From 36036b5901223591e7e21e8b73d8cd1fb034f4cb Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 16 May 2017 15:43:50 +0200 Subject: Finish the Step 1 calculator including tests Some cleaning up. PELMO facilities do not currently work at my end, as I have no working wine installation on this computer --- docs/reference/PELMO_runs.html | 143 +++++++++++++++++++---------------------- 1 file changed, 66 insertions(+), 77 deletions(-) (limited to 'docs/reference/PELMO_runs.html') 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 @@ - + + + @@ -79,7 +81,7 @@ installed into the package installation directory of PELMO.installeRwine.

- 
PELMO_runs(runs, psm_dir = ".", version = "5.5.3", PELMO_base = "auto",
+    
PELMO_runs(runs, psm_dir = ".", version = "5.5.3", PELMO_base = "auto",
   execute = TRUE, cores = getOption("mc.cores", 2L), evaluate = TRUE,
   overwrite = FALSE)
 
@@ -89,28 +91,45 @@ and run using wine.

 evaluate_PELMO(runs, version = "5.5.3", PELMO_base = "auto")

     
     
 Arguments

-    

-      
runs

-      
A list of lists. Each inner lists has an element named 'psm'
+    
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
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,
 as used in FOCUS_PELMO_crops,
 that hold character vectors of three letter scenario acronyms
-as used in FOCUS_GW_scenarios_2012.
-      
psm_dir

-      
The directory where the psm files are located

-      
version

-      
The FOCUS PELMO version

-      
PELMO_base

-      
Where the FOCUS PELMO installation is located

-      
execute

-      
Should PELMO be executed directly?

-      
cores

-      
The number of cores to execute PELMO runs in parallel

-      
evaluate

-      
Should the results be returned?

-      
overwrite

-      
Should existing run directories be overwritten?

-    
+as used in FOCUS_GW_scenarios_2012.
psm_dir
The directory where the psm files are located
version
The FOCUS PELMO version
PELMO_base
Where the FOCUS PELMO installation is located
execute
Should PELMO be executed directly?
cores
The number of cores to execute PELMO runs in parallel
evaluate
Should the results be returned?
overwrite
Should existing run directories be overwritten?

     
     
Value

 
@@ -126,65 +145,35 @@ the period.plm file generated by the FOCUS PELMO GUI.

     
References

 
     
PELMO.installeR https://jranke.github.io/PELMO.installeR

-    
Wine https://winehq.org

-    
PELMO test results http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/gw/models/pelmo/test-results/test_results_FOCUS_PELMO_5_5_3.doc

+
Wine https://winehq.org

+
PELMO test results http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/gw/models/pelmo/test-results/test_results_FOCUS_PELMO_5_5_3.doc

     
 
     
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)
#> $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 
-#>     229.448       0.524      57.021 

-# 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
-#> 
-#> 

+    
# 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)
+})