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diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html index ed7975e..3b64c6e 100644 --- a/docs/reference/PELMO_runs.html +++ b/docs/reference/PELMO_runs.html @@ -150,30 +150,60 @@ the period.plm file generated by the FOCUS PELMO GUI.</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <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> + <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 +#> 219.860 0.960 55.449 </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> </div> <div class="col-md-3 hidden-xs hidden-sm" 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