docs

docs/cellcoal.manual.v1.html

@@ -326,9 +326,9 @@ <h1>2. Citation</h1>
 <div id="getting-started" class="section level1">
 <h1>3. Getting started</h1>
 <ol style="list-style-type: decimal">
-<li><p><strong>Download</strong>: get the program from the GitHub repository at <a href="https://github.com/dapogon/cellcoal" class="uri">https://github.com/dapogon/cellcoal</a>. Under the Code tab you will see a section call <em>releas</em>e. Click on it download the source code in .zip (or tar.gz) format. Then unzip the <em>cellcoal-x.y.z.zip</em> file (for example, cellcoal-1.0.0.zip). You should see now a folder called <em>cellcoal-x.y.z</em>.Move into the folder to compile and run the program.</p></li>
+<li><p><strong>Download</strong>: get the program from the GitHub repository at <a href="https://github.com/dapogon/cellcoal" class="uri">https://github.com/dapogon/cellcoal</a>. Under the Code tab you will see a section call <em>release</em>. Click on it download the source code in .zip (or tar.gz) format. Then unzip the <em>cellcoal-x.y.z.zip</em> file (for example, cellcoal-1.0.0.zip). You should see now a folder called <em>cellcoal-x.y.z</em>.Move into the folder to compile and run the program.</p></li>
 <li><p><strong>Compile</strong>: type <code>make</code>. The program should compile without much problem in Linux/MacOSX. A Makefile is provided for the gcc compiler. The executable file will be located in the bin folder.</p></li>
-<li><p><strong>Run</strong>: type <code>./cellcoal</code>. In this case, the program arguments will be read from a file called <em>parameters</em>. Alternatively, arguments can be entered directly in the command line.</p></li>
+<li><p><strong>Run</strong>: type <code>./cellcoal</code>. In this case, the program arguments will be read from a file called <em>parameters</em>. Alternatively, arguments can be entered directly in the command line, or from a specific parameter file with a different name.</p></li>
 <li><p><strong>Inspect results</strong>: Once the run is finished, different output files will be written inside a folder called <em>results</em>.</p></li>
 </ol>
 </div>
@@ -338,6 +338,8 @@ <h1>4. Basic usage</h1>
 <p>If no arguments are passed in the command line, CellCoal will look for a file called <em>parameters</em> in the current working directory:</p>
 <p><code>./cellcoal</code></p>
 <p>The <em>parameters</em> file is a text file that contains the different arguments for the program. The arguments correspond to different letters whose case (uppercase or lowercase) makes a difference. Comments within brackets are allowed. To avoid unexpected problems, users are encouraged to maintain the same order of the arguments as in the example files. For clarity, the example parameters files are divided in different blocks or sections including related arguments.</p>
+<p>Alternatively, users can specify their own parameter file <strong>(option -F)</strong>, for example:</p>
+<p><code>./ cellcoal -Fmyparameters.txt</code></p>
 <p>Otherwise, CellCoal will run under the arguments specified in the command line, using default values for the absent arguments:</p>
 <p><code>./ cellcoal -n100 -s20 -l1000 -e10000 -g1.0e-04 -k1 -i1 -b1 -j250 -p0.0 -f0.3 0.2 0.2 0.3 -r0.00 0.03 0.12 0.04 0.11 0.00 0.02 0.68 0.68 0.02 0.00 0.11 0.04 0.12 0.03 0.00 -1 -2 -3 -4 -6 -9 -v -x -#200011</code></p>
 <p>A brief usage guide plus the current default values for the different parameters can be obtained with the argument -h:</p>
@@ -903,6 +905,11 @@ <h2>6.6 Other options</h2>
 <p><strong>-##: seed</strong></p>
 <p>Seed for the random number generator. If no seed is specified, the current time will be used as seed.</p>
 </div>
+<div id="parameter-file-name-at-the-command-line" class="section level2">
+<h2>6.7 Parameter file name at the command line</h2>
+<p>By default, the parameter file is called <em>parameters</em>. Alternatively, the user can indicate the name of the parameter file name at the command line with the <strong>option -F</strong>, like this:</p>
+<p><code>./cellcoal -Fmyparameterfile.txt</code></p>
+</div>
 </div>
 <div id="default-settings" class="section level1">
 <h1>7. Default settings</h1>