From a2e24495c01f837474b69263a9861a89050cbfd1 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 21 Jul 2017 11:15:41 +0200 Subject: New Option for Step 1, fix example, update docs Also add the reference file for testing Step12 input file generation --- docs/reference/PEC_sw_focus.html | 67 ++++++++++++++++++++++++++++++++------ docs/reference/PELMO_runs.html | 2 +- docs/reference/chent_focus_sw.html | 22 +++++++++++-- docs/reference/index.html | 2 +- docs/reference/pesticide.txt | 3 ++ 5 files changed, 81 insertions(+), 15 deletions(-) create mode 100644 docs/reference/pesticide.txt (limited to 'docs/reference') diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html index 7331d42..50651ae 100644 --- a/docs/reference/PEC_sw_focus.html +++ b/docs/reference/PEC_sw_focus.html @@ -6,7 +6,7 @@ -Calculate FOCUS Step 1 PEC surface water — PEC_sw_focus • pfm +Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus • pfm @@ -68,19 +68,25 @@
-

Calculate FOCUS Step 1 PEC surface water

+

Calculate PEC surface water at FOCUS Step 1

-

This is reimplementation of Step 1 of the FOCUS Step 1 and 2 calculator -version 3.2, authored by Michael Klein. Note that results for multiple +

This is reimplementation of the FOCUS Step 1 and 2 calculator version 3.2, +authored by Michael Klein, in R. Note that results for multiple applications should be compared to the corresponding results for a single application. At current, this is not done automatically in -this implementation.

+this implementation. Only Step 1 PECs are calculated. However, +input files are generated that are suitable as input also for Step 2 +to be used with the FOCUS calculator.

- 
PEC_sw_focus(parent, rate, n = 1, i = NA, met = NULL, f_drift = NA,
-  f_rd = 0.1, scenario = FOCUS_Step_12_scenarios$names)
+ 
PEC_sw_focus(parent, rate, n = 1, i = NA, comment = "", met = NULL,
+  f_drift = NA, f_rd = 0.1, scenario = FOCUS_Step_12_scenarios$names,
+  region = c("n", "s"), season = c(NA, "of", "mm", "js"),
+  interception = c("no interception", "minimal crop cover",
+  "average crop cover", "full canopy"), met_form_water = TRUE,
+  txt_file = "pesticide.txt", overwrite = FALSE, append = TRUE)

Arguments

@@ -103,6 +109,10 @@ applications are given explicitly

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
i

The application interval
comment

A comment for the input file

met

A list containing metabolite specific parameters. e.g. @@ -127,6 +137,42 @@ parent or a metabolite

The name of the scenario. Must be one of the scenario names given in FOCUS_Step_12_scenarios
region

'n' for Northern Europe or 's' for Southern Europe. If NA, only +Step 1 PECsw are calculated

season

'of' for October to February, 'mm' for March to May, and 'js' +for June to September. If NA, only step 1 PECsw are calculated

interception

One of 'no interception' (default), 'minimal crop cover', +'average crop cover' or 'full canopy'

met_form_water

Should the metabolite formation in water be taken into +account? This can be switched off to check the influence and to compare +with previous versions of the Steps 12 calculator

txt_file

the name, and potentially the full path to the +Steps.12 input text file to which the specification of the run(s) +should be written

overwrite

Should an existing file a the location specified in +txt_file be overwritten?

append

Should the input text file be appended?

Note

@@ -151,7 +197,7 @@ names given in FOCUS_Step_12_scenar

Examples

# Parent only
-dummy_1 <- chent_focus_sw(cwsat = 6000, DT50_ws = 6, Koc = 344.8)
+dummy_1 <- chent_focus_sw("Dummy 1", cwsat = 6000, DT50_ws = 6, Koc = 344.8)
 PEC_sw_focus(dummy_1, 3000, f_drift = 0)
#> $f_drift
 #> [1] 0
 #> 
@@ -198,8 +244,9 @@ names given in FOCUS_Step_12_scenar
 #> [1] 2362.075
 #> 

 # Metabolite
-new_dummy <- chent_focus_sw(mw = 250, Koc = 100)
-M1 <- chent_focus_sw(mw = 100, cwsat = 100, DT50_ws = 100, Koc = 50, max_ws = 0, max_soil = 0.5)
+new_dummy <- chent_focus_sw("New Dummy", mw = 250, Koc = 100)
+M1 <- chent_focus_sw("M1", mw = 100, cwsat = 100, DT50_ws = 100, Koc = 50,
+  max_ws = 0, max_soil = 0.5)
 PEC_sw_focus(new_dummy, 1000, scenario = "cereals, winter", met = M1)
#> $f_drift
 #> [1] 0.02759
 #> 
diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html
index 25afcf0..f2df73a 100644
--- a/docs/reference/PELMO_runs.html
+++ b/docs/reference/PELMO_runs.html
@@ -190,7 +190,7 @@ the period.plm file generated by the FOCUS PELMO GUI.

 #> 
 #> 
# We get exactly the same PECgw values (on Linux, calling PELMO using Wine).
 print(time_1)
#>        User      System verstrichen 
-#>     218.736       0.940      54.948 

+#>     218.452       0.788      55.054 

 # Demonstrate some results with metabolites.
 runs_2 <- list(list(psm = 'Pesticide_D_1_May_every_other_year_mets',
                     win = c("Cha", "Ham", "Kre")))
diff --git a/docs/reference/chent_focus_sw.html b/docs/reference/chent_focus_sw.html
index bd3d084..8e95618 100644
--- a/docs/reference/chent_focus_sw.html
+++ b/docs/reference/chent_focus_sw.html
@@ -75,12 +75,16 @@
     
Create a chemical compound object for FOCUS Step 1 calculations

     
 
-    
chent_focus_sw(Koc, DT50_ws = NA, cwsat = 1000, mw = NA, max_soil = 1,
-  max_ws = 1)

+    
chent_focus_sw(name, Koc, DT50_ws = NA, DT50_soil = NA, DT50_water = NA,
+  DT50_sediment = NA, cwsat = 1000, mw = NA, max_soil = 1, max_ws = 1)

     
     
 Arguments

     
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
-      
+      
diff --git a/docs/reference/index.html b/docs/reference/index.html
index a6ae657..9973635 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -191,7 +191,7 @@ published by the JKI

-          
+          

     
name
Length one character vector containing the name

     

       Koc
       
Partition coefficient between organic carbon and water
@@ -90,13 +94,25 @@ in L/kg.

       DT50_ws
       
Half-life in water/sediment systems in days

     
DT50_soil
Half-life in soil in days
DT50_water
Half-life in water in days (Step 2)
DT50_sediment
Half-life in sediment in days (Step 2)

     

       cwsat
       
Water solubility in mg/L

     

     

       mw
Molar weight in g/mol
Molar weight in g/mol.

     

     

       max_soil
           
             
PEC_sw_focus 

           
Calculate FOCUS Step 1 PEC surface water
Calculate PEC surface water at FOCUS Step 1

         

           
           
diff --git a/docs/reference/pesticide.txt b/docs/reference/pesticide.txt
new file mode 100644
index 0000000..e4c6dac
--- /dev/null
+++ b/docs/reference/pesticide.txt
@@ -0,0 +1,3 @@
+Active Substance	Compound	Comment	Mol mass a.i.	Mol mass met.	Water solubility	KOC assessed compound	KOC parent compound	DT50	Max. in Water	Max. in Soil asessed compound	App. Rate	Number of App.	Time between app.	App. Type	DT50 soil parent compound	DT50 soil	DT50 water	DT50 sediment	Region / Season	Interception class
+Dummy 1 cereals, spring n NA	Dummy 1 cereals, winter s of	Dummy 1 citrus n mm	Dummy 1 cotton s js	Dummy 1 field beans n NA	Dummy 1 grass / alfalfa s of	Dummy 1 hops n mm	Dummy 1 legumes s js	Dummy 1 maize n NA	Dummy 1 oil seed rape, spring s of	Dummy 1 oil seed rape, winter n mm	Dummy 1 olives s js	Dummy 1 pome / stone fruit, early applns n NA	Dummy 1 pome / stone fruit, late applns s of	Dummy 1 potatoes n mm	Dummy 1 soybeans s js	Dummy 1 sugar beets n NA	Dummy 1 sunflowers s of	Dummy 1 tobacco n mm	Dummy 1 vegetables, bulb s js	Dummy 1 vegetables, fruiting n NA	Dummy 1 vegetables, leafy s of	Dummy 1 vegetables, root n mm	Dummy 1 vines, early applns s js	Dummy 1 vines, late applns n NA	Dummy 1 appln, aerial s of	Dummy 1 appln, hand (crop < 50 cm) n mm	Dummy 1 appln, hand (crop > 50 cm) s js	Dummy 1 no drift (incorp or seed trtmt) n NA	Dummy 1 cereals, spring n NA	Dummy 1 cereals, winter s of	Dummy 1 citrus n mm	Dummy 1 cotton s js	Dummy 1 field beans n NA	Dummy 1 grass / alfalfa s of	Dummy 1 hops n mm	Dummy 1 legumes s js	Dummy 1 maize n NA	Dummy 1 oil seed rape, spring s of	Dummy 1 oil seed rape, winter n mm	Dummy 1 olives s js	Dummy 1 pome / stone fruit, early applns n NA	Dummy 1 pome / stone fruit, late applns s of	Dummy 1 potatoes n mm	Dummy 1 soybeans s js	Dummy 1 sugar beets n NA	Dummy 1 sunflowers s of	Dummy 1 tobacco n mm	Dummy 1 vegetables, bulb s js	Dummy 1 vegetables, fruiting n NA	Dummy 1 vegetables, leafy s of	Dummy 1 vegetables, root n mm	Dummy 1 vines, early applns s js	Dummy 1 vines, late applns n NA	Dummy 1 appln, aerial s of	Dummy 1 appln, hand (crop < 50 cm) n mm	Dummy 1 appln, hand (crop > 50 cm) s js	Dummy 1 no drift (incorp or seed trtmt) n NA		  -99.00	  -99.00	 6000.00	  344.80	0.00E+00	    6.00	0.00E+00	0.00E+00	 3000.00	    1.00	0.00E+00	0.00E+00	    1.00	    2.00	    3.00	    4.00	    5.00	    6.00	    7.00	    8.00	    9.00	   10.00	   11.00	   12.00	   13.00	   14.00	   15.00	   16.00	   17.00	   18.00	   19.00	   20.00	   21.00	   22.00	   23.00	   24.00	   25.00	   26.00	   27.00	   28.00	0.00E+00	  -99.00	  -99.00	  -99.00	0.00E+00	    1.00
+M1 cereals, winter n NA	M1 cereals, winter s of	M1 cereals, winter n mm	M1 cereals, winter s js	M1 cereals, winter n NA	M1 cereals, winter s of	M1 cereals, winter n mm	M1 cereals, winter s js		  250.00	  100.00	  100.00	   50.00	  100.00	  100.00	0.00E+00	   50.00	 1000.00	    1.00	0.00E+00	    1.00	  -99.00	  -99.00	  -99.00	  -99.00	0.00E+00	    1.00
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