Fix #30 and add plot and jags.View tests

6 files changed, 107 insertions, 35 deletions

diff --git a/R/densityplot.R b/R/densityplot.R
index b350f0a..2f7209b 100644
--- a/R/densityplot.R
+++ b/R/densityplot.R
@@ -24,36 +24,41 @@ param_density <- function(x, parameter, m_labels=FALSE){
   
   #Get samples
   vals <- mcmc_to_mat(x$samples[,parameter])
-  
-  # Get bandwidth, one value for all chains
-  bw <- mean(apply(vals, 2, stats::bw.nrd0))
+ 
+  if(any(is.na(vals))){
+    plot(1:nrow(vals), rep(0, nrow(vals)), type='n',
+         xlab='Value', ylab='Density', main=paste('Density of',parameter))
+  } else {
+    # Get bandwidth, one value for all chains
+    bw <- mean(apply(vals, 2, stats::bw.nrd0))
 
-  from <- min(vals) - 3*bw  # these are 'density's defaults...
-  to <- max(vals) + 3*bw    # ... use these if no constraints
-  xx <- vals
-  mult <- 1
+    from <- min(vals) - 3*bw  # these are 'density's defaults...
+    to <- max(vals) + 3*bw    # ... use these if no constraints
+    xx <- vals
+    mult <- 1
 
-  # Check for non-negative constraint or probability
-  if (min(vals) >= 0 && min(vals) < 2 * bw) { # it's non-negative
-    from <- 0
-    xx <- rbind(vals, -vals)
-    mult <- 2
-  }
-  if (min(vals) >= 0 && max(vals) <= 1 &&
+    # Check for non-negative constraint or probability
+    if (min(vals) >= 0 && min(vals) < 2 * bw) { # it's non-negative
+      from <- 0
+      xx <- rbind(vals, -vals)
+      mult <- 2
+    }
+    if (min(vals) >= 0 && max(vals) <= 1 &&
         (min(vals) < 2 * bw || 1 - max(vals) < 2 * bw)) { # it's a probability
-    xx <- rbind(vals, -vals, 2-vals)
-    mult <- 3
-    to <- 1
-  }
+      xx <- rbind(vals, -vals, 2-vals)
+      mult <- 3
+      to <- 1
+    }
 
-  # Get densities
-  dens <- apply(xx, 2, function(x) stats::density(x, bw=bw, from=from, to=to)$y) * mult
+    # Get densities
+    dens <- apply(xx, 2, function(x) stats::density(x, bw=bw, from=from, to=to)$y) * mult
 
-  # Draw plot
-  x <- seq(from, to, length=nrow(dens))
-  cols <- grDevices::rainbow(ncol(vals))
-  graphics::matplot(x, dens, type='l', lty=1, col=cols,
-      xlab='Value', ylab='Density', main=paste('Density of',parameter))
+    # Draw plot
+    x <- seq(from, to, length=nrow(dens))
+    cols <- grDevices::rainbow(ncol(vals))
+    graphics::matplot(x, dens, type='l', lty=1, col=cols,
+        xlab='Value', ylab='Density', main=paste('Density of',parameter))
+  }
 
   #Add margin labels if necessary
   if(m_labels){
diff --git a/R/jags_View.R b/R/jags_View.R
index 0bae3e0..4ab0460 100644
--- a/R/jags_View.R
+++ b/R/jags_View.R
@@ -8,7 +8,7 @@ jags.View <- function(x, title, digits=3){
   }
   # Organize columns
   if(x$mcmc.info$n.chains!=1){y = x$summary[,c(1,2,3,5,7,10,11,8,9)]
-  } else {y = x$summary[,c(1,2,3,5,7,8,9)]}
+  } else {y = x$summary[,c(1,2,3,5,7,10,11)]}
   z <-  as.data.frame(round(as.matrix(y),digits))
   if(is.vector(y)){
     z <- as.data.frame(t(z))
diff --git a/R/traceplot.R b/R/traceplot.R
index 755d3aa..66069fb 100644
--- a/R/traceplot.R
+++ b/R/traceplot.R
@@ -30,9 +30,16 @@ param_trace <- function(x, parameter, m_labels=FALSE){
 
   #Draw plot
   cols <- grDevices::rainbow(ncol(vals))
-  graphics::matplot(1:nrow(vals), vals, type='l', lty=1, col=cols,
+
+  if(all(is.na(vals))){
+    plot(1:nrow(vals), rep(0, nrow(vals)), type='n',
+              xlab="Iterations", ylab="Value",
+              main=bquote(.(parameter)*","~hat(R) == .(Rhat)))
+  } else {
+    graphics::matplot(1:nrow(vals), vals, type='l', lty=1, col=cols,
                  xlab='Iterations', ylab='Value',
                  main=bquote(.(parameter)*","~hat(R) == .(Rhat)))
+  }
 
   #Add margin labels if necessary
   if(m_labels){
@@ -40,6 +47,3 @@ param_trace <- function(x, parameter, m_labels=FALSE){
     graphics::mtext("Value", side=2, line=1.5, outer=TRUE)
   }
 }
-
-#General function for setting up plots
-# get_plot_info now has its own file
diff --git a/R/whiskerplot.R b/R/whiskerplot.R
index 8b09bf1..0e85236 100644
--- a/R/whiskerplot.R
+++ b/R/whiskerplot.R
@@ -27,11 +27,15 @@ whiskerplot <- function(x,parameters,quantiles=c(0.025,0.975),
 
   #Plot parameter means
   n <- length(parameters)
-  graphics::plot(1:n, post_stats[1,], xaxt="n", 
-                 ylim=range(post_stats), xlim=c(0,n+1),
+  graphics::plot(1:n, post_stats[1,], xaxt="n", type='n',
+                 ylim=range(post_stats, na.rm=TRUE), xlim=c(0,n+1),
                  xlab="Parameters", 
                  ylab=paste0('Parameter mean and quantiles (',quantiles[1],
-                            ' - ',quantiles[2],')'), pch=19, cex=1.5, ...)
+                            ' - ',quantiles[2],')'), ...)
+  for (i in 1:n){
+    if(any(is.na(post_stats[,i]))) next
+    graphics::points(i, post_stats[1,i], cex=1.5, pch=19)
+  }
   graphics::axis(side=1, at=1:n, labels=parameters)
   graphics::box()
   
diff --git a/inst/tinytest/test_jags.R b/inst/tinytest/test_jags.R
index 2218dfc..be64ffb 100644
--- a/inst/tinytest/test_jags.R
+++ b/inst/tinytest/test_jags.R
@@ -193,6 +193,18 @@ expect_true(all(is.na(out$summary[,"Rhat"])))
 expect_true(all(is.na(out$summary[,"n.eff"])))
 expect_true(all(out$summary["alpha",3:7] == out$summary["alpha",3]))
 
+# test jags.View---------------------------------------------------------------
+at_home <- identical( Sys.getenv("AT_HOME"), "TRUE" )
+if(at_home){
+  ref <- readRDS("longley_reference_fit.Rds")
+  test <- jags.View(ref)
+  expect_equal(ncol(test), 10)
+  expect_equal(colnames(test)[7:10], c("overlap0", "f", "Rhat", "n.eff"))
+  test2 <- jags.View(out)
+  expect_equal(ncol(test2), 8)
+  expect_equal(colnames(test)[7:8], c("overlap0", "f"))
+}
+
 # Error when user tries to set seed--------------------------------------------
 expect_error(jags(data = data, inits = inits, parameters.to.save = params,
             model.file = modfile, n.chains = 1, n.adapt = 100, n.iter = 100,
@@ -244,8 +256,6 @@ expect_equal(nrow(out$summary), 21)
 expect_equal(rownames(out$summary)[20], "mu[1,2]")
 
 # When no stochastic nodes (and deviance is not calculated)--------------------
-library(jagsUI)
-
 data <- list(a = 1, b = Inf)
 
 modfile <- tempfile()
diff --git a/inst/tinytest/test_plots.R b/inst/tinytest/test_plots.R
new file mode 100644
index 0000000..4e06f39
--- /dev/null
+++ b/inst/tinytest/test_plots.R
@@ -0,0 +1,49 @@
+# Handle missing values in plots-----------------------------------------------
+ref <- readRDS('longley_reference_fit.Rds')
+
+# Rhat_min
+pdf(NULL)
+test1 <- traceplot(ref, Rhat_min=1.0005)
+expect_equal(test1, NULL)
+expect_error(traceplot(ref, Rhat_min=1.1))
+dev.off()
+
+# Plotting array parameter
+pdf(NULL)
+test2 <- traceplot(ref, "mu", ask=FALSE)
+expect_equal(test2, NULL)
+dev.off()
+
+# Plotting range
+pdf(NULL)
+test3 <- traceplot(ref, "mu[1:4]", ask=FALSE)
+expect_equal(test3, NULL)
+dev.off()
+
+# Handling NAs
+for (i in 1:3){
+  ref$samples[[i]][,'alpha'] <- NA
+}
+ref$samples[[1]][,"beta"] <- NA
+ref$samples[[1]][1,"sigma"] <- NA
+ref$summary["alpha","Rhat"] <- NA
+
+pdf(NULL)
+test4 <- traceplot(ref, c("alpha", "beta", "sigma"))
+expect_equal(test4, NULL)
+test5 <- whiskerplot(ref, c("alpha", "beta", "sigma"))
+expect_equal(test5, NULL)
+# Not ideal, maybe fix someday
+test6 <- densityplot(ref, c("alpha", "beta", "sigma"))
+expect_equal(test6, NULL)
+test7 <- plot(ref, ask=FALSE)
+expect_equal(test7, NULL)
+dev.off()
+
+# Incorrect object
+expect_error(traceplot(ref$samples))
+# Parameter not found
+expect_error(traceplot(ref, "fake"))
+expect_error(densityplot(ref, "fake"))
+expect_error(whiskerplot(ref, "fake"))
+expect_error(plot(ref, "fake"))