Correct psm file in the example with metabolites

10 files changed, 613 insertions, 7 deletions

diff --git a/ChangeLog b/ChangeLog
index 6923efa..9cb0481 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,18 @@
+commit 39d202b0a0f833c756bc98fb4961483de1b15353
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2017-01-30 16:14:15 +0100
+
+    Ignore windows binary builds in git and in R package
+
+commit e6bb9654679f43af6958d6e28cb5206abb91d574
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2017-01-30 16:10:30 +0100
+
+    Test reproducing the FOCUS Summary information
+    
+    generated from the FOCUS PELMO GUI, as copied into the text files
+    in the testdata directory.
+
 commit 80b451ddb4e749041c2b216603274a012dc83d59
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Date:   2017-01-30 14:28:23 +0100
diff --git a/R/PELMO_runs.R b/R/PELMO_runs.R
index 3d4f03b..e5a78ff 100644
--- a/R/PELMO_runs.R
+++ b/R/PELMO_runs.R
@@ -12,7 +12,7 @@
 #' run directory, holding the results for all FOCUS periods, equivalent to
 #' the period.plm file generated by the FOCUS PELMO GUI.
 #'
-#' @return If evaluate is TRUE, a list of lists of data frames holding the
+#' @return If evaluate is TRUE, a list of lists of matrices holding the
 #'   PEC data.
 #' @param runs 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,
@@ -29,7 +29,31 @@
 #' @references PELMO.installeR \url{https://jranke.github.io/PELMO.installeR}
 #'
 #' Wine \url{https://winehq.org}
+#'
+#' PELMO test results \url{http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/gw/models/pelmo/test-results/test_results_FOCUS_PELMO_5_5_3.doc}
 #' @export
+#' @examples
+#' # Reproduce the official test results for annual application of Pesticide D
+#' # to winter cereals at the day before emergence
+#' runs_1 <- list(
+#'   list(psm = 'Pesticide_D',
+#'        win = c("Cha", "Ham", "Jok", "Kre", "Oke", "Pia", "Por", "Sev", "Thi")),
+#'   list(psm = 'Pesticide_D_1_day_pre_em_every_third_year',
+#'        pot = c("Cha", "Ham", "Jok", "Kre", "Oke", "Pia", "Por", "Sev", "Thi")))
+#' time_1 <- system.time(
+#'   PECgw_1 <- PELMO_runs(runs_1, psm_dir = system.file("testdata", package = "pfm"),
+#'     cores = 6, overwrite = TRUE)
+#' )
+#' print(PECgw_1)
+#' # We get exactly the same PECgw values (on Linux, calling PELMO using Wine).
+#' print(time_1)
+#'
+#' # Demonstrate some results with metabolites.
+#' runs_2 <- list(list(psm = 'Pesticide_D_1_May_every_other_year_mets',
+#'                     win = c("Cha", "Ham", "Kre")))
+#' PECgw_2 <- PELMO_runs(runs_2, psm_dir = system.file("testdata", package = "pfm"),
+#'   cores = 3, overwrite = TRUE)
+#' print(PECgw_2)
 PELMO_runs <- function(runs, psm_dir = ".", version = "5.5.3", PELMO_base = "auto",
                        execute = TRUE, cores = getOption("mc.cores", 2L),
                        evaluate = TRUE, overwrite = FALSE)
@@ -142,13 +166,11 @@ PELMO_runs <- function(runs, psm_dir = ".", version = "5.5.3", PELMO_base = "aut
     # the exe file from this directory
     file.copy(file.path(PELMO_base, "lf90.eer"), run_dir)
   }
-  run_list[[7]]
-  setup_run(run_list[[7]])
 
   lapply(run_list, setup_run)
 
   if (execute) {
-    run_PELMO(runs, version = version, PELMO_base = PELMO_base)
+    run_PELMO(runs, version = version, PELMO_base = PELMO_base, cores = cores)
   }
 
   if (evaluate) {
diff --git a/README.md b/README.md
index 3e7c869..98529e6 100644
--- a/README.md
+++ b/README.md
@@ -41,3 +41,5 @@ One recent nice example of the usage of this package is the visualisation
 of a time weighted average for a sawtooth curve obtained from several overlays
 of mkinfit predictions as shown [here](http://jranke.github.io/pfm/reference/plot.one_box.html).
 
+Another, even more recent example shows how FOCUS PELMO can be run in parallel under Linux
+as shown [here](http://jranke.github.io/pfm/reference/PELMO_runs.html).
diff --git a/docs/index.html b/docs/index.html
index db22eb0..0c53fe9 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -75,6 +75,7 @@ this program. If not, see &lt;http:<span class="er">//</span>www.gnu.org/license
 <h2 class="hasAnchor">
 <a href="#examples" class="anchor"> </a>Examples</h2>
 <p>One recent nice example of the usage of this package is the visualisation of a time weighted average for a sawtooth curve obtained from several overlays of mkinfit predictions as shown <a href="http://jranke.github.io/pfm/reference/plot.one_box.html">here</a>.</p>
+<p>Another, even more recent example shows how FOCUS PELMO can be run in parallel under Linux as shown <a href="http://jranke.github.io/pfm/reference/PELMO_runs.html">here</a>.</p>
 </div>
 </div>
   </div>
diff --git a/docs/reference/PELMO_path.html b/docs/reference/PELMO_path.html
index 79aa89d..ab24341 100644
--- a/docs/reference/PELMO_path.html
+++ b/docs/reference/PELMO_path.html
@@ -73,7 +73,7 @@
     <p>Create a path of run directories as the PELMO GUI does</p>
     
 
-    <pre><span class='fu'>PELMO_path</span>(<span class='no'>psm</span>, <span class='no'>crop</span>, <span class='no'>scenario</span>)</pre>
+    <pre><span class='fu'>PELMO_path</span>(<span class='no'>psm</span>, <span class='no'>crop</span>, <span class='kw'>scenario</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
     <dl class="dl-horizontal">
diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html
index 03b7b7b..e299b7c 100644
--- a/docs/reference/PELMO_runs.html
+++ b/docs/reference/PELMO_runs.html
@@ -112,20 +112,93 @@ as used in <code><a href='FOCUS_GW_scenarios_2012.html'>FOCUS_GW_scenarios_2012<
       <dd>Should an existing run directories be overwritten</dd>
     </dl>
     
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>If evaluate is TRUE, a list of lists of matrices holding the
+  PEC data.</p>
+    
+    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+    <p>As a side effect, an R data file (period_pfm.rda) is generated in each
+run directory, holding the results for all FOCUS periods, equivalent to
+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>
     
 
+    <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'>&lt;-</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'>&lt;-</span> <span class='fu'>system.time</span>(
+  <span class='no'>PECgw_1</span> <span class='kw'>&lt;-</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'>#&gt; $Pesticide_D
+#&gt; $Pesticide_D$win
+#&gt;     FOCUS DUMMY D
+#&gt; Cha         0.025
+#&gt; Ham         1.621
+#&gt; Jok         0.388
+#&gt; Kre         0.467
+#&gt; Oke         1.608
+#&gt; Pia         0.848
+#&gt; Por         2.386
+#&gt; Sev         0.009
+#&gt; Thi         0.030
+#&gt; 
+#&gt; 
+#&gt; $Pesticide_D_1_day_pre_em_every_third_year
+#&gt; $Pesticide_D_1_day_pre_em_every_third_year$pot
+#&gt;     FOCUS DUMMY D
+#&gt; Cha         0.010
+#&gt; Ham         0.014
+#&gt; Jok         0.009
+#&gt; Kre         0.027
+#&gt; Oke         0.085
+#&gt; Pia         0.051
+#&gt; Por         0.021
+#&gt; Sev         0.000
+#&gt; Thi         0.001
+#&gt; 
+#&gt; </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'>#&gt;        User      System verstrichen 
+#&gt;     231.892       0.496      57.056 </div><div class='input'>
+<span class='co'># Demonstrate some results with metabolites.</span>
+<span class='no'>runs_2</span> <span class='kw'>&lt;-</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'>&lt;-</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'>#&gt; $Pesticide_D_1_May_every_other_year_mets
+#&gt; $Pesticide_D_1_May_every_other_year_mets$win
+#&gt;     FOCUS DUMMY D      M1    M2
+#&gt; Cha         0.001 126.195 0.000
+#&gt; Ham         0.054  82.196 0.001
+#&gt; Kre         0.103  75.494 0.001
+#&gt; 
+#&gt; </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
     <ul class="nav nav-pills nav-stacked">
       <li><a href="#arguments">Arguments</a></li>
       
+      <li><a href="#value">Value</a></li>
+
+      <li><a href="#details">Details</a></li>
+
       <li><a href="#references">References</a></li>
-          </ul>
+      
+      <li><a href="#examples">Examples</a></li>
+    </ul>
 
   </div>
 </div>
diff --git a/inst/testdata/Pesticide_D.psm b/inst/testdata/Pesticide_D.psm
new file mode 100644
index 0000000..8204f3c
--- /dev/null
+++ b/inst/testdata/Pesticide_D.psm
@@ -0,0 +1,68 @@
+<COMMENT>
+Pesticide D, 1 day before emergence     <FOCUS DUMMY D>
+<END COMMENT>
+<NUMBER OF SOIL HORIZONS>
+ 0 
+<END NUMBER OF SOIL HORIZONS>
+<APPLICATION>
+ 1    0    9    <number of locations absolute app/relative app>
+026            <number of application location>
+-01  00  01   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  02   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  03   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  04   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  05   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  06   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  07   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  08   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  09   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  10   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  11   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  12   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  13   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  14   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  15   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  16   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  17   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  18   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  19   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  20   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  21   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  22   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  23   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  24   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  25   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  26   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+ 1    <pesticide appl. flag: 1=soil 2 =linear 3=exp. foliar 4=manually
+<END APPLICATION>
+<FLAGS>
+ 1   1   <henry(0=direct 1=calc.)  kd_flag(0=direct 1=calc.)>
+<END FLAGS>
+<VOLATILIZATION>
+<henry       solub.      molmass     vap.press   diff air    depth volat.  Hv        Temperature>
+  3.33E-04   90    300     1.00E-04   0.0498    0.1    98400    20 
+  6.67E-10   180    300     4.00E-04   0.0498    0.1    98400    30 
+<END VOLATILIZATION>
+<PLANT UPTAKE>
+ 0.5      <plant uptake factor
+<END PLANT UPTAKE>
+<DEGRADATION>
+<degrate    degtemp     q10         moist-abs   moist-rel   moist-exp   rel deg neq sites
+  0.00E+00   0           0           0           0           0         0        <Met A1>
+  0.00E+00   20          2           19          0           0         0        <Met B1>
+  0.00E+00   20          2           19          0           0         0        <Met C1>
+  0.00E+00   20          2           19          0           0         0        <Met D1>
+ 0.0346570   20          2.2         0           100         0.7       0        <BR/CO2>
+ 0                 <0 = degradation according to degradation factors, 1 = constant with depth,2 individual,3 = degradation according to degradation factors, 4 = constant with depth,5 individual, >2 deg in liquid phase only)
+<PHOTODEGRADATION>
+<rate 1/n>  <I_Ref W/mē>
+ 0   500  0   0  0   0  0   0  0   0 
+<END DEGRADATION>
+<ADSORPTION>
+<Koc-value    Fr.exp.Koc  pH          pKa     limit for Freundl.  ann.incr.> <k_doc> <% change> KOC2      pH2 f_neq       kdes>
+ 60          0.9        -99          20          0                0      0     1    -99    -99     0     0 
+<END ADSORPTION>
+<DEPTH DEPENDENT SORPTION AND TRANSFORMATION VALUES>
+<Kd          Fr.exp.     Met A1   Met B1   Met C1   Met D1   BR/CO2 >
+<END DEPTH DEPENDENT>
+<END PSM>
diff --git a/inst/testdata/Pesticide_D_1_May_every_other_year_mets.psm b/inst/testdata/Pesticide_D_1_May_every_other_year_mets.psm
new file mode 100644
index 0000000..cf91533
--- /dev/null
+++ b/inst/testdata/Pesticide_D_1_May_every_other_year_mets.psm
@@ -0,0 +1,336 @@
+<COMMENT>
+Pesticide D, 1 May C H every other year     <FOCUS DUMMY D>
+<END COMMENT>
+<NUMBER OF SOIL HORIZONS>
+ 0 
+<END NUMBER OF SOIL HORIZONS>
+<APPLICATION>
+ 10    0    0    <number of locations absolute app/relative app>
+022            <number of application location>
+01  01  01   0    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  01  02   0    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  01  03   0    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  01  04   0    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  01  05   0    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  01  06   0    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  01  07   0    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  01  08   0    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  01  09   0    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  01  10   0    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  01  11   0    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  01  12   0    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  01  13   0    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  01  14   0    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  01  15   0    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  01  16   0    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  01  17   0    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  01  18   0    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  01  19   0    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  01  20   0    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  01  21   0    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  01  22   0    0    0    0    0   <day month year app_rate app_depth frpex time>
+023         C   <number of application location>
+01  05  01   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  03   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  05   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  07   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  09   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  11   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  13   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  15   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  17   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  19   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  21   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  23   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  25   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  27   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  29   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  31   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  33   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  35   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  37   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  39   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  41   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  43   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  45   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+023         H   <number of application location>
+01  05  01   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  03   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  05   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  07   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  09   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  11   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  13   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  15   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  17   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  19   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  21   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  23   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  25   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  27   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  29   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  31   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  33   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  35   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  37   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  39   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  41   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  43   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  45   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+023         J   <number of application location>
+01  05  01   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  03   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  05   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  07   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  09   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  11   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  13   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  15   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  17   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  19   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  21   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  23   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  25   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  27   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  29   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  31   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  33   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  35   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  37   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  39   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  41   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  43   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  45   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+023         K   <number of application location>
+01  05  01   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  03   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  05   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  07   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  09   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  11   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  13   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  15   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  17   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  19   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  21   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  23   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  25   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  27   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  29   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  31   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  33   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  35   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  37   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  39   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  41   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  43   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  45   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+023         N   <number of application location>
+01  05  01   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  03   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  05   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  07   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  09   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  11   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  13   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  15   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  17   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  19   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  21   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  23   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  25   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  27   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  29   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  31   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  33   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  35   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  37   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  39   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  41   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  43   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  45   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+023         P   <number of application location>
+01  05  01   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  03   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  05   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  07   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  09   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  11   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  13   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  15   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  17   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  19   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  21   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  23   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  25   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  27   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  29   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  31   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  33   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  35   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  37   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  39   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  41   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  43   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  45   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+023         O   <number of application location>
+01  05  01   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  03   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  05   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  07   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  09   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  11   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  13   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  15   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  17   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  19   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  21   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  23   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  25   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  27   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  29   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  31   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  33   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  35   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  37   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  39   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  41   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  43   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  45   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+023         S   <number of application location>
+01  05  01   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  03   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  05   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  07   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  09   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  11   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  13   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  15   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  17   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  19   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  21   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  23   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  25   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  27   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  29   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  31   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  33   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  35   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  37   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  39   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  41   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  43   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  45   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+023         T   <number of application location>
+01  05  01   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  03   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  05   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  07   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  09   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  11   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  13   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  15   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  17   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  19   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  21   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  23   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  25   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  27   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  29   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  31   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  33   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  35   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  37   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  39   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  41   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  43   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+01  05  45   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+ 1    <pesticide appl. flag: 1=soil 2 =linear 3=exp. foliar 4=manually
+<END APPLICATION>
+<FLAGS>
+ 1   1   <henry(0=direct 1=calc.)  kd_flag(0=direct 1=calc.)>
+<END FLAGS>
+<VOLATILIZATION>
+<henry       solub.      molmass     vap.press   diff air    depth volat.  Hv        Temperature>
+  3.33E-04   90    300     1.00E-04   0.0498    0.1    98400    20 
+  6.67E-10   180    300     4.00E-04   0.0498    0.1    98400    30 
+<END VOLATILIZATION>
+<PLANT UPTAKE>
+ 0.5      <plant uptake factor
+<END PLANT UPTAKE>
+<DEGRADATION>
+<degrate    degtemp     q10         moist-abs   moist-rel   moist-exp   rel deg neq sites
+ 0.0277260   20          2.2         0           100         0.7       0        <Met A1>
+ 0.0069310   20          2.2         0           100         0.7       0        <Met B1>
+  0.00E+00   20          2           19          0           0         0        <Met C1>
+  0.00E+00   20          2           19          0           0         0        <Met D1>
+  0.00E+00   20          2.2         0           100         0.7       0        <BR/CO2>
+ 0                 <0 = degradation according to degradation factors, 1 = constant with depth,2 individual,3 = degradation according to degradation factors, 4 = constant with depth,5 individual, >2 deg in liquid phase only)
+<PHOTODEGRADATION>
+<rate 1/n>  <I_Ref W/mē>
+ 0   500  0   0  0   0  0   0  0   0 
+<END DEGRADATION>
+<ADSORPTION>
+<Koc-value    Fr.exp.Koc  pH          pKa     limit for Freundl.  ann.incr.> <k_doc> <% change> KOC2      pH2 f_neq       kdes>
+ 60          0.9        -99          20          0                0      0     1    -99    -99     0     0 
+<END ADSORPTION>
+<DEPTH DEPENDENT SORPTION AND TRANSFORMATION VALUES>
+<Kd          Fr.exp.     Met A1   Met B1   Met C1   Met D1   BR/CO2 >
+<END DEPTH DEPENDENT>
+###############################################
+<COMMENT>
+METABOLITE A1     M1
+<END COMMENT>
+<FLAGS>
+ 1   <kd_flag(0=direct 1=calc.)>
+<END FLAGS>
+<MOLMASS>
+ 200 
+<END MOLMASS>
+<PLANT UPTAKE>
+ 0      <plant uptake factor>
+<END PLANT UPTAKE>
+<DEGRADATION>
+<degrate    degtemp     q10         moist-abs   moist-rel   moist-exp  <rel deg in neq sites>
+  0.00E+00   20          2.58        0           100         0.7       0        <Met B1>
+  0.00E+00   20          2.58        0           100         0.7       0        <Met A2>
+  0.00E+00   20          2.58        0           100         0.7       0        <Met B2>
+ 0.0023100   20          2.2         0           100         0.7       0        <BR/CO2>
+ 0                 <0 = degradation according to degradation factors, 1 = constant with depth,2 individual,3 = degradation according to degradation factors, 4 = constant with depth,5 individual, >2 deg in liquid phase only)
+<END DEGRADATION>
+<ADSORPTION>
+<Koc-value    Fr.exp.Koc  pH          pKa     limit for Freundl.  ann.incr.> <k_doc> <% change> KOC2      pH2    f_neq       kdes>
+10          0.9         -99          20         0.01              0      0     1    -99    -99     0     0 
+<END ADSORPTION>
+<DEPTH DEPENDENT SORPTION AND TRANSFORMATION VALUES>
+<Kd          Fr.exp.     Met B1   Met A2   Met B2   BR/CO2 >
+<END DEPTH DEPENDENT>
+###############################################
+<COMMENT>
+METABOLITE B1     M2
+<END COMMENT>
+<FLAGS>
+ 1   <kd_flag(0=direct 1=calc.)>
+<END FLAGS>
+<MOLMASS>
+ 200 
+<END MOLMASS>
+<PLANT UPTAKE>
+ 0      <plant uptake factor>
+<END PLANT UPTAKE>
+<DEGRADATION>
+<degrate    degtemp     q10         moist-abs   moist-rel   moist-exp  <rel deg in neq sites>
+  0.00E+00   20          2.58        0           100         0.7       0        <Met C1>
+  0.00E+00   20          2.58        0           100         0.7       0        <Met B2>
+  0.00E+00   20          2.58        0           100         0.7       0        <Met C2>
+ 0.0693150   20          2.2         0           100         0.7       0        <BR/CO2>
+ 0                 <0 = degradation according to degradation factors, 1 = constant with depth,2 individual,3 = degradation according to degradation factors, 4 = constant with depth,5 individual, >2 deg in liquid phase only)
+<END DEGRADATION>
+<ADSORPTION>
+<Koc-value    Fr.exp.Koc  pH          pKa     limit for Freundl.  ann.incr.> <k_doc> <% change> KOC2      pH2    f_neq       kdes>
+1000        0.9         -99          20         0.01              0      0     1    -99    -99     0     0 
+<END ADSORPTION>
+<DEPTH DEPENDENT SORPTION AND TRANSFORMATION VALUES>
+<Kd          Fr.exp.     Met C1   Met B2   Met C2   BR/CO2 >
+<END DEPTH DEPENDENT>
+<END PSM>
diff --git a/inst/testdata/Pesticide_D_1_day_pre_em_every_third_year.psm b/inst/testdata/Pesticide_D_1_day_pre_em_every_third_year.psm
new file mode 100644
index 0000000..c6f5945
--- /dev/null
+++ b/inst/testdata/Pesticide_D_1_day_pre_em_every_third_year.psm
@@ -0,0 +1,64 @@
+<COMMENT>
+Pesticide D, 1 day before emergence     <FOCUS DUMMY D>
+<END COMMENT>
+<NUMBER OF SOIL HORIZONS>
+ 0 
+<END NUMBER OF SOIL HORIZONS>
+<APPLICATION>
+ 1    0    9    <number of locations absolute app/relative app>
+022            <number of application location>
+-01  00  01   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  04   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  07   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  10   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  13   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  16   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  19   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  22   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  25   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  28   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  31   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  34   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  37   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  40   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  43   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  46   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  49   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  52   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  55   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  58   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  61   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+-01  00  64   1    0    0    0    0   <day month year app_rate app_depth frpex time>
+ 1    <pesticide appl. flag: 1=soil 2 =linear 3=exp. foliar 4=manually
+<END APPLICATION>
+<FLAGS>
+ 1   1   <henry(0=direct 1=calc.)  kd_flag(0=direct 1=calc.)>
+<END FLAGS>
+<VOLATILIZATION>
+<henry       solub.      molmass     vap.press   diff air    depth volat.  Hv        Temperature>
+  3.33E-04   90    300     1.00E-04   0.0498    0.1    98400    20 
+  6.67E-10   180    300     4.00E-04   0.0498    0.1    98400    30 
+<END VOLATILIZATION>
+<PLANT UPTAKE>
+ 0.5      <plant uptake factor
+<END PLANT UPTAKE>
+<DEGRADATION>
+<degrate    degtemp     q10         moist-abs   moist-rel   moist-exp   rel deg neq sites
+  0.00E+00   0           0           0           0           0         0        <Met A1>
+  0.00E+00   20          2           19          0           0         0        <Met B1>
+  0.00E+00   20          2           19          0           0         0        <Met C1>
+  0.00E+00   20          2           19          0           0         0        <Met D1>
+ 0.0346570   20          2.2         0           100         0.7       0        <BR/CO2>
+ 0                 <0 = degradation according to degradation factors, 1 = constant with depth,2 individual,3 = degradation according to degradation factors, 4 = constant with depth,5 individual, >2 deg in liquid phase only)
+<PHOTODEGRADATION>
+<rate 1/n>  <I_Ref W/mē>
+ 0   500  0   0  0   0  0   0  0   0 
+<END DEGRADATION>
+<ADSORPTION>
+<Koc-value    Fr.exp.Koc  pH          pKa     limit for Freundl.  ann.incr.> <k_doc> <% change> KOC2      pH2 f_neq       kdes>
+ 60          0.9        -99          20          0                0      0     1    -99    -99     0     0 
+<END ADSORPTION>
+<DEPTH DEPENDENT SORPTION AND TRANSFORMATION VALUES>
+<Kd          Fr.exp.     Met A1   Met B1   Met C1   Met D1   BR/CO2 >
+<END DEPTH DEPENDENT>
+<END PSM>
diff --git a/man/PELMO_runs.Rd b/man/PELMO_runs.Rd
index 60519bd..ce5c7af 100644
--- a/man/PELMO_runs.Rd
+++ b/man/PELMO_runs.Rd
@@ -37,7 +37,7 @@ as used in \code{\link{FOCUS_GW_scenarios_2012}}.}
 \item{overwrite}{Should an existing run directories be overwritten}
 }
 \value{
-If evaluate is TRUE, a list of lists of data frames holding the
+If evaluate is TRUE, a list of lists of matrices holding the
   PEC data.
 }
 \description{
@@ -54,8 +54,33 @@ As a side effect, an R data file (period_pfm.rda) is generated in each
 run directory, holding the results for all FOCUS periods, equivalent to
 the period.plm file generated by the FOCUS PELMO GUI.
 }
+\examples{
+# Reproduce the official test results for annual application of Pesticide D
+# to winter cereals at the day before emergence
+runs_1 <- list(
+  list(psm = 'Pesticide_D',
+       win = c("Cha", "Ham", "Jok", "Kre", "Oke", "Pia", "Por", "Sev", "Thi")),
+  list(psm = 'Pesticide_D_1_day_pre_em_every_third_year',
+       pot = c("Cha", "Ham", "Jok", "Kre", "Oke", "Pia", "Por", "Sev", "Thi")))
+time_1 <- system.time(
+  PECgw_1 <- PELMO_runs(runs_1, psm_dir = system.file("testdata", package = "pfm"),
+    cores = 6, overwrite = TRUE)
+)
+print(PECgw_1)
+# We get exactly the same PECgw values (on Linux, calling PELMO using Wine).
+print(time_1)
+
+# Demonstrate some results with metabolites.
+runs_2 <- list(list(psm = 'Pesticide_D_1_May_every_other_year_mets',
+                    win = c("Cha", "Ham", "Kre")))
+PECgw_2 <- PELMO_runs(runs_2, psm_dir = system.file("testdata", package = "pfm"),
+  cores = 3, overwrite = TRUE)
+print(PECgw_2)
+}
 \references{
 PELMO.installeR \url{https://jranke.github.io/PELMO.installeR}
 
 Wine \url{https://winehq.org}
+
+PELMO test results \url{http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/gw/models/pelmo/test-results/test_results_FOCUS_PELMO_5_5_3.doc}
 }