From 4835e20d1d08203657ab616600286ad9dfd71344 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 24 May 2017 15:46:44 +0200 Subject: Re-enable PELMO examples and tests - Add .gitattributes to make sure CRLF line endings are kept for PELMO .psm files - Update static docs --- docs/reference/PELMO_runs.html | 78 ++++++++++++++++++++++++----------- docs/reference/one_box-2.png | Bin 5599 -> 5841 bytes docs/reference/one_box-4.png | Bin 5426 -> 5660 bytes docs/reference/one_box-8.png | Bin 9671 -> 10226 bytes docs/reference/plot.TOXSWA_cwa-2.png | Bin 7427 -> 7786 bytes docs/reference/plot.one_box-2.png | Bin 5653 -> 5891 bytes docs/reference/plot.one_box-4.png | Bin 10315 -> 10742 bytes docs/reference/plot.one_box-8.png | Bin 13307 -> 13953 bytes docs/reference/sawtooth-2.png | Bin 6018 -> 6217 bytes docs/reference/sawtooth-6.png | Bin 13307 -> 13953 bytes 10 files changed, 54 insertions(+), 24 deletions(-) (limited to 'docs') 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.

Examples

- 
# At the moment I can not run the examples, as my wine installation is not working
-not_run({
-  # 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)
-})
+ 
# 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)
#> $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
+#> 
+#> 
# We get exactly the same PECgw values (on Linux, calling PELMO using Wine).
+print(time_1)
#>        User      System verstrichen 
+#>     219.860       0.960      55.449 

+# 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)
#> $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
+#> 
+#>