Merge pull request #635 from stan-dev/fix/laplace-output-docs

Update laplace output documentation

Author: mitzimorris

docs/2_32/cmdstan-guide-2_32.pdf

@@ -425,13 +425,12 @@ <h2><span class="header-section-number">13.1</span> Configuration</h2>
 <h2><span class="header-section-number">13.2</span> CSV output</h2>
 <p>The output file consists of the following pieces of information:</p>
 <ul>
-<li><p>The full set of configuration options available for the <code>log_prob</code> method is
+<li><p>The full set of configuration options available for the <code>laplace</code> method is
 reported at the beginning of the output file as CSV comments.</p></li>
-<li><p>Output columns for all model parameters on the constrained scale,
-followed by columns <code>log_p</code> and <code>log_q</code>,
-the unnormalized log density and the unnormalized density of the
-Laplace approximation, respectively.
+<li><p>Output columns <code>log_p__</code> and <code>log_q__</code>, the unnormalized log density and the
+unnormalized density of the Laplace approximation, respectively.
 These can be used for diagnostics and importance sampling.</p></li>
+<li><p>Output columns for all model parameters on the constrained scale.</p></li>
 </ul>
 </div>
 <div id="example" class="section level2" number="13.3">
@@ -479,11 +478,11 @@ <h2><span class="header-section-number">13.3</span> Example</h2>
 #   profile_file = profile.csv (Default)
 # num_threads = 1 (Default)
 # stanc_version = stanc3 v2.31.0-7-g20444266
-# stancflags = 
-theta,log_p,log_q
-0.0498545,-9.4562,-2.33997
-0.182898,-6.9144,-0.0117349
-0.376428,-7.18171,-0.746034
+# stancflags =
+log_p__,log_q__,theta
+-9.4562,-2.33997,0.0498545
+-6.9144,-0.0117349,0.182898
+-7.18171,-0.746034,0.376428
 ...</code></pre>
 
 </div>

docs/2_32/cmdstan-guide/laplace-sampling.html

@@ -425,13 +425,12 @@ <h2><span class="header-section-number">13.1</span> Configuration</h2>
 <h2><span class="header-section-number">13.2</span> CSV output</h2>
 <p>The output file consists of the following pieces of information:</p>
 <ul>
-<li><p>The full set of configuration options available for the <code>log_prob</code> method is
+<li><p>The full set of configuration options available for the <code>laplace</code> method is
 reported at the beginning of the output file as CSV comments.</p></li>
-<li><p>Output columns for all model parameters on the constrained scale,
-followed by columns <code>log_p</code> and <code>log_q</code>,
-the unnormalized log density and the unnormalized density of the
-Laplace approximation, respectively.
+<li><p>Output columns <code>log_p__</code> and <code>log_q__</code>, the unnormalized log density and the
+unnormalized density of the Laplace approximation, respectively.
 These can be used for diagnostics and importance sampling.</p></li>
+<li><p>Output columns for all model parameters on the constrained scale.</p></li>
 </ul>
 </div>
 <div id="example" class="section level2" number="13.3">
@@ -479,11 +478,11 @@ <h2><span class="header-section-number">13.3</span> Example</h2>
 #   profile_file = profile.csv (Default)
 # num_threads = 1 (Default)
 # stanc_version = stanc3 v2.31.0-7-g20444266
-# stancflags = 
-theta,log_p,log_q
-0.0498545,-9.4562,-2.33997
-0.182898,-6.9144,-0.0117349
-0.376428,-7.18171,-0.746034
+# stancflags =
+log_p__,log_q__,theta
+-9.4562,-2.33997,0.0498545
+-6.9144,-0.0117349,0.182898
+-7.18171,-0.746034,0.376428
 ...</code></pre>
 
 </div>

docs/2_32/cmdstan-guide/search_index.json

@@ -40,15 +40,15 @@ method default setting, `jacobian=1`, should be used.
 
 The output file consists of the following pieces of information:
 
-- The full set of configuration options available for the `log_prob` method is
+- The full set of configuration options available for the `laplace` method is
   reported at the beginning of the output file as CSV comments.
 
-- Output columns for all model parameters on the constrained scale,
-followed by columns `log_p` and `log_q`, 
-the unnormalized log density and the unnormalized density of the
-Laplace approximation, respectively.
+- Output columns `log_p__` and `log_q__`, the unnormalized log density and the
+unnormalized density of the Laplace approximation, respectively.
 These can be used for diagnostics and importance sampling.
 
+- Output columns for all model parameters on the constrained scale.
+
 ## Example
 
 To get an approximate estimate of the mode and standard deviation of the
@@ -102,11 +102,10 @@ The header and first few data rows of the output sample are shown below.
 #   profile_file = profile.csv (Default)
 # num_threads = 1 (Default)
 # stanc_version = stanc3 v2.31.0-7-g20444266
-# stancflags = 
-theta,log_p,log_q
-0.0498545,-9.4562,-2.33997
-0.182898,-6.9144,-0.0117349
-0.376428,-7.18171,-0.746034
+# stancflags =
+log_p__,log_q__,theta
+-9.4562,-2.33997,0.0498545
+-6.9144,-0.0117349,0.182898
+-7.18171,-0.746034,0.376428
 ...
 ```
-