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Diffstat (limited to 'docs/reference/PELMO_runs.html')
| -rw-r--r-- | docs/reference/PELMO_runs.html | 143 |
1 files changed, 66 insertions, 77 deletions
diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html index 4b7f7fb..7fcbba8 100644 --- a/docs/reference/PELMO_runs.html +++ b/docs/reference/PELMO_runs.html @@ -25,12 +25,14 @@ <script src="../pkgdown.js"></script> <!-- mathjax --> -<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> <!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--> + + </head> <body> @@ -79,7 +81,7 @@ installed into the package installation directory of <code>PELMO.installeR</code and run using <code>wine</code>.</p> - <pre><span class='fu'>PELMO_runs</span>(<span class='no'>runs</span>, <span class='kw'>psm_dir</span> <span class='kw'>=</span> <span class='st'>"."</span>, <span class='kw'>version</span> <span class='kw'>=</span> <span class='st'>"5.5.3"</span>, <span class='kw'>PELMO_base</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <pre class="usage"><span class='fu'>PELMO_runs</span>(<span class='no'>runs</span>, <span class='kw'>psm_dir</span> <span class='kw'>=</span> <span class='st'>"."</span>, <span class='kw'>version</span> <span class='kw'>=</span> <span class='st'>"5.5.3"</span>, <span class='kw'>PELMO_base</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>execute</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'>getOption</span>(<span class='st'>"mc.cores"</span>, <span class='fl'>2L</span>), <span class='kw'>evaluate</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) @@ -89,28 +91,45 @@ and run using <code>wine</code>.</p> <span class='fu'>evaluate_PELMO</span>(<span class='no'>runs</span>, <span class='kw'>version</span> <span class='kw'>=</span> <span class='st'>"5.5.3"</span>, <span class='kw'>PELMO_base</span> <span class='kw'>=</span> <span class='st'>"auto"</span>)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> - <dl class="dl-horizontal"> - <dt>runs</dt> - <dd>A list of lists. Each inner lists has an element named 'psm' + <table class="ref-arguments"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>runs</th> + <td><p>A list of lists. Each inner lists has an element named 'psm' that holds the psm string, and elements named using three letter crop acronyms, as used in <code><a href='FOCUS_PELMO_crops.html'>FOCUS_PELMO_crops</a></code>, that hold character vectors of three letter scenario acronyms -as used in <code><a href='FOCUS_GW_scenarios_2012.html'>FOCUS_GW_scenarios_2012</a></code>.</dd> - <dt>psm_dir</dt> - <dd>The directory where the psm files are located</dd> - <dt>version</dt> - <dd>The FOCUS PELMO version</dd> - <dt>PELMO_base</dt> - <dd>Where the FOCUS PELMO installation is located</dd> - <dt>execute</dt> - <dd>Should PELMO be executed directly?</dd> - <dt>cores</dt> - <dd>The number of cores to execute PELMO runs in parallel</dd> - <dt>evaluate</dt> - <dd>Should the results be returned?</dd> - <dt>overwrite</dt> - <dd>Should existing run directories be overwritten?</dd> - </dl> +as used in <code><a href='FOCUS_GW_scenarios_2012.html'>FOCUS_GW_scenarios_2012</a></code>.</p></td> + </tr> + <tr> + <th>psm_dir</th> + <td><p>The directory where the psm files are located</p></td> + </tr> + <tr> + <th>version</th> + <td><p>The FOCUS PELMO version</p></td> + </tr> + <tr> + <th>PELMO_base</th> + <td><p>Where the FOCUS PELMO installation is located</p></td> + </tr> + <tr> + <th>execute</th> + <td><p>Should PELMO be executed directly?</p></td> + </tr> + <tr> + <th>cores</th> + <td><p>The number of cores to execute PELMO runs in parallel</p></td> + </tr> + <tr> + <th>evaluate</th> + <td><p>Should the results be returned?</p></td> + </tr> + <tr> + <th>overwrite</th> + <td><p>Should existing run directories be overwritten?</p></td> + </tr> + </table> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> @@ -126,65 +145,35 @@ 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://jranke.github.io/PELMO.installeR'>https://jranke.github.io/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>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> - <pre class="examples"><div class='input'><span class='co'># Reproduce the official test results for annual application of Pesticide D</span> -<span class='co'># to winter cereals at the day before emergence</span> -<span class='no'>runs_1</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'</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'>"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='fu'>list</span>(<span class='kw'>psm</span> <span class='kw'>=</span> <span class='st'>'Pesticide_D_1_day_pre_em_every_third_year'</span>, - <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='fu'>print</span>(<span class='no'>PECgw_1</span>)</div><div class='output co'>#> $Pesticide_D -#> $Pesticide_D$win -#> FOCUS DUMMY D -#> Cha 0.025 -#> Ham 1.621 -#> Jok 0.388 -#> Kre 0.467 -#> Oke 1.608 -#> Pia 0.848 -#> Por 2.386 -#> Sev 0.009 -#> Thi 0.030 -#> -#> -#> $Pesticide_D_1_day_pre_em_every_third_year -#> $Pesticide_D_1_day_pre_em_every_third_year$pot -#> FOCUS DUMMY D -#> Cha 0.010 -#> Ham 0.014 -#> Jok 0.009 -#> Kre 0.027 -#> Oke 0.085 -#> Pia 0.051 -#> Por 0.021 -#> Sev 0.000 -#> Thi 0.001 -#> -#> </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 -#> 229.448 0.524 57.021 </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>))) -<span class='no'>PECgw_2</span> <span class='kw'><-</span> <span class='fu'>PELMO_runs</span>(<span class='no'>runs_2</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'>3</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>print</span>(<span class='no'>PECgw_2</span>)</div><div class='output co'>#> $Pesticide_D_1_May_every_other_year_mets -#> $Pesticide_D_1_May_every_other_year_mets$win -#> FOCUS DUMMY D M1 M2 -#> Cha 0.001 126.195 0.000 -#> Ham 0.054 82.196 0.001 -#> Kre 0.103 75.494 0.001 -#> -#> </div></pre> + <pre class="examples"><div class='input'><span class='co'># At the moment I can not run the examples, as my wine installation is not working</span> +<span class='fu'>not_run</span>({ + <span class='co'># Reproduce the official test results for annual application of Pesticide D</span> + <span class='co'># to winter cereals at the day before emergence</span> + <span class='no'>runs_1</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'</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'>"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='fu'>list</span>(<span class='kw'>psm</span> <span class='kw'>=</span> <span class='st'>'Pesticide_D_1_day_pre_em_every_third_year'</span>, + <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='fu'>print</span>(<span class='no'>PECgw_1</span>) + <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>) + + <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>))) + <span class='no'>PECgw_2</span> <span class='kw'><-</span> <span class='fu'>PELMO_runs</span>(<span class='no'>runs_2</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'>3</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='fu'>print</span>(<span class='no'>PECgw_2</span>) +})</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> |