Re-enable PELMO examples and tests

- Add .gitattributes to make sure CRLF line endings are kept for PELMO
.psm files
- Update static docs

17 files changed, 89 insertions, 49 deletions

diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 0000000..d60e817
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1 @@
+inst/testdata/*.psm text eol=crlf
diff --git a/ChangeLog b/ChangeLog
index 6f5775d..f749300 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,15 @@
+commit 539ea37b45ddc41b36dd199f06ffe5936ab13f21
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2017-05-17 12:23:38 +0200
+
+    Documentation fix
+
+commit 62bffd4873bc53fa9cd81336efa716b220c83e0a
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2017-05-17 09:36:22 +0200
+
+    Simplify tests where possible
+
 commit d60bb9c0b52c8e0452bfbe507e60d5f651589cc8
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Date:   2017-05-16 18:57:16 +0200
diff --git a/DESCRIPTION b/DESCRIPTION
index 484970a..fcefaa4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: pfm
 Type: Package
 Title: Utilities for Pesticide Fate Modelling
 Version: 0.4-3
-Date: 2017-05-17
+Date: 2017-05-24
 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", 
                   role = c("aut", "cre", "cph"))
 Description: Utilities for simple calculations of predicted environmental
diff --git a/R/PELMO_runs.R b/R/PELMO_runs.R
index c0d1266..432231e 100644
--- a/R/PELMO_runs.R
+++ b/R/PELMO_runs.R
@@ -33,8 +33,6 @@
 #' 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
-#' # At the moment I can not run the examples, as my wine installation is not working
-#' \dontrun{
 #' # Reproduce the official test results for annual application of Pesticide D
 #' # to winter cereals at the day before emergence
 #' runs_1 <- list(
@@ -56,7 +54,6 @@
 #' 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)
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'>&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>)
-  <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'>&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></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'>&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;     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'>&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>
diff --git a/docs/reference/one_box-2.png b/docs/reference/one_box-2.png
index a43ff32..4788607 100644
--- a/docs/reference/one_box-2.png
+++ b/docs/reference/one_box-2.png
diff --git a/docs/reference/one_box-4.png b/docs/reference/one_box-4.png
index 63d59ff..f7730a4 100644
--- a/docs/reference/one_box-4.png
+++ b/docs/reference/one_box-4.png
diff --git a/docs/reference/one_box-8.png b/docs/reference/one_box-8.png
index 963775a..da3d439 100644
--- a/docs/reference/one_box-8.png
+++ b/docs/reference/one_box-8.png
diff --git a/docs/reference/plot.TOXSWA_cwa-2.png b/docs/reference/plot.TOXSWA_cwa-2.png
index 6f9de30..01737fa 100644
--- a/docs/reference/plot.TOXSWA_cwa-2.png
+++ b/docs/reference/plot.TOXSWA_cwa-2.png
diff --git a/docs/reference/plot.one_box-2.png b/docs/reference/plot.one_box-2.png
index 89b52df..4c6cb92 100644
--- a/docs/reference/plot.one_box-2.png
+++ b/docs/reference/plot.one_box-2.png
diff --git a/docs/reference/plot.one_box-4.png b/docs/reference/plot.one_box-4.png
index eeb88e3..1a1a7c6 100644
--- a/docs/reference/plot.one_box-4.png
+++ b/docs/reference/plot.one_box-4.png
diff --git a/docs/reference/plot.one_box-8.png b/docs/reference/plot.one_box-8.png
index 6998974..aa74981 100644
--- a/docs/reference/plot.one_box-8.png
+++ b/docs/reference/plot.one_box-8.png
diff --git a/docs/reference/sawtooth-2.png b/docs/reference/sawtooth-2.png
index 1270a14..548c87d 100644
--- a/docs/reference/sawtooth-2.png
+++ b/docs/reference/sawtooth-2.png
diff --git a/docs/reference/sawtooth-6.png b/docs/reference/sawtooth-6.png
index 6998974..aa74981 100644
--- a/docs/reference/sawtooth-6.png
+++ b/docs/reference/sawtooth-6.png
diff --git a/man/PELMO_runs.Rd b/man/PELMO_runs.Rd
index a86e0fd..f936d8c 100644
--- a/man/PELMO_runs.Rd
+++ b/man/PELMO_runs.Rd
@@ -55,8 +55,6 @@ run directory, holding the results for all FOCUS periods, equivalent to
 the period.plm file generated by the FOCUS PELMO GUI.
 }
 \examples{
-# At the moment I can not run the examples, as my wine installation is not working
-\dontrun{
 # Reproduce the official test results for annual application of Pesticide D
 # to winter cereals at the day before emergence
 runs_1 <- list(
@@ -79,7 +77,6 @@ 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://pkgdown.jrwb.de/PELMO.installeR}
 
diff --git a/test.log b/test.log
index c94222b..2963aae 100644
--- a/test.log
+++ b/test.log
@@ -13,21 +13,10 @@ Check max_twa for parent mkinfit models against analytical solutions: .
 Simple PEC sediment calculations: .
 Simple PEC soil calculations: ...........
 Simple PEC surface water calculations with drift entry: ..
-Create PELMO runs from psm files and execute them: SSSSS
+Create PELMO runs from psm files and execute them: ...........................................................................................................................................................................................................................
 Actual and time weighted average concentrations for SFO kinetics: .
 FOCUS Step 1 calculations: .........
 Read and analyse TOXSWA cwa files: .......
 UK drainage PEC calculations: ............
 
-Skipped --------------------------------------------------------------------------------------------
-1. PELMO paths are correctly created (@test_PELMO.R#23) - A wine installation is needed for this test
-
-2. PELMO runs are correctly set up (@test_PELMO.R#38) - A wine installation is needed for this test
-
-3. PELMO runs can be run and give the expected result files (@test_PELMO.R#62) - A wine installation is needed for this test
-
-4. PELMO runs are correctly evaluated (@test_PELMO.R#94) - A wine installation is needed for this test
-
-5. PECgw from FOCUS summary files can be reproduced (@test_PELMO.R#152) - A wine installation is needed for this test
-
 DONE ===============================================================================================
diff --git a/tests/testthat/test_PELMO.R b/tests/testthat/test_PELMO.R
index e6d3a0f..be0b410 100644
--- a/tests/testthat/test_PELMO.R
+++ b/tests/testthat/test_PELMO.R
@@ -19,8 +19,13 @@ runs <- list(
     psm = "Pesticide_D_1_May_every_other_year_mets",
     win = names(FOCUS_GW_scenarios_2012$names)))
 
+# Check if we have wine on the path
+wine_installed <- system('wine --version', ignore.stdout = TRUE) == 0
+
 test_that("PELMO paths are correctly created", {
-  skip("A wine installation is needed for this test")
+  if (!wine_installed) {
+    skip("A wine installation is needed for this test")
+  }
   psm_paths = c(
      PELMO_path(runs[[1]]$psm, "fbe", "Por"),
      PELMO_path(runs[[2]]$psm, "pot", "Ham"),
@@ -35,7 +40,9 @@ test_that("PELMO paths are correctly created", {
 })
 
 test_that("PELMO runs are correctly set up", {
-  skip("A wine installation is needed for this test")
+  if (!wine_installed) {
+    skip("A wine installation is needed for this test")
+  }
 
   # Prepare runs in analogy to the test archive
   PELMO_runs(runs, psm_dir = PELMO_base, execute = FALSE, evaluate = FALSE, overwrite = TRUE)
@@ -59,7 +66,10 @@ test_that("PELMO runs are correctly set up", {
 })
 
 test_that("PELMO runs can be run and give the expected result files", {
-  skip("A wine installation is needed for this test")
+  if (!wine_installed) {
+    skip("A wine installation is needed for this test")
+  }
+
   run_PELMO(runs, cores = 7)
 
   plm_files <- c("CHEM.PLM", "ECHO.PLM",
@@ -88,10 +98,12 @@ test_that("PELMO runs can be run and give the expected result files", {
   }
 })
 
-# pfm_PECgw <- evaluate_PELMO(runs)
+pfm_PECgw <- evaluate_PELMO(runs)
 
 test_that("PELMO runs are correctly evaluated", {
-  skip("A wine installation is needed for this test")
+  if (!wine_installed) {
+    skip("A wine installation is needed for this test")
+  }
 
   # Check that if output is the same as in the test archive
   for (run in runs) {
@@ -149,7 +161,9 @@ test_that("PELMO runs are correctly evaluated", {
 })
 
 test_that("PECgw from FOCUS summary files can be reproduced", {
-  skip("A wine installation is needed for this test")
+  if (!wine_installed) {
+    skip("A wine installation is needed for this test")
+  }
   focus_summary <- list()
 
   for (run in runs) {