Reorganize files

11 files changed, 147 insertions, 145 deletions

diff --git a/R/print.R b/R/S3_methods.R
index bb593ec..6df687a 100644
--- a/R/print.R
+++ b/R/S3_methods.R
@@ -1,4 +1,32 @@
+# Summary method
+summary.jagsUI <- function(object, ...){
+  object$summary
+}
+
+#Plot method
+plot.jagsUI <- function(x, parameters=NULL, per_plot=4, ask=NULL, ...){
+
+  if(is.null(ask))
+    ask <- grDevices::dev.interactive(orNone = TRUE)
+  plot_info <- get_plot_info(x, parameters, NULL, ask)
+  dims <- c(min(length(plot_info$params), per_plot), 2)
+  if(length(plot_info$params) <= per_plot)
+    ask <- FALSE
+  new_par <- list(mfrow = dims, mar = c(4,4,2.5,1), oma=c(0,0,0,0), ask=ask)
+   
+  #Handle par()
+  old_par <- graphics::par(new_par)
+  on.exit(graphics::par(old_par))  
+  
+
+  #Make plot
+  for (i in plot_info$params){
+    param_trace(x, i)
+    param_density(x, i)
+  }
+}
 
+# Print method
 print.jagsUI <- function(x,digits=3,...){
 
   mc <- x$mcmc.info
diff --git a/R/autojags.R b/R/autojags.R
index 4c67f43..3b1f809 100644
--- a/R/autojags.R
+++ b/R/autojags.R
@@ -184,4 +184,42 @@ autojags <- function(data,inits=NULL,parameters.to.save,model.file,n.chains,n.ad
   
   
 }
+ 
+
+test.Rhat <- function(samples,cutoff,params.omit,verbose=TRUE){
+  
+  params <- colnames(samples[[1]])
+  expand <- sapply(strsplit(params, "\\["), "[", 1)
+  
+  gd <- function(hold){
+    r <- try(gelman.diag(hold, autoburnin=FALSE)$psrf[1], silent=TRUE)
+    if(inherits(r, "try-error") || !is.finite(r)) {
+      r <- NA
+    }
+    return(r)
+  }
+  
+  failure <- FALSE
+  index <- 1
+  while (failure==FALSE && index <= length(params)){
+    
+    if(!expand[index]%in%params.omit){
+      test <- gd(samples[,index])
+    } else {test <- 1}
+    
+    if(is.na(test)){test <- 1}
+   
+    if(test>cutoff){failure=TRUE
+    } else {index <- index + 1}
+  }
   
+  if(failure==TRUE&verbose){
+    cat('.......Convergence check failed for parameter \'',params[index],'\'\n',sep="")
+  }
+  if(failure==FALSE&verbose){
+    cat('.......All parameters converged.','\n\n')
+  }
+  
+  return(failure)
+  
+}
diff --git a/R/bindmcmc.R b/R/bindmcmc.R
deleted file mode 100644
index 451e6a8..0000000
--- a/R/bindmcmc.R
+++ /dev/null
@@ -1,19 +0,0 @@
-
-bind.mcmc <- function(mcmc.list1,mcmc.list2,start,n.new.iter){
-  
-  nchains <- length(mcmc.list1)
-  
-  samples <- list()
-  
-  for (i in 1:nchains){
-    
-    d <- rbind(mcmc.list1[[i]],mcmc.list2[[i]])
-    
-    samples[[i]] <- mcmc(data=d,start=start,end=(end(mcmc.list1[[i]])+n.new.iter),thin=thin(mcmc.list1[i]))
-    
-  }
-  
-  return(as.mcmc.list(samples))
-  
-  
-}
\ No newline at end of file
diff --git a/R/mcmc_tools.R b/R/mcmc_tools.R
index 612fda5..1c867a1 100644
--- a/R/mcmc_tools.R
+++ b/R/mcmc_tools.R
@@ -80,3 +80,25 @@ get_inds <- function(param, params_raw){
 has_one_parameter <- function(mcmc_list){
   coda::nvar(mcmc_list) == 1
 }
+
+
+#------------------------------------------------------------------------------
+# Bind two mcmc.lists together
+bind.mcmc <- function(mcmc.list1,mcmc.list2,start,n.new.iter){
+  
+  nchains <- length(mcmc.list1)
+  
+  samples <- list()
+  
+  for (i in 1:nchains){
+    
+    d <- rbind(mcmc.list1[[i]],mcmc.list2[[i]])
+    
+    samples[[i]] <- mcmc(data=d,start=start,end=(end(mcmc.list1[[i]])+n.new.iter),thin=thin(mcmc.list1[i]))
+    
+  }
+  
+  return(as.mcmc.list(samples))
+  
+  
+}
diff --git a/R/plot.R b/R/plot.R
deleted file mode 100644
index 17108cf..0000000
--- a/R/plot.R
+++ /dev/null
@@ -1,23 +0,0 @@
-
-#Plot method for jagsUI objects
-plot.jagsUI <- function(x, parameters=NULL, per_plot=4, ask=NULL, ...){
-
-  if(is.null(ask))
-    ask <- grDevices::dev.interactive(orNone = TRUE)
-  plot_info <- get_plot_info(x, parameters, NULL, ask)
-  dims <- c(min(length(plot_info$params), per_plot), 2)
-  if(length(plot_info$params) <= per_plot)
-    ask <- FALSE
-  new_par <- list(mfrow = dims, mar = c(4,4,2.5,1), oma=c(0,0,0,0), ask=ask)
-   
-  #Handle par()
-  old_par <- graphics::par(new_par)
-  on.exit(graphics::par(old_par))  
-  
-
-  #Make plot
-  for (i in plot_info$params){
-    param_trace(x, i)
-    param_density(x, i)
-  }
-}
diff --git a/R/get_plot_info.R b/R/plot_tools.R
index ac0ae42..7b58b91 100644
--- a/R/get_plot_info.R
+++ b/R/plot_tools.R
@@ -1,5 +1,9 @@
+#Check that an object is the right class---------------------------------------
+check_class <- function(output){
+  if(!inherits(output, "jagsUI")) stop("Requires jagsUI object")
+}
 
-#General function for setting up plots
+#General function for setting up plots-----------------------------------------
 # Called by densityplot, traceplot, and plot.jagsUI
 # plot.jagsUI only uses the 'params' component in the output, ignores the rest
 get_plot_info <- function(x, parameters, layout, ask, Rhat_min=NULL){
@@ -50,9 +54,9 @@ get_plot_info <- function(x, parameters, layout, ask, Rhat_min=NULL){
   list(params=parameters, new_par=new_par, per_plot=per_plot)
 }
 
-
-has_brackets <- function(x){
-  grepl("\\[.*\\]", x)
+# Parameter name tools---------------------------------------------------------
+expand_params <- function(params){
+  unlist(lapply(params, expand_brackets))
 }
 
 expand_brackets <- function(x){
@@ -64,6 +68,6 @@ expand_brackets <- function(x){
   paste0(pname, "[",rng,"]")
 }
 
-expand_params <- function(params){
-  unlist(lapply(params, expand_brackets))
+has_brackets <- function(x){
+  grepl("\\[.*\\]", x)
 }
diff --git a/R/summary.R b/R/summary.R
deleted file mode 100644
index 4cdeffd..0000000
--- a/R/summary.R
+++ /dev/null
@@ -1,3 +0,0 @@
-summary.jagsUI <- function(object, ...){
-  object$summary
-}
diff --git a/R/testrhat.R b/R/testrhat.R
deleted file mode 100644
index 5c85448..0000000
--- a/R/testrhat.R
+++ /dev/null
@@ -1,38 +0,0 @@
-
-test.Rhat <- function(samples,cutoff,params.omit,verbose=TRUE){
-  
-  params <- colnames(samples[[1]])
-  expand <- sapply(strsplit(params, "\\["), "[", 1)
-  
-  gd <- function(hold){
-    r <- try(gelman.diag(hold, autoburnin=FALSE)$psrf[1], silent=TRUE)
-    if(inherits(r, "try-error") || !is.finite(r)) {
-      r <- NA
-    }
-    return(r)
-  }
-  
-  failure <- FALSE
-  index <- 1
-  while (failure==FALSE && index <= length(params)){
-    
-    if(!expand[index]%in%params.omit){
-      test <- gd(samples[,index])
-    } else {test <- 1}
-    
-    if(is.na(test)){test <- 1}
-   
-    if(test>cutoff){failure=TRUE
-    } else {index <- index + 1}
-  }
-  
-  if(failure==TRUE&verbose){
-    cat('.......Convergence check failed for parameter \'',params[index],'\'\n',sep="")
-  }
-  if(failure==FALSE&verbose){
-    cat('.......All parameters converged.','\n\n')
-  }
-  
-  return(failure)
-  
-}
\ No newline at end of file
diff --git a/R/update.R b/R/update.R
index b731851..048a0c3 100644
--- a/R/update.R
+++ b/R/update.R
@@ -1,4 +1,4 @@
-
+# update method for jagsUI class-----------------------------------------------
 update.jagsUI <- function(object, parameters.to.save=NULL, 
                           n.adapt=NULL, n.iter, n.thin=NULL, 
                           modules=c('glm'), factories=NULL,
@@ -72,3 +72,51 @@ update.jagsUI <- function(object, parameters.to.save=NULL,
   
   return(output) 
 }
+
+# update method for jagsUIbasic class------------------------------------------
+update.jagsUIbasic <- function(object, parameters.to.save=NULL, 
+                               n.adapt=NULL, n.iter, n.thin=NULL, 
+                               modules=c('glm'), factories=NULL, 
+                               DIC=NULL, verbose=TRUE, ...){
+  
+  # Set up parameters
+  if(is.null(parameters.to.save)){
+    params_long <- colnames(object$samples[[1]])
+    parameters.to.save <- unique(sapply(strsplit(params_long, "\\["), "[", 1))
+  }
+  
+  #Set up DIC monitoring
+  if(is.null(DIC)){
+    DIC <- 'deviance' %in% parameters.to.save
+  } else {
+    if(DIC & (!'deviance' %in% parameters.to.save)){
+      parameters.to.save <- c(parameters.to.save, 'deviance')
+    } else if(!DIC & 'deviance' %in% parameters.to.save){
+      parameters.to.save <- parameters.to.save[parameters.to.save != 'deviance']
+    }
+  }
+
+  # Set up MCMC info
+  mcmc.info <- list(n.chains = length(object$samples), n.adapt = n.adapt, 
+                    n.iter = n.iter, n.burnin = 0,
+                    n.thin = ifelse(is.null(n.thin), thin(object$samples), n.thin),
+                    n.cores = object$n.cores)
+
+  parallel <- names(object$model[1]) == "cluster1"
+
+  # Run JAGS via rjags
+  rjags_out <- run_rjags(data=NULL, inits=NULL, parameters.to.save, modfile=NULL,
+                         mcmc.info, modules, factories, DIC, parallel, !verbose,
+                         model.object = object$model, update=TRUE)
+
+  # Report time
+  if(verbose) cat('MCMC took', rjags_out$elapsed.min, 'minutes.\n')
+  
+  # Create output object
+  output <- list(samples = order_samples(rjags_out$samples, parameters.to.save),
+                 model = rjags_out$m, 
+                 n.cores = object$n.cores)
+  class(output) <- 'jagsUIbasic'
+  
+  return(output) 
+}
diff --git a/R/updatebasic.R b/R/updatebasic.R
deleted file mode 100644
index 97fd512..0000000
--- a/R/updatebasic.R
+++ /dev/null
@@ -1,47 +0,0 @@
-
-update.jagsUIbasic <- function(object, parameters.to.save=NULL, 
-                               n.adapt=NULL, n.iter, n.thin=NULL, 
-                               modules=c('glm'), factories=NULL, 
-                               DIC=NULL, verbose=TRUE, ...){
-  
-  # Set up parameters
-  if(is.null(parameters.to.save)){
-    params_long <- colnames(object$samples[[1]])
-    parameters.to.save <- unique(sapply(strsplit(params_long, "\\["), "[", 1))
-  }
-  
-  #Set up DIC monitoring
-  if(is.null(DIC)){
-    DIC <- 'deviance' %in% parameters.to.save
-  } else {
-    if(DIC & (!'deviance' %in% parameters.to.save)){
-      parameters.to.save <- c(parameters.to.save, 'deviance')
-    } else if(!DIC & 'deviance' %in% parameters.to.save){
-      parameters.to.save <- parameters.to.save[parameters.to.save != 'deviance']
-    }
-  }
-
-  # Set up MCMC info
-  mcmc.info <- list(n.chains = length(object$samples), n.adapt = n.adapt, 
-                    n.iter = n.iter, n.burnin = 0,
-                    n.thin = ifelse(is.null(n.thin), thin(object$samples), n.thin),
-                    n.cores = object$n.cores)
-
-  parallel <- names(object$model[1]) == "cluster1"
-
-  # Run JAGS via rjags
-  rjags_out <- run_rjags(data=NULL, inits=NULL, parameters.to.save, modfile=NULL,
-                         mcmc.info, modules, factories, DIC, parallel, !verbose,
-                         model.object = object$model, update=TRUE)
-
-  # Report time
-  if(verbose) cat('MCMC took', rjags_out$elapsed.min, 'minutes.\n')
-  
-  # Create output object
-  output <- list(samples = order_samples(rjags_out$samples, parameters.to.save),
-                 model = rjags_out$m, 
-                 n.cores = object$n.cores)
-  class(output) <- 'jagsUIbasic'
-  
-  return(output) 
-}
diff --git a/R/utils.R b/R/utils.R
deleted file mode 100644
index 9458c63..0000000
--- a/R/utils.R
+++ /dev/null
@@ -1,8 +0,0 @@
-
-
-#--- from process_output ---------------------------------------------------------------------------
-#Check that an object is the right class
-check_class <- function(output){
-  if(!inherits(output, "jagsUI")) stop("Requires jagsUI object")
-}
-#------------------------------------------------------------------------------