)
yhat <- m * x + c
MSE <- sum((y - yhat) ^ 2) / n
converged = F
iterations = 0
while(converged == F) {
## Implement the gradient descent algorithm
m_new <- m - learn_rate * ((1 / n) * (sum((yhat - y) * x)))
c_new <- c - learn_rate * ((1 / n) * (sum(yhat - y)))
m <- m_new
c <- c_new
yhat <- m * x + c
MSE_new <- sum((y - yhat) ^ 2) / n
if(MSE - MSE_new <= conv_threshold) {
abline(c, m)
converged = T
return(paste("Optimal intercept:", c, "Optimal slope:", m))
}
iterations = iterations + 1
if(iterations > max_iter) {
abline(c, m)
converged = T
return(paste("Optimal intercept:", c, "Optimal slope:", m))
}
}
return(paste("MSE=", MSE))
}
AND:
grad <- function(x, y, theta) { # note that for readability, I redefined theta as a column vector
gradient <- 1/m* t(x) %*% (x %*% theta - y)
return(gradient)
}
grad.descent <- function(x, maxit, alpha){
theta <- matrix(rep(0, length=ncol(x)), ncol = 1)
for (i in 1:maxit) {
theta <- theta - alpha * grad(x, y, theta)
}
return(theta)
}
If someone could explain why these two functions are producing different results I would greatly appreciate it. I also want to make sure that I am in fact implementing the gradient descent correctly.
Lastly, how can I plot the results of the descent with varying learning rates and superimpose this data over the results of the regression itself?
EDIT
Here are the results of running the two algorithms with alpha = .005 and 10,000 iterations:
1)
> gradientDesc(trainingDS, y, 0.005, 0.001, 32, 10000)
TEXT_SHOW_BACKTRACE environmental variable.
[1] "Optimal intercept: 2183458.95872599 Optimal slope: 62417773.0184353"
2)
> print(grad.descent(x, 10000, .005))
[,1]
x0 8.3681113
season 19.8399837
mnth -0.3515479
hr 8.0269388
holiday -16.2429750
weekday 1.9615369
workingday 7.6063719
weathersit -12.0611266
temp 157.5315413
atemp 138.8019732
hum -162.7948299
windspeed 31.5442471
To give you an example of how to write functions like this in a slightly better way, consider the following:
gradientDesc <- function(x, y, learn_rate, conv_threshold, max_iter) {
n <- nrow(x)
m <- runif(ncol(x), 0, 1) # m is a vector of dimension ncol(x), 1
yhat <- x %*% m # since x already contains a constant, no need to add another one
MSE <- sum((y - yhat) ^ 2) / n
converged = F
iterations = 0
while(converged == F) {
m <- m - learn_rate * ( 1/n * t(x) %*% (yhat - y))
yhat <- x %*% m
MSE_new <- sum((y - yhat) ^ 2) / n
if( abs(MSE - MSE_new) <= conv_threshold) {
converged = T
}
iterations = iterations + 1
MSE <- MSE_new
if(iterations >= max_iter) break
}
return(list(converged = converged,
num_iterations = iterations,
MSE = MSE_new,
coefs = m) )
}
For comparison:
ols <- solve(t(x)%*%x)%*%t(x)%*%y
Now,
out <- gradientDesc(x,y, 0.005, 1e-7, 200000)
data.frame(ols, out$coefs)
ols out.coefs
x0 33.0663095 35.2995589
season 18.5603565 18.5779534
mnth -0.1441603 -0.1458521
hr 7.4374031 7.4420685
holiday -21.0608520 -21.3284449
weekday 1.5115838 1.4813259
workingday 5.9953383 5.9643950
weathersit -0.2990723 -0.4073493
temp 100.0719903 147.1157262
atemp 226.9828394 174.0260534
hum -225.7411524 -225.2686640
windspeed 12.3671942 9.5792498
Here, x refers to your x as defined in your first code chunk. Note the similarity between the coefficients. However, also note that
out$converged
[1] FALSE
so that you could increase the accuracy by increasing the number of iterations or by playing around with the step size. It might also help to scale your variables first.

Maximum likelihood estimation of the log-normal distribution using R

I'm trying to estimate a linear model with a log-normal distributed error term. I already have working code for a linear model with normally distributed errors:
library(Ecdat)
library(assertthat)
library(maxLik)
# Load the data
data(Wages1)
# Check what R says
summary(lm(wage ~ school + exper + sex, data = Wages1))
# Use maxLik from package maxLik
# The likelihood function
my_log_lik_pos <- function(theta, data){
y <- data[, 1]
x <- data[, -1]
beta <- head(theta, -1)
sigma <- tail(theta, 1)
xb <- x%*%beta
are_equal(dim(xb), c(nrow(my_data), 1))
return(sum(log(dnorm(y, mean = xb, sd = sigma))))
}
# Bind the data
my_data <- cbind(Wages1$wage, 1, Wages1$school, Wages1$exper, Wages1$sex)
my_problem <- maxLik(my_log_lik_pos, data = my_data,
start = rep(1,5), method = "BFGS")
summary(my_problem)
I get approximately the same results. Now I try to do the same, but using the log-normal likelihood. For this, I have to first simulate some data:
true_beta <- c(0.1, 0.2, 0.3, 0.4, 0.5)
ys <- my_data[, -1] %*% head(true_beta, -1) +
rlnorm(nrow(my_data), 0, tail(true_beta, 1))
my_data_2 <- cbind(ys, my_data[, -1])
And the log-likelihood function:
my_log_lik_lognorm <- function(theta, data){
y <- data[, 1]
x <- data[, -1]
beta <- head(theta, -1)
sigma <- tail(theta, 1)
xb <- x%*%beta
are_equal(dim(xb), c(nrow(data), 1))
return(sum(log(dlnorm(y, mean = xb, sd = sigma))))
}
my_problem2 <- maxLik(my_log_lik_lognorm, data = my_data_2,
start = rep(0.2,5), method = "BFGS")
summary(my_problem2)
The estimated parameters should be around the values of true_beta, but for some reason I find completely different values. I tried with different methods, different starting values but to no avail. I'm sure that I'm missing something obvious, but I don't see what.
Am I right to assume that the log-likelihood of the log-normal distribution is:
sum(log(dlnorm(y, mean = .., sd = ...))
Unless I'm mistaken, this is the definition of the log-likelihood (sum of the logs of the densities).
I found the issue: it seems the problem is not my log-likelihood function. When I try to estimate the model with glm:
summary(glm(ys ~ school + exper + sex, family=gaussian(link="log"), data=Wages1))
I get the same result as with maxLik and my log-likelihood. It would seem the problem comes from when I tried to simulate some data:
ys <- my_data[, -1] %*% head(true_beta, -1) +
rlnorm(nrow(my_data), 0, tail(true_beta, 1))
The correct way to simulate the data:
ys <- rlnorm(nrow(my_data), my_data[, -1] %*% head(true_beta, -1), tail(true_beta, 1))
Now everything works!

OpenBUGS error undefined variable

I'm working on a binomial mixture model using OpenBUGS and R package R2OpenBUGS. I've successfully built simpler models, but once I add another level for imperfect detection, I consistently receive the error variable X is not defined in model or in data set. I've tried a number of different things, including changing the structure of my data and entering my data directly into OpenBUGS. I'm posting this in the hope that someone else has experience with this error, and perhaps knows why OpenBUGS is not recognizing variable X even though it is clearly defined as far as I can tell.
I've also gotten the error expected the collection operator c error pos 8 - this is not an error I've been getting previously, but I am similarly stumped.
Both the model and the data-simulation function come from Kery's Introduction to WinBUGS for Ecologists (2010). I will note that the data set here is in lieu of my own data, which is similar.
I am including the function to build the dataset as well as the model. Apologies for the length.
# Simulate data: 200 sites, 3 sampling rounds, 3 factors of the level 'trt',
# and continuous covariate 'X'
data.fn <- function(nsite = 180, nrep = 3, xmin = -1, xmax = 1, alpha.vec = c(0.01,0.2,0.4,1.1,0.01,0.2), beta0 = 1, beta1 = -1, ntrt = 3){
y <- array(dim = c(nsite, nrep)) # Array for counts
X <- sort(runif(n = nsite, min = xmin, max = xmax)) # covariate values, sorted
# Relationship expected abundance - covariate
x2 <- rep(1:ntrt, rep(60, ntrt)) # Indicator for population
trt <- factor(x2, labels = c("CT", "CM", "CC"))
Xmat <- model.matrix(~ trt*X)
lin.pred <- Xmat[,] %*% alpha.vec # Value of lin.predictor
lam <- exp(lin.pred)
# Add Poisson noise: draw N from Poisson(lambda)
N <- rpois(n = nsite, lambda = lam)
table(N) # Distribution of abundances across sites
sum(N > 0) / nsite # Empirical occupancy
totalN <- sum(N) ; totalN
# Observation process
# Relationship detection prob - covariate
p <- plogis(beta0 + beta1 * X)
# Make a 'census' (i.e., go out and count things)
for (i in 1:nrep){
y[,i] <- rbinom(n = nsite, size = N, prob = p)
}
# Return stuff
return(list(nsite = nsite, nrep = nrep, ntrt = ntrt, X = X, alpha.vec = alpha.vec, beta0 = beta0, beta1 = beta1, lam = lam, N = N, totalN = totalN, p = p, y = y, trt = trt))
}
data <- data.fn()
And here is the model:
sink("nmix1.txt")
cat("
model {
# Priors
for (i in 1:3){ # 3 treatment levels (factor)
alpha0[i] ~ dnorm(0, 0.01)
alpha1[i] ~ dnorm(0, 0.01)
}
beta0 ~ dnorm(0, 0.01)
beta1 ~ dnorm(0, 0.01)
# Likelihood
for (i in 1:180) { # 180 sites
C[i] ~ dpois(lambda[i])
log(lambda[i]) <- log.lambda[i]
log.lambda[i] <- alpha0[trt[i]] + alpha1[trt[i]]*X[i]
for (j in 1:3){ # each site sampled 3 times
y[i,j] ~ dbin(p[i,j], C[i])
lp[i,j] <- beta0 + beta1*X[i]
p[i,j] <- exp(lp[i,j])/(1+exp(lp[i,j]))
}
}
# Derived quantities
}
",fill=TRUE)
sink()
# Bundle data
trt <- data$trt
y <- data$y
X <- data$X
ntrt <- 3
# Standardise covariates
s.X <- (X - mean(X))/sd(X)
win.data <- list(C = y, trt = as.numeric(trt), X = s.X)
# Inits function
inits <- function(){ list(alpha0 = rnorm(ntrt, 0, 2),
alpha1 = rnorm(ntrt, 0, 2),
beta0 = rnorm(1,0,2), beta1 = rnorm(1,0,2))}
# Parameters to estimate
parameters <- c("alpha0", "alpha1", "beta0", "beta1")
# MCMC settings
ni <- 1200
nb <- 200
nt <- 2
nc <- 3
# Start Markov chains
out <- bugs(data = win.data, inits, parameters, "nmix1.txt", n.thin=nt,
n.chains=nc, n.burnin=nb, n.iter=ni, debug = TRUE)
Note: This answer has gone through a major revision, after I noticed another problem with the code.
If I understand your model correctly, you are mixing up the y and N from the simulated data, and what is passed as C to Bugs. You are passing the y variable (a matrix) to the C variable in the Bugs model, but this is accessed as a vector. From what I can see C is representing the number of "trials" in your binomial draw (actual abundances), i.e. N in your data set. The variable y (a matrix) is called the same thing in both the simulated data and in the Bugs model.
This is a reformulation of your model, as I understand it, and this runs ok:
sink("nmix1.txt")
cat("
model {
# Priors
for (i in 1:3){ # 3 treatment levels (factor)
alpha0[i] ~ dnorm(0, 0.01)
alpha1[i] ~ dnorm(0, 0.01)
}
beta0 ~ dnorm(0, 0.01)
beta1 ~ dnorm(0, 0.01)
# Likelihood
for (i in 1:180) { # 180 sites
C[i] ~ dpois(lambda[i])
log(lambda[i]) <- log.lambda[i]
log.lambda[i] <- alpha0[trt[i]] + alpha1[trt[i]]*X[i]
for (j in 1:3){ # each site sampled 3 times
y[i,j] ~ dbin(p[i,j], C[i])
lp[i,j] <- beta0 + beta1*X[i]
p[i,j] <- exp(lp[i,j])/(1+exp(lp[i,j]))
}
}
# Derived quantities
}
",fill=TRUE)
sink()
# Bundle data
trt <- data$trt
y <- data$y
X <- data$X
N<- data$N
ntrt <- 3
# Standardise covariates
s.X <- (X - mean(X))/sd(X)
win.data <- list(y = y, trt = as.numeric(trt), X = s.X, C= N)
# Inits function
inits <- function(){ list(alpha0 = rnorm(ntrt, 0, 2),
alpha1 = rnorm(ntrt, 0, 2),
beta0 = rnorm(1,0,2), beta1 = rnorm(1,0,2))}
# Parameters to estimate
parameters <- c("alpha0", "alpha1", "beta0", "beta1")
# MCMC settings
ni <- 1200
nb <- 200
nt <- 2
nc <- 3
# Start Markov chains
out <- bugs(data = win.data, inits, parameters, "nmix1.txt", n.thin=nt,
n.chains=nc, n.burnin=nb, n.iter=ni, debug = TRUE)
Overall, the results from this model looks ok, but there are long autocorrelation lags for beta0 and beta1. The estimate of beta1 also seems a bit off(~= -0.4), so you might want to recheck the Bugs model specification, so that it is matching the simulation model (i.e. that you are fitting the correct statistical model). At the moment, I'm not sure that it does, but I don't have the time to check further right now.
I got the same message trying to pass a factor to OpenBUGS. Like so,
Ndata <- list(yrs=N$yrs, site=N$site), ... )
The variable "site" was not passed by the "bugs" function. It simply was not in list passed
to OpenBUGS
I solved the problem by passing site as numeric,
Ndata <- list(yrs=N$yrs, site=as.numeric(N$site)), ... )

jags.parallel: setting less clusters than chains: "Error in res[[ch]] : subscript out of bounds"

I have only 2 core CPU so logically I want to set only two parallel threads/clusters for jags.parallel. unfortunatelly, when I try it and the number of chains is 3 or 4, jags fails with an error:
Error in res[[ch]] : subscript out of bounds
Is lower number of threads (than chains) not allowed?
I have not encountered such statement in the documentation. Anyway, it doesn't make sense to run 4 chains in 4 threads/clusters, when your CPU only has 2 cores! Threads will fight for CPU, caches won't be used optimally and the result will be much slower than using 2 threads only.
Full code:
set.seed(123)
### 14.1.2. Data generation
n.site <- 10
x <- gl(n = 2, k = n.site, labels = c("grassland", "arable"))
eps <- rnorm(2*n.site, mean = 0, sd = 0.5)# Normal random effect
lambda.OD <- exp(0.69 +(0.92*(as.numeric(x)-1) + eps) )
lambda.Poisson <- exp(0.69 +(0.92*(as.numeric(x)-1)) ) # For comparison
C.OD <- rpois(n = 2*n.site, lambda = lambda.OD)
C.Poisson <- rpois(n = 2*n.site, lambda = lambda.Poisson)
### 14.1.4. Analysis using WinBUGS
# Define model
sink("Poisson.OD.t.test.txt")
cat("
model {
# Priors
alpha ~ dnorm(0,0.001)
beta ~ dnorm(0,0.001)
sigma ~ dunif(0, 10)
tau <- 1 / (sigma * sigma)
maybe_overdisp <- mean(exp_eps[])
# Likelihood
for (i in 1:n) {
C.OD[i] ~ dpois(lambda[i])
log(lambda[i]) <- alpha + beta *x[i] #+ eps[i]
eps[i] ~ dnorm(0, tau)
exp_eps[i] <- exp(eps[i])
}
}
",fill=TRUE)
sink()
# Bundle data
x = as.numeric(x)-1
n = length(x)
win.data <- list(C.OD = C.OD, x = as.numeric(x)-1, n = length(x))
# Inits function
inits <- function(){ list(alpha=rlnorm(1), beta=rlnorm(1), sigma = rlnorm(1))}
# Parameters to estimate
params <- c("lambda","alpha", "beta", "sigma", "maybe_overdisp")
# MCMC settings
nc <- 3 # Number of chains
ni <- 3000 # Number of draws from posterior per chain
nb <- 1000 # Number of draws to discard as burn-in
nt <- 5 # Thinning rate
require(R2jags)
# THIS WORKS FINE
out <- R2jags::jags(win.data, inits, params, "Poisson.OD.t.test.txt",
nc, ni, nb, nt);
# THIS PRODUCES ERROR
out <- do.call(jags.parallel, list(names(win.data), inits, params, "Poisson.OD.t.test.txt",
nc, ni, nb, nt, n.cluster = 2));

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