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/404.html | 117 +++------ docs/authors.html | 136 ++++------ docs/index.html | 82 +++--- docs/pkgdown.css | 83 ++++--- docs/pkgdown.js | 4 +- docs/pkgdown.yml | 6 +- docs/reference/PEC_soil.html | 477 ++++++++++++++++------------------- docs/reference/PEC_sw_focus.html | 522 +++++++++++++++++---------------------- docs/reference/TOXSWA_cwa.html | 412 +++++++++++++++--------------- docs/reference/index.html | 365 ++++++--------------------- docs/reference/reexports.html | 83 +++++++ docs/sitemap.xml | 12 + 12 files changed, 981 insertions(+), 1318 deletions(-) create mode 100644 docs/reference/reexports.html (limited to 'docs') diff --git a/docs/404.html b/docs/404.html index acdca31..c0581a0 100644 --- a/docs/404.html +++ b/docs/404.html @@ -1,66 +1,27 @@ - - - - + + + + - Page not found (404) • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + - - - - -
-
- + +
+ + + - - -
+
+
-
- +
+ + - - diff --git a/docs/authors.html b/docs/authors.html index e4155eb..b945040 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,66 +1,12 @@ - - - - - - - -Authors • pfm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -Authors and Citation • 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 @@ + +
-
- - +
+ +

Build Status codecov

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.

-

Site built with pkgdown 1.6.1.

+

+

Site built with pkgdown 2.0.7.

@@ -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 -#>
-
- +
-
- +
- - + + 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 - - - - - - - - - - - - - + + -
-
- -
- -
+
+
+

Format

+

An R6Class generator object.

+
+
+

Public fields

+

filename
+

Length one character vector holding the filename.

-

Format

-

An R6Class generator object.

-

Public fields

+
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

+

+
+
+

Methods

-

Public methods

- - -


-

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 +


+

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.

-

Arguments

-

-
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

+ + +
+ + + +
+ +
+ + +
+ +
+

Site built with pkgdown 2.0.7.

+
+ +
+ + + + + + + + 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