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Diffstat (limited to 'docs/reference/PELMO_runs.html')
| -rw-r--r-- | docs/reference/PELMO_runs.html | 33 |
1 files changed, 27 insertions, 6 deletions
diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html index 3d70c32..1c2aabe 100644 --- a/docs/reference/PELMO_runs.html +++ b/docs/reference/PELMO_runs.html @@ -18,12 +18,25 @@ <!-- Font Awesome icons --> <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> <script src="../jquery.sticky-kit.min.js"></script> <script src="../pkgdown.js"></script> + + +<meta property="og:title" content="Set up runs for FOCUS PELMO — PELMO_runs" /> +<meta property="og:description" content="Per default, the runs are not only set up but also executed with FOCUS +PELMO, the results are processed and returned. Currently, only FOCUS PELMO +as installed on Linux (or other Unix systems) +using the install_PELMO from the PELMO.installeR package +maintained on github is supported. In such installations, FOCUS PELMO is +installed into the package installation directory of PELMO.installeR +and run using wine." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -51,6 +64,12 @@ <div id="navbar" class="navbar-collapse collapse"> <ul class="nav navbar-nav"> <li> + <a href="../index.html"> + <span class="fa fa-home fa-lg"></span> + + </a> +</li> +<li> <a href="../reference/index.html">Reference</a> </li> </ul> @@ -144,9 +163,9 @@ the period.plm file generated by the FOCUS PELMO GUI.</p> <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> - <p>PELMO.installeR <a href = 'https://pkgdown.jrwb.de/PELMO.installeR'>https://pkgdown.jrwb.de/PELMO.installeR</a></p> -<p>Wine <a href = 'https://winehq.org'>https://winehq.org</a></p> -<p>PELMO test results <a href = 'http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/gw/models/pelmo/test-results/test_results_FOCUS_PELMO_5_5_3.doc'>http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/gw/models/pelmo/test-results/test_results_FOCUS_PELMO_5_5_3.doc</a></p> + <p>PELMO.installeR <a href='https://pkgdown.jrwb.de/PELMO.installeR'>https://pkgdown.jrwb.de/PELMO.installeR</a></p> +<p>Wine <a href='https://winehq.org'>https://winehq.org</a></p> +<p>PELMO test results <a href='http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/gw/models/pelmo/test-results/test_results_FOCUS_PELMO_5_5_3.doc'>http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/gw/models/pelmo/test-results/test_results_FOCUS_PELMO_5_5_3.doc</a></p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> @@ -159,7 +178,7 @@ the period.plm file generated by the FOCUS PELMO GUI.</p> <span class='kw'>pot</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Cha"</span>, <span class='st'>"Ham"</span>, <span class='st'>"Jok"</span>, <span class='st'>"Kre"</span>, <span class='st'>"Oke"</span>, <span class='st'>"Pia"</span>, <span class='st'>"Por"</span>, <span class='st'>"Sev"</span>, <span class='st'>"Thi"</span>))) <span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'>system.time</span>( <span class='no'>PECgw_1</span> <span class='kw'><-</span> <span class='fu'>PELMO_runs</span>(<span class='no'>runs_1</span>, <span class='kw'>psm_dir</span> <span class='kw'>=</span> <span class='fu'>system.file</span>(<span class='st'>"testdata"</span>, <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>), - <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>6</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>15</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) ) <span class='fu'>print</span>(<span class='no'>PECgw_1</span>)</div><div class='output co'>#> $Pesticide_D #> $Pesticide_D$win @@ -190,7 +209,9 @@ the period.plm file generated by the FOCUS PELMO GUI.</p> #> #> </div><div class='input'><span class='co'># We get exactly the same PECgw values (on Linux, calling PELMO using Wine).</span> <span class='fu'>print</span>(<span class='no'>time_1</span>)</div><div class='output co'>#> User System verstrichen -#> 218.536 1.056 55.555 </div><div class='input'> +#> 220.760 1.509 30.234 </div><div class='input'><span class='kw'>if</span>(!<span class='fu'>inherits</span>(<span class='fu'>try</span>(<span class='no'>cpuinfo</span> <span class='kw'><-</span> <span class='fu'>readLines</span>(<span class='st'>"/proc/cpuinfo"</span>)), <span class='st'>"try-error"</span>)) { + <span class='fu'>cat</span>(<span class='fu'>gsub</span>(<span class='st'>"model name\t: "</span>, <span class='st'>"CPU model: "</span>, <span class='no'>cpuinfo</span>[<span class='fu'>grep</span>(<span class='st'>"model name"</span>, <span class='no'>cpuinfo</span>)[<span class='fl'>1</span>]])) +}</div><div class='output co'>#> CPU model: AMD Ryzen 7 1700 Eight-Core Processor</div><div class='input'> <span class='co'># Demonstrate some results with metabolites.</span> <span class='no'>runs_2</span> <span class='kw'><-</span> <span class='fu'>list</span>(<span class='fu'>list</span>(<span class='kw'>psm</span> <span class='kw'>=</span> <span class='st'>'Pesticide_D_1_May_every_other_year_mets'</span>, <span class='kw'>win</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Cha"</span>, <span class='st'>"Ham"</span>, <span class='st'>"Kre"</span>))) @@ -228,7 +249,7 @@ the period.plm file generated by the FOCUS PELMO GUI.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> </div> </footer> |