Merge pull request #31 from nimble-dev/joss

Fix vignette formatting detail.  Add some DOIs to paper.bib.

compareMCMCs/doc/compareMCMCs.R

@@ -102,8 +102,8 @@ res$nimble$metrics
 MCMCmetric_quartiles <- function(result, options) {
   p25 <- apply(result$samples, 2, quantile, probs = 0.25)
   p75 <- apply(result$samples, 2, quantile, probs = 0.75)
-  ## q25 and q75 are named vectors with names matching model parameters
-  ## i.e. column names of result$samples
+  # q25 and q75 are named vectors with names matching model parameters
+  # i.e. column names of result$samples
   maxDiff <- max(p75-p25)
   list(byParameter = list(p25 = p25,
                           p75 = p75),
@@ -133,8 +133,8 @@ res <- compareMCMCs(modelInfo,
                                        niter = 2000,
                                        burnin = 100))
 
-## We will look at the result using combineMetrics
-## rather than generating new html pages.
+# We will look at the result using combineMetrics
+# rather than generating new html pages.
 combineMetrics(res)
 
 ## -----------------------------------------------------------------------------
@@ -145,7 +145,7 @@ conversions <- list(nimble = reparam,
 applyConversions(res, conversions)
 clearMetrics(res)
 addMetrics(res) # use default metrics
-combineMetrics(res) ## An easy way to see that it worked
+combineMetrics(res) # An easy way to see that it worked
 
 ## -----------------------------------------------------------------------------
 combineMetrics(res, include_times = TRUE)

compareMCMCs/doc/compareMCMCs.Rmd

@@ -203,8 +203,8 @@ Let's look at an example of each.  Say we want to make a metric that calculates
 MCMCmetric_quartiles <- function(result, options) {
   p25 <- apply(result$samples, 2, quantile, probs = 0.25)
   p75 <- apply(result$samples, 2, quantile, probs = 0.75)
-  ## q25 and q75 are named vectors with names matching model parameters
-  ## i.e. column names of result$samples
+  # q25 and q75 are named vectors with names matching model parameters
+  # i.e. column names of result$samples
   maxDiff <- max(p75-p25)
   list(byParameter = list(p25 = p25,
                           p75 = p75),
@@ -254,8 +254,8 @@ res <- compareMCMCs(modelInfo,
                                        niter = 2000,
                                        burnin = 100))
 
-## We will look at the result using combineMetrics
-## rather than generating new html pages.
+# We will look at the result using combineMetrics
+# rather than generating new html pages.
 combineMetrics(res)
 ```
 
@@ -273,7 +273,7 @@ conversions <- list(nimble = reparam,
 applyConversions(res, conversions)
 clearMetrics(res)
 addMetrics(res) # use default metrics
-combineMetrics(res) ## An easy way to see that it worked
+combineMetrics(res) # An easy way to see that it worked
 ```
 
 ## How to specify conversions

compareMCMCs/doc/example1.html

@@ -12,11 +12,11 @@ <h1>example1</h1>
 <a href='#p4'>MCMC efficiency details</a><br>
 <a href='#p5'>Posterior summaries</a><br><h2 id='p1'>MCMC sampling time</h2>
 <!-- html table generated in R 4.1.2 by xtable 1.8-4 package -->
-<!-- Fri Jan  7 14:52:53 2022 -->
+<!-- Wed Jan 12 15:21:55 2022 -->
 <table border=1>
 <tr> <th> MCMC </th> <th> burnin </th> <th> post-burnin </th> <th> total sampling </th>  </tr>
   <tr> <td> jags </td> <td align="right"> 0.00 </td> <td align="right"> 0.01 </td> <td align="right"> 0.01 </td> </tr>
-  <tr> <td> stan </td> <td align="right"> 0.00 </td> <td align="right"> 0.07 </td> <td align="right"> 0.07 </td> </tr>
+  <tr> <td> stan </td> <td align="right"> 0.01 </td> <td align="right"> 0.07 </td> <td align="right"> 0.08 </td> </tr>
   <tr> <td> nimble </td> <td align="right"> 0.00 </td> <td align="right"> 0.00 </td> <td align="right"> 0.00 </td> </tr>
   <tr> <td> nimble_slice </td> <td align="right"> 0.00 </td> <td align="right"> 0.00 </td> <td align="right"> 0.00 </td> </tr>
    </table>

compareMCMCs/doc/example2.html

@@ -12,10 +12,10 @@ <h1>example2</h1>
 <a href='#p4'>MCMC efficiency details</a><br>
 <a href='#p5'>Posterior summaries</a><br><h2 id='p1'>MCMC sampling time</h2>
 <!-- html table generated in R 4.1.2 by xtable 1.8-4 package -->
-<!-- Fri Jan  7 14:53:09 2022 -->
+<!-- Wed Jan 12 15:22:10 2022 -->
 <table border=1>
 <tr> <th> MCMC </th> <th> burnin </th> <th> post-burnin </th> <th> total sampling </th>  </tr>
-  <tr> <td> jags </td> <td align="right"> 0.00 </td> <td align="right"> 0.00 </td> <td align="right"> 0.00 </td> </tr>
+  <tr> <td> jags </td> <td align="right"> 0.00 </td> <td align="right"> 0.00 </td> <td align="right"> 0.01 </td> </tr>
   <tr> <td> nimble </td> <td align="right"> 0.00 </td> <td align="right"> 0.00 </td> <td align="right"> 0.00 </td> </tr>
   <tr> <td> nimble_slice </td> <td align="right"> 0.00 </td> <td align="right"> 0.01 </td> <td align="right"> 0.01 </td> </tr>
    </table>

compareMCMCs/vignettes/compareMCMCs.Rmd

@@ -203,8 +203,8 @@ Let's look at an example of each.  Say we want to make a metric that calculates
 MCMCmetric_quartiles <- function(result, options) {
   p25 <- apply(result$samples, 2, quantile, probs = 0.25)
   p75 <- apply(result$samples, 2, quantile, probs = 0.75)
-  ## q25 and q75 are named vectors with names matching model parameters
-  ## i.e. column names of result$samples
+  # q25 and q75 are named vectors with names matching model parameters
+  # i.e. column names of result$samples
   maxDiff <- max(p75-p25)
   list(byParameter = list(p25 = p25,
                           p75 = p75),

paper.bib

@@ -82,6 +82,7 @@ @article{lunn2009bugs
   number    = {25},
   pages     = {3049--3067},
   year      = {2009},
+  doi       = {10.1002/sim.3680},
   publisher = {Wiley Online Library}
 }
 
@@ -93,6 +94,7 @@ @article{lunn2000winbugs
   number    = {4},
   pages     = {325--337},
   year      = {2000},
+  doi       = {10.1023/A:1008929526011},
   publisher = {Springer}
 }