Apply a Bayesian model (JAGS) for various iterations

Question

Consider the following data frame:

set.seed(5678)
sub_df<- data.frame(clustersize= rep(1, 4), 
            lepsp= c("A", "B", "C", "D"), 
            dens= round(runif(4, c(0, 1)), 3), 
            db= sample(1:10, 4, replace=TRUE))

Let's say I wanted to run the following Bayes linear model which returns samples, an mc.array object:

library("rjags")
library("coda")
dataForJags <- list(dens=sub_df$dens, db=sub_df$db, N=length(sub_df$dens))


model<-"model{
  for(i in 1:N){
  dens[i] ~ dnorm(mu[i], tau)  
  # identity
  mu[i] <- int + beta1*db[i] 
  }
  tau ~ dgamma(0.1,0.1)
  int ~ dnorm(0, 0.001)
  beta1 ~ dnorm(0, 0.001) 
  }"

 ##compile
 
 mod1 <- jags.model(textConnection(model),data= dataForJags,n.chains=2)
 
 ##samples returns a list of mcarray objects  
 
 samples<-jags.samples(model= mod1,variable.names=c("beta1", 
 "int","mu","tau"),n.iter=100000)

Given that samples$beta1[,,] represents random samples from the posterior distribution of the parameters of the jags model, then to summarize, my next step would be to calculate the mean and the 95% credible intervals of the posterior distribution. So I would use:

coeff_output<- round(quantile(samples$beta1[,,],probs=c(0.5,0.025,0.975)),3)

Now, let's say my actual data frame has multiple levels of clustersize.

set.seed(5672)
df<- data.frame(clustersize= c(rep(1, 4), rep(2,4), rep(3, 3)), 
            lepsp= c("A", "B", "C", "D", "B", "C", "D", "E", "A", "D", "F"), 
            dens= round(runif(11, c(0, 1)), 3), 
            db= sample(1:10, 11, replace=TRUE))

How would I run this model for each level of clustersize separately and compile the output into a single result data frame using a forloop or apply function? For each level of clustersize, the resulting mc.array object samples should be output to result_list and the coeff_output should be output to a data frame result_coeff.

Below I calculate the output for each clustersize separately, to produce the expected result list and data frame.

 #clustersize==1
 sub_df1<- data.frame(clustersize= rep(1, 4), 
                 lepsp= c("A", "B", "C", "D"), 
                 dens= round(runif(4, c(0, 1)), 3), 
                 db= sample(1:10, 4, replace=TRUE))

dataForJags <- list(dens=sub_df$dens, db=sub_df$db, N=length(sub_df$dens))
model<-"model{
for(i in 1:N){
dens[i] ~ dnorm(mu[i], tau)  
mu[i] <- int + beta1*db[i] 
}
tau ~ dgamma(0.1,0.1)
int ~ dnorm(0, 0.001)
beta1 ~ dnorm(0, 0.001) 
}"

mod1 <- jags.model(textConnection(model),data= dataForJags,n.chains=2)

samples1<-jags.samples(model= mod1,variable.names=c("beta1", 
"int","mu","tau"),n.iter=100000)

coeff_output1<- 
data.frame(as.list(round(quantile(samples1$beta1[,,],probs=c(0.5,0.025,0.975)),3)))

#clustersize==2
sub_df2<- data.frame(clustersize=  rep(2,4), 
                 lepsp= c( "B", "C", "D", "E"), 
                 dens= round(runif(4, c(0, 1)), 3), 
                 db= sample(1:10, 4, replace=TRUE))
dataForJags <- list(dens=sub_df$dens, db=sub_df$db, N=length(sub_df$dens))
model<-"model{
for(i in 1:N){
dens[i] ~ dnorm(mu[i], tau)  
mu[i] <- int + beta1*db[i] 
}
tau ~ dgamma(0.1,0.1)
int ~ dnorm(0, 0.001)
beta1 ~ dnorm(0, 0.001) 
}"

mod1 <- jags.model(textConnection(model),data= dataForJags,n.chains=2)

samples2<-jags.samples(model= mod1,variable.names=c("beta1", 
 "int","mu","tau"),n.iter=100000)

coeff_output2<- 
data.frame(as.list(round(quantile(samples2$beta1[,,],probs=c(0.5,0.025,0.975)),3)))    

#clustersize==3
sub_df3<- data.frame(clustersize= rep(3, 3), 
                 lepsp= c("A", "D", "F"), 
                 dens= round(runif(3, c(0, 1)), 3), 
                 db= sample(1:10, 3, replace=TRUE))
dataForJags <- list(dens=sub_df$dens, db=sub_df$db, N=length(sub_df$dens))
model<-"model{
for(i in 1:N){
dens[i] ~ dnorm(mu[i], tau)  
mu[i] <- int + beta1*db[i] 
}
tau ~ dgamma(0.1,0.1)
int ~ dnorm(0, 0.001)
beta1 ~ dnorm(0, 0.001) 
}"

mod1 <- jags.model(textConnection(model),data= dataForJags,n.chains=2)

samples3<-jags.samples(model= mod1,variable.names=c("beta1", 
"int","mu","tau"),n.iter=100000)

coeff_output3<- 
data.frame(as.list(round(quantile(samples3$beta1[,,],probs=c(0.5,0.025,0.975)),3)))

Desired final output:

result_list<- list(samples1, samples2, samples3)

result_coeff<-rbind(coeff_output1, coeff_output2, coeff_output3)

Here is a link to the actual data frame. The solution should be able to process a large dataframe with clustersizes up to 600.

download.file("https://drive.google.com/file/d/1ZYIQtb_QHbYsInDGkta-5P2EJrFRDf22/view?usp=sharing",temp)

Felton

Just FYI, the download.file() link you posted does not work for grabbing the actual dataset. I had to get it manually by downloading via my browser. – Regionalism

Answer 1

There are a few issues to consider here, which are caused by the scale of what you're trying to do. You are creating over 550 different jags.sample objects with 100000 iterations each, and then trying to store all of them in a single list. On most machines, this will cause memory issues: the output is simply too large.

There are at least two ways that we can deal with this:

1. Take measures to reduce the memory usage of our input data by as much as possible.
2. Tune our JAGS output so that it does not save so many iterations from each chain.

I've made a number of modifications to your code that should allow it to work with your actual dataset.

Creating Input Data:

In your original code, clustersize and db both have the data type numeric, even though they only need to be integers. The numeric type takes 8 bytes, while the integer type only takes 4 bytes. If we coerce these two columns to the integer type, we can actually reduce the memory size of the list of dataframes in the next step by about 30%.

library("tidyverse")

#### Load Raw Data ####
df <- read_csv("example.csv") %>%
  select(-1) %>%
  mutate(clustersize = as.integer(clustersize),
         db = as.integer(db))

Initial JAGS Tuning

You are using far too many iterations for each of your chains; niter = 100000 is extremely high. You should also be specifying a burn-in period using n.burn, an adaptation period using n.adapt, and a thinning parameter using thin. The thinning parameter is especially important here - this directly reduces the number of iterations that we are saving from each chain. A thinning parameter of 50 means that we are only saving every 50th result.

There are post-hoc methods for selecting your thinning parameters, burn-in, and adaptation period, but that discussion is beyond the scope of SO. For some basic information on what all of these arguments do, there is an excellent answer here: https://mcmap.net/q/2034162/-how-to-interpret-some-syntax-n-adapt-update-in-jags. For now, I've provided values that will allow this code to run on your entire dataset, but I recommend that you carefully select the values that you use for your final analysis.

Using tidybayes

The following solution uses the tidybayes package. This provides a clean output and allows us to neatly row-bind all of the coefficient summaries into a single dataframe. Note that we use coda.samples() instead of jags.samples(), because this provides a more universal MCMC object that we can pass to spread_draws(). We also use dplyr::group_split() which is slightly more computationally efficient than split().

library("rjags")
library("coda")
library("tidybayes")

set.seed(5672)
result <- df %>% group_split(clustersize) %>% map(~{
  
  dataForJags <- list(dens=.x$dens, db=.x$db, N=length(.x$dens))
  
  # Declare model structure
  mod1 <- jags.model(textConnection(model),
                     data=dataForJags,
                     n.chains=2)
  
  # samples returns a list of mcmc objects  
  samples<-coda.samples(model=mod1,
                        variable.names=c("beta1","int","mu","tau"),
                        n.burn=10000,
                        n.adapt=5000,
                        n.iter=25000,
                        thin=50
  )
  # Extract individual draws
  samp <- spread_draws(samples, beta1)
  
  # Summarize 95% credible intervals
  coeff_output <- spread_draws(samples, beta1) %>%
    median_qi(beta1)

  list(samples = samp, coeff_output = coeff_output)
}) %>% transpose()

# List of sample objects
result$samples
# Dataframe of coefficient estimates and 95% credible intervals
result_coeff <- bind_rows(result$coeff_output, .id = "clustersize")

Regionalism

can you help me out how Jags works for training and testing datasets, please! I don't have that much experience about JAGS and please help me out! – Irfan

Answer 2

You can use map from purrr package and split over the different clustersize:

library(rjags)
library(coda)
library(purrr)

set.seed(5678)
set.seed(5672)
df<- data.frame(clustersize= c(rep(1, 4), rep(2,4), rep(3, 3)), 
                lepsp= c("A", "B", "C", "D", "B", "C", "D", "E", "A", "D", "F"), 
                dens= round(runif(11, c(0, 1)), 3), 
                db= sample(1:10, 11, replace=TRUE))

model<-"model{
  for(i in 1:N){
  dens[i] ~ dnorm(mu[i], tau)  
  # identity
  mu[i] <- int + beta1*db[i] 
  }
  tau ~ dgamma(0.1,0.1)
  int ~ dnorm(0, 0.001)
  beta1 ~ dnorm(0, 0.001) 
  }"

# split data for different clustersize and calculate result
result <- df %>% split(.$clustersize) %>% map(~{

    dataForJags <- list(dens=.x$dens, db=.x$db, N=length(.x$dens))

    ##compile
    mod1 <- jags.model(textConnection(model),data= dataForJags,n.chains=2)

    ##samples returns a list of mcarray objects  
    samples<-jags.samples(model= mod1,variable.names=c("beta1","int","mu","tau"),n.iter=100000)
    coeff_output<- data.frame(as.list(round(quantile(samples$beta1[,,],probs=c(0.5,0.025,0.975)),3)))
    list(samples = samples, coeff_output = coeff_output)
    }) %>% transpose()

result$samples
result$coeff_output

Note the use of purrr::transpose to transform the final result in a list for samples and a list for coefs as per you request.

Alcaraz

This works on the example dataframe. Any Idea why I get the following error message on the actual dataframe where cluster sizes go up to 600? Error: vector memory exhausted (limit reached?) – Felton

I edited the original post to include a link to the actual dataframe that the solution should be able to process. – Felton

did you try to run your example code just on sub_df <- newdata %>% filter(clustersize ==1) which gives a subset of 773 rows ? it almost stuck my computer and gave me following error : 'impossible to allocate a 1.2Go vector'. If I run this with parameter n.iter = 1000 instead of n.iter = 100000 everything works perfectly. – Alcaraz

You still have a JAGS tuning problem and I won't be able to help you on this, The iteration problem which is your question works fine. – Alcaraz

@Danielle, did you manage to make all iterations work? – Alcaraz