rebuild book

docs/index.html

@@ -288,7 +288,7 @@ <h2>Setup<div class="tooltip"><button class="internal-link-btn" onclick="copy_li
 script</a>
 by executing the line below to install all requirements to compile the
 book:</p>
-<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="index.html#cb3-1" tabindex="-1"></a><span class="fu">source</span>(<span class="st">"https://raw.githubusercontent.com/rformassspectrometry/docs/main/install_docs_deps.R"</span>)</span></code></pre></div>
+<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="index.html#cb3-1" tabindex="-1"></a><span class="fu">source</span>(<span class="st">"https://raw.githubusercontent.com/rformassspectrometry/book/main/install_docs_deps.R"</span>)</span></code></pre></div>
 </div>
 <div id="acknowledgments" class="section level2 unnumbered">
 <h2>Acknowledgments<div class="tooltip"><button class="internal-link-btn" onclick="copy_link('acknowledgments')" onmouseout="reset_tooltip('acknowledgments-tooltip')"><span class="tooltiptext" id="acknowledgments-tooltip">Copy link</span><i class="fa fa-link"></i></button></div>

docs/sec-id.html

@@ -1125,7 +1125,7 @@ <h2>
 ##  [local]  QEP2LC6_HeLa_50ng_251120_03-calib.mzID.gz
 ##  [local]  QEP2LC6_HeLa_50ng_251120_03-calib.mzML
 ##  [remote] QEP2LC6_HeLa_50ng_251120_03.raw
-##  [remote] QEP2LC6_HeLa_50ng_251120_04-calib.mzID.gz
+##  [local]  QEP2LC6_HeLa_50ng_251120_04-calib.mzID.gz
 ##  ...</code></pre>
 <div class="sourceCode" id="cb207"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb207-1"><a href="sec-id.html#cb207-1" tabindex="-1"></a>(mzids <span class="ot">&lt;-</span> <span class="fu">pxget</span>(PXD022816, <span class="fu">grep</span>(<span class="st">"mzID"</span>, <span class="fu">pxfiles</span>(PXD022816))[<span class="dv">1</span><span class="sc">:</span><span class="dv">3</span>]))</span></code></pre></div>
 <pre><code>## Project PXD022816 files (32):
@@ -1138,7 +1138,7 @@ <h2>
 ##  [local]  QEP2LC6_HeLa_50ng_251120_03-calib.mzID.gz
 ##  [local]  QEP2LC6_HeLa_50ng_251120_03-calib.mzML
 ##  [remote] QEP2LC6_HeLa_50ng_251120_03.raw
-##  [remote] QEP2LC6_HeLa_50ng_251120_04-calib.mzID.gz
+##  [local]  QEP2LC6_HeLa_50ng_251120_04-calib.mzID.gz
 ##  ...</code></pre>
 <pre><code>## Warning in rep(as.integer(len), length = length(str)): partial argument match
 ## of 'length' to 'length.out'</code></pre>
@@ -1163,7 +1163,7 @@ <h2>
 ##  [local]  QEP2LC6_HeLa_50ng_251120_03-calib.mzID.gz
 ##  [local]  QEP2LC6_HeLa_50ng_251120_03-calib.mzML
 ##  [remote] QEP2LC6_HeLa_50ng_251120_03.raw
-##  [remote] QEP2LC6_HeLa_50ng_251120_04-calib.mzID.gz
+##  [local]  QEP2LC6_HeLa_50ng_251120_04-calib.mzID.gz
 ##  ...</code></pre>
 <pre><code>## Warning in rep(as.integer(len), length = length(str)): partial argument match
 ## of 'length' to 'length.out'</code></pre>
@@ -1388,7 +1388,7 @@ <h2>
 ## 77          2   3563.78     26314
 ##  ... 65 more variables/columns.
 ## Processing:
-##  Switch backend from MsBackendMzR to MsBackendDataFrame [Mon Mar 18 09:11:06 2024]</code></pre>
+##  Switch backend from MsBackendMzR to MsBackendDataFrame [Mon Mar 18 14:05:02 2024]</code></pre>
 <div class="sourceCode" id="cb257"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb257-1"><a href="sec-id.html#cb257-1" tabindex="-1"></a>cmat <span class="ot">&lt;-</span> <span class="fu">compareSpectra</span>(sp_O43175)</span>
 <span id="cb257-2"><a href="sec-id.html#cb257-2" tabindex="-1"></a><span class="fu">rownames</span>(cmat) <span class="ot">&lt;-</span></span>
 <span id="cb257-3"><a href="sec-id.html#cb257-3" tabindex="-1"></a>    <span class="fu">colnames</span>(cmat) <span class="ot">&lt;-</span> <span class="fu">strtrim</span>(sp_O43175<span class="sc">$</span>sequence, <span class="dv">3</span>)</span>

docs/sec-raw.html

@@ -491,7 +491,7 @@ <h3>
 ## 1862         1   259.752       931
 ##  ... 33 more variables/columns.
 ## Processing:
-##  Switch backend from MsBackendMzR to MsBackendMemory [Mon Mar 18 09:10:18 2024]</code></pre>
+##  Switch backend from MsBackendMzR to MsBackendMemory [Mon Mar 18 14:04:22 2024]</code></pre>
 <ul>
 <li>
 <code>MsBackendHdf5Peaks</code>: similar to <code>MsBackendMzR</code> this backend reads peak data
@@ -523,7 +523,7 @@ <h3>
 ##  20171016_POOL_POS_1_105-134.h5
 ##  20171016_POOL_POS_3_105-134.h5
 ## Processing:
-##  Switch backend from MsBackendMzR to MsBackendHdf5Peaks [Mon Mar 18 09:10:24 2024]</code></pre>
+##  Switch backend from MsBackendMzR to MsBackendHdf5Peaks [Mon Mar 18 14:04:29 2024]</code></pre>
 <div class="sourceCode" id="cb56"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb56-1"><a href="sec-raw.html#cb56-1" tabindex="-1"></a><span class="fu">table</span>(sp_hdf5<span class="sc">$</span>dataOrigin)</span></code></pre></div>
 <pre><code>## 
 ## /home/lgatto/disk/R/x86_64-pc-linux-gnu-library/4.3/msdata/sciex/20171016_POOL_POS_1_105-134.mzML 
@@ -532,9 +532,9 @@ <h3>
 ##                                                                                               931</code></pre>
 <div class="sourceCode" id="cb58"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb58-1"><a href="sec-raw.html#cb58-1" tabindex="-1"></a><span class="fu">table</span>(sp_hdf5<span class="sc">$</span>dataStorage)</span></code></pre></div>
 <pre><code>## 
-## /tmp/RtmpKu4Alm/20171016_POOL_POS_1_105-134.h5 
+## /tmp/RtmpJ3ldDf/20171016_POOL_POS_1_105-134.h5 
 ##                                            931 
-## /tmp/RtmpKu4Alm/20171016_POOL_POS_3_105-134.h5 
+## /tmp/RtmpJ3ldDf/20171016_POOL_POS_3_105-134.h5 
 ##                                            931</code></pre>
 <p>All of the above mentioned backends support changing all of their their spectra
 variables, <strong>except</strong> the <code>MsBackendMzR</code> that does not support changing m/z or
@@ -658,7 +658,7 @@ <h2>
 ## file(s):
 ## 678521a4fbe2_TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML
 ## Processing:
-##  Filter: select parent/children scans for 2807 [Mon Mar 18 09:10:25 2024]</code></pre>
+##  Filter: select parent/children scans for 2807 [Mon Mar 18 14:04:29 2024]</code></pre>
 <p class="solution-end">
 <span class="fa fa-square-o solution-icon"></span>
 </p>
@@ -972,8 +972,8 @@ <h2>
 ## file(s):
 ## 20171016_POOL_POS_3_105-134.mzML
 ## Processing:
-##  Filter: select data origin(s) /home/lgatto/disk/R/x86_64-pc-linux-gnu-library/4.3/msdata/sciex/20171016_POOL_POS_3_105-134.mzML [Mon Mar 18 09:10:26 2024]
-##  Filter: select retention time [175..189] on MS level(s) 1 [Mon Mar 18 09:10:26 2024]</code></pre>
+##  Filter: select data origin(s) /home/lgatto/disk/R/x86_64-pc-linux-gnu-library/4.3/msdata/sciex/20171016_POOL_POS_3_105-134.mzML [Mon Mar 18 14:04:31 2024]
+##  Filter: select retention time [175..189] on MS level(s) 1 [Mon Mar 18 14:04:31 2024]</code></pre>
 <p class="solution-end">
 <span class="fa fa-square-o solution-icon"></span>
 </p>
@@ -1059,7 +1059,7 @@ <h3>
 ## 20171016_POOL_POS_3_105-134.mzML
 ## Lazy evaluation queue: 1 processing step(s)
 ## Processing:
-##  Remove peaks with intensities outside [10, Inf] in spectra of MS level(s) 1. [Mon Mar 18 09:10:26 2024]</code></pre>
+##  Remove peaks with intensities outside [10, Inf] in spectra of MS level(s) 1. [Mon Mar 18 14:04:31 2024]</code></pre>
 <div class="sourceCode" id="cb86"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb86-1"><a href="sec-raw.html#cb86-1" tabindex="-1"></a><span class="fu">min</span>(<span class="fu">intensity</span>(sp_sciex[<span class="dv">1</span>]))</span></code></pre></div>
 <pre><code>## [1] 412</code></pre>
 <div class="sourceCode" id="cb88"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb88-1"><a href="sec-raw.html#cb88-1" tabindex="-1"></a>sp_sciex<span class="sc">@</span>processingQueue</span></code></pre></div>