update vignettes, fix bug in hist()

Author: pglpm

vignettes/vignette_start.htm

@@ -1301,7 +1301,7 @@ <h3>“Learning” and extrapolating from the sample data</h3>
 <span id="cb5-12"><a href="#cb5-12" tabindex="-1"></a><span class="do">## </span></span>
 <span id="cb5-13"><a href="#cb5-13" tabindex="-1"></a><span class="do">##  *************************************************** </span></span>
 <span id="cb5-14"><a href="#cb5-14" tabindex="-1"></a><span class="do">##  Saving output in directory</span></span>
-<span id="cb5-15"><a href="#cb5-15" tabindex="-1"></a><span class="do">##  penguin_inference-261031T120155-vrt8_dat10_smp3600 </span></span>
+<span id="cb5-15"><a href="#cb5-15" tabindex="-1"></a><span class="do">##  penguin_inference-261031T122336-vrt8_dat10_smp3600 </span></span>
 <span id="cb5-16"><a href="#cb5-16" tabindex="-1"></a><span class="do">##  *************************************************** </span></span>
 <span id="cb5-17"><a href="#cb5-17" tabindex="-1"></a><span class="do">## Starting Monte Carlo sampling of 3600 samples by 60 chains</span></span>
 <span id="cb5-18"><a href="#cb5-18" tabindex="-1"></a><span class="do">## in a space of 1027 (effectively 3851) dimensions.</span></span>
@@ -1312,7 +1312,7 @@ <h3>“Learning” and extrapolating from the sample data</h3>
 <span id="cb5-23"><a href="#cb5-23" tabindex="-1"></a><span class="do">## this can take tens of minutes. Please wait...</span></span>
 <span id="cb5-24"><a href="#cb5-24" tabindex="-1"></a><span class="do">## Compiled core 1. Number of samplers: 1078.       </span></span>
 <span id="cb5-25"><a href="#cb5-25" tabindex="-1"></a><span class="do">## Estimating remaining time, please be patient...</span></span>
-<span id="cb5-26"><a href="#cb5-26" tabindex="-1"></a><span class="do">## Sampling. Core 4 estimated end time: 2026-10-31 12:09</span></span>
+<span id="cb5-26"><a href="#cb5-26" tabindex="-1"></a><span class="do">## Sampling. Core 4 estimated end time: 2026-10-31 12:31</span></span>
 <span id="cb5-27"><a href="#cb5-27" tabindex="-1"></a><span class="do">## Finished Monte Carlo sampling.                                 </span></span>
 <span id="cb5-28"><a href="#cb5-28" tabindex="-1"></a><span class="do">## Highest number of Monte Carlo iterations across chains: 3600 </span></span>
 <span id="cb5-29"><a href="#cb5-29" tabindex="-1"></a><span class="do">## Highest number of used mixture components: 10 </span></span>
@@ -1327,14 +1327,14 @@ <h3>“Learning” and extrapolating from the sample data</h3>
 <span id="cb5-38"><a href="#cb5-38" tabindex="-1"></a><span class="do">## </span></span>
 <span id="cb5-39"><a href="#cb5-39" tabindex="-1"></a><span class="do">## Plotting final Monte Carlo traces and marginal samples...</span></span>
 <span id="cb5-40"><a href="#cb5-40" tabindex="-1"></a><span class="do">## </span></span>
-<span id="cb5-41"><a href="#cb5-41" tabindex="-1"></a><span class="do">## Total computation time: 4.3 mins </span></span>
-<span id="cb5-42"><a href="#cb5-42" tabindex="-1"></a><span class="do">## Average total time per chain: 0.071 mins </span></span>
-<span id="cb5-43"><a href="#cb5-43" tabindex="-1"></a><span class="do">## Max total memory used: approx 3500 MB</span></span>
-<span id="cb5-44"><a href="#cb5-44" tabindex="-1"></a><span class="do">## Max memory used per core: approx 860 MB</span></span>
-<span id="cb5-45"><a href="#cb5-45" tabindex="-1"></a><span class="do">## </span></span>
-<span id="cb5-46"><a href="#cb5-46" tabindex="-1"></a><span class="do">## Removing temporary output files.</span></span>
-<span id="cb5-47"><a href="#cb5-47" tabindex="-1"></a><span class="do">## Finished.</span></span>
-<span id="cb5-48"><a href="#cb5-48" tabindex="-1"></a><span class="do">## </span></span>
+<span id="cb5-41"><a href="#cb5-41" tabindex="-1"></a><span class="do">## Total computation time: 4.7 mins </span></span>
+<span id="cb5-42"><a href="#cb5-42" tabindex="-1"></a><span class="do">## Average preparation &amp; finalization time: 1 mins </span></span>
+<span id="cb5-43"><a href="#cb5-43" tabindex="-1"></a><span class="do">## Average Monte Carlo time per chain: 13 secs </span></span>
+<span id="cb5-44"><a href="#cb5-44" tabindex="-1"></a><span class="do">## Max total memory used: approx 3500 MB</span></span>
+<span id="cb5-45"><a href="#cb5-45" tabindex="-1"></a><span class="do">## Max memory used per core: approx 860 MB</span></span>
+<span id="cb5-46"><a href="#cb5-46" tabindex="-1"></a><span class="do">## ## </span></span>
+<span id="cb5-47"><a href="#cb5-47" tabindex="-1"></a><span class="do">## Removing temporary output files.</span></span>
+<span id="cb5-48"><a href="#cb5-48" tabindex="-1"></a><span class="do">## Finished.</span></span>
 <span id="cb5-49"><a href="#cb5-49" tabindex="-1"></a><span class="do">## </span></span>
 <span id="cb5-50"><a href="#cb5-50" tabindex="-1"></a><span class="do">## Closing connections to cores.</span></span></code></pre></div>
 <p>The initial output gives a summary of the sample size, number of
@@ -1794,7 +1794,7 @@ <h3>Updating what we’ve learnt</h3>
 <span id="cb20-12"><a href="#cb20-12" tabindex="-1"></a><span class="do">## </span></span>
 <span id="cb20-13"><a href="#cb20-13" tabindex="-1"></a><span class="do">##  *************************************************** </span></span>
 <span id="cb20-14"><a href="#cb20-14" tabindex="-1"></a><span class="do">##  Saving output in directory</span></span>
-<span id="cb20-15"><a href="#cb20-15" tabindex="-1"></a><span class="do">##  __learn_penguin_60-261031T120159-vrt8_dat60_smp3600 </span></span>
+<span id="cb20-15"><a href="#cb20-15" tabindex="-1"></a><span class="do">##  penguin_inference-261031T122341-vrt8_dat60_smp3600 </span></span>
 <span id="cb20-16"><a href="#cb20-16" tabindex="-1"></a><span class="do">##  *************************************************** </span></span>
 <span id="cb20-17"><a href="#cb20-17" tabindex="-1"></a><span class="do">## Starting Monte Carlo sampling of 3600 samples by 60 chains</span></span>
 <span id="cb20-18"><a href="#cb20-18" tabindex="-1"></a><span class="do">## in a space of 1027 (effectively 16651) dimensions.</span></span>
@@ -1805,7 +1805,7 @@ <h3>Updating what we’ve learnt</h3>
 <span id="cb20-23"><a href="#cb20-23" tabindex="-1"></a><span class="do">## this can take tens of minutes. Please wait...</span></span>
 <span id="cb20-24"><a href="#cb20-24" tabindex="-1"></a><span class="do">## Compiled core 1. Number of samplers: 1328.       </span></span>
 <span id="cb20-25"><a href="#cb20-25" tabindex="-1"></a><span class="do">## Estimating remaining time, please be patient...</span></span>
-<span id="cb20-26"><a href="#cb20-26" tabindex="-1"></a><span class="do">## Sampling. Core 1 estimated end time: 2026-10-31 12:17</span></span>
+<span id="cb20-26"><a href="#cb20-26" tabindex="-1"></a><span class="do">## Sampling. Core 1 estimated end time: 2026-10-31 12:39</span></span>
 <span id="cb20-27"><a href="#cb20-27" tabindex="-1"></a><span class="do">## Finished Monte Carlo sampling.                                 </span></span>
 <span id="cb20-28"><a href="#cb20-28" tabindex="-1"></a><span class="do">## Highest number of Monte Carlo iterations across chains: 14235 </span></span>
 <span id="cb20-29"><a href="#cb20-29" tabindex="-1"></a><span class="do">## Highest number of used mixture components: 19 </span></span>
@@ -1820,17 +1820,17 @@ <h3>Updating what we’ve learnt</h3>
 <span id="cb20-38"><a href="#cb20-38" tabindex="-1"></a><span class="do">## </span></span>
 <span id="cb20-39"><a href="#cb20-39" tabindex="-1"></a><span class="do">## Plotting final Monte Carlo traces and marginal samples...</span></span>
 <span id="cb20-40"><a href="#cb20-40" tabindex="-1"></a><span class="do">## </span></span>
-<span id="cb20-41"><a href="#cb20-41" tabindex="-1"></a><span class="do">## Total computation time: 13 mins </span></span>
-<span id="cb20-42"><a href="#cb20-42" tabindex="-1"></a><span class="do">## Average total time per chain: 0.21 mins </span></span>
-<span id="cb20-43"><a href="#cb20-43" tabindex="-1"></a><span class="do">## Max total memory used: approx 3600 MB</span></span>
-<span id="cb20-44"><a href="#cb20-44" tabindex="-1"></a><span class="do">## Max memory used per core: approx 900 MB</span></span>
-<span id="cb20-45"><a href="#cb20-45" tabindex="-1"></a><span class="do">## </span></span>
-<span id="cb20-46"><a href="#cb20-46" tabindex="-1"></a><span class="do">## Removing temporary output files.</span></span>
-<span id="cb20-47"><a href="#cb20-47" tabindex="-1"></a><span class="do">## Finished.</span></span>
-<span id="cb20-48"><a href="#cb20-48" tabindex="-1"></a><span class="do">## </span></span>
+<span id="cb20-41"><a href="#cb20-41" tabindex="-1"></a><span class="do">## Total computation time: 12 mins </span></span>
+<span id="cb20-42"><a href="#cb20-42" tabindex="-1"></a><span class="do">## Average preparation &amp; finalization time: 1.2 mins </span></span>
+<span id="cb20-43"><a href="#cb20-43" tabindex="-1"></a><span class="do">## Average Monte Carlo time per chain: 40 secs </span></span>
+<span id="cb20-44"><a href="#cb20-44" tabindex="-1"></a><span class="do">## Max total memory used: approx 3600 MB</span></span>
+<span id="cb20-45"><a href="#cb20-45" tabindex="-1"></a><span class="do">## Max memory used per core: approx 950 MB</span></span>
+<span id="cb20-46"><a href="#cb20-46" tabindex="-1"></a><span class="do">## </span></span>
+<span id="cb20-47"><a href="#cb20-47" tabindex="-1"></a><span class="do">## Removing temporary output files.</span></span>
+<span id="cb20-48"><a href="#cb20-48" tabindex="-1"></a><span class="do">## Finished.</span></span>
 <span id="cb20-49"><a href="#cb20-49" tabindex="-1"></a><span class="do">## </span></span>
 <span id="cb20-50"><a href="#cb20-50" tabindex="-1"></a><span class="do">## Closing connections to cores.</span></span></code></pre></div>
-<p>The calculation with 60 sample data took around 4 GB and 15 minutes
+<p>The calculation with 60 sample data took around 4 GB and 12 minutes
 on 4 cores.</p>
 <p>The results of this updated inference are now stored in the
 compressed file <code>&#39;learn.rds&#39;</code> within the new output