Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014 • pfm

From 396ba6c42252426a132be56b9f417786a1f276e3 Mon Sep 17 00:00:00 2001 From: Ranke Johannes Date: Tue, 13 Aug 2024 10:58:16 +0200 Subject: Support units in drift, runoff und sediment PECs --- docs/reference/EFSA_GW_interception_2014.html | 47 ++- docs/reference/EFSA_washoff_2017.html | 47 ++- docs/reference/FOCUS_GW_scenarios_2012.html | 51 ++-- docs/reference/FOCUS_Step_12_scenarios.html | 51 ++-- docs/reference/FOMC_actual_twa.html | 55 ++-- docs/reference/GUS.chent.html | 8 + docs/reference/GUS.html | 87 +++--- docs/reference/GUS.numeric.html | 8 + docs/reference/PEC_soil.html | 101 +++---- docs/reference/PEC_sw_drainage_UK.html | 71 ++--- docs/reference/PEC_sw_drift.html | 110 +++---- docs/reference/PEC_sw_exposit_drainage.html | 77 +++-- docs/reference/PEC_sw_exposit_runoff.html | 138 +++++---- docs/reference/PEC_sw_focus.html | 85 +++--- docs/reference/PEC_sw_sed.html | 90 +++--- docs/reference/SFO_actual_twa.html | 53 ++-- docs/reference/SSLRC_mobility_classification.html | 59 ++-- docs/reference/TOXSWA_cwa.html | 55 ++-- docs/reference/TSCF.html | 57 ++-- docs/reference/drift_data_JKI.html | 54 ++-- docs/reference/drift_parameters_focus.html | 51 ++-- docs/reference/drift_percentages_rautmann.html | 59 ++-- docs/reference/endpoint.html | 79 +++-- docs/reference/index.html | 346 ++++++++++++---------- docs/reference/max_twa.html | 61 ++-- docs/reference/one_box.character.html | 8 + docs/reference/one_box.mkinfit.html | 8 + docs/reference/one_box.numeric.html | 8 + docs/reference/perc_runoff_exposit.html | 73 ++--- docs/reference/perc_runoff_reduction_exposit.html | 49 ++- docs/reference/print.GUS_result.html | 8 + docs/reference/set_nd_nq.html | 8 + docs/reference/set_nd_nq_focus.html | 8 + docs/reference/soil_DT50.html | 8 + docs/reference/soil_Kfoc.html | 8 + docs/reference/soil_N.html | 8 + docs/reference/soil_scenario_data_EFSA_2015.html | 51 ++-- docs/reference/soil_scenario_data_EFSA_2017.html | 51 ++-- docs/reference/soil_sorption.html | 8 + docs/reference/twa.one_box.html | 8 + 40 files changed, 1070 insertions(+), 1142 deletions(-) create mode 100644 docs/reference/GUS.chent.html create mode 100644 docs/reference/GUS.numeric.html create mode 100644 docs/reference/one_box.character.html create mode 100644 docs/reference/one_box.mkinfit.html create mode 100644 docs/reference/one_box.numeric.html create mode 100644 docs/reference/print.GUS_result.html create mode 100644 docs/reference/set_nd_nq.html create mode 100644 docs/reference/set_nd_nq_focus.html create mode 100644 docs/reference/soil_DT50.html create mode 100644 docs/reference/soil_Kfoc.html create mode 100644 docs/reference/soil_N.html create mode 100644 docs/reference/soil_sorption.html create mode 100644 docs/reference/twa.one_box.html (limited to 'docs/reference') diff --git a/docs/reference/EFSA_GW_interception_2014.html b/docs/reference/EFSA_GW_interception_2014.html index 555509e..cf97c02 100644 --- a/docs/reference/EFSA_GW_interception_2014.html +++ b/docs/reference/EFSA_GW_interception_2014.html @@ -1,43 +1,34 @@ -Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014 • pfm +Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014 • pfm - -

- + +

@@ -78,23 +69,23 @@ products of these active substances in soil. EFSA Journal #> Winter cereals 0 0.00 0.20 0.80 0.90 0.90 0.90 0.80 0.80 0.80

-

- - + + diff --git a/docs/reference/EFSA_washoff_2017.html b/docs/reference/EFSA_washoff_2017.html index 3603cda..a6b51d9 100644 --- a/docs/reference/EFSA_washoff_2017.html +++ b/docs/reference/EFSA_washoff_2017.html @@ -1,43 +1,34 @@ -Subset of EFSA crop washoff default values — EFSA_washoff_2017 • pfm +Subset of EFSA crop washoff default values — EFSA_washoff_2017 • pfm - -

- + +

@@ -78,23 +69,23 @@ doi:10.2903/j.efsa.2017.4982

#> Winter cereals NA 0.10 0.40 0.60 0.55 0.55 0.55 0.60 0.60 0.40

-

- - + + diff --git a/docs/reference/FOCUS_GW_scenarios_2012.html b/docs/reference/FOCUS_GW_scenarios_2012.html index 20140cc..b2295c5 100644 --- a/docs/reference/FOCUS_GW_scenarios_2012.html +++ b/docs/reference/FOCUS_GW_scenarios_2012.html @@ -1,45 +1,36 @@ -A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012 • pfm +A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012 • pfm - -

- + +

@@ -130,23 +121,23 @@ http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf

#>

-

- - + + diff --git a/docs/reference/FOCUS_Step_12_scenarios.html b/docs/reference/FOCUS_Step_12_scenarios.html index aab1d87..536b974 100644 --- a/docs/reference/FOCUS_Step_12_scenarios.html +++ b/docs/reference/FOCUS_Step_12_scenarios.html @@ -1,45 +1,36 @@ -Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios • pfm +Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios • pfm - -

- + +

@@ -101,23 +92,23 @@ calculations in a matrix called 'rd'.

#> list()

-

- - + + diff --git a/docs/reference/FOMC_actual_twa.html b/docs/reference/FOMC_actual_twa.html index b66cd35..1e0fd64 100644 --- a/docs/reference/FOMC_actual_twa.html +++ b/docs/reference/FOMC_actual_twa.html @@ -1,43 +1,34 @@ -Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa • pfm +Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa • pfm - -

- + +

@@ -63,15 +54,17 @@ Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Versi

Arguments

-

alpha

@@ -97,23 +90,23 @@ Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Versi #> 100 0.09088729 0.2397608

-

On this page

+ - - + + diff --git a/docs/reference/GUS.chent.html b/docs/reference/GUS.chent.html new file mode 100644 index 0000000..15d3826 --- /dev/null +++ b/docs/reference/GUS.chent.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/GUS.html b/docs/reference/GUS.html index 7638dcd..a613d98 100644 --- a/docs/reference/GUS.html +++ b/docs/reference/GUS.html @@ -1,47 +1,38 @@ -Groundwater ubiquity score based on Gustafson (1989) — GUS • pfmGroundwater ubiquity score based on Gustafson (1989) — GUS • pfm +$$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$"> - -

- + +

@@ -56,10 +47,10 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$

Usage

GUS(...)
 
-# S3 method for numeric
+# S3 method for class 'numeric'
 GUS(DT50, Koc, ...)
 
-# S3 method for chent
+# S3 method for class 'chent'
 GUS(
   chent,
   degradation_value = "DT50ref",
@@ -71,18 +62,20 @@ $$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$
   ...
 )
 
-# S3 method for GUS_result
+# S3 method for class 'GUS_result'
 print(x, ..., digits = 1)

Arguments

-

...

Value

- - -

A list with the DT50 and Koc used as well as the resulting score +

A list with the DT50 and Koc used as well as the resulting score of class GUS_result

@@ -162,23 +153,23 @@ toxicology and chemistry 8(4) 339–57.

Johannes Ranke

-

- - + + diff --git a/docs/reference/GUS.numeric.html b/docs/reference/GUS.numeric.html new file mode 100644 index 0000000..15d3826 --- /dev/null +++ b/docs/reference/GUS.numeric.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html index 46c92f4..e86dd6d 100644 --- a/docs/reference/PEC_soil.html +++ b/docs/reference/PEC_soil.html @@ -1,51 +1,42 @@ -Calculate predicted environmental concentrations in soil — PEC_soil • pfmCalculate predicted environmental concentrations in soil — PEC_soil • pfm +and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017)."> - -

- + +

@@ -88,99 +79,101 @@ and in the EFSA guidance on PEC soil calculations (EFSA, 2015, 2017).

Arguments

-

rate

Value

- - -

The predicted concentration in soil

+

The predicted concentration in soil

Details

@@ -305,23 +296,23 @@ doi:10.2903/j.efsa.2015.4093

Kom = 100, scenarios = "EFSA_2015", porewater = TRUE)

-

- - + + diff --git a/docs/reference/PEC_sw_drainage_UK.html b/docs/reference/PEC_sw_drainage_UK.html index 3996f9c..d8b885f 100644 --- a/docs/reference/PEC_sw_drainage_UK.html +++ b/docs/reference/PEC_sw_drainage_UK.html @@ -1,45 +1,36 @@ -Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK • pfm +Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK • pfm - -

- + +

@@ -64,40 +55,40 @@ published on the CRC website

Arguments

-

rate

Value

- - -

The predicted concentration in surface water in µg/L

+

The predicted concentration in surface water in µg/L

References

@@ -120,23 +111,23 @@ accessed 2019-09-27

#> [1] 8.076923

-

- - + + diff --git a/docs/reference/PEC_sw_drift.html b/docs/reference/PEC_sw_drift.html index 1fe8465..cc6fefd 100644 --- a/docs/reference/PEC_sw_drift.html +++ b/docs/reference/PEC_sw_drift.html @@ -1,47 +1,38 @@ -Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift • pfmCalculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift • pfm +with input via spray drift."> - -

- + +

@@ -57,7 +48,7 @@ with input via spray drift.

PEC_sw_drift(
   rate,
   applications = 1,
-  water_depth = 30,
+  water_depth = as_units("30 cm"),
   drift_percentages = NULL,
   drift_data = c("JKI", "RF"),
   crop_group_JKI = c("Ackerbau", "Obstbau frueh", "Obstbau spaet", "Weinbau frueh",
@@ -66,7 +57,7 @@ with input via spray drift.
     "fruit, early", "aerial"),
   distances = c(1, 5, 10, 20),
   formula = c("Rautmann", "FOCUS"),
-  water_width = 100,
+  water_width = as_units("100 cm"),
   side_angle = 90,
   rate_units = "g/ha",
   PEC_units = "µg/L"
@@ -75,71 +66,78 @@ with input via spray drift.
 
     
     Arguments
-    rate
-Application rate in units specified below
 
 
-applications
+rate
+Application rate in units specified below, or with units defined via the
+units package.
+
+
+applications
 Number of applications for selection of drift percentile
 
 
-water_depth
+water_depth
 Depth of the water body in cm
 
 
-drift_percentages
+drift_percentages
 Percentage drift values for which to calculate PECsw.
 Overrides 'drift_data' and 'distances' if not NULL.
 
 
-drift_data
+drift_data
 Source of drift percentage data. If 'JKI', the drift_data_JKI
 included in the package is used. If 'RF', the Rautmann drift data are calculated
 either in the original form or integrated over the width of the water body, depending
 on the 'formula' argument.
 
 
-crop_group_JKI
+crop_group_JKI
 When using the 'JKI' drift data, one of the German names
 as used in drift_parameters_focus.
 
 
-crop_group_focus
+crop_group_focus
 One of the crop groups as used in drift_parameters_focus
 
 
-distances
+distances
 The distances in m for which to get PEC values
 
 
-formula
+formula
 By default, the original Rautmann formula is used. If you
 specify "FOCUS", mean drift input over the width of the water body is
 calculated as described in Chapter 5.4.5 of the FOCUS surface water guidance
 
 
-water_width
+water_width
 Width of the water body in cm
 
 
-side_angle
+side_angle
 The angle of the side of the water relative to the bottom which
 is assumed to be horizontal, in degrees. The SYNOPS model assumes 45 degrees here.
 
 
-rate_units
-Defaults to g/ha
+rate_units
+Defaults to g/ha. For backwards compatibility, only used
+if the specified rate does not have units::units].
 
 
-PEC_units
+PEC_units
 Requested units for the calculated PEC. Only µg/L currently supported
 
 
     
     Value
-    
-
-The predicted concentration in surface water
+    The predicted concentration in surface water
+    
+    
+    Details
+    It is recommened to specify the arguments rate, water_depth and
+water_width using units::units from the units package.
     
     
     See also
@@ -153,16 +151,19 @@ is assumed to be horizontal, in degrees. The SYNOPS model assumes 45 degrees her
     
     Examples
     PEC_sw_drift(100)
+#> Units: [µg/L]
 #>        1 m        5 m       10 m       20 m 
 #> 0.92333333 0.19000000 0.09666667 0.05000000 
 # Alternatively, we can use the formula for a single application to
 # "Ackerbau" from the paper
 PEC_sw_drift(100, drift_data = "RF")
+#> Units: [µg/L]
 #>        1 m        5 m       10 m       20 m 
 #> 0.91976667 0.19064473 0.09680051 0.04915079 
 
 # This makes it possible to also use different distances
 PEC_sw_drift(100, distances = c(1, 3, 5, 6, 10, 20, 50, 100), drift_data = "RF")
+#> Units: [µg/L]
 #>        1 m        3 m        5 m        6 m       10 m       20 m       50 m 
 #> 0.91976667 0.31415827 0.19064473 0.15951494 0.09680051 0.04915079 0.02006434 
 #>      100 m 
@@ -171,6 +172,7 @@ is assumed to be horizontal, in degrees. The SYNOPS model assumes 45 degrees her
 # or consider aerial application
 PEC_sw_drift(100, distances = c(1, 3, 5, 6, 10, 20, 50, 100), drift_data = "RF", 
   crop_group_focus = "aerial")
+#> Units: [µg/L]
 #>        1 m        3 m        5 m        6 m       10 m       20 m       50 m 
 #> 16.8233333 11.0585820  9.0986174  8.4866460  6.9825178  4.7004640  1.8820816 
 #>      100 m 
@@ -178,6 +180,7 @@ is assumed to be horizontal, in degrees. The SYNOPS model assumes 45 degrees her
 
 # Using custom drift percentages is also supported
 PEC_sw_drift(100, drift_percentages = c(2.77, 0.95, 0.57, 0.48, 0.29, 0.15, 0.06, 0.03))
+#> Units: [µg/L]
 #>     2.77 %     0.95 %     0.57 %     0.48 %     0.29 %     0.15 %     0.06 % 
 #> 0.92333333 0.31666667 0.19000000 0.16000000 0.09666667 0.05000000 0.02000000 
 #>     0.03 % 
@@ -186,39 +189,44 @@ is assumed to be horizontal, in degrees. The SYNOPS model assumes 45 degrees her
 # The influence of assuming a 45° angle of the sides of the waterbody and the width of the 
 # waterbody can be illustrated
 PEC_sw_drift(100)
+#> Units: [µg/L]
 #>        1 m        5 m       10 m       20 m 
 #> 0.92333333 0.19000000 0.09666667 0.05000000 
 PEC_sw_drift(100, drift_data = "RF")
+#> Units: [µg/L]
 #>        1 m        5 m       10 m       20 m 
 #> 0.91976667 0.19064473 0.09680051 0.04915079 
 PEC_sw_drift(100, drift_data = "RF", formula = "FOCUS")
+#> Units: [µg/L]
 #>        1 m        5 m       10 m       20 m 
 #> 0.64246407 0.17414541 0.09235842 0.04798749 
 PEC_sw_drift(100, drift_data = "RF", formula = "FOCUS", side_angle = 45)
+#> Units: [µg/L]
 #>        1 m        5 m       10 m       20 m 
 #> 0.91780582 0.24877916 0.13194060 0.06855356 
 PEC_sw_drift(100, drift_data = "RF", formula = "FOCUS", side_angle = 45, water_width = 200)
+#> Units: [µg/L]
 #>        1 m        5 m       10 m       20 m 
-#> 0.30085000 0.09468652 0.05201349 0.02758547 
+#> 0.60169999 0.18937304 0.10402698 0.05517095 
 
     
-


 
 
     
-  
Developed by Johannes Ranke.
+  Developed by Johannes Ranke.
 
 
 
-  
Site built with pkgdown 2.0.7.
+  Site built with pkgdown 2.1.0.


 
-  
 
-  
+
+
 
   
 
diff --git a/docs/reference/PEC_sw_exposit_drainage.html b/docs/reference/PEC_sw_exposit_drainage.html
index 5da26c6..7468fe6 100644
--- a/docs/reference/PEC_sw_exposit_drainage.html
+++ b/docs/reference/PEC_sw_exposit_drainage.html
@@ -1,56 +1,47 @@
 
-Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage • pfm
+details, see the discussion of the function arguments below.'>
     Skip to contents
-    
 
-


-    
+
+    
+
     pfm
 
-    0.6.1
+    0.6.3
+
 
-    
     
 
     
-      
-  Reference
-
-      

-        
-
-      
-  
-    
-     
-  
-
+      Reference
+Changelog
+      

+ 
+
       
 
-    
+


 
   
-      Calculate PEC surface water due to drainage as in Exposit 3
-      Source: R/PEC_sw_exposit_runoff.R
+
+      Calculate PEC surface water due to drainage as in Exposit 3
+      Source: R/PEC_sw_exposit.R
       PEC_sw_exposit_drainage.Rd
     
 
@@ -86,49 +77,49 @@ details, see the discussion of the function arguments below.
     
     
     Arguments
-    rate
+
+
+rate
 The application rate in g/ha
 
 
-interception
+interception
 The fraction intercepted by the crop
 
 
-Koc
+Koc
 The sorption coefficient to soil organic carbon used to determine the mobility. A trigger
 value of 550 L/kg is used in order to decide if Koc >> 500.
 
 
-mobility
+mobility
 Overrides what is determined from the Koc.
 
 
-DT50
+DT50
 The soil half-life in days
 
 
-t_drainage
+t_drainage
 The time between application and the drainage event, where degradation occurs, in days
 
 
-V_ditch
+V_ditch
 The volume of the ditch is assumed to be 1 m * 100 m * 30 cm = 30 m3
 
 
-V_drainage
+V_drainage
 The drainage volume, equivalent to 1 mm precipitation on 1 ha for spring/summer or 10 mm for
 autumn/winter/early spring.
 
 
-dilution
+dilution
 The dilution factor


     Value
-    
-
-A list containing the following components

perc_runoff

-

- - + + diff --git a/docs/reference/PEC_sw_exposit_runoff.html b/docs/reference/PEC_sw_exposit_runoff.html index 21731f3..cd57c99 100644 --- a/docs/reference/PEC_sw_exposit_runoff.html +++ b/docs/reference/PEC_sw_exposit_runoff.html @@ -1,46 +1,37 @@ -Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff • pfm +Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff • pfm - -

- + +

@@ -55,11 +46,11 @@ in the worksheet "Konzept Runoff".

rate, interception = 0, Koc, - DT50 = Inf, - t_runoff = 3, + DT50 = set_units(Inf, "d"), + t_runoff = set_units(3, "days"), exposit_reduction_version = c("3.02", "3.01a", "3.01a2", "2.0"), - V_ditch = 30, - V_event = 100, + V_ditch = set_units(30, "m3"), + V_event = set_units(100, "m3"), dilution = 2 )

@@ -71,27 +62,29 @@ in the worksheet "Konzept Runoff".

Arguments

-

rate

Value

- - -

A list containing the following components

perc_runoff

+

+

Details

+

It is recommened to specify the arguments rate, Koc, DT50, t_runoff, V_ditch and V_event +using units::units from the units package.

+

See also

perc_runoff_exposit for runoff loss percentages and perc_runoff_reduction_exposit for runoff reduction percentages used

@@ -140,18 +136,18 @@ for the different distances. If the rate was given in g/ha, the PECsw are in mic #> 0.248 0.001 #> #> $runoff -#> dissolved bound total -#> No buffer 1.240 0.00500 1.24500 -#> 5 m 0.744 0.00300 0.74700 -#> 10 m 0.496 0.00075 0.49675 -#> 20 m 0.248 0.00025 0.24825 +#> dissolved bound total +#> No buffer 1.240 [g] 0.00500 [g] 1.24500 [g] +#> 5 m 0.744 [g] 0.00300 [g] 0.74700 [g] +#> 10 m 0.496 [g] 0.00075 [g] 0.49675 [g] +#> 20 m 0.248 [g] 0.00025 [g] 0.24825 [g] #> #> $PEC_sw_runoff -#> dissolved bound total -#> No buffer 4.769231 0.019230769 4.788462 -#> 5 m 4.133333 0.016666667 4.150000 -#> 10 m 3.542857 0.005357143 3.548214 -#> 20 m 2.480000 0.002500000 2.482500 +#> dissolved bound total +#> No buffer 4.769231 [µg/L] 0.019230769 [µg/L] 4.788462 [µg/L] +#> 5 m 4.133333 [µg/L] 0.016666667 [µg/L] 4.150000 [µg/L] +#> 10 m 3.542857 [µg/L] 0.005357143 [µg/L] 3.548214 [µg/L] +#> 20 m 2.480000 [µg/L] 0.002500000 [µg/L] 2.482500 [µg/L] #> PEC_sw_exposit_runoff(600, Koc = 10000, DT50 = 195, exposit = "3.01a") #> $perc_runoff @@ -159,42 +155,42 @@ for the different distances. If the rate was given in g/ha, the PECsw are in mic #> 0.037 0.159 #> #> $runoff -#> dissolved bound total -#> No buffer 0.21964521 0.94388078 1.16352600 -#> 3 m 0.16473391 0.66071655 0.82545046 -#> 5 m 0.13178713 0.56632847 0.69811560 -#> 6 m 0.12080487 0.42474635 0.54555122 -#> 10 m 0.08785809 0.14158212 0.22944020 -#> 20 m 0.04392904 0.04719404 0.09112308 +#> dissolved bound total +#> No buffer 0.21964521 [g] 0.94388078 [g] 1.16352600 [g] +#> 3 m 0.16473391 [g] 0.66071655 [g] 0.82545046 [g] +#> 5 m 0.13178713 [g] 0.56632847 [g] 0.69811560 [g] +#> 6 m 0.12080487 [g] 0.42474635 [g] 0.54555122 [g] +#> 10 m 0.08785809 [g] 0.14158212 [g] 0.22944020 [g] +#> 20 m 0.04392904 [g] 0.04719404 [g] 0.09112308 [g] #> #> $PEC_sw_runoff -#> dissolved bound total -#> No buffer 0.8447893 3.6303107 4.4751000 -#> 3 m 0.7844472 3.1462693 3.9307165 -#> 5 m 0.7321507 3.1462693 3.8784200 -#> 6 m 0.7106169 2.4985080 3.2091248 -#> 10 m 0.6275578 1.0113008 1.6388586 -#> 20 m 0.4392904 0.4719404 0.9112308 +#> dissolved bound total +#> No buffer 0.8447893 [µg/L] 3.6303107 [µg/L] 4.4751000 [µg/L] +#> 3 m 0.7844472 [µg/L] 3.1462693 [µg/L] 3.9307165 [µg/L] +#> 5 m 0.7321507 [µg/L] 3.1462693 [µg/L] 3.8784200 [µg/L] +#> 6 m 0.7106169 [µg/L] 2.4985080 [µg/L] 3.2091248 [µg/L] +#> 10 m 0.6275578 [µg/L] 1.0113008 [µg/L] 1.6388586 [µg/L] +#> 20 m 0.4392904 [µg/L] 0.4719404 [µg/L] 0.9112308 [µg/L] #>

-

On this page

+ - - + + diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html index d9d06de..d91d957 100644 --- a/docs/reference/PEC_sw_focus.html +++ b/docs/reference/PEC_sw_focus.html @@ -1,55 +1,46 @@ -Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus • pfmCalculate PEC surface water at FOCUS Step 1 — PEC_sw_focus • pfm +the FOCUS calculator."> - -

- + +

@@ -89,85 +80,87 @@ the FOCUS calculator.

Arguments

-

parent

@@ -294,23 +287,23 @@ http://esdac.jrc.ec.europa.eu/projects/stepsonetwo

#>

-

- - + + diff --git a/docs/reference/PEC_sw_sed.html b/docs/reference/PEC_sw_sed.html index c4b0fd8..6d377c9 100644 --- a/docs/reference/PEC_sw_sed.html +++ b/docs/reference/PEC_sw_sed.html @@ -1,48 +1,36 @@ -Calculate predicted environmental concentrations in sediment from surface -water concentrations — PEC_sw_sed • pfm +Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed • pfm - -

- + +

@@ -58,50 +46,50 @@ PEC calculator

PEC_sw, percentage = 100, method = "percentage", - sediment_depth = 5, - water_depth = 30, - sediment_density = 1.3, + sediment_depth = set_units(5, "cm"), + water_depth = set_units(30, "cm"), + sediment_density = set_units(1.3, "kg/L"), PEC_sed_units = c("µg/kg", "mg/kg") )

Arguments

-

PEC_sw

Value

- - -

The predicted concentration in sediment

+

The predicted concentration in sediment

Author

@@ -110,28 +98,30 @@ g/cm3)

Examples

-

PEC_sw_sed(PEC_sw_drift(100, distances = 1), percentage = 50)
-#>      1 m 
-#> 2.130769 
+    library(pfm)
+library(units)
+#> udunits database from /usr/share/xml/udunits/udunits2.xml
+PEC_sw_sed(PEC_sw_drift(100, distances = 1), percentage = 50)
+#> 2.130769 [µg/kg]


-  On this page
+  On this page


 
 
     
-  
Developed by Johannes Ranke.
+  Developed by Johannes Ranke.
 
 
 
-  
Site built with pkgdown 2.0.7.
+  Site built with pkgdown 2.1.0.


 
-  
 
-  
+
+
 
   
 
diff --git a/docs/reference/SFO_actual_twa.html b/docs/reference/SFO_actual_twa.html
index 6dc6862..186b9f3 100644
--- a/docs/reference/SFO_actual_twa.html
+++ b/docs/reference/SFO_actual_twa.html
@@ -1,43 +1,34 @@
 
-Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa • pfm
+Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa • pfm
     Skip to contents
-    
 
-


-    
+
+    
+
     pfm
 
-    0.6.1
+    0.6.3
+
 
-    
     
 
     
-      
-  Reference
-
-      

-        
-
-      
-  
-    
-     
-  
-
+      Reference
+Changelog
+      

+ 
+
       
 
-    
+


 
   
-      Actual and maximum moving window time average concentrations for SFO kinetics
+
+      Actual and maximum moving window time average concentrations for SFO kinetics
       Source: R/SFO_actual_twa.R
       SFO_actual_twa.Rd
     
@@ -59,11 +50,13 @@ Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Versi
     
     
     Arguments
-    DT50
+
+
+DT50
 The half-life.
 
 
-times
+times
 The output times, and window sizes for time weighted average concentrations
 
 
@@ -89,23 +82,23 @@ Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Versi
 #> 100 0.0009765625 0.1441286

-

- - + + diff --git a/docs/reference/SSLRC_mobility_classification.html b/docs/reference/SSLRC_mobility_classification.html index 1874128..3463b3c 100644 --- a/docs/reference/SSLRC_mobility_classification.html +++ b/docs/reference/SSLRC_mobility_classification.html @@ -1,45 +1,36 @@ -Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification • pfm +Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification • pfm - -

- + +

@@ -56,15 +47,15 @@ checked against the spreadsheet published on the CRD website

Arguments

-

Koc

Value

- - -

A list containing the classification and the percentage of the +

A list containing the classification and the percentage of the compound transported per 10 mm drain water

@@ -100,23 +91,23 @@ accessed 2019-09-27

#>

-

- - + + diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html index 281315a..f620349 100644 --- a/docs/reference/TOXSWA_cwa.html +++ b/docs/reference/TOXSWA_cwa.html @@ -1,51 +1,42 @@ -R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa • pfmR6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa • pfm +by read.TOXSWA_cwa."> - -

- + +

@@ -61,7 +52,7 @@ by read.TOXSWA_cwa.

Format

-

An R6Class generator object.

+

An R6Class generator object.

Public fields

@@ -103,7 +94,7 @@ for the requested moving window sizes in days.

Methods

- +

Public methods

@@ -264,23 +255,23 @@ suspended matter will be used.

#> 1 55.083 40.58401 0.459 55.083 379.433 15.80971

-

- - + + diff --git a/docs/reference/TSCF.html b/docs/reference/TSCF.html index 8391cb4..f611a53 100644 --- a/docs/reference/TSCF.html +++ b/docs/reference/TSCF.html @@ -1,53 +1,44 @@ -Estimation of the transpiration stream concentration factor — TSCF • pfmEstimation of the transpiration stream concentration factor — TSCF • pfm +or ionic."> - -

- + +

@@ -68,11 +59,13 @@ or ionic.

Arguments

-

log_Kow

@@ -98,23 +91,23 @@ by plant roots. Environ. Sci. Technol 43, 324 - 329

-

- - + + diff --git a/docs/reference/drift_data_JKI.html b/docs/reference/drift_data_JKI.html index 5d9c11e..064264f 100644 --- a/docs/reference/drift_data_JKI.html +++ b/docs/reference/drift_data_JKI.html @@ -1,48 +1,36 @@ -Deposition from spray drift expressed as percent of the applied dose as -published by the JKI — drift_data_JKI • pfm +Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI • pfm - -

- + +

@@ -288,23 +276,23 @@ included.

#>

-

- - + + diff --git a/docs/reference/drift_parameters_focus.html b/docs/reference/drift_parameters_focus.html index 3f54160..6d3f679 100644 --- a/docs/reference/drift_parameters_focus.html +++ b/docs/reference/drift_parameters_focus.html @@ -1,49 +1,40 @@ -Regression parameters for the Rautmann drift data — drift_parameters_focus • pfmRegression parameters for the Rautmann drift data — drift_parameters_focus • pfm +as its licence is not clear."> - -

- + +

@@ -111,23 +102,23 @@ Bundesanst. Land- Forstwirtsch. 383, 133-141

#> [6] "fruit, early" "aerial"

-

- - + + diff --git a/docs/reference/drift_percentages_rautmann.html b/docs/reference/drift_percentages_rautmann.html index ae5ca03..bee0e60 100644 --- a/docs/reference/drift_percentages_rautmann.html +++ b/docs/reference/drift_percentages_rautmann.html @@ -1,43 +1,34 @@ -Calculate drift percentages based on Rautmann data — drift_percentages_rautmann • pfm +Calculate drift percentages based on Rautmann data — drift_percentages_rautmann • pfm - -

- + +

@@ -60,25 +51,27 @@

Arguments

-

distances

@@ -135,23 +128,23 @@ FOrum for the Co-ordination of pesticde fate models and their USe.

-

- - + + diff --git a/docs/reference/endpoint.html b/docs/reference/endpoint.html index 6705770..228d77f 100644 --- a/docs/reference/endpoint.html +++ b/docs/reference/endpoint.html @@ -1,49 +1,40 @@ -Retrieve endpoint information from the chyaml field of a chent object — endpoint • pfmRetrieve endpoint information from the chyaml field of a chent object — endpoint • pfm +this function."> - -

- + +

@@ -94,59 +85,59 @@ this function.

Arguments

-

chent

Value

- - -

The result from applying the aggregator function to +

The result from applying the aggregator function to the values converted to a numeric vector, rounded to the given number of significant digits, or, if raw = TRUE, the values as a character value, retaining any implicit @@ -160,23 +151,23 @@ facilitate dealing with such data in R. In pesticide fate modelling, this exponent is often called 1/n.

-

- - + + diff --git a/docs/reference/index.html b/docs/reference/index.html index aaa499d..97f59b5 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,337 +1,365 @@ -Function reference • pfm +Package index • pfm - -

- + +

General utility functions

- -

Functions that are independent of specific fate modelling areas

- -

- - - +

Functions that are independent of specific fate modelling areas

+ + +

+ + +

- - geomean() + + geomean() +: Calculate the geometric mean

- - one_box() + + one_box() +: Create a time series of decline data

- - plot(<one_box>) + + plot(<one_box>) +: Plot time series of decline data

- - sawtooth() + + sawtooth() +: Create decline time series for multiple applications

- - twa() + + twa() +: Calculate a time weighted average concentration

- - max_twa() + + max_twa() +: The maximum time weighted average concentration for a moving window

- - pfm_degradation() + + pfm_degradation() +: Calculate a time course of relative concentrations based on an mkinmod model

- - SFO_actual_twa() + + SFO_actual_twa() +: Actual and maximum moving window time average concentrations for SFO kinetics

- - FOMC_actual_twa() + + FOMC_actual_twa() +: Actual and maximum moving window time average concentrations for FOMC kinetics

- - reexports set_nd_nq set_nd_nq_focus + + reexports set_nd_nq set_nd_nq_focus +: Objects exported from other packages

- - TSCF() + + TSCF() +: Estimation of the transpiration stream concentration factor

Predicted environmental concentrations in soil

- - - -

- - - + + + +

+ + +

- - PEC_soil() + + PEC_soil() +: Calculate predicted environmental concentrations in soil

- - PEC_soil_mets() + + PEC_soil_mets() +: Calculate initial and accumulation PEC soil for a set of metabolites

- - soil_scenario_data_EFSA_2015 + + soil_scenario_data_EFSA_2015 +: Properties of the predefined scenarios from the EFSA guidance from 2015

- - soil_scenario_data_EFSA_2017 + + soil_scenario_data_EFSA_2017 +: Properties of the predefined scenarios from the EFSA guidance from 2017

- - PEC_FOMC_accu_rel() + + PEC_FOMC_accu_rel() +: Get the relative accumulation of an FOMC model over multiples of an interval

- - EFSA_washoff_2017 + + EFSA_washoff_2017 +: Subset of EFSA crop washoff default values

Predicted environmental concentrations in groundwater

- - - -

- - - + + + +

+ + +

- - FOCUS_GW_scenarios_2012 + + FOCUS_GW_scenarios_2012 +: A very small subset of the FOCUS Groundwater scenario definitions

- - EFSA_GW_interception_2014 + + EFSA_GW_interception_2014 +: Subset of EFSA crop interception default values for groundwater modelling

Predicted environmental concentrations in surface water

- - - -

- - - + + + +

+ + +

- - PEC_sw_drift() + + PEC_sw_drift() +: Calculate predicted environmental concentrations in surface water due to drift

- - drift_data_JKI + + drift_data_JKI +: Deposition from spray drift expressed as percent of the applied dose as -published by the JKI; Deposition from spray drift expressed as percent of the applied dose as published by the JKI

- - drift_parameters_focus + + drift_parameters_focus +: Regression parameters for the Rautmann drift data

- - drift_percentages_rautmann() + + drift_percentages_rautmann() +: Calculate drift percentages based on Rautmann data

- - PEC_sw_drainage_UK() + + PEC_sw_drainage_UK() +: Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method

- - PEC_sw_sed() + + PEC_sw_sed() +: Calculate predicted environmental concentrations in sediment from surface -water concentrations; Calculate predicted environmental concentrations in sediment from surface water concentrations

- - PEC_sw_focus() + + PEC_sw_focus() +: Calculate PEC surface water at FOCUS Step 1

- - chent_focus_sw() + + chent_focus_sw() +: Create a chemical compound object for FOCUS Step 1 calculations

- - FOCUS_Step_12_scenarios + + FOCUS_Step_12_scenarios +: Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator

- - PEC_sw_exposit_drainage() + + PEC_sw_exposit_drainage() +: Calculate PEC surface water due to drainage as in Exposit 3

- - PEC_sw_exposit_runoff() + + PEC_sw_exposit_runoff() +: Calculate PEC surface water due to runoff and erosion as in Exposit 3

- - perc_runoff_exposit + + perc_runoff_exposit +: Runoff loss percentages as used in Exposit 3

- - perc_runoff_reduction_exposit + + perc_runoff_reduction_exposit +: Runoff reduction percentages as used in Exposit

- - TOXSWA_cwa + + TOXSWA_cwa +: R6 class for holding TOXSWA water concentration data and associated statistics

- - read.TOXSWA_cwa() + + read.TOXSWA_cwa() +: Read TOXSWA surface water concentrations

- - plot(<TOXSWA_cwa>) + + plot(<TOXSWA_cwa>) +: Plot TOXSWA surface water concentrations

Classifications and indicators

- -

Evaluating environmental fate properties

- -

- - - +

Evaluating environmental fate properties

+ + +

+ + +

- - SSLRC_mobility_classification() + + SSLRC_mobility_classification() +: Determine the SSLRC mobility classification for a chemical substance from its Koc

- - GUS() print(<GUS_result>) + + GUS() print(<GUS_result>) +: Groundwater ubiquity score based on Gustafson (1989)

Work with chent objects containing relevant information

- - - -

- - - + + + +

+ + +

- - endpoint() soil_DT50() soil_Kfoc() soil_N() soil_sorption() + + endpoint() soil_DT50() soil_Kfoc() soil_N() soil_sorption() +: Retrieve endpoint information from the chyaml field of a chent object

Utilities

- - - -

- - - + + + +

+ + +

- - get_vertex() + + get_vertex() +: Fit a parabola through three points

-

- - + + diff --git a/docs/reference/max_twa.html b/docs/reference/max_twa.html index 4d469eb..74eeb46 100644 --- a/docs/reference/max_twa.html +++ b/docs/reference/max_twa.html @@ -1,51 +1,42 @@ -The maximum time weighted average concentration for a moving window — max_twa • pfmThe maximum time weighted average concentration for a moving window — max_twa • pfm +max_twa."> - -

- + +

@@ -65,17 +56,19 @@ for finding the maximum. It is therefore recommended to check this using

Arguments

-

x

Details

-

The method working directly on fitted mkinfit objects uses the +

The method working directly on fitted mkinfit objects uses the equations given in the PEC soil section of the FOCUS guidance and is restricted SFO, FOMC and DFOP models and to the parent compound

@@ -109,29 +102,29 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, #> parent #> 21 #> -pred_FOMC <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) +pred_FOMC <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) max_twa(pred_FOMC) #> 21 #> 18.22124

-

- - + + diff --git a/docs/reference/one_box.character.html b/docs/reference/one_box.character.html new file mode 100644 index 0000000..b2bfb92 --- /dev/null +++ b/docs/reference/one_box.character.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/one_box.mkinfit.html b/docs/reference/one_box.mkinfit.html new file mode 100644 index 0000000..b2bfb92 --- /dev/null +++ b/docs/reference/one_box.mkinfit.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/one_box.numeric.html b/docs/reference/one_box.numeric.html new file mode 100644 index 0000000..b2bfb92 --- /dev/null +++ b/docs/reference/one_box.numeric.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/perc_runoff_exposit.html b/docs/reference/perc_runoff_exposit.html index 2311d09..a1afbde 100644 --- a/docs/reference/perc_runoff_exposit.html +++ b/docs/reference/perc_runoff_exposit.html @@ -1,44 +1,35 @@ -Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit • pfm +Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit • pfm - -

- + +

@@ -77,37 +68,37 @@ adjacent water body bound to eroding particles

Examples

print(perc_runoff_exposit)
 #>              Koc_lower_bound dissolved bound
-#> 0-20                       0     0.110 0.000
-#> >20-50                    20     0.151 0.000
-#> >50-100                   50     0.197 0.000
-#> >100-200                 100     0.248 0.001
-#> >200-500                 200     0.224 0.004
-#> >500-1000                500     0.184 0.020
-#> >1000-2000              1000     0.133 0.042
-#> >2000-5000              2000     0.084 0.091
-#> >5000-10000             5000     0.037 0.159
-#> >10000-20000           10000     0.031 0.192
-#> >20000-50000           20000     0.014 0.291
-#> >50000                 50000     0.001 0.451
+#> 0-20                0 [L/kg]     0.110 0.000
+#> >20-50             20 [L/kg]     0.151 0.000
+#> >50-100            50 [L/kg]     0.197 0.000
+#> >100-200          100 [L/kg]     0.248 0.001
+#> >200-500          200 [L/kg]     0.224 0.004
+#> >500-1000         500 [L/kg]     0.184 0.020
+#> >1000-2000       1000 [L/kg]     0.133 0.042
+#> >2000-5000       2000 [L/kg]     0.084 0.091
+#> >5000-10000      5000 [L/kg]     0.037 0.159
+#> >10000-20000    10000 [L/kg]     0.031 0.192
+#> >20000-50000    20000 [L/kg]     0.014 0.291
+#> >50000          50000 [L/kg]     0.001 0.451

-

- - + + diff --git a/docs/reference/perc_runoff_reduction_exposit.html b/docs/reference/perc_runoff_reduction_exposit.html index 24a199e..5bb3a57 100644 --- a/docs/reference/perc_runoff_reduction_exposit.html +++ b/docs/reference/perc_runoff_reduction_exposit.html @@ -1,44 +1,35 @@ -Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit • pfm +Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit • pfm - -

- + +

@@ -103,23 +94,23 @@ The variant 3.01a2 was introduced for consistency with previous calculations per #>

-

- - + + diff --git a/docs/reference/print.GUS_result.html b/docs/reference/print.GUS_result.html new file mode 100644 index 0000000..15d3826 --- /dev/null +++ b/docs/reference/print.GUS_result.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/set_nd_nq.html b/docs/reference/set_nd_nq.html new file mode 100644 index 0000000..2291be7 --- /dev/null +++ b/docs/reference/set_nd_nq.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/set_nd_nq_focus.html b/docs/reference/set_nd_nq_focus.html new file mode 100644 index 0000000..2291be7 --- /dev/null +++ b/docs/reference/set_nd_nq_focus.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/soil_DT50.html b/docs/reference/soil_DT50.html new file mode 100644 index 0000000..2224ee0 --- /dev/null +++ b/docs/reference/soil_DT50.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/soil_Kfoc.html b/docs/reference/soil_Kfoc.html new file mode 100644 index 0000000..2224ee0 --- /dev/null +++ b/docs/reference/soil_Kfoc.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/soil_N.html b/docs/reference/soil_N.html new file mode 100644 index 0000000..2224ee0 --- /dev/null +++ b/docs/reference/soil_N.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/soil_scenario_data_EFSA_2015.html b/docs/reference/soil_scenario_data_EFSA_2015.html index 41f1078..b65586c 100644 --- a/docs/reference/soil_scenario_data_EFSA_2015.html +++ b/docs/reference/soil_scenario_data_EFSA_2015.html @@ -1,47 +1,38 @@ -Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015 • pfmProperties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015 • pfm +scenario and model adjustment factors from p. 15 and p. 17 are included."> - -

- + +

@@ -91,23 +82,23 @@ active substances in soil. EFSA Journal 13(4) 4093 #> CLS 4

-

- - + + diff --git a/docs/reference/soil_scenario_data_EFSA_2017.html b/docs/reference/soil_scenario_data_EFSA_2017.html index b1adfab..1a6157a 100644 --- a/docs/reference/soil_scenario_data_EFSA_2017.html +++ b/docs/reference/soil_scenario_data_EFSA_2017.html @@ -1,47 +1,38 @@ -Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017 • pfmProperties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017 • pfm +scenario and model adjustment factors from p. 16 and p. 18 are included."> - -

- + +

@@ -124,23 +115,23 @@ active substances in soil. EFSA Journal 15(10) 4982 #> And 3 more differences ...

-

- - + + diff --git a/docs/reference/soil_sorption.html b/docs/reference/soil_sorption.html new file mode 100644 index 0000000..2224ee0 --- /dev/null +++ b/docs/reference/soil_sorption.html @@ -0,0 +1,8 @@ + + + + + + + + diff --git a/docs/reference/twa.one_box.html b/docs/reference/twa.one_box.html new file mode 100644 index 0000000..9372dd5 --- /dev/null +++ b/docs/reference/twa.one_box.html @@ -0,0 +1,8 @@ + + + + + + + + -- cgit v1.2.1