From 97d0465a296ef1f5ae4502f9374ae339c0a8148e Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sun, 12 Nov 2023 21:10:41 +0100 Subject: Update static docs --- docs/reference/PEC_sw_focus.html | 522 +++++++++++++++++---------------------- 1 file changed, 227 insertions(+), 295 deletions(-) (limited to 'docs/reference/PEC_sw_focus.html') diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html index 8242f6a..55a7400 100644 --- a/docs/reference/PEC_sw_focus.html +++ b/docs/reference/PEC_sw_focus.html @@ -1,70 +1,18 @@ - - - - - - - -Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus • pfm - - - - - - - - - - - - - - + + -
-
- -
- -
+

Calculate PEC surface water at FOCUS Step 1

@@ -121,115 +55,114 @@ input files are generated that are suitable as input also for Step 2 to be used with the FOCUS calculator.

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

Arguments

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
parent

A list containing substance specific parameters, e.g. -conveniently generated by chent_focus_sw.

rate

The application rate in g/ha. Overriden when -applications are given explicitly

n

The number of applications

i

The application interval

comment

A comment for the input file

met

A list containing metabolite specific parameters. e.g. -conveniently generated by chent_focus_sw. If not NULL, -the PEC is calculated for this compound, not the parent.

f_drift

The fraction of the application rate reaching the waterbody +

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

Arguments

+
parent
+

A list containing substance specific parameters, e.g. +conveniently generated by [chent_focus_sw].

+ + +
rate
+

The application rate in g/ha. Overriden when +applications are given explicitly

+ + +
n
+

The number of applications

+ + +
i
+

The application interval

+ + +
comment
+

A comment for the input file

+ + +
met
+

A list containing metabolite specific parameters. e.g. +conveniently generated by [chent_focus_sw]. If not NULL, +the PEC is calculated for this compound, not the parent.

+ + +
f_drift
+

The fraction of the application rate reaching the waterbody via drift. If NA, this is derived from the scenario name and the number of applications via the drift data defined by the -FOCUS_Step_12_scenarios

f_rd

The fraction of the amount applied reaching the waterbody via +[FOCUS_Step_12_scenarios]

+ + +
f_rd
+

The fraction of the amount applied reaching the waterbody via runoff/drainage. At Step 1, it is assumed to be 10 -parent or a metabolite

scenario

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

region

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

season

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

interception

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

met_form_water

Should the metabolite formation in water be taken into +parent or a metabolite

+ + +
scenario
+

The name of the scenario. Must be one of the scenario +names given in [FOCUS_Step_12_scenarios]

+ + +
region
+

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

+ + +
season
+

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

+ + +
interception
+

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

+ + +
met_form_water
+

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

txt_file

the name, and potentially the full path to the +with previous versions of the Steps 12 calculator

+ + +
txt_file
+

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

overwrite

Should an existing file a the location specified in -txt_file be overwritten? Only takes effect if append is FALSE.

append

Should the input text file be appended?

- -

Note

+should be written

+ + +
overwrite
+

Should an existing file a the location specified in +txt_file be overwritten? Only takes effect if append is FALSE.

+ +
append
+

Should the input text file be appended?

+ +
+
+

Note

The formulas for input to the waterbody via runoff/drainage of the parent and subsequent formation of the metabolite in water is not documented in the model description coming with the calculator. As one would @@ -237,142 +170,141 @@ should be written

multiplying the application rate with the molar weight correction and the formation fraction in water/sediment systems.

Step 2 is not implemented.

-

References

- +
+
+

References

FOCUS (2014) Generic guidance for Surface Water Scenarios (version 1.4). FOrum for the Co-ordination of pesticde fate models and their USe. http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic

Website of the Steps 1 and 2 calculator at the Joint Research Center of the European Union: http://esdac.jrc.ec.europa.eu/projects/stepsonetwo

+
-

Examples

- 
# Parent only
-dummy_1 <- chent_focus_sw("Dummy 1", cwsat = 6000, DT50_ws = 6, Koc = 344.8)
-PEC_sw_focus(dummy_1, 3000, f_drift = 0, overwrite = TRUE, append = FALSE)
#> $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
-#>
-
- +
-
-
-

Developed by Johannes Ranke.

+
+

Developed by Johannes Ranke.

-

Site built with pkgdown 1.4.1.

+

Site built with pkgdown 2.0.7.

-
-
+
- - + + -- cgit v1.2.1 From d66bd4aa0bf9c4d9b8793a4e308c9e80691b440f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sun, 12 Nov 2023 21:40:01 +0100 Subject: Enable links to source, upgrade to bootstrap 5 --- docs/reference/PEC_sw_focus.html | 104 +++++++++++++++++++++------------------ 1 file changed, 55 insertions(+), 49 deletions(-) (limited to 'docs/reference/PEC_sw_focus.html') diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html index 55a7400..78f6453 100644 --- a/docs/reference/PEC_sw_focus.html +++ b/docs/reference/PEC_sw_focus.html @@ -1,5 +1,11 @@ -Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus • pfmCalculate PEC surface water at FOCUS Step 1 — PEC_sw_focus • pfm + + Skip to contents -
-
-
-
-

Calculate PEC surface water at FOCUS Step 1

- +
+
+
+
+

Calculate PEC surface water at FOCUS Step 1

+ Source: R/PEC_sw_focus.R +
PEC_sw_focus.Rd
-
+

This is a reimplementation of the FOCUS Step 1 and 2 calculator version 3.2, authored by Michael Klein, in R. Note that results for multiple applications should be compared to the corresponding results for a @@ -55,7 +64,8 @@ input files are generated that are suitable as input also for Step 2 to be used with the FOCUS calculator.

-
+
+

Usage

PEC_sw_focus(
   parent,
   rate,
@@ -77,8 +87,8 @@ to be used with the FOCUS calculator.

 )
-
-

Arguments

+
+

Arguments

parent

A list containing substance specific parameters, e.g. conveniently generated by [chent_focus_sw].

@@ -161,8 +171,8 @@ should be written

Should the input text file be appended?

-
-

Note

+
+

Note

The formulas for input to the waterbody via runoff/drainage of the parent and subsequent formation of the metabolite in water is not documented in the model description coming with the calculator. As one would @@ -171,8 +181,8 @@ should be written

correction and the formation fraction in water/sediment systems.

Step 2 is not implemented.

-
-

References

+
+

References

FOCUS (2014) Generic guidance for Surface Water Scenarios (version 1.4). FOrum for the Co-ordination of pesticde fate models and their USe. http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic

@@ -181,8 +191,8 @@ should be written

http://esdac.jrc.ec.europa.eu/projects/stepsonetwo

-
-

Examples

+
+

Examples

# 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, overwrite = TRUE, append = FALSE)
@@ -284,26 +294,22 @@ should be written

 #>
-
- -
+
-
+

Developed by Johannes Ranke.

-
+

Site built with pkgdown 2.0.7.

-
+
- -- cgit v1.2.1 From 4079a2c496aa4e8c6dc2a93afedcbedbf7a852b5 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sun, 12 Nov 2023 21:59:34 +0100 Subject: Enable markdown and rebuild docs --- docs/reference/PEC_sw_focus.html | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) (limited to 'docs/reference/PEC_sw_focus.html') diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html index 78f6453..e758347 100644 --- a/docs/reference/PEC_sw_focus.html +++ b/docs/reference/PEC_sw_focus.html @@ -91,7 +91,7 @@ to be used with the FOCUS calculator.

Arguments

parent

A list containing substance specific parameters, e.g. -conveniently generated by [chent_focus_sw].

+conveniently generated by chent_focus_sw.

rate
@@ -113,7 +113,7 @@ applications are given explicitly

met

A list containing metabolite specific parameters. e.g. -conveniently generated by [chent_focus_sw]. If not NULL, +conveniently generated by chent_focus_sw. If not NULL, the PEC is calculated for this compound, not the parent.

@@ -121,18 +121,18 @@ the PEC is calculated for this compound, not the parent.

The fraction of the application rate reaching the waterbody via drift. If NA, this is derived from the scenario name and the number of applications via the drift data defined by the -[FOCUS_Step_12_scenarios]

+FOCUS_Step_12_scenarios

f_rd

The fraction of the amount applied reaching the waterbody via -runoff/drainage. At Step 1, it is assumed to be 10 +runoff/drainage. At Step 1, it is assumed to be 10%, be it the parent or a metabolite

scenario

The name of the scenario. Must be one of the scenario -names given in [FOCUS_Step_12_scenarios]

+names given in FOCUS_Step_12_scenarios

region
@@ -174,21 +174,21 @@ should be written

Note

The formulas for input to the waterbody via runoff/drainage of the - parent and subsequent formation of the metabolite in water is not - documented in the model description coming with the calculator. As one would - expect, this appears to be (as we get the same results) calculated by - multiplying the application rate with the molar weight - correction and the formation fraction in water/sediment systems.

+parent and subsequent formation of the metabolite in water is not +documented in the model description coming with the calculator. As one would +expect, this appears to be (as we get the same results) calculated by +multiplying the application rate with the molar weight +correction and the formation fraction in water/sediment systems.

Step 2 is not implemented.

References

FOCUS (2014) Generic guidance for Surface Water Scenarios (version 1.4). - FOrum for the Co-ordination of pesticde fate models and their USe. - http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic

+FOrum for the Co-ordination of pesticde fate models and their USe. +http://esdac.jrc.ec.europa.eu/public_path/projects_data/focus/sw/docs/Generic%20FOCUS_SWS_vc1.4.pdf

Website of the Steps 1 and 2 calculator at the Joint Research - Center of the European Union: - http://esdac.jrc.ec.europa.eu/projects/stepsonetwo

+Center of the European Union: +http://esdac.jrc.ec.europa.eu/projects/stepsonetwo

-- cgit v1.2.1