Authors

+ + + +

+
Johannes Ranke. Author, maintainer. +
+

Citation

+ -

-
Johannes Ranke. Author, maintainer, copyright holder. -
-

Johannes Ranke (2023). +pfm: Utilities for Pesticide Fate Modelling. +R package version 0.6.0, https://pkgdown.jrwb.de/pfm. +

@Manual{,
+  title = {pfm: Utilities for Pesticide Fate Modelling},
+  author = {{Johannes Ranke}},
+  year = {2023},
+  note = {R package version 0.6.0},
+  url = {https://pkgdown.jrwb.de/pfm},
+}

@@ -118,22 +70,20 @@ -

- - + + diff --git a/docs/index.html b/docs/index.html index fd7cfd1..9b6e441 100644 --- a/docs/index.html +++ b/docs/index.html @@ -21,6 +21,8 @@ + +

- - +

+ +

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

The easiest way to install the package is probably to use drat:

Installation +

The easiest way to install the package is probably to use drat:

-install.packages("drat")
-drat::addRepo("jranke")
-install.packages("pfm")

install.packages("drat")
+drat::addRepo("jranke")
+install.packages("pfm")

Alternatively you can install the package using the devtools package. Using quick = TRUE skips docs, multiple-architecture builds, demos, and vignettes.

-library(devtools)
-install_github("jranke/pfm", quick = TRUE)

library(devtools)
+install_github("jranke/pfm", quick = TRUE)

-Use

Please refer to the reference.

Use +

Please refer to the reference.

-Examples

One recent nice example of the usage of this package is the visualisation of a time weighted average for a sawtooth curve obtained from several overlays of mkinfit predictions as shown here.

Examples +

One recent nice example of the usage of this package is the visualisation of a time weighted average for a sawtooth curve obtained from several overlays of mkinfit predictions as shown here.

@@ -131,5 +133,7 @@ + + diff --git a/docs/pkgdown.css b/docs/pkgdown.css index 1273238..80ea5b8 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -56,8 +56,10 @@ img.icon { float: right; } -img { +/* Ensure in-page images don't run outside their container */ +.contents img { max-width: 100%; + height: auto; } /* Fix bug in bootstrap (only seen in firefox) */ @@ -78,11 +80,10 @@ dd { /* Section anchors ---------------------------------*/ a.anchor { - margin-left: -30px; - display:inline-block; - width: 30px; - height: 30px; - visibility: hidden; + display: none; + margin-left: 5px; + width: 20px; + height: 20px; background-image: url(./link.svg); background-repeat: no-repeat; @@ -90,17 +91,15 @@ a.anchor { background-position: center center; } -.hasAnchor:hover a.anchor { - visibility: visible; -} - -@media (max-width: 767px) { - .hasAnchor:hover a.anchor { - visibility: hidden; - } +h1:hover .anchor, +h2:hover .anchor, +h3:hover .anchor, +h4:hover .anchor, +h5:hover .anchor, +h6:hover .anchor { + display: inline-block; } - /* Fixes for fixed navbar --------------------------*/ .contents h1, .contents h2, .contents h3, .contents h4 { @@ -264,31 +263,26 @@ table { /* Syntax highlighting ---------------------------------------------------- */ -pre { - word-wrap: normal; - word-break: normal; - border: 1px solid #eee; -} - -pre, code { +pre, code, pre code { background-color: #f8f8f8; color: #333; } +pre, pre code { + white-space: pre-wrap; + word-break: break-all; + overflow-wrap: break-word; +} -pre code { - overflow: auto; - word-wrap: normal; - white-space: pre; +pre { + border: 1px solid #eee; } -pre .img { +pre .img, pre .r-plt { margin: 5px 0; } -pre .img img { +pre .img img, pre .r-plt img { background-color: #fff; - display: block; - height: auto; } code a, pre a { @@ -305,9 +299,8 @@ a.sourceLine:hover { .kw {color: #264D66;} /* keyword */ .co {color: #888888;} /* comment */ -.message { color: black; font-weight: bolder;} -.error { color: orange; font-weight: bolder;} -.warning { color: #6A0366; font-weight: bolder;} +.error {font-weight: bolder;} +.warning {font-weight: bolder;} /* Clipboard --------------------------*/ @@ -365,3 +358,27 @@ mark { content: ""; } } + +/* Section anchors --------------------------------- + Added in pandoc 2.11: https://github.com/jgm/pandoc-templates/commit/9904bf71 +*/ + +div.csl-bib-body { } +div.csl-entry { + clear: both; +} +.hanging-indent div.csl-entry { + margin-left:2em; + text-indent:-2em; +} +div.csl-left-margin { + min-width:2em; + float:left; +} +div.csl-right-inline { + margin-left:2em; + padding-left:1em; +} +div.csl-indent { + margin-left: 2em; +} diff --git a/docs/pkgdown.js b/docs/pkgdown.js index 7e7048f..6f0eee4 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -80,7 +80,7 @@ $(document).ready(function() { var copyButton = ""; - $(".examples, div.sourceCode").addClass("hasCopyButton"); + $("div.sourceCode").addClass("hasCopyButton"); // Insert copy buttons: $(copyButton).prependTo(".hasCopyButton"); @@ -91,7 +91,7 @@ // Initialize clipboard: var clipboardBtnCopies = new ClipboardJS('[data-clipboard-copy]', { text: function(trigger) { - return trigger.parentNode.textContent; + return trigger.parentNode.textContent.replace(/\n#>[^\n]*/g, ""); } }); diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index cc57584..b223f0d 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,8 +1,8 @@ -pandoc: 2.9.2.1 -pkgdown: 1.6.1 +pandoc: 2.17.1.1 +pkgdown: 2.0.7 pkgdown_sha: ~ articles: {} -last_built: 2021-11-18T23:17Z +last_built: 2023-11-12T20:09Z urls: reference: https://pkgdown.jrwb.de/pfm/reference article: https://pkgdown.jrwb.de/pfm/articles diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html index 3e405a5..e531fab 100644 --- a/docs/reference/PEC_soil.html +++ b/docs/reference/PEC_soil.html @@ -1,68 +1,16 @@ - - - - - - - -Calculate predicted environmental concentrations in soil — PEC_soil • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Calculate predicted environmental concentrations in soil — PEC_soil • pfm - - - - - - - - - - - - - - + + -

- -

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
-)

- -

Arguments

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

rate	Application rate in units specified below
rate_units	Defaults to g/ha
interception	The fraction of the application rate that does not reach the soil
mixing_depth	Mixing depth in cm
PEC_units	Requested units for the calculated PEC. Only mg/kg currently supported
PEC_pw_units	Only mg/L currently supported
interval	Period of the deeper mixing. The default is NA, i.e. no + + `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 +)` + + + + Arguments + rate + Application rate in units specified below + + + rate_units + Defaults to g/ha + + + interception + The fraction of the application rate that does not reach the soil + + + mixing_depth + Mixing depth in cm + + + PEC_units + Requested units for the calculated PEC. Only mg/kg currently supported + + + PEC_pw_units + Only mg/L currently supported + + + interval + Period of the deeper mixing. The default is NA, i.e. no deeper mixing. For annual deeper mixing, set this to 365 when degradation -units are in days
n_periods	Number of periods to be considered for long term PEC calculations
tillage_depth	Periodic (see interval) deeper mixing in cm
leaching_depth	EFSA (2017) uses the mixing depth (ecotoxicological +units are in days + + + n_periods + Number of periods to be considered for long term PEC calculations + + + tillage_depth + Periodic (see interval) deeper mixing in cm + + + leaching_depth + EFSA (2017) uses the mixing depth (ecotoxicological evaluation depth) to calculate leaching for annual crops where tillage takes place. By default, losses from the layer down to the tillage -depth are taken into account in this implementation.
crop	Ignored for scenarios other than EFSA_2017. Only annual crops +depth are taken into account in this implementation. + + + crop + Ignored for scenarios other than EFSA_2017. Only annual crops are supported when these scenarios are used. Only crops with a single cropping -cycle per year are currently supported.
cultivation	Does mechanical cultivation in the sense of EFSA (2017) +cycle per year are currently supported. + + + cultivation + Does mechanical cultivation in the sense of EFSA (2017) take place, i.e. twice a year to a depth of 5 cm? Ignored for scenarios -other than EFSA_2017
chent	An optional chent object holding substance specific information. Can -also be a name for the substance as a character string
DT50	If specified, overrides soil DT50 endpoints from a chent object +other than EFSA_2017 + + + chent + An optional chent object holding substance specific information. Can +also be a name for the substance as a character string + + + DT50 + If specified, overrides soil DT50 endpoints from a chent object If DT50 is not specified here and not available from the chent object, zero -degradation is assumed
FOMC	If specified, it should be a named numeric vector containing +degradation is assumed + + + FOMC + If specified, it should be a named numeric vector containing the FOMC parameters alpha and beta. This overrides any other degradation endpoints, and the degradation during the interval and after the maximum PEC -is calculated using these parameters without temperature correction
Koc	If specified, overrides Koc endpoints from a chent object
Kom	Calculated from Koc by default, but can explicitly be specified -as Kom here
t_avg	Averaging times for time weighted average concentrations
t_act	Time series for actual concentrations
scenarios	If this is 'default', the DT50 will be used without correction +is calculated using these parameters without temperature correction + + + Koc + If specified, overrides Koc endpoints from a chent object + + + Kom + Calculated from Koc by default, but can explicitly be specified +as Kom here + + + t_avg + Averaging times for time weighted average concentrations + + + t_act + Time series for actual concentrations + + + scenarios + If this is 'default', the DT50 will be used without correction and soil properties as specified in the REACH guidance (R.16, Table R.16-9) are used for porewater PEC calculations. If this is "EFSA_2015", the DT50 is taken to be a modelling half-life at 20°C and pF2 (for when -'chents' is specified, the DegT50 with destination 'PECgw' will be used), +'chent' is specified, the DegT50 with destination 'PECgw' will be used), and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also -model and scenario adjustment factors from the EFSA guidance are used.
leaching	Should leaching be taken into account? The default is FALSE, -except when the EFSA_2017 scenarios are used.
porewater	Should equilibrium porewater concentrations be estimated +model and scenario adjustment factors from the EFSA guidance are used. + + + leaching + Should leaching be taken into account? The default is FALSE, +except when the EFSA_2017 scenarios are used. + + + porewater + Should equilibrium porewater concentrations be estimated based on Kom and the organic carbon fraction of the soil instead of total soil concentrations? Based on equation (7) given in the PPR panel opinion (EFSA 2012, p. 24) and the scenarios specified in the EFSA guidance (2015, -p. 13).

+p. 13).

Value

- -

The predicted concentration in soil

Details

Value

+ +

The predicted concentration in soil

Details

This assumes that the complete load to soil during the time specified by 'interval' (typically 365 days) is dosed at once. As in the PPR panel opinion cited below (EFSA PPR panel 2012), only temperature correction using the Arrhenius equation is performed.

Total soil and porewater PEC values for the scenarios as defined in the EFSA guidance (2017, p. 14/15) can easily be calculated.

Note

- +

Note

While time weighted average (TWA) concentrations given in the examples from the EFSA guidance from 2015 (p. 80) are be reproduced, this is not true for the TWA concentrations given for the same example in the EFSA guidance @@ -289,8 +226,9 @@ from 2017 (p. 92).

e.g. in the EFSA scenarios, the DT50 for groundwater modelling (destination 'PECgw') is taken from the chent object, otherwise the DT50 with destination 'PECsoil'.

References

- +

References

EFSA Panel on Plant Protection Products and their Residues (2012) Scientific Opinion on the science behind the guidance for scenario selection and scenario parameterisation for predicting environmental @@ -306,75 +244,80 @@ from 2017 (p. 92).

protection products and transformation products of these active substances in soil. EFSA Journal 13(4) 4093 doi:10.2903/j.efsa.2015.4093

- -

Examples

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)

- +

Author

Johannes Ranke

+ +

Examples

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)
+

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

- -

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
-#>

- +

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
+#> 
+

- - + + diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html index 16dc5db..c8622df 100644 --- a/docs/reference/TOXSWA_cwa.html +++ b/docs/reference/TOXSWA_cwa.html @@ -1,71 +1,16 @@ - - - - - - - -R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -R6 class for holding TOXSWA water concentration data and associated statistics — TOXSWA_cwa • pfm - - - - - - - - - - - - - + + -

- -

R6 class for holding TOXSWA water concentration data and associated statistics

@@ -117,179 +48,236 @@ by read.TOXSWA_cwa." /> and some associated statistics. like maximum moving window average concentrations, and dataframes holding the events exceeding specified thresholds. Usually, an instance of this class will be generated -by read.TOXSWA_cwa.

+by read.TOXSWA_cwa.

Format

An R6Class generator object.

Public fields

filename: Length one character vector holding the filename.
basedir: Length one character vector holding the directory where the file came from.
filename: Length one character vector holding the filename.
zipfile: If not null, giving the path to the zip file from which the file was read.
basedir: Length one character vector holding the directory where the file came from.
zipfile: If not null, giving the path to the zip file from which the file was read.
segment: Length one integer, specifying for which segment the cwa data were read.
segment: Length one integer, specifying for which segment the cwa data were read.
substance: The TOXSWA name of the substance.
substance: The TOXSWA name of the substance.
cwas: Dataframe holding the concentrations.
events: List of dataframes holding the event statistics for each threshold.
cwas: Dataframe holding the concentrations.
windows: Matrix of maximum time weighted average concentrations (TWAC_max) + +
events: List of dataframes holding the event statistics for each threshold.
windows: Matrix of maximum time weighted average concentrations (TWAC_max) and areas under the curve in µg/day * h (AUC_max_h) or µg/day * d (AUC_max_d) for the requested moving window sizes in days.

Methods

Public methods

- -

TOXSWA_cwa$new()
TOXSWA_cwa$moving_windows()
TOXSWA_cwa$get_events()
TOXSWA_cwa$print()
TOXSWA_cwa$clone()

Method `new()`

Create a TOXSWA_cwa object from a file

Usage

TOXSWA_cwa$new(
-  filename,
-  basedir,
-  zipfile = NULL,
-  segment = "last",
-  substance = "parent",
-  total = FALSE
-)

- -

Arguments

filename

The filename

- -

basedir

The directory to look in

- -

zipfile

Optional path to a zipfile holding the file

- -

segment

Either "last" or the number of the segment for which to read the data

- -

substance

The TOXSWA substance name (for TOXSWA 4 or higher)

- -

total

Should total concentrations be read in? If FALSE, free concentrations are read

- -

Method `moving_windows()`

Add to the `windows` field described above.

Usage

TOXSWA_cwa$moving_windows(windows, total = FALSE)

- -

Arguments

windows

Window sizes in days

- -

total

If TRUE, the total concentration including the amount adsorbed to +

Public methods

+ +

TOXSWA_cwa$new()
TOXSWA_cwa$moving_windows()
TOXSWA_cwa$get_events()
TOXSWA_cwa$print()
TOXSWA_cwa$clone()

Method `new()`

Create a TOXSWA_cwa object from a file

Usage

TOXSWA_cwa$new(
+  filename,
+  basedir,
+  zipfile = NULL,
+  segment = "last",
+  substance = "parent",
+  total = FALSE
+)

+ +

Arguments

filename: The filename
basedir: The directory to look in
zipfile: Optional path to a zipfile holding the file
segment: Either "last" or the number of the segment for which to read the data
substance: The TOXSWA substance name (for TOXSWA 4 or higher)
total: Should total concentrations be read in? If FALSE, free concentrations are read

+ +

Method `moving_windows()`

Add to the `windows` field described above.

Usage

TOXSWA_cwa$moving_windows(windows, total = FALSE)

+ +

Arguments

windows: Window sizes in days
total: If TRUE, the total concentration including the amount adsorbed to suspended matter will be used.

Method `get_events()`

+ +

Method `get_events()`

Populate a datataframe with event information for the specified threshold value. The resulting dataframe is stored in the `events` -field of the object.

Usage

TOXSWA_cwa$get_events(thresholds, total = FALSE)

+field of the object.

Usage

TOXSWA_cwa$get_events(thresholds, total = FALSE)

+ +

Arguments

thresholds: Threshold values in µg/L.
thresholds: Threshold values in µg/L.
total: If TRUE, the total concentration including the amount adsorbed to +
total: If TRUE, the total concentration including the amount adsorbed to suspended matter will be used.

Method `print()`

Print a `TOXSWA_cwa` object

Usage

TOXSWA_cwa$print()

- -

Method `clone()`

The objects of this class are cloneable with this method.

Usage

TOXSWA_cwa$clone(deep = FALSE)

- -

Arguments

deep

Whether to make a deep clone.

- -

- - - -

Examples

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)
#> <TOXSWA_cwa> 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

+ +

Method `print()`

Print a `TOXSWA_cwa` object

Usage

TOXSWA_cwa$print()

+ + +

Method `clone()`

The objects of this class are cloneable with this method.

Usage

TOXSWA_cwa$clone(deep = FALSE)

+ +

Arguments

deep: Whether to make a deep clone.

+ +

Examples

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)
+#> <TOXSWA_cwa> 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
+

- - + + diff --git a/docs/reference/index.html b/docs/reference/index.html index fed30cc..e5af0b7 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,66 +1,12 @@ - - - - - - - -Function reference • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Function reference • pfm - - - - + + -

- -

- - - - - - - - - - -

General utility functions

Functions that are independent of specific fate modelling areas

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

+ General utility functions + Functions that are independent of specific fate modelling areas
+
`geomean()`	Calculate the geometric mean
+
`one_box()`	Create a time series of decline data
+
`plot(<one_box>)`	Plot time series of decline data
+
`sawtooth()`	Create decline time series for multiple applications
+
`twa()`	Calculate a time weighted average concentration
+
`max_twa()`	The maximum time weighted average concentration for a moving window
+
`pfm_degradation()`	Calculate a time course of relative concentrations based on an mkinmod model
+
`SFO_actual_twa()`	Actual and maximum moving window time average concentrations for SFO kinetics
+
`FOMC_actual_twa()`	Actual and maximum moving window time average concentrations for FOMC kinetics
- `set_nd_nq()` `set_nd_nq_focus()` -	Set non-detects and unquantified values in residue series without replicates
+
+ `reexports` `set_nd_nq` `set_nd_nq_focus` +	Objects exported from other packages
`TSCF()`	Estimation of the transpiration stream concentration factor
- Predicted environmental concentrations in soil +
+ Predicted environmental concentrations in soil
+
`PEC_soil()`	Calculate predicted environmental concentrations in soil
+
`PEC_soil_mets()`	Calculate initial and accumulation PEC soil for a set of metabolites
+
`soil_scenario_data_EFSA_2015`	Properties of the predefined scenarios from the EFSA guidance from 2015
+
`soil_scenario_data_EFSA_2017`	Properties of the predefined scenarios from the EFSA guidance from 2017
+
`PEC_FOMC_accu_rel()`	Get the relative accumulation of an FOMC model over multiples of an interval
+
`EFSA_washoff_2017`	Subset of EFSA crop washoff default values
- Predicted environmental concentrations in groundwater +
+ Predicted environmental concentrations in groundwater
+
`FOCUS_GW_scenarios_2012`	A very small subset of the FOCUS Groundwater scenario definitions
+
`EFSA_GW_interception_2014`	Subset of EFSA crop interception default values for groundwater modelling
- Predicted environmental concentrations in surface water +
+ Predicted environmental concentrations in surface water
+
`PEC_sw_drift()`	Calculate predicted environmental concentrations in surface water due to drift
+
`drift_data_JKI`	Deposition from spray drift expressed as percent of the applied dose as published by the JKI
+
`PEC_sw_drainage_UK()`	Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method
+
`PEC_sw_sed()`	Calculate predicted environmental concentrations in sediment from surface water concentrations
+
`PEC_sw_focus()`	Calculate PEC surface water at FOCUS Step 1
+
`chent_focus_sw()`	Create a chemical compound object for FOCUS Step 1 calculations
+
`FOCUS_Step_12_scenarios`	Step 1/2 scenario data as distributed with the FOCUS Step 1/2 calculator
+
`PEC_sw_exposit_drainage()`	Calculate PEC surface water due to drainage as in Exposit 3
+
`PEC_sw_exposit_runoff()`	Calculate PEC surface water due to runoff and erosion as in Exposit 3
+
`perc_runoff_exposit`	Runoff loss percentages as used in Exposit 3
+
`perc_runoff_reduction_exposit`	Runoff reduction percentages as used in Exposit
+
`TOXSWA_cwa`	R6 class for holding TOXSWA water concentration data and associated statistics
+
`read.TOXSWA_cwa()`	Read TOXSWA surface water concentrations
+
`plot(<TOXSWA_cwa>)`	Plot TOXSWA surface water concentrations
- Classifications and indicators - Evaluating environmental fate properties +
+ Classifications and indicators + Evaluating environmental fate properties
+
`SSLRC_mobility_classification()`	Determine the SSLRC mobility classification for a chemical substance from its Koc
+
`GUS()` `print(<GUS_result>)`	Groundwater ubiquity score based on Gustafson (1989)
- Work with chent objects containing relevant information +
+ Work with chent objects containing relevant information
+
`endpoint()` `soil_DT50()` `soil_Kfoc()` `soil_N()` `soil_sorption()`	Retrieve endpoint information from the chyaml field of a chent object
- Utilities +
+ Utilities
+
`get_vertex()`	Fit a parabola through three points

- +

- - + + diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html new file mode 100644 index 0000000..2f410e4 --- /dev/null +++ b/docs/reference/reexports.html @@ -0,0 +1,83 @@ + +Objects exported from other packages — reexports • pfm + + +

+ + + +

+ + +

These objects are imported from other packages. Follow the links +below to see their documentation.

mkin: set_nd_nq, set_nd_nq_focus

+ + + +

+ +

+ + +

+ + + + + + + + diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 0c507b6..6ba511d 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -1,5 +1,11 @@ + + https://pkgdown.jrwb.de/pfm/404.html + + + https://pkgdown.jrwb.de/pfm/authors.html + https://pkgdown.jrwb.de/pfm/index.html @@ -75,6 +81,9 @@ https://pkgdown.jrwb.de/pfm/reference/get_vertex.html + + https://pkgdown.jrwb.de/pfm/reference/index.html + https://pkgdown.jrwb.de/pfm/reference/max_twa.html @@ -99,6 +108,9 @@ https://pkgdown.jrwb.de/pfm/reference/read.TOXSWA_cwa.html + + https://pkgdown.jrwb.de/pfm/reference/reexports.html + https://pkgdown.jrwb.de/pfm/reference/sawtooth.html -- cgit v1.2.1

Page not found (404)

Authors

Authors

Citation

-pfm

pfm +

-Installation

Installation +

-Use

Use +

-Examples

Examples +

License

License

Developers

Citation

Dev status

Developers

Calculate predicted environmental concentrations in soil

Arguments

Arguments

Value

Details

Value

Details

Note

Note

References

References

Examples

Contents

Author

Examples

Calculate PEC surface water at FOCUS Step 1

Arguments

Arguments

Note

Note

References

References

Examples

Contents

Examples

R6 class for holding TOXSWA water concentration data and associated statistics

Format

Public fields

Format

Public fields

Methods

Methods

Public methods

Method new()

Usage

Arguments

Method moving_windows()

Usage

Arguments

Public methods

Method new()

Usage

Arguments

Method moving_windows()

Usage

Arguments

Method get_events()

Method get_events()

Usage

Usage

Arguments

Arguments

Method print()

Usage

Method clone()

Usage

Arguments

Examples

Method print()

Usage

Method clone()

Usage

Method `new()`

Method `moving_windows()`

Method `new()`

Method `moving_windows()`

Method `get_events()`

Method `get_events()`

Method `print()`

Method `clone()`

Method `print()`

Method `clone()`