A very small subset of the FOCUS Groundwater scenario defitions

...	Included in the generic to allow for further arguments later. Therefore +this also had to be added to the specific methods.
DT50	Half-life of the chemical in soil. Should be a field half-life according to Gustafson (1989). However, leaching to the sub-soil can not completely be excluded in field dissipation experiments and Gustafson did not refer to any normalisation procedure, but says the field study should -be conducted under use conditions. - Koc - The sorption constant normalised to organic carbon. Gustafson +be conducted under use conditions.
Koc	The sorption constant normalised to organic carbon. Gustafson does not mention the nonlinearity of the sorption constant commonly found and usually described by Freundlich sorption, therefore it is unclear at which reference concentration the Koc should be observed -(and if the reference concentration would be in soil or in porewater). - chent - If a chent is given with appropriate information present in its -chyaml field, this information is used, with defaults specified below. - degradation_value - Which of the available degradation values should -be used? - lab_field - Should laboratory or field half-lives be used? This +(and if the reference concentration would be in soil or in porewater).
chent	If a chent is given with appropriate information present in its +chyaml field, this information is used, with defaults specified below.
degradation_value	Which of the available degradation values should +be used?
lab_field	Should laboratory or field half-lives be used? This defaults to lab in this implementation, in order to avoid double-accounting for mobility. If comparability with the original GUS values given by Gustafson (1989) is desired, non-normalised first-order -field half-lives obtained under actual use conditions should be used. - redox - Aerobic or anaerobic degradation data - sorption_value - Which of the available sorption values should be used? +field half-lives obtained under actual use conditions should be used.
redox	Aerobic or anaerobic degradation data
sorption_value	Which of the available sorption values should be used? Defaults to Kfoc as this is what is generally available from the European pesticide peer review process. These values generally use a reference concentration of 1 mg/L in porewater, that means they would be expected to -be Koc values at a concentration of 1 mg/L in the water phase. - degradation_aggregator - Function for aggregating half-lives - sorption_aggregator - Function for aggregation Koc values - x - An object of class GUS_result to be printed - digits - The number of digits used in the print method - +be Koc values at a concentration of 1 mg/L in the water phase.
degradation_aggregator	Function for aggregating half-lives
sorption_aggregator	Function for aggregation Koc values
x	An object of class GUS_result to be printed
digits	The number of digits used in the print method

rate	Application rate in units specified below
rate_units	Defaults to g/ha
interception	The fraction of the application rate that does not reach the soil
mixing_depth	Mixing depth in cm
PEC_units	Requested units for the calculated PEC. Only mg/kg currently supported
PEC_pw_units	Only mg/L currently supported
interval	Period of the deeper mixing, defaults to 365, which is a year if +rate units are in days
n_periods	Number of periods to be considered for long term PEC calculations
tillage_depth	Periodic (see interval) deeper mixing in cm
chent	An optional chent object holding substance specific information. Can +also be a name for the substance as a character string
DT50	If specified, overrides soil DT50 endpoints from a chent object If DT50 is not specified here and not available from the chent object, zero -degradation is assumed - Koc - If specified, overrides Koc endpoints from a chent object - Kom - Calculated from Koc by default, but can explicitly be specified -as Kom here - t_avg - Averaging times for time weighted average concentrations - scenarios - If this is 'default', the DT50 will be used without correction +degradation is assumed
Koc	If specified, overrides Koc endpoints from a chent object
Kom	Calculated from Koc by default, but can explicitly be specified +as Kom here
t_avg	Averaging times for time weighted average concentrations
scenarios	If this is 'default', the DT50 will be used without correction and soil properties as specified in the REACH guidance (R.16, Table -R.16-9) are used for porewater PEC calculations. If this is "EFSA_2015", +R.16-9) are used for porewater PEC calculations. If this is "EFSA_2015", the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when -'chents' is specified, the DegT50 with destination 'PECgw' will be used), +'chents' is specified, the DegT50 with destination 'PECgw' will be used), and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also -model and scenario adjustment factors from the EFSA guidance are used. - porewater - Should equilibrium porewater concentrations be estimated +model and scenario adjustment factors from the EFSA guidance are used.
porewater	Should equilibrium porewater concentrations be estimated based on Kom and the organic carbon fraction of the soil instead of total soil concentrations? Based on equation (7) given in the PPR panel opinion (EFSA 2012, p. 24) and the scenarios specified in the EFSA guidance (2015, -p. 13). - +p. 13).

rate	Application rate in g/ha
interception	The fraction of the application rate that does not reach the soil
Koc	The sorption coefficient normalised to organic carbon in L/kg
latest_application	Latest application date, formatted as e.g. "01 July"
soil_DT50	Soil degradation half-life, if SFO kinetics are to be used
model	The soil degradation model to be used. Either one of "FOMC", +"DFOP", "HS", or "IORE", or an mkinmod object
model_parms	A named numeric vector containing the model parameters

rate	Application rate in units specified below
applications	Number of applications for selection of drift percentile
water_depth	Depth of the water body in cm
drift_percentages	Percentage drift values for which to calculate PECsw. +'drift_data' and 'distances' if not NULL.
drift_data	Source of drift percentage data
crop	Crop name (use German names for JKI data), defaults to "Ackerbau"
distances	The distances in m for which to get PEC values
rate_units	Defaults to g/ha
PEC_units	Requested units for the calculated PEC. Only µg/L currently supported

parent	A list containing substance specific parameters
rate	The application rate in g/ha. Overriden when +applications are given explicitly
n	The number of applications
i	The application interval
met	A list containing metabolite specific parameters. If not NULL, +the PEC is calculated for this compound, not the parent.
f_drift	The fraction of the application rate reaching the waterbody +via drift. If NA, this is derived from the scenario name and the number +of applications via the drift data defined by the +`FOCUS_Step_12_scenarios`
f_rd	The fraction of the amount applied reaching the waterbody via +runoff/drainage. At Step 1, it is assumed to be 10 +parent or a metabolite
scenario	The name of the scenario. Must be one of the scenario +names given in `FOCUS_Step_12_scenarios`

PEC_sw	Numeric vector or matrix of surface water concentrations in µg/L for +which the corresponding sediment concentration is to be estimated
percentage	The percentage in sediment, used for the percentage method
method	The method used for the calculation
sediment_depth	Depth of the sediment layer
water_depth	Depth of the water body in cm
sediment_density	The density of the sediment in L/kg (equivalent to +g/cm3)
PEC_sed_units	The units of the estimated sediment PEC value

psm	The psm identifier
crop	The PELMO crop acronym
scenario	The scenario

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?


     Contents
diff --git a/docs/reference/FOCUS_Step_12_scenarios.html b/docs/reference/FOCUS_Step_12_scenarios.html
new file mode 100644
index 0000000..37bb2fd
--- /dev/null
+++ b/docs/reference/FOCUS_Step_12_scenarios.html
@@ -0,0 +1,285 @@
+
+
+
+  
+  
+
+
+
+Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios • pfm
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+  
+
+  
+    
+      
+      
+  
+    
+      
+      pfm
+    
+    
+      
+        
+  Reference
+
+      
+      
+      
+        
+      
+    

+  

+

+
+      
+      
+
+      
+  
+    
+    Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator
+    
+
+    
+    The data were extracted from the scenario.txt file using the R code shown below.
+The text file is not included in the package as its licence is not clear.
+    
+
+        
+    Format
+
+    A list containing the scenario names in a character vector called 'names',
+  the drift percentiles in a matrix called 'drift', interception percentages in
+  a matrix called 'interception' and the runoff/drainage percentages for Step 2
+  calculations in a matrix called 'rd'.
+    
+
+    Examples
+    
+not_run({
+    # This is the code that was used to extract the data
+    scenario_path <- "inst/extdata/FOCUS_Step_12_scenarios.txt"
+    scenarios <- readLines(scenario_path)[9:38]
+    FOCUS_Step_12_scenarios <- list()
+    sce <- read.table(text = scenarios, sep = "\t", header = TRUE, check.names = FALSE,
+      stringsAsFactors = FALSE)
+    FOCUS_Step_12_scenarios$names = sce$Crop
+    rownames(sce) <- sce$Crop
+    FOCUS_Step_12_scenarios$drift = sce[, 3:11]
+    FOCUS_Step_12_scenarios$interception = sce[, 12:15]
+    sce_2 <- readLines(scenario_path)[41:46]
+    rd <- read.table(text = sce_2, sep = "\t")[1:2]
+    rd_mat <- matrix(rd$V2, nrow = 3, byrow = FALSE)
+    dimnames(rd_mat) = list(Time = c("Oct-Feb", "Mar-May", "Jun-Sep"),
+                            Region = c("North", "South"))
+    FOCUS_Step_12_scenarios$rd = rd_mat
+    save(FOCUS_Step_12_scenarios, file = "data/FOCUS_Step_12_scenarios.RData")
+})
+
+# And this is the resulting data
+FOCUS_Step_12_scenarios
#> $names
+#>  [1] "cereals, spring"                  "cereals, winter"                 
+#>  [3] "citrus"                           "cotton"                          
+#>  [5] "field beans"                      "grass / alfalfa"                 
+#>  [7] "hops"                             "legumes"                         
+#>  [9] "maize"                            "oil seed rape, spring"           
+#> [11] "oil seed rape, winter"            "olives"                          
+#> [13] "pome / stone fruit, early applns" "pome / stone fruit, late applns" 
+#> [15] "potatoes"                         "soybeans"                        
+#> [17] "sugar beets"                      "sunflowers"                      
+#> [19] "tobacco"                          "vegetables, bulb"                
+#> [21] "vegetables, fruiting"             "vegetables, leafy"               
+#> [23] "vegetables, root"                 "vines, early applns"             
+#> [25] "vines, late applns"               "appln, aerial"                   
+#> [27] "appln, hand (crop < 50 cm)"       "appln, hand (crop > 50 cm)"      
+#> [29] "no drift (incorp or seed trtmt)" 
+#> 
+#> $drift
+#>                                       1      2      3      4      5      6
+#> cereals, spring                   2.759  2.438  2.024  1.862  1.794  1.631
+#> cereals, winter                   2.759  2.438  2.024  1.862  1.794  1.631
+#> citrus                           15.725 12.129 11.011 10.124  9.743  9.204
+#> cotton                            2.759  2.438  2.024  1.862  1.794  1.631
+#> field beans                       2.759  2.438  2.024  1.862  1.794  1.631
+#> grass / alfalfa                   2.759  2.438  2.024  1.862  1.794  1.631
+#> hops                             19.326 17.723 15.928 15.378 15.114 14.902
+#> legumes                           2.759  2.438  2.024  1.862  1.794  1.631
+#> maize                             2.759  2.438  2.024  1.862  1.794  1.631
+#> oil seed rape, spring             2.759  2.438  2.024  1.862  1.794  1.631
+#> oil seed rape, winter             2.759  2.438  2.024  1.862  1.794  1.631
+#> olives                           15.725 12.129 11.011 10.124  9.743  9.204
+#> pome / stone fruit, early applns 29.197 25.531 23.960 23.603 23.116 22.760
+#> pome / stone fruit, late applns  15.725 12.129 11.011 10.124  9.743  9.204
+#> potatoes                          2.759  2.438  2.024  1.862  1.794  1.631
+#> soybeans                          2.759  2.438  2.024  1.862  1.794  1.631
+#> sugar beets                       2.759  2.438  2.024  1.862  1.794  1.631
+#> sunflowers                        2.759  2.438  2.024  1.862  1.794  1.631
+#> tobacco                           2.759  2.438  2.024  1.862  1.794  1.631
+#> vegetables, bulb                  2.759  2.438  2.024  1.862  1.794  1.631
+#> vegetables, fruiting              2.759  2.438  2.024  1.862  1.794  1.631
+#> vegetables, leafy                 2.759  2.438  2.024  1.862  1.794  1.631
+#> vegetables, root                  2.759  2.438  2.024  1.862  1.794  1.631
+#> vines, early applns               2.699  2.496  2.546  2.499  2.398  2.336
+#> vines, late applns                8.028  7.119  6.898  6.631  6.636  6.431
+#> appln, aerial                    33.200 33.200 33.200 33.200 33.200 33.200
+#> appln, hand (crop < 50 cm)        2.759  2.438  2.024  1.862  1.794  1.631
+#> appln, hand (crop > 50 cm)        8.028  7.119  6.898  6.631  6.636  6.431
+#> no drift (incorp or seed trtmt)   0.000  0.000  0.000  0.000  0.000  0.000
+#>                                       7      8     >8
+#> cereals, spring                   1.578  1.512  1.512
+#> cereals, winter                   1.578  1.512  1.512
+#> citrus                            9.102  8.656  8.656
+#> cotton                            1.578  1.512  1.512
+#> field beans                       1.578  1.512  1.512
+#> grass / alfalfa                   1.578  1.512  1.512
+#> hops                             14.628 13.520 13.520
+#> legumes                           1.578  1.512  1.512
+#> maize                             1.578  1.512  1.512
+#> oil seed rape, spring             1.578  1.512  1.512
+#> oil seed rape, winter             1.578  1.512  1.512
+#> olives                            9.102  8.656  8.656
+#> pome / stone fruit, early applns 22.690 22.241 22.241
+#> pome / stone fruit, late applns   9.102  8.656  8.656
+#> potatoes                          1.578  1.512  1.512
+#> soybeans                          1.578  1.512  1.512
+#> sugar beets                       1.578  1.512  1.512
+#> sunflowers                        1.578  1.512  1.512
+#> tobacco                           1.578  1.512  1.512
+#> vegetables, bulb                  1.578  1.512  1.512
+#> vegetables, fruiting              1.578  1.512  1.512
+#> vegetables, leafy                 1.578  1.512  1.512
+#> vegetables, root                  1.578  1.512  1.512
+#> vines, early applns               2.283  2.265  2.265
+#> vines, late applns                6.227  6.173  6.173
+#> appln, aerial                    33.200 33.200 33.200
+#> appln, hand (crop < 50 cm)        1.578  1.512  1.512
+#> appln, hand (crop > 50 cm)        6.227  6.173  6.173
+#> no drift (incorp or seed trtmt)   0.000  0.000  0.000
+#> 
+#> $interception
+#>                                  no interception minimal crop cover
+#> cereals, spring                                0               0.00
+#> cereals, winter                                0               0.00
+#> citrus                                         0               0.80
+#> cotton                                         0               0.30
+#> field beans                                    0               0.25
+#> grass / alfalfa                                0               0.40
+#> hops                                           0               0.20
+#> legumes                                        0               0.25
+#> maize                                          0               0.25
+#> oil seed rape, spring                          0               0.40
+#> oil seed rape, winter                          0               0.40
+#> olives                                         0               0.70
+#> pome / stone fruit, early applns               0               0.20
+#> pome / stone fruit, late applns                0               0.20
+#> potatoes                                       0               0.15
+#> soybeans                                       0               0.20
+#> sugar beets                                    0               0.20
+#> sunflowers                                     0               0.20
+#> tobacco                                        0               0.20
+#> vegetables, bulb                               0               0.10
+#> vegetables, fruiting                           0               0.25
+#> vegetables, leafy                              0               0.25
+#> vegetables, root                               0               0.25
+#> vines, early applns                            0               0.40
+#> vines, late applns                             0               0.40
+#> appln, aerial                                  0               0.20
+#> appln, hand (crop < 50 cm)                     0               0.20
+#> appln, hand (crop > 50 cm)                     0               0.20
+#> no drift (incorp or seed trtmt)                0               0.00
+#>                                  average crop cover full canopy
+#> cereals, spring                                0.20        0.70
+#> cereals, winter                                0.20        0.70
+#> citrus                                         0.80        0.80
+#> cotton                                         0.60        0.75
+#> field beans                                    0.40        0.70
+#> grass / alfalfa                                0.60        0.75
+#> hops                                           0.50        0.70
+#> legumes                                        0.50        0.70
+#> maize                                          0.50        0.75
+#> oil seed rape, spring                          0.70        0.75
+#> oil seed rape, winter                          0.70        0.75
+#> olives                                         0.70        0.70
+#> pome / stone fruit, early applns               0.40        0.65
+#> pome / stone fruit, late applns                0.40        0.65
+#> potatoes                                       0.50        0.70
+#> soybeans                                       0.50        0.75
+#> sugar beets                                    0.70        0.75
+#> sunflowers                                     0.50        0.75
+#> tobacco                                        0.70        0.75
+#> vegetables, bulb                               0.25        0.40
+#> vegetables, fruiting                           0.50        0.70
+#> vegetables, leafy                              0.40        0.70
+#> vegetables, root                               0.50        0.70
+#> vines, early applns                            0.50        0.60
+#> vines, late applns                             0.50        0.60
+#> appln, aerial                                  0.50        0.70
+#> appln, hand (crop < 50 cm)                     0.50        0.70
+#> appln, hand (crop > 50 cm)                     0.50        0.70
+#> no drift (incorp or seed trtmt)                0.00        0.00
+#> 
+#> $rd
+#>          Region
+#> Time      North South
+#>   Oct-Feb     5     4
+#>   Mar-May     2     4
+#>   Jun-Sep     2     3
+#> 
+  
+  
+    Contents
+    
+      
+      Format
+      
+      Examples
+    
+
+  
+
+
+      
+      
+  Developed by Johannes Ranke.
+
+
+
+  Site built with pkgdown.
+
+
+      
+   
+
+  
+
diff --git a/docs/reference/GUS.html b/docs/reference/GUS.html
index f65c6fd..6f29e72 100644
--- a/docs/reference/GUS.html
+++ b/docs/reference/GUS.html
@@ -25,12 +25,14 @@
 
 
 
-
+
 
 
+
+
   
 
   
@@ -75,7 +77,7 @@ the following equation
 $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$
     
 
-

GUS(...)
+    GUS(...)
 
 # S3 method for numeric
 GUS(DT50, Koc, ...)
@@ -89,51 +91,76 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$
 print(x, ..., digits = 1)
     
      Arguments
-    
-      ...
-      Included in the generic to allow for further arguments later. Therefore
-this also had to be added to the specific methods.
-      DT50
-      Half-life of the chemical in soil. Should be a field
+    
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    ... Included in the generic to allow for further arguments later. Therefore
+this also had to be added to the specific methods.
DT50 Half-life of the chemical in soil. Should be a field
 half-life according to Gustafson (1989). However, leaching to the sub-soil
 can not completely be excluded in field dissipation experiments and Gustafson
 did not refer to any normalisation procedure, but says the field study should
-be conducted under use conditions.
-      
Koc
-      The sorption constant normalised to organic carbon. Gustafson
+be conducted under use conditions.
Koc The sorption constant normalised to organic carbon. Gustafson
 does not mention the nonlinearity of the sorption constant commonly
 found and usually described by Freundlich sorption, therefore it is 
 unclear at which reference concentration the Koc should be observed
-(and if the reference concentration would be in soil or in porewater).
-      
chent
-      If a chent is given with appropriate information present in its
-chyaml field, this information is used, with defaults specified below.
-      degradation_value
-      Which of the available degradation values should 
-be used?
-      lab_field
-      Should laboratory or field half-lives be used? This
+(and if the reference concentration would be in soil or in porewater).
chent If a chent is given with appropriate information present in its
+chyaml field, this information is used, with defaults specified below.
degradation_value Which of the available degradation values should 
+be used?
lab_field Should laboratory or field half-lives be used? This
 defaults to lab in this implementation, in order to avoid
 double-accounting for mobility. If comparability with the original GUS
 values given by Gustafson (1989) is desired, non-normalised first-order
-field half-lives obtained under actual use conditions should be used.
-      
redox
-      Aerobic or anaerobic degradation data
-      sorption_value
-      Which of the available sorption values should be used?
+field half-lives obtained under actual use conditions should be used.
redox Aerobic or anaerobic degradation data
sorption_value Which of the available sorption values should be used?
 Defaults to Kfoc as this is what is generally available from the European
 pesticide peer review process. These values generally use a reference
 concentration of 1 mg/L in porewater, that means they would be expected to
-be Koc values at a concentration of 1 mg/L in the water phase.
-      
degradation_aggregator
-      Function for aggregating half-lives
-      sorption_aggregator
-      Function for aggregation Koc values
-      x
-      An object of class GUS_result to be printed
-      digits
-      The number of digits used in the print method
-    
+be Koc values at a concentration of 1 mg/L in the water phase.
degradation_aggregator Function for aggregating half-lives
sorption_aggregator Function for aggregation Koc values
x An object of class GUS_result to be printed
digits The number of digits used in the print method
     
     Value
 
diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html
index 0449f8e..4b1b7b9 100644
--- a/docs/reference/PEC_soil.html
+++ b/docs/reference/PEC_soil.html
@@ -25,12 +25,14 @@
 
 
 
-
+
 
 
+
+
   
 
   
@@ -76,62 +78,95 @@ attempt is made at calculating a long term maximum concentration using
 the concepts layed out for example in the PPR panel opinion (EFSA 2012).
     
 
-    PEC_soil(rate, rate_units = "g/ha", interception = 0, mixing_depth = 5,
+    PEC_soil(rate, rate_units = "g/ha", interception = 0, mixing_depth = 5,
   PEC_units = "mg/kg", PEC_pw_units = "mg/L", interval = NA,
   n_periods = Inf, tillage_depth = 20, chent = NA, DT50 = NA,
   Koc = NA, Kom = Koc/1.724, t_avg = 0, scenarios = c("default",
   "EFSA_2015"), porewater = FALSE)
     
      Arguments
-    
-      rate
-      Application rate in units specified below
-      rate_units
-      Defaults to g/ha
-      interception
-      The fraction of the application rate that does not reach the soil
-      mixing_depth
-      Mixing depth in cm
-      PEC_units
-      Requested units for the calculated PEC. Only mg/kg currently supported
-      PEC_pw_units
-      Only mg/L currently supported
-      interval
-      Period of the deeper mixing, defaults to 365, which is a year if
-rate units are in days
-      n_periods
-      Number of periods to be considered for long term PEC calculations
-      tillage_depth
-      Periodic (see interval) deeper mixing in cm
-      chent
-      An optional chent object holding substance specific information. Can 
-also be a name for the substance as a character string
-      DT50
-      If specified, overrides soil DT50 endpoints from a chent object
+    
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    rate Application rate in units specified below
rate_units Defaults to g/ha
interception The fraction of the application rate that does not reach the soil
mixing_depth Mixing depth in cm
PEC_units Requested units for the calculated PEC. Only mg/kg currently supported
PEC_pw_units Only mg/L currently supported
interval Period of the deeper mixing, defaults to 365, which is a year if
+rate units are in days
n_periods Number of periods to be considered for long term PEC calculations
tillage_depth Periodic (see interval) deeper mixing in cm
chent An optional chent object holding substance specific information. Can 
+also be a name for the substance as a character string
DT50 If specified, overrides soil DT50 endpoints from a chent object
 If DT50 is not specified here and not available from the chent object, zero
-degradation is assumed
-      
Koc
-      If specified, overrides Koc endpoints from a chent object
-      Kom
-      Calculated from Koc by default, but can explicitly be specified
-as Kom here
-      t_avg
-      Averaging times for time weighted average concentrations
-      scenarios
-      If this is 'default', the DT50 will be used without correction
+degradation is assumed
Koc If specified, overrides Koc endpoints from a chent object
Kom Calculated from Koc by default, but can explicitly be specified
+as Kom here
t_avg Averaging times for time weighted average concentrations
scenarios If this is 'default', the DT50 will be used without correction
 and soil properties as specified in the REACH guidance (R.16, Table
-R.16-9) are used for porewater PEC calculations.  If this is "EFSA_2015",
+R.16-9) are used for porewater PEC calculations.  If this is "EFSA_2015",
 the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when
-'chents' is specified, the DegT50 with destination 'PECgw' will be used),
+'chents' is specified, the DegT50 with destination 'PECgw' will be used),
 and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also
-model and scenario adjustment factors from the EFSA guidance are used.
-      
porewater
-      Should equilibrium porewater concentrations be estimated
+model and scenario adjustment factors from the EFSA guidance are used.
porewater Should equilibrium porewater concentrations be estimated
 based on Kom and the organic carbon fraction of the soil instead of total
 soil concentrations?  Based on equation (7) given in the PPR panel opinion
 (EFSA 2012, p. 24) and the scenarios specified in the EFSA guidance (2015,
-p. 13).
-    
+p. 13).
     
     Value
 
@@ -140,18 +175,18 @@ p. 13).
     Details
 
     This assumes that the complete load to soil during the time specified by
-'interval' (typically 365 days) is dosed at once. As in the PPR panel
+'interval' (typically 365 days) is dosed at once. As in the PPR panel
 opinion cited below (PPR panel 2012), only temperature correction using the
 Arrhenius equation is performed.
-    Total soil and porewater PEC values for the scenarios as defined in the EFSA
+
Total soil and porewater PEC values for the scenarios as defined in the EFSA
 guidance (2015, p. 13) can easily be calculated.
     
     Note
 
     If temperature information is available in the selected scenarios, as
   e.g. in the EFSA scenarios, the DT50 for groundwater modelling
-  (destination 'PECgw') is taken from the chent object, otherwise the DT50
-  with destination 'PECsoil'.
+  (destination 'PECgw') is taken from the chent object, otherwise the DT50
+  with destination 'PECsoil'.
     
     References
 
@@ -160,7 +195,7 @@ guidance (2015, p. 13) can easily be calculated.
   selection and scenario parameterisation for predicting environmental
   concentrations of plant protection products in soil. EFSA Journal
   10(2) 2562, doi:10.2903/j.efsa.2012.2562
-    EFSA (European Food Safety Authority) (2015) EFSA guidance document for
+
EFSA (European Food Safety Authority) (2015) EFSA guidance document for
   predicting environmental concentrations of active substances of plant
   protection products and transformation products of these active substances
   in soil. EFSA Journal 13(4) 4093
diff --git a/docs/reference/PEC_sw_drainage_UK.html b/docs/reference/PEC_sw_drainage_UK.html
index db0f85f..e52eeb8 100644
--- a/docs/reference/PEC_sw_drainage_UK.html
+++ b/docs/reference/PEC_sw_drainage_UK.html
@@ -25,12 +25,14 @@
 
 
 
-
+
 
 
+
+
   
 
   
@@ -74,27 +76,42 @@
 published on the CRC website
     
 
-    PEC_sw_drainage_UK(rate, interception = 0, Koc, latest_application = NULL,
+    PEC_sw_drainage_UK(rate, interception = 0, Koc, latest_application = NULL,
   soil_DT50 = NULL, model = NULL, model_parms = NULL)
     
      Arguments
-    
-      rate
-      Application rate in g/ha
-      interception
-      The fraction of the application rate that does not reach the soil
-      Koc
-      The sorption coefficient normalised to organic carbon in L/kg
-      latest_application
-      Latest application date, formatted as e.g. "01 July"
-      soil_DT50
-      Soil degradation half-life, if SFO kinetics are to be used
-      model
-      The soil degradation model to be used. Either one of "FOMC",
-"DFOP", "HS", or "IORE", or an mkinmod object
-      model_parms
-      A named numeric vector containing the model parameters
-    
+    
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    rate Application rate in g/ha
interception The fraction of the application rate that does not reach the soil
Koc The sorption coefficient normalised to organic carbon in L/kg
latest_application Latest application date, formatted as e.g. "01 July"
soil_DT50 Soil degradation half-life, if SFO kinetics are to be used
model The soil degradation model to be used. Either one of "FOMC",
+"DFOP", "HS", or "IORE", or an mkinmod object
model_parms A named numeric vector containing the model parameters
     
     Value
 
diff --git a/docs/reference/PEC_sw_drift.html b/docs/reference/PEC_sw_drift.html
index a168de3..e52546b 100644
--- a/docs/reference/PEC_sw_drift.html
+++ b/docs/reference/PEC_sw_drift.html
@@ -25,12 +25,14 @@
 
 
 
-
+
 
 
+
+
   
 
   
@@ -75,32 +77,51 @@ concentration in surface water based on complete, instantaneous mixing
 with input via spray drift.
     
 
-    PEC_sw_drift(rate, applications = 1, water_depth = 30,
+    PEC_sw_drift(rate, applications = 1, water_depth = 30,
   drift_percentages = NULL, drift_data = "JKI", crop = "Ackerbau",
   distances = c(1, 5, 10, 20), rate_units = "g/ha", PEC_units = "µg/L")
     
      Arguments
-    
-      rate
-      Application rate in units specified below
-      applications
-      Number of applications for selection of drift percentile
-      water_depth
-      Depth of the water body in cm
-      drift_percentages
-      Percentage drift values for which to calculate PECsw.
-'drift_data' and 'distances' if not NULL.
-      drift_data
-      Source of drift percentage data
-      crop
-      Crop name (use German names for JKI data), defaults to "Ackerbau"
-      distances
-      The distances in m for which to get PEC values
-      rate_units
-      Defaults to g/ha
-      PEC_units
-      Requested units for the calculated PEC. Only µg/L currently supported
-    
+    
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    rate Application rate in units specified below
applications Number of applications for selection of drift percentile
water_depth Depth of the water body in cm
drift_percentages Percentage drift values for which to calculate PECsw.
+'drift_data' and 'distances' if not NULL.
drift_data Source of drift percentage data
crop Crop name (use German names for JKI data), defaults to "Ackerbau"
distances The distances in m for which to get PEC values
rate_units Defaults to g/ha
PEC_units Requested units for the calculated PEC. Only µg/L currently supported
     
     Value
 
diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html
new file mode 100644
index 0000000..c5cbfe7
--- /dev/null
+++ b/docs/reference/PEC_sw_focus.html
@@ -0,0 +1,272 @@
+
+
+
+  
+  
+
+
+
+Calculate FOCUS Step 1 PEC surface water — PEC_sw_focus • pfm
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+  
+
+  
+    
+      
+      
+  
+    
+      
+      pfm
+    
+    
+      
+        
+  Reference
+
+      
+      
+      
+        
+      
+    

+  

+

+
+      
+      
+
+      
+  
+    
+    Calculate FOCUS Step 1 PEC surface water
+    
+
+    
+    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
+applications should be compared to the corresponding results for a
+single application. At current, this is not done automatically in
+this implementation.
+    
+
+    PEC_sw_focus(parent, rate, n = 1, i = NA, met = NULL, f_drift = NA,
+  f_rd = 0.1, scenario = FOCUS_Step_12_scenarios$names)
+    
+     Arguments
+    
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    parent A list containing substance specific parameters
rate The application rate in g/ha. Overriden when
+applications are given explicitly
n The number of applications
i The application interval
met A list containing metabolite specific parameters. If not NULL, 
+the PEC is calculated for this compound, not the parent.
f_drift The fraction of the application rate reaching the waterbody
+via drift. If NA, this is derived from the scenario name and the number
+of applications via the drift data defined by the 
+FOCUS_Step_12_scenarios
f_rd The fraction of the amount applied reaching the waterbody via
+runoff/drainage. At Step 1, it is assumed to be 10
+parent or a metabolite
scenario The name of the scenario. Must be one of the scenario
+names given in FOCUS_Step_12_scenarios
+    
+    Note
+
+    The formulas for input to the waterbody via runoff/drainage of the
+  parent and subsequent formation of the metabolite in water is not
+  documented in the model description coming with the calculator
+Step 2 is not implemented
+    
+    References
+
+    FOCUS (2014) Generic guidance for Surface Water Scenarios (version 1.4).
+ FOrum for the Co-ordination of pesticde fate models and their USe.
+ http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic
+Website of the Steps 1 and 2 calculator at the Joint Research
+  Center of the European Union:
+  http://esdac.jrc.ec.europa.eu/projects/stepsonetwo
+    
+
+    Examples
+    # Parent only
+dummy_1 <- chent_focus_sw(cwsat = 6000, DT50_ws = 6, Koc = 344.8)
+PEC_sw_focus(dummy_1, 3000, f_drift = 0)
#> $f_drift
+#> [1] 0
+#> 
+#> $eq_rate_drift_s
+#> [1] 3000
+#> 
+#> $eq_rate_rd_s
+#> [1] 3000
+#> 
+#> $eq_rate_rd_parent_s
+#> [1] NA
+#> 
+#> $input_drift_s
+#> [1] 0
+#> 
+#> $input_rd_s
+#> [1] 300
+#> 
+#> $f_rd_sw
+#> [1] 0.6850566
+#> 
+#> $f_rd_sed
+#> [1] 0.3149434
+#> 
+#> $PEC
+#>      type
+#> Time         PECsw  TWAECsw       PECsed TWAECsed
+#>   0   6.850566e+02       NA 2.362075e+03       NA
+#>   1   6.103161e+02 647.6864 2.104370e+03 2233.223
+#>   2   5.437298e+02       NA 1.874780e+03       NA
+#>   4   4.315586e+02       NA 1.488014e+03       NA
+#>   7   3.051580e+02       NA 1.052185e+03       NA
+#>   14  1.359325e+02       NA 4.686951e+02       NA
+#>   21  6.055102e+01       NA 2.087799e+02       NA
+#>   28  2.697241e+01       NA 9.300089e+01       NA
+#>   42  5.352005e+00       NA 1.845371e+01       NA
+#>   50  2.123945e+00       NA 7.323361e+00       NA
+#>   100 6.585062e-03       NA 2.270529e-02       NA
+#> 
+#> $PEC_sw_max
+#> [1] 685.0566
+#> 
+#> $PEC_sed_max
+#> [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)
+PEC_sw_focus(new_dummy, 1000, scenario = "cereals, winter", met = M1)
#> $f_drift
+#> [1] 0.02759
+#> 
+#> $eq_rate_drift_s
+#> [1] 0
+#> 
+#> $eq_rate_rd_s
+#> [1] 200
+#> 
+#> $eq_rate_rd_parent_s
+#> [1] 0
+#> 
+#> $input_drift_s
+#> [1] 0
+#> 
+#> $input_rd_s
+#> [1] 20
+#> 
+#> $f_rd_sw
+#> [1] 0.9375
+#> 
+#> $f_rd_sed
+#> [1] 0.0625
+#> 
+#> $PEC
+#>      type
+#> Time     PECsw  TWAECsw   PECsed TWAECsed
+#>   0   62.50000       NA 31.25000       NA
+#>   1   62.06828 62.28414 31.03414 31.14207
+#>   2   61.63954       NA 30.81977       NA
+#>   4   60.79093       NA 30.39547       NA
+#>   7   59.53987       NA 29.76994       NA
+#>   14  56.71995       NA 28.35997       NA
+#>   21  54.03358       NA 27.01679       NA
+#>   28  51.47444       NA 25.73722       NA
+#>   42  46.71404       NA 23.35702       NA
+#>   50  44.19417       NA 22.09709       NA
+#>   100 31.25000       NA 15.62500       NA
+#> 
+#> $PEC_sw_max
+#> [1] 62.5
+#> 
+#> $PEC_sed_max
+#> [1] 31.25
+#> 
+  
+  
+    Contents
+    
+      Arguments
+      
+      Note
+
+      References
+      
+      Examples
+    
+
+  
+
+
+      
+      
+  Developed by Johannes Ranke.
+
+
+
+  Site built with pkgdown.
+
+
+      
+   
+
+  
+
diff --git a/docs/reference/PEC_sw_sed.html b/docs/reference/PEC_sw_sed.html
index 6ede4c7..ceb8ea3 100644
--- a/docs/reference/PEC_sw_sed.html
+++ b/docs/reference/PEC_sw_sed.html
@@ -7,7 +7,7 @@
 
 
 Calculate predicted environmental concentrations in sediment from surface
- — PEC_sw_sed • pfm
+water concentrations — PEC_sw_sed • pfm
 
 
 
@@ -26,12 +26,14 @@
 
 
 
-
+
 
 
+
+
   
 
   
@@ -68,37 +70,52 @@
   
     
     Calculate predicted environmental concentrations in sediment from surface
-
+water concentrations
     
 
     
-    The method 'percentage' is equivalent to what is used in the CRD spreadsheet
+    
The method 'percentage' is equivalent to what is used in the CRD spreadsheet
 PEC calculator
     
 
-    PEC_sw_sed(PEC_sw, percentage = 100, method = "percentage",
+    PEC_sw_sed(PEC_sw, percentage = 100, method = "percentage",
   sediment_depth = 5, water_depth = 30, sediment_density = 1.3,
   PEC_sed_units = c("µg/kg", "mg/kg"))
     
      Arguments
-    
-      PEC_sw
-      Numeric vector or matrix of surface water concentrations in µg/L for
-which the corresponding sediment concentration is to be estimated
-      percentage
-      The percentage in sediment, used for the percentage method
-      method
-      The method used for the calculation
-      sediment_depth
-      Depth of the sediment layer
-      water_depth
-      Depth of the water body in cm
-      sediment_density
-      The density of the sediment in L/kg (equivalent to
-g/cm3)
-      PEC_sed_units
-      The units of the estimated sediment PEC value
-    
+    
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    PEC_sw Numeric vector or matrix of surface water concentrations in µg/L for
+which the corresponding sediment concentration is to be estimated
percentage The percentage in sediment, used for the percentage method
method The method used for the calculation
sediment_depth Depth of the sediment layer
water_depth Depth of the water body in cm
sediment_density The density of the sediment in L/kg (equivalent to
+g/cm3)
PEC_sed_units The units of the estimated sediment PEC value
     
     Value
 
diff --git a/docs/reference/PELMO_path.html b/docs/reference/PELMO_path.html
index ab24341..d19d640 100644
--- a/docs/reference/PELMO_path.html
+++ b/docs/reference/PELMO_path.html
@@ -25,12 +25,14 @@
 
 
 
-
+
 
 
+
+
   
 
   
@@ -73,17 +75,24 @@
     Create a path of run directories as the PELMO GUI does
     
 
-    PELMO_path(psm, crop, scenario = NA)
+    PELMO_path(psm, crop, scenario = NA)
     
      Arguments
-    
-      psm
-      The psm identifier
-      crop
-      The PELMO crop acronym
-      scenario
-      The scenario
-    
+    
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    psm The psm identifier
crop The PELMO crop acronym
scenario The scenario
     
 
   
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)
+})

DT50	The half-life.
times	The output times, and window sizes for time weighted average concentrations

Koc	The sorption coefficient normalised to organic carbon in L/kg

Koc	Partition coefficient between organic carbon and water +in L/kg.
DT50_ws	Half-life in water/sediment systems in days
cwsat	Water solubility in mg/L
mw	Molar weight in g/mol
max_soil	Maximum observed fraction (dimensionless) in soil
max_ws	Maximum observed fraction (dimensionless) in water/sediment +systems

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 - check_psm_files - Should we check if the psm file exists - +as used in `FOCUS_GW_scenarios_2012`.
psm_dir	The directory where the psm files are located
check_psm_files	Should we check if the psm file exists

chent	The chent object to get the information from
medium	The medium for which information is sought
type	The information type
lab_field	If not NA, do we want laboratory or field endpoints
redox	If not NA, are we looking for aerobic or anaerobic data
value	The name of the value we want. The list given in the +usage section is not exclusive
aggregator	The aggregator function. Can be mean, +`geomean`, or identity, for example.
raw	Should the number(s) be returned as stored in the chent object (could be a character value) to retain original information -about precision? - signif - How many significant digits do we want - values - The values to be returned - aggregators - A named vector of aggregator functions to be used - +about precision?
signif	How many significant digits do we want
values	The values to be returned
aggregators	A named vector of aggregator functions to be used

c_period	A numeric vector of values to calculate the percentile from
old	Should the old calculation method be used (the 17th highest value)?

x	Vector of numbers
na.rm	Should NA values be omitted?

chem_file	The full path to a CHEM*.PLM file

psm_file	The path to the .psm file
location_code	The location code

General utility functions

Functions that are independent of specific fate modelling areas

- - -

Calculate the geometric mean

geomean

- -

Create a time series of decline data

- -

Plot time series of decline data

plot.one_box

- -

Create decline time series for multiple applications

sawtooth

- -

Calculate a time weighted average concentration

twa
twa.one_box

- -

The maximum time weighted average concentration for a moving window

max_twa

Predicted environmental concentrations in soil

+ - -

Calculate predicted environmental concentrations in soil

PEC_soil

- -

Properties of the predefined scenarios from the EFSA guidance from 2015

soil_scenario_data_EFSA_2015

Predicted environmental concentrations in groundwater

+ + + + - -

Set up runs for FOCUS PELMO

Predicted environmental concentrations in surface water

- - -

Calculate predicted environmental concentrations in surface water due to drift

PEC_sw_drift

- -

Deposition from spray drift expressed as percent of the applied dose as -

drift_data_JKI

- -

Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method

PEC_sw_drainage_UK

- -

R6 class for holding TOXSWA cwa concentration data and associated statistics

TOXSWA_cwa

- -

Read TOXSWA surface water concentrations

read.TOXSWA_cwa

- -

Plot TOXSWA surface water concentrations

plot.TOXSWA_cwa

Classifications and indicators

Evaluating environmental fate properties

- - -

Determine the SSLRC mobility classification for a chemical substance from its Koc

SSLRC_mobility_classification

- -

Groundwater ubiquity score based on Gustafson (1989)

- + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ General utility functions + Functions that are independent of specific fate modelling areas +
+ `geomean` +	Calculate the geometric mean
+ `one_box` +	Create a time series of decline data
+ `plot` +	Plot time series of decline data
+ `sawtooth` +	Create decline time series for multiple applications
+ `twa` +	Calculate a time weighted average concentration
+ `max_twa` +	The maximum time weighted average concentration for a moving window
+ Predicted environmental concentrations in soil + +
+ `PEC_soil` +	Calculate predicted environmental concentrations in soil
+ `soil_scenario_data_EFSA_2015` +	Properties of the predefined scenarios from the EFSA guidance from 2015
+ Predicted environmental concentrations in groundwater + +
+ `PELMO_runs` `run_PELMO` `evaluate_PELMO` +	Set up runs for FOCUS PELMO
+ Predicted environmental concentrations in surface water + +
+ `PEC_sw_drift` +	Calculate predicted environmental concentrations in surface water due to drift
+ `drift_data_JKI` +	Deposition from spray drift expressed as percent of the applied dose as +published by the JKI
+ `PEC_sw_drainage_UK` +	Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method
+ `PEC_sw_focus` +	Calculate FOCUS Step 1 PEC surface water
+ `TOXSWA_cwa` +	R6 class for holding TOXSWA cwa concentration data and associated statistics
+ `read.TOXSWA_cwa` +	Read TOXSWA surface water concentrations
+ `plot` +	Plot TOXSWA surface water concentrations
+ Classifications and indicators + Evaluating environmental fate properties +
+ `SSLRC_mobility_classification` +	Determine the SSLRC mobility classification for a chemical substance from its Koc
+ `GUS` `print` +	Groundwater ubiquity score based on Gustafson (1989)

diff --git a/docs/reference/max_twa.html b/docs/reference/max_twa.html index f78da58..431bbd7 100644 --- a/docs/reference/max_twa.html +++ b/docs/reference/max_twa.html @@ -25,12 +25,14 @@ - + + + @@ -77,15 +79,20 @@ for finding the maximum. It is therefore recommended to check this using max_twa.

max_twa(x, window = 21)

max_twa(x, window = 21)

Arguments

x: An object of type one_box
window: The size of the moving window

+ + + + + + + + + + +

x	An object of type `one_box`
window	The size of the moving window

Details

diff --git a/docs/reference/one_box-12.png b/docs/reference/one_box-12.png deleted file mode 100644 index 31e2f4b..0000000 Binary files a/docs/reference/one_box-12.png and /dev/null differ diff --git a/docs/reference/one_box-6.png b/docs/reference/one_box-6.png deleted file mode 100644 index 10ebb35..0000000 Binary files a/docs/reference/one_box-6.png and /dev/null differ diff --git a/docs/reference/one_box.html b/docs/reference/one_box.html index 800ca66..931e722 100644 --- a/docs/reference/one_box.html +++ b/docs/reference/one_box.html @@ -25,12 +25,14 @@ - + + + @@ -73,7 +75,7 @@

Create a time series of decline data

one_box(x, ini, ..., t_end = 100, res = 0.01)
+    one_box(x, ini, ..., t_end = 100, res = 0.01)
 
 # S3 method for numeric
 one_box(x, ini = 1, ..., t_end = 100, res = 0.01)
@@ -86,28 +88,41 @@
 one_box(x, ini = "model", ..., t_end = 100, res = 0.01)
     
      Arguments
-    
-      x
-      When numeric, this is the half-life to be used for an exponential
+    
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    x When numeric, this is the half-life to be used for an exponential
 decline. When a character string specifying a parent decline model is given
 e.g. FOMC, parms must contain the corresponding paramters.
 If x is an mkinfit object, the decline is calculated from this
-object.
-      
ini
-      The initial amount. If x is an mkinfit object, and
-ini is 'model', the fitted initial concentrations are used. Otherwise, ini
+object.
ini The initial amount. If x is an mkinfit object, and
+ini is 'model', the fitted initial concentrations are used. Otherwise, ini
 must be numeric. If it has length one, it is used for the parent and
 initial values of metabolites are zero, otherwise, it must give values for
-all observed variables.
-      
...
-      Further arguments passed to methods
-      t_end
-      End of the time series
-      res
-      Resolution of the time series
-      parms
-      A named numeric vector containing the model parameters
-    
+all observed variables.
... Further arguments passed to methods
t_end End of the time series
res Resolution of the time series
parms A named numeric vector containing the model parameters
     
     Value
 
diff --git a/docs/reference/pfm_degradation.html b/docs/reference/pfm_degradation.html
index d98778b..9198f6b 100644
--- a/docs/reference/pfm_degradation.html
+++ b/docs/reference/pfm_degradation.html
@@ -25,12 +25,14 @@
 
 
 
-
+
 
 
+
+
   
 
   
@@ -73,27 +75,40 @@
     Calculate a time course of relative concentrations based on an mkinmod model
     
 
-    pfm_degradation(model = "SFO", DT50 = 1000, parms = c(k_parent_sink =
+    pfm_degradation(model = "SFO", DT50 = 1000, parms = c(k_parent_sink =
   log(2)/DT50), years = 1, step_days = 1, times = seq(0, years * 365, by =
   step_days))
     
      Arguments
-    
-      model
-      The degradation model to be used. Either a parent only model like
-'SFO' or 'FOMC', or an mkinmod object
-      DT50
-      The half-life. This is only used when simple exponential decline
-is calculated (SFO model).
-      parms
-      The parameters used for the degradation model
-      years
-      For how many years should the degradation be predicted?
-      step_days
-      What step size in days should the output have?
-      times
-      The output times
-    
+    
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    model The degradation model to be used. Either a parent only model like
+'SFO' or 'FOMC', or an mkinmod object
DT50 The half-life. This is only used when simple exponential decline
+is calculated (SFO model).
parms The parameters used for the degradation model
years For how many years should the degradation be predicted?
step_days What step size in days should the output have?
times The output times
     
 
     Examples
diff --git a/docs/reference/plot.TOXSWA_cwa.html b/docs/reference/plot.TOXSWA_cwa.html
index 7cbe238..5375673 100644
--- a/docs/reference/plot.TOXSWA_cwa.html
+++ b/docs/reference/plot.TOXSWA_cwa.html
@@ -25,12 +25,14 @@
 
 
 
-
+
 
 
+
+
   
 
   
@@ -74,30 +76,45 @@
 segment of a TOXSWA surface water body.
     
 
-    # S3 method for TOXSWA_cwa
+    # S3 method for TOXSWA_cwa
 plot(x, time_column = c("datetime", "t", "t_firstjan",
   "t_rel_to_max"), xlab = "default", ylab = "default", add = FALSE,
   total = FALSE, LC_TIME = "C", ...)
     
      Arguments
-    
-      x
-      The TOXSWA_cwa object to be plotted.
-      time_column
-      What should be used for the time axis. If "t_firstjan" is chosen,
-the time is given in days relative to the first of January in the first year.
-      xlab, ylab
-      Labels for x and y axis.
-      add
-      Should we add to an existing plot?
-      total
-      Should the total concentration in water be plotted, including substance sorbed
-to suspended matter?
-      LC_TIME
-      Specification of the locale used to format dates
-      ...
-      Further arguments passed to plot if we are not adding to an existing plot
-    
+    
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    x The TOXSWA_cwa object to be plotted.
time_column What should be used for the time axis. If "t_firstjan" is chosen,
+the time is given in days relative to the first of January in the first year.
xlab, ylab Labels for x and y axis.
add Should we add to an existing plot?
total Should the total concentration in water be plotted, including substance sorbed
+to suspended matter?
LC_TIME Specification of the locale used to format dates
... Further arguments passed to plot if we are not adding to an existing plot
     
 
     Examples
diff --git a/docs/reference/plot.one_box.html b/docs/reference/plot.one_box.html
index 4c3cb82..0a876e3 100644
--- a/docs/reference/plot.one_box.html
+++ b/docs/reference/plot.one_box.html
@@ -25,12 +25,14 @@
 
 
 
-
+
 
 
+
+
   
 
   
@@ -73,32 +75,49 @@
     Plot time series of decline data
     
 
-    # S3 method for one_box
+    # S3 method for one_box
 plot(x, xlim = range(time(x)), ylim = c(0, max(x)),
   xlab = "Time", ylab = "Residue", max_twa = NULL,
   max_twa_var = dimnames(x)[[2]][1], ...)
     
      Arguments
-    
-      x
-      The object of type one_box to be plotted
-      xlim
-      Limits for the x axis
-      ylim
-      Limits for the y axis
-      xlab
-      Label for the x axis
-      ylab
-      Label for the y axis
-      max_twa
-      If a numeric value is given, the maximum time weighted
-average concentration(s) is/are shown in the graph.
-      max_twa_var
-      Variable for which the maximum time weighted average should
-be shown if max_twa is not NULL.
-      ...
-      Further arguments passed to methods
-    
+    
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    x The object of type one_box to be plotted
xlim Limits for the x axis
ylim Limits for the y axis
xlab Label for the x axis
ylab Label for the y axis
max_twa If a numeric value is given, the maximum time weighted
+average concentration(s) is/are shown in the graph.
max_twa_var Variable for which the maximum time weighted average should
+be shown if max_twa is not NULL.
... Further arguments passed to methods
     
     See also
 
diff --git a/docs/reference/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html
index 3afec9c..30e29cd 100644
--- a/docs/reference/read.TOXSWA_cwa.html
+++ b/docs/reference/read.TOXSWA_cwa.html
@@ -25,12 +25,14 @@
 
 
 
-
+
 
 
+
+
   
 
   
@@ -77,37 +79,54 @@ segment are imported. As TOXSWA 4 reports the values at the end of the hour
 of the hourly averages (ConLiqWatLay).
     
 
-    read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL, segment = "last",
+    read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL, segment = "last",
   substance = "parent", total = FALSE, windows = NULL,
   thresholds = NULL)
     
      Arguments
-    
-      filename
-      The filename of the cwa file (TOXSWA 2.x.y  or similar) or the
-out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).
-      basedir
-      The path to the directory where the cwa file resides.
-      zipfile
-      Optional path to a zip file containing the cwa file.
-      segment
-      The segment for which the data should be read. Either "last", or 
-the segment number.
-      substance
-      For TOXSWA 4 .out files, the default value "parent" leads
+    
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    filename The filename of the cwa file (TOXSWA 2.x.y  or similar) or the
+out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).
basedir The path to the directory where the cwa file resides.
zipfile Optional path to a zip file containing the cwa file.
segment The segment for which the data should be read. Either "last", or 
+the segment number.
substance For TOXSWA 4 .out files, the default value "parent" leads
 to reading concentrations of the parent compound. Alternatively, the substance
-of interested can be selected by its code name.
-      
total
-      Set this to TRUE in order to read total concentrations as well. This is 
+of interested can be selected by its code name.
total Set this to TRUE in order to read total concentrations as well. This is 
 only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa
-files. For .cwa files, the total concentration is always read as well.
-      
windows
-      Numeric vector of width of moving windows in days, for calculating
-maximum time weighted average concentrations and areas under the curve.
-      thresholds
-      Numeric vector of threshold concentrations in µg/L for
-generating event statistics.
-    
+files. For .cwa files, the total concentration is always read as well.
windows Numeric vector of width of moving windows in days, for calculating
+maximum time weighted average concentrations and areas under the curve.
thresholds Numeric vector of threshold concentrations in µg/L for
+generating event statistics.
     
     Value
 
diff --git a/docs/reference/run_PELMO.html b/docs/reference/run_PELMO.html
deleted file mode 100644
index 067d3c1..0000000
--- a/docs/reference/run_PELMO.html
+++ /dev/null
@@ -1,119 +0,0 @@
-
-
-
-  
-  
-
-
-
-Run PELMO — run_PELMO • pfm
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-  
-
-  
-    
-      
-      
-  
-    
-      
-      pfm
-    
-    
-      
-        
-  Reference
-
-      
-      
-      
-        
-      
-    

-  

-

-
-      
-      
-
-      
-  
-    
-    Run PELMO
-    
-
-    
-    Run PELMO
-    
-
-    run_PELMO(runs, version = "5.5.3", PELMO_base = "auto",
-  cores = getOption("mc.cores", 2L))
-    
-     Arguments
-    
-      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.
-      version
-      The FOCUS PELMO version
-      PELMO_base
-      Where the FOCUS PELMO installation is located
-      cores
-      The number of cores to execute PELMO runs in parallel
-    
-    
-
-  
-  
-    Contents
-    
-      Arguments
-                
-
-  
-
-
-      
-      
-  Developed by Johannes Ranke.
-
-
-
-  Site built with pkgdown.
-
-
-      
-   
-
-  
-
diff --git a/docs/reference/sawtooth-8.png b/docs/reference/sawtooth-8.png
deleted file mode 100644
index 161ecb4..0000000
Binary files a/docs/reference/sawtooth-8.png and /dev/null differ
diff --git a/docs/reference/sawtooth.html b/docs/reference/sawtooth.html
index be43745..0d5c9a9 100644
--- a/docs/reference/sawtooth.html
+++ b/docs/reference/sawtooth.html
@@ -25,12 +25,14 @@
 
 
 
-
+
 
 
+
+
   
 
   
@@ -75,22 +77,31 @@ application pattern specified in applications is repeated ni.
     
 
-    sawtooth(x, n = 1, i = 365, applications = data.frame(time = seq(0, 0 + n
+    sawtooth(x, n = 1, i = 365, applications = data.frame(time = seq(0, 0 + n
   * i, length.out = n), amount = 1))
     
      Arguments
-    
-      x
-      A one_box object
-      n
-      The number of applications. If applications is specified, n is ignored
-      i
-      The interval between applications. If applications is specified, i
-is ignored
-      applications
-      A data frame holding the application times in the first column and
-the corresponding amounts applied in the second column.
-    
+    
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    x A one_box object
n The number of applications. If applications is specified, n is ignored
i The interval between applications. If applications is specified, i
+is ignored
applications A data frame holding the application times in the first column and
+the corresponding amounts applied in the second column.
     
 
     Examples
diff --git a/docs/reference/soil_scenario_data_EFSA_2015.html b/docs/reference/soil_scenario_data_EFSA_2015.html
index f842d08..39841ed 100644
--- a/docs/reference/soil_scenario_data_EFSA_2015.html
+++ b/docs/reference/soil_scenario_data_EFSA_2015.html
@@ -25,12 +25,14 @@
 
 
 
-
+
 
 
+
+
   
 
   
@@ -92,24 +94,24 @@ doi:10.2903/j.efsa.2015.4093
     
 
     Examples
-    ## Not run: ------------------------------------
-#   # This is the code that was used to define the data
-#   soil_scenario_data_EFSA_2015 <- data.frame(
-#     Zone = rep(c("North", "Central", "South"), 2),
-#     Country = c("Estonia", "Germany", "France", "Denmark", "Czech Republik", "Spain"),
-#     T_arit = c(4.7, 8.0, 11.0, 8.2, 9.1, 12.8),
-#     T_arr = c(7.0, 10.1, 12.3, 9.8, 11.2, 14.7),
-#     Texture = c("Coarse", "Coarse", "Medium fine", "Medium", "Medium", "Medium"),
-#     f_om = c(0.118, 0.086, 0.048, 0.023, 0.018, 0.011),
-#     theta_fc = c(0.244, 0.244, 0.385, 0.347, 0.347, 0.347),
-#     rho = c(0.95, 1.05, 1.22, 1.39, 1.43, 1.51),
-#     f_sce = c(3, 2, 2, 2, 1.5, 1.5),
-#     f_mod = c(2, 2, 2, 4, 4, 4),
-#     stringsAsFactors = FALSE,
-#     row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS")
-#   )
-#   save(soil_scenario_data_EFSA_2015, file = '../data/soil_scenario_data_EFSA_2015.RData')
-## ---------------------------------------------
+    not_run({
+    # This is the code that was used to define the data
+    soil_scenario_data_EFSA_2015 <- data.frame(
+      Zone = rep(c("North", "Central", "South"), 2),
+      Country = c("Estonia", "Germany", "France", "Denmark", "Czech Republik", "Spain"),
+      T_arit = c(4.7, 8.0, 11.0, 8.2, 9.1, 12.8),
+      T_arr = c(7.0, 10.1, 12.3, 9.8, 11.2, 14.7),
+      Texture = c("Coarse", "Coarse", "Medium fine", "Medium", "Medium", "Medium"),
+      f_om = c(0.118, 0.086, 0.048, 0.023, 0.018, 0.011),
+      theta_fc = c(0.244, 0.244, 0.385, 0.347, 0.347, 0.347),
+      rho = c(0.95, 1.05, 1.22, 1.39, 1.43, 1.51),
+      f_sce = c(3, 2, 2, 2, 1.5, 1.5),
+      f_mod = c(2, 2, 2, 4, 4, 4),
+      stringsAsFactors = FALSE,
+      row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS")
+    )
+    save(soil_scenario_data_EFSA_2015, file = '../data/soil_scenario_data_EFSA_2015.RData')
+})
 
 # And this is the resulting dataframe
 soil_scenario_data_EFSA_2015
#>        Zone        Country T_arit T_arr     Texture  f_om theta_fc  rho f_sce
diff --git a/docs/reference/sum_periods.html b/docs/reference/sum_periods.html
index 66466ac..147a698 100644
--- a/docs/reference/sum_periods.html
+++ b/docs/reference/sum_periods.html
@@ -25,12 +25,14 @@
 
 
 
-
+
 
 
+
+
   
 
   
@@ -73,13 +75,27 @@
     Sum up values according to FOCUS periods
     
 
-    sum_periods(annual, interval)
-        
+    sum_periods(annual, interval)
+    
+     Arguments
+    
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    annual The annual flux as obtained by get_flux
interval The interval in years
+    
 
   
   
     Contents
     
+      Arguments
                 
 
   
diff --git a/docs/reference/twa.html b/docs/reference/twa.html
index 414b372..32fa459 100644
--- a/docs/reference/twa.html
+++ b/docs/reference/twa.html
@@ -25,12 +25,14 @@
 
 
 
-
+
 
 
+
+
   
 
   
@@ -75,18 +77,23 @@ the earliest possible time for the maximum in the time series returned
 is after one window has passed.
     
 
-    twa(x, window = 21)
+    twa(x, window = 21)
 
 # S3 method for one_box
 twa(x, window = 21)
     
      Arguments
-    
-      x
-      An object of type one_box
-      window
-      The size of the moving window
-    
+    
+    
+    
+      
+      
+    
+    
+      
+      
+    
+    x An object of type one_box
window The size of the moving window
     
     See also
 
-- 
cgit v1.2.1

x	A `one_box` object
n	The number of applications. If `applications` is specified, `n` is ignored
i	The interval between applications. If `applications` is specified, `i` +is ignored
applications	A data frame holding the application times in the first column and +the corresponding amounts applied in the second column.

x	When numeric, this is the half-life to be used for an exponential decline. When a character string specifying a parent decline model is given e.g. `FOMC`, `parms` must contain the corresponding paramters. If x is an `mkinfit` object, the decline is calculated from this -object. - ini - The initial amount. If x is an `mkinfit` object, and -ini is 'model', the fitted initial concentrations are used. Otherwise, ini +object.
ini	The initial amount. If x is an `mkinfit` object, and +ini is 'model', the fitted initial concentrations are used. Otherwise, ini must be numeric. If it has length one, it is used for the parent and initial values of metabolites are zero, otherwise, it must give values for -all observed variables. - ... - Further arguments passed to methods - t_end - End of the time series - res - Resolution of the time series - parms - A named numeric vector containing the model parameters - +all observed variables.
...	Further arguments passed to methods
t_end	End of the time series
res	Resolution of the time series
parms	A named numeric vector containing the model parameters

model	The degradation model to be used. Either a parent only model like +'SFO' or 'FOMC', or an mkinmod object
DT50	The half-life. This is only used when simple exponential decline +is calculated (SFO model).
parms	The parameters used for the degradation model
years	For how many years should the degradation be predicted?
step_days	What step size in days should the output have?
times	The output times

x	The TOXSWA_cwa object to be plotted.
time_column	What should be used for the time axis. If "t_firstjan" is chosen, +the time is given in days relative to the first of January in the first year.
xlab, ylab	Labels for x and y axis.
add	Should we add to an existing plot?
total	Should the total concentration in water be plotted, including substance sorbed +to suspended matter?
LC_TIME	Specification of the locale used to format dates
...	Further arguments passed to `plot` if we are not adding to an existing plot

x	The object of type `one_box` to be plotted
xlim	Limits for the x axis
ylim	Limits for the y axis
xlab	Label for the x axis
ylab	Label for the y axis
max_twa	If a numeric value is given, the maximum time weighted +average concentration(s) is/are shown in the graph.
max_twa_var	Variable for which the maximum time weighted average should +be shown if max_twa is not NULL.
...	Further arguments passed to methods

filename	The filename of the cwa file (TOXSWA 2.x.y or similar) or the +out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).
basedir	The path to the directory where the cwa file resides.
zipfile	Optional path to a zip file containing the cwa file.
segment	The segment for which the data should be read. Either "last", or +the segment number.
substance	For TOXSWA 4 .out files, the default value "parent" leads to reading concentrations of the parent compound. Alternatively, the substance -of interested can be selected by its code name. - total - Set this to TRUE in order to read total concentrations as well. This is +of interested can be selected by its code name.
total	Set this to TRUE in order to read total concentrations as well. This is only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa -files. For .cwa files, the total concentration is always read as well. - windows - Numeric vector of width of moving windows in days, for calculating -maximum time weighted average concentrations and areas under the curve. - thresholds - Numeric vector of threshold concentrations in µg/L for -generating event statistics. - +files. For .cwa files, the total concentration is always read as well.
windows	Numeric vector of width of moving windows in days, for calculating +maximum time weighted average concentrations and areas under the curve.
thresholds	Numeric vector of threshold concentrations in µg/L for +generating event statistics.

annual	The annual flux as obtained by `get_flux`
interval	The interval in years

A very small subset of the FOCUS Groundwater scenario defitions

A very small subset of the FOCUS Groundwater scenario definitions

Format

Examples

Format

Examples

Contents

Format

Contents

Format

Examples

Contents

Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator

Format

Examples

Contents

Arguments

Value

Arguments

Value

Details

Note

References

Arguments

Value

Arguments

Value

Calculate FOCUS Step 1 PEC surface water

Arguments

Note

References

Examples

Contents

Calculate predicted environmental concentrations in sediment from surface -

Arguments

Value

Arguments

Arguments

Value

References

Examples

Contents

Arguments

Source

Arguments

Value

Examples

Format

Methods

Examples

Create a chemical compound object for FOCUS Step 1 calculations

Arguments

Value

Contents

Arguments

Deposition from spray drift expressed as percent of the applied dose as -

Source

Examples

Arguments

Value

Evaluate PELMO runs

Arguments

Contents

Arguments

Arguments

Value

Arguments

Contents

Arguments

Contents

Function reference

version 0.4-2

+ Reference + version 0.4-3 +

General utility functions

Predicted environmental concentrations in soil

Predicted environmental concentrations in groundwater

Predicted environmental concentrations in surface water

Classifications and indicators

General utility functions

Predicted environmental concentrations in soil