Page not found (404) • 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/404.html | 56 ++-- docs/authors.html | 58 ++-- docs/index.html | 61 ++-- docs/news/index.html | 57 ++++ 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 + docs/search.json | 2 +- docs/sitemap.xml | 177 +++-------- 46 files changed, 1241 insertions(+), 1382 deletions(-) create mode 100644 docs/news/index.html 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') diff --git a/docs/404.html b/docs/404.html index 7e83442..e41a30d 100644 --- a/docs/404.html +++ b/docs/404.html @@ -8,56 +8,44 @@ Page not found (404) • pfm - - - - + - -

- + +

Content not found. Please use links in the navbar. @@ -67,21 +55,19 @@ Content not found. Please use links in the navbar.

- - + + diff --git a/docs/authors.html b/docs/authors.html index fac5267..937daa8 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,87 +1,79 @@ -Authors and Citation • pfm +Authors and Citation • pfm - -

- + +

Authors

- +

Johannes Ranke. Author, maintainer.

Citation

Source: DESCRIPTION

Johannes Ranke (2024). pfm: Utilities for Pesticide Fate Modelling. -R package version 0.6.2, https://github.com/jranke/pfm, https://pkgdown.jrwb.de/pfm. +R package version 0.6.3, https://github.com/jranke/pfm, https://pkgdown.jrwb.de/pfm.

@Manual{,
   title = {pfm: Utilities for Pesticide Fate Modelling},
   author = {{Johannes Ranke}},
   year = {2024},
-  note = {R package version 0.6.2, https://github.com/jranke/pfm},
+  note = {R package version 0.6.3, https://github.com/jranke/pfm},
   url = {https://pkgdown.jrwb.de/pfm},
 }

- - + + diff --git a/docs/index.html b/docs/index.html index 1c37ff1..590ed7b 100644 --- a/docs/index.html +++ b/docs/index.html @@ -5,66 +5,49 @@ - Utilities for Pesticide Fate Modelling • pfm - - - - - + + + - -

- + +

The R package pfm provides some utilities for fate modelling, including dealing with FOCUS pesticide fate modelling tools, (currently only TOXSWA cwa and out files), made available under the GNU public license.

Installation @@ -145,21 +128,19 @@ Korkaric M, Hanke I, Grossar D, Neuweiler R, Christ B, Wirth J, Hochstrasser M,
-
-
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/news/index.html b/docs/news/index.html new file mode 100644 index 0000000..f2f50d7 --- /dev/null +++ b/docs/news/index.html @@ -0,0 +1,57 @@ + +Changelog • pfm + + + +

+ +

version 0.6.3

R/{PEC_sw_drift,PEC_sw_exposit_runoff,PEC_sw_sed}.R: Make use of the units package.

+ + +

+ + + + + + + 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

- - + + 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

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

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.

+ - - + + 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

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.

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 @@ + + + + + + + + diff --git a/docs/search.json b/docs/search.json index 223c957..56f0991 100644 --- a/docs/search.json +++ b/docs/search.json @@ -1 +1 @@ -[{"path":"https://pkgdown.jrwb.de/pfm/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Johannes Ranke. Author, maintainer.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Johannes Ranke (2024). pfm: Utilities Pesticide Fate Modelling. R package version 0.6.2, https://github.com/jranke/pfm, https://pkgdown.jrwb.de/pfm.","code":"@Manual{, title = {pfm: Utilities for Pesticide Fate Modelling}, author = {{Johannes Ranke}}, year = {2024}, note = {R package version 0.6.2, https://github.com/jranke/pfm}, url = {https://pkgdown.jrwb.de/pfm}, }"},{"path":"https://pkgdown.jrwb.de/pfm/index.html","id":"pfm","dir":"","previous_headings":"","what":"Utilities for Pesticide Fate Modelling","title":"Utilities for Pesticide Fate Modelling","text":"R package pfm provides utilities fate modelling, including dealing FOCUS pesticide fate modelling tools, (currently TOXSWA cwa files), made available GNU public license.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Utilities for Pesticide Fate Modelling","text":"easiest way install package probably use r-universe repo: Alternatively can install package using remotes package. Using quick = TRUE skips docs, multiple-architecture builds, demos, vignettes.","code":"install.packages(\"pfm\", repos = c(\"https://jranke.r-universe.dev\", \"https://cran.r-project.org\")) remotes::install_github(\"jranke/pfm\", quick = TRUE)"},{"path":"https://pkgdown.jrwb.de/pfm/index.html","id":"use","dir":"","previous_headings":"","what":"Use","title":"Utilities for Pesticide Fate Modelling","text":"Please refer reference.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/index.html","id":"examples","dir":"","previous_headings":"","what":"Examples","title":"Utilities for Pesticide Fate Modelling","text":"One recent nice example usage package visualisation time weighted average sawtooth curve obtained several overlays mkinfit predictions shown .","code":""},{"path":"https://pkgdown.jrwb.de/pfm/index.html","id":"applications","dir":"","previous_headings":"","what":"Applications","title":"Utilities for Pesticide Fate Modelling","text":"Calculations predicted environmental concentrations using package used publications Agroscope.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_GW_interception_2014.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014","title":"Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014","text":"Subset EFSA crop interception default values groundwater modelling","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_GW_interception_2014.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014","text":"","code":"EFSA_GW_interception_2014"},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_GW_interception_2014.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014","text":"matrix containing interception values, currently selected crops","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_GW_interception_2014.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014","text":"European Food Safety Authority (2014) EFSA Guidance Document evaluating laboratory field dissipation studies obtain DegT50 values active substances plant protection products transformation products active substances soil. EFSA Journal 12(5):3662, 37 pp., doi:10.2903/j.efsa.2014.3662","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_GW_interception_2014.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014","text":"","code":"EFSA_GW_interception_2014 #> BBCH #> Crop 0x 1x 2x 3x 4x 5x 6x 7x 8x 9x #> Beans (field + vegetable) 0 0.25 0.40 0.40 0.70 0.70 0.70 0.70 0.70 0.80 #> Peas 0 0.35 0.55 0.55 0.85 0.85 0.85 0.85 0.85 0.85 #> Summer oilseed rape 0 0.40 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.90 #> Winter oilseed rape 0 0.40 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.90 #> Tomatoes 0 0.50 0.70 0.70 0.80 0.80 0.80 0.80 0.80 0.50 #> Spring cereals 0 0.00 0.20 0.80 0.90 0.90 0.90 0.80 0.80 0.80 #> Winter cereals 0 0.00 0.20 0.80 0.90 0.90 0.90 0.80 0.80 0.80"},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_washoff_2017.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset of EFSA crop washoff default values — EFSA_washoff_2017","title":"Subset of EFSA crop washoff default values — EFSA_washoff_2017","text":"Subset EFSA crop washoff default values","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_washoff_2017.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset of EFSA crop washoff default values — EFSA_washoff_2017","text":"","code":"EFSA_washoff_2017"},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_washoff_2017.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Subset of EFSA crop washoff default values — EFSA_washoff_2017","text":"matrix containing wash-factors, currently selected crops","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_washoff_2017.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Subset of EFSA crop washoff default values — EFSA_washoff_2017","text":"European Food Safety Authority (2017) EFSA guidance document predicting environmental concentrations active substances plant protection products transformation products active substances soil. EFSA Journal 15(10) 4982 doi:10.2903/j.efsa.2017.4982","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_washoff_2017.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subset of EFSA crop washoff default values — EFSA_washoff_2017","text":"","code":"EFSA_washoff_2017 #> BBCH #> Crop 0x 1x 2x 3x 4x 5x 6x 7x 8x 9x #> Beans (field + vegetable) NA 0.60 0.75 0.75 0.80 0.80 0.80 0.80 0.80 0.35 #> Peas NA 0.40 0.60 0.60 0.65 0.65 0.65 0.65 0.65 0.35 #> Summer oilseed rape NA 0.40 0.50 0.50 0.60 0.60 0.60 0.60 0.60 0.50 #> Winter oilseed rape NA 0.10 0.40 0.40 0.55 0.55 0.55 0.55 0.55 0.30 #> Tomatoes NA 0.55 0.75 0.75 0.70 0.70 0.70 0.70 0.70 0.35 #> Spring cereals NA 0.40 0.50 0.50 0.65 0.65 0.65 0.65 0.65 0.55 #> Winter cereals NA 0.10 0.40 0.60 0.55 0.55 0.55 0.60 0.60 0.40"},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_GW_scenarios_2012.html","id":null,"dir":"Reference","previous_headings":"","what":"A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012","title":"A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012","text":"Currently, scenario names acronyms small subset soil definitions provided. soil definitions page 46ff. FOCUS (2012).","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_GW_scenarios_2012.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012","text":"","code":"FOCUS_GW_scenarios_2012"},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_GW_scenarios_2012.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012","text":"object class list length 2.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_GW_scenarios_2012.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012","text":"FOCUS (2012) Generic guidance Tier 1 FOCUS ground water assessments. Version 2.1. FOrum Co-ordination pesticde fate models USe. http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_GW_scenarios_2012.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012","text":"","code":"FOCUS_GW_scenarios_2012 #> $names #> Cha Ham Jok Kre Oke #> \"Châteadun\" \"Hamburg\" \"Jokioinen\" \"Kremsmünster\" \"Okehampton\" #> Pia Por Sev Thi #> \"Piacenza\" \"Porto\" \"Sevilla\" \"Thiva\" #> #> $soils #> location horizon number pH_H2O perc_clay perc_oc rel_deg #> 1 Cha Ap 1 8.0 30.0 1.39 1.0 #> 2 Cha B1 2 8.1 31.0 0.93 0.5 #> 3 Cha B2 3 8.2 25.0 0.70 0.5 #> 4 Cha II C1 4 8.5 26.0 0.30 0.3 #> 5 Cha II C1 5 8.5 26.0 0.30 0.0 #> 6 Cha II C2 6 8.5 24.0 0.27 0.0 #> 7 Cha M 7 8.3 31.0 0.21 0.0 #> 8 Ham Ap 1 6.4 7.2 1.50 1.0 #> 9 Ham BvI 2 5.6 6.7 1.00 0.5 #> 10 Ham BvII 3 5.6 0.9 0.20 0.3 #> 11 Ham Bv/Cv 4 5.7 0.0 0.00 0.3 #> 12 Ham Cv 5 5.5 0.0 0.00 0.3 #> 13 Ham Cv 6 5.5 0.0 0.00 0.0 #> 14 Jok Ap 1 6.2 3.6 4.06 1.0 #> 15 Jok Bs 2 5.6 1.8 0.84 0.5 #> 16 Jok BC1 3 5.4 1.2 0.36 0.3 #> 17 Jok BC2 4 5.4 1.7 0.29 0.3 #> 18 Jok BC2 5 5.4 1.7 0.29 0.0 #> 19 Jok Cg 6 5.3 1.9 0.21 0.0 #> 20 Kre 1 7.7 14.0 3.60 1.0 #> 21 Kre 2 7.0 25.0 1.00 0.5 #> 22 Kre 3 7.1 27.0 0.50 0.5 #> 23 Kre 4 7.1 27.0 0.50 0.3 #> 24 Kre 5 7.1 27.0 0.50 0.0 #> 25 Oke A 1 5.8 18.0 2.20 1.0 #> 26 Oke Bw1 2 6.3 17.0 0.70 0.5 #> 27 Oke BC 3 6.5 14.0 0.40 0.3 #> 28 Oke C 4 6.6 9.0 0.10 0.3 #> 29 Oke C 5 6.6 9.0 0.10 0.0 #> 30 Pia Ap 1 7.0 15.0 1.26 1.0 #> 31 Pia Ap 2 7.0 15.0 1.26 0.5 #> 32 Pia Bw 3 6.3 7.0 0.47 0.5 #> 33 Pia Bw 4 6.3 7.0 0.47 0.3 #> 34 Pia 2C 5 6.4 0.0 0.00 0.3 #> 35 Pia 2C 6 6.4 0.0 0.00 0.0 #> 36 Por 1 4.9 10.0 1.42 1.0 #> 37 Por 2 4.8 8.0 0.78 0.5 #> 38 Por 3 4.8 8.0 0.78 0.3 #> 39 Por 4 4.8 8.0 0.78 0.0 #> 40 Sev 1 7.3 14.0 0.93 1.0 #> 41 Sev 2 7.3 13.0 0.93 1.0 #> 42 Sev 3 7.8 15.0 0.70 0.5 #> 43 Sev 4 8.1 16.0 0.58 0.3 #> 44 Sev 5 8.1 16.0 0.58 0.0 #> 45 Sev 6 8.2 22.0 0.49 0.0 #> 46 Thi Ap1 1 7.7 25.3 0.74 1.0 #> 47 Thi Ap2 2 7.7 25.3 0.74 0.5 #> 48 Thi Bw 3 7.8 29.6 0.57 0.5 #> 49 Thi Bw 4 7.8 31.9 0.31 0.3 #> 50 Thi Ck1 5 7.8 32.9 0.18 0.3 #> 51 Thi Ck1 6 7.8 32.9 0.18 0.0 #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_Step_12_scenarios.html","id":null,"dir":"Reference","previous_headings":"","what":"Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios","title":"Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios","text":"data extracted scenario.txt file using R code shown . text file included package licence clear.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_Step_12_scenarios.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios","text":"list containing scenario names character vector called 'names', drift percentiles matrix called 'drift', interception percentages matrix called 'interception' runoff/drainage percentages Step 2 calculations matrix called 'rd'.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_Step_12_scenarios.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios","text":"","code":"# \\dontrun{ # 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] #> Warning: cannot open file 'inst/extdata/FOCUS_Step_12_scenarios.txt': No such file or directory #> Error in file(con, \"r\"): cannot open the connection FOCUS_Step_12_scenarios <- list() sce <- read.table(text = scenarios, sep = \"\\t\", header = TRUE, check.names = FALSE, stringsAsFactors = FALSE) #> Error in eval(expr, envir, enclos): object 'scenarios' not found FOCUS_Step_12_scenarios$names = sce$Crop #> Error in eval(expr, envir, enclos): object 'sce' not found rownames(sce) <- sce$Crop #> Error in eval(expr, envir, enclos): object 'sce' not found FOCUS_Step_12_scenarios$drift = sce[, 3:11] #> Error in eval(expr, envir, enclos): object 'sce' not found FOCUS_Step_12_scenarios$interception = sce[, 12:15] #> Error in eval(expr, envir, enclos): object 'sce' not found sce_2 <- readLines(scenario_path)[41:46] #> Warning: cannot open file 'inst/extdata/FOCUS_Step_12_scenarios.txt': No such file or directory #> Error in file(con, \"r\"): cannot open the connection rd <- read.table(text = sce_2, sep = \"\\t\")[1:2] #> Error in eval(expr, envir, enclos): object 'sce_2' not found rd_mat <- matrix(rd$V2, nrow = 3, byrow = FALSE) #> Error in eval(expr, envir, enclos): object 'rd' not found dimnames(rd_mat) = list(Time = c(\"Oct-Feb\", \"Mar-May\", \"Jun-Sep\"), Region = c(\"North\", \"South\")) #> Error: object 'rd_mat' not found FOCUS_Step_12_scenarios$rd = rd_mat #> Error in eval(expr, envir, enclos): object 'rd_mat' not found save(FOCUS_Step_12_scenarios, file = \"data/FOCUS_Step_12_scenarios.RData\") #> Warning: cannot open compressed file 'data/FOCUS_Step_12_scenarios.RData', probable reason 'No such file or directory' #> Error in gzfile(file, \"wb\"): cannot open the connection # } # And this is the resulting data FOCUS_Step_12_scenarios #> list()"},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.html","id":null,"dir":"Reference","previous_headings":"","what":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","title":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","text":"Actual maximum moving window time average concentrations FOMC kinetics","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","text":"","code":"FOMC_actual_twa( alpha = 1.0001, beta = 10, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100) )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","text":"FOCUS (2014) Generic Guidance Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration, Version 1.1, 18 December 2014, p. 251","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","text":"alpha Parameter FOMC model beta Parameter FOMC model times output times, window sizes time weighted average concentrations","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","text":"","code":"FOMC_actual_twa(alpha = 1.0001, beta = 10) #> actual twa #> 0 1.00000000 NaN #> 1 0.90908224 0.9530973 #> 2 0.83331814 0.9115995 #> 4 0.71426168 0.8411664 #> 7 0.58820408 0.7580202 #> 14 0.41663019 0.6253074 #> 21 0.32254415 0.5387324 #> 28 0.26312277 0.4767543 #> 42 0.19227599 0.3925054 #> 50 0.16663681 0.3583198 #> 100 0.09088729 0.2397608"},{"path":"https://pkgdown.jrwb.de/pfm/reference/GUS.html","id":null,"dir":"Reference","previous_headings":"","what":"Groundwater ubiquity score based on Gustafson (1989) — GUS","title":"Groundwater ubiquity score based on Gustafson (1989) — GUS","text":"groundwater ubiquity score GUS calculated according following equation $$GUS = \\log_{10} DT50_{soil} (4 - \\log_{10} K_{oc})$$","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/GUS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Groundwater ubiquity score based on Gustafson (1989) — GUS","text":"","code":"GUS(...) # S3 method for numeric GUS(DT50, Koc, ...) # S3 method for chent GUS( chent, degradation_value = \"DT50ref\", lab_field = \"laboratory\", redox = \"aerobic\", sorption_value = \"Kfoc\", degradation_aggregator = geomean, sorption_aggregator = geomean, ... ) # S3 method for GUS_result print(x, ..., digits = 1)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/GUS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Groundwater ubiquity score based on Gustafson (1989) — GUS","text":"... Included generic allow arguments later. Therefore also added specific methods. DT50 Half-life chemical soil. field half-life according Gustafson (1989). However, leaching sub-soil can completely excluded field dissipation experiments Gustafson refer normalisation procedure, says field study conducted use conditions. Koc sorption constant normalised organic carbon. Gustafson mention nonlinearity sorption constant commonly found usually described Freundlich sorption, therefore unclear reference concentration Koc observed (reference concentration soil porewater). chent chent given appropriate information present chyaml field, information used, defaults specified . degradation_value available degradation values used? lab_field laboratory field half-lives used? defaults lab implementation, order avoid double-accounting mobility. comparability original GUS values given Gustafson (1989) desired, non-normalised first-order field half-lives obtained actual use conditions used. redox Aerobic anaerobic degradation data sorption_value available sorption values used? Defaults Kfoc generally available European pesticide peer review process. values generally use reference concentration 1 mg/L porewater, means expected Koc values concentration 1 mg/L water phase. degradation_aggregator Function aggregating half-lives sorption_aggregator Function aggregation Koc values x object class GUS_result printed digits number digits used print method","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/GUS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Groundwater ubiquity score based on Gustafson (1989) — GUS","text":"list DT50 Koc used well resulting score class GUS_result","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/GUS.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Groundwater ubiquity score based on Gustafson (1989) — GUS","text":"Gustafson, David . (1989) Groundwater ubiquity score: simple method assessing pesticide leachability. Environmental toxicology chemistry 8(4) 339–57.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/GUS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Groundwater ubiquity score based on Gustafson (1989) — GUS","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_FOMC_accu_rel.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel","title":"Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel","text":"Get relative accumulation FOMC model multiples interval","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_FOMC_accu_rel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel","text":"","code":"PEC_FOMC_accu_rel(n, interval, FOMC)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_FOMC_accu_rel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel","text":"n number applications interval Time applications FOMC Named numeric vector containing FOMC parameters alpha beta","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_FOMC_accu_rel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel","text":"numeric vector containing n accumulation factors n applications","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate predicted environmental concentrations in soil — PEC_soil","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"basic calculation contaminant concentration bulk soil based complete, instantaneous mixing. interval given, attempt made calculating long term maximum concentration using concepts layed PPR panel opinion (EFSA PPR panel 2012 EFSA guidance PEC soil calculations (EFSA, 2015, 2017).","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"","code":"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, leaching_depth = tillage_depth, crop = \"annual\", cultivation = FALSE, chent = NA, DT50 = NA, FOMC = NA, Koc = NA, Kom = Koc/1.724, t_avg = 0, t_act = NULL, scenarios = c(\"default\", \"EFSA_2017\", \"EFSA_2015\"), leaching = scenarios == \"EFSA_2017\", porewater = FALSE )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"rate Application rate units specified rate_units Defaults g/ha interception fraction application rate reach soil mixing_depth Mixing depth cm PEC_units Requested units calculated PEC. mg/kg currently supported PEC_pw_units mg/L currently supported interval Period deeper mixing. default NA, .e. deeper mixing. annual deeper mixing, set 365 degradation units days n_periods Number periods considered long term PEC calculations tillage_depth Periodic (see interval) deeper mixing cm leaching_depth EFSA (2017) uses mixing depth (ecotoxicological evaluation depth) calculate leaching annual crops tillage takes place. default, losses layer tillage depth taken account implementation. crop Ignored scenarios EFSA_2017. annual crops supported scenarios used. crops single cropping cycle per year currently supported. cultivation mechanical cultivation sense EFSA (2017) take place, .e. twice year depth 5 cm? Ignored scenarios EFSA_2017 chent optional chent object holding substance specific information. Can also name substance character string DT50 specified, overrides soil DT50 endpoints chent object DT50 specified available chent object, zero degradation assumed FOMC specified, named numeric vector containing FOMC parameters alpha beta. overrides degradation endpoints, degradation interval maximum PEC calculated using parameters without temperature correction Koc specified, overrides Koc endpoints chent object Kom Calculated Koc default, can explicitly specified Kom t_avg Averaging times time weighted average concentrations t_act Time series actual concentrations scenarios 'default', DT50 used without correction soil properties specified REACH guidance (R.16, Table R.16-9) used porewater PEC calculations. \"EFSA_2015\", DT50 taken modelling half-life 20°C pF2 ('chent' specified, DegT50 destination 'PECgw' used), corrected using Arrhenius activation energy 65.4 kJ/mol. Also model scenario adjustment factors EFSA guidance used. leaching leaching taken account? default FALSE, except EFSA_2017 scenarios used. porewater equilibrium porewater concentrations estimated based Kom organic carbon fraction soil instead total soil concentrations? Based equation (7) given PPR panel opinion (EFSA 2012, p. 24) scenarios specified EFSA guidance (2015, p. 13).","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"predicted concentration soil","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"assumes complete load soil time specified 'interval' (typically 365 days) dosed . PPR panel opinion cited (EFSA PPR panel 2012), temperature correction using Arrhenius equation performed. Total soil porewater PEC values scenarios defined EFSA guidance (2017, p. 14/15) can easily calculated.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"time weighted average (TWA) concentrations given examples EFSA guidance 2015 (p. 80) reproduced, true TWA concentrations given example EFSA guidance 2017 (p. 92). According EFSA guidance (EFSA, 2017, p. 43), leaching taken account EFSA 2017 scenarios, using evaluation depth (mixing depth) depth layer leaching takes place. However, amount leaching evaluation depth (often 5 cm) partly mixed back tillage, default function use tillage depth calculation leaching rate. temperature information available selected scenarios, e.g. EFSA scenarios, DT50 groundwater modelling (destination 'PECgw') taken chent object, otherwise DT50 destination 'PECsoil'.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"EFSA Panel Plant Protection Products Residues (2012) Scientific Opinion science behind guidance scenario selection scenario parameterisation predicting environmental concentrations plant protection products soil. EFSA Journal 10(2) 2562, doi:10.2903/j.efsa.2012.2562 EFSA (European Food Safety Authority) 2017) EFSA guidance document predicting environmental concentrations active substances plant protection products transformation products active substances soil. EFSA Journal 15(10) 4982 doi:10.2903/j.efsa.2017.4982 EFSA (European Food Safety Authority) (2015) EFSA guidance document predicting environmental concentrations active substances plant protection products transformation products active substances soil. EFSA Journal 13(4) 4093 doi:10.2903/j.efsa.2015.4093","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"","code":"PEC_soil(100, interception = 0.25) #> scenario #> t_avg default #> 0 0.1 # This is example 1 starting at p. 92 of the EFSA guidance (2017) # Note that TWA concentrations differ from the ones given in the guidance # for an unknown reason (the values from EFSA (2015) can be reproduced). PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), Kom = 1000, scenarios = \"EFSA_2017\") #> scenario #> t_avg CTN CTC CTS #> 0 19.76834 13.8619 10.53795 #> 21 19.59345 13.7169 10.39882 PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), Kom = 1000, scenarios = \"EFSA_2017\", porewater = TRUE) #> scenario #> t_avg CLN CLC CLS #> 0 0.5541984 0.6779249 0.9816693 #> 21 0.5484576 0.6693125 0.9609119 # This is example 1 starting at p. 79 of the EFSA guidance (2015) PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), scenarios = \"EFSA_2015\") #> scenario #> t_avg CTN CTC CTS #> 0 21.96827 11.53750 9.145259 #> 21 21.78517 11.40701 9.017370 PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), Kom = 1000, scenarios = \"EFSA_2015\", porewater = TRUE) #> scenario #> t_avg CLN CLC CLS #> 0 0.7589401 0.6674322 0.9147861 #> 21 0.7506036 0.6590345 0.8987279 # The following is from example 4 starting at p. 85 of the EFSA guidance (2015) # Metabolite M2 # Calculate total and porewater soil concentrations for tier 1 scenarios # Relative molar mass is 100/300, formation fraction is 0.7 * 1 results_pfm <- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_avg = c(0, 21), scenarios = \"EFSA_2015\") results_pfm_pw <- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_av = c(0, 21), Kom = 100, scenarios = \"EFSA_2015\", porewater = TRUE)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil_mets.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets","title":"Calculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets","text":"Calculate initial accumulation PEC soil set metabolites","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil_mets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets","text":"","code":"PEC_soil_mets(rate, mw_parent, mets, interval = 365, ...)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil_mets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets","text":"rate Application rate units specified mw_parent molecular weight parent compound mets dataframe metabolite identifiers rownames columns \"mw\", \"occ\" \"DT50\" holding molecular weight, maximum occurrence soil soil DT50 interval interval accumulation calculations ... arguments passed PEC_soil","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"implements method specified UK data requirements handbook checked spreadsheet published CRC website","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"","code":"PEC_sw_drainage_UK( rate, interception = 0, Koc, latest_application = NULL, soil_DT50 = NULL, model = NULL, model_parms = NULL )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"rate Application rate g/ha interception fraction application rate reach soil Koc sorption coefficient normalised organic carbon L/kg latest_application Latest application date, formatted e.g. \"01 July\" soil_DT50 Soil degradation half-life, SFO kinetics used model soil degradation model used. Either one \"FOMC\", \"DFOP\", \"HS\", \"IORE\", mkinmod object model_parms named numeric vector containing model parameters","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"predicted concentration surface water µg/L","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"HSE's Chemicals Regulation Division (CRD) Active substance PECsw calculations (UK specific authorisation requests) https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm accessed 2019-09-27 Drainage PECs Version 1.0 (2015) Spreadsheet published https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx accessed 2019-09-27","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"","code":"PEC_sw_drainage_UK(150, Koc = 100) #> [1] 8.076923"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"basic, vectorised form simple calculation contaminant concentration surface water based complete, instantaneous mixing input via spray drift.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"","code":"PEC_sw_drift( rate, applications = 1, water_depth = 30, drift_percentages = NULL, drift_data = c(\"JKI\", \"RF\"), crop_group_JKI = c(\"Ackerbau\", \"Obstbau frueh\", \"Obstbau spaet\", \"Weinbau frueh\", \"Weinbau spaet\", \"Hopfenbau\", \"Flaechenkulturen > 900 l/ha\", \"Gleisanlagen\"), crop_group_focus = c(\"arable\", \"hops\", \"vines, late\", \"vines, early\", \"fruit, late\", \"fruit, early\", \"aerial\"), distances = c(1, 5, 10, 20), formula = c(\"Rautmann\", \"FOCUS\"), water_width = 100, side_angle = 90, rate_units = \"g/ha\", PEC_units = \"µg/L\" )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"rate Application rate units specified applications Number applications selection drift percentile water_depth Depth water body cm drift_percentages Percentage drift values calculate PECsw. Overrides 'drift_data' 'distances' NULL. drift_data Source drift percentage data. 'JKI', drift_data_JKI included package used. 'RF', Rautmann drift data calculated either original form integrated width water body, depending 'formula' argument. crop_group_JKI using 'JKI' drift data, one German names used drift_parameters_focus. crop_group_focus One crop groups used drift_parameters_focus distances distances m get PEC values formula default, original Rautmann formula used. specify \"FOCUS\", mean drift input width water body calculated described Chapter 5.4.5 FOCUS surface water guidance water_width Width water body cm side_angle angle side water relative bottom assumed horizontal, degrees. SYNOPS model assumes 45 degrees . rate_units Defaults g/ha PEC_units Requested units calculated PEC. µg/L currently supported","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"predicted concentration surface water","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"","code":"PEC_sw_drift(100) #> 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\") #> 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\") #> 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 #> 0.01018774 # 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\") #> 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 #> 0.9417586 # 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)) #> 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 % #> 0.01000000 # 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) #> 1 m 5 m 10 m 20 m #> 0.92333333 0.19000000 0.09666667 0.05000000 PEC_sw_drift(100, drift_data = \"RF\") #> 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\") #> 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) #> 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) #> 1 m 5 m 10 m 20 m #> 0.30085000 0.09468652 0.05201349 0.02758547"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","title":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","text":"reimplementation calculation described Exposit 3.02 spreadsheet file, worksheet \"Konzept Drainage\". Although four groups compounds (\"Gefährdungsgruppen\"), one distinction made calculations, compounds low mobility (group 1) compounds modest high mobility (groups 2, 3 4). implementation, group derived Koc, given explicitly. details, see discussion function arguments .","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","text":"","code":"PEC_sw_exposit_drainage( rate, interception = 0, Koc = NA, mobility = c(NA, \"low\", \"high\"), DT50 = Inf, t_drainage = 3, V_ditch = 30, V_drainage = c(spring = 10, autumn = 100), dilution = 2 )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","text":"Excel 3.02 spreadsheet available https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","text":"rate application rate g/ha interception fraction intercepted crop Koc sorption coefficient soil organic carbon used determine mobility. trigger value 550 L/kg used order decide Koc >> 500. mobility Overrides determined Koc. DT50 soil half-life days t_drainage time application drainage event, degradation occurs, days V_ditch volume ditch assumed 1 m * 100 m * 30 cm = 30 m3 V_drainage drainage volume, equivalent 1 mm precipitation 1 ha spring/summer 10 mm autumn/winter/early spring. dilution dilution factor","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","text":"list containing following components perc_runoff runoff percentages dissolved bound substance runoff matrix containing dissolved bound input different distances PEC_sw_runoff matrix containing PEC values dissolved bound substance different distances. rate given g/ha, PECsw microg/L.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","text":"","code":"PEC_sw_exposit_drainage(500, Koc = 150) #> $perc_drainage_total #> spring autumn #> 0.2 1.0 #> #> $perc_peak #> spring autumn #> 12.5 25.0 #> #> $PEC_sw_drainage #> spring autumn #> 1.562500 4.807692 #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"reimplementation calculation described Exposit 3.02 spreadsheet file, worksheet \"Konzept Runoff\".","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"","code":"PEC_sw_exposit_runoff( rate, interception = 0, Koc, DT50 = Inf, t_runoff = 3, exposit_reduction_version = c(\"3.02\", \"3.01a\", \"3.01a2\", \"2.0\"), V_ditch = 30, V_event = 100, dilution = 2 )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"Excel 3.02 spreadsheet available https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"rate application rate g/ha interception fraction intercepted crop Koc sorption coefficient soil organic carbon DT50 soil half-life days t_runoff time application runoff event, degradation occurs, days exposit_reduction_version version reduction factors used. \"3.02\" current version used Germany, \"3.01a\" version additional percentages 3 m 6 m buffer zones used Switzerland. \"3.01a2\" version introduced consistency previous calculations performed 3 m buffer zone Switzerland, reduction applied dissolved bound fraction. V_ditch volume ditch assumed 1 m * 100 m * 30 cm = 30 m3 V_event unreduced runoff volume, equivalent 10 mm precipitation 1 ha dilution dilution factor","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"list containing following components perc_runoff runoff percentages dissolved bound substance runoff matrix containing dissolved bound input different distances PEC_sw_runoff matrix containing PEC values dissolved bound substance different distances. rate given g/ha, PECsw microg/L.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"","code":"PEC_sw_exposit_runoff(500, Koc = 150) #> $perc_runoff #> dissolved bound #> 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 #> #> $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 #> PEC_sw_exposit_runoff(600, Koc = 10000, DT50 = 195, exposit = \"3.01a\") #> $perc_runoff #> dissolved bound #> 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 #> #> $PEC_sw_runoff #> dissolved bound total #> No buffer 0.8447893 3.6303107 4.4751000 #> 3 m 0.7844472 3.1462693 3.9307165 #> 5 m 0.7321507 3.1462693 3.8784200 #> 6 m 0.7106169 2.4985080 3.2091248 #> 10 m 0.6275578 1.0113008 1.6388586 #> 20 m 0.4392904 0.4719404 0.9112308 #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","title":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","text":"reimplementation FOCUS Step 1 2 calculator version 3.2, authored Michael Klein, R. Note results multiple applications compared corresponding results single application. current, done automatically implementation. Step 1 PECs calculated. However, input files can generated suitable input FOCUS calculator.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","text":"","code":"PEC_sw_focus( parent, rate, n = 1, i = NA, comment = \"\", met = NULL, f_drift = NA, f_rd = 0.1, scenario = FOCUS_Step_12_scenarios$names, region = c(\"n\", \"s\"), season = c(NA, \"of\", \"mm\", \"js\"), interception = c(\"no interception\", \"minimal crop cover\", \"average crop cover\", \"full canopy\"), met_form_water = TRUE, txt_file = \"pesticide.txt\", overwrite = FALSE, append = FALSE )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","text":"parent list containing substance specific parameters, e.g. conveniently generated chent_focus_sw. rate application rate g/ha. Overriden applications given explicitly n number applications application interval comment comment input file met list containing metabolite specific parameters. e.g. conveniently generated chent_focus_sw. NULL, PEC calculated compound, parent. f_drift fraction application rate reaching waterbody via drift. NA, derived scenario name number applications via drift data defined FOCUS_Step_12_scenarios f_rd fraction amount applied reaching waterbody via runoff/drainage. Step 1, assumed 10%, parent metabolite scenario name scenario. Must one scenario names given FOCUS_Step_12_scenarios region 'n' Northern Europe 's' Southern Europe. NA, Step 1 PECsw calculated season '' October February, 'mm' March May, 'js' June September. NA, step 1 PECsw calculated interception One 'interception' (default), 'minimal crop cover', 'average crop cover' 'full canopy' met_form_water metabolite formation water taken account? can switched check influence compare previous versions Steps 12 calculator txt_file name, potentially full path Steps.12 input text file specification run(s) written overwrite existing file location specified txt_file overwritten? takes effect append FALSE. append input text file appended, exists?","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","text":"formulas input waterbody via runoff/drainage parent subsequent formation metabolite water documented model description coming calculator. one expect, appears (get results) calculated multiplying application rate molar weight correction formation fraction water/sediment systems. Step 2 implemented.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","text":"FOCUS (2014) Generic guidance Surface Water Scenarios (version 1.4). FOrum Co-ordination pesticde fate models USe. http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic%20FOCUS_SWS_vc1.4.pdf Website Steps 1 2 calculator Joint Research Center European Union: http://esdac.jrc.ec.europa.eu/projects/stepsonetwo","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","text":"","code":"# Parent only dummy_1 <- chent_focus_sw(\"Dummy 1\", cwsat = 6000, DT50_ws = 6, Koc = 344.8) PEC_sw_focus(dummy_1, 3000, f_drift = 0) #> $f_drift #> [1] 0 #> #> $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+02 647.68635 2.104370e+03 2233.2225 #> 2 5.437298e+02 612.03420 1.874780e+03 2110.2939 #> 4 4.315586e+02 548.76030 1.488014e+03 1892.1255 #> 7 3.051580e+02 469.88375 1.052185e+03 1620.1592 #> 14 1.359325e+02 339.57370 4.686951e+02 1170.8501 #> 21 6.055102e+01 257.45458 2.087799e+02 887.7034 #> 28 2.697241e+01 203.47173 9.300089e+01 701.5705 #> 42 5.352005e+00 140.10377 1.845371e+01 483.0778 #> 50 2.123945e+00 118.24602 7.323361e+00 407.7123 #> 100 6.585062e-03 59.30629 2.270529e-02 204.4881 #> #> $PEC_sw_max #> [1] 685.0566 #> #> $PEC_sed_max #> [1] 2362.075 #> # Metabolite new_dummy <- chent_focus_sw(\"New Dummy\", mw = 250, Koc = 100) M1 <- chent_focus_sw(\"M1\", mw = 100, cwsat = 100, DT50_ws = 100, Koc = 50, max_ws = 0, max_soil = 0.5) PEC_sw_focus(new_dummy, 1000, scenario = \"cereals, winter\", met = M1) #> $f_drift #> [1] 0.02759 #> #> $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 62.06890 30.81977 31.03445 #> 4 60.79093 61.64158 30.39547 30.82079 #> 7 59.53987 61.00800 29.76994 30.50400 #> 14 56.71995 59.56326 28.35997 29.78163 #> 21 54.03358 58.16414 27.01679 29.08207 #> 28 51.47444 56.80902 25.73722 28.40451 #> 42 46.71404 54.22460 23.35702 27.11230 #> 50 44.19417 52.81945 22.09709 26.40973 #> 100 31.25000 45.08422 15.62500 22.54211 #> #> $PEC_sw_max #> [1] 62.5 #> #> $PEC_sed_max #> [1] 31.25 #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate predicted environmental concentrations in sediment from surface\nwater concentrations — PEC_sw_sed","title":"Calculate predicted environmental concentrations in sediment from surface\nwater concentrations — PEC_sw_sed","text":"method 'percentage' equivalent used CRD spreadsheet PEC calculator","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate predicted environmental concentrations in sediment from surface\nwater concentrations — PEC_sw_sed","text":"","code":"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\") )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate predicted environmental concentrations in sediment from surface\nwater concentrations — PEC_sw_sed","text":"PEC_sw Numeric vector matrix surface water concentrations µg/L corresponding sediment concentration estimated percentage percentage sediment, used percentage method method method used calculation sediment_depth Depth sediment layer water_depth Depth water body cm sediment_density density sediment L/kg (equivalent g/cm3) PEC_sed_units units estimated sediment PEC value","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate predicted environmental concentrations in sediment from surface\nwater concentrations — PEC_sw_sed","text":"predicted concentration sediment","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate predicted environmental concentrations in sediment from surface\nwater concentrations — PEC_sw_sed","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate predicted environmental concentrations in sediment from surface\nwater concentrations — PEC_sw_sed","text":"","code":"PEC_sw_sed(PEC_sw_drift(100, distances = 1), percentage = 50) #> 1 m #> 2.130769"},{"path":"https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.html","id":null,"dir":"Reference","previous_headings":"","what":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","title":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","text":"Actual maximum moving window time average concentrations SFO kinetics","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","text":"","code":"SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100))"},{"path":"https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","text":"FOCUS (2014) Generic Guidance Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration, Version 1.1, 18 December 2014, p. 251","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","text":"DT50 half-life. times output times, window sizes time weighted average concentrations","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","text":"","code":"SFO_actual_twa(10) #> actual twa #> 0 1.0000000000 NaN #> 1 0.9330329915 0.9661297 #> 2 0.8705505633 0.9337803 #> 4 0.7578582833 0.8733416 #> 7 0.6155722067 0.7923030 #> 14 0.3789291416 0.6400113 #> 21 0.2332582479 0.5267498 #> 28 0.1435872944 0.4412651 #> 42 0.0544094102 0.3248093 #> 50 0.0312500000 0.2795222 #> 100 0.0009765625 0.1441286"},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"implements method specified UK data requirements handbook checked spreadsheet published CRD website","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"","code":"SSLRC_mobility_classification(Koc)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"Koc sorption coefficient normalised organic carbon L/kg","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"list containing classification percentage compound transported per 10 mm drain water","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"HSE's Chemicals Regulation Division (CRD) Active substance PECsw calculations (UK specific authorisation requests) https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm accessed 2019-09-27 Drainage PECs Version 1.0 (2015) Spreadsheet published https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx accessed 2019-09-27","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"","code":"SSLRC_mobility_classification(100) #> $`Mobility classification` #> [1] \"Moderately mobile\" #> #> $`Percentage drained per mm of drain water` #> [1] 0.7 #> SSLRC_mobility_classification(10000) #> $`Mobility classification` #> [1] \"Non mobile\" #> #> $`Percentage drained per mm of drain water` #> [1] 0.008 #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"R6 class holding TOXSWA water concentration (cwa) data associated statistics. like maximum moving window average concentrations, dataframes holding events exceeding specified thresholds. Usually, instance class generated read.TOXSWA_cwa.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"R6Class generator object.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"filename Length one character vector holding filename. basedir Length one character vector holding directory file came . zipfile null, giving path zip file file read. segment Length one integer, specifying segment cwa data read. substance TOXSWA name substance. cwas Dataframe holding concentrations. events List dataframes holding event statistics threshold. windows Matrix maximum time weighted average concentrations (TWAC_max) areas curve µg/day * h (AUC_max_h) µg/day * d (AUC_max_d) requested moving window sizes days.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"TOXSWA_cwa$new() TOXSWA_cwa$moving_windows() TOXSWA_cwa$get_events() TOXSWA_cwa$print() TOXSWA_cwa$clone()","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"Create TOXSWA_cwa object file","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"TOXSWA_cwa$new( filename, basedir, zipfile = NULL, segment = \"last\", substance = \"parent\", total = FALSE )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"filename filename basedir directory look zipfile Optional path zipfile holding file segment Either \"last\" number segment read data substance TOXSWA substance name (TOXSWA 4 higher) total total concentrations read ? FALSE, free concentrations read","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"method-moving-windows-","dir":"Reference","previous_headings":"","what":"Method moving_windows()","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"Add windows field described .","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"TOXSWA_cwa$moving_windows(windows, total = FALSE)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"windows Window sizes days total TRUE, total concentration including amount adsorbed suspended matter used.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"method-get-events-","dir":"Reference","previous_headings":"","what":"Method get_events()","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"Populate datataframe event information specified threshold value. resulting dataframe stored events field object.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"TOXSWA_cwa$get_events(thresholds, total = FALSE)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"thresholds Threshold values µg/L. total TRUE, total concentration including amount adsorbed suspended matter used.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"Print TOXSWA_cwa object","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"TOXSWA_cwa$print()"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"TOXSWA_cwa$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"H_sw_R1_stream <- read.TOXSWA_cwa(\"00003s_pa.cwa\", basedir = \"SwashProjects/project_H_sw/TOXSWA\", zipfile = system.file(\"testdata/SwashProjects.zip\", package = \"pfm\")) H_sw_R1_stream$get_events(c(2, 10)) H_sw_R1_stream$moving_windows(c(7, 21)) print(H_sw_R1_stream) #> data from file 00003s_pa.cwa segment 20 #> datetime t t_firstjan t_rel_to_max cwa_mug_per_L #> 20 1978-10-01 00:00:00 0.000 273.0000 -55.333 0 #> 40 1978-10-01 01:00:00 0.042 273.0417 -55.291 0 #> 60 1978-10-01 02:00:00 0.083 273.0833 -55.250 0 #> 80 1978-10-01 03:00:00 0.125 273.1250 -55.208 0 #> 100 1978-10-01 04:00:00 0.167 273.1667 -55.166 0 #> 120 1978-10-01 05:00:00 0.208 273.2083 -55.125 0 #> cwa_tot_mug_per_L #> 20 0 #> 40 0 #> 60 0 #> 80 0 #> 100 0 #> 120 0 #> Moving window analysis #> window max_TWAC max_AUC_h max_AUC_d #> 1 7 days 2.3926551 401.9660 16.74859 #> 2 21 days 0.8369248 421.8101 17.57542 #> Event statistics for threshold 2 #> t_start cwa_max duration pre_interval AUC_h AUC_d #> 1 44.375 4.167238 0.208 44.375 17.77202 0.740501 #> 2 55.042 40.584010 0.583 10.459 398.21189 16.592162 #> Event statistics for threshold 10 #> t_start cwa_max duration pre_interval AUC_h AUC_d #> 1 55.083 40.58401 0.459 55.083 379.433 15.80971"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TSCF.html","id":null,"dir":"Reference","previous_headings":"","what":"Estimation of the transpiration stream concentration factor — TSCF","title":"Estimation of the transpiration stream concentration factor — TSCF","text":"FOCUS groundwater guidance (FOCUS 2014, p. 41) states reliable measured log Kow neutral pH must available order apply Briggs equation. clarified can regarded reliable, equation stated produced non-ionic compounds, suggesting compound ionogenic (weak acid/base) ionic.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TSCF.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Estimation of the transpiration stream concentration factor — TSCF","text":"","code":"TSCF(log_Kow, method = c(\"briggs82\", \"dettenmaier09\"))"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TSCF.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Estimation of the transpiration stream concentration factor — TSCF","text":"log_Kow decadic logarithm octanol-water partition constant method Short name estimation method.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TSCF.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Estimation of the transpiration stream concentration factor — TSCF","text":"Dettenmaier equation given show views subject exist.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TSCF.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Estimation of the transpiration stream concentration factor — TSCF","text":"FOCUS (2014) Generic Guidance Tier 1 FOCUS Ground Water Assessments. Version 2.2, May 2014 Dettenmaier EM, Doucette WJ Bugbee B (2009) Chemical hydrophobicity uptake plant roots. Environ. Sci. Technol 43, 324 - 329","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TSCF.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Estimation of the transpiration stream concentration factor — TSCF","text":"","code":"plot(TSCF, -1, 5, xlab = \"log Kow\", ylab = \"TSCF\", ylim = c(0, 1.1)) TSCF_2 <- function(x) TSCF(x, method = \"dettenmaier09\") curve(TSCF_2, -1, 5, add = TRUE, lty = 2) legend(\"topright\", lty = 1:2, bty = \"n\", legend = c(\"Briggs et al. (1982)\", \"Dettenmaier et al. (2009)\"))"},{"path":"https://pkgdown.jrwb.de/pfm/reference/chent_focus_sw.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw","title":"Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw","text":"Create chemical compound object FOCUS Step 1 calculations","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/chent_focus_sw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw","text":"","code":"chent_focus_sw( name, Koc, DT50_ws = NA, DT50_soil = NA, DT50_water = NA, DT50_sediment = NA, cwsat = 1000, mw = NA, max_soil = 1, max_ws = 1 )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/chent_focus_sw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw","text":"name Length one character vector containing name Koc Partition coefficient organic carbon water L/kg. DT50_ws Half-life water/sediment systems days DT50_soil Half-life soil days DT50_water Half-life water days (Step 2) DT50_sediment Half-life sediment days (Step 2) cwsat Water solubility mg/L mw Molar weight g/mol. max_soil Maximum observed fraction (dimensionless) soil max_ws Maximum observed fraction (dimensionless) water/sediment systems","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/chent_focus_sw.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw","text":"list substance specific properties","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.html","id":null,"dir":"Reference","previous_headings":"","what":"Deposition from spray drift expressed as percent of the applied dose as\npublished by the JKI — drift_data_JKI","title":"Deposition from spray drift expressed as percent of the applied dose as\npublished by the JKI — drift_data_JKI","text":"Deposition spray drift expressed percent applied dose published German Julius-Kühn Institute (JKI).","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Deposition from spray drift expressed as percent of the applied dose as\npublished by the JKI — drift_data_JKI","text":"","code":"drift_data_JKI"},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Deposition from spray drift expressed as percent of the applied dose as\npublished by the JKI — drift_data_JKI","text":"list currently containing matrices spray drift percentage data field crops (Ackerbau), Pome/stone fruit, early late (Obstbau frueh, spaet).","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Deposition from spray drift expressed as percent of the applied dose as\npublished by the JKI — drift_data_JKI","text":"JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html 2015-06-11, present 2024-01-31 Rautmann, D., Streloke, M Winkler, R (2001) New basic drift values authorization procedure plant protection products Mitt. Biol. Bundesanst. Land- Forstwirtsch. 383, 133-141","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Deposition from spray drift expressed as percent of the applied dose as\npublished by the JKI — drift_data_JKI","text":"data extracted spreadsheet cited using R code given file data_generation/drift_data_JKI.R installed package. file included package, licence clear. Additional spray drift values taken publication Rautmann et al. (2001). Specifically, values early vines, values 3 m buffer incomplete spreadsheet. Note vegetables, ornamentals small fruit, values field crops used crops < 50 cm, vales late vines used crops > 50 cm. JKI spreadsheet, indicated values used spray applications handheld/knapsack equipment (tragbare Spritz- und Sprühgerate). Values non-professional use listed JKI spreadsheet included.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Deposition from spray drift expressed as percent of the applied dose as\npublished by the JKI — drift_data_JKI","text":"","code":"drift_data_JKI #> [[1]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 2.77 NA NA NA NA #> 3 0.95 29.20 15.73 2.70 8.02 #> 5 0.57 19.89 8.41 1.18 3.62 #> 10 0.29 11.81 3.60 0.39 1.23 #> 15 0.20 5.55 1.81 0.20 0.65 #> 20 0.15 2.77 1.09 0.13 0.42 #> 30 0.10 1.04 0.54 0.07 0.22 #> 40 0.07 0.52 0.32 0.04 0.14 #> 50 0.06 0.30 0.22 0.03 0.10 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 4.440 NA #> 3 19.33 NA 0.018721696 #> 5 11.57 0.180 0.014363896 #> 10 5.77 0.050 0.010026007 #> 15 3.84 0.020 0.008124366 #> 20 1.79 0.012 0.006998158 #> 30 0.56 0.005 0.005670811 #> 40 0.25 0.003 NA #> 50 0.13 0.002 0.004350831 #> #> [[2]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 2.38 NA NA NA NA #> 3 0.79 25.53 12.13 2.53 7.23 #> 5 0.47 16.87 6.81 1.09 3.22 #> 10 0.24 9.61 3.11 0.35 1.07 #> 15 0.16 5.61 1.58 0.18 0.56 #> 20 0.12 2.59 0.90 0.11 0.36 #> 30 0.08 0.87 0.40 0.06 0.19 #> 40 0.06 0.40 0.23 0.03 0.12 #> 50 0.05 0.22 0.15 0.02 0.08 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 3.780 NA #> 3 17.73 NA NA #> 5 9.60 0.160 NA #> 10 4.18 0.040 NA #> 15 2.57 0.020 NA #> 20 1.21 0.011 NA #> 30 0.38 0.005 NA #> 40 0.17 0.003 NA #> 50 0.09 0.002 NA #> #> [[3]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 2.01 NA NA NA NA #> 3 0.68 23.96 11.01 2.49 6.90 #> 5 0.41 15.79 6.04 1.04 3.07 #> 10 0.20 8.96 2.67 0.32 1.02 #> 15 0.14 4.24 1.39 0.16 0.54 #> 20 0.10 2.01 0.80 0.10 0.34 #> 30 0.07 0.70 0.36 0.05 0.18 #> 40 0.05 0.33 0.21 0.03 0.11 #> 50 0.04 0.19 0.13 0.02 0.08 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 3.420 NA #> 3 15.93 NA NA #> 5 8.57 0.150 NA #> 10 3.70 0.040 NA #> 15 2.26 0.020 NA #> 20 1.05 0.010 NA #> 30 0.34 0.004 NA #> 40 0.15 0.003 NA #> 50 0.08 0.002 NA #> #> [[4]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 1.85 NA NA NA NA #> 3 0.62 23.61 10.12 2.44 6.71 #> 5 0.38 15.42 5.60 1.02 2.99 #> 10 0.19 8.66 2.50 0.31 0.99 #> 15 0.13 4.01 1.28 0.16 0.52 #> 20 0.10 1.89 0.75 0.10 0.33 #> 30 0.06 0.66 0.35 0.05 0.17 #> 40 0.05 0.31 0.20 0.03 0.11 #> 50 0.04 0.17 0.13 0.02 0.08 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 2.290 NA #> 3 15.38 NA NA #> 5 8.26 0.120 NA #> 10 3.55 0.030 NA #> 15 2.17 0.020 NA #> 20 0.93 0.009 NA #> 30 0.31 0.004 NA #> 40 0.14 0.002 NA #> 50 0.08 0.002 NA #> #> [[5]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 1.75 NA NA NA NA #> 3 0.59 23.12 9.74 2.37 6.59 #> 5 0.36 15.06 5.41 1.00 2.93 #> 10 0.18 8.42 2.43 0.31 0.98 #> 15 0.12 3.83 1.24 0.15 0.51 #> 20 0.09 1.81 0.72 0.09 0.33 #> 30 0.06 0.63 0.34 0.05 0.17 #> 40 0.05 0.30 0.20 0.03 0.11 #> 50 0.04 0.17 0.13 0.02 0.08 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 2.120 NA #> 3 15.12 NA NA #> 5 7.99 0.110 NA #> 10 3.36 0.030 NA #> 15 2.03 0.010 NA #> 20 0.88 0.008 NA #> 30 0.29 0.004 NA #> 40 0.14 0.002 NA #> 50 0.07 0.002 NA #> #> [[6]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 1.64 NA NA NA NA #> 3 0.56 22.76 9.21 2.29 6.41 #> 5 0.34 14.64 5.18 0.97 2.85 #> 10 0.17 8.04 2.38 0.30 0.95 #> 15 0.11 3.71 1.20 0.15 0.50 #> 20 0.09 1.75 0.68 0.09 0.32 #> 30 0.06 0.61 0.31 0.05 0.17 #> 40 0.04 0.29 0.17 0.03 0.11 #> 50 0.03 0.16 0.11 0.02 0.07 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 1.980 NA #> 3 14.90 NA NA #> 5 7.79 0.100 NA #> 10 3.23 0.030 NA #> 15 1.93 0.010 NA #> 20 0.83 0.008 NA #> 30 0.28 0.004 NA #> 40 0.13 0.002 NA #> 50 0.07 0.001 NA #> #> [[7]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 1.61 NA NA NA NA #> 3 0.55 22.69 9.10 2.24 6.33 #> 5 0.33 14.45 5.11 0.94 2.81 #> 10 0.17 7.83 2.33 0.29 0.94 #> 15 0.11 3.62 1.20 0.15 0.49 #> 20 0.08 1.71 0.67 0.09 0.31 #> 30 0.06 0.60 0.30 0.05 0.16 #> 40 0.04 0.28 0.17 0.03 0.10 #> 50 0.03 0.16 0.11 0.02 0.07 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 1.930 NA #> 3 14.63 NA NA #> 5 7.60 0.100 NA #> 10 3.13 0.030 NA #> 15 1.86 0.010 NA #> 20 0.81 0.008 NA #> 30 0.26 0.004 NA #> 40 0.12 0.002 NA #> 50 0.06 0.001 NA #> #> [[8]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 1.52 NA NA NA NA #> 3 0.52 22.24 8.66 2.16 6.26 #> 5 0.31 14.09 4.92 0.91 2.78 #> 10 0.16 7.58 2.29 0.28 0.93 #> 15 0.11 3.48 1.14 0.14 0.49 #> 20 0.08 1.65 0.65 0.09 0.31 #> 30 0.05 0.57 0.29 0.04 0.16 #> 40 0.04 0.27 0.16 0.03 0.10 #> 50 0.03 0.15 0.11 0.02 0.07 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 1.640 NA #> 3 13.53 NA NA #> 5 7.15 0.090 NA #> 10 3.01 0.020 NA #> 15 1.82 0.010 NA #> 20 0.78 0.007 NA #> 30 0.25 0.003 NA #> 40 0.12 0.002 NA #> 50 0.06 0.001 NA #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.html","id":null,"dir":"Reference","previous_headings":"","what":"Regression parameters for the Rautmann drift data — drift_parameters_focus","title":"Regression parameters for the Rautmann drift data — drift_parameters_focus","text":"parameters extracted Appendix B FOCUS surface water guidance using R code given file data_generation/drift_parameters_focus.R installed package. appendix included package, licence clear.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Regression parameters for the Rautmann drift data — drift_parameters_focus","text":"","code":"drift_parameters_focus"},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Regression parameters for the Rautmann drift data — drift_parameters_focus","text":"tibble::tibble.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Regression parameters for the Rautmann drift data — drift_parameters_focus","text":"hinge distance, Inf substituted cases hinge distance given data, way parameters C D never used distance B used case distance smaller hinge distance.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Regression parameters for the Rautmann drift data — drift_parameters_focus","text":"FOCUS (2014) Generic guidance Surface Water Scenarios (version 1.4). FOrum Co-ordination pesticde fate models USe. http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic%20FOCUS_SWS_vc1.4.pdf FOCUS (2001) FOCUS Surface Water Scenarios EU Evaluation Process 91/414/EEC. Report FOCUS Working Group Surface Water Scenarios, EC Document Reference SANCO/4802/2001-rev.2. 245, Appendix B. https://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/FOCUS_SWS_APPENDIX_B.doc Rautmann, D., Streloke, M Winkler, R (2001) New basic drift values authorization procedure plant protection products Mitt. Biol. Bundesanst. Land- Forstwirtsch. 383, 133-141","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Regression parameters for the Rautmann drift data — drift_parameters_focus","text":"","code":"drift_parameters_focus #> # A tibble: 49 × 8 #> crop_group n_apps percentile A B C D hinge #> #> 1 arable 1 90 2.76 -0.978 NA NA Inf #> 2 arable 2 82 2.44 -1.01 NA NA Inf #> 3 arable 3 77 2.02 -0.996 NA NA Inf #> 4 arable 4 74 1.86 -0.986 NA NA Inf #> 5 arable 5 72 1.79 -0.994 NA NA Inf #> 6 arable 6 70 1.63 -0.986 NA NA Inf #> 7 arable 7 69 1.58 -0.981 NA NA Inf #> 8 arable 8 67 1.51 -0.983 NA NA Inf #> 9 hops 1 90 58.2 -1.00 8655. -2.84 15.3 #> 10 hops 2 82 66.2 -1.20 5555. -2.82 15.3 #> # ℹ 39 more rows unique(drift_parameters_focus$crop_group) #> [1] \"arable\" \"hops\" \"vines, late\" \"vines, early\" \"fruit, late\" #> [6] \"fruit, early\" \"aerial\""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_percentages_rautmann.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate drift percentages based on Rautmann data — drift_percentages_rautmann","title":"Calculate drift percentages based on Rautmann data — drift_percentages_rautmann","text":"Calculate drift percentages based Rautmann data","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_percentages_rautmann.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate drift percentages based on Rautmann data — drift_percentages_rautmann","text":"","code":"drift_percentages_rautmann( distances, applications = 1, crop_group_focus = c(\"arable\", \"hops\", \"vines, late\", \"vines, early\", \"fruit, late\", \"fruit, early\", \"aerial\"), formula = c(\"Rautmann\", \"FOCUS\"), widths = 1 )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_percentages_rautmann.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate drift percentages based on Rautmann data — drift_percentages_rautmann","text":"distances distances m get PEC values applications Number applications selection drift percentile crop_group_focus One crop groups used drift_parameters_focus formula default, original Rautmann formula used. specify \"FOCUS\", mean drift input width water body calculated described Chapter 5.4.5 FOCUS surface water guidance widths widths water bodies (used FOCUS formula)","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_percentages_rautmann.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate drift percentages based on Rautmann data — drift_percentages_rautmann","text":"FOCUS (2014) Generic guidance Surface Water Scenarios (version 1.4). FOrum Co-ordination pesticde fate models USe. http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic%20FOCUS_SWS_vc1.4.pdf","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_percentages_rautmann.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate drift percentages based on Rautmann data — drift_percentages_rautmann","text":"","code":"# Compare JKI data with Rautmann formula # One application on field crops, for 1 m, 3 m and 5 m distance drift_data_JKI[[1]][as.character(c(1, 3, 5)), \"Ackerbau\"] #> 1 3 5 #> 2.77 0.95 0.57 drift_percentages_rautmann(c(1, 3, 5)) #> [1] 2.7593000 0.9424748 0.5719342 drift_percentages_rautmann(c(1, 3, 5), formula = \"FOCUS\") #> [1] 1.9273922 0.8160023 0.5224362 # One application to early or late fruit crops drift_data_JKI[[1]][as.character(c(3, 5, 20, 50)), \"Obstbau frueh\"] #> 3 5 20 50 #> 29.20 19.89 2.77 0.30 drift_percentages_rautmann(c(3, 5, 20, 50), crop_group = \"fruit, early\") #> [1] 29.1973659 19.8844422 2.7618138 0.3012008 drift_percentages_rautmann(c(3, 5, 20, 50), crop_group = \"fruit, early\", formula = \"FOCUS\") #> [1] 26.1193421 18.5428680 2.6038558 0.2940792 drift_data_JKI[[1]][as.character(c(3, 5, 20, 50)), \"Obstbau spaet\"] #> 3 5 20 50 #> 15.73 8.41 1.09 0.22 drift_percentages_rautmann(c(3, 5, 20, 50), crop_group = \"fruit, late\") #> [1] 15.7246994 8.4108487 1.0813887 0.2155992 drift_percentages_rautmann(c(3, 5, 20, 50), crop_group = \"fruit, late\", formula = \"FOCUS\") #> [1] 13.1414350 7.5123244 1.0359007 0.2118734 # We get a continuum if the waterbody covers the hinge distance # (11.4 m for 1 early app to fruit) x <- seq(3, 30, by = 0.1) d <- drift_percentages_rautmann(x, crop_group = \"fruit, early\", formula = \"FOCUS\") plot(x, d, type = \"l\", xlab = \"Distance of near edge [m]\", ylab = \"Mean drift percentage over waterbody width\", main = \"One application to fruit, early\") abline(v = 11.4, lty = 2)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/endpoint.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve endpoint information from the chyaml field of a chent object — endpoint","title":"Retrieve endpoint information from the chyaml field of a chent object — endpoint","text":"R6 class objects class chent represent chemical entities can hold list information loaded chemical yaml file chyaml field. information extracted optionally aggregated function.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/endpoint.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve endpoint information from the chyaml field of a chent object — endpoint","text":"","code":"endpoint( chent, medium = \"soil\", type = c(\"degradation\", \"sorption\"), lab_field = c(NA, \"laboratory\", \"field\"), redox = c(NA, \"aerobic\", \"anaerobic\"), value = c(\"DT50ref\", \"Kfoc\", \"N\"), aggregator = geomean, raw = FALSE, signif = 3 ) soil_DT50( chent, aggregator = geomean, signif = 3, lab_field = \"laboratory\", value = \"DT50ref\", redox = \"aerobic\", raw = FALSE ) soil_Kfoc(chent, aggregator = geomean, signif = 3, value = \"Kfoc\", raw = FALSE) soil_N(chent, aggregator = mean, signif = 3, raw = FALSE) soil_sorption( chent, values = c(\"Kfoc\", \"N\"), aggregators = c(Kfoc = geomean, Koc = geomean, N = mean), signif = c(Kfoc = 3, N = 3), raw = FALSE )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/endpoint.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve endpoint information from the chyaml field of a chent object — endpoint","text":"chent chent object get information medium medium information sought type information type lab_field NA, want laboratory field endpoints redox NA, looking aerobic anaerobic data value name value want. list given usage section exclusive aggregator aggregator function. Can mean, geomean, identity, example. raw number(s) returned stored chent object (character value) retain original information precision? signif many significant digits want values values returned aggregators named vector aggregator functions used","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/endpoint.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve endpoint information from the chyaml field of a chent object — endpoint","text":"result applying aggregator function values converted numeric vector, rounded given number significant digits, , raw = TRUE, values character value, retaining implicit information precision may present.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/endpoint.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Retrieve endpoint information from the chyaml field of a chent object — endpoint","text":"functions soil_* functions extract soil specific endpoints. Freundlich exponent, capital letter N used order facilitate dealing data R. pesticide fate modelling, exponent often called 1/n.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/geomean.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate the geometric mean — geomean","title":"Calculate the geometric mean — geomean","text":"Based posts thread Stackoverflow http://stackoverflow.com/questions/2602583/geometric-mean----built-function returns NA NA values present na.rm = FALSE (default). negative values present, gives error message. least one element vector 0, returns 0.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/geomean.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate the geometric mean — geomean","text":"","code":"geomean(x, na.rm = FALSE)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/geomean.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate the geometric mean — geomean","text":"x Vector numbers na.rm NA values omitted?","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/geomean.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate the geometric mean — geomean","text":"geometric mean","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/geomean.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate the geometric mean — geomean","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/geomean.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate the geometric mean — geomean","text":"","code":"geomean(c(1, 3, 9)) #> [1] 3 geomean(c(1, 3, NA, 9)) #> [1] NA geomean(c(1, -3, 9)) # returns an error #> Error in geomean(c(1, -3, 9)): Only defined for positive numbers"},{"path":"https://pkgdown.jrwb.de/pfm/reference/get_vertex.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit a parabola through three points — get_vertex","title":"Fit a parabola through three points — get_vertex","text":"inspired answer stackoverflow https://stackoverflow.com//717791","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/get_vertex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit a parabola through three points — get_vertex","text":"","code":"get_vertex(x, y)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/get_vertex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit a parabola through three points — get_vertex","text":"x Three x coordinates y Three y coordinates","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/max_twa.html","id":null,"dir":"Reference","previous_headings":"","what":"The maximum time weighted average concentration for a moving window — max_twa","title":"The maximum time weighted average concentration for a moving window — max_twa","text":"generate time series using sawtooth, need make sure length time series allows finding maximum. therefore recommended check using plot.one_box using window size argument max_twa.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/max_twa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The maximum time weighted average concentration for a moving window — max_twa","text":"","code":"max_twa(x, window = 21)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/max_twa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The maximum time weighted average concentration for a moving window — max_twa","text":"x object type one_box window size moving window","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/max_twa.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"The maximum time weighted average concentration for a moving window — max_twa","text":"method working directly fitted mkinfit objects uses equations given PEC soil section FOCUS guidance restricted SFO, FOMC DFOP models parent compound","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/max_twa.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"The maximum time weighted average concentration for a moving window — max_twa","text":"FOCUS (2006) “Guidance Document Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/max_twa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"The maximum time weighted average concentration for a moving window — max_twa","text":"","code":"pred <- sawtooth(one_box(10), applications = data.frame(time = c(0, 7), amount = c(1, 1))) max_twa(pred) #> $max #> parent #> 0.9537545 #> #> $window_start #> parent #> 0 #> #> $window_end #> parent #> 21 #> pred_FOMC <- mkinfit(\"FOMC\", FOCUS_2006_C, quiet = TRUE) max_twa(pred_FOMC) #> 21 #> 18.22124"},{"path":"https://pkgdown.jrwb.de/pfm/reference/one_box.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a time series of decline data — one_box","title":"Create a time series of decline data — one_box","text":"Create time series decline data","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/one_box.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a time series of decline data — one_box","text":"","code":"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) # S3 method for character one_box(x, ini = 1, parms, ..., t_end = 100, res = 0.01) # S3 method for mkinfit one_box(x, ini = \"model\", ..., t_end = 100, res = 0.01)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/one_box.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a time series of decline data — one_box","text":"x numeric, half-life used exponential decline. character string specifying parent decline model given e.g. FOMC, parms must contain corresponding parameters. x mkinfit object, decline calculated object. ini initial amount. x mkinfit object, ini 'model', fitted initial concentrations used. Otherwise, ini must numeric. length one, used parent initial values metabolites zero, otherwise, must give values observed variables. ... arguments passed methods t_end End time series res Resolution time series parms named numeric vector containing model parameters","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/one_box.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a time series of decline data — one_box","text":"object class one_box, inheriting ts.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/one_box.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a time series of decline data — one_box","text":"","code":"# Only use a half-life pred_0 <- one_box(10) plot(pred_0) # Use a fitted mkinfit model require(mkin) fit <- mkinfit(\"FOMC\", FOCUS_2006_C, quiet = TRUE) pred_1 <- one_box(fit) plot(pred_1) # Use a model with more than one observed variable m_2 <- mkinmod(parent = mkinsub(\"SFO\", \"m1\"), m1 = mkinsub(\"SFO\")) #> Temporary DLL for differentials generated and loaded fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) #> Warning: Observations with value of zero were removed from the data pred_2 <- one_box(fit_2, ini = \"model\") plot(pred_2)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_exposit.html","id":null,"dir":"Reference","previous_headings":"","what":"Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit","title":"Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit","text":"table loss percentages used Exposit 3 twelve different Koc classes","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_exposit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit","text":"","code":"perc_runoff_exposit"},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_exposit.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit","text":"data frame percentage values dissolved fraction fraction bound eroding particles, Koc classes used row names Koc_lower_bound lower bound Koc class dissolved percentage applied substance transferred adjacent water body dissolved phase bound percentage applied substance transferred adjacent water body bound eroding particles","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_exposit.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit","text":"Excel 3.02 spreadsheet available https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_exposit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit","text":"","code":"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"},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_reduction_exposit.html","id":null,"dir":"Reference","previous_headings":"","what":"Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit","title":"Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit","text":"table runoff reduction percentages used Exposit 3 different vegetated buffer widths","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_reduction_exposit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit","text":"","code":"perc_runoff_reduction_exposit"},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_reduction_exposit.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit","text":"named list data frames reduction percentage values dissolved fraction fraction bound eroding particles, vegetated buffer widths row names. names list items Exposit versions values taken. dissolved reduction percentage dissolved phase bound reduction percentage particulate phase","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_reduction_exposit.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit","text":"Excel 3.02 spreadsheet available https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html Agroscope version 3.01a additional runoff factors 3 m 6 m buffer zones received Muris Korkaric (published). variant 3.01a2 introduced consistency previous calculations performed Agroscope 3 m buffer zone.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_reduction_exposit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit","text":"","code":"print(perc_runoff_reduction_exposit) #> $`3.02` #> dissolved bound #> No buffer 0 0 #> 5 m 40 40 #> 10 m 60 85 #> 20 m 80 95 #> #> $`3.01a` #> dissolved bound #> No buffer 0 0 #> 3 m 25 30 #> 5 m 40 40 #> 6 m 45 55 #> 10 m 60 85 #> 20 m 80 95 #> #> $`3.01a2` #> dissolved bound #> No buffer 0 0 #> 3 m 25 25 #> #> $`2.0` #> dissolved bound #> No buffer 0.0 0.0 #> 20 m 97.5 97.5 #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/pfm_degradation.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation","title":"Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation","text":"Calculate time course relative concentrations based mkinmod model","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/pfm_degradation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation","text":"","code":"pfm_degradation( model = \"SFO\", DT50 = 1000, parms = c(k_parent = log(2)/DT50), years = 1, step_days = 1, times = seq(0, years * 365, by = step_days) )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/pfm_degradation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation","text":"model degradation model used. Either parent model like 'SFO' 'FOMC', mkinmod object DT50 half-life. used simple exponential decline calculated (SFO model). parms parameters used degradation model years many years degradation predicted? step_days step size days output ? times output times","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/pfm_degradation.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/pfm_degradation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation","text":"","code":"head(pfm_degradation(\"SFO\", DT50 = 10)) #> time parent #> 0 0 1.0000000 #> 1 1 0.9330330 #> 2 2 0.8705506 #> 3 3 0.8122524 #> 4 4 0.7578583 #> 5 5 0.7071068"},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.TOXSWA_cwa.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa","title":"Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa","text":"Plot TOXSWA hourly concentrations chemical substance specific segment TOXSWA surface water body.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.TOXSWA_cwa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa","text":"","code":"# S3 method for TOXSWA_cwa plot( x, time_column = c(\"datetime\", \"t\", \"t_firstjan\", \"t_rel_to_max\"), xlab = \"default\", ylab = \"default\", add = FALSE, threshold_factor = 1000, thin_low = 1, total = FALSE, LC_TIME = \"C\", ... )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.TOXSWA_cwa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa","text":"x TOXSWA_cwa object plotted. time_column used time axis. \"t_firstjan\" chosen, time given days relative first January first year. xlab, ylab Labels x y axis. add add existing plot? threshold_factor factor data lower maximum order get thinned plotting (see next argument). thin_low integer greater 1, data close zero (smaller 1/threshold_factor maximum) series thinned factor order decrease amount data included plots total total concentration water plotted, including substance sorbed suspended matter? LC_TIME Specification locale used format dates ... arguments passed plot adding existing plot","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.TOXSWA_cwa.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.TOXSWA_cwa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa","text":"","code":"H_sw_D4_pond <- read.TOXSWA_cwa(\"00001p_pa.cwa\", basedir = \"SwashProjects/project_H_sw/TOXSWA\", zipfile = system.file(\"testdata/SwashProjects.zip\", package = \"pfm\")) plot(H_sw_D4_pond) plot(H_sw_D4_pond, time_column = \"t\") plot(H_sw_D4_pond, time_column = \"t_firstjan\") plot(H_sw_D4_pond, time_column = \"t_rel_to_max\") H_sw_R1_stream <- read.TOXSWA_cwa(\"00003s_pa.cwa\", basedir = \"SwashProjects/project_H_sw/TOXSWA\", zipfile = system.file(\"testdata/SwashProjects.zip\", package = \"pfm\")) plot(H_sw_R1_stream, time_column = \"t_rel_to_max\")"},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.one_box.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot time series of decline data — plot.one_box","title":"Plot time series of decline data — plot.one_box","text":"Plot time series decline data","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.one_box.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot time series of decline data — plot.one_box","text":"","code":"# 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], ... )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.one_box.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot time series of decline data — plot.one_box","text":"x object type one_box plotted xlim Limits x axis ylim Limits y axis xlab Label x axis ylab Label y axis max_twa numeric value given, maximum time weighted average concentration(s) /shown graph. max_twa_var Variable maximum time weighted average shown max_twa NULL. ... arguments passed methods","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.one_box.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot time series of decline data — plot.one_box","text":"","code":"dfop_pred <- one_box(\"DFOP\", parms = c(k1 = 0.2, k2 = 0.02, g = 0.7)) plot(dfop_pred) plot(sawtooth(dfop_pred, 3, 7), max_twa = 21) # Use a fitted mkinfit model m_2 <- mkinmod(parent = mkinsub(\"SFO\", \"m1\"), m1 = mkinsub(\"SFO\")) #> Temporary DLL for differentials generated and loaded fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) #> Warning: Observations with value of zero were removed from the data pred_2 <- one_box(fit_2, ini = 1) pred_2_saw <- sawtooth(pred_2, 2, 7) plot(pred_2_saw, max_twa = 21, max_twa_var = \"m1\")"},{"path":"https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html","id":null,"dir":"Reference","previous_headings":"","what":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","title":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","text":"Read TOXSWA hourly concentrations chemical substance specific segment TOXSWA surface water body. Per default, data last segment imported. TOXSWA 4 reports values end hour (ConLiqWatLayCur) summary file, use value well instead hourly averages (ConLiqWatLay). TOXSWA 5.5.3 variable renamed ConLiqWatLay file.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","text":"","code":"read.TOXSWA_cwa( filename, basedir = \".\", zipfile = NULL, segment = \"last\", substance = \"parent\", total = FALSE, windows = NULL, thresholds = NULL )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","text":"filename filename cwa file (TOXSWA 2.x.y similar) file using FOCUS TOXSWA 4 (.e. TOXSWA 4.4.2) higher. basedir path directory cwa file resides. zipfile Optional path zip file containing cwa file. segment segment data read. Either \"last\", segment number. substance .files, default value \"parent\" leads reading concentrations parent compound. Alternatively, substance interested can selected code name. total Set TRUE order read total concentrations well. necessary .files generated TOXSWA 4.4.2 similar, .cwa files. .cwa files, total concentration always read well. windows Numeric vector width moving windows days, calculating maximum time weighted average concentrations areas curve. thresholds Numeric vector threshold concentrations µg/L generating event statistics.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","text":"instance R6 object class TOXSWA_cwa.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","text":"","code":"H_sw_D4_pond <- read.TOXSWA_cwa(\"00001p_pa.cwa\", basedir = \"SwashProjects/project_H_sw/TOXSWA\", zipfile = system.file(\"testdata/SwashProjects.zip\", package = \"pfm\"))"},{"path":"https://pkgdown.jrwb.de/pfm/reference/reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Objects exported from other packages — reexports","title":"Objects exported from other packages — reexports","text":"objects imported packages. Follow links see documentation. mkin set_nd_nq, set_nd_nq_focus","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/sawtooth.html","id":null,"dir":"Reference","previous_headings":"","what":"Create decline time series for multiple applications — sawtooth","title":"Create decline time series for multiple applications — sawtooth","text":"application pattern specified applications, n disregarded.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/sawtooth.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create decline time series for multiple applications — sawtooth","text":"","code":"sawtooth( x, n = 1, i = 365, applications = data.frame(time = seq(0, (n - 1) * i, length.out = n), amount = 1) )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/sawtooth.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create decline time series for multiple applications — sawtooth","text":"x one_box object n number applications. applications specified, n ignored interval applications. applications specified, ignored applications data frame holding application times first column corresponding amounts applied second column.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/sawtooth.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create decline time series for multiple applications — sawtooth","text":"","code":"applications = data.frame(time = seq(0, 14, by = 7), amount = c(1, 2, 3)) pred <- one_box(10) plot(sawtooth(pred, applications = applications)) m_2 <- mkinmod(parent = mkinsub(\"SFO\", \"m1\"), m1 = mkinsub(\"SFO\")) #> Temporary DLL for differentials generated and loaded fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) #> Warning: Observations with value of zero were removed from the data pred_2 <- one_box(fit_2, ini = 1) pred_2_saw <- sawtooth(pred_2, 2, 7) plot(pred_2_saw, max_twa = 21, max_twa_var = \"m1\") max_twa(pred_2_saw) #> $max #> parent m1 #> 0.7834481 0.8617049 #> #> $window_start #> parent m1 #> 0.00 26.85 #> #> $window_end #> parent m1 #> 21.00 47.85 #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.html","id":null,"dir":"Reference","previous_headings":"","what":"Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015","title":"Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015","text":"Properties predefined scenarios used Tier 1, Tier 2A Tier 3A concentration soil given EFSA guidance (2015, p. 13/14). Also, scenario model adjustment factors p. 15 p. 17 included.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015","text":"","code":"soil_scenario_data_EFSA_2015"},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015","text":"data frame one row scenario. Row names scenario codes, e.g. CTN Northern scenario total concentration soil. Columns mostly self-explanatory. rho dry bulk density top soil.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015","text":"EFSA (European Food Safety Authority) (2015) EFSA guidance document predicting environmental concentrations active substances plant protection products transformation products active substances soil. EFSA Journal 13(4) 4093 doi:10.2903/j.efsa.2015.4093","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015","text":"","code":"soil_scenario_data_EFSA_2015 #> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce #> CTN North Estonia 4.7 7.0 Coarse 0.118 0.244 0.95 3.0 #> CTC Central Germany 8.0 10.1 Coarse 0.086 0.244 1.05 2.0 #> CTS South France 11.0 12.3 Medium fine 0.048 0.385 1.22 2.0 #> CLN North Denmark 8.2 9.8 Medium 0.023 0.347 1.39 2.0 #> CLC Central Czech Republik 9.1 11.2 Medium 0.018 0.347 1.43 1.5 #> CLS South Spain 12.8 14.7 Medium 0.011 0.347 1.51 1.5 #> f_mod #> CTN 2 #> CTC 2 #> CTS 2 #> CLN 4 #> CLC 4 #> CLS 4"},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2017.html","id":null,"dir":"Reference","previous_headings":"","what":"Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017","title":"Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017","text":"Properties predefined scenarios used Tier 1, Tier 2A Tier 3A concentration soil given EFSA guidance (2017, p. 14/15). Also, scenario model adjustment factors p. 16 p. 18 included.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2017.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017","text":"","code":"soil_scenario_data_EFSA_2017"},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2017.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017","text":"data frame one row scenario. Row names scenario codes, e.g. CTN Northern scenario total concentration soil. Columns mostly self-explanatory. rho dry bulk density top soil.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2017.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017","text":"EFSA (European Food Safety Authority) (2017) EFSA guidance document predicting environmental concentrations active substances plant protection products transformation products active substances soil. EFSA Journal 15(10) 4982 doi:10.2903/j.efsa.2017.4982","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2017.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017","text":"","code":"soil_scenario_data_EFSA_2017 #> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce f_mod #> CTN North Estonia 5.7 7.6 Coarse 0.220 0.244 0.707 1.4 3 #> CTC Central Poland 7.4 9.3 Coarse 0.122 0.244 0.934 1.4 3 #> CTS South France 10.2 11.7 Medium 0.070 0.349 1.117 1.4 3 #> CLN North Denmark 8.0 9.2 Medium 0.025 0.349 1.371 1.6 4 #> CLC Central Austria 9.3 11.3 Medium 0.018 0.349 1.432 1.6 4 #> CLS South Spain 15.4 16.7 Medium 0.010 0.349 1.521 1.6 4 #> FOCUS_zone prec #> CTN Hamburg 639 #> CTC Hamburg 617 #> CTS Hamburg 667 #> CLN Hamburg 602 #> CLC Châteaudun 589 #> CLS Sevilla 526 waldo::compare(soil_scenario_data_EFSA_2017, soil_scenario_data_EFSA_2015) #> `old` is length 12 #> `new` is length 10 #> #> `names(old)[8:12]`: \"rho\" \"f_sce\" \"f_mod\" \"FOCUS_zone\" \"prec\" #> `names(new)[8:10]`: \"rho\" \"f_sce\" \"f_mod\" #> #> `old$Country`: \"Estonia\" \"Poland\" \"France\" \"Denmark\" \"Austria\" \"Spain\" #> `new$Country`: \"Estonia\" \"Germany\" \"France\" \"Denmark\" \"Czech Republik\" \"Spain\" #> #> `old$T_arit`: 5.7 7.4 10.2 8.0 9.3 15.4 #> `new$T_arit`: 4.7 8.0 11.0 8.2 9.1 12.8 #> #> `old$T_arr`: 7.6 9.3 11.7 9.2 11.3 16.7 #> `new$T_arr`: 7.0 10.1 12.3 9.8 11.2 14.7 #> #> `old$Texture`: \"Coarse\" \"Coarse\" \"Medium\" \"Medium\" \"Medium\" \"Medium\" #> `new$Texture`: \"Coarse\" \"Coarse\" \"Medium fine\" \"Medium\" \"Medium\" \"Medium\" #> #> `old$f_om`: 0.220 0.122 0.070 0.025 0.018 0.010 #> `new$f_om`: 0.118 0.086 0.048 0.023 0.018 0.011 #> #> `old$theta_fc`: 0.244 0.244 0.349 0.349 0.349 0.349 #> `new$theta_fc`: 0.244 0.244 0.385 0.347 0.347 0.347 #> #> `old$rho`: 0.707 0.934 1.117 1.371 1.432 1.521 #> `new$rho`: 0.950 1.050 1.220 1.390 1.430 1.510 #> #> `old$f_sce`: 1.4 1.4 1.4 1.6 1.6 1.6 #> `new$f_sce`: 3.0 2.0 2.0 2.0 1.5 1.5 #> #> And 3 more differences ..."},{"path":"https://pkgdown.jrwb.de/pfm/reference/twa.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate a time weighted average concentration — twa","title":"Calculate a time weighted average concentration — twa","text":"moving average built using values past, earliest possible time maximum time series returned one window passed.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/twa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate a time weighted average concentration — twa","text":"","code":"twa(x, window = 21) # S3 method for one_box twa(x, window = 21)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/twa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate a time weighted average concentration — twa","text":"x object type one_box window size moving window","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/twa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate a time weighted average concentration — twa","text":"","code":"pred <- sawtooth(one_box(10), applications = data.frame(time = c(0, 7), amount = c(1, 1))) max_twa(pred) #> $max #> parent #> 0.9537545 #> #> $window_start #> parent #> 0 #> #> $window_end #> parent #> 21 #>"}] +[{"path":"https://pkgdown.jrwb.de/pfm/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Johannes Ranke. Author, maintainer.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Johannes Ranke (2024). pfm: Utilities Pesticide Fate Modelling. R package version 0.6.3, https://github.com/jranke/pfm, https://pkgdown.jrwb.de/pfm.","code":"@Manual{, title = {pfm: Utilities for Pesticide Fate Modelling}, author = {{Johannes Ranke}}, year = {2024}, note = {R package version 0.6.3, https://github.com/jranke/pfm}, url = {https://pkgdown.jrwb.de/pfm}, }"},{"path":"https://pkgdown.jrwb.de/pfm/index.html","id":"pfm","dir":"","previous_headings":"","what":"Utilities for Pesticide Fate Modelling","title":"Utilities for Pesticide Fate Modelling","text":"R package pfm provides utilities fate modelling, including dealing FOCUS pesticide fate modelling tools, (currently TOXSWA cwa files), made available GNU public license.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Utilities for Pesticide Fate Modelling","text":"easiest way install package probably use r-universe repo: Alternatively can install package using remotes package. Using quick = TRUE skips docs, multiple-architecture builds, demos, vignettes.","code":"install.packages(\"pfm\", repos = c(\"https://jranke.r-universe.dev\", \"https://cran.r-project.org\")) remotes::install_github(\"jranke/pfm\", quick = TRUE)"},{"path":"https://pkgdown.jrwb.de/pfm/index.html","id":"use","dir":"","previous_headings":"","what":"Use","title":"Utilities for Pesticide Fate Modelling","text":"Please refer reference.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/index.html","id":"examples","dir":"","previous_headings":"","what":"Examples","title":"Utilities for Pesticide Fate Modelling","text":"One recent nice example usage package visualisation time weighted average sawtooth curve obtained several overlays mkinfit predictions shown .","code":""},{"path":"https://pkgdown.jrwb.de/pfm/index.html","id":"applications","dir":"","previous_headings":"","what":"Applications","title":"Utilities for Pesticide Fate Modelling","text":"Calculations predicted environmental concentrations using package used publications Agroscope.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_GW_interception_2014.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014","title":"Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014","text":"Subset EFSA crop interception default values groundwater modelling","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_GW_interception_2014.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014","text":"","code":"EFSA_GW_interception_2014"},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_GW_interception_2014.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014","text":"matrix containing interception values, currently selected crops","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_GW_interception_2014.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014","text":"European Food Safety Authority (2014) EFSA Guidance Document evaluating laboratory field dissipation studies obtain DegT50 values active substances plant protection products transformation products active substances soil. EFSA Journal 12(5):3662, 37 pp., doi:10.2903/j.efsa.2014.3662","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_GW_interception_2014.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subset of EFSA crop interception default values for groundwater modelling — EFSA_GW_interception_2014","text":"","code":"EFSA_GW_interception_2014 #> BBCH #> Crop 0x 1x 2x 3x 4x 5x 6x 7x 8x 9x #> Beans (field + vegetable) 0 0.25 0.40 0.40 0.70 0.70 0.70 0.70 0.70 0.80 #> Peas 0 0.35 0.55 0.55 0.85 0.85 0.85 0.85 0.85 0.85 #> Summer oilseed rape 0 0.40 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.90 #> Winter oilseed rape 0 0.40 0.80 0.80 0.80 0.80 0.80 0.80 0.80 0.90 #> Tomatoes 0 0.50 0.70 0.70 0.80 0.80 0.80 0.80 0.80 0.50 #> Spring cereals 0 0.00 0.20 0.80 0.90 0.90 0.90 0.80 0.80 0.80 #> Winter cereals 0 0.00 0.20 0.80 0.90 0.90 0.90 0.80 0.80 0.80"},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_washoff_2017.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset of EFSA crop washoff default values — EFSA_washoff_2017","title":"Subset of EFSA crop washoff default values — EFSA_washoff_2017","text":"Subset EFSA crop washoff default values","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_washoff_2017.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset of EFSA crop washoff default values — EFSA_washoff_2017","text":"","code":"EFSA_washoff_2017"},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_washoff_2017.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Subset of EFSA crop washoff default values — EFSA_washoff_2017","text":"matrix containing wash-factors, currently selected crops","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_washoff_2017.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Subset of EFSA crop washoff default values — EFSA_washoff_2017","text":"European Food Safety Authority (2017) EFSA guidance document predicting environmental concentrations active substances plant protection products transformation products active substances soil. EFSA Journal 15(10) 4982 doi:10.2903/j.efsa.2017.4982","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/EFSA_washoff_2017.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subset of EFSA crop washoff default values — EFSA_washoff_2017","text":"","code":"EFSA_washoff_2017 #> BBCH #> Crop 0x 1x 2x 3x 4x 5x 6x 7x 8x 9x #> Beans (field + vegetable) NA 0.60 0.75 0.75 0.80 0.80 0.80 0.80 0.80 0.35 #> Peas NA 0.40 0.60 0.60 0.65 0.65 0.65 0.65 0.65 0.35 #> Summer oilseed rape NA 0.40 0.50 0.50 0.60 0.60 0.60 0.60 0.60 0.50 #> Winter oilseed rape NA 0.10 0.40 0.40 0.55 0.55 0.55 0.55 0.55 0.30 #> Tomatoes NA 0.55 0.75 0.75 0.70 0.70 0.70 0.70 0.70 0.35 #> Spring cereals NA 0.40 0.50 0.50 0.65 0.65 0.65 0.65 0.65 0.55 #> Winter cereals NA 0.10 0.40 0.60 0.55 0.55 0.55 0.60 0.60 0.40"},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_GW_scenarios_2012.html","id":null,"dir":"Reference","previous_headings":"","what":"A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012","title":"A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012","text":"Currently, scenario names acronyms small subset soil definitions provided. soil definitions page 46ff. FOCUS (2012).","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_GW_scenarios_2012.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012","text":"","code":"FOCUS_GW_scenarios_2012"},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_GW_scenarios_2012.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012","text":"object class list length 2.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_GW_scenarios_2012.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012","text":"FOCUS (2012) Generic guidance Tier 1 FOCUS ground water assessments. Version 2.1. FOrum Co-ordination pesticde fate models USe. http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_GW_scenarios_2012.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"A very small subset of the FOCUS Groundwater scenario definitions — FOCUS_GW_scenarios_2012","text":"","code":"FOCUS_GW_scenarios_2012 #> $names #> Cha Ham Jok Kre Oke #> \"Châteadun\" \"Hamburg\" \"Jokioinen\" \"Kremsmünster\" \"Okehampton\" #> Pia Por Sev Thi #> \"Piacenza\" \"Porto\" \"Sevilla\" \"Thiva\" #> #> $soils #> location horizon number pH_H2O perc_clay perc_oc rel_deg #> 1 Cha Ap 1 8.0 30.0 1.39 1.0 #> 2 Cha B1 2 8.1 31.0 0.93 0.5 #> 3 Cha B2 3 8.2 25.0 0.70 0.5 #> 4 Cha II C1 4 8.5 26.0 0.30 0.3 #> 5 Cha II C1 5 8.5 26.0 0.30 0.0 #> 6 Cha II C2 6 8.5 24.0 0.27 0.0 #> 7 Cha M 7 8.3 31.0 0.21 0.0 #> 8 Ham Ap 1 6.4 7.2 1.50 1.0 #> 9 Ham BvI 2 5.6 6.7 1.00 0.5 #> 10 Ham BvII 3 5.6 0.9 0.20 0.3 #> 11 Ham Bv/Cv 4 5.7 0.0 0.00 0.3 #> 12 Ham Cv 5 5.5 0.0 0.00 0.3 #> 13 Ham Cv 6 5.5 0.0 0.00 0.0 #> 14 Jok Ap 1 6.2 3.6 4.06 1.0 #> 15 Jok Bs 2 5.6 1.8 0.84 0.5 #> 16 Jok BC1 3 5.4 1.2 0.36 0.3 #> 17 Jok BC2 4 5.4 1.7 0.29 0.3 #> 18 Jok BC2 5 5.4 1.7 0.29 0.0 #> 19 Jok Cg 6 5.3 1.9 0.21 0.0 #> 20 Kre 1 7.7 14.0 3.60 1.0 #> 21 Kre 2 7.0 25.0 1.00 0.5 #> 22 Kre 3 7.1 27.0 0.50 0.5 #> 23 Kre 4 7.1 27.0 0.50 0.3 #> 24 Kre 5 7.1 27.0 0.50 0.0 #> 25 Oke A 1 5.8 18.0 2.20 1.0 #> 26 Oke Bw1 2 6.3 17.0 0.70 0.5 #> 27 Oke BC 3 6.5 14.0 0.40 0.3 #> 28 Oke C 4 6.6 9.0 0.10 0.3 #> 29 Oke C 5 6.6 9.0 0.10 0.0 #> 30 Pia Ap 1 7.0 15.0 1.26 1.0 #> 31 Pia Ap 2 7.0 15.0 1.26 0.5 #> 32 Pia Bw 3 6.3 7.0 0.47 0.5 #> 33 Pia Bw 4 6.3 7.0 0.47 0.3 #> 34 Pia 2C 5 6.4 0.0 0.00 0.3 #> 35 Pia 2C 6 6.4 0.0 0.00 0.0 #> 36 Por 1 4.9 10.0 1.42 1.0 #> 37 Por 2 4.8 8.0 0.78 0.5 #> 38 Por 3 4.8 8.0 0.78 0.3 #> 39 Por 4 4.8 8.0 0.78 0.0 #> 40 Sev 1 7.3 14.0 0.93 1.0 #> 41 Sev 2 7.3 13.0 0.93 1.0 #> 42 Sev 3 7.8 15.0 0.70 0.5 #> 43 Sev 4 8.1 16.0 0.58 0.3 #> 44 Sev 5 8.1 16.0 0.58 0.0 #> 45 Sev 6 8.2 22.0 0.49 0.0 #> 46 Thi Ap1 1 7.7 25.3 0.74 1.0 #> 47 Thi Ap2 2 7.7 25.3 0.74 0.5 #> 48 Thi Bw 3 7.8 29.6 0.57 0.5 #> 49 Thi Bw 4 7.8 31.9 0.31 0.3 #> 50 Thi Ck1 5 7.8 32.9 0.18 0.3 #> 51 Thi Ck1 6 7.8 32.9 0.18 0.0 #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_Step_12_scenarios.html","id":null,"dir":"Reference","previous_headings":"","what":"Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios","title":"Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios","text":"data extracted scenario.txt file using R code shown . text file included package licence clear.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_Step_12_scenarios.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios","text":"list containing scenario names character vector called 'names', drift percentiles matrix called 'drift', interception percentages matrix called 'interception' runoff/drainage percentages Step 2 calculations matrix called 'rd'.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOCUS_Step_12_scenarios.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator — FOCUS_Step_12_scenarios","text":"","code":"# \\dontrun{ # 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] #> Warning: cannot open file 'inst/extdata/FOCUS_Step_12_scenarios.txt': No such file or directory #> Error in file(con, \"r\"): cannot open the connection FOCUS_Step_12_scenarios <- list() sce <- read.table(text = scenarios, sep = \"\\t\", header = TRUE, check.names = FALSE, stringsAsFactors = FALSE) #> Error in eval(expr, envir, enclos): object 'scenarios' not found FOCUS_Step_12_scenarios$names = sce$Crop #> Error in eval(expr, envir, enclos): object 'sce' not found rownames(sce) <- sce$Crop #> Error in eval(expr, envir, enclos): object 'sce' not found FOCUS_Step_12_scenarios$drift = sce[, 3:11] #> Error in eval(expr, envir, enclos): object 'sce' not found FOCUS_Step_12_scenarios$interception = sce[, 12:15] #> Error in eval(expr, envir, enclos): object 'sce' not found sce_2 <- readLines(scenario_path)[41:46] #> Warning: cannot open file 'inst/extdata/FOCUS_Step_12_scenarios.txt': No such file or directory #> Error in file(con, \"r\"): cannot open the connection rd <- read.table(text = sce_2, sep = \"\\t\")[1:2] #> Error in eval(expr, envir, enclos): object 'sce_2' not found rd_mat <- matrix(rd$V2, nrow = 3, byrow = FALSE) #> Error in eval(expr, envir, enclos): object 'rd' not found dimnames(rd_mat) = list(Time = c(\"Oct-Feb\", \"Mar-May\", \"Jun-Sep\"), Region = c(\"North\", \"South\")) #> Error: object 'rd_mat' not found FOCUS_Step_12_scenarios$rd = rd_mat #> Error in eval(expr, envir, enclos): object 'rd_mat' not found save(FOCUS_Step_12_scenarios, file = \"data/FOCUS_Step_12_scenarios.RData\") #> Warning: cannot open compressed file 'data/FOCUS_Step_12_scenarios.RData', probable reason 'No such file or directory' #> Error in gzfile(file, \"wb\"): cannot open the connection # } # And this is the resulting data FOCUS_Step_12_scenarios #> list()"},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.html","id":null,"dir":"Reference","previous_headings":"","what":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","title":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","text":"Actual maximum moving window time average concentrations FOMC kinetics","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","text":"","code":"FOMC_actual_twa( alpha = 1.0001, beta = 10, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100) )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","text":"FOCUS (2014) Generic Guidance Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration, Version 1.1, 18 December 2014, p. 251","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","text":"alpha Parameter FOMC model beta Parameter FOMC model times output times, window sizes time weighted average concentrations","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/FOMC_actual_twa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Actual and maximum moving window time average concentrations for FOMC kinetics — FOMC_actual_twa","text":"","code":"FOMC_actual_twa(alpha = 1.0001, beta = 10) #> actual twa #> 0 1.00000000 NaN #> 1 0.90908224 0.9530973 #> 2 0.83331814 0.9115995 #> 4 0.71426168 0.8411664 #> 7 0.58820408 0.7580202 #> 14 0.41663019 0.6253074 #> 21 0.32254415 0.5387324 #> 28 0.26312277 0.4767543 #> 42 0.19227599 0.3925054 #> 50 0.16663681 0.3583198 #> 100 0.09088729 0.2397608"},{"path":"https://pkgdown.jrwb.de/pfm/reference/GUS.html","id":null,"dir":"Reference","previous_headings":"","what":"Groundwater ubiquity score based on Gustafson (1989) — GUS","title":"Groundwater ubiquity score based on Gustafson (1989) — GUS","text":"groundwater ubiquity score GUS calculated according following equation $$GUS = \\log_{10} DT50_{soil} (4 - \\log_{10} K_{oc})$$","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/GUS.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Groundwater ubiquity score based on Gustafson (1989) — GUS","text":"","code":"GUS(...) # S3 method for class 'numeric' GUS(DT50, Koc, ...) # S3 method for class 'chent' GUS( chent, degradation_value = \"DT50ref\", lab_field = \"laboratory\", redox = \"aerobic\", sorption_value = \"Kfoc\", degradation_aggregator = geomean, sorption_aggregator = geomean, ... ) # S3 method for class 'GUS_result' print(x, ..., digits = 1)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/GUS.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Groundwater ubiquity score based on Gustafson (1989) — GUS","text":"... Included generic allow arguments later. Therefore also added specific methods. DT50 Half-life chemical soil. field half-life according Gustafson (1989). However, leaching sub-soil can completely excluded field dissipation experiments Gustafson refer normalisation procedure, says field study conducted use conditions. Koc sorption constant normalised organic carbon. Gustafson mention nonlinearity sorption constant commonly found usually described Freundlich sorption, therefore unclear reference concentration Koc observed (reference concentration soil porewater). chent chent given appropriate information present chyaml field, information used, defaults specified . degradation_value available degradation values used? lab_field laboratory field half-lives used? defaults lab implementation, order avoid double-accounting mobility. comparability original GUS values given Gustafson (1989) desired, non-normalised first-order field half-lives obtained actual use conditions used. redox Aerobic anaerobic degradation data sorption_value available sorption values used? Defaults Kfoc generally available European pesticide peer review process. values generally use reference concentration 1 mg/L porewater, means expected Koc values concentration 1 mg/L water phase. degradation_aggregator Function aggregating half-lives sorption_aggregator Function aggregation Koc values x object class GUS_result printed digits number digits used print method","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/GUS.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Groundwater ubiquity score based on Gustafson (1989) — GUS","text":"list DT50 Koc used well resulting score class GUS_result","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/GUS.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Groundwater ubiquity score based on Gustafson (1989) — GUS","text":"Gustafson, David . (1989) Groundwater ubiquity score: simple method assessing pesticide leachability. Environmental toxicology chemistry 8(4) 339–57.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/GUS.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Groundwater ubiquity score based on Gustafson (1989) — GUS","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_FOMC_accu_rel.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel","title":"Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel","text":"Get relative accumulation FOMC model multiples interval","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_FOMC_accu_rel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel","text":"","code":"PEC_FOMC_accu_rel(n, interval, FOMC)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_FOMC_accu_rel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel","text":"n number applications interval Time applications FOMC Named numeric vector containing FOMC parameters alpha beta","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_FOMC_accu_rel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the relative accumulation of an FOMC model over multiples of an interval — PEC_FOMC_accu_rel","text":"numeric vector containing n accumulation factors n applications","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate predicted environmental concentrations in soil — PEC_soil","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"basic calculation contaminant concentration bulk soil based complete, instantaneous mixing. interval given, attempt made calculating long term maximum concentration using concepts layed PPR panel opinion (EFSA PPR panel 2012 EFSA guidance PEC soil calculations (EFSA, 2015, 2017).","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"","code":"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, leaching_depth = tillage_depth, crop = \"annual\", cultivation = FALSE, chent = NA, DT50 = NA, FOMC = NA, Koc = NA, Kom = Koc/1.724, t_avg = 0, t_act = NULL, scenarios = c(\"default\", \"EFSA_2017\", \"EFSA_2015\"), leaching = scenarios == \"EFSA_2017\", porewater = FALSE )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"rate Application rate units specified rate_units Defaults g/ha interception fraction application rate reach soil mixing_depth Mixing depth cm PEC_units Requested units calculated PEC. mg/kg currently supported PEC_pw_units mg/L currently supported interval Period deeper mixing. default NA, .e. deeper mixing. annual deeper mixing, set 365 degradation units days n_periods Number periods considered long term PEC calculations tillage_depth Periodic (see interval) deeper mixing cm leaching_depth EFSA (2017) uses mixing depth (ecotoxicological evaluation depth) calculate leaching annual crops tillage takes place. default, losses layer tillage depth taken account implementation. crop Ignored scenarios EFSA_2017. annual crops supported scenarios used. crops single cropping cycle per year currently supported. cultivation mechanical cultivation sense EFSA (2017) take place, .e. twice year depth 5 cm? Ignored scenarios EFSA_2017 chent optional chent object holding substance specific information. Can also name substance character string DT50 specified, overrides soil DT50 endpoints chent object DT50 specified available chent object, zero degradation assumed FOMC specified, named numeric vector containing FOMC parameters alpha beta. overrides degradation endpoints, degradation interval maximum PEC calculated using parameters without temperature correction Koc specified, overrides Koc endpoints chent object Kom Calculated Koc default, can explicitly specified Kom t_avg Averaging times time weighted average concentrations t_act Time series actual concentrations scenarios 'default', DT50 used without correction soil properties specified REACH guidance (R.16, Table R.16-9) used porewater PEC calculations. \"EFSA_2015\", DT50 taken modelling half-life 20°C pF2 ('chent' specified, DegT50 destination 'PECgw' used), corrected using Arrhenius activation energy 65.4 kJ/mol. Also model scenario adjustment factors EFSA guidance used. leaching leaching taken account? default FALSE, except EFSA_2017 scenarios used. porewater equilibrium porewater concentrations estimated based Kom organic carbon fraction soil instead total soil concentrations? Based equation (7) given PPR panel opinion (EFSA 2012, p. 24) scenarios specified EFSA guidance (2015, p. 13).","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"predicted concentration soil","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"assumes complete load soil time specified 'interval' (typically 365 days) dosed . PPR panel opinion cited (EFSA PPR panel 2012), temperature correction using Arrhenius equation performed. Total soil porewater PEC values scenarios defined EFSA guidance (2017, p. 14/15) can easily calculated.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"time weighted average (TWA) concentrations given examples EFSA guidance 2015 (p. 80) reproduced, true TWA concentrations given example EFSA guidance 2017 (p. 92). According EFSA guidance (EFSA, 2017, p. 43), leaching taken account EFSA 2017 scenarios, using evaluation depth (mixing depth) depth layer leaching takes place. However, amount leaching evaluation depth (often 5 cm) partly mixed back tillage, default function use tillage depth calculation leaching rate. temperature information available selected scenarios, e.g. EFSA scenarios, DT50 groundwater modelling (destination 'PECgw') taken chent object, otherwise DT50 destination 'PECsoil'.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"EFSA Panel Plant Protection Products Residues (2012) Scientific Opinion science behind guidance scenario selection scenario parameterisation predicting environmental concentrations plant protection products soil. EFSA Journal 10(2) 2562, doi:10.2903/j.efsa.2012.2562 EFSA (European Food Safety Authority) 2017) EFSA guidance document predicting environmental concentrations active substances plant protection products transformation products active substances soil. EFSA Journal 15(10) 4982 doi:10.2903/j.efsa.2017.4982 EFSA (European Food Safety Authority) (2015) EFSA guidance document predicting environmental concentrations active substances plant protection products transformation products active substances soil. EFSA Journal 13(4) 4093 doi:10.2903/j.efsa.2015.4093","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate predicted environmental concentrations in soil — PEC_soil","text":"","code":"PEC_soil(100, interception = 0.25) #> scenario #> t_avg default #> 0 0.1 # This is example 1 starting at p. 92 of the EFSA guidance (2017) # Note that TWA concentrations differ from the ones given in the guidance # for an unknown reason (the values from EFSA (2015) can be reproduced). PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), Kom = 1000, scenarios = \"EFSA_2017\") #> scenario #> t_avg CTN CTC CTS #> 0 19.76834 13.8619 10.53795 #> 21 19.59345 13.7169 10.39882 PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), Kom = 1000, scenarios = \"EFSA_2017\", porewater = TRUE) #> scenario #> t_avg CLN CLC CLS #> 0 0.5541984 0.6779249 0.9816693 #> 21 0.5484576 0.6693125 0.9609119 # This is example 1 starting at p. 79 of the EFSA guidance (2015) PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), scenarios = \"EFSA_2015\") #> scenario #> t_avg CTN CTC CTS #> 0 21.96827 11.53750 9.145259 #> 21 21.78517 11.40701 9.017370 PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), Kom = 1000, scenarios = \"EFSA_2015\", porewater = TRUE) #> scenario #> t_avg CLN CLC CLS #> 0 0.7589401 0.6674322 0.9147861 #> 21 0.7506036 0.6590345 0.8987279 # The following is from example 4 starting at p. 85 of the EFSA guidance (2015) # Metabolite M2 # Calculate total and porewater soil concentrations for tier 1 scenarios # Relative molar mass is 100/300, formation fraction is 0.7 * 1 results_pfm <- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_avg = c(0, 21), scenarios = \"EFSA_2015\") results_pfm_pw <- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_av = c(0, 21), Kom = 100, scenarios = \"EFSA_2015\", porewater = TRUE)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil_mets.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets","title":"Calculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets","text":"Calculate initial accumulation PEC soil set metabolites","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil_mets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets","text":"","code":"PEC_soil_mets(rate, mw_parent, mets, interval = 365, ...)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_soil_mets.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate initial and accumulation PEC soil for a set of metabolites — PEC_soil_mets","text":"rate Application rate units specified mw_parent molecular weight parent compound mets dataframe metabolite identifiers rownames columns \"mw\", \"occ\" \"DT50\" holding molecular weight, maximum occurrence soil soil DT50 interval interval accumulation calculations ... arguments passed PEC_soil","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"implements method specified UK data requirements handbook checked spreadsheet published CRC website","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"","code":"PEC_sw_drainage_UK( rate, interception = 0, Koc, latest_application = NULL, soil_DT50 = NULL, model = NULL, model_parms = NULL )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"rate Application rate g/ha interception fraction application rate reach soil Koc sorption coefficient normalised organic carbon L/kg latest_application Latest application date, formatted e.g. \"01 July\" soil_DT50 Soil degradation half-life, SFO kinetics used model soil degradation model used. Either one \"FOMC\", \"DFOP\", \"HS\", \"IORE\", mkinmod object model_parms named numeric vector containing model parameters","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"predicted concentration surface water µg/L","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"HSE's Chemicals Regulation Division (CRD) Active substance PECsw calculations (UK specific authorisation requests) https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm accessed 2019-09-27 Drainage PECs Version 1.0 (2015) Spreadsheet published https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx accessed 2019-09-27","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drainage_UK.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method — PEC_sw_drainage_UK","text":"","code":"PEC_sw_drainage_UK(150, Koc = 100) #> [1] 8.076923"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"basic, vectorised form simple calculation contaminant concentration surface water based complete, instantaneous mixing input via spray drift.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"","code":"PEC_sw_drift( rate, applications = 1, 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\", \"Weinbau spaet\", \"Hopfenbau\", \"Flaechenkulturen > 900 l/ha\", \"Gleisanlagen\"), crop_group_focus = c(\"arable\", \"hops\", \"vines, late\", \"vines, early\", \"fruit, late\", \"fruit, early\", \"aerial\"), distances = c(1, 5, 10, 20), formula = c(\"Rautmann\", \"FOCUS\"), water_width = as_units(\"100 cm\"), side_angle = 90, rate_units = \"g/ha\", PEC_units = \"µg/L\" )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"rate Application rate units specified , units defined via units package. applications Number applications selection drift percentile water_depth Depth water body cm drift_percentages Percentage drift values calculate PECsw. Overrides 'drift_data' 'distances' NULL. drift_data Source drift percentage data. 'JKI', drift_data_JKI included package used. 'RF', Rautmann drift data calculated either original form integrated width water body, depending 'formula' argument. crop_group_JKI using 'JKI' drift data, one German names used drift_parameters_focus. crop_group_focus One crop groups used drift_parameters_focus distances distances m get PEC values formula default, original Rautmann formula used. specify \"FOCUS\", mean drift input width water body calculated described Chapter 5.4.5 FOCUS surface water guidance water_width Width water body cm side_angle angle side water relative bottom assumed horizontal, degrees. SYNOPS model assumes 45 degrees . rate_units Defaults g/ha. backwards compatibility, used specified rate units::units]. PEC_units Requested units calculated PEC. µg/L currently supported","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"predicted concentration surface water","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"recommened specify arguments rate, water_depth water_width using units::units units package.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_drift.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift","text":"","code":"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 #> 0.01018774 # 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 #> 0.9417586 # 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 % #> 0.01000000 # 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 #> 0.60169999 0.18937304 0.10402698 0.05517095"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","title":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","text":"reimplementation calculation described Exposit 3.02 spreadsheet file, worksheet \"Konzept Drainage\". Although four groups compounds (\"Gefährdungsgruppen\"), one distinction made calculations, compounds low mobility (group 1) compounds modest high mobility (groups 2, 3 4). implementation, group derived Koc, given explicitly. details, see discussion function arguments .","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","text":"","code":"PEC_sw_exposit_drainage( rate, interception = 0, Koc = NA, mobility = c(NA, \"low\", \"high\"), DT50 = Inf, t_drainage = 3, V_ditch = 30, V_drainage = c(spring = 10, autumn = 100), dilution = 2 )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","text":"Excel 3.02 spreadsheet available https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","text":"rate application rate g/ha interception fraction intercepted crop Koc sorption coefficient soil organic carbon used determine mobility. trigger value 550 L/kg used order decide Koc >> 500. mobility Overrides determined Koc. DT50 soil half-life days t_drainage time application drainage event, degradation occurs, days V_ditch volume ditch assumed 1 m * 100 m * 30 cm = 30 m3 V_drainage drainage volume, equivalent 1 mm precipitation 1 ha spring/summer 10 mm autumn/winter/early spring. dilution dilution factor","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","text":"list containing following components perc_runoff runoff percentages dissolved bound substance runoff matrix containing dissolved bound input different distances PEC_sw_runoff matrix containing PEC values dissolved bound substance different distances. rate given g/ha, PECsw microg/L.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_drainage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate PEC surface water due to drainage as in Exposit 3 — PEC_sw_exposit_drainage","text":"","code":"PEC_sw_exposit_drainage(500, Koc = 150) #> $perc_drainage_total #> spring autumn #> 0.2 1.0 #> #> $perc_peak #> spring autumn #> 12.5 25.0 #> #> $PEC_sw_drainage #> spring autumn #> 1.562500 4.807692 #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"reimplementation calculation described Exposit 3.02 spreadsheet file, worksheet \"Konzept Runoff\".","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"","code":"PEC_sw_exposit_runoff( rate, interception = 0, Koc, 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 = set_units(30, \"m3\"), V_event = set_units(100, \"m3\"), dilution = 2 )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"Excel 3.02 spreadsheet available https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"rate application rate g/ha interception fraction intercepted crop Koc sorption coefficient soil organic carbon DT50 soil half-life days t_runoff time application runoff event, degradation occurs, days exposit_reduction_version version reduction factors used. \"3.02\" current version used Germany, \"3.01a\" version additional percentages 3 m 6 m buffer zones used Switzerland. \"3.01a2\" version introduced consistency previous calculations performed 3 m buffer zone Switzerland, reduction applied dissolved bound fraction. V_ditch volume ditch assumed 1 m * 100 m * 30 cm = 30 m3 V_event unreduced runoff volume, equivalent 10 mm precipitation 1 ha dilution dilution factor","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"list containing following components perc_runoff runoff percentages dissolved bound substance runoff matrix containing dissolved bound input different distances PEC_sw_runoff matrix containing PEC values dissolved bound substance different distances. rate given g/ha, PECsw microg/L.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"recommened specify arguments rate, Koc, DT50, t_runoff, V_ditch V_event using units::units units package.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_exposit_runoff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate PEC surface water due to runoff and erosion as in Exposit 3 — PEC_sw_exposit_runoff","text":"","code":"PEC_sw_exposit_runoff(500, Koc = 150) #> $perc_runoff #> dissolved bound #> 0.248 0.001 #> #> $runoff #> 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 [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 #> dissolved bound #> 0.037 0.159 #> #> $runoff #> 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] #> #> $PEC_sw_runoff #> dissolved bound total #> No buffer 0.8447893 [µg/L] 3.6303107 [µg/L] 4.4751000 [µg/L] #> 3 m 0.7844472 [µg/L] 3.1462693 [µg/L] 3.9307165 [µg/L] #> 5 m 0.7321507 [µg/L] 3.1462693 [µg/L] 3.8784200 [µg/L] #> 6 m 0.7106169 [µg/L] 2.4985080 [µg/L] 3.2091248 [µg/L] #> 10 m 0.6275578 [µg/L] 1.0113008 [µg/L] 1.6388586 [µg/L] #> 20 m 0.4392904 [µg/L] 0.4719404 [µg/L] 0.9112308 [µg/L] #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","title":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","text":"reimplementation FOCUS Step 1 2 calculator version 3.2, authored Michael Klein, R. Note results multiple applications compared corresponding results single application. current, done automatically implementation. Step 1 PECs calculated. However, input files can generated suitable input FOCUS calculator.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","text":"","code":"PEC_sw_focus( parent, rate, n = 1, i = NA, comment = \"\", met = NULL, f_drift = NA, f_rd = 0.1, scenario = FOCUS_Step_12_scenarios$names, region = c(\"n\", \"s\"), season = c(NA, \"of\", \"mm\", \"js\"), interception = c(\"no interception\", \"minimal crop cover\", \"average crop cover\", \"full canopy\"), met_form_water = TRUE, txt_file = \"pesticide.txt\", overwrite = FALSE, append = FALSE )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","text":"parent list containing substance specific parameters, e.g. conveniently generated chent_focus_sw. rate application rate g/ha. Overriden applications given explicitly n number applications application interval comment comment input file met list containing metabolite specific parameters. e.g. conveniently generated chent_focus_sw. NULL, PEC calculated compound, parent. f_drift fraction application rate reaching waterbody via drift. NA, derived scenario name number applications via drift data defined FOCUS_Step_12_scenarios f_rd fraction amount applied reaching waterbody via runoff/drainage. Step 1, assumed 10%, parent metabolite scenario name scenario. Must one scenario names given FOCUS_Step_12_scenarios region 'n' Northern Europe 's' Southern Europe. NA, Step 1 PECsw calculated season '' October February, 'mm' March May, 'js' June September. NA, step 1 PECsw calculated interception One 'interception' (default), 'minimal crop cover', 'average crop cover' 'full canopy' met_form_water metabolite formation water taken account? can switched check influence compare previous versions Steps 12 calculator txt_file name, potentially full path Steps.12 input text file specification run(s) written overwrite existing file location specified txt_file overwritten? takes effect append FALSE. append input text file appended, exists?","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","text":"formulas input waterbody via runoff/drainage parent subsequent formation metabolite water documented model description coming calculator. one expect, appears (get results) calculated multiplying application rate molar weight correction formation fraction water/sediment systems. Step 2 implemented.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","text":"FOCUS (2014) Generic guidance Surface Water Scenarios (version 1.4). FOrum Co-ordination pesticde fate models USe. http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic%20FOCUS_SWS_vc1.4.pdf Website Steps 1 2 calculator Joint Research Center European Union: http://esdac.jrc.ec.europa.eu/projects/stepsonetwo","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_focus.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus","text":"","code":"# Parent only dummy_1 <- chent_focus_sw(\"Dummy 1\", cwsat = 6000, DT50_ws = 6, Koc = 344.8) PEC_sw_focus(dummy_1, 3000, f_drift = 0) #> $f_drift #> [1] 0 #> #> $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+02 647.68635 2.104370e+03 2233.2225 #> 2 5.437298e+02 612.03420 1.874780e+03 2110.2939 #> 4 4.315586e+02 548.76030 1.488014e+03 1892.1255 #> 7 3.051580e+02 469.88375 1.052185e+03 1620.1592 #> 14 1.359325e+02 339.57370 4.686951e+02 1170.8501 #> 21 6.055102e+01 257.45458 2.087799e+02 887.7034 #> 28 2.697241e+01 203.47173 9.300089e+01 701.5705 #> 42 5.352005e+00 140.10377 1.845371e+01 483.0778 #> 50 2.123945e+00 118.24602 7.323361e+00 407.7123 #> 100 6.585062e-03 59.30629 2.270529e-02 204.4881 #> #> $PEC_sw_max #> [1] 685.0566 #> #> $PEC_sed_max #> [1] 2362.075 #> # Metabolite new_dummy <- chent_focus_sw(\"New Dummy\", mw = 250, Koc = 100) M1 <- chent_focus_sw(\"M1\", mw = 100, cwsat = 100, DT50_ws = 100, Koc = 50, max_ws = 0, max_soil = 0.5) PEC_sw_focus(new_dummy, 1000, scenario = \"cereals, winter\", met = M1) #> $f_drift #> [1] 0.02759 #> #> $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 62.06890 30.81977 31.03445 #> 4 60.79093 61.64158 30.39547 30.82079 #> 7 59.53987 61.00800 29.76994 30.50400 #> 14 56.71995 59.56326 28.35997 29.78163 #> 21 54.03358 58.16414 27.01679 29.08207 #> 28 51.47444 56.80902 25.73722 28.40451 #> 42 46.71404 54.22460 23.35702 27.11230 #> 50 44.19417 52.81945 22.09709 26.40973 #> 100 31.25000 45.08422 15.62500 22.54211 #> #> $PEC_sw_max #> [1] 62.5 #> #> $PEC_sed_max #> [1] 31.25 #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed","title":"Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed","text":"method 'percentage' equivalent used CRD spreadsheet PEC calculator","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed","text":"","code":"PEC_sw_sed( PEC_sw, percentage = 100, method = \"percentage\", 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\") )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed","text":"PEC_sw Numeric vector matrix surface water concentrations µg/L corresponding sediment concentration estimated percentage percentage sediment, used percentage method method method used calculation sediment_depth Depth sediment layer water_depth Depth water body cm sediment_density density sediment kg/L (equivalent g/cm3) PEC_sed_units units estimated sediment PEC value","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed","text":"predicted concentration sediment","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/PEC_sw_sed.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate predicted environmental concentrations in sediment from surface water concentrations — PEC_sw_sed","text":"","code":"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]"},{"path":"https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.html","id":null,"dir":"Reference","previous_headings":"","what":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","title":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","text":"Actual maximum moving window time average concentrations SFO kinetics","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","text":"","code":"SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100))"},{"path":"https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","text":"FOCUS (2014) Generic Guidance Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration, Version 1.1, 18 December 2014, p. 251","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","text":"DT50 half-life. times output times, window sizes time weighted average concentrations","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SFO_actual_twa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa","text":"","code":"SFO_actual_twa(10) #> actual twa #> 0 1.0000000000 NaN #> 1 0.9330329915 0.9661297 #> 2 0.8705505633 0.9337803 #> 4 0.7578582833 0.8733416 #> 7 0.6155722067 0.7923030 #> 14 0.3789291416 0.6400113 #> 21 0.2332582479 0.5267498 #> 28 0.1435872944 0.4412651 #> 42 0.0544094102 0.3248093 #> 50 0.0312500000 0.2795222 #> 100 0.0009765625 0.1441286"},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"implements method specified UK data requirements handbook checked spreadsheet published CRD website","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"","code":"SSLRC_mobility_classification(Koc)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"Koc sorption coefficient normalised organic carbon L/kg","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"list containing classification percentage compound transported per 10 mm drain water","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"HSE's Chemicals Regulation Division (CRD) Active substance PECsw calculations (UK specific authorisation requests) https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/active-substance-uk.htm accessed 2019-09-27 Drainage PECs Version 1.0 (2015) Spreadsheet published https://www.hse.gov.uk/pesticides/topics/pesticide-approvals/pesticides-registration/data-requirements-handbook/fate/pec-tools-2015/PEC%20sw-sed%20(drainage).xlsx accessed 2019-09-27","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/SSLRC_mobility_classification.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification","text":"","code":"SSLRC_mobility_classification(100) #> $`Mobility classification` #> [1] \"Moderately mobile\" #> #> $`Percentage drained per mm of drain water` #> [1] 0.7 #> SSLRC_mobility_classification(10000) #> $`Mobility classification` #> [1] \"Non mobile\" #> #> $`Percentage drained per mm of drain water` #> [1] 0.008 #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":null,"dir":"Reference","previous_headings":"","what":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"R6 class holding TOXSWA water concentration (cwa) data associated statistics. like maximum moving window average concentrations, dataframes holding events exceeding specified thresholds. Usually, instance class generated read.TOXSWA_cwa.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"R6Class generator object.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"filename Length one character vector holding filename. basedir Length one character vector holding directory file came . zipfile null, giving path zip file file read. segment Length one integer, specifying segment cwa data read. substance TOXSWA name substance. cwas Dataframe holding concentrations. events List dataframes holding event statistics threshold. windows Matrix maximum time weighted average concentrations (TWAC_max) areas curve µg/day * h (AUC_max_h) µg/day * d (AUC_max_d) requested moving window sizes days.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"TOXSWA_cwa$new() TOXSWA_cwa$moving_windows() TOXSWA_cwa$get_events() TOXSWA_cwa$print() TOXSWA_cwa$clone()","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"Create TOXSWA_cwa object file","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"TOXSWA_cwa$new( filename, basedir, zipfile = NULL, segment = \"last\", substance = \"parent\", total = FALSE )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"filename filename basedir directory look zipfile Optional path zipfile holding file segment Either \"last\" number segment read data substance TOXSWA substance name (TOXSWA 4 higher) total total concentrations read ? FALSE, free concentrations read","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"method-moving-windows-","dir":"Reference","previous_headings":"","what":"Method moving_windows()","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"Add windows field described .","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"TOXSWA_cwa$moving_windows(windows, total = FALSE)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"windows Window sizes days total TRUE, total concentration including amount adsorbed suspended matter used.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"method-get-events-","dir":"Reference","previous_headings":"","what":"Method get_events()","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"Populate datataframe event information specified threshold value. resulting dataframe stored events field object.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"usage-2","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"TOXSWA_cwa$get_events(thresholds, total = FALSE)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"thresholds Threshold values µg/L. total TRUE, total concentration including amount adsorbed suspended matter used.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"method-print-","dir":"Reference","previous_headings":"","what":"Method print()","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"Print TOXSWA_cwa object","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"usage-3","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"TOXSWA_cwa$print()"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"usage-4","dir":"Reference","previous_headings":"","what":"Usage","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"TOXSWA_cwa$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"arguments-3","dir":"Reference","previous_headings":"","what":"Arguments","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TOXSWA_cwa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa","text":"","code":"H_sw_R1_stream <- read.TOXSWA_cwa(\"00003s_pa.cwa\", basedir = \"SwashProjects/project_H_sw/TOXSWA\", zipfile = system.file(\"testdata/SwashProjects.zip\", package = \"pfm\")) H_sw_R1_stream$get_events(c(2, 10)) H_sw_R1_stream$moving_windows(c(7, 21)) print(H_sw_R1_stream) #> data from file 00003s_pa.cwa segment 20 #> datetime t t_firstjan t_rel_to_max cwa_mug_per_L #> 20 1978-10-01 00:00:00 0.000 273.0000 -55.333 0 #> 40 1978-10-01 01:00:00 0.042 273.0417 -55.291 0 #> 60 1978-10-01 02:00:00 0.083 273.0833 -55.250 0 #> 80 1978-10-01 03:00:00 0.125 273.1250 -55.208 0 #> 100 1978-10-01 04:00:00 0.167 273.1667 -55.166 0 #> 120 1978-10-01 05:00:00 0.208 273.2083 -55.125 0 #> cwa_tot_mug_per_L #> 20 0 #> 40 0 #> 60 0 #> 80 0 #> 100 0 #> 120 0 #> Moving window analysis #> window max_TWAC max_AUC_h max_AUC_d #> 1 7 days 2.3926551 401.9660 16.74859 #> 2 21 days 0.8369248 421.8101 17.57542 #> Event statistics for threshold 2 #> t_start cwa_max duration pre_interval AUC_h AUC_d #> 1 44.375 4.167238 0.208 44.375 17.77202 0.740501 #> 2 55.042 40.584010 0.583 10.459 398.21189 16.592162 #> Event statistics for threshold 10 #> t_start cwa_max duration pre_interval AUC_h AUC_d #> 1 55.083 40.58401 0.459 55.083 379.433 15.80971"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TSCF.html","id":null,"dir":"Reference","previous_headings":"","what":"Estimation of the transpiration stream concentration factor — TSCF","title":"Estimation of the transpiration stream concentration factor — TSCF","text":"FOCUS groundwater guidance (FOCUS 2014, p. 41) states reliable measured log Kow neutral pH must available order apply Briggs equation. clarified can regarded reliable, equation stated produced non-ionic compounds, suggesting compound ionogenic (weak acid/base) ionic.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TSCF.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Estimation of the transpiration stream concentration factor — TSCF","text":"","code":"TSCF(log_Kow, method = c(\"briggs82\", \"dettenmaier09\"))"},{"path":"https://pkgdown.jrwb.de/pfm/reference/TSCF.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Estimation of the transpiration stream concentration factor — TSCF","text":"log_Kow decadic logarithm octanol-water partition constant method Short name estimation method.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TSCF.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Estimation of the transpiration stream concentration factor — TSCF","text":"Dettenmaier equation given show views subject exist.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TSCF.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Estimation of the transpiration stream concentration factor — TSCF","text":"FOCUS (2014) Generic Guidance Tier 1 FOCUS Ground Water Assessments. Version 2.2, May 2014 Dettenmaier EM, Doucette WJ Bugbee B (2009) Chemical hydrophobicity uptake plant roots. Environ. Sci. Technol 43, 324 - 329","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/TSCF.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Estimation of the transpiration stream concentration factor — TSCF","text":"","code":"plot(TSCF, -1, 5, xlab = \"log Kow\", ylab = \"TSCF\", ylim = c(0, 1.1)) TSCF_2 <- function(x) TSCF(x, method = \"dettenmaier09\") curve(TSCF_2, -1, 5, add = TRUE, lty = 2) legend(\"topright\", lty = 1:2, bty = \"n\", legend = c(\"Briggs et al. (1982)\", \"Dettenmaier et al. (2009)\"))"},{"path":"https://pkgdown.jrwb.de/pfm/reference/chent_focus_sw.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw","title":"Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw","text":"Create chemical compound object FOCUS Step 1 calculations","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/chent_focus_sw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw","text":"","code":"chent_focus_sw( name, Koc, DT50_ws = NA, DT50_soil = NA, DT50_water = NA, DT50_sediment = NA, cwsat = 1000, mw = NA, max_soil = 1, max_ws = 1 )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/chent_focus_sw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw","text":"name Length one character vector containing name Koc Partition coefficient organic carbon water L/kg. DT50_ws Half-life water/sediment systems days DT50_soil Half-life soil days DT50_water Half-life water days (Step 2) DT50_sediment Half-life sediment days (Step 2) cwsat Water solubility mg/L mw Molar weight g/mol. max_soil Maximum observed fraction (dimensionless) soil max_ws Maximum observed fraction (dimensionless) water/sediment systems","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/chent_focus_sw.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a chemical compound object for FOCUS Step 1 calculations — chent_focus_sw","text":"list substance specific properties","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.html","id":null,"dir":"Reference","previous_headings":"","what":"Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI","title":"Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI","text":"Deposition spray drift expressed percent applied dose published German Julius-Kühn Institute (JKI).","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI","text":"","code":"drift_data_JKI"},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI","text":"list currently containing matrices spray drift percentage data field crops (Ackerbau), Pome/stone fruit, early late (Obstbau frueh, spaet).","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI","text":"JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html 2015-06-11, present 2024-01-31 Rautmann, D., Streloke, M Winkler, R (2001) New basic drift values authorization procedure plant protection products Mitt. Biol. Bundesanst. Land- Forstwirtsch. 383, 133-141","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI","text":"data extracted spreadsheet cited using R code given file data_generation/drift_data_JKI.R installed package. file included package, licence clear. Additional spray drift values taken publication Rautmann et al. (2001). Specifically, values early vines, values 3 m buffer incomplete spreadsheet. Note vegetables, ornamentals small fruit, values field crops used crops < 50 cm, vales late vines used crops > 50 cm. JKI spreadsheet, indicated values used spray applications handheld/knapsack equipment (tragbare Spritz- und Sprühgerate). Values non-professional use listed JKI spreadsheet included.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_data_JKI.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Deposition from spray drift expressed as percent of the applied dose as published by the JKI — drift_data_JKI","text":"","code":"drift_data_JKI #> [[1]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 2.77 NA NA NA NA #> 3 0.95 29.20 15.73 2.70 8.02 #> 5 0.57 19.89 8.41 1.18 3.62 #> 10 0.29 11.81 3.60 0.39 1.23 #> 15 0.20 5.55 1.81 0.20 0.65 #> 20 0.15 2.77 1.09 0.13 0.42 #> 30 0.10 1.04 0.54 0.07 0.22 #> 40 0.07 0.52 0.32 0.04 0.14 #> 50 0.06 0.30 0.22 0.03 0.10 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 4.440 NA #> 3 19.33 NA 0.018721696 #> 5 11.57 0.180 0.014363896 #> 10 5.77 0.050 0.010026007 #> 15 3.84 0.020 0.008124366 #> 20 1.79 0.012 0.006998158 #> 30 0.56 0.005 0.005670811 #> 40 0.25 0.003 NA #> 50 0.13 0.002 0.004350831 #> #> [[2]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 2.38 NA NA NA NA #> 3 0.79 25.53 12.13 2.53 7.23 #> 5 0.47 16.87 6.81 1.09 3.22 #> 10 0.24 9.61 3.11 0.35 1.07 #> 15 0.16 5.61 1.58 0.18 0.56 #> 20 0.12 2.59 0.90 0.11 0.36 #> 30 0.08 0.87 0.40 0.06 0.19 #> 40 0.06 0.40 0.23 0.03 0.12 #> 50 0.05 0.22 0.15 0.02 0.08 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 3.780 NA #> 3 17.73 NA NA #> 5 9.60 0.160 NA #> 10 4.18 0.040 NA #> 15 2.57 0.020 NA #> 20 1.21 0.011 NA #> 30 0.38 0.005 NA #> 40 0.17 0.003 NA #> 50 0.09 0.002 NA #> #> [[3]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 2.01 NA NA NA NA #> 3 0.68 23.96 11.01 2.49 6.90 #> 5 0.41 15.79 6.04 1.04 3.07 #> 10 0.20 8.96 2.67 0.32 1.02 #> 15 0.14 4.24 1.39 0.16 0.54 #> 20 0.10 2.01 0.80 0.10 0.34 #> 30 0.07 0.70 0.36 0.05 0.18 #> 40 0.05 0.33 0.21 0.03 0.11 #> 50 0.04 0.19 0.13 0.02 0.08 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 3.420 NA #> 3 15.93 NA NA #> 5 8.57 0.150 NA #> 10 3.70 0.040 NA #> 15 2.26 0.020 NA #> 20 1.05 0.010 NA #> 30 0.34 0.004 NA #> 40 0.15 0.003 NA #> 50 0.08 0.002 NA #> #> [[4]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 1.85 NA NA NA NA #> 3 0.62 23.61 10.12 2.44 6.71 #> 5 0.38 15.42 5.60 1.02 2.99 #> 10 0.19 8.66 2.50 0.31 0.99 #> 15 0.13 4.01 1.28 0.16 0.52 #> 20 0.10 1.89 0.75 0.10 0.33 #> 30 0.06 0.66 0.35 0.05 0.17 #> 40 0.05 0.31 0.20 0.03 0.11 #> 50 0.04 0.17 0.13 0.02 0.08 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 2.290 NA #> 3 15.38 NA NA #> 5 8.26 0.120 NA #> 10 3.55 0.030 NA #> 15 2.17 0.020 NA #> 20 0.93 0.009 NA #> 30 0.31 0.004 NA #> 40 0.14 0.002 NA #> 50 0.08 0.002 NA #> #> [[5]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 1.75 NA NA NA NA #> 3 0.59 23.12 9.74 2.37 6.59 #> 5 0.36 15.06 5.41 1.00 2.93 #> 10 0.18 8.42 2.43 0.31 0.98 #> 15 0.12 3.83 1.24 0.15 0.51 #> 20 0.09 1.81 0.72 0.09 0.33 #> 30 0.06 0.63 0.34 0.05 0.17 #> 40 0.05 0.30 0.20 0.03 0.11 #> 50 0.04 0.17 0.13 0.02 0.08 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 2.120 NA #> 3 15.12 NA NA #> 5 7.99 0.110 NA #> 10 3.36 0.030 NA #> 15 2.03 0.010 NA #> 20 0.88 0.008 NA #> 30 0.29 0.004 NA #> 40 0.14 0.002 NA #> 50 0.07 0.002 NA #> #> [[6]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 1.64 NA NA NA NA #> 3 0.56 22.76 9.21 2.29 6.41 #> 5 0.34 14.64 5.18 0.97 2.85 #> 10 0.17 8.04 2.38 0.30 0.95 #> 15 0.11 3.71 1.20 0.15 0.50 #> 20 0.09 1.75 0.68 0.09 0.32 #> 30 0.06 0.61 0.31 0.05 0.17 #> 40 0.04 0.29 0.17 0.03 0.11 #> 50 0.03 0.16 0.11 0.02 0.07 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 1.980 NA #> 3 14.90 NA NA #> 5 7.79 0.100 NA #> 10 3.23 0.030 NA #> 15 1.93 0.010 NA #> 20 0.83 0.008 NA #> 30 0.28 0.004 NA #> 40 0.13 0.002 NA #> 50 0.07 0.001 NA #> #> [[7]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 1.61 NA NA NA NA #> 3 0.55 22.69 9.10 2.24 6.33 #> 5 0.33 14.45 5.11 0.94 2.81 #> 10 0.17 7.83 2.33 0.29 0.94 #> 15 0.11 3.62 1.20 0.15 0.49 #> 20 0.08 1.71 0.67 0.09 0.31 #> 30 0.06 0.60 0.30 0.05 0.16 #> 40 0.04 0.28 0.17 0.03 0.10 #> 50 0.03 0.16 0.11 0.02 0.07 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 1.930 NA #> 3 14.63 NA NA #> 5 7.60 0.100 NA #> 10 3.13 0.030 NA #> 15 1.86 0.010 NA #> 20 0.81 0.008 NA #> 30 0.26 0.004 NA #> 40 0.12 0.002 NA #> 50 0.06 0.001 NA #> #> [[8]] #> crop #> distance Ackerbau Obstbau frueh Obstbau spaet Weinbau frueh Weinbau spaet #> 1 1.52 NA NA NA NA #> 3 0.52 22.24 8.66 2.16 6.26 #> 5 0.31 14.09 4.92 0.91 2.78 #> 10 0.16 7.58 2.29 0.28 0.93 #> 15 0.11 3.48 1.14 0.14 0.49 #> 20 0.08 1.65 0.65 0.09 0.31 #> 30 0.05 0.57 0.29 0.04 0.16 #> 40 0.04 0.27 0.16 0.03 0.10 #> 50 0.03 0.15 0.11 0.02 0.07 #> crop #> distance Hopfenbau Flaechenkulturen > 900 l/ha Gleisanlagen #> 1 NA 1.640 NA #> 3 13.53 NA NA #> 5 7.15 0.090 NA #> 10 3.01 0.020 NA #> 15 1.82 0.010 NA #> 20 0.78 0.007 NA #> 30 0.25 0.003 NA #> 40 0.12 0.002 NA #> 50 0.06 0.001 NA #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.html","id":null,"dir":"Reference","previous_headings":"","what":"Regression parameters for the Rautmann drift data — drift_parameters_focus","title":"Regression parameters for the Rautmann drift data — drift_parameters_focus","text":"parameters extracted Appendix B FOCUS surface water guidance using R code given file data_generation/drift_parameters_focus.R installed package. appendix included package, licence clear.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Regression parameters for the Rautmann drift data — drift_parameters_focus","text":"","code":"drift_parameters_focus"},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Regression parameters for the Rautmann drift data — drift_parameters_focus","text":"tibble::tibble.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Regression parameters for the Rautmann drift data — drift_parameters_focus","text":"hinge distance, Inf substituted cases hinge distance given data, way parameters C D never used distance B used case distance smaller hinge distance.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Regression parameters for the Rautmann drift data — drift_parameters_focus","text":"FOCUS (2014) Generic guidance Surface Water Scenarios (version 1.4). FOrum Co-ordination pesticde fate models USe. http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic%20FOCUS_SWS_vc1.4.pdf FOCUS (2001) FOCUS Surface Water Scenarios EU Evaluation Process 91/414/EEC. Report FOCUS Working Group Surface Water Scenarios, EC Document Reference SANCO/4802/2001-rev.2. 245, Appendix B. https://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/FOCUS_SWS_APPENDIX_B.doc Rautmann, D., Streloke, M Winkler, R (2001) New basic drift values authorization procedure plant protection products Mitt. Biol. Bundesanst. Land- Forstwirtsch. 383, 133-141","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_parameters_focus.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Regression parameters for the Rautmann drift data — drift_parameters_focus","text":"","code":"drift_parameters_focus #> # A tibble: 49 × 8 #> crop_group n_apps percentile A B C D hinge #> #> 1 arable 1 90 2.76 -0.978 NA NA Inf #> 2 arable 2 82 2.44 -1.01 NA NA Inf #> 3 arable 3 77 2.02 -0.996 NA NA Inf #> 4 arable 4 74 1.86 -0.986 NA NA Inf #> 5 arable 5 72 1.79 -0.994 NA NA Inf #> 6 arable 6 70 1.63 -0.986 NA NA Inf #> 7 arable 7 69 1.58 -0.981 NA NA Inf #> 8 arable 8 67 1.51 -0.983 NA NA Inf #> 9 hops 1 90 58.2 -1.00 8655. -2.84 15.3 #> 10 hops 2 82 66.2 -1.20 5555. -2.82 15.3 #> # ℹ 39 more rows unique(drift_parameters_focus$crop_group) #> [1] \"arable\" \"hops\" \"vines, late\" \"vines, early\" \"fruit, late\" #> [6] \"fruit, early\" \"aerial\""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_percentages_rautmann.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate drift percentages based on Rautmann data — drift_percentages_rautmann","title":"Calculate drift percentages based on Rautmann data — drift_percentages_rautmann","text":"Calculate drift percentages based Rautmann data","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_percentages_rautmann.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate drift percentages based on Rautmann data — drift_percentages_rautmann","text":"","code":"drift_percentages_rautmann( distances, applications = 1, crop_group_focus = c(\"arable\", \"hops\", \"vines, late\", \"vines, early\", \"fruit, late\", \"fruit, early\", \"aerial\"), formula = c(\"Rautmann\", \"FOCUS\"), widths = 1 )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_percentages_rautmann.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate drift percentages based on Rautmann data — drift_percentages_rautmann","text":"distances distances m get PEC values applications Number applications selection drift percentile crop_group_focus One crop groups used drift_parameters_focus formula default, original Rautmann formula used. specify \"FOCUS\", mean drift input width water body calculated described Chapter 5.4.5 FOCUS surface water guidance widths widths water bodies (used FOCUS formula)","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_percentages_rautmann.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate drift percentages based on Rautmann data — drift_percentages_rautmann","text":"FOCUS (2014) Generic guidance Surface Water Scenarios (version 1.4). FOrum Co-ordination pesticde fate models USe. http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic%20FOCUS_SWS_vc1.4.pdf","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/drift_percentages_rautmann.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate drift percentages based on Rautmann data — drift_percentages_rautmann","text":"","code":"# Compare JKI data with Rautmann formula # One application on field crops, for 1 m, 3 m and 5 m distance drift_data_JKI[[1]][as.character(c(1, 3, 5)), \"Ackerbau\"] #> 1 3 5 #> 2.77 0.95 0.57 drift_percentages_rautmann(c(1, 3, 5)) #> [1] 2.7593000 0.9424748 0.5719342 drift_percentages_rautmann(c(1, 3, 5), formula = \"FOCUS\") #> [1] 1.9273922 0.8160023 0.5224362 # One application to early or late fruit crops drift_data_JKI[[1]][as.character(c(3, 5, 20, 50)), \"Obstbau frueh\"] #> 3 5 20 50 #> 29.20 19.89 2.77 0.30 drift_percentages_rautmann(c(3, 5, 20, 50), crop_group = \"fruit, early\") #> [1] 29.1973659 19.8844422 2.7618138 0.3012008 drift_percentages_rautmann(c(3, 5, 20, 50), crop_group = \"fruit, early\", formula = \"FOCUS\") #> [1] 26.1193421 18.5428680 2.6038558 0.2940792 drift_data_JKI[[1]][as.character(c(3, 5, 20, 50)), \"Obstbau spaet\"] #> 3 5 20 50 #> 15.73 8.41 1.09 0.22 drift_percentages_rautmann(c(3, 5, 20, 50), crop_group = \"fruit, late\") #> [1] 15.7246994 8.4108487 1.0813887 0.2155992 drift_percentages_rautmann(c(3, 5, 20, 50), crop_group = \"fruit, late\", formula = \"FOCUS\") #> [1] 13.1414350 7.5123244 1.0359007 0.2118734 # We get a continuum if the waterbody covers the hinge distance # (11.4 m for 1 early app to fruit) x <- seq(3, 30, by = 0.1) d <- drift_percentages_rautmann(x, crop_group = \"fruit, early\", formula = \"FOCUS\") plot(x, d, type = \"l\", xlab = \"Distance of near edge [m]\", ylab = \"Mean drift percentage over waterbody width\", main = \"One application to fruit, early\") abline(v = 11.4, lty = 2)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/endpoint.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve endpoint information from the chyaml field of a chent object — endpoint","title":"Retrieve endpoint information from the chyaml field of a chent object — endpoint","text":"R6 class objects class chent represent chemical entities can hold list information loaded chemical yaml file chyaml field. information extracted optionally aggregated function.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/endpoint.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve endpoint information from the chyaml field of a chent object — endpoint","text":"","code":"endpoint( chent, medium = \"soil\", type = c(\"degradation\", \"sorption\"), lab_field = c(NA, \"laboratory\", \"field\"), redox = c(NA, \"aerobic\", \"anaerobic\"), value = c(\"DT50ref\", \"Kfoc\", \"N\"), aggregator = geomean, raw = FALSE, signif = 3 ) soil_DT50( chent, aggregator = geomean, signif = 3, lab_field = \"laboratory\", value = \"DT50ref\", redox = \"aerobic\", raw = FALSE ) soil_Kfoc(chent, aggregator = geomean, signif = 3, value = \"Kfoc\", raw = FALSE) soil_N(chent, aggregator = mean, signif = 3, raw = FALSE) soil_sorption( chent, values = c(\"Kfoc\", \"N\"), aggregators = c(Kfoc = geomean, Koc = geomean, N = mean), signif = c(Kfoc = 3, N = 3), raw = FALSE )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/endpoint.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve endpoint information from the chyaml field of a chent object — endpoint","text":"chent chent object get information medium medium information sought type information type lab_field NA, want laboratory field endpoints redox NA, looking aerobic anaerobic data value name value want. list given usage section exclusive aggregator aggregator function. Can mean, geomean, identity, example. raw number(s) returned stored chent object (character value) retain original information precision? signif many significant digits want values values returned aggregators named vector aggregator functions used","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/endpoint.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve endpoint information from the chyaml field of a chent object — endpoint","text":"result applying aggregator function values converted numeric vector, rounded given number significant digits, , raw = TRUE, values character value, retaining implicit information precision may present.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/endpoint.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Retrieve endpoint information from the chyaml field of a chent object — endpoint","text":"functions soil_* functions extract soil specific endpoints. Freundlich exponent, capital letter N used order facilitate dealing data R. pesticide fate modelling, exponent often called 1/n.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/geomean.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate the geometric mean — geomean","title":"Calculate the geometric mean — geomean","text":"Based posts thread Stackoverflow http://stackoverflow.com/questions/2602583/geometric-mean----built-function returns NA NA values present na.rm = FALSE (default). negative values present, gives error message. least one element vector 0, returns 0.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/geomean.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate the geometric mean — geomean","text":"","code":"geomean(x, na.rm = FALSE)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/geomean.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate the geometric mean — geomean","text":"x Vector numbers na.rm NA values omitted?","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/geomean.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate the geometric mean — geomean","text":"geometric mean","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/geomean.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate the geometric mean — geomean","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/geomean.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate the geometric mean — geomean","text":"","code":"geomean(c(1, 3, 9)) #> [1] 3 geomean(c(1, 3, NA, 9)) #> [1] NA geomean(c(1, -3, 9)) # returns an error #> Error in geomean(c(1, -3, 9)): Only defined for positive numbers"},{"path":"https://pkgdown.jrwb.de/pfm/reference/get_vertex.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit a parabola through three points — get_vertex","title":"Fit a parabola through three points — get_vertex","text":"inspired answer stackoverflow https://stackoverflow.com//717791","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/get_vertex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit a parabola through three points — get_vertex","text":"","code":"get_vertex(x, y)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/get_vertex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit a parabola through three points — get_vertex","text":"x Three x coordinates y Three y coordinates","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/max_twa.html","id":null,"dir":"Reference","previous_headings":"","what":"The maximum time weighted average concentration for a moving window — max_twa","title":"The maximum time weighted average concentration for a moving window — max_twa","text":"generate time series using sawtooth, need make sure length time series allows finding maximum. therefore recommended check using plot.one_box using window size argument max_twa.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/max_twa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"The maximum time weighted average concentration for a moving window — max_twa","text":"","code":"max_twa(x, window = 21)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/max_twa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"The maximum time weighted average concentration for a moving window — max_twa","text":"x object type one_box window size moving window","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/max_twa.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"The maximum time weighted average concentration for a moving window — max_twa","text":"method working directly fitted mkinfit objects uses equations given PEC soil section FOCUS guidance restricted SFO, FOMC DFOP models parent compound","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/max_twa.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"The maximum time weighted average concentration for a moving window — max_twa","text":"FOCUS (2006) “Guidance Document Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/max_twa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"The maximum time weighted average concentration for a moving window — max_twa","text":"","code":"pred <- sawtooth(one_box(10), applications = data.frame(time = c(0, 7), amount = c(1, 1))) max_twa(pred) #> $max #> parent #> 0.9537545 #> #> $window_start #> parent #> 0 #> #> $window_end #> parent #> 21 #> pred_FOMC <- mkinfit(\"FOMC\", FOCUS_2006_C, quiet = TRUE) max_twa(pred_FOMC) #> 21 #> 18.22124"},{"path":"https://pkgdown.jrwb.de/pfm/reference/one_box.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a time series of decline data — one_box","title":"Create a time series of decline data — one_box","text":"Create time series decline data","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/one_box.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a time series of decline data — one_box","text":"","code":"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) # S3 method for character one_box(x, ini = 1, parms, ..., t_end = 100, res = 0.01) # S3 method for mkinfit one_box(x, ini = \"model\", ..., t_end = 100, res = 0.01)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/one_box.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a time series of decline data — one_box","text":"x numeric, half-life used exponential decline. character string specifying parent decline model given e.g. FOMC, parms must contain corresponding parameters. x mkinfit object, decline calculated object. ini initial amount. x mkinfit object, ini 'model', fitted initial concentrations used. Otherwise, ini must numeric. length one, used parent initial values metabolites zero, otherwise, must give values observed variables. ... arguments passed methods t_end End time series res Resolution time series parms named numeric vector containing model parameters","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/one_box.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a time series of decline data — one_box","text":"object class one_box, inheriting ts.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/one_box.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a time series of decline data — one_box","text":"","code":"# Only use a half-life pred_0 <- one_box(10) plot(pred_0) # Use a fitted mkinfit model require(mkin) fit <- mkinfit(\"FOMC\", FOCUS_2006_C, quiet = TRUE) pred_1 <- one_box(fit) plot(pred_1) # Use a model with more than one observed variable m_2 <- mkinmod(parent = mkinsub(\"SFO\", \"m1\"), m1 = mkinsub(\"SFO\")) #> Temporary DLL for differentials generated and loaded fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) #> Warning: Observations with value of zero were removed from the data pred_2 <- one_box(fit_2, ini = \"model\") plot(pred_2)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_exposit.html","id":null,"dir":"Reference","previous_headings":"","what":"Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit","title":"Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit","text":"table loss percentages used Exposit 3 twelve different Koc classes","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_exposit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit","text":"","code":"perc_runoff_exposit"},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_exposit.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit","text":"data frame percentage values dissolved fraction fraction bound eroding particles, Koc classes used row names Koc_lower_bound lower bound Koc class dissolved percentage applied substance transferred adjacent water body dissolved phase bound percentage applied substance transferred adjacent water body bound eroding particles","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_exposit.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit","text":"Excel 3.02 spreadsheet available https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_exposit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Runoff loss percentages as used in Exposit 3 — perc_runoff_exposit","text":"","code":"print(perc_runoff_exposit) #> Koc_lower_bound dissolved bound #> 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"},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_reduction_exposit.html","id":null,"dir":"Reference","previous_headings":"","what":"Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit","title":"Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit","text":"table runoff reduction percentages used Exposit 3 different vegetated buffer widths","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_reduction_exposit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit","text":"","code":"perc_runoff_reduction_exposit"},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_reduction_exposit.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit","text":"named list data frames reduction percentage values dissolved fraction fraction bound eroding particles, vegetated buffer widths row names. names list items Exposit versions values taken. dissolved reduction percentage dissolved phase bound reduction percentage particulate phase","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_reduction_exposit.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit","text":"Excel 3.02 spreadsheet available https://www.bvl.bund.de/SharedDocs/Downloads/04_Pflanzenschutzmittel/zul_umwelt_exposit.html Agroscope version 3.01a additional runoff factors 3 m 6 m buffer zones received Muris Korkaric (published). variant 3.01a2 introduced consistency previous calculations performed Agroscope 3 m buffer zone.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/perc_runoff_reduction_exposit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Runoff reduction percentages as used in Exposit — perc_runoff_reduction_exposit","text":"","code":"print(perc_runoff_reduction_exposit) #> $`3.02` #> dissolved bound #> No buffer 0 0 #> 5 m 40 40 #> 10 m 60 85 #> 20 m 80 95 #> #> $`3.01a` #> dissolved bound #> No buffer 0 0 #> 3 m 25 30 #> 5 m 40 40 #> 6 m 45 55 #> 10 m 60 85 #> 20 m 80 95 #> #> $`3.01a2` #> dissolved bound #> No buffer 0 0 #> 3 m 25 25 #> #> $`2.0` #> dissolved bound #> No buffer 0.0 0.0 #> 20 m 97.5 97.5 #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/pfm_degradation.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation","title":"Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation","text":"Calculate time course relative concentrations based mkinmod model","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/pfm_degradation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation","text":"","code":"pfm_degradation( model = \"SFO\", DT50 = 1000, parms = c(k_parent = log(2)/DT50), years = 1, step_days = 1, times = seq(0, years * 365, by = step_days) )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/pfm_degradation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation","text":"model degradation model used. Either parent model like 'SFO' 'FOMC', mkinmod object DT50 half-life. used simple exponential decline calculated (SFO model). parms parameters used degradation model years many years degradation predicted? step_days step size days output ? times output times","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/pfm_degradation.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/pfm_degradation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation","text":"","code":"head(pfm_degradation(\"SFO\", DT50 = 10)) #> time parent #> 0 0 1.0000000 #> 1 1 0.9330330 #> 2 2 0.8705506 #> 3 3 0.8122524 #> 4 4 0.7578583 #> 5 5 0.7071068"},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.TOXSWA_cwa.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa","title":"Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa","text":"Plot TOXSWA hourly concentrations chemical substance specific segment TOXSWA surface water body.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.TOXSWA_cwa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa","text":"","code":"# S3 method for TOXSWA_cwa plot( x, time_column = c(\"datetime\", \"t\", \"t_firstjan\", \"t_rel_to_max\"), xlab = \"default\", ylab = \"default\", add = FALSE, threshold_factor = 1000, thin_low = 1, total = FALSE, LC_TIME = \"C\", ... )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.TOXSWA_cwa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa","text":"x TOXSWA_cwa object plotted. time_column used time axis. \"t_firstjan\" chosen, time given days relative first January first year. xlab, ylab Labels x y axis. add add existing plot? threshold_factor factor data lower maximum order get thinned plotting (see next argument). thin_low integer greater 1, data close zero (smaller 1/threshold_factor maximum) series thinned factor order decrease amount data included plots total total concentration water plotted, including substance sorbed suspended matter? LC_TIME Specification locale used format dates ... arguments passed plot adding existing plot","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.TOXSWA_cwa.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.TOXSWA_cwa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa","text":"","code":"H_sw_D4_pond <- read.TOXSWA_cwa(\"00001p_pa.cwa\", basedir = \"SwashProjects/project_H_sw/TOXSWA\", zipfile = system.file(\"testdata/SwashProjects.zip\", package = \"pfm\")) plot(H_sw_D4_pond) plot(H_sw_D4_pond, time_column = \"t\") plot(H_sw_D4_pond, time_column = \"t_firstjan\") plot(H_sw_D4_pond, time_column = \"t_rel_to_max\") H_sw_R1_stream <- read.TOXSWA_cwa(\"00003s_pa.cwa\", basedir = \"SwashProjects/project_H_sw/TOXSWA\", zipfile = system.file(\"testdata/SwashProjects.zip\", package = \"pfm\")) plot(H_sw_R1_stream, time_column = \"t_rel_to_max\")"},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.one_box.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot time series of decline data — plot.one_box","title":"Plot time series of decline data — plot.one_box","text":"Plot time series decline data","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.one_box.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot time series of decline data — plot.one_box","text":"","code":"# 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], ... )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.one_box.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot time series of decline data — plot.one_box","text":"x object type one_box plotted xlim Limits x axis ylim Limits y axis xlab Label x axis ylab Label y axis max_twa numeric value given, maximum time weighted average concentration(s) /shown graph. max_twa_var Variable maximum time weighted average shown max_twa NULL. ... arguments passed methods","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/plot.one_box.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot time series of decline data — plot.one_box","text":"","code":"dfop_pred <- one_box(\"DFOP\", parms = c(k1 = 0.2, k2 = 0.02, g = 0.7)) plot(dfop_pred) plot(sawtooth(dfop_pred, 3, 7), max_twa = 21) # Use a fitted mkinfit model m_2 <- mkinmod(parent = mkinsub(\"SFO\", \"m1\"), m1 = mkinsub(\"SFO\")) #> Temporary DLL for differentials generated and loaded fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) #> Warning: Observations with value of zero were removed from the data pred_2 <- one_box(fit_2, ini = 1) pred_2_saw <- sawtooth(pred_2, 2, 7) plot(pred_2_saw, max_twa = 21, max_twa_var = \"m1\")"},{"path":"https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html","id":null,"dir":"Reference","previous_headings":"","what":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","title":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","text":"Read TOXSWA hourly concentrations chemical substance specific segment TOXSWA surface water body. Per default, data last segment imported. TOXSWA 4 reports values end hour (ConLiqWatLayCur) summary file, use value well instead hourly averages (ConLiqWatLay). TOXSWA 5.5.3 variable renamed ConLiqWatLay file.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","text":"","code":"read.TOXSWA_cwa( filename, basedir = \".\", zipfile = NULL, segment = \"last\", substance = \"parent\", total = FALSE, windows = NULL, thresholds = NULL )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","text":"filename filename cwa file (TOXSWA 2.x.y similar) file using FOCUS TOXSWA 4 (.e. TOXSWA 4.4.2) higher. basedir path directory cwa file resides. zipfile Optional path zip file containing cwa file. segment segment data read. Either \"last\", segment number. substance .files, default value \"parent\" leads reading concentrations parent compound. Alternatively, substance interested can selected code name. total Set TRUE order read total concentrations well. necessary .files generated TOXSWA 4.4.2 similar, .cwa files. .cwa files, total concentration always read well. windows Numeric vector width moving windows days, calculating maximum time weighted average concentrations areas curve. thresholds Numeric vector threshold concentrations µg/L generating event statistics.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","text":"instance R6 object class TOXSWA_cwa.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read TOXSWA surface water concentrations — read.TOXSWA_cwa","text":"","code":"H_sw_D4_pond <- read.TOXSWA_cwa(\"00001p_pa.cwa\", basedir = \"SwashProjects/project_H_sw/TOXSWA\", zipfile = system.file(\"testdata/SwashProjects.zip\", package = \"pfm\"))"},{"path":"https://pkgdown.jrwb.de/pfm/reference/reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Objects exported from other packages — reexports","title":"Objects exported from other packages — reexports","text":"objects imported packages. Follow links see documentation. mkin set_nd_nq, set_nd_nq_focus","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/sawtooth.html","id":null,"dir":"Reference","previous_headings":"","what":"Create decline time series for multiple applications — sawtooth","title":"Create decline time series for multiple applications — sawtooth","text":"application pattern specified applications, n disregarded.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/sawtooth.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create decline time series for multiple applications — sawtooth","text":"","code":"sawtooth( x, n = 1, i = 365, applications = data.frame(time = seq(0, (n - 1) * i, length.out = n), amount = 1) )"},{"path":"https://pkgdown.jrwb.de/pfm/reference/sawtooth.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create decline time series for multiple applications — sawtooth","text":"x one_box object n number applications. applications specified, n ignored interval applications. applications specified, ignored applications data frame holding application times first column corresponding amounts applied second column.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/sawtooth.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create decline time series for multiple applications — sawtooth","text":"","code":"applications = data.frame(time = seq(0, 14, by = 7), amount = c(1, 2, 3)) pred <- one_box(10) plot(sawtooth(pred, applications = applications)) m_2 <- mkinmod(parent = mkinsub(\"SFO\", \"m1\"), m1 = mkinsub(\"SFO\")) #> Temporary DLL for differentials generated and loaded fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) #> Warning: Observations with value of zero were removed from the data pred_2 <- one_box(fit_2, ini = 1) pred_2_saw <- sawtooth(pred_2, 2, 7) plot(pred_2_saw, max_twa = 21, max_twa_var = \"m1\") max_twa(pred_2_saw) #> $max #> parent m1 #> 0.7834481 0.8617049 #> #> $window_start #> parent m1 #> 0.00 26.85 #> #> $window_end #> parent m1 #> 21.00 47.85 #>"},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.html","id":null,"dir":"Reference","previous_headings":"","what":"Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015","title":"Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015","text":"Properties predefined scenarios used Tier 1, Tier 2A Tier 3A concentration soil given EFSA guidance (2015, p. 13/14). Also, scenario model adjustment factors p. 15 p. 17 included.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015","text":"","code":"soil_scenario_data_EFSA_2015"},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015","text":"data frame one row scenario. Row names scenario codes, e.g. CTN Northern scenario total concentration soil. Columns mostly self-explanatory. rho dry bulk density top soil.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015","text":"EFSA (European Food Safety Authority) (2015) EFSA guidance document predicting environmental concentrations active substances plant protection products transformation products active substances soil. EFSA Journal 13(4) 4093 doi:10.2903/j.efsa.2015.4093","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2015.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015","text":"","code":"soil_scenario_data_EFSA_2015 #> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce #> CTN North Estonia 4.7 7.0 Coarse 0.118 0.244 0.95 3.0 #> CTC Central Germany 8.0 10.1 Coarse 0.086 0.244 1.05 2.0 #> CTS South France 11.0 12.3 Medium fine 0.048 0.385 1.22 2.0 #> CLN North Denmark 8.2 9.8 Medium 0.023 0.347 1.39 2.0 #> CLC Central Czech Republik 9.1 11.2 Medium 0.018 0.347 1.43 1.5 #> CLS South Spain 12.8 14.7 Medium 0.011 0.347 1.51 1.5 #> f_mod #> CTN 2 #> CTC 2 #> CTS 2 #> CLN 4 #> CLC 4 #> CLS 4"},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2017.html","id":null,"dir":"Reference","previous_headings":"","what":"Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017","title":"Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017","text":"Properties predefined scenarios used Tier 1, Tier 2A Tier 3A concentration soil given EFSA guidance (2017, p. 14/15). Also, scenario model adjustment factors p. 16 p. 18 included.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2017.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017","text":"","code":"soil_scenario_data_EFSA_2017"},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2017.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017","text":"data frame one row scenario. Row names scenario codes, e.g. CTN Northern scenario total concentration soil. Columns mostly self-explanatory. rho dry bulk density top soil.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2017.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017","text":"EFSA (European Food Safety Authority) (2017) EFSA guidance document predicting environmental concentrations active substances plant protection products transformation products active substances soil. EFSA Journal 15(10) 4982 doi:10.2903/j.efsa.2017.4982","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/soil_scenario_data_EFSA_2017.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Properties of the predefined scenarios from the EFSA guidance from 2017 — soil_scenario_data_EFSA_2017","text":"","code":"soil_scenario_data_EFSA_2017 #> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce f_mod #> CTN North Estonia 5.7 7.6 Coarse 0.220 0.244 0.707 1.4 3 #> CTC Central Poland 7.4 9.3 Coarse 0.122 0.244 0.934 1.4 3 #> CTS South France 10.2 11.7 Medium 0.070 0.349 1.117 1.4 3 #> CLN North Denmark 8.0 9.2 Medium 0.025 0.349 1.371 1.6 4 #> CLC Central Austria 9.3 11.3 Medium 0.018 0.349 1.432 1.6 4 #> CLS South Spain 15.4 16.7 Medium 0.010 0.349 1.521 1.6 4 #> FOCUS_zone prec #> CTN Hamburg 639 #> CTC Hamburg 617 #> CTS Hamburg 667 #> CLN Hamburg 602 #> CLC Châteaudun 589 #> CLS Sevilla 526 waldo::compare(soil_scenario_data_EFSA_2017, soil_scenario_data_EFSA_2015) #> `old` is length 12 #> `new` is length 10 #> #> `names(old)[8:12]`: \"rho\" \"f_sce\" \"f_mod\" \"FOCUS_zone\" \"prec\" #> `names(new)[8:10]`: \"rho\" \"f_sce\" \"f_mod\" #> #> `old$Country`: \"Estonia\" \"Poland\" \"France\" \"Denmark\" \"Austria\" \"Spain\" #> `new$Country`: \"Estonia\" \"Germany\" \"France\" \"Denmark\" \"Czech Republik\" \"Spain\" #> #> `old$T_arit`: 5.7 7.4 10.2 8.0 9.3 15.4 #> `new$T_arit`: 4.7 8.0 11.0 8.2 9.1 12.8 #> #> `old$T_arr`: 7.6 9.3 11.7 9.2 11.3 16.7 #> `new$T_arr`: 7.0 10.1 12.3 9.8 11.2 14.7 #> #> `old$Texture`: \"Coarse\" \"Coarse\" \"Medium\" \"Medium\" \"Medium\" \"Medium\" #> `new$Texture`: \"Coarse\" \"Coarse\" \"Medium fine\" \"Medium\" \"Medium\" \"Medium\" #> #> `old$f_om`: 0.220 0.122 0.070 0.025 0.018 0.010 #> `new$f_om`: 0.118 0.086 0.048 0.023 0.018 0.011 #> #> `old$theta_fc`: 0.244 0.244 0.349 0.349 0.349 0.349 #> `new$theta_fc`: 0.244 0.244 0.385 0.347 0.347 0.347 #> #> `old$rho`: 0.707 0.934 1.117 1.371 1.432 1.521 #> `new$rho`: 0.950 1.050 1.220 1.390 1.430 1.510 #> #> `old$f_sce`: 1.4 1.4 1.4 1.6 1.6 1.6 #> `new$f_sce`: 3.0 2.0 2.0 2.0 1.5 1.5 #> #> And 3 more differences ..."},{"path":"https://pkgdown.jrwb.de/pfm/reference/twa.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate a time weighted average concentration — twa","title":"Calculate a time weighted average concentration — twa","text":"moving average built using values past, earliest possible time maximum time series returned one window passed.","code":""},{"path":"https://pkgdown.jrwb.de/pfm/reference/twa.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate a time weighted average concentration — twa","text":"","code":"twa(x, window = 21) # S3 method for one_box twa(x, window = 21)"},{"path":"https://pkgdown.jrwb.de/pfm/reference/twa.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate a time weighted average concentration — twa","text":"x object type one_box window size moving window","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/pfm/reference/twa.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate a time weighted average concentration — twa","text":"","code":"pred <- sawtooth(one_box(10), applications = data.frame(time = c(0, 7), amount = c(1, 1))) max_twa(pred) #> $max #> parent #> 0.9537545 #> #> $window_start #> parent #> 0 #> #> $window_end #> parent #> 21 #>"},{"path":"https://pkgdown.jrwb.de/pfm/news/index.html","id":"version-063","dir":"Changelog","previous_headings":"","what":"version 0.6.3","title":"version 0.6.3","text":"R/{PEC_sw_drift,PEC_sw_exposit_runoff,PEC_sw_sed}.R: Make use units package.","code":""}] diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 2ec8e59..8dc19ce 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -1,132 +1,47 @@ - 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