diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2017-01-18 22:41:01 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2017-01-18 22:50:14 +0100 |
| commit | a76221d87485029444c8e684022ca606a0c7e68d (patch) | |
| tree | c95052ee51b35f6c5ab87bd6f27ef2877f536838 | |
| parent | a1d9f93138c2cfed92a683e37e72c737d52b7ad7 (diff) | |
Update static docs using pkgdown
- Add _pkgdown.yml for a structured function/data reference
- Make seealso links active
- Make mkinfit calls quiet
- Use pkgdown branch from pull request hadley/pkgdown#229 to have topics
ordered
73 files changed, 3840 insertions, 10450 deletions
diff --git a/GNUmakefile b/GNUmakefile index 5d396fc..f449880 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -26,10 +26,10 @@ roxygen: "$(R_HOME)/bin/Rscript" -e 'library(devtools); document()' @echo "DONE." -sd: roxygen +pd: roxygen @echo "Building static documentation..." # suppressWarnings to get rid of mbcsToSbcs warnings when plotting the 'µ' character - "$(R_HOME)/bin/Rscript" -e 'suppressWarnings(staticdocs::build_site())' + "$(R_HOME)/bin/Rscript" -e 'suppressWarnings(pkgdown::build_site())' @echo "DONE." $(TGZ): $(pkgfiles) @@ -35,13 +35,13 @@ #' #' # Use a fitted mkinfit model #' require(mkin) -#' fit <- mkinfit("FOMC", FOCUS_2006_C) +#' fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) #' pred_1 <- one_box(fit) #' plot(pred_1) #' #' # Use a model with more than one observed variable #' m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")) -#' fit_2 <- mkinfit(m_2, FOCUS_2006_D) +#' fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) #' pred_2 <- one_box(fit_2) #' plot(pred_2) one_box <- function(x, @@ -138,7 +138,7 @@ plot.one_box <- function(x, #' plot(sawtooth(pred, applications = applications)) #' #' m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")) -#' fit_2 <- mkinfit(m_2, FOCUS_2006_D) +#' fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) #' pred_2 <- one_box(fit_2) #' pred_2_saw <- sawtooth(pred_2, 2, 7) #' plot(pred_2_saw, max_twa = 21, max_twa_var = "m1") @@ -178,7 +178,7 @@ sawtooth <- function(x, n = 1, i = 365, #' #' @param x An object of type \code{\link{one_box}} #' @param window The size of the moving window -#' @seealso max_twa +#' @seealso \code{\link{max_twa}} #' @export #' @examples #' pred <- sawtooth(one_box(10), @@ -200,7 +200,7 @@ twa.one_box <- function(x, window = 21) #' The maximum time weighted average concentration for a moving window #' -#' @seealso twa +#' @seealso \code{\link{twa}} #' @inheritParams twa #' @export max_twa <- function(x, window = 21) UseMethod("max_twa") diff --git a/_pkgdown.yml b/_pkgdown.yml new file mode 100644 index 0000000..ff5f43d --- /dev/null +++ b/_pkgdown.yml @@ -0,0 +1,32 @@ +title: pfm + +template: + bootswatch: spacelab + +reference: + - title: General utility functions + desc: Functions that are independent of specific fate modelling areas + contents: + - geomean + - one_box + - plot.one_box + - sawtooth + - twa + - max_twa + - title: Predicted environmental concentrations in soil + contents: + - PEC_soil + - soil_scenario_data_EFSA_2015 + - title: Predicted environmental concentrations in surface water + contents: + - PEC_sw_drift + - drift_data_JKI + - PEC_sw_drainage_UK + - TOXSWA_cwa + - read.TOXSWA_cwa + - plot.TOXSWA_cwa + - title: Classifications and indicators + desc: Evaluating environmental fate properties + contents: + - SSLRC_mobility_classification + - GUS diff --git a/docs/FOCUS_GW_scenarios_2012.html b/docs/FOCUS_GW_scenarios_2012.html deleted file mode 100644 index 275e7e4..0000000 --- a/docs/FOCUS_GW_scenarios_2012.html +++ /dev/null @@ -1,157 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>FOCUS_GW_scenarios_2012. pfm 0.3-8</title> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=""> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">pfm 0.3-8</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> - </div> - </div> -</div> - - - <div class="container"> - <header> - - </header> - - <h1>A very small subset of the FOCUS Groundwater scenario defitions</h1> - -<div class="row"> - <div class="span8"> - - <div class="Description"> - <h2>Description</h2> - - <p>Currently, only a small subset of the soil definitions are provided.</p> - - </div> - - <div class="References"> - <h2>References</h2> - - <p>FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1. - FOrum for the Co-ordination of pesticde fate models and their USe. - http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf</p> - - </div> - - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'><span class="symbol">FOCUS_GW_scenarios_2012</span></div> -<div class='output'>$names - Cha Ham Jok Kre Oke - "Châteaudun" "Hamburg" "Jokioinen" "Kremsmünster" "Okehampton" - Pia Por Sev Thi - "Piacenza" "Porto" "Sevilla" "Thiva" - -$soils - location horizon number pH_H2O perc_clay perc_oc rel_deg -1 Cha Ap 1 8.0 30.0 1.39 1.0 -2 Cha B1 2 8.1 31.0 0.93 0.5 -3 Cha B2 3 8.2 25.0 0.70 0.5 -4 Cha II C1 4 8.5 26.0 0.30 0.3 -5 Cha II C1 5 8.5 26.0 0.30 0.0 -6 Cha II C2 6 8.5 24.0 0.27 0.0 -7 Cha M 7 8.3 31.0 0.21 0.0 -8 Ham Ap 1 6.4 7.2 1.50 1.0 -9 Ham BvI 2 5.6 6.7 1.00 0.5 -10 Ham BvII 3 5.6 0.9 0.20 0.3 -11 Ham Bv/Cv 4 5.7 0.0 0.00 0.3 -12 Ham Cv 5 5.5 0.0 0.00 0.3 -13 Ham Cv 6 5.5 0.0 0.00 0.0 -14 Jok Ap 1 6.2 3.6 4.06 1.0 -15 Jok Bs 2 5.6 1.8 0.84 0.5 -16 Jok BC1 3 5.4 1.2 0.36 0.3 -17 Jok BC2 4 5.4 1.7 0.29 0.3 -18 Jok BC2 5 5.4 1.7 0.29 0.0 -19 Jok Cg 6 5.3 1.9 0.21 0.0 -20 Kre <NA> 1 7.7 14.0 3.60 1.0 -21 Kre <NA> 2 7.0 25.0 1.00 0.5 -22 Kre <NA> 3 7.1 27.0 0.50 0.5 -23 Kre <NA> 4 7.1 27.0 0.50 0.3 -24 Kre <NA> 5 7.1 27.0 0.50 0.0 -25 Oke A 1 5.8 18.0 2.20 1.0 -26 Oke Bw1 2 6.3 17.0 0.70 0.5 -27 Oke BC 3 6.5 14.0 0.40 0.3 -28 Oke C 4 6.6 9.0 0.10 0.3 -29 Oke C 5 6.6 9.0 0.10 0.0 -30 Pia Ap 1 7.0 15.0 1.26 1.0 -31 Pia Ap 2 7.0 15.0 1.26 0.5 -32 Pia Bw 3 6.3 7.0 0.47 0.5 -33 Pia Bw 4 6.3 7.0 0.47 0.3 -34 Pia 2C 5 6.4 0.0 0.00 0.3 -35 Pia 2C 6 6.4 0.0 0.00 0.0 -36 Por <NA> 1 4.9 10.0 1.42 1.0 -37 Por <NA> 2 4.8 8.0 0.78 0.5 -38 Por <NA> 3 4.8 8.0 0.78 0.3 -39 Por <NA> 4 4.8 8.0 0.78 0.0 -40 Sev <NA> 1 7.3 14.0 0.93 1.0 -41 Sev <NA> 2 7.3 13.0 0.93 1.0 -42 Sev <NA> 3 7.8 15.0 0.70 0.5 -43 Sev <NA> 4 8.1 16.0 0.58 0.3 -44 Sev <NA> 5 8.1 16.0 0.58 0.0 -45 Sev <NA> 6 8.2 22.0 0.49 0.0 -46 Thi Ap1 1 7.7 25.3 0.74 1.0 -47 Thi Ap2 2 7.7 25.3 0.74 0.5 -48 Thi Bw 3 7.8 29.6 0.57 0.5 -49 Thi Bw 4 7.8 31.9 0.31 0.3 -50 Thi Ck1 5 7.8 32.9 0.18 0.3 -51 Thi Ck1 6 7.8 32.9 0.18 0.0 - -</div></pre> - </div> - <div class="span4 sidebar"> - <!-- <ul> - <li>FOCUS_GW_scenarios_2012</li> - </ul> - <ul> - - </ul> --> - - - - - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/docs/GUS.html b/docs/GUS.html deleted file mode 100644 index cb4e10e..0000000 --- a/docs/GUS.html +++ /dev/null @@ -1,171 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>GUS. pfm 0.3-8</title> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=" -Johannes Ranke -"> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">pfm 0.3-8</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> - </div> - </div> -</div> - - - <div class="container"> - <header> - - </header> - - <h1>Groundwater ubiquity score based on Gustafson (1989)</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><span class="functioncall"><a href='GUS.html'>GUS</a></span><span class="keyword">(</span><span class="symbol">...</span><span class="keyword">)</span> - -<span class="comment"># S3 method for numeric</span> -<span class="functioncall"><a href='GUS.html'>GUS</a></span><span class="keyword">(</span><span class="symbol">DT50</span><span class="keyword">,</span> <span class="symbol">Koc</span><span class="keyword">,</span> <span class="symbol">...</span><span class="keyword">)</span> - -<span class="comment"># S3 method for chent</span> -<span class="functioncall"><a href='GUS.html'>GUS</a></span><span class="keyword">(</span><span class="symbol">chent</span><span class="keyword">,</span> <span class="argument">degradation_value</span> <span class="argument">=</span> <span class="string">"DT50ref"</span><span class="keyword">,</span> - <span class="argument">lab_field</span> <span class="argument">=</span> <span class="string">"laboratory"</span><span class="keyword">,</span> <span class="argument">redox</span> <span class="argument">=</span> <span class="string">"aerobic"</span><span class="keyword">,</span> <span class="argument">sorption_value</span> <span class="argument">=</span> <span class="string">"Kfoc"</span><span class="keyword">,</span> - <span class="argument">degradation_aggregator</span> <span class="argument">=</span> <span class="symbol">geomean</span><span class="keyword">,</span> <span class="argument">sorption_aggregator</span> <span class="argument">=</span> <span class="symbol">geomean</span><span class="keyword">,</span> <span class="symbol">...</span><span class="keyword">)</span> - -<span class="comment"># S3 method for GUS_result</span> -<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/print'>print</a></span><span class="keyword">(</span><span class="symbol">x</span><span class="keyword">,</span> <span class="symbol">...</span><span class="keyword">,</span> <span class="argument">digits</span> <span class="argument">=</span> <span class="number">1</span><span class="keyword">)</span></pre> - - <h2>Arguments</h2> - <dl> - <dt>...</dt> - <dd>Included in the generic to allow for further arguments later. Therefore -this also had to be added to the specific methods.</dd> - <dt>DT50</dt> - <dd>Half-life of the chemical in soil. Should be a field -half-life according to Gustafson (1989). However, leaching to the sub-soil -can not completely be excluded in field dissipation experiments and Gustafson -did not refer to any normalisation procedure, but says the field study should -be conducted under use conditions.</dd> - <dt>Koc</dt> - <dd>The sorption constant normalised to organic carbon. Gustafson -does not mention the nonlinearity of the sorption constant commonly -found and usually described by Freundlich sorption, therefore it is -unclear at which reference concentration the Koc should be observed -(and if the reference concentration would be in soil or in porewater).</dd> - <dt>chent</dt> - <dd>If a chent is given with appropriate information present in its -chyaml field, this information is used, with defaults specified below.</dd> - <dt>degradation_value</dt> - <dd>Which of the available degradation values should -be used?</dd> - <dt>lab_field</dt> - <dd>Should laboratory or field half-lives be used? This -defaults to lab in this implementation, in order to avoid -double-accounting for mobility. If comparability with the original GUS -values given by Gustafson (1989) is desired, non-normalised first-order -field half-lives obtained under actual use conditions should be used.</dd> - <dt>redox</dt> - <dd>Aerobic or anaerobic degradation data</dd> - <dt>sorption_value</dt> - <dd>Which of the available sorption values should be used? -Defaults to Kfoc as this is what is generally available from the European -pesticide peer review process. These values generally use a reference -concentration of 1 mg/L in porewater, that means they would be expected to -be Koc values at a concentration of 1 mg/L in the water phase.</dd> - <dt>degradation_aggregator</dt> - <dd>Function for aggregating half-lives</dd> - <dt>sorption_aggregator</dt> - <dd>Function for aggregation Koc values</dd> - <dt>x</dt> - <dd>An object of class GUS_result to be printed</dd> - <dt>digits</dt> - <dd>The number of digits used in the print method</dd> - </dl> - - <div class="Value"> - <h2>Value</h2> - - <p><dl> -A list with the DT50 and Koc used as well as the resulting score - of class GUS_result -</dl></p> - - </div> - - <div class="Description"> - <h2>Description</h2> - - <p>The groundwater ubiquity score GUS is calculated according to -the following equation -$$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$</p> - - </div> - - <div class="References"> - <h2>References</h2> - - <p>Gustafson, David I. (1989) Groundwater ubiquity score: a simple -method for assessing pesticide leachability. <em>Environmental -toxicology and chemistry</em> <b>8</b>(4) 339–57.</p> - - </div> - </div> - <div class="span4 sidebar"> - <!-- <ul> - <li>GUS</li><li>GUS.chent</li><li>GUS.numeric</li><li>print.GUS_result</li> - </ul> - <ul> - - </ul> --> - - - - <h2>Author</h2> - -Johannes Ranke - - - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/docs/PEC_soil.html b/docs/PEC_soil.html deleted file mode 100644 index 9a10757..0000000 --- a/docs/PEC_soil.html +++ /dev/null @@ -1,231 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>PEC_soil. pfm 0.3-8</title> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=" -Johannes Ranke -"> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">pfm 0.3-8</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> - </div> - </div> -</div> - - - <div class="container"> - <header> - - </header> - - <h1>Calculate predicted environmental concentrations in soil</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><span class="functioncall"><a href='PEC_soil.html'>PEC_soil</a></span><span class="keyword">(</span><span class="symbol">rate</span><span class="keyword">,</span> <span class="argument">rate_units</span> <span class="argument">=</span> <span class="string">"g/ha"</span><span class="keyword">,</span> <span class="argument">interception</span> <span class="argument">=</span> <span class="number">0</span><span class="keyword">,</span> <span class="argument">mixing_depth</span> <span class="argument">=</span> <span class="number">5</span><span class="keyword">,</span> - <span class="argument">PEC_units</span> <span class="argument">=</span> <span class="string">"mg/kg"</span><span class="keyword">,</span> <span class="argument">PEC_pw_units</span> <span class="argument">=</span> <span class="string">"mg/L"</span><span class="keyword">,</span> <span class="argument">interval</span> <span class="argument">=</span> <span class="number">NA</span><span class="keyword">,</span> - <span class="argument">n_periods</span> <span class="argument">=</span> <span class="number">Inf</span><span class="keyword">,</span> <span class="argument">tillage_depth</span> <span class="argument">=</span> <span class="number">20</span><span class="keyword">,</span> <span class="argument">chent</span> <span class="argument">=</span> <span class="number">NA</span><span class="keyword">,</span> <span class="argument">DT50</span> <span class="argument">=</span> <span class="number">NA</span><span class="keyword">,</span> - <span class="argument">Koc</span> <span class="argument">=</span> <span class="number">NA</span><span class="keyword">,</span> <span class="argument">Kom</span> <span class="argument">=</span> <span class="symbol">Koc</span><span class="keyword">/</span><span class="number">1.724</span><span class="keyword">,</span> <span class="argument">t_avg</span> <span class="argument">=</span> <span class="number">0</span><span class="keyword">,</span> <span class="argument">scenarios</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"default"</span><span class="keyword">,</span> - <span class="string">"EFSA_2015"</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">porewater</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">)</span></pre> - - <h2>Arguments</h2> - <dl> - <dt>rate</dt> - <dd>Application rate in units specified below</dd> - <dt>rate_units</dt> - <dd>Defaults to g/ha</dd> - <dt>interception</dt> - <dd>The fraction of the application rate that does not reach the soil</dd> - <dt>mixing_depth</dt> - <dd>Mixing depth in cm</dd> - <dt>PEC_units</dt> - <dd>Requested units for the calculated PEC. Only mg/kg currently supported</dd> - <dt>PEC_pw_units</dt> - <dd>Only mg/L currently supported</dd> - <dt>interval</dt> - <dd>Period of the deeper mixing, defaults to 365, which is a year if -rate units are in days</dd> - <dt>n_periods</dt> - <dd>Number of periods to be considered for long term PEC calculations</dd> - <dt>tillage_depth</dt> - <dd>Periodic (see interval) deeper mixing in cm</dd> - <dt>chent</dt> - <dd>An optional chent object holding substance specific information. Can -also be a name for the substance as a character string</dd> - <dt>DT50</dt> - <dd>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</dd> - <dt>Koc</dt> - <dd>If specified, overrides Koc endpoints from a chent object</dd> - <dt>Kom</dt> - <dd>Calculated from Koc by default, but can explicitly be specified -as Kom here</dd> - <dt>t_avg</dt> - <dd>Averaging times for time weighted average concentrations</dd> - <dt>scenarios</dt> - <dd>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), -and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also -model and scenario adjustment factors from the EFSA guidance are used.</dd> - <dt>porewater</dt> - <dd>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).</dd> - </dl> - - <div class="Value"> - <h2>Value</h2> - - <p><dl> -The predicted concentration in soil -</dl></p> - - </div> - - <div class="Description"> - <h2>Description</h2> - - <p>This is a basic calculation of a contaminant concentration in bulk soil -based on complete, instantaneous mixing. If an interval is given, an -attempt is made at calculating a long term maximum concentration using -the concepts layed out for example in the PPR panel opinion (EFSA 2012).</p> - - </div> - - <div class="Details"> - <h2>Details</h2> - - <p>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 (PPR panel 2012), only temperature correction using the -Arrhenius equation is performed.</p> - - <p>Total soil and porewater PEC values for the scenarios as defined in the EFSA -guidance (2015, p. 13) can easily be calculated.</p> - - </div> - - <div class="Note"> - <h2>Note</h2> - - <p>If temperature information is available in the selected scenarios, as - 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'.</p> - - </div> - - <div class="References"> - <h2>References</h2> - - <p>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 - concentrations of plant protection products in soil. <em>EFSA Journal</em> - <b>10</b>(2) 2562, doi:10.2903/j.efsa.2012.2562</p> - - <p>EFSA (European Food Safety Authority) (2015) EFSA guidance document for - predicting environmental concentrations of active substances of plant - protection products and transformation products of these active substances - in soil. <em>EFSA Journal</em> <b>13</b>(4) 4093 - doi:10.2903/j.efsa.2015.4093</p> - - </div> - - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'><span class="functioncall"><a href='PEC_soil.html'>PEC_soil</a></span><span class="keyword">(</span><span class="number">100</span><span class="keyword">,</span> <span class="argument">interception</span> <span class="argument">=</span> <span class="number">0.25</span><span class="keyword">)</span></div> -<div class='output'> scenario -t_avg default - 0 0.1 -</div> -<div class='input'> -<span class="comment"># This is example 1 starting at p. 79 of the EFSA guidance (2015)</span> -<span class="functioncall"><a href='PEC_soil.html'>PEC_soil</a></span><span class="keyword">(</span><span class="number">1000</span><span class="keyword">,</span> <span class="argument">interval</span> <span class="argument">=</span> <span class="number">365</span><span class="keyword">,</span> <span class="argument">DT50</span> <span class="argument">=</span> <span class="number">250</span><span class="keyword">,</span> <span class="argument">t_avg</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">0</span><span class="keyword">,</span> <span class="number">21</span><span class="keyword">)</span><span class="keyword">,</span> - <span class="argument">scenarios</span> <span class="argument">=</span> <span class="string">"EFSA_2015"</span><span class="keyword">)</span></div> -<div class='output'> scenario -t_avg CTN CTC CTS - 0 21.96827 11.53750 9.145259 - 21 21.78517 11.40701 9.017370 -</div> -<div class='input'><span class="functioncall"><a href='PEC_soil.html'>PEC_soil</a></span><span class="keyword">(</span><span class="number">1000</span><span class="keyword">,</span> <span class="argument">interval</span> <span class="argument">=</span> <span class="number">365</span><span class="keyword">,</span> <span class="argument">DT50</span> <span class="argument">=</span> <span class="number">250</span><span class="keyword">,</span> <span class="argument">t_av</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">0</span><span class="keyword">,</span> <span class="number">21</span><span class="keyword">)</span><span class="keyword">,</span> - <span class="argument">Kom</span> <span class="argument">=</span> <span class="number">1000</span><span class="keyword">,</span> <span class="argument">scenarios</span> <span class="argument">=</span> <span class="string">"EFSA_2015"</span><span class="keyword">,</span> <span class="argument">porewater</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span></div> -<div class='output'> scenario -t_avg CLN CLC CLS - 0 0.7589401 0.6674322 0.9147861 - 21 0.7506036 0.6590345 0.8987279 -</div> -<div class='input'> -<span class="comment"># The following is from example 4 starting at p. 85 of the EFSA guidance (2015)</span> -<span class="comment"># Metabolite M2</span> -<span class="comment"># Calculate total and porewater soil concentrations for tier 1 scenarios</span> -<span class="comment"># Relative molar mass is 100/300, formation fraction is 0.7 * 1</span> -<span class="symbol">results_pfm</span> <span class="assignement"><-</span> <span class="functioncall"><a href='PEC_soil.html'>PEC_soil</a></span><span class="keyword">(</span><span class="number">100</span><span class="keyword">/</span><span class="number">300</span> <span class="keyword">*</span> <span class="number">0.7</span> <span class="keyword">*</span> <span class="number">1</span> <span class="keyword">*</span> <span class="number">1000</span><span class="keyword">,</span> <span class="argument">interval</span> <span class="argument">=</span> <span class="number">365</span><span class="keyword">,</span> <span class="argument">DT50</span> <span class="argument">=</span> <span class="number">250</span><span class="keyword">,</span> <span class="argument">t_avg</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">0</span><span class="keyword">,</span> <span class="number">21</span><span class="keyword">)</span><span class="keyword">,</span> - <span class="argument">scenarios</span> <span class="argument">=</span> <span class="string">"EFSA_2015"</span><span class="keyword">)</span> -<span class="symbol">results_pfm_pw</span> <span class="assignement"><-</span> <span class="functioncall"><a href='PEC_soil.html'>PEC_soil</a></span><span class="keyword">(</span><span class="number">100</span><span class="keyword">/</span><span class="number">300</span> <span class="keyword">*</span> <span class="number">0.7</span> <span class="keyword">*</span> <span class="number">1000</span><span class="keyword">,</span> <span class="argument">interval</span> <span class="argument">=</span> <span class="number">365</span><span class="keyword">,</span> <span class="argument">DT50</span> <span class="argument">=</span> <span class="number">250</span><span class="keyword">,</span> <span class="argument">t_av</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">0</span><span class="keyword">,</span> <span class="number">21</span><span class="keyword">)</span><span class="keyword">,</span> - <span class="argument">Kom</span> <span class="argument">=</span> <span class="number">100</span><span class="keyword">,</span> <span class="argument">scenarios</span> <span class="argument">=</span> <span class="string">"EFSA_2015"</span><span class="keyword">,</span> <span class="argument">porewater</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span></div></pre> - </div> - <div class="span4 sidebar"> - <!-- <ul> - <li>PEC_soil</li> - </ul> - <ul> - - </ul> --> - - - - <h2>Author</h2> - -Johannes Ranke - - - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/docs/PEC_sw_drainage_UK.html b/docs/PEC_sw_drainage_UK.html deleted file mode 100644 index 9c28968..0000000 --- a/docs/PEC_sw_drainage_UK.html +++ /dev/null @@ -1,127 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>PEC_sw_drainage_UK. pfm 0.3-8</title> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=" -Johannes Ranke -"> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">pfm 0.3-8</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> - </div> - </div> -</div> - - - <div class="container"> - <header> - - </header> - - <h1>Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><span class="functioncall"><a href='PEC_sw_drainage_UK.html'>PEC_sw_drainage_UK</a></span><span class="keyword">(</span><span class="symbol">rate</span><span class="keyword">,</span> <span class="argument">interception</span> <span class="argument">=</span> <span class="number">0</span><span class="keyword">,</span> <span class="symbol">Koc</span><span class="keyword">,</span> <span class="argument">latest_application</span> <span class="argument">=</span> NULL<span class="keyword">,</span> - <span class="argument">soil_DT50</span> <span class="argument">=</span> NULL<span class="keyword">,</span> <span class="argument">model</span> <span class="argument">=</span> NULL<span class="keyword">,</span> <span class="argument">model_parms</span> <span class="argument">=</span> NULL<span class="keyword">)</span></pre> - - <h2>Arguments</h2> - <dl> - <dt>rate</dt> - <dd>Application rate in g/ha</dd> - <dt>interception</dt> - <dd>The fraction of the application rate that does not reach the soil</dd> - <dt>Koc</dt> - <dd>The sorption coefficient normalised to organic carbon in L/kg</dd> - <dt>latest_application</dt> - <dd>Latest application date, formatted as e.g. "01 July"</dd> - <dt>soil_DT50</dt> - <dd>Soil degradation half-life, if SFO kinetics are to be used</dd> - <dt>model</dt> - <dd>The soil degradation model to be used. Either one of "FOMC", -"DFOP", "HS", or "IORE", or an mkinmod object</dd> - <dt>model_parms</dt> - <dd>A named numeric vector containing the model parameters</dd> - </dl> - - <div class="Value"> - <h2>Value</h2> - - <p><dl> -The predicted concentration in surface water in µg/L -</dl></p> - - </div> - - <div class="Description"> - <h2>Description</h2> - - <p>This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet -published on the CRC website</p> - - </div> - - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'><span class="functioncall"><a href='PEC_sw_drainage_UK.html'>PEC_sw_drainage_UK</a></span><span class="keyword">(</span><span class="number">150</span><span class="keyword">,</span> <span class="argument">Koc</span> <span class="argument">=</span> <span class="number">100</span><span class="keyword">)</span></div> -<div class='output'>[1] 8.076923 -</div></pre> - </div> - <div class="span4 sidebar"> - <!-- <ul> - <li>PEC_sw_drainage_UK</li> - </ul> - <ul> - - </ul> --> - - - - <h2>Author</h2> - -Johannes Ranke - - - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/docs/PEC_sw_drift.html b/docs/PEC_sw_drift.html deleted file mode 100644 index 3654d2f..0000000 --- a/docs/PEC_sw_drift.html +++ /dev/null @@ -1,134 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>PEC_sw_drift. pfm 0.3-8</title> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=" -Johannes Ranke -"> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">pfm 0.3-8</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> - </div> - </div> -</div> - - - <div class="container"> - <header> - - </header> - - <h1>Calculate predicted environmental concentrations in surface water due to drift</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><span class="functioncall"><a href='PEC_sw_drift.html'>PEC_sw_drift</a></span><span class="keyword">(</span><span class="symbol">rate</span><span class="keyword">,</span> <span class="argument">applications</span> <span class="argument">=</span> <span class="number">1</span><span class="keyword">,</span> <span class="argument">water_depth</span> <span class="argument">=</span> <span class="number">30</span><span class="keyword">,</span> - <span class="argument">drift_percentages</span> <span class="argument">=</span> NULL<span class="keyword">,</span> <span class="argument">drift_data</span> <span class="argument">=</span> <span class="string">"JKI"</span><span class="keyword">,</span> <span class="argument">crop</span> <span class="argument">=</span> <span class="string">"Ackerbau"</span><span class="keyword">,</span> - <span class="argument">distances</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">1</span><span class="keyword">,</span> <span class="number">5</span><span class="keyword">,</span> <span class="number">10</span><span class="keyword">,</span> <span class="number">20</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">rate_units</span> <span class="argument">=</span> <span class="string">"g/ha"</span><span class="keyword">,</span> <span class="argument">PEC_units</span> <span class="argument">=</span> <span class="string">"µg/L"</span><span class="keyword">)</span></pre> - - <h2>Arguments</h2> - <dl> - <dt>rate</dt> - <dd>Application rate in units specified below</dd> - <dt>applications</dt> - <dd>Number of applications for selection of drift percentile</dd> - <dt>water_depth</dt> - <dd>Depth of the water body in cm</dd> - <dt>drift_percentages</dt> - <dd>Percentage drift values for which to calculate PECsw. -'drift_data' and 'distances' if not NULL.</dd> - <dt>drift_data</dt> - <dd>Source of drift percentage data</dd> - <dt>crop</dt> - <dd>Crop name (use German names for JKI data), defaults to "Ackerbau"</dd> - <dt>distances</dt> - <dd>The distances in m for which to get PEC values</dd> - <dt>rate_units</dt> - <dd>Defaults to g/ha</dd> - <dt>PEC_units</dt> - <dd>Requested units for the calculated PEC. Only µg/L currently supported</dd> - </dl> - - <div class="Value"> - <h2>Value</h2> - - <p><dl> -The predicted concentration in surface water -</dl></p> - - </div> - - <div class="Description"> - <h2>Description</h2> - - <p>This is a basic, vectorised form of a simple calculation of a contaminant -concentration in surface water based on complete, instantaneous mixing -with input via spray drift.</p> - - </div> - - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'><span class="functioncall"><a href='PEC_sw_drift.html'>PEC_sw_drift</a></span><span class="keyword">(</span><span class="number">100</span><span class="keyword">)</span></div> -<div class='output'> 1 m 5 m 10 m 20 m -0.92333333 0.19000000 0.09666667 0.05000000 -</div></pre> - </div> - <div class="span4 sidebar"> - <!-- <ul> - <li>PEC_sw_drift</li> - </ul> - <ul> - - </ul> --> - - - - <h2>Author</h2> - -Johannes Ranke - - - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/docs/PEC_sw_sed.html b/docs/PEC_sw_sed.html deleted file mode 100644 index 8161eda..0000000 --- a/docs/PEC_sw_sed.html +++ /dev/null @@ -1,131 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>PEC_sw_sed. pfm 0.3-8</title> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=" -Johannes Ranke -"> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">pfm 0.3-8</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> - </div> - </div> -</div> - - - <div class="container"> - <header> - - </header> - - <h1>Calculate predicted environmental concentrations in sediment from surface -water concentrations</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><span class="functioncall"><a href='PEC_sw_sed.html'>PEC_sw_sed</a></span><span class="keyword">(</span><span class="symbol">PEC_sw</span><span class="keyword">,</span> <span class="argument">percentage</span> <span class="argument">=</span> <span class="number">100</span><span class="keyword">,</span> <span class="argument">method</span> <span class="argument">=</span> <span class="string">"percentage"</span><span class="keyword">,</span> - <span class="argument">sediment_depth</span> <span class="argument">=</span> <span class="number">5</span><span class="keyword">,</span> <span class="argument">water_depth</span> <span class="argument">=</span> <span class="number">30</span><span class="keyword">,</span> <span class="argument">sediment_density</span> <span class="argument">=</span> <span class="number">1.3</span><span class="keyword">,</span> - <span class="argument">PEC_sed_units</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"µg/kg"</span><span class="keyword">,</span> <span class="string">"mg/kg"</span><span class="keyword">)</span><span class="keyword">)</span></pre> - - <h2>Arguments</h2> - <dl> - <dt>PEC_sw</dt> - <dd>Numeric vector or matrix of surface water concentrations in µg/L for -which the corresponding sediment concentration is to be estimated</dd> - <dt>percentage</dt> - <dd>The percentage in sediment, used for the percentage method</dd> - <dt>method</dt> - <dd>The method used for the calculation</dd> - <dt>sediment_depth</dt> - <dd>Depth of the sediment layer</dd> - <dt>water_depth</dt> - <dd>Depth of the water body in cm</dd> - <dt>sediment_density</dt> - <dd>The density of the sediment in L/kg (equivalent to -g/cm3)</dd> - <dt>PEC_sed_units</dt> - <dd>The units of the estimated sediment PEC value</dd> - </dl> - - <div class="Value"> - <h2>Value</h2> - - <p><dl> -The predicted concentration in sediment -</dl></p> - - </div> - - <div class="Description"> - <h2>Description</h2> - - <p>The method 'percentage' is equivalent to what is used in the CRD spreadsheet -PEC calculator</p> - - </div> - - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'><span class="functioncall"><a href='PEC_sw_sed.html'>PEC_sw_sed</a></span><span class="keyword">(</span><span class="functioncall"><a href='PEC_sw_drift.html'>PEC_sw_drift</a></span><span class="keyword">(</span><span class="number">100</span><span class="keyword">,</span> <span class="argument">distances</span> <span class="argument">=</span> <span class="number">1</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">percentage</span> <span class="argument">=</span> <span class="number">50</span><span class="keyword">)</span></div> -<div class='output'> 1 m -2.130769 -</div></pre> - </div> - <div class="span4 sidebar"> - <!-- <ul> - <li>PEC_sw_sed</li> - </ul> - <ul> - - </ul> --> - - - - <h2>Author</h2> - -Johannes Ranke - - - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/docs/SFO_actual_twa.html b/docs/SFO_actual_twa.html deleted file mode 100644 index 053457d..0000000 --- a/docs/SFO_actual_twa.html +++ /dev/null @@ -1,126 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>SFO_actual_twa. pfm 0.3-8</title> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=" -Johannes Ranke -"> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">pfm 0.3-8</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> - </div> - </div> -</div> - - - <div class="container"> - <header> - - </header> - - <h1>Actual and maximum moving window time average concentrations for SFO kinetics</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><span class="functioncall"><a href='SFO_actual_twa.html'>SFO_actual_twa</a></span><span class="keyword">(</span><span class="argument">DT50</span> <span class="argument">=</span> <span class="number">1000</span><span class="keyword">,</span> <span class="argument">times</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">0</span><span class="keyword">,</span> <span class="number">1</span><span class="keyword">,</span> <span class="number">2</span><span class="keyword">,</span> <span class="number">4</span><span class="keyword">,</span> <span class="number">7</span><span class="keyword">,</span> <span class="number">14</span><span class="keyword">,</span> <span class="number">21</span><span class="keyword">,</span> <span class="number">28</span><span class="keyword">,</span> <span class="number">42</span><span class="keyword">,</span> <span class="number">50</span><span class="keyword">,</span> - <span class="number">100</span><span class="keyword">)</span><span class="keyword">)</span></pre> - - <h2>Arguments</h2> - <dl> - <dt>DT50</dt> - <dd>The half-life.</dd> - <dt>times</dt> - <dd>The output times, and window sizes for time weighted average concentrations</dd> - </dl> - - <div class="Source"> - <h2>Source</h2> - - <p>FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation - Kinetics from Environmental Fate Studies on Pesticides in EU Registratin, Version 1.1, - 18 December 2014, p. 251</p> - - </div> - - <div class="Description"> - <h2>Description</h2> - - <p>Actual and maximum moving window time average concentrations for SFO kinetics</p> - - </div> - - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'><span class="functioncall"><a href='SFO_actual_twa.html'>SFO_actual_twa</a></span><span class="keyword">(</span><span class="number">10</span><span class="keyword">)</span></div> -<div class='output'> actual twa -0 1.0000000000 NaN -1 0.9330329915 0.9661297 -2 0.8705505633 0.9337803 -4 0.7578582833 0.8733416 -7 0.6155722067 0.7923030 -14 0.3789291416 0.6400113 -21 0.2332582479 0.5267498 -28 0.1435872944 0.4412651 -42 0.0544094102 0.3248093 -50 0.0312500000 0.2795222 -100 0.0009765625 0.1441286 -</div></pre> - </div> - <div class="span4 sidebar"> - <!-- <ul> - <li>SFO_actual_twa</li> - </ul> - <ul> - - </ul> --> - - - - <h2>Author</h2> - -Johannes Ranke - - - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/docs/SSLRC_mobility_classification.html b/docs/SSLRC_mobility_classification.html deleted file mode 100644 index 7a57c50..0000000 --- a/docs/SSLRC_mobility_classification.html +++ /dev/null @@ -1,119 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>SSLRC_mobility_classification. pfm 0.3-8</title> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=" -Johannes Ranke -"> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">pfm 0.3-8</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> - </div> - </div> -</div> - - - <div class="container"> - <header> - - </header> - - <h1>Determine the SSLRC mobility classification for a chemical substance from its Koc</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><span class="functioncall"><a href='SSLRC_mobility_classification.html'>SSLRC_mobility_classification</a></span><span class="keyword">(</span><span class="symbol">Koc</span><span class="keyword">)</span></pre> - - <h2>Arguments</h2> - <dl> - <dt>Koc</dt> - <dd>The sorption coefficient normalised to organic carbon in L/kg</dd> - </dl> - - <div class="Value"> - <h2>Value</h2> - - <p><dl> -A list containing the classification and the percentage of the - compound transported per 10 mm drain water -</dl></p> - - </div> - - <div class="Description"> - <h2>Description</h2> - - <p>This implements the method specified in the UK data requirements handbook and was -checked against the spreadsheet published on the CRC website</p> - - </div> - - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'><span class="functioncall"><a href='SSLRC_mobility_classification.html'>SSLRC_mobility_classification</a></span><span class="keyword">(</span><span class="number">100</span><span class="keyword">)</span></div> -<div class='output'>$`Mobility classification` -[1] "Moderately mobile" - -$`Percentage drained per mm of drain water` -[1] 0.7 - -</div></pre> - </div> - <div class="span4 sidebar"> - <!-- <ul> - <li>SSLRC_mobility_classification</li> - </ul> - <ul> - - </ul> --> - - - - <h2>Author</h2> - -Johannes Ranke - - - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/docs/TOXSWA_cwa.html b/docs/TOXSWA_cwa.html deleted file mode 100644 index 561af84..0000000 --- a/docs/TOXSWA_cwa.html +++ /dev/null @@ -1,179 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>TOXSWA_cwa. pfm 0.3-8</title> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=""> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">pfm 0.3-8</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> - </div> - </div> -</div> - - - <div class="container"> - <header> - - </header> - - <h1>R6 class for holding TOXSWA cwa concentration data and associated statistics</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><span class="symbol">TOXSWA_cwa</span></pre> - - <div class="Format"> - <h2>Format</h2> - - <p>An <code><a href='http://www.rdocumentation.org/packages/R6/topics/R6Class'>R6Class</a></code> generator object.</p> - - </div> - - <div class="Description"> - <h2>Description</h2> - - <p>An R6 class for holding TOXSWA cwa concentration data and some associated statistics. -Usually, an instance of this class will be generated by <code><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></code>.</p> - - </div> - - <div class="Fields"> - <h2>Fields</h2> - - <p></p> - - <p><dl> -<dt><code>filename</code></dt><dd>Length one character vector.</dd></p> - - <p><dt><code>basedir</code></dt><dd>Length one character vector.</dd></p> - - <p><dt><code>segment</code></dt><dd>Length one integer, specifying for which segment the cwa data were read.</dd></p> - - <p><dt><code>cwas</code></dt><dd>Dataframe holding the concentrations.</dd></p> - - <p><dt><code>events</code></dt><dd>List of dataframes holding the event statistics for each threshold.</dd></p> - - <p><dt><code>windows</code></dt><dd>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.</dd></p> - - <p></dl></p> - - </div> - - <div class="Methods"> - <h2>Methods</h2> - - <p></p> - - <p><dl> - <dt><code>get_events(threshold, total = FALSE)</code></dt><dd> - Populate a datataframe with event information for the specified threshold value - in µg/L. If <code>total = TRUE</code>, the total concentration including the amount - adsorbed to suspended matter will be used. The resulting dataframe is stored in the - <code>events</code> field of the object. - </dd></p> - - <p><dt><code>moving_windows(windows, total = FALSE)</code></dt><dd> - Add to the <code>windows</code> field described above. - Again, if <code>total = TRUE</code>, the total concentration including the amount - adsorbed to suspended matter will be used. - </dd></p> - - <p></dl></p> - - <p></p> - - </div> - - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'><span class="symbol">H_sw_R1_stream</span> <span class="assignement"><-</span> <span class="functioncall"><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span><span class="keyword">(</span><span class="string">"00003s_pa.cwa"</span><span class="keyword">,</span> - <span class="argument">basedir</span> <span class="argument">=</span> <span class="string">"SwashProjects/project_H_sw/TOXSWA"</span><span class="keyword">,</span> - <span class="argument">zipfile</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/devtools/topics/system.file'>system.file</a></span><span class="keyword">(</span><span class="string">"testdata/SwashProjects.zip"</span><span class="keyword">,</span> - <span class="argument">package</span> <span class="argument">=</span> <span class="string">"pfm"</span><span class="keyword">)</span><span class="keyword">)</span> -<span class="symbol">H_sw_R1_stream</span><span class="keyword">$</span><span class="functioncall">get_events</span><span class="keyword">(</span><span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">2</span><span class="keyword">,</span> <span class="number">10</span><span class="keyword">)</span><span class="keyword">)</span> -<span class="symbol">H_sw_R1_stream</span><span class="keyword">$</span><span class="functioncall">moving_windows</span><span class="keyword">(</span><span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">7</span><span class="keyword">,</span> <span class="number">21</span><span class="keyword">)</span><span class="keyword">)</span> -<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/print'>print</a></span><span class="keyword">(</span><span class="symbol">H_sw_R1_stream</span><span class="keyword">)</span></div> -<div class='output'><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 -</div></pre> - </div> - <div class="span4 sidebar"> - <!-- <ul> - <li>TOXSWA_cwa</li> - </ul> - <ul> - <li>data</li> - </ul> --> - - - - - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/docs/authors.html b/docs/authors.html new file mode 100644 index 0000000..0830cef --- /dev/null +++ b/docs/authors.html @@ -0,0 +1,97 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Authors • pfm</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="pkgdown.css" rel="stylesheet"> +<script src="jquery.sticky-kit.min.js"></script> +<script src="pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container template-authors"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="index.html">pfm</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="contents col-md-12"> + <div class="page-header"> + <h1>Authors</h1> + </div> + + <ul class="list-unstyled"> + <li> + <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder. + </p> + </li> + </ul> + + </div> + +</div> + + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/css/bootstrap-responsive.css b/docs/css/bootstrap-responsive.css deleted file mode 100644 index 06e55c0..0000000 --- a/docs/css/bootstrap-responsive.css +++ /dev/null @@ -1,815 +0,0 @@ -/*! - * Bootstrap Responsive v2.0.4 - * - * Copyright 2012 Twitter, Inc - * Licensed under the Apache License v2.0 - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Designed and built with all the love in the world @twitter by @mdo and @fat. - */ - -.clearfix { - *zoom: 1; -} - -.clearfix:before, -.clearfix:after { - display: table; - content: ""; -} - -.clearfix:after { - clear: both; -} - -.hide-text { - font: 0/0 a; - color: transparent; - text-shadow: 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-(Obstbau frueh, spaet).</p> - - </div> - - <div class="Source"> - <h2>Source</h2> - - <p>JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved -from -http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html -on 2015-06-11</p> - - </div> - - <div class="Description"> - <h2>Description</h2> - - <p>Deposition from spray drift expressed as percent of the applied dose as -published by the German Julius-Kühn Institute (JKI).</p> - - </div> - - <div class="Details"> - <h2>Details</h2> - - <p>The data were extracted from the spreadsheet cited below using the R code -given in the example section. The spreadsheet is not included in the package -as its licence is not clear.</p> - - </div> - - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'> -<span class="comment">## Not run: ------------------------------------</span> -<span class="comment"># # This is the code that was used to extract the data</span> -<span class="comment"># library(readxl)</span> -<span class="comment"># abdrift_path <- "inst/extdata/Tabelle der Abdrifteckwerte.xls"</span> -<span class="comment"># JKI_crops <- c("Ackerbau", "Obstbau frueh", "Obstbau spaet")</span> -<span class="comment"># names(JKI_crops) <- c("Field crops", "Pome/stone fruit, early", "Pome/stone fruit, late")</span> -<span class="comment"># drift_data_JKI <- list()</span> -<span class="comment"># </span> -<span class="comment"># for (n in 1:8) {</span> -<span class="comment"># drift_data_raw <- read_excel(abdrift_path, sheet = n + 1, skip = 2)</span> -<span class="comment"># drift_data <- as.matrix(drift_data_raw[1:9, 2:4]) </span> -<span class="comment"># dimnames(drift_data) <- list(distance = as.integer(drift_data_raw[1:9, 1]),</span> -<span class="comment"># crop = JKI_crops)</span> -<span class="comment"># drift_data_JKI[[n]] <- drift_data</span> -<span class="comment"># }</span> -<span class="comment"># save(drift_data_JKI, file = "data/drift_data_JKI.RData")</span> -<span class="comment">## ---------------------------------------------</span> - -<span class="comment"># And this is the resulting data</span> -<span class="symbol">drift_data_JKI</span></div> -<div class='output'>[[1]] - crop -distance Ackerbau Obstbau frueh Obstbau spaet - 1 2.77 NA NA - 3 NA 29.20 15.73 - 5 0.57 19.89 8.41 - 10 0.29 11.81 3.60 - 15 0.20 5.55 1.81 - 20 0.15 2.77 1.09 - 30 0.10 1.04 0.54 - 40 0.07 0.52 0.32 - 50 0.06 0.30 0.22 - -[[2]] - crop -distance Ackerbau Obstbau frueh Obstbau spaet - 1 2.38 NA NA - 3 NA 25.53 12.13 - 5 0.47 16.87 6.81 - 10 0.24 9.61 3.11 - 15 0.16 5.61 1.58 - 20 0.12 2.59 0.90 - 30 0.08 0.87 0.40 - 40 0.06 0.40 0.23 - 50 0.05 0.22 0.15 - -[[3]] - crop -distance Ackerbau Obstbau frueh Obstbau spaet - 1 2.01 NA NA - 3 NA 23.96 11.01 - 5 0.41 15.79 6.04 - 10 0.20 8.96 2.67 - 15 0.14 4.24 1.39 - 20 0.10 2.01 0.80 - 30 0.07 0.70 0.36 - 40 0.05 0.33 0.21 - 50 0.04 0.19 0.13 - -[[4]] - crop -distance Ackerbau Obstbau frueh Obstbau spaet - 1 1.85 NA NA - 3 NA 23.61 10.12 - 5 0.38 15.42 5.60 - 10 0.19 8.66 2.50 - 15 0.13 4.01 1.28 - 20 0.10 1.89 0.75 - 30 0.06 0.66 0.35 - 40 0.05 0.31 0.20 - 50 0.04 0.17 0.13 - -[[5]] - crop -distance Ackerbau Obstbau frueh Obstbau spaet - 1 1.75 NA NA - 3 NA 23.12 9.74 - 5 0.36 15.06 5.41 - 10 0.18 8.42 2.43 - 15 0.12 3.83 1.24 - 20 0.09 1.81 0.72 - 30 0.06 0.63 0.34 - 40 0.05 0.30 0.20 - 50 0.04 0.17 0.13 - -[[6]] - crop -distance Ackerbau Obstbau frueh Obstbau spaet - 1 1.64 NA NA - 3 NA 22.76 9.21 - 5 0.34 14.64 5.18 - 10 0.17 8.04 2.38 - 15 0.11 3.71 1.20 - 20 0.09 1.75 0.68 - 30 0.06 0.61 0.31 - 40 0.04 0.29 0.17 - 50 0.03 0.16 0.11 - -[[7]] - crop -distance Ackerbau Obstbau frueh Obstbau spaet - 1 1.61 NA NA - 3 NA 22.69 9.10 - 5 0.33 14.45 5.11 - 10 0.17 7.83 2.33 - 15 0.11 3.62 1.20 - 20 0.08 1.71 0.67 - 30 0.06 0.60 0.30 - 40 0.04 0.28 0.17 - 50 0.03 0.16 0.11 - -[[8]] - crop -distance Ackerbau Obstbau frueh Obstbau spaet - 1 1.52 NA NA - 3 NA 22.24 8.66 - 5 0.31 14.09 4.92 - 10 0.16 7.58 2.29 - 15 0.11 3.48 1.14 - 20 0.08 1.65 0.65 - 30 0.05 0.57 0.29 - 40 0.04 0.27 0.16 - 50 0.03 0.15 0.11 - -</div></pre> - </div> - <div class="span4 sidebar"> - <!-- <ul> - <li>drift_data_JKI</li> - </ul> - <ul> - <li>datasets</li> - </ul> --> - - - - - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. 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\ No newline at end of file diff --git a/docs/endpoint.html b/docs/endpoint.html deleted file mode 100644 index 58696a9..0000000 --- a/docs/endpoint.html +++ /dev/null @@ -1,158 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>endpoint. pfm 0.3-8</title> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=""> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">pfm 0.3-8</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> - </div> - </div> -</div> - - - <div class="container"> - <header> - - </header> - - <h1>Retrieve endpoint information from the chyaml field of a chent object</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><span class="functioncall"><a href='endpoint.html'>endpoint</a></span><span class="keyword">(</span><span class="symbol">chent</span><span class="keyword">,</span> <span class="argument">medium</span> <span class="argument">=</span> <span class="string">"soil"</span><span class="keyword">,</span> <span class="argument">type</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"degradation"</span><span class="keyword">,</span> <span class="string">"sorption"</span><span class="keyword">)</span><span class="keyword">,</span> - <span class="argument">lab_field</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">NA</span><span class="keyword">,</span> <span class="string">"laboratory"</span><span class="keyword">,</span> <span class="string">"field"</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">redox</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">NA</span><span class="keyword">,</span> <span class="string">"aerobic"</span><span class="keyword">,</span> - <span class="string">"anaerobic"</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">value</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"DT50ref"</span><span class="keyword">,</span> <span class="string">"Kfoc"</span><span class="keyword">,</span> <span class="string">"N"</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">aggregator</span> <span class="argument">=</span> <span class="symbol">geomean</span><span class="keyword">,</span> - <span class="argument">raw</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">,</span> <span class="argument">signif</span> <span class="argument">=</span> <span class="number">3</span><span class="keyword">)</span> - -<span class="functioncall"><a href='endpoint.html'>soil_DT50</a></span><span class="keyword">(</span><span class="symbol">chent</span><span class="keyword">,</span> <span class="argument">aggregator</span> <span class="argument">=</span> <span class="symbol">geomean</span><span class="keyword">,</span> <span class="argument">signif</span> <span class="argument">=</span> <span class="number">3</span><span class="keyword">,</span> - <span class="argument">lab_field</span> <span class="argument">=</span> <span class="string">"laboratory"</span><span class="keyword">,</span> <span class="argument">value</span> <span class="argument">=</span> <span class="string">"DT50ref"</span><span class="keyword">,</span> <span class="argument">redox</span> <span class="argument">=</span> <span class="string">"aerobic"</span><span class="keyword">,</span> - <span class="argument">raw</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">)</span> - -<span class="functioncall"><a href='endpoint.html'>soil_Kfoc</a></span><span class="keyword">(</span><span class="symbol">chent</span><span class="keyword">,</span> <span class="argument">aggregator</span> <span class="argument">=</span> <span class="symbol">geomean</span><span class="keyword">,</span> <span class="argument">signif</span> <span class="argument">=</span> <span class="number">3</span><span class="keyword">,</span> <span class="argument">value</span> <span class="argument">=</span> <span class="string">"Kfoc"</span><span class="keyword">,</span> - <span class="argument">raw</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">)</span> - -<span class="functioncall"><a href='endpoint.html'>soil_N</a></span><span class="keyword">(</span><span class="symbol">chent</span><span class="keyword">,</span> <span class="argument">aggregator</span> <span class="argument">=</span> <span class="symbol">mean</span><span class="keyword">,</span> <span class="argument">signif</span> <span class="argument">=</span> <span class="number">3</span><span class="keyword">,</span> <span class="argument">raw</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">)</span> - -<span class="functioncall"><a href='endpoint.html'>soil_sorption</a></span><span class="keyword">(</span><span class="symbol">chent</span><span class="keyword">,</span> <span class="argument">values</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"Kfoc"</span><span class="keyword">,</span> <span class="string">"N"</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">aggregators</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">Kfoc</span> <span class="argument">=</span> - <span class="symbol">geomean</span><span class="keyword">,</span> <span class="argument">Koc</span> <span class="argument">=</span> <span class="symbol">geomean</span><span class="keyword">,</span> <span class="argument">N</span> <span class="argument">=</span> <span class="symbol">mean</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">signif</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="argument">Kfoc</span> <span class="argument">=</span> <span class="number">3</span><span class="keyword">,</span> <span class="argument">N</span> <span class="argument">=</span> <span class="number">3</span><span class="keyword">)</span><span class="keyword">,</span> - <span class="argument">raw</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">)</span></pre> - - <h2>Arguments</h2> - <dl> - <dt>chent</dt> - <dd>The chent object to get the information from</dd> - <dt>medium</dt> - <dd>The medium for which information is sought</dd> - <dt>type</dt> - <dd>The information type</dd> - <dt>lab_field</dt> - <dd>If not NA, do we want laboratory or field endpoints</dd> - <dt>redox</dt> - <dd>If not NA, are we looking for aerobic or anaerobic data</dd> - <dt>value</dt> - <dd>The name of the value we want. The list given in the -usage section is not exclusive</dd> - <dt>aggregator</dt> - <dd>The aggregator function. Can be mean, -<code><a href='geomean.html'>geomean</a></code>, or identity, for example.</dd> - <dt>raw</dt> - <dd>Should the number(s) be returned as stored in the chent -object (could be a character value) to retain original information -about precision?</dd> - <dt>signif</dt> - <dd>How many significant digits do we want</dd> - <dt>values</dt> - <dd>The values to be returned</dd> - <dt>aggregators</dt> - <dd>A named vector of aggregator functions to be used</dd> - </dl> - - <div class="Value"> - <h2>Value</h2> - - <p><dl> -The result from applying the aggregator function to - the values converted to a numeric vector, rounded to the - given number of significant digits, or, if raw = TRUE, - the values as a character value, retaining any implicit - information on precision that may be present. -</dl></p> - - </div> - - <div class="Description"> - <h2>Description</h2> - - <p>R6 class objects of class chent represent chemical entities -and can hold a list of information loaded from a chemical yaml file in their -chyaml field. Such information is extracted and optionally aggregated by -this function.</p> - - </div> - - <div class="Details"> - <h2>Details</h2> - - <p>The functions <code>soil_*</code> are functions to extract soil specific endpoints. -For the Freundlich exponent, the capital letter <code>N</code> is used in order to -facilitate dealing with such data in R. In pesticide fate modelling, this -exponent is often called 1/n.</p> - - </div> - </div> - <div class="span4 sidebar"> - <!-- <ul> - <li>endpoint</li><li>soil_DT50</li><li>soil_Kfoc</li><li>soil_N</li><li>soil_sorption</li> - </ul> - <ul> - - </ul> --> - - - - - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/docs/geomean.html b/docs/geomean.html deleted file mode 100644 index 3530c32..0000000 --- a/docs/geomean.html +++ /dev/null @@ -1,121 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>geomean. pfm 0.3-8</title> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=" -Johannes Ranke -"> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">pfm 0.3-8</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> - </div> - </div> -</div> - - - <div class="container"> - <header> - - </header> - - <h1>Calculate the geometric mean</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><span class="functioncall"><a href='geomean.html'>geomean</a></span><span class="keyword">(</span><span class="symbol">x</span><span class="keyword">,</span> <span class="argument">na.rm</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span></pre> - - <h2>Arguments</h2> - <dl> - <dt>x</dt> - <dd>Vector of numbers</dd> - <dt>na.rm</dt> - <dd>Should NA values be omitted?</dd> - </dl> - - <div class="Value"> - <h2>Value</h2> - - <p><dl> -The geometric mean -</dl></p> - - </div> - - <div class="Description"> - <h2>Description</h2> - - <p>Based on some posts in a thread on Stackoverflow -<a href = 'http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in'>http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in</a> -This function checks for negative values, removes NA values per default and -returns 0 if at least one element of the vector is 0.</p> - - </div> - - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'><span class="functioncall"><a href='geomean.html'>geomean</a></span><span class="keyword">(</span><span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">1</span><span class="keyword">,</span> <span class="number">3</span><span class="keyword">,</span> <span class="number">9</span><span class="keyword">)</span><span class="keyword">)</span></div> -<div class='output'>[1] 3 -</div> -<div class='input'><span class="functioncall"><a href='geomean.html'>geomean</a></span><span class="keyword">(</span><span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="number">1</span><span class="keyword">,</span> <span class="number">3</span><span class="keyword">,</span> <span class="number">NA</span><span class="keyword">,</span> <span class="number">9</span><span class="keyword">)</span><span class="keyword">)</span></div> -<div class='output'>[1] 3 -</div> -<div class='input'><span class="comment">## Not run: geomean(c(1, -3, 9)) # returns an error</span></div></pre> - </div> - <div class="span4 sidebar"> - <!-- <ul> - <li>geomean</li> - </ul> - <ul> - - </ul> --> - - - - <h2>Author</h2> - -Johannes Ranke - - - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/docs/img/glyphicons-halflings-white.png b/docs/img/glyphicons-halflings-white.png Binary files differdeleted file mode 100644 index 3bf6484..0000000 --- a/docs/img/glyphicons-halflings-white.png +++ /dev/null diff --git a/docs/img/glyphicons-halflings.png b/docs/img/glyphicons-halflings.png Binary files differdeleted file mode 100644 index 79bc568..0000000 --- a/docs/img/glyphicons-halflings.png +++ /dev/null diff --git a/docs/index.html b/docs/index.html index a82dcae..4aa129c 100644 --- a/docs/index.html +++ b/docs/index.html @@ -1,65 +1,55 @@ <!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>Home. pfm 0.3-8</title> +<!-- Generated by pkgdown: do not edit by hand --><html> +<head> +<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> +<meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=""> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> +<title>Utilities for Pesticide Fate Modelling • pfm</title> +<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> +<!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"> +<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><!-- mathjax --><script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">pfm 0.3-8</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> +</head> +<body> + <div class="container template-home"> + <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="index.html">pfm</a> </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> +<li> + <a href="reference/index.html">Reference</a> +</li> + </ul> +<ul class="nav navbar-nav navbar-right"></ul> +</div> +<!--/.nav-collapse --> </div> +<!--/.container --> </div> +<!--/.navbar --> - - <div class="container"> - <header> - - </header> - <div class="row"> - <div class="span8"> - <h1>pfm</h1> - -<p>The R package <strong>pfm</strong> provides some utilities for dealing with FOCUS pesticide fate modelling tools, -(currently only TOXSWA cwa and out files), made available under the GNU public license. -This means:</p> - -<pre><code>This program is free software: you can redistribute it and/or modify it under + </header><div class="row"> + <div class="contents col-md-9"> + <div id="pfm" class="section level1"> +<div class="page-header"><h1 class="hasAnchor"> +<a href="#pfm" class="anchor"> </a>pfm</h1></div> +<p>The R package <strong>pfm</strong> provides some utilities for dealing with FOCUS pesticide fate modelling tools, (currently only TOXSWA cwa and out files), made available under the GNU public license. This means:</p> +<div class="sourceCode"><pre class="sourceCode R"><code class="sourceCode r">This program is free software:<span class="st"> </span>you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software -Foundation, either version 3 of the License, or (at your option) any later +Foundation, either version <span class="dv">3</span> of the License, <span class="kw">or</span> (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT @@ -68,49 +58,32 @@ FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with -this program. If not, see <http://www.gnu.org/licenses/> -</code></pre> - -<h2>Installation</h2> - -<p>You can install the package from <a href="http://github.com/jranke/pfm">github</a>, e.g. -using the <code>devtools</code> package. Using <code>quick = TRUE</code> skips docs, -multiple-architecture builds, demos, and vignettes, to make installation as -fast and painless as possible.</p> - -<pre><code class="r">library(devtools) -install_github("jranke/pfm", subdir = "pkg", quick = TRUE) -</code></pre> - -<h2>Use</h2> - -<h3>Analyse TOXSWA output</h3> - +this program. If not, see <http:<span class="er">//</span>www.gnu.org/licenses/<span class="er">></span></code></pre></div> +<div id="installation" class="section level2"> +<h2 class="hasAnchor"> +<a href="#installation" class="anchor"> </a>Installation</h2> +<p>You can install the package from <a href="http://github.com/jranke/pfm">github</a>, e.g. using the <code>devtools</code> package. Using <code>quick = TRUE</code> skips docs, multiple-architecture builds, demos, and vignettes, to make installation as fast and painless as possible.</p> +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(devtools) +<span class="kw">install_github</span>(<span class="st">"jranke/pfm"</span>, <span class="dt">subdir =</span> <span class="st">"pkg"</span>, <span class="dt">quick =</span> <span class="ot">TRUE</span>)</code></pre></div> +</div> +<div id="use" class="section level2"> +<h2 class="hasAnchor"> +<a href="#use" class="anchor"> </a>Use</h2> +<div id="analyse-toxswa-output" class="section level3"> +<h3 class="hasAnchor"> +<a href="#analyse-toxswa-output" class="anchor"> </a>Analyse TOXSWA output</h3> <p>Read in and analyse a cwa file:</p> - -<pre><code class="r">library(pfm, quietly = TRUE) -</code></pre> - +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(pfm, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</code></pre></div> <pre><code>## ## Initialize Python Version 2.7.9 (default, Jun 29 2016, 13:11:10) -## [GCC 4.9.2] -</code></pre> - -<pre><code class="r">example_cwa <- read.TOXSWA_cwa("00003s_pa.cwa") -plot(example_cwa) -</code></pre> - -<p><img src="README_files/figure-html/unnamed-chunk-3-1.png" width="672" /></p> - -<p>Get events above thresholds of 20 and 100 µg/L, -and do a moving window analysis for windows of 7 days -and 21 days, print the results:</p> - -<pre><code class="r">example_cwa$get_events(c(20, 100)) -example_cwa$moving_windows(c(7, 21)) -print(example_cwa) -</code></pre> - +## [GCC 4.9.2]</code></pre> +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">example_cwa <-<span class="st"> </span><span class="kw"><a href="reference/read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></span>(<span class="st">"00003s_pa.cwa"</span>) +<span class="kw">plot</span>(example_cwa)</code></pre></div> +<p><img src="README_files/figure-html/unnamed-chunk-3-1.png" width="672"></p> +<p>Get events above thresholds of 20 and 100 µg/L, and do a moving window analysis for windows of 7 days and 21 days, print the results:</p> +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">example_cwa$<span class="kw">get_events</span>(<span class="kw">c</span>(<span class="dv">20</span>, <span class="dv">100</span>)) +example_cwa$<span class="kw">moving_windows</span>(<span class="kw">c</span>(<span class="dv">7</span>, <span class="dv">21</span>)) +<span class="kw">print</span>(example_cwa)</code></pre></div> <pre><code>## <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 @@ -134,35 +107,23 @@ print(example_cwa) ## t_start cwa_max duration pre_interval AUC_h AUC_d ## 1 55.083 40.58401 0.417 55.083 365.7912 15.2413 ## Event statistics for threshold 100 -## No events found -</code></pre> - -<p>This can also be done with out files, the function reads -out files from current TOXSWA versions as well as cwa files -from old TOXSWA versions.</p> - -<h3>Calculate PEC soil</h3> - -<p>Simple PEC soil calculation for an application rate of 100 g/ha and -25% interception, assuming complete mixing into 5 cm and a soil bulk -density of 1.5 kg/L, output in mg/kg:</p> - -<pre><code class="r">PEC_soil(100, interception = 0.25) -</code></pre> - +## No events found</code></pre> +<p>This can also be done with out files, the function reads out files from current TOXSWA versions as well as cwa files from old TOXSWA versions.</p> +</div> +<div id="calculate-pec-soil" class="section level3"> +<h3 class="hasAnchor"> +<a href="#calculate-pec-soil" class="anchor"> </a>Calculate PEC soil</h3> +<p>Simple PEC soil calculation for an application rate of 100 g/ha and 25% interception, assuming complete mixing into 5 cm and a soil bulk density of 1.5 kg/L, output in mg/kg:</p> +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="reference/PEC_soil.html">PEC_soil</a></span>(<span class="dv">100</span>, <span class="dt">interception =</span> <span class="fl">0.25</span>)</code></pre></div> <pre><code>## scenario ## t_avg default -## 0 0.1 -</code></pre> - -<h3>Rautmann drift data</h3> - -<p>Some of the drift percentage data published by the JKI are included. To -see the data for one application:</p> - -<pre><code class="r">drift_data_JKI[1] -</code></pre> - +## 0 0.1</code></pre> +</div> +<div id="rautmann-drift-data" class="section level3"> +<h3 class="hasAnchor"> +<a href="#rautmann-drift-data" class="anchor"> </a>Rautmann drift data</h3> +<p>Some of the drift percentage data published by the JKI are included. To see the data for one application:</p> +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">drift_data_JKI[<span class="dv">1</span>]</code></pre></div> <pre><code>## [[1]] ## crop ## distance Ackerbau Obstbau frueh Obstbau spaet @@ -174,35 +135,41 @@ see the data for one application:</p> ## 20 0.15 2.77 1.09 ## 30 0.10 1.04 0.54 ## 40 0.07 0.52 0.32 -## 50 0.06 0.30 0.22 -</code></pre> - -<h3>PEC surface water due to drift</h3> - -<p>Initial PEC values for an application of 100 g/ha in the vicinity of a 30 cm -deep water body are obtained using</p> +## 50 0.06 0.30 0.22</code></pre> +</div> +<div id="pec-surface-water-due-to-drift" class="section level3"> +<h3 class="hasAnchor"> +<a href="#pec-surface-water-due-to-drift" class="anchor"> </a>PEC surface water due to drift</h3> +<p>Initial PEC values for an application of 100 g/ha in the vicinity of a 30 cm deep water body are obtained using</p> +<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="reference/PEC_sw_drift.html">PEC_sw_drift</a></span>(<span class="dv">100</span>, <span class="dt">applications =</span> <span class="dv">1</span>)</code></pre></div> +<pre><code>## 1 m 5 m 10 m 20 m +## 0.92333333 0.19000000 0.09666667 0.05000000</code></pre> +</div> +</div> +</div> + </div> -<pre><code class="r">PEC_sw_drift(100, applications = 1) -</code></pre> + <div class="col-md-3" id="sidebar"> + <h2>License</h2> +<p>GPL</p> +<h2>Developers</h2> +<ul class="list-unstyled"> +<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> </li> +</ul> +</div> +</div> -<pre><code>## 1 m 5 m 10 m 20 m -## 0.92333333 0.19000000 0.09666667 0.05000000 -</code></pre> - </div> + <footer><div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> - <div class="span3 offset1 sidebar"> - <h2>Authors</h2> - <ul> - <li><a href='mailto:jranke@uni-bremen.de'>Johannes Ranke</a> [aut, cre, cph]</li> - </ul> - </div> +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> </div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. 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\ No newline at end of file +</html> diff --git a/docs/jquery.sticky-kit.min.js b/docs/jquery.sticky-kit.min.js new file mode 100644 index 0000000..e2a3c6d --- /dev/null +++ b/docs/jquery.sticky-kit.min.js @@ -0,0 +1,9 @@ +/* + Sticky-kit v1.1.2 | WTFPL | Leaf Corcoran 2015 | http://leafo.net +*/ +(function(){var b,f;b=this.jQuery||window.jQuery;f=b(window);b.fn.stick_in_parent=function(d){var A,w,J,n,B,K,p,q,k,E,t;null==d&&(d={});t=d.sticky_class;B=d.inner_scrolling;E=d.recalc_every;k=d.parent;q=d.offset_top;p=d.spacer;w=d.bottoming;null==q&&(q=0);null==k&&(k=void 0);null==B&&(B=!0);null==t&&(t="is_stuck");A=b(document);null==w&&(w=!0);J=function(a,d,n,C,F,u,r,G){var v,H,m,D,I,c,g,x,y,z,h,l;if(!a.data("sticky_kit")){a.data("sticky_kit",!0);I=A.height();g=a.parent();null!=k&&(g=g.closest(k)); +if(!g.length)throw"failed to find stick parent";v=m=!1;(h=null!=p?p&&a.closest(p):b("<div />"))&&h.css("position",a.css("position"));x=function(){var c,f,e;if(!G&&(I=A.height(),c=parseInt(g.css("border-top-width"),10),f=parseInt(g.css("padding-top"),10),d=parseInt(g.css("padding-bottom"),10),n=g.offset().top+c+f,C=g.height(),m&&(v=m=!1,null==p&&(a.insertAfter(h),h.detach()),a.css({position:"",top:"",width:"",bottom:""}).removeClass(t),e=!0),F=a.offset().top-(parseInt(a.css("margin-top"),10)||0)-q, +u=a.outerHeight(!0),r=a.css("float"),h&&h.css({width:a.outerWidth(!0),height:u,display:a.css("display"),"vertical-align":a.css("vertical-align"),"float":r}),e))return l()};x();if(u!==C)return D=void 0,c=q,z=E,l=function(){var b,l,e,k;if(!G&&(e=!1,null!=z&&(--z,0>=z&&(z=E,x(),e=!0)),e||A.height()===I||x(),e=f.scrollTop(),null!=D&&(l=e-D),D=e,m?(w&&(k=e+u+c>C+n,v&&!k&&(v=!1,a.css({position:"fixed",bottom:"",top:c}).trigger("sticky_kit:unbottom"))),e<F&&(m=!1,c=q,null==p&&("left"!==r&&"right"!==r||a.insertAfter(h), +h.detach()),b={position:"",width:"",top:""},a.css(b).removeClass(t).trigger("sticky_kit:unstick")),B&&(b=f.height(),u+q>b&&!v&&(c-=l,c=Math.max(b-u,c),c=Math.min(q,c),m&&a.css({top:c+"px"})))):e>F&&(m=!0,b={position:"fixed",top:c},b.width="border-box"===a.css("box-sizing")?a.outerWidth()+"px":a.width()+"px",a.css(b).addClass(t),null==p&&(a.after(h),"left"!==r&&"right"!==r||h.append(a)),a.trigger("sticky_kit:stick")),m&&w&&(null==k&&(k=e+u+c>C+n),!v&&k)))return v=!0,"static"===g.css("position")&&g.css({position:"relative"}), +a.css({position:"absolute",bottom:d,top:"auto"}).trigger("sticky_kit:bottom")},y=function(){x();return l()},H=function(){G=!0;f.off("touchmove",l);f.off("scroll",l);f.off("resize",y);b(document.body).off("sticky_kit:recalc",y);a.off("sticky_kit:detach",H);a.removeData("sticky_kit");a.css({position:"",bottom:"",top:"",width:""});g.position("position","");if(m)return null==p&&("left"!==r&&"right"!==r||a.insertAfter(h),h.remove()),a.removeClass(t)},f.on("touchmove",l),f.on("scroll",l),f.on("resize", +y),b(document.body).on("sticky_kit:recalc",y),a.on("sticky_kit:detach",H),setTimeout(l,0)}};n=0;for(K=this.length;n<K;n++)d=this[n],J(b(d));return this}}).call(this); diff --git a/docs/js/bootstrap.js b/docs/js/bootstrap.js deleted file mode 100644 index 5d6e65b..0000000 --- a/docs/js/bootstrap.js +++ /dev/null @@ -1,1825 +0,0 @@ -/* =================================================== - * bootstrap-transition.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#transitions - * =================================================== - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ========================================================== */ - - -!function ($) { - - $(function () { - - "use strict"; // jshint ;_; - - - /* CSS TRANSITION SUPPORT (http://www.modernizr.com/) - * ======================================================= */ - - $.support.transition = (function () { - - var transitionEnd = (function () { - - var el = document.createElement('bootstrap') - , transEndEventNames = { - 'WebkitTransition' : 'webkitTransitionEnd' - , 'MozTransition' : 'transitionend' - , 'OTransition' : 'oTransitionEnd' - , 'msTransition' : 'MSTransitionEnd' - , 'transition' : 'transitionend' - } - , name - - for (name in transEndEventNames){ - if (el.style[name] !== undefined) { - return transEndEventNames[name] - } - } - - }()) - - return transitionEnd && { - end: transitionEnd - } - - })() - - }) - -}(window.jQuery);/* ========================================================== - * bootstrap-alert.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#alerts - * ========================================================== - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ========================================================== */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* ALERT CLASS DEFINITION - * ====================== */ - - var dismiss = '[data-dismiss="alert"]' - , Alert = function (el) { - $(el).on('click', dismiss, this.close) - } - - Alert.prototype.close = function (e) { - var $this = $(this) - , selector = $this.attr('data-target') - , $parent - - if (!selector) { - selector = $this.attr('href') - selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7 - } - - $parent = $(selector) - - e && e.preventDefault() - - $parent.length || ($parent = $this.hasClass('alert') ? $this : $this.parent()) - - $parent.trigger(e = $.Event('close')) - - if (e.isDefaultPrevented()) return - - $parent.removeClass('in') - - function removeElement() { - $parent - .trigger('closed') - .remove() - } - - $.support.transition && $parent.hasClass('fade') ? - $parent.on($.support.transition.end, removeElement) : - removeElement() - } - - - /* ALERT PLUGIN DEFINITION - * ======================= */ - - $.fn.alert = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('alert') - if (!data) $this.data('alert', (data = new Alert(this))) - if (typeof option == 'string') data[option].call($this) - }) - } - - $.fn.alert.Constructor = Alert - - - /* ALERT DATA-API - * ============== */ - - $(function () { - $('body').on('click.alert.data-api', dismiss, Alert.prototype.close) - }) - -}(window.jQuery);/* ============================================================ - * bootstrap-button.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#buttons - * ============================================================ - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ============================================================ */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* BUTTON PUBLIC CLASS DEFINITION - * ============================== */ - - var Button = function (element, options) { - this.$element = $(element) - this.options = $.extend({}, $.fn.button.defaults, options) - } - - Button.prototype.setState = function (state) { - var d = 'disabled' - , $el = this.$element - , data = $el.data() - , val = $el.is('input') ? 'val' : 'html' - - state = state + 'Text' - data.resetText || $el.data('resetText', $el[val]()) - - $el[val](data[state] || this.options[state]) - - // push to event loop to allow forms to submit - setTimeout(function () { - state == 'loadingText' ? - $el.addClass(d).attr(d, d) : - $el.removeClass(d).removeAttr(d) - }, 0) - } - - Button.prototype.toggle = function () { - var $parent = this.$element.parent('[data-toggle="buttons-radio"]') - - $parent && $parent - .find('.active') - .removeClass('active') - - this.$element.toggleClass('active') - } - - - /* BUTTON PLUGIN DEFINITION - * ======================== */ - - $.fn.button = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('button') - , options = typeof option == 'object' && option - if (!data) $this.data('button', (data = new Button(this, options))) - if (option == 'toggle') data.toggle() - else if (option) data.setState(option) - }) - } - - $.fn.button.defaults = { - loadingText: 'loading...' - } - - $.fn.button.Constructor = Button - - - /* BUTTON DATA-API - * =============== */ - - $(function () { - $('body').on('click.button.data-api', '[data-toggle^=button]', function ( e ) { - var $btn = $(e.target) - if (!$btn.hasClass('btn')) $btn = $btn.closest('.btn') - $btn.button('toggle') - }) - }) - -}(window.jQuery);/* ========================================================== - * bootstrap-carousel.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#carousel - * ========================================================== - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ========================================================== */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* CAROUSEL CLASS DEFINITION - * ========================= */ - - var Carousel = function (element, options) { - this.$element = $(element) - this.options = options - this.options.slide && this.slide(this.options.slide) - this.options.pause == 'hover' && this.$element - .on('mouseenter', $.proxy(this.pause, this)) - .on('mouseleave', $.proxy(this.cycle, this)) - } - - Carousel.prototype = { - - cycle: function (e) { - if (!e) this.paused = false - this.options.interval - && !this.paused - && (this.interval = setInterval($.proxy(this.next, this), this.options.interval)) - return this - } - - , to: function (pos) { - var $active = this.$element.find('.active') - , children = $active.parent().children() - , activePos = children.index($active) - , that = this - - if (pos > (children.length - 1) || pos < 0) return - - if (this.sliding) { - return this.$element.one('slid', function () { - that.to(pos) - }) - } - - if (activePos == pos) { - return this.pause().cycle() - } - - return this.slide(pos > activePos ? 'next' : 'prev', $(children[pos])) - } - - , pause: function (e) { - if (!e) this.paused = true - clearInterval(this.interval) - this.interval = null - return this - } - - , next: function () { - if (this.sliding) return - return this.slide('next') - } - - , prev: function () { - if (this.sliding) return - return this.slide('prev') - } - - , slide: function (type, next) { - var $active = this.$element.find('.active') - , $next = next || $active[type]() - , isCycling = this.interval - , direction = type == 'next' ? 'left' : 'right' - , fallback = type == 'next' ? 'first' : 'last' - , that = this - , e = $.Event('slide') - - this.sliding = true - - isCycling && this.pause() - - $next = $next.length ? $next : this.$element.find('.item')[fallback]() - - if ($next.hasClass('active')) return - - if ($.support.transition && this.$element.hasClass('slide')) { - this.$element.trigger(e) - if (e.isDefaultPrevented()) return - $next.addClass(type) - $next[0].offsetWidth // force reflow - $active.addClass(direction) - $next.addClass(direction) - this.$element.one($.support.transition.end, function () { - $next.removeClass([type, direction].join(' ')).addClass('active') - $active.removeClass(['active', direction].join(' ')) - that.sliding = false - setTimeout(function () { that.$element.trigger('slid') }, 0) - }) - } else { - this.$element.trigger(e) - if (e.isDefaultPrevented()) return - $active.removeClass('active') - $next.addClass('active') - this.sliding = false - this.$element.trigger('slid') - } - - isCycling && this.cycle() - - return this - } - - } - - - /* CAROUSEL PLUGIN DEFINITION - * ========================== */ - - $.fn.carousel = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('carousel') - , options = $.extend({}, $.fn.carousel.defaults, typeof option == 'object' && option) - if (!data) $this.data('carousel', (data = new Carousel(this, options))) - if (typeof option == 'number') data.to(option) - else if (typeof option == 'string' || (option = options.slide)) data[option]() - else if (options.interval) data.cycle() - }) - } - - $.fn.carousel.defaults = { - interval: 5000 - , pause: 'hover' - } - - $.fn.carousel.Constructor = Carousel - - - /* CAROUSEL DATA-API - * ================= */ - - $(function () { - $('body').on('click.carousel.data-api', '[data-slide]', function ( e ) { - var $this = $(this), href - , $target = $($this.attr('data-target') || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7 - , options = !$target.data('modal') && $.extend({}, $target.data(), $this.data()) - $target.carousel(options) - e.preventDefault() - }) - }) - -}(window.jQuery);/* ============================================================= - * bootstrap-collapse.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#collapse - * ============================================================= - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ============================================================ */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* COLLAPSE PUBLIC CLASS DEFINITION - * ================================ */ - - var Collapse = function (element, options) { - this.$element = $(element) - this.options = $.extend({}, $.fn.collapse.defaults, options) - - if (this.options.parent) { - this.$parent = $(this.options.parent) - } - - this.options.toggle && this.toggle() - } - - Collapse.prototype = { - - constructor: Collapse - - , dimension: function () { - var hasWidth = this.$element.hasClass('width') - return hasWidth ? 'width' : 'height' - } - - , show: function () { - var dimension - , scroll - , actives - , hasData - - if (this.transitioning) return - - dimension = this.dimension() - scroll = $.camelCase(['scroll', dimension].join('-')) - actives = this.$parent && this.$parent.find('> .accordion-group > .in') - - if (actives && actives.length) { - hasData = actives.data('collapse') - if (hasData && hasData.transitioning) return - actives.collapse('hide') - hasData || actives.data('collapse', null) - } - - this.$element[dimension](0) - this.transition('addClass', $.Event('show'), 'shown') - this.$element[dimension](this.$element[0][scroll]) - } - - , hide: function () { - var dimension - if (this.transitioning) return - dimension = this.dimension() - this.reset(this.$element[dimension]()) - this.transition('removeClass', $.Event('hide'), 'hidden') - this.$element[dimension](0) - } - - , reset: function (size) { - var dimension = this.dimension() - - this.$element - .removeClass('collapse') - [dimension](size || 'auto') - [0].offsetWidth - - this.$element[size !== null ? 'addClass' : 'removeClass']('collapse') - - return this - } - - , transition: function (method, startEvent, completeEvent) { - var that = this - , complete = function () { - if (startEvent.type == 'show') that.reset() - that.transitioning = 0 - that.$element.trigger(completeEvent) - } - - this.$element.trigger(startEvent) - - if (startEvent.isDefaultPrevented()) return - - this.transitioning = 1 - - this.$element[method]('in') - - $.support.transition && this.$element.hasClass('collapse') ? - this.$element.one($.support.transition.end, complete) : - complete() - } - - , toggle: function () { - this[this.$element.hasClass('in') ? 'hide' : 'show']() - } - - } - - - /* COLLAPSIBLE PLUGIN DEFINITION - * ============================== */ - - $.fn.collapse = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('collapse') - , options = typeof option == 'object' && option - if (!data) $this.data('collapse', (data = new Collapse(this, options))) - if (typeof option == 'string') data[option]() - }) - } - - $.fn.collapse.defaults = { - toggle: true - } - - $.fn.collapse.Constructor = Collapse - - - /* COLLAPSIBLE DATA-API - * ==================== */ - - $(function () { - $('body').on('click.collapse.data-api', '[data-toggle=collapse]', function ( e ) { - var $this = $(this), href - , target = $this.attr('data-target') - || e.preventDefault() - || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '') //strip for ie7 - , option = $(target).data('collapse') ? 'toggle' : $this.data() - $(target).collapse(option) - }) - }) - -}(window.jQuery);/* ============================================================ - * bootstrap-dropdown.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#dropdowns - * ============================================================ - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ============================================================ */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* DROPDOWN CLASS DEFINITION - * ========================= */ - - var toggle = '[data-toggle="dropdown"]' - , Dropdown = function (element) { - var $el = $(element).on('click.dropdown.data-api', this.toggle) - $('html').on('click.dropdown.data-api', function () { - $el.parent().removeClass('open') - }) - } - - Dropdown.prototype = { - - constructor: Dropdown - - , toggle: function (e) { - var $this = $(this) - , $parent - , selector - , isActive - - if ($this.is('.disabled, :disabled')) return - - selector = $this.attr('data-target') - - if (!selector) { - selector = $this.attr('href') - selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7 - } - - $parent = $(selector) - $parent.length || ($parent = $this.parent()) - - isActive = $parent.hasClass('open') - - clearMenus() - - if (!isActive) $parent.toggleClass('open') - - return false - } - - } - - function clearMenus() { - $(toggle).parent().removeClass('open') - } - - - /* DROPDOWN PLUGIN DEFINITION - * ========================== */ - - $.fn.dropdown = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('dropdown') - if (!data) $this.data('dropdown', (data = new Dropdown(this))) - if (typeof option == 'string') data[option].call($this) - }) - } - - $.fn.dropdown.Constructor = Dropdown - - - /* APPLY TO STANDARD DROPDOWN ELEMENTS - * =================================== */ - - $(function () { - $('html').on('click.dropdown.data-api', clearMenus) - $('body') - .on('click.dropdown', '.dropdown form', function (e) { e.stopPropagation() }) - .on('click.dropdown.data-api', toggle, Dropdown.prototype.toggle) - }) - -}(window.jQuery);/* ========================================================= - * bootstrap-modal.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#modals - * ========================================================= - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ========================================================= */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* MODAL CLASS DEFINITION - * ====================== */ - - var Modal = function (content, options) { - this.options = options - this.$element = $(content) - .delegate('[data-dismiss="modal"]', 'click.dismiss.modal', $.proxy(this.hide, this)) - } - - Modal.prototype = { - - constructor: Modal - - , toggle: function () { - return this[!this.isShown ? 'show' : 'hide']() - } - - , show: function () { - var that = this - , e = $.Event('show') - - this.$element.trigger(e) - - if (this.isShown || e.isDefaultPrevented()) return - - $('body').addClass('modal-open') - - this.isShown = true - - escape.call(this) - backdrop.call(this, function () { - var transition = $.support.transition && that.$element.hasClass('fade') - - if (!that.$element.parent().length) { - that.$element.appendTo(document.body) //don't move modals dom position - } - - that.$element - .show() - - if (transition) { - that.$element[0].offsetWidth // force reflow - } - - that.$element.addClass('in') - - transition ? - that.$element.one($.support.transition.end, function () { that.$element.trigger('shown') }) : - that.$element.trigger('shown') - - }) - } - - , hide: function (e) { - e && e.preventDefault() - - var that = this - - e = $.Event('hide') - - this.$element.trigger(e) - - if (!this.isShown || e.isDefaultPrevented()) return - - this.isShown = false - - $('body').removeClass('modal-open') - - escape.call(this) - - this.$element.removeClass('in') - - $.support.transition && this.$element.hasClass('fade') ? - hideWithTransition.call(this) : - hideModal.call(this) - } - - } - - - /* MODAL PRIVATE METHODS - * ===================== */ - - function hideWithTransition() { - var that = this - , timeout = setTimeout(function () { - that.$element.off($.support.transition.end) - hideModal.call(that) - }, 500) - - this.$element.one($.support.transition.end, function () { - clearTimeout(timeout) - hideModal.call(that) - }) - } - - function hideModal(that) { - this.$element - .hide() - .trigger('hidden') - - backdrop.call(this) - } - - function backdrop(callback) { - var that = this - , animate = this.$element.hasClass('fade') ? 'fade' : '' - - if (this.isShown && this.options.backdrop) { - var doAnimate = $.support.transition && animate - - this.$backdrop = $('<div class="modal-backdrop ' + animate + '" />') - .appendTo(document.body) - - if (this.options.backdrop != 'static') { - this.$backdrop.click($.proxy(this.hide, this)) - } - - if (doAnimate) this.$backdrop[0].offsetWidth // force reflow - - this.$backdrop.addClass('in') - - doAnimate ? - this.$backdrop.one($.support.transition.end, callback) : - callback() - - } else if (!this.isShown && this.$backdrop) { - this.$backdrop.removeClass('in') - - $.support.transition && this.$element.hasClass('fade')? - this.$backdrop.one($.support.transition.end, $.proxy(removeBackdrop, this)) : - removeBackdrop.call(this) - - } else if (callback) { - callback() - } - } - - function removeBackdrop() { - this.$backdrop.remove() - this.$backdrop = null - } - - function escape() { - var that = this - if (this.isShown && this.options.keyboard) { - $(document).on('keyup.dismiss.modal', function ( e ) { - e.which == 27 && that.hide() - }) - } else if (!this.isShown) { - $(document).off('keyup.dismiss.modal') - } - } - - - /* MODAL PLUGIN DEFINITION - * ======================= */ - - $.fn.modal = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('modal') - , options = $.extend({}, $.fn.modal.defaults, $this.data(), typeof option == 'object' && option) - if (!data) $this.data('modal', (data = new Modal(this, options))) - if (typeof option == 'string') data[option]() - else if (options.show) data.show() - }) - } - - $.fn.modal.defaults = { - backdrop: true - , keyboard: true - , show: true - } - - $.fn.modal.Constructor = Modal - - - /* MODAL DATA-API - * ============== */ - - $(function () { - $('body').on('click.modal.data-api', '[data-toggle="modal"]', function ( e ) { - var $this = $(this), href - , $target = $($this.attr('data-target') || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7 - , option = $target.data('modal') ? 'toggle' : $.extend({}, $target.data(), $this.data()) - - e.preventDefault() - $target.modal(option) - }) - }) - -}(window.jQuery);/* =========================================================== - * bootstrap-tooltip.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#tooltips - * Inspired by the original jQuery.tipsy by Jason Frame - * =========================================================== - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ========================================================== */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* TOOLTIP PUBLIC CLASS DEFINITION - * =============================== */ - - var Tooltip = function (element, options) { - this.init('tooltip', element, options) - } - - Tooltip.prototype = { - - constructor: Tooltip - - , init: function (type, element, options) { - var eventIn - , eventOut - - this.type = type - this.$element = $(element) - this.options = this.getOptions(options) - this.enabled = true - - if (this.options.trigger != 'manual') { - eventIn = this.options.trigger == 'hover' ? 'mouseenter' : 'focus' - eventOut = this.options.trigger == 'hover' ? 'mouseleave' : 'blur' - this.$element.on(eventIn, this.options.selector, $.proxy(this.enter, this)) - this.$element.on(eventOut, this.options.selector, $.proxy(this.leave, this)) - } - - this.options.selector ? - (this._options = $.extend({}, this.options, { trigger: 'manual', selector: '' })) : - this.fixTitle() - } - - , getOptions: function (options) { - options = $.extend({}, $.fn[this.type].defaults, options, this.$element.data()) - - if (options.delay && typeof options.delay == 'number') { - options.delay = { - show: options.delay - , hide: options.delay - } - } - - return options - } - - , enter: function (e) { - var self = $(e.currentTarget)[this.type](this._options).data(this.type) - - if (!self.options.delay || !self.options.delay.show) return self.show() - - clearTimeout(this.timeout) - self.hoverState = 'in' - this.timeout = setTimeout(function() { - if (self.hoverState == 'in') self.show() - }, self.options.delay.show) - } - - , leave: function (e) { - var self = $(e.currentTarget)[this.type](this._options).data(this.type) - - if (this.timeout) clearTimeout(this.timeout) - if (!self.options.delay || !self.options.delay.hide) return self.hide() - - self.hoverState = 'out' - this.timeout = setTimeout(function() { - if (self.hoverState == 'out') self.hide() - }, self.options.delay.hide) - } - - , show: function () { - var $tip - , inside - , pos - , actualWidth - , actualHeight - , placement - , tp - - if (this.hasContent() && this.enabled) { - $tip = this.tip() - this.setContent() - - if (this.options.animation) { - $tip.addClass('fade') - } - - placement = typeof this.options.placement == 'function' ? - this.options.placement.call(this, $tip[0], this.$element[0]) : - this.options.placement - - inside = /in/.test(placement) - - $tip - .remove() - .css({ top: 0, left: 0, display: 'block' }) - .appendTo(inside ? this.$element : document.body) - - pos = this.getPosition(inside) - - actualWidth = $tip[0].offsetWidth - actualHeight = $tip[0].offsetHeight - - switch (inside ? placement.split(' ')[1] : placement) { - case 'bottom': - tp = {top: pos.top + pos.height, left: pos.left + pos.width / 2 - actualWidth / 2} - break - case 'top': - tp = {top: pos.top - actualHeight, left: pos.left + pos.width / 2 - actualWidth / 2} - break - case 'left': - tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left - actualWidth} - break - case 'right': - tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left + pos.width} - break - } - - $tip - .css(tp) - .addClass(placement) - .addClass('in') - } - } - - , isHTML: function(text) { - // html string detection logic adapted from jQuery - return typeof text != 'string' - || ( text.charAt(0) === "<" - && text.charAt( text.length - 1 ) === ">" - && text.length >= 3 - ) || /^(?:[^<]*<[\w\W]+>[^>]*$)/.exec(text) - } - - , setContent: function () { - var $tip = this.tip() - , title = this.getTitle() - - $tip.find('.tooltip-inner')[this.isHTML(title) ? 'html' : 'text'](title) - $tip.removeClass('fade in top bottom left right') - } - - , hide: function () { - var that = this - , $tip = this.tip() - - $tip.removeClass('in') - - function removeWithAnimation() { - var timeout = setTimeout(function () { - $tip.off($.support.transition.end).remove() - }, 500) - - $tip.one($.support.transition.end, function () { - clearTimeout(timeout) - $tip.remove() - }) - } - - $.support.transition && this.$tip.hasClass('fade') ? - removeWithAnimation() : - $tip.remove() - } - - , fixTitle: function () { - var $e = this.$element - if ($e.attr('title') || typeof($e.attr('data-original-title')) != 'string') { - $e.attr('data-original-title', $e.attr('title') || '').removeAttr('title') - } - } - - , hasContent: function () { - return this.getTitle() - } - - , getPosition: function (inside) { - return $.extend({}, (inside ? {top: 0, left: 0} : this.$element.offset()), { - width: this.$element[0].offsetWidth - , height: this.$element[0].offsetHeight - }) - } - - , getTitle: function () { - var title - , $e = this.$element - , o = this.options - - title = $e.attr('data-original-title') - || (typeof o.title == 'function' ? o.title.call($e[0]) : o.title) - - return title - } - - , tip: function () { - return this.$tip = this.$tip || $(this.options.template) - } - - , validate: function () { - if (!this.$element[0].parentNode) { - this.hide() - this.$element = null - this.options = null - } - } - - , enable: function () { - this.enabled = true - } - - , disable: function () { - this.enabled = false - } - - , toggleEnabled: function () { - this.enabled = !this.enabled - } - - , toggle: function () { - this[this.tip().hasClass('in') ? 'hide' : 'show']() - } - - } - - - /* TOOLTIP PLUGIN DEFINITION - * ========================= */ - - $.fn.tooltip = function ( option ) { - return this.each(function () { - var $this = $(this) - , data = $this.data('tooltip') - , options = typeof option == 'object' && option - if (!data) $this.data('tooltip', (data = new Tooltip(this, options))) - if (typeof option == 'string') data[option]() - }) - } - - $.fn.tooltip.Constructor = Tooltip - - $.fn.tooltip.defaults = { - animation: true - , placement: 'top' - , selector: false - , template: '<div class="tooltip"><div class="tooltip-arrow"></div><div class="tooltip-inner"></div></div>' - , trigger: 'hover' - , title: '' - , delay: 0 - } - -}(window.jQuery); -/* =========================================================== - * bootstrap-popover.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#popovers - * =========================================================== - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * =========================================================== */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* POPOVER PUBLIC CLASS DEFINITION - * =============================== */ - - var Popover = function ( element, options ) { - this.init('popover', element, options) - } - - - /* NOTE: POPOVER EXTENDS BOOTSTRAP-TOOLTIP.js - ========================================== */ - - Popover.prototype = $.extend({}, $.fn.tooltip.Constructor.prototype, { - - constructor: Popover - - , setContent: function () { - var $tip = this.tip() - , title = this.getTitle() - , content = this.getContent() - - $tip.find('.popover-title')[this.isHTML(title) ? 'html' : 'text'](title) - $tip.find('.popover-content > *')[this.isHTML(content) ? 'html' : 'text'](content) - - $tip.removeClass('fade top bottom left right in') - } - - , hasContent: function () { - return this.getTitle() || this.getContent() - } - - , getContent: function () { - var content - , $e = this.$element - , o = this.options - - content = $e.attr('data-content') - || (typeof o.content == 'function' ? o.content.call($e[0]) : o.content) - - return content - } - - , tip: function () { - if (!this.$tip) { - this.$tip = $(this.options.template) - } - return this.$tip - } - - }) - - - /* POPOVER PLUGIN DEFINITION - * ======================= */ - - $.fn.popover = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('popover') - , options = typeof option == 'object' && option - if (!data) $this.data('popover', (data = new Popover(this, options))) - if (typeof option == 'string') data[option]() - }) - } - - $.fn.popover.Constructor = Popover - - $.fn.popover.defaults = $.extend({} , $.fn.tooltip.defaults, { - placement: 'right' - , content: '' - , template: '<div class="popover"><div class="arrow"></div><div class="popover-inner"><h3 class="popover-title"></h3><div class="popover-content"><p></p></div></div></div>' - }) - -}(window.jQuery);/* ============================================================= - * bootstrap-scrollspy.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#scrollspy - * ============================================================= - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ============================================================== */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* SCROLLSPY CLASS DEFINITION - * ========================== */ - - function ScrollSpy( element, options) { - var process = $.proxy(this.process, this) - , $element = $(element).is('body') ? $(window) : $(element) - , href - this.options = $.extend({}, $.fn.scrollspy.defaults, options) - this.$scrollElement = $element.on('scroll.scroll.data-api', process) - this.selector = (this.options.target - || ((href = $(element).attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7 - || '') + ' .nav li > a' - this.$body = $('body') - this.refresh() - this.process() - } - - ScrollSpy.prototype = { - - constructor: ScrollSpy - - , refresh: function () { - var self = this - , $targets - - this.offsets = $([]) - this.targets = $([]) - - $targets = this.$body - .find(this.selector) - .map(function () { - var $el = $(this) - , href = $el.data('target') || $el.attr('href') - , $href = /^#\w/.test(href) && $(href) - return ( $href - && href.length - && [[ $href.position().top, href ]] ) || null - }) - .sort(function (a, b) { return a[0] - b[0] }) - .each(function () { - self.offsets.push(this[0]) - self.targets.push(this[1]) - }) - } - - , process: function () { - var scrollTop = this.$scrollElement.scrollTop() + this.options.offset - , scrollHeight = this.$scrollElement[0].scrollHeight || this.$body[0].scrollHeight - , maxScroll = scrollHeight - this.$scrollElement.height() - , offsets = this.offsets - , targets = this.targets - , activeTarget = this.activeTarget - , i - - if (scrollTop >= maxScroll) { - return activeTarget != (i = targets.last()[0]) - && this.activate ( i ) - } - - for (i = offsets.length; i--;) { - activeTarget != targets[i] - && scrollTop >= offsets[i] - && (!offsets[i + 1] || scrollTop <= offsets[i + 1]) - && this.activate( targets[i] ) - } - } - - , activate: function (target) { - var active - , selector - - this.activeTarget = target - - $(this.selector) - .parent('.active') - .removeClass('active') - - selector = this.selector - + '[data-target="' + target + '"],' - + this.selector + '[href="' + target + '"]' - - active = $(selector) - .parent('li') - .addClass('active') - - if (active.parent('.dropdown-menu')) { - active = active.closest('li.dropdown').addClass('active') - } - - active.trigger('activate') - } - - } - - - /* SCROLLSPY PLUGIN DEFINITION - * =========================== */ - - $.fn.scrollspy = function ( option ) { - return this.each(function () { - var $this = $(this) - , data = $this.data('scrollspy') - , options = typeof option == 'object' && option - if (!data) $this.data('scrollspy', (data = new ScrollSpy(this, options))) - if (typeof option == 'string') data[option]() - }) - } - - $.fn.scrollspy.Constructor = ScrollSpy - - $.fn.scrollspy.defaults = { - offset: 10 - } - - - /* SCROLLSPY DATA-API - * ================== */ - - $(function () { - $('[data-spy="scroll"]').each(function () { - var $spy = $(this) - $spy.scrollspy($spy.data()) - }) - }) - -}(window.jQuery);/* ======================================================== - * bootstrap-tab.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#tabs - * ======================================================== - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ======================================================== */ - - -!function ($) { - - "use strict"; // jshint ;_; - - - /* TAB CLASS DEFINITION - * ==================== */ - - var Tab = function ( element ) { - this.element = $(element) - } - - Tab.prototype = { - - constructor: Tab - - , show: function () { - var $this = this.element - , $ul = $this.closest('ul:not(.dropdown-menu)') - , selector = $this.attr('data-target') - , previous - , $target - , e - - if (!selector) { - selector = $this.attr('href') - selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7 - } - - if ( $this.parent('li').hasClass('active') ) return - - previous = $ul.find('.active a').last()[0] - - e = $.Event('show', { - relatedTarget: previous - }) - - $this.trigger(e) - - if (e.isDefaultPrevented()) return - - $target = $(selector) - - this.activate($this.parent('li'), $ul) - this.activate($target, $target.parent(), function () { - $this.trigger({ - type: 'shown' - , relatedTarget: previous - }) - }) - } - - , activate: function ( element, container, callback) { - var $active = container.find('> .active') - , transition = callback - && $.support.transition - && $active.hasClass('fade') - - function next() { - $active - .removeClass('active') - .find('> .dropdown-menu > .active') - .removeClass('active') - - element.addClass('active') - - if (transition) { - element[0].offsetWidth // reflow for transition - element.addClass('in') - } else { - element.removeClass('fade') - } - - if ( element.parent('.dropdown-menu') ) { - element.closest('li.dropdown').addClass('active') - } - - callback && callback() - } - - transition ? - $active.one($.support.transition.end, next) : - next() - - $active.removeClass('in') - } - } - - - /* TAB PLUGIN DEFINITION - * ===================== */ - - $.fn.tab = function ( option ) { - return this.each(function () { - var $this = $(this) - , data = $this.data('tab') - if (!data) $this.data('tab', (data = new Tab(this))) - if (typeof option == 'string') data[option]() - }) - } - - $.fn.tab.Constructor = Tab - - - /* TAB DATA-API - * ============ */ - - $(function () { - $('body').on('click.tab.data-api', '[data-toggle="tab"], [data-toggle="pill"]', function (e) { - e.preventDefault() - $(this).tab('show') - }) - }) - -}(window.jQuery);/* ============================================================= - * bootstrap-typeahead.js v2.0.4 - * http://twitter.github.com/bootstrap/javascript.html#typeahead - * ============================================================= - * Copyright 2012 Twitter, Inc. - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - * ============================================================ */ - - -!function($){ - - "use strict"; // jshint ;_; - - - /* TYPEAHEAD PUBLIC CLASS DEFINITION - * ================================= */ - - var Typeahead = function (element, options) { - this.$element = $(element) - this.options = $.extend({}, $.fn.typeahead.defaults, options) - this.matcher = this.options.matcher || this.matcher - this.sorter = this.options.sorter || this.sorter - this.highlighter = this.options.highlighter || this.highlighter - this.updater = this.options.updater || this.updater - this.$menu = $(this.options.menu).appendTo('body') - this.source = this.options.source - this.shown = false - this.listen() - } - - Typeahead.prototype = { - - constructor: Typeahead - - , select: function () { - var val = this.$menu.find('.active').attr('data-value') - this.$element - .val(this.updater(val)) - .change() - return this.hide() - } - - , updater: function (item) { - return item - } - - , show: function () { - var pos = $.extend({}, this.$element.offset(), { - height: this.$element[0].offsetHeight - }) - - this.$menu.css({ - top: pos.top + pos.height - , left: pos.left - }) - - this.$menu.show() - this.shown = true - return this - } - - , hide: function () { - this.$menu.hide() - this.shown = false - return this - } - - , lookup: function (event) { - var that = this - , items - , q - - this.query = this.$element.val() - - if (!this.query) { - return this.shown ? this.hide() : this - } - - items = $.grep(this.source, function (item) { - return that.matcher(item) - }) - - items = this.sorter(items) - - if (!items.length) { - return this.shown ? this.hide() : this - } - - return this.render(items.slice(0, this.options.items)).show() - } - - , matcher: function (item) { - return ~item.toLowerCase().indexOf(this.query.toLowerCase()) - } - - , sorter: function (items) { - var beginswith = [] - , caseSensitive = [] - , caseInsensitive = [] - , item - - while (item = items.shift()) { - if (!item.toLowerCase().indexOf(this.query.toLowerCase())) beginswith.push(item) - else if (~item.indexOf(this.query)) caseSensitive.push(item) - else caseInsensitive.push(item) - } - - return beginswith.concat(caseSensitive, caseInsensitive) - } - - , highlighter: function (item) { - var query = this.query.replace(/[\-\[\]{}()*+?.,\\\^$|#\s]/g, '\\$&') - return item.replace(new RegExp('(' + query + ')', 'ig'), function ($1, match) { - return '<strong>' + match + '</strong>' - }) - } - - , render: function (items) { - var that = this - - items = $(items).map(function (i, item) { - i = $(that.options.item).attr('data-value', item) - i.find('a').html(that.highlighter(item)) - return i[0] - }) - - items.first().addClass('active') - this.$menu.html(items) - return this - } - - , next: function (event) { - var active = this.$menu.find('.active').removeClass('active') - , next = active.next() - - if (!next.length) { - next = $(this.$menu.find('li')[0]) - } - - next.addClass('active') - } - - , prev: function (event) { - var active = this.$menu.find('.active').removeClass('active') - , prev = active.prev() - - if (!prev.length) { - prev = this.$menu.find('li').last() - } - - prev.addClass('active') - } - - , listen: function () { - this.$element - .on('blur', $.proxy(this.blur, this)) - .on('keypress', $.proxy(this.keypress, this)) - .on('keyup', $.proxy(this.keyup, this)) - - if ($.browser.webkit || $.browser.msie) { - this.$element.on('keydown', $.proxy(this.keypress, this)) - } - - this.$menu - .on('click', $.proxy(this.click, this)) - .on('mouseenter', 'li', $.proxy(this.mouseenter, this)) - } - - , keyup: function (e) { - switch(e.keyCode) { - case 40: // down arrow - case 38: // up arrow - break - - case 9: // tab - case 13: // enter - if (!this.shown) return - this.select() - break - - case 27: // escape - if (!this.shown) return - this.hide() - break - - default: - this.lookup() - } - - e.stopPropagation() - e.preventDefault() - } - - , keypress: function (e) { - if (!this.shown) return - - switch(e.keyCode) { - case 9: // tab - case 13: // enter - case 27: // escape - e.preventDefault() - break - - case 38: // up arrow - if (e.type != 'keydown') break - e.preventDefault() - this.prev() - break - - case 40: // down arrow - if (e.type != 'keydown') break - e.preventDefault() - this.next() - break - } - - e.stopPropagation() - } - - , blur: function (e) { - var that = this - setTimeout(function () { that.hide() }, 150) - } - - , click: function (e) { - e.stopPropagation() - e.preventDefault() - this.select() - } - - , mouseenter: function (e) { - this.$menu.find('.active').removeClass('active') - $(e.currentTarget).addClass('active') - } - - } - - - /* TYPEAHEAD PLUGIN DEFINITION - * =========================== */ - - $.fn.typeahead = function (option) { - return this.each(function () { - var $this = $(this) - , data = $this.data('typeahead') - , options = typeof option == 'object' && option - if (!data) $this.data('typeahead', (data = new Typeahead(this, options))) - if (typeof option == 'string') data[option]() - }) - } - - $.fn.typeahead.defaults = { - source: [] - , items: 8 - , menu: '<ul class="typeahead dropdown-menu"></ul>' - , item: '<li><a href="#"></a></li>' - } - - $.fn.typeahead.Constructor = Typeahead - - - /* TYPEAHEAD DATA-API - * ================== */ - - $(function () { - $('body').on('focus.typeahead.data-api', '[data-provide="typeahead"]', function (e) { - var $this = $(this) - if ($this.data('typeahead')) return - e.preventDefault() - $this.typeahead($this.data()) - }) - }) - -}(window.jQuery);
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\ No newline at end of file diff --git a/docs/link.svg b/docs/link.svg new file mode 100644 index 0000000..88ad827 --- /dev/null +++ b/docs/link.svg @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="utf-8"?> +<!-- Generator: Adobe Illustrator 19.2.1, SVG Export Plug-In . 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Either a parent only model like -'SFO' or 'FOMC', or an mkinmod object</dd> - <dt>DT50</dt> - <dd>The half-life. This is only used when simple exponential decline -is calculated (SFO model).</dd> - <dt>parms</dt> - <dd>The parameters used for the degradation model</dd> - <dt>years</dt> - <dd>For how many years should the degradation be predicted?</dd> - <dt>step_days</dt> - <dd>What step size in days should the output have?</dd> - <dt>times</dt> - <dd>The output times</dd> - </dl> - - <div class="Description"> - <h2>Description</h2> - - <p>Calculate a time course of relative concentrations based on an mkinmod model</p> - - </div> - - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'><span class="functioncall"><a href='http://www.rdocumentation.org/packages/utils/topics/head'>head</a></span><span class="keyword">(</span><span class="functioncall"><a href='pfm_degradation.html'>pfm_degradation</a></span><span class="keyword">(</span><span class="string">"SFO"</span><span class="keyword">,</span> <span class="argument">DT50</span> <span class="argument">=</span> <span class="number">10</span><span class="keyword">)</span><span class="keyword">)</span></div> -<div class='output'> time parent -1 0 1.0000000 -2 1 0.9330330 -3 2 0.8705506 -4 3 0.8122524 -5 4 0.7578583 -6 5 0.7071068 -</div></pre> - </div> - <div class="span4 sidebar"> - <!-- <ul> - <li>pfm_degradation</li> - </ul> - <ul> - - </ul> --> - - - - <h2>Author</h2> - -Johannes Ranke - - - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
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+} + +/* Fixes for fixed navbar --------------------------*/ + +.contents h1, .contents h2, .contents h3, .contents h4 { + padding-top: 60px; + margin-top: -60px; +} + +/* Sidebar --------------------------*/ + +#sidebar { + margin-top: 30px; +} +#sidebar h2 { + font-size: 1.5em; + margin-top: 1em; +} + +#sidebar h2:first-child { + margin-top: 0; +} + +#sidebar .list-unstyled li { + margin-bottom: 0.5em; +} + +/* Syntax highlighting ---------------------------------------------------- */ + +code { + background-color: #f7f7f7; + color: #333; +} +code a { + color: #375f84; +} + +.warning { color: red; } +.message { font-weight: bolder; } +.error { color: red; font-weight: bolder; } + +.fl,.number {color:rgb(21,20,181);} +.fu,.functioncall {color:#264D66 ;} +.ch,.st,.string {color:#375D81 ;} +.kw,.keyword {color:black;} +.argument {color:#264D66 ;} +.co,.comment {color: #777;} +.formalargs {color: #264D66;} +.eqformalargs {color:#264D66;} +.slot {font-style:italic;} +.symbol {color:black ;} +.prompt {color:black ;} + +pre img { + background-color: #fff; + display: block; +} diff --git a/docs/pkgdown.js b/docs/pkgdown.js new file mode 100644 index 0000000..c8b38c4 --- /dev/null +++ b/docs/pkgdown.js @@ -0,0 +1,8 @@ +$(function() { + $("#sidebar").stick_in_parent({offset_top: 40}); + $('body').scrollspy({ + target: '#sidebar', + offset: 60 + }); + +}); diff --git a/docs/plot.TOXSWA_cwa-2.png b/docs/plot.TOXSWA_cwa-2.png Binary files differdeleted file mode 100644 index 764c7f4..0000000 --- a/docs/plot.TOXSWA_cwa-2.png +++ /dev/null diff --git a/docs/plot.TOXSWA_cwa.html b/docs/plot.TOXSWA_cwa.html deleted file mode 100644 index 87dae02..0000000 --- a/docs/plot.TOXSWA_cwa.html +++ /dev/null @@ -1,124 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>plot.TOXSWA_cwa. pfm 0.3-8</title> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=" -Johannes Ranke -"> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">pfm 0.3-8</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> - </div> - </div> -</div> - - - <div class="container"> - <header> - - </header> - - <h1>Plot TOXSWA surface water concentrations</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><span class="comment"># S3 method for TOXSWA_cwa</span> -<span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">x</span><span class="keyword">,</span> <span class="argument">time_column</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"datetime"</span><span class="keyword">,</span> <span class="string">"t"</span><span class="keyword">,</span> <span class="string">"t_firstjan"</span><span class="keyword">,</span> - <span class="string">"t_rel_to_max"</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">xlab</span> <span class="argument">=</span> <span class="string">"default"</span><span class="keyword">,</span> <span class="argument">ylab</span> <span class="argument">=</span> <span class="string">"default"</span><span class="keyword">,</span> <span class="argument">add</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">,</span> - <span class="argument">total</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">,</span> <span class="argument">LC_TIME</span> <span class="argument">=</span> <span class="string">"C"</span><span class="keyword">,</span> <span class="symbol">...</span><span class="keyword">)</span></pre> - - <h2>Arguments</h2> - <dl> - <dt>x</dt> - <dd>The TOXSWA_cwa object to be plotted.</dd> - <dt>time_column</dt> - <dd>What should be used for the time axis. If "t_firstjan" is chosen, -the time is given in days relative to the first of January in the first year.</dd> - <dt>xlab, ylab</dt> - <dd>Labels for x and y axis.</dd> - <dt>add</dt> - <dd>Should we add to an existing plot?</dd> - <dt>total</dt> - <dd>Should the total concentration in water be plotted, including substance sorbed -to suspended matter?</dd> - <dt>LC_TIME</dt> - <dd>Specification of the locale used to format dates</dd> - <dt>...</dt> - <dd>Further arguments passed to <code>plot</code> if we are not adding to an existing plot</dd> - </dl> - - <div class="Description"> - <h2>Description</h2> - - <p>Plot TOXSWA hourly concentrations of a chemical substance in a specific -segment of a TOXSWA surface water body.</p> - - </div> - - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'><span class="symbol">H_sw_D4_pond</span> <span class="assignement"><-</span> <span class="functioncall"><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span><span class="keyword">(</span><span class="string">"00001p_pa.cwa"</span><span class="keyword">,</span> - <span class="argument">basedir</span> <span class="argument">=</span> <span class="string">"SwashProjects/project_H_sw/TOXSWA"</span><span class="keyword">,</span> - <span class="argument">zipfile</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/devtools/topics/system.file'>system.file</a></span><span class="keyword">(</span><span class="string">"testdata/SwashProjects.zip"</span><span class="keyword">,</span> - <span class="argument">package</span> <span class="argument">=</span> <span class="string">"pfm"</span><span class="keyword">)</span><span class="keyword">)</span> -<span class="functioncall"><a href='http://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span><span class="keyword">(</span><span class="symbol">H_sw_D4_pond</span><span class="keyword">)</span></div> -<p><img src='plot.TOXSWA_cwa-2.png' alt='' width='540' height='400' /></p></pre> - </div> - <div class="span4 sidebar"> - <!-- <ul> - <li>plot.TOXSWA_cwa</li> - </ul> - <ul> - - </ul> --> - - - - <h2>Author</h2> - -Johannes Ranke - - - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/docs/read.TOXSWA_cwa.html b/docs/read.TOXSWA_cwa.html deleted file mode 100644 index cc34733..0000000 --- a/docs/read.TOXSWA_cwa.html +++ /dev/null @@ -1,142 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>read.TOXSWA_cwa. pfm 0.3-8</title> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=" -Johannes Ranke -"> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">pfm 0.3-8</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> - </div> - </div> -</div> - - - <div class="container"> - <header> - - </header> - - <h1>Read TOXSWA surface water concentrations</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><span class="functioncall"><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span><span class="keyword">(</span><span class="symbol">filename</span><span class="keyword">,</span> <span class="argument">basedir</span> <span class="argument">=</span> <span class="string">"."</span><span class="keyword">,</span> <span class="argument">zipfile</span> <span class="argument">=</span> NULL<span class="keyword">,</span> <span class="argument">segment</span> <span class="argument">=</span> <span class="string">"last"</span><span class="keyword">,</span> - <span class="argument">substance</span> <span class="argument">=</span> <span class="string">"parent"</span><span class="keyword">,</span> <span class="argument">total</span> <span class="argument">=</span> <span class="number">FALSE</span><span class="keyword">,</span> <span class="argument">windows</span> <span class="argument">=</span> NULL<span class="keyword">,</span> - <span class="argument">thresholds</span> <span class="argument">=</span> NULL<span class="keyword">)</span></pre> - - <h2>Arguments</h2> - <dl> - <dt>filename</dt> - <dd>The filename of the cwa file (TOXSWA 2.x.y or similar) or the -out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).</dd> - <dt>basedir</dt> - <dd>The path to the directory where the cwa file resides.</dd> - <dt>zipfile</dt> - <dd>Optional path to a zip file containing the cwa file.</dd> - <dt>segment</dt> - <dd>The segment for which the data should be read. Either "last", or -the segment number.</dd> - <dt>substance</dt> - <dd>For TOXSWA 4 .out files, the default value "parent" leads -to reading concentrations of the parent compound. Alternatively, the substance -of interested can be selected by its code name.</dd> - <dt>total</dt> - <dd>Set this to TRUE in order to read total concentrations as well. This is -only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa -files. For .cwa files, the total concentration is always read as well.</dd> - <dt>windows</dt> - <dd>Numeric vector of width of moving windows in days, for calculating -maximum time weighted average concentrations and areas under the curve.</dd> - <dt>thresholds</dt> - <dd>Numeric vector of threshold concentrations in µg/L for -generating event statistics.</dd> - </dl> - - <div class="Value"> - <h2>Value</h2> - - <p><dl> -An instance of an R6 object of class -<code><a href='TOXSWA_cwa.html'>TOXSWA_cwa</a></code>. -</dl></p> - - </div> - - <div class="Description"> - <h2>Description</h2> - - <p>Read TOXSWA hourly concentrations of a chemical substance in a specific -segment of a TOXSWA surface water body. Per default, the data for the last -segment are imported. As TOXSWA 4 reports the values at the end of the hour -(ConLiqWatLayCur) in its summary file, we use this value as well instead -of the hourly averages (ConLiqWatLay).</p> - - </div> - - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'><span class="symbol">H_sw_D4_pond</span> <span class="assignement"><-</span> <span class="functioncall"><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span><span class="keyword">(</span><span class="string">"00001p_pa.cwa"</span><span class="keyword">,</span> - <span class="argument">basedir</span> <span class="argument">=</span> <span class="string">"SwashProjects/project_H_sw/TOXSWA"</span><span class="keyword">,</span> - <span class="argument">zipfile</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/devtools/topics/system.file'>system.file</a></span><span class="keyword">(</span><span class="string">"testdata/SwashProjects.zip"</span><span class="keyword">,</span> - <span class="argument">package</span> <span class="argument">=</span> <span class="string">"pfm"</span><span class="keyword">)</span><span class="keyword">)</span></div></pre> - </div> - <div class="span4 sidebar"> - <!-- <ul> - <li>read.TOXSWA_cwa</li> - </ul> - <ul> - - </ul> --> - - - - <h2>Author</h2> - -Johannes Ranke - - - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/docs/reference.html b/docs/reference.html deleted file mode 100644 index 83e788a..0000000 --- a/docs/reference.html +++ /dev/null @@ -1,164 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>Function reference. pfm 0.3-8</title> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=""> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">pfm 0.3-8</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> - </div> - </div> -</div> - - - <div class="container"> - <header> - - </header> - - <div class="row"> - <div class="span8"> - <h2>Function reference</h2> - - <h3>Degradation</h3> - <p>Functions related to degradation</p> - - - <ul class="index"> - - <li> - <code><a href="pfm_degradation.html">pfm_degradation</a></code><br />Calculate a time course of relative concentrations based on an mkinmod model</li> - - <li> - <code><a href="SFO_actual_twa.html">SFO_actual_twa</a></code><br />Actual and maximum moving window time average concentrations for SFO kinetics</li> - - </ul> - <h3>Mobility</h3> - <p>Indicators related to mobility</p> - - - <ul class="index"> - - <li> - <code><a href="GUS.html">GUS</a></code>(GUS.chent, GUS.numeric, print.GUS_result)<br />Groundwater ubiquity score based on Gustafson (1989)</li> - - <li> - <code><a href="SSLRC_mobility_classification.html">SSLRC_mobility_classification</a></code><br />Determine the SSLRC mobility classification for a chemical substance from its Koc</li> - - </ul> - <h3>Soil</h3> - <p>Predicted environmental concentrations in soil</p> - - - <ul class="index"> - - <li> - <code><a href="PEC_soil.html">PEC_soil</a></code><br />Calculate predicted environmental concentrations in soil</li> - - <li> - <code><a href="soil_scenario_data_EFSA_2015.html">soil_scenario_data_EFSA_2015</a></code><br />Properties of the predefined scenarios from the EFSA guidance from 2015</li> - - </ul> - <h3>Surface water</h3> - <p>Predicted environmental concentrations in surface water</p> - - - <ul class="index"> - - <li> - <code><a href="PEC_sw_drift.html">PEC_sw_drift</a></code><br />Calculate predicted environmental concentrations in surface water due to drift</li> - - <li> - <code><a href="PEC_sw_sed.html">PEC_sw_sed</a></code><br />Calculate predicted environmental concentrations in sediment from surface -water concentrations</li> - - <li> - <code><a href="drift_data_JKI.html">drift_data_JKI</a></code><br />Deposition from spray drift expressed as percent of the applied dose as -published by the JKI</li> - - <li> - <code><a href="PEC_sw_drainage_UK.html">PEC_sw_drainage_UK</a></code><br />Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method</li> - - <li> - <code><a href="TOXSWA_cwa.html">TOXSWA_cwa</a></code><br />R6 class for holding TOXSWA cwa concentration data and associated statistics</li> - - <li> - <code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></code><br />Read TOXSWA surface water concentrations</li> - - <li> - <code><a href="plot.TOXSWA_cwa.html">plot.TOXSWA_cwa</a></code><br />Plot TOXSWA surface water concentrations</li> - - </ul> - <h3>Groundwater</h3> - <p>Predicted environmental concentrations in groundwater</p> - - - <ul class="index"> - - <li> - <code><a href="FOCUS_GW_scenarios_2012.html">FOCUS_GW_scenarios_2012</a></code><br />A very small subset of the FOCUS Groundwater scenario defitions</li> - - </ul> - <h3>Chemical entities</h3> - <p>Work with input stored in chemical entites as R objects using the chent package</p> - - - <ul class="index"> - - <li> - <code><a href="endpoint.html">endpoint</a></code>(soil_DT50, soil_Kfoc, soil_N, soil_sorption)<br />Retrieve endpoint information from the chyaml field of a chent object</li> - - </ul> - <h3>General</h3> - <p>Utilities that are generally useful</p> - - - <ul class="index"> - - <li> - <code><a href="geomean.html">geomean</a></code><br />Calculate the geometric mean</li> - - </ul> - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/docs/reference/FOCUS_GW_scenarios_2012.html b/docs/reference/FOCUS_GW_scenarios_2012.html new file mode 100644 index 0000000..64b42e9 --- /dev/null +++ b/docs/reference/FOCUS_GW_scenarios_2012.html @@ -0,0 +1,171 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>A very small subset of the FOCUS Groundwater scenario defitions — FOCUS_GW_scenarios_2012 • pfm</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">pfm</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>A very small subset of the FOCUS Groundwater scenario defitions</h1> + </div> + + + <p>Currently, only a small subset of the soil definitions are provided.</p> + + + + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> + + <p>FOCUS (2012) Generic guidance for Tier 1 FOCUS ground water assessments. Version 2.1. + FOrum for the Co-ordination of pesticde fate models and their USe. + http://focus.jrc.ec.europa.eu/gw/docs/Generic_guidance_FOCV2_1.pdf</p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='no'>FOCUS_GW_scenarios_2012</span></div><div class='output co'>#> $names +#> Cha Ham Jok Kre Oke +#> "Châteaudun" "Hamburg" "Jokioinen" "Kremsmünster" "Okehampton" +#> Pia Por Sev Thi +#> "Piacenza" "Porto" "Sevilla" "Thiva" +#> +#> $soils +#> location horizon number pH_H2O perc_clay perc_oc rel_deg +#> 1 Cha Ap 1 8.0 30.0 1.39 1.0 +#> 2 Cha B1 2 8.1 31.0 0.93 0.5 +#> 3 Cha B2 3 8.2 25.0 0.70 0.5 +#> 4 Cha II C1 4 8.5 26.0 0.30 0.3 +#> 5 Cha II C1 5 8.5 26.0 0.30 0.0 +#> 6 Cha II C2 6 8.5 24.0 0.27 0.0 +#> 7 Cha M 7 8.3 31.0 0.21 0.0 +#> 8 Ham Ap 1 6.4 7.2 1.50 1.0 +#> 9 Ham BvI 2 5.6 6.7 1.00 0.5 +#> 10 Ham BvII 3 5.6 0.9 0.20 0.3 +#> 11 Ham Bv/Cv 4 5.7 0.0 0.00 0.3 +#> 12 Ham Cv 5 5.5 0.0 0.00 0.3 +#> 13 Ham Cv 6 5.5 0.0 0.00 0.0 +#> 14 Jok Ap 1 6.2 3.6 4.06 1.0 +#> 15 Jok Bs 2 5.6 1.8 0.84 0.5 +#> 16 Jok BC1 3 5.4 1.2 0.36 0.3 +#> 17 Jok BC2 4 5.4 1.7 0.29 0.3 +#> 18 Jok BC2 5 5.4 1.7 0.29 0.0 +#> 19 Jok Cg 6 5.3 1.9 0.21 0.0 +#> 20 Kre <NA> 1 7.7 14.0 3.60 1.0 +#> 21 Kre <NA> 2 7.0 25.0 1.00 0.5 +#> 22 Kre <NA> 3 7.1 27.0 0.50 0.5 +#> 23 Kre <NA> 4 7.1 27.0 0.50 0.3 +#> 24 Kre <NA> 5 7.1 27.0 0.50 0.0 +#> 25 Oke A 1 5.8 18.0 2.20 1.0 +#> 26 Oke Bw1 2 6.3 17.0 0.70 0.5 +#> 27 Oke BC 3 6.5 14.0 0.40 0.3 +#> 28 Oke C 4 6.6 9.0 0.10 0.3 +#> 29 Oke C 5 6.6 9.0 0.10 0.0 +#> 30 Pia Ap 1 7.0 15.0 1.26 1.0 +#> 31 Pia Ap 2 7.0 15.0 1.26 0.5 +#> 32 Pia Bw 3 6.3 7.0 0.47 0.5 +#> 33 Pia Bw 4 6.3 7.0 0.47 0.3 +#> 34 Pia 2C 5 6.4 0.0 0.00 0.3 +#> 35 Pia 2C 6 6.4 0.0 0.00 0.0 +#> 36 Por <NA> 1 4.9 10.0 1.42 1.0 +#> 37 Por <NA> 2 4.8 8.0 0.78 0.5 +#> 38 Por <NA> 3 4.8 8.0 0.78 0.3 +#> 39 Por <NA> 4 4.8 8.0 0.78 0.0 +#> 40 Sev <NA> 1 7.3 14.0 0.93 1.0 +#> 41 Sev <NA> 2 7.3 13.0 0.93 1.0 +#> 42 Sev <NA> 3 7.8 15.0 0.70 0.5 +#> 43 Sev <NA> 4 8.1 16.0 0.58 0.3 +#> 44 Sev <NA> 5 8.1 16.0 0.58 0.0 +#> 45 Sev <NA> 6 8.2 22.0 0.49 0.0 +#> 46 Thi Ap1 1 7.7 25.3 0.74 1.0 +#> 47 Thi Ap2 2 7.7 25.3 0.74 0.5 +#> 48 Thi Bw 3 7.8 29.6 0.57 0.5 +#> 49 Thi Bw 4 7.8 31.9 0.31 0.3 +#> 50 Thi Ck1 5 7.8 32.9 0.18 0.3 +#> 51 Thi Ck1 6 7.8 32.9 0.18 0.0 +#> </div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + + <li><a href="#references">References</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/GUS.html b/docs/reference/GUS.html new file mode 100644 index 0000000..f65c6fd --- /dev/null +++ b/docs/reference/GUS.html @@ -0,0 +1,181 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Groundwater ubiquity score based on Gustafson (1989) — GUS • pfm</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">pfm</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Groundwater ubiquity score based on Gustafson (1989)</h1> + </div> + + + <p>The groundwater ubiquity score GUS is calculated according to +the following equation +$$GUS = \log_{10} DT50_{soil} (4 - \log_{10} K_{oc})$$</p> + + + <pre><span class='fu'>GUS</span>(<span class='no'>...</span>) + +<span class='co'># S3 method for numeric</span> +<span class='fu'>GUS</span>(<span class='no'>DT50</span>, <span class='no'>Koc</span>, <span class='no'>...</span>) + +<span class='co'># S3 method for chent</span> +<span class='fu'>GUS</span>(<span class='no'>chent</span>, <span class='kw'>degradation_value</span> <span class='kw'>=</span> <span class='st'>"DT50ref"</span>, + <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='st'>"laboratory"</span>, <span class='kw'>redox</span> <span class='kw'>=</span> <span class='st'>"aerobic"</span>, <span class='kw'>sorption_value</span> <span class='kw'>=</span> <span class='st'>"Kfoc"</span>, + <span class='kw'>degradation_aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>sorption_aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='no'>...</span>) + +<span class='co'># S3 method for GUS_result</span> +<span class='fu'>print</span>(<span class='no'>x</span>, <span class='no'>...</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <dl class="dl-horizontal"> + <dt>...</dt> + <dd>Included in the generic to allow for further arguments later. Therefore +this also had to be added to the specific methods.</dd> + <dt>DT50</dt> + <dd>Half-life of the chemical in soil. Should be a field +half-life according to Gustafson (1989). However, leaching to the sub-soil +can not completely be excluded in field dissipation experiments and Gustafson +did not refer to any normalisation procedure, but says the field study should +be conducted under use conditions.</dd> + <dt>Koc</dt> + <dd>The sorption constant normalised to organic carbon. Gustafson +does not mention the nonlinearity of the sorption constant commonly +found and usually described by Freundlich sorption, therefore it is +unclear at which reference concentration the Koc should be observed +(and if the reference concentration would be in soil or in porewater).</dd> + <dt>chent</dt> + <dd>If a chent is given with appropriate information present in its +chyaml field, this information is used, with defaults specified below.</dd> + <dt>degradation_value</dt> + <dd>Which of the available degradation values should +be used?</dd> + <dt>lab_field</dt> + <dd>Should laboratory or field half-lives be used? This +defaults to lab in this implementation, in order to avoid +double-accounting for mobility. If comparability with the original GUS +values given by Gustafson (1989) is desired, non-normalised first-order +field half-lives obtained under actual use conditions should be used.</dd> + <dt>redox</dt> + <dd>Aerobic or anaerobic degradation data</dd> + <dt>sorption_value</dt> + <dd>Which of the available sorption values should be used? +Defaults to Kfoc as this is what is generally available from the European +pesticide peer review process. These values generally use a reference +concentration of 1 mg/L in porewater, that means they would be expected to +be Koc values at a concentration of 1 mg/L in the water phase.</dd> + <dt>degradation_aggregator</dt> + <dd>Function for aggregating half-lives</dd> + <dt>sorption_aggregator</dt> + <dd>Function for aggregation Koc values</dd> + <dt>x</dt> + <dd>An object of class GUS_result to be printed</dd> + <dt>digits</dt> + <dd>The number of digits used in the print method</dd> + </dl> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>A list with the DT50 and Koc used as well as the resulting score + of class GUS_result</p> + + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> + + <p>Gustafson, David I. (1989) Groundwater ubiquity score: a simple +method for assessing pesticide leachability. <em>Environmental +toxicology and chemistry</em> <b>8</b>(4) 339–57.</p> + + + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#references">References</a></li> + </ul> + + <h2>Author</h2> + +Johannes Ranke + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html new file mode 100644 index 0000000..0449f8e --- /dev/null +++ b/docs/reference/PEC_soil.html @@ -0,0 +1,229 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Calculate predicted environmental concentrations in soil — PEC_soil • pfm</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">pfm</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Calculate predicted environmental concentrations in soil</h1> + </div> + + + <p>This is a basic calculation of a contaminant concentration in bulk soil +based on complete, instantaneous mixing. If an interval is given, an +attempt is made at calculating a long term maximum concentration using +the concepts layed out for example in the PPR panel opinion (EFSA 2012).</p> + + + <pre><span class='fu'>PEC_soil</span>(<span class='no'>rate</span>, <span class='kw'>rate_units</span> <span class='kw'>=</span> <span class='st'>"g/ha"</span>, <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>mixing_depth</span> <span class='kw'>=</span> <span class='fl'>5</span>, + <span class='kw'>PEC_units</span> <span class='kw'>=</span> <span class='st'>"mg/kg"</span>, <span class='kw'>PEC_pw_units</span> <span class='kw'>=</span> <span class='st'>"mg/L"</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>NA</span>, + <span class='kw'>n_periods</span> <span class='kw'>=</span> <span class='fl'>Inf</span>, <span class='kw'>tillage_depth</span> <span class='kw'>=</span> <span class='fl'>20</span>, <span class='kw'>chent</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>NA</span>, + <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='no'>Koc</span>/<span class='fl'>1.724</span>, <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"default"</span>, + <span class='st'>"EFSA_2015"</span>), <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <dl class="dl-horizontal"> + <dt>rate</dt> + <dd>Application rate in units specified below</dd> + <dt>rate_units</dt> + <dd>Defaults to g/ha</dd> + <dt>interception</dt> + <dd>The fraction of the application rate that does not reach the soil</dd> + <dt>mixing_depth</dt> + <dd>Mixing depth in cm</dd> + <dt>PEC_units</dt> + <dd>Requested units for the calculated PEC. Only mg/kg currently supported</dd> + <dt>PEC_pw_units</dt> + <dd>Only mg/L currently supported</dd> + <dt>interval</dt> + <dd>Period of the deeper mixing, defaults to 365, which is a year if +rate units are in days</dd> + <dt>n_periods</dt> + <dd>Number of periods to be considered for long term PEC calculations</dd> + <dt>tillage_depth</dt> + <dd>Periodic (see interval) deeper mixing in cm</dd> + <dt>chent</dt> + <dd>An optional chent object holding substance specific information. Can +also be a name for the substance as a character string</dd> + <dt>DT50</dt> + <dd>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</dd> + <dt>Koc</dt> + <dd>If specified, overrides Koc endpoints from a chent object</dd> + <dt>Kom</dt> + <dd>Calculated from Koc by default, but can explicitly be specified +as Kom here</dd> + <dt>t_avg</dt> + <dd>Averaging times for time weighted average concentrations</dd> + <dt>scenarios</dt> + <dd>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), +and corrected using an Arrhenius activation energy of 65.4 kJ/mol. Also +model and scenario adjustment factors from the EFSA guidance are used.</dd> + <dt>porewater</dt> + <dd>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).</dd> + </dl> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>The predicted concentration in soil</p> + + <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> + + <p>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 (PPR panel 2012), only temperature correction using the +Arrhenius equation is performed.</p> + <p>Total soil and porewater PEC values for the scenarios as defined in the EFSA +guidance (2015, p. 13) can easily be calculated.</p> + + <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> + + <p>If temperature information is available in the selected scenarios, as + 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'.</p> + + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> + + <p>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 + concentrations of plant protection products in soil. <em>EFSA Journal</em> + <b>10</b>(2) 2562, doi:10.2903/j.efsa.2012.2562</p> + <p>EFSA (European Food Safety Authority) (2015) EFSA guidance document for + predicting environmental concentrations of active substances of plant + protection products and transformation products of these active substances + in soil. <em>EFSA Journal</em> <b>13</b>(4) 4093 + doi:10.2903/j.efsa.2015.4093</p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='fu'>PEC_soil</span>(<span class='fl'>100</span>, <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0.25</span>)</div><div class='output co'>#> scenario +#> t_avg default +#> 0 0.1</div><div class='input'> +<span class='co'># This is example 1 starting at p. 79 of the EFSA guidance (2015)</span> +<span class='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>21</span>), + <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>)</div><div class='output co'>#> scenario +#> t_avg CTN CTC CTS +#> 0 21.96827 11.53750 9.145259 +#> 21 21.78517 11.40701 9.017370</div><div class='input'><span class='fu'>PEC_soil</span>(<span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_av</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>21</span>), + <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>, <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> scenario +#> t_avg CLN CLC CLS +#> 0 0.7589401 0.6674322 0.9147861 +#> 21 0.7506036 0.6590345 0.8987279</div><div class='input'> +<span class='co'># The following is from example 4 starting at p. 85 of the EFSA guidance (2015)</span> +<span class='co'># Metabolite M2</span> +<span class='co'># Calculate total and porewater soil concentrations for tier 1 scenarios</span> +<span class='co'># Relative molar mass is 100/300, formation fraction is 0.7 * 1</span> +<span class='no'>results_pfm</span> <span class='kw'><-</span> <span class='fu'>PEC_soil</span>(<span class='fl'>100</span>/<span class='fl'>300</span> * <span class='fl'>0.7</span> * <span class='fl'>1</span> * <span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_avg</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>21</span>), + <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>) +<span class='no'>results_pfm_pw</span> <span class='kw'><-</span> <span class='fu'>PEC_soil</span>(<span class='fl'>100</span>/<span class='fl'>300</span> * <span class='fl'>0.7</span> * <span class='fl'>1000</span>, <span class='kw'>interval</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>t_av</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>21</span>), + <span class='kw'>Kom</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>scenarios</span> <span class='kw'>=</span> <span class='st'>"EFSA_2015"</span>, <span class='kw'>porewater</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#details">Details</a></li> + + <li><a href="#note">Note</a></li> + + <li><a href="#references">References</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + <h2>Author</h2> + +Johannes Ranke + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/PEC_sw_drainage_UK.html b/docs/reference/PEC_sw_drainage_UK.html new file mode 100644 index 0000000..db0f85f --- /dev/null +++ b/docs/reference/PEC_sw_drainage_UK.html @@ -0,0 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class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">pfm</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method</h1> + </div> + + + <p>This implements the method specified in the UK data requirements handbook and was checked against the spreadsheet +published on the CRC website</p> + + + <pre><span class='fu'>PEC_sw_drainage_UK</span>(<span class='no'>rate</span>, <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='no'>Koc</span>, <span class='kw'>latest_application</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, + <span class='kw'>soil_DT50</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>model</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>model_parms</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <dl class="dl-horizontal"> + <dt>rate</dt> + <dd>Application rate in g/ha</dd> + <dt>interception</dt> + <dd>The fraction of the application rate that does not reach the soil</dd> + <dt>Koc</dt> + <dd>The sorption coefficient normalised to organic carbon in L/kg</dd> + <dt>latest_application</dt> + <dd>Latest application date, formatted as e.g. "01 July"</dd> + <dt>soil_DT50</dt> + <dd>Soil degradation half-life, if SFO kinetics are to be used</dd> + <dt>model</dt> + <dd>The soil degradation model to be used. Either one of "FOMC", +"DFOP", "HS", or "IORE", or an mkinmod object</dd> + <dt>model_parms</dt> + <dd>A named numeric vector containing the model parameters</dd> + </dl> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>The predicted concentration in surface water in µg/L</p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='fu'>PEC_sw_drainage_UK</span>(<span class='fl'>150</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>100</span>)</div><div class='output co'>#> [1] 8.076923</div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + <h2>Author</h2> + +Johannes Ranke + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/PEC_sw_drift.html b/docs/reference/PEC_sw_drift.html new file mode 100644 index 0000000..a168de3 --- /dev/null +++ b/docs/reference/PEC_sw_drift.html @@ -0,0 +1,144 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Calculate predicted environmental concentrations in surface water due to drift — PEC_sw_drift • pfm</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">pfm</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Calculate predicted environmental concentrations in surface water due to drift</h1> + </div> + + + <p>This is a basic, vectorised form of a simple calculation of a contaminant +concentration in surface water based on complete, instantaneous mixing +with input via spray drift.</p> + + + <pre><span class='fu'>PEC_sw_drift</span>(<span class='no'>rate</span>, <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>water_depth</span> <span class='kw'>=</span> <span class='fl'>30</span>, + <span class='kw'>drift_percentages</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>drift_data</span> <span class='kw'>=</span> <span class='st'>"JKI"</span>, <span class='kw'>crop</span> <span class='kw'>=</span> <span class='st'>"Ackerbau"</span>, + <span class='kw'>distances</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>, <span class='fl'>5</span>, <span class='fl'>10</span>, <span class='fl'>20</span>), <span class='kw'>rate_units</span> <span class='kw'>=</span> <span class='st'>"g/ha"</span>, <span class='kw'>PEC_units</span> <span class='kw'>=</span> <span class='st'>"µg/L"</span>)</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <dl class="dl-horizontal"> + <dt>rate</dt> + <dd>Application rate in units specified below</dd> + <dt>applications</dt> + <dd>Number of applications for selection of drift percentile</dd> + <dt>water_depth</dt> + <dd>Depth of the water body in cm</dd> + <dt>drift_percentages</dt> + <dd>Percentage drift values for which to calculate PECsw. +'drift_data' and 'distances' if not NULL.</dd> + <dt>drift_data</dt> + <dd>Source of drift percentage data</dd> + <dt>crop</dt> + <dd>Crop name (use German names for JKI data), defaults to "Ackerbau"</dd> + <dt>distances</dt> + <dd>The distances in m for which to get PEC values</dd> + <dt>rate_units</dt> + <dd>Defaults to g/ha</dd> + <dt>PEC_units</dt> + <dd>Requested units for the calculated PEC. Only µg/L currently supported</dd> + </dl> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>The predicted concentration in surface water</p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='fu'>PEC_sw_drift</span>(<span class='fl'>100</span>)</div><div class='output co'>#> 1 m 5 m 10 m 20 m +#> 0.92333333 0.19000000 0.09666667 0.05000000 </div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + <h2>Author</h2> + +Johannes Ranke + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/PEC_sw_sed.html b/docs/reference/PEC_sw_sed.html new file mode 100644 index 0000000..6ede4c7 --- /dev/null +++ b/docs/reference/PEC_sw_sed.html @@ -0,0 +1,142 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Calculate predicted environmental concentrations in sediment from surface + — PEC_sw_sed • pfm</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">pfm</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Calculate predicted environmental concentrations in sediment from surface +</h1> + </div> + + + <p>The method 'percentage' is equivalent to what is used in the CRD spreadsheet +PEC calculator</p> + + + <pre><span class='fu'>PEC_sw_sed</span>(<span class='no'>PEC_sw</span>, <span class='kw'>percentage</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"percentage"</span>, + <span class='kw'>sediment_depth</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>water_depth</span> <span class='kw'>=</span> <span class='fl'>30</span>, <span class='kw'>sediment_density</span> <span class='kw'>=</span> <span class='fl'>1.3</span>, + <span class='kw'>PEC_sed_units</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"µg/kg"</span>, <span class='st'>"mg/kg"</span>))</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <dl class="dl-horizontal"> + <dt>PEC_sw</dt> + <dd>Numeric vector or matrix of surface water concentrations in µg/L for +which the corresponding sediment concentration is to be estimated</dd> + <dt>percentage</dt> + <dd>The percentage in sediment, used for the percentage method</dd> + <dt>method</dt> + <dd>The method used for the calculation</dd> + <dt>sediment_depth</dt> + <dd>Depth of the sediment layer</dd> + <dt>water_depth</dt> + <dd>Depth of the water body in cm</dd> + <dt>sediment_density</dt> + <dd>The density of the sediment in L/kg (equivalent to +g/cm3)</dd> + <dt>PEC_sed_units</dt> + <dd>The units of the estimated sediment PEC value</dd> + </dl> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>The predicted concentration in sediment</p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='fu'>PEC_sw_sed</span>(<span class='fu'><a href='PEC_sw_drift.html'>PEC_sw_drift</a></span>(<span class='fl'>100</span>, <span class='kw'>distances</span> <span class='kw'>=</span> <span class='fl'>1</span>), <span class='kw'>percentage</span> <span class='kw'>=</span> <span class='fl'>50</span>)</div><div class='output co'>#> 1 m +#> 2.130769 </div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + <h2>Author</h2> + +Johannes Ranke + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/SFO_actual_twa.html b/docs/reference/SFO_actual_twa.html new file mode 100644 index 0000000..4285191 --- /dev/null +++ b/docs/reference/SFO_actual_twa.html @@ -0,0 +1,138 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Actual and maximum moving window time average concentrations for SFO kinetics — SFO_actual_twa • pfm</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">pfm</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Actual and maximum moving window time average concentrations for SFO kinetics</h1> + </div> + + + <p>Actual and maximum moving window time average concentrations for SFO kinetics</p> + + + <pre><span class='fu'>SFO_actual_twa</span>(<span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>4</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>21</span>, <span class='fl'>28</span>, <span class='fl'>42</span>, <span class='fl'>50</span>, + <span class='fl'>100</span>))</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <dl class="dl-horizontal"> + <dt>DT50</dt> + <dd>The half-life.</dd> + <dt>times</dt> + <dd>The output times, and window sizes for time weighted average concentrations</dd> + </dl> + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + + <p>FOCUS (2014) Generic Guidance for Estimating Persistence and Degradation + Kinetics from Environmental Fate Studies on Pesticides in EU Registratin, Version 1.1, + 18 December 2014, p. 251</p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='fu'>SFO_actual_twa</span>(<span class='fl'>10</span>)</div><div class='output co'>#> actual twa +#> 0 1.0000000000 NaN +#> 1 0.9330329915 0.9661297 +#> 2 0.8705505633 0.9337803 +#> 4 0.7578582833 0.8733416 +#> 7 0.6155722067 0.7923030 +#> 14 0.3789291416 0.6400113 +#> 21 0.2332582479 0.5267498 +#> 28 0.1435872944 0.4412651 +#> 42 0.0544094102 0.3248093 +#> 50 0.0312500000 0.2795222 +#> 100 0.0009765625 0.1441286</div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#source">Source</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + <h2>Author</h2> + +Johannes Ranke + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/SSLRC_mobility_classification.html b/docs/reference/SSLRC_mobility_classification.html new file mode 100644 index 0000000..f207a7a --- /dev/null +++ b/docs/reference/SSLRC_mobility_classification.html @@ -0,0 +1,129 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Determine the SSLRC mobility classification for a chemical substance from its Koc — SSLRC_mobility_classification • pfm</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">pfm</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Determine the SSLRC mobility classification for a chemical substance from its Koc</h1> + </div> + + + <p>This implements the method specified in the UK data requirements handbook and was +checked against the spreadsheet published on the CRC website</p> + + + <pre><span class='fu'>SSLRC_mobility_classification</span>(<span class='no'>Koc</span>)</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <dl class="dl-horizontal"> + <dt>Koc</dt> + <dd>The sorption coefficient normalised to organic carbon in L/kg</dd> + </dl> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>A list containing the classification and the percentage of the + compound transported per 10 mm drain water</p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='fu'>SSLRC_mobility_classification</span>(<span class='fl'>100</span>)</div><div class='output co'>#> $`Mobility classification` +#> [1] "Moderately mobile" +#> +#> $`Percentage drained per mm of drain water` +#> [1] 0.7 +#> </div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + <h2>Author</h2> + +Johannes Ranke + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html new file mode 100644 index 0000000..3f9310a --- /dev/null +++ b/docs/reference/TOXSWA_cwa.html @@ -0,0 +1,178 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>R6 class for holding TOXSWA cwa concentration data and associated statistics — TOXSWA_cwa • pfm</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">pfm</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>R6 class for holding TOXSWA cwa concentration data and associated statistics</h1> + </div> + + + <p>An R6 class for holding TOXSWA cwa concentration data and some associated statistics. +Usually, an instance of this class will be generated by <code><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></code>.</p> + + + <pre><span class='no'>TOXSWA_cwa</span></pre> + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + + <p>An <code>R6Class</code> generator object.</p> + + <h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2> + + <p></p> + <p><dl class='dl-horizontal'> +<dt><code>filename</code></dt><dd>Length one character vector.</dd></p> + <p><dt><code>basedir</code></dt><dd>Length one character vector.</dd></p> + <p><dt><code>segment</code></dt><dd>Length one integer, specifying for which segment the cwa data were read.</dd></p> + <p><dt><code>cwas</code></dt><dd>Dataframe holding the concentrations.</dd></p> + <p><dt><code>events</code></dt><dd>List of dataframes holding the event statistics for each threshold.</dd></p> + <p><dt><code>windows</code></dt><dd>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.</dd> +</dl></p> + + <h2 class="hasAnchor" id="methods"><a class="anchor" href="#methods"></a>Methods</h2> + + <p></p> + <p><dl class='dl-horizontal'> + <dt><code>get_events(threshold, total = FALSE)</code></dt><dd> + Populate a datataframe with event information for the specified threshold value + in µg/L. If <code>total = TRUE</code>, the total concentration including the amount + adsorbed to suspended matter will be used. The resulting dataframe is stored in the + <code>events</code> field of the object. + </dd> + <dt><code>moving_windows(windows, total = FALSE)</code></dt><dd> + Add to the <code>windows</code> field described above. + Again, if <code>total = TRUE</code>, the total concentration including the amount + adsorbed to suspended matter will be used. + </dd> +</dl></p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='no'>H_sw_R1_stream</span> <span class='kw'><-</span> <span class='fu'><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span>(<span class='st'>"00003s_pa.cwa"</span>, + <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>, + <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'>system.file</span>(<span class='st'>"testdata/SwashProjects.zip"</span>, + <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>)) +<span class='no'>H_sw_R1_stream</span>$<span class='fu'>get_events</span>(<span class='fu'>c</span>(<span class='fl'>2</span>, <span class='fl'>10</span>)) +<span class='no'>H_sw_R1_stream</span>$<span class='fu'>moving_windows</span>(<span class='fu'>c</span>(<span class='fl'>7</span>, <span class='fl'>21</span>)) +<span class='fu'>print</span>(<span class='no'>H_sw_R1_stream</span>)</div><div class='output co'>#> <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</div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + + <li><a href="#format">Format</a></li> + + <li><a href="#fields">Fields</a></li> + + <li><a href="#methods">Methods</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/drift_data_JKI.html b/docs/reference/drift_data_JKI.html new file mode 100644 index 0000000..527c1cb --- /dev/null +++ b/docs/reference/drift_data_JKI.html @@ -0,0 +1,255 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Deposition from spray drift expressed as percent of the applied dose as + — drift_data_JKI • pfm</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">pfm</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Deposition from spray drift expressed as percent of the applied dose as +</h1> + </div> + + + <p>Deposition from spray drift expressed as percent of the applied dose as +published by the German Julius-Kühn Institute (JKI).</p> + + + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + + <p>A list currently containing matrices with spray drift percentage +data for field crops (Ackerbau), and Pome/stone fruit, early and late +(Obstbau frueh, spaet).</p> + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + + <p>JKI (2010) Spreadsheet 'Tabelle der Abdrifteckwerte.xls', retrieved +from +http://www.jki.bund.de/no_cache/de/startseite/institute/anwendungstechnik/abdrift-eckwerte.html +on 2015-06-11</p> + + <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> + + <p>The data were extracted from the spreadsheet cited below using the R code +given in the example section. The spreadsheet is not included in the package +as its licence is not clear.</p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'> +<span class='co'>## Not run: ------------------------------------</span> +<span class='co'># # This is the code that was used to extract the data</span> +<span class='co'># library(readxl)</span> +<span class='co'># abdrift_path <- "inst/extdata/Tabelle der Abdrifteckwerte.xls"</span> +<span class='co'># JKI_crops <- c("Ackerbau", "Obstbau frueh", "Obstbau spaet")</span> +<span class='co'># names(JKI_crops) <- c("Field crops", "Pome/stone fruit, early", "Pome/stone fruit, late")</span> +<span class='co'># drift_data_JKI <- list()</span> +<span class='co'># </span> +<span class='co'># for (n in 1:8) {</span> +<span class='co'># drift_data_raw <- read_excel(abdrift_path, sheet = n + 1, skip = 2)</span> +<span class='co'># drift_data <- as.matrix(drift_data_raw[1:9, 2:4]) </span> +<span class='co'># dimnames(drift_data) <- list(distance = as.integer(drift_data_raw[1:9, 1]),</span> +<span class='co'># crop = JKI_crops)</span> +<span class='co'># drift_data_JKI[[n]] <- drift_data</span> +<span class='co'># }</span> +<span class='co'># save(drift_data_JKI, file = "data/drift_data_JKI.RData")</span> +<span class='co'>## ---------------------------------------------</span> + +<span class='co'># And this is the resulting data</span> +<span class='no'>drift_data_JKI</span></div><div class='output co'>#> [[1]] +#> crop +#> distance Ackerbau Obstbau frueh Obstbau spaet +#> 1 2.77 NA NA +#> 3 NA 29.20 15.73 +#> 5 0.57 19.89 8.41 +#> 10 0.29 11.81 3.60 +#> 15 0.20 5.55 1.81 +#> 20 0.15 2.77 1.09 +#> 30 0.10 1.04 0.54 +#> 40 0.07 0.52 0.32 +#> 50 0.06 0.30 0.22 +#> +#> [[2]] +#> crop +#> distance Ackerbau Obstbau frueh Obstbau spaet +#> 1 2.38 NA NA +#> 3 NA 25.53 12.13 +#> 5 0.47 16.87 6.81 +#> 10 0.24 9.61 3.11 +#> 15 0.16 5.61 1.58 +#> 20 0.12 2.59 0.90 +#> 30 0.08 0.87 0.40 +#> 40 0.06 0.40 0.23 +#> 50 0.05 0.22 0.15 +#> +#> [[3]] +#> crop +#> distance Ackerbau Obstbau frueh Obstbau spaet +#> 1 2.01 NA NA +#> 3 NA 23.96 11.01 +#> 5 0.41 15.79 6.04 +#> 10 0.20 8.96 2.67 +#> 15 0.14 4.24 1.39 +#> 20 0.10 2.01 0.80 +#> 30 0.07 0.70 0.36 +#> 40 0.05 0.33 0.21 +#> 50 0.04 0.19 0.13 +#> +#> [[4]] +#> crop +#> distance Ackerbau Obstbau frueh Obstbau spaet +#> 1 1.85 NA NA +#> 3 NA 23.61 10.12 +#> 5 0.38 15.42 5.60 +#> 10 0.19 8.66 2.50 +#> 15 0.13 4.01 1.28 +#> 20 0.10 1.89 0.75 +#> 30 0.06 0.66 0.35 +#> 40 0.05 0.31 0.20 +#> 50 0.04 0.17 0.13 +#> +#> [[5]] +#> crop +#> distance Ackerbau Obstbau frueh Obstbau spaet +#> 1 1.75 NA NA +#> 3 NA 23.12 9.74 +#> 5 0.36 15.06 5.41 +#> 10 0.18 8.42 2.43 +#> 15 0.12 3.83 1.24 +#> 20 0.09 1.81 0.72 +#> 30 0.06 0.63 0.34 +#> 40 0.05 0.30 0.20 +#> 50 0.04 0.17 0.13 +#> +#> [[6]] +#> crop +#> distance Ackerbau Obstbau frueh Obstbau spaet +#> 1 1.64 NA NA +#> 3 NA 22.76 9.21 +#> 5 0.34 14.64 5.18 +#> 10 0.17 8.04 2.38 +#> 15 0.11 3.71 1.20 +#> 20 0.09 1.75 0.68 +#> 30 0.06 0.61 0.31 +#> 40 0.04 0.29 0.17 +#> 50 0.03 0.16 0.11 +#> +#> [[7]] +#> crop +#> distance Ackerbau Obstbau frueh Obstbau spaet +#> 1 1.61 NA NA +#> 3 NA 22.69 9.10 +#> 5 0.33 14.45 5.11 +#> 10 0.17 7.83 2.33 +#> 15 0.11 3.62 1.20 +#> 20 0.08 1.71 0.67 +#> 30 0.06 0.60 0.30 +#> 40 0.04 0.28 0.17 +#> 50 0.03 0.16 0.11 +#> +#> [[8]] +#> crop +#> distance Ackerbau Obstbau frueh Obstbau spaet +#> 1 1.52 NA NA +#> 3 NA 22.24 8.66 +#> 5 0.31 14.09 4.92 +#> 10 0.16 7.58 2.29 +#> 15 0.11 3.48 1.14 +#> 20 0.08 1.65 0.65 +#> 30 0.05 0.57 0.29 +#> 40 0.04 0.27 0.16 +#> 50 0.03 0.15 0.11 +#> </div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + + <li><a href="#format">Format</a></li> + + <li><a href="#source">Source</a></li> + + <li><a href="#details">Details</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/endpoint.html b/docs/reference/endpoint.html new file mode 100644 index 0000000..57a7652 --- /dev/null +++ b/docs/reference/endpoint.html @@ -0,0 +1,170 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Retrieve endpoint information from the chyaml field of a chent object — endpoint • pfm</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link 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class="col-md-9 contents"> + <div class="page-header"> + <h1>Retrieve endpoint information from the chyaml field of a chent object</h1> + </div> + + + <p>R6 class objects of class chent represent chemical entities +and can hold a list of information loaded from a chemical yaml file in their +chyaml field. Such information is extracted and optionally aggregated by +this function.</p> + + + <pre><span class='fu'>endpoint</span>(<span class='no'>chent</span>, <span class='kw'>medium</span> <span class='kw'>=</span> <span class='st'>"soil"</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"degradation"</span>, <span class='st'>"sorption"</span>), + <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>NA</span>, <span class='st'>"laboratory"</span>, <span class='st'>"field"</span>), <span class='kw'>redox</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>NA</span>, <span class='st'>"aerobic"</span>, + <span class='st'>"anaerobic"</span>), <span class='kw'>value</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"DT50ref"</span>, <span class='st'>"Kfoc"</span>, <span class='st'>"N"</span>), <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, + <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>) + +<span class='fu'>soil_DT50</span>(<span class='no'>chent</span>, <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>, + <span class='kw'>lab_field</span> <span class='kw'>=</span> <span class='st'>"laboratory"</span>, <span class='kw'>value</span> <span class='kw'>=</span> <span class='st'>"DT50ref"</span>, <span class='kw'>redox</span> <span class='kw'>=</span> <span class='st'>"aerobic"</span>, + <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) + +<span class='fu'>soil_Kfoc</span>(<span class='no'>chent</span>, <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>value</span> <span class='kw'>=</span> <span class='st'>"Kfoc"</span>, + <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) + +<span class='fu'>soil_N</span>(<span class='no'>chent</span>, <span class='kw'>aggregator</span> <span class='kw'>=</span> <span class='no'>mean</span>, <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) + +<span class='fu'>soil_sorption</span>(<span class='no'>chent</span>, <span class='kw'>values</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Kfoc"</span>, <span class='st'>"N"</span>), <span class='kw'>aggregators</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>Kfoc</span> <span class='kw'>=</span> + <span class='no'>geomean</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='no'>geomean</span>, <span class='kw'>N</span> <span class='kw'>=</span> <span class='no'>mean</span>), <span class='kw'>signif</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>Kfoc</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>N</span> <span class='kw'>=</span> <span class='fl'>3</span>), + <span class='kw'>raw</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <dl class="dl-horizontal"> + <dt>chent</dt> + <dd>The chent object to get the information from</dd> + <dt>medium</dt> + <dd>The medium for which information is sought</dd> + <dt>type</dt> + <dd>The information type</dd> + <dt>lab_field</dt> + <dd>If not NA, do we want laboratory or field endpoints</dd> + <dt>redox</dt> + <dd>If not NA, are we looking for aerobic or anaerobic data</dd> + <dt>value</dt> + <dd>The name of the value we want. The list given in the +usage section is not exclusive</dd> + <dt>aggregator</dt> + <dd>The aggregator function. Can be mean, +<code><a href='geomean.html'>geomean</a></code>, or identity, for example.</dd> + <dt>raw</dt> + <dd>Should the number(s) be returned as stored in the chent +object (could be a character value) to retain original information +about precision?</dd> + <dt>signif</dt> + <dd>How many significant digits do we want</dd> + <dt>values</dt> + <dd>The values to be returned</dd> + <dt>aggregators</dt> + <dd>A named vector of aggregator functions to be used</dd> + </dl> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>The result from applying the aggregator function to + the values converted to a numeric vector, rounded to the + given number of significant digits, or, if raw = TRUE, + the values as a character value, retaining any implicit + information on precision that may be present.</p> + + <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> + + <p>The functions <code>soil_*</code> are functions to extract soil specific endpoints. +For the Freundlich exponent, the capital letter <code>N</code> is used in order to +facilitate dealing with such data in R. In pesticide fate modelling, this +exponent is often called 1/n.</p> + + + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#details">Details</a></li> + </ul> + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/geomean.html b/docs/reference/geomean.html new file mode 100644 index 0000000..4634f99 --- /dev/null +++ b/docs/reference/geomean.html @@ -0,0 +1,127 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, 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class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Calculate the geometric mean</h1> + </div> + + + <p>Based on some posts in a thread on Stackoverflow +<a href = 'http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in'>http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in</a> +This function checks for negative values, removes NA values per default and +returns 0 if at least one element of the vector is 0.</p> + + + <pre><span class='fu'>geomean</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <dl class="dl-horizontal"> + <dt>x</dt> + <dd>Vector of numbers</dd> + <dt>na.rm</dt> + <dd>Should NA values be omitted?</dd> + </dl> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>The geometric mean</p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='fu'>geomean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>9</span>))</div><div class='output co'>#> [1] 3</div><div class='input'><span class='fu'>geomean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>NA</span>, <span class='fl'>9</span>))</div><div class='output co'>#> [1] 3</div><div class='input'><span class='co'>## Not run: geomean(c(1, -3, 9)) # returns an error</span></div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + <h2>Author</h2> + +Johannes Ranke + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/index.html b/docs/reference/index.html new file mode 100644 index 0000000..e458048 --- /dev/null +++ b/docs/reference/index.html @@ -0,0 +1,195 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Function reference • pfm</title> + +<!-- jquery --> +<script 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class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9"> + <div class="page-header"> + <h1>Function reference</h1> + <h4>version 0.4-1</h4> + </div> + + <div class="contents"> + <h2 id="section-general-utility-functions" class="hasAnchor"><a href="#section-general-utility-functions" class="anchor"></a>General utility functions</h2> + <p class="section-desc"><p>Functions that are independent of specific fate modelling areas</p></p> + + + <p><a href="geomean.html">Calculate the geometric mean</a></p> + <ul> + <li><code><a href="geomean.html">geomean</a></code></li> + </ul> + + <p><a href="one_box.html">Create a time series of decline data</a></p> + <ul> + <li><code><a href="one_box.html">one_box</a></code></li><li><code><a href="one_box.html">one_box.numeric</a></code></li><li><code><a href="one_box.html">one_box.mkinfit</a></code></li> + </ul> + + <p><a href="plot.one_box.html">Plot time series of decline data</a></p> + <ul> + <li><code><a href="plot.one_box.html">plot.one_box</a></code></li> + </ul> + + <p><a href="sawtooth.html">Create decline time series for multiple applications</a></p> + <ul> + <li><code><a href="sawtooth.html">sawtooth</a></code></li> + </ul> + + <p><a href="twa.html">Calculate a time weighted average concentration</a></p> + <ul> + <li><code><a href="twa.html">twa</a></code></li><li><code><a href="twa.html">twa.one_box</a></code></li> + </ul> + + <p><a href="max_twa.html">The maximum time weighted average concentration for a moving window</a></p> + <ul> + <li><code><a href="max_twa.html">max_twa</a></code></li> + </ul> + <h2 id="section-predicted-environmental-concentrations-in-soil" class="hasAnchor"><a href="#section-predicted-environmental-concentrations-in-soil" class="anchor"></a>Predicted environmental concentrations in soil</h2> + <p class="section-desc"></p> + + + <p><a href="PEC_soil.html">Calculate predicted environmental concentrations in soil</a></p> + <ul> + <li><code><a href="PEC_soil.html">PEC_soil</a></code></li> + </ul> + + <p><a href="soil_scenario_data_EFSA_2015.html">Properties of the predefined scenarios from the EFSA guidance from 2015</a></p> + <ul> + <li><code><a href="soil_scenario_data_EFSA_2015.html">soil_scenario_data_EFSA_2015</a></code></li> + </ul> + <h2 id="section-predicted-environmental-concentrations-in-surface-water" class="hasAnchor"><a href="#section-predicted-environmental-concentrations-in-surface-water" class="anchor"></a>Predicted environmental concentrations in surface water</h2> + <p class="section-desc"></p> + + + <p><a href="PEC_sw_drift.html">Calculate predicted environmental concentrations in surface water due to drift</a></p> + <ul> + <li><code><a href="PEC_sw_drift.html">PEC_sw_drift</a></code></li> + </ul> + + <p><a href="drift_data_JKI.html">Deposition from spray drift expressed as percent of the applied dose as +</a></p> + <ul> + <li><code><a href="drift_data_JKI.html">drift_data_JKI</a></code></li> + </ul> + + <p><a href="PEC_sw_drainage_UK.html">Calculate initial predicted environmental concentrations in surface water due to drainage using the UK method</a></p> + <ul> + <li><code><a href="PEC_sw_drainage_UK.html">PEC_sw_drainage_UK</a></code></li> + </ul> + + <p><a href="TOXSWA_cwa.html">R6 class for holding TOXSWA cwa concentration data and associated statistics</a></p> + <ul> + <li><code><a href="TOXSWA_cwa.html">TOXSWA_cwa</a></code></li> + </ul> + + <p><a href="read.TOXSWA_cwa.html">Read TOXSWA surface water concentrations</a></p> + <ul> + <li><code><a href="read.TOXSWA_cwa.html">read.TOXSWA_cwa</a></code></li> + </ul> + + <p><a href="plot.TOXSWA_cwa.html">Plot TOXSWA surface water concentrations</a></p> + <ul> + <li><code><a href="plot.TOXSWA_cwa.html">plot.TOXSWA_cwa</a></code></li> + </ul> + <h2 id="section-classifications-and-indicators" class="hasAnchor"><a href="#section-classifications-and-indicators" class="anchor"></a>Classifications and indicators</h2> + <p class="section-desc"><p>Evaluating environmental fate properties</p></p> + + + <p><a href="SSLRC_mobility_classification.html">Determine the SSLRC mobility classification for a chemical substance from its Koc</a></p> + <ul> + <li><code><a href="SSLRC_mobility_classification.html">SSLRC_mobility_classification</a></code></li> + </ul> + + <p><a href="GUS.html">Groundwater ubiquity score based on Gustafson (1989)</a></p> + <ul> + <li><code><a href="GUS.html">GUS</a></code></li><li><code><a href="GUS.html">GUS.numeric</a></code></li><li><code><a href="GUS.html">GUS.chent</a></code></li><li><code><a href="GUS.html">print.GUS_result</a></code></li> + </ul> + + </div> + </div> + + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#section-general-utility-functions">General utility functions</a></li> + <li><a href="#section-predicted-environmental-concentrations-in-soil">Predicted environmental concentrations in soil</a></li> + <li><a href="#section-predicted-environmental-concentrations-in-surface-water">Predicted environmental concentrations in surface water</a></li> + <li><a href="#section-classifications-and-indicators">Classifications and indicators</a></li> + </ul> + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/max_twa.html b/docs/reference/max_twa.html new file mode 100644 index 0000000..4bb1be9 --- /dev/null +++ b/docs/reference/max_twa.html @@ -0,0 +1,116 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta 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+ </button> + <a class="navbar-brand" href="../index.html">pfm</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>The maximum time weighted average concentration for a moving window</h1> + </div> + + + <p>The maximum time weighted average concentration for a moving window</p> + + + <pre><span class='fu'>max_twa</span>(<span class='no'>x</span>, <span class='kw'>window</span> <span class='kw'>=</span> <span class='fl'>21</span>)</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <dl class="dl-horizontal"> + <dt>x</dt> + <dd>An object of type <code><a href='one_box.html'>one_box</a></code></dd> + <dt>window</dt> + <dd>The size of the moving window</dd> + </dl> + + <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> + + <p><code><a href='twa.html'>twa</a></code></p> + + + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#see-also">See also</a></li> + </ul> + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/one_box-12.png b/docs/reference/one_box-12.png Binary files differnew file mode 100644 index 0000000..31e2f4b --- /dev/null +++ b/docs/reference/one_box-12.png diff --git a/docs/reference/one_box-2.png 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http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Create a time series of decline data — one_box • pfm</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">pfm</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Create a time series of decline data</h1> + </div> + + + <p>The time series starts with the amount specified for the first application. +This does not create objects of type <code>ts</code>.</p> + + + <pre><span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='no'>...</span>) + +<span class='co'># S3 method for numeric</span> +<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='no'>...</span>) + +<span class='co'># S3 method for mkinfit</span> +<span class='fu'>one_box</span>(<span class='no'>x</span>, <span class='kw'>t_end</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>res</span> <span class='kw'>=</span> <span class='fl'>0.01</span>, <span class='no'>...</span>)</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <dl class="dl-horizontal"> + <dt>x</dt> + <dd>When numeric, this is the half-life to be used for an exponential +decline. If x is an mkinfit object, the decline is calculated from this object</dd> + <dt>t_end</dt> + <dd>End of the time series</dd> + <dt>res</dt> + <dd>Resolution of the time series</dd> + <dt>...</dt> + <dd>Further arguments passed to methods</dd> + </dl> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='co'># Only use a half-life</span> +<span class='no'>pred_0</span> <span class='kw'><-</span> <span class='fu'>one_box</span>(<span class='fl'>10</span>) +<span class='fu'>plot</span>(<span class='no'>pred_0</span>)</div><img src='one_box-2.png' alt='' width='540' height='400' /><div class='input'> +<span class='co'># Use a fitted mkinfit model</span> +<span class='fu'>require</span>(<span class='no'>mkin</span>) +<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='no'>pred_1</span> <span class='kw'><-</span> <span class='fu'>one_box</span>(<span class='no'>fit</span>) +<span class='fu'>plot</span>(<span class='no'>pred_1</span>)</div><img src='one_box-4.png' alt='' width='540' height='400' /><div class='input'> +<span class='co'># Use a model with more than one observed variable</span> +<span class='no'>m_2</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='no'>pred_2</span> <span class='kw'><-</span> <span class='fu'>one_box</span>(<span class='no'>fit_2</span>) +<span class='fu'>plot</span>(<span class='no'>pred_2</span>)</div><img src='one_box-8.png' alt='' width='540' height='400' /></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/pfm_degradation.html b/docs/reference/pfm_degradation.html new file mode 100644 index 0000000..d98778b --- /dev/null +++ b/docs/reference/pfm_degradation.html @@ -0,0 +1,136 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Calculate a time course of relative concentrations based on an mkinmod model — pfm_degradation • pfm</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">pfm</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Calculate a time course of relative concentrations based on an mkinmod model</h1> + </div> + + + <p>Calculate a time course of relative concentrations based on an mkinmod model</p> + + + <pre><span class='fu'>pfm_degradation</span>(<span class='kw'>model</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> + <span class='fu'>log</span>(<span class='fl'>2</span>)/<span class='no'>DT50</span>), <span class='kw'>years</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>step_days</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>times</span> <span class='kw'>=</span> <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='no'>years</span> * <span class='fl'>365</span>, <span class='kw'>by</span> <span class='kw'>=</span> + <span class='no'>step_days</span>))</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <dl class="dl-horizontal"> + <dt>model</dt> + <dd>The degradation model to be used. Either a parent only model like +'SFO' or 'FOMC', or an mkinmod object</dd> + <dt>DT50</dt> + <dd>The half-life. This is only used when simple exponential decline +is calculated (SFO model).</dd> + <dt>parms</dt> + <dd>The parameters used for the degradation model</dd> + <dt>years</dt> + <dd>For how many years should the degradation be predicted?</dd> + <dt>step_days</dt> + <dd>What step size in days should the output have?</dd> + <dt>times</dt> + <dd>The output times</dd> + </dl> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='fu'>head</span>(<span class='fu'>pfm_degradation</span>(<span class='st'>"SFO"</span>, <span class='kw'>DT50</span> <span class='kw'>=</span> <span class='fl'>10</span>))</div><div class='output co'>#> time parent +#> 1 0 1.0000000 +#> 2 1 0.9330330 +#> 3 2 0.8705506 +#> 4 3 0.8122524 +#> 5 4 0.7578583 +#> 6 5 0.7071068</div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + <h2>Author</h2> + +Johannes Ranke + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/plot.TOXSWA_cwa-2.png b/docs/reference/plot.TOXSWA_cwa-2.png Binary files differnew file mode 100644 index 0000000..6f9de30 --- /dev/null +++ b/docs/reference/plot.TOXSWA_cwa-2.png diff --git a/docs/reference/plot.TOXSWA_cwa.html b/docs/reference/plot.TOXSWA_cwa.html new file mode 100644 index 0000000..7cbe238 --- /dev/null +++ b/docs/reference/plot.TOXSWA_cwa.html @@ -0,0 +1,138 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Plot TOXSWA surface water concentrations — plot.TOXSWA_cwa • pfm</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">pfm</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Plot TOXSWA surface water concentrations</h1> + </div> + + + <p>Plot TOXSWA hourly concentrations of a chemical substance in a specific +segment of a TOXSWA surface water body.</p> + + + <pre><span class='co'># S3 method for TOXSWA_cwa</span> +<span class='fu'>plot</span>(<span class='no'>x</span>, <span class='kw'>time_column</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"datetime"</span>, <span class='st'>"t"</span>, <span class='st'>"t_firstjan"</span>, + <span class='st'>"t_rel_to_max"</span>), <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"default"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"default"</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>LC_TIME</span> <span class='kw'>=</span> <span class='st'>"C"</span>, <span class='no'>...</span>)</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <dl class="dl-horizontal"> + <dt>x</dt> + <dd>The TOXSWA_cwa object to be plotted.</dd> + <dt>time_column</dt> + <dd>What should be used for the time axis. If "t_firstjan" is chosen, +the time is given in days relative to the first of January in the first year.</dd> + <dt>xlab, ylab</dt> + <dd>Labels for x and y axis.</dd> + <dt>add</dt> + <dd>Should we add to an existing plot?</dd> + <dt>total</dt> + <dd>Should the total concentration in water be plotted, including substance sorbed +to suspended matter?</dd> + <dt>LC_TIME</dt> + <dd>Specification of the locale used to format dates</dd> + <dt>...</dt> + <dd>Further arguments passed to <code>plot</code> if we are not adding to an existing plot</dd> + </dl> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='no'>H_sw_D4_pond</span> <span class='kw'><-</span> <span class='fu'><a href='read.TOXSWA_cwa.html'>read.TOXSWA_cwa</a></span>(<span class='st'>"00001p_pa.cwa"</span>, + <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>, + <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'>system.file</span>(<span class='st'>"testdata/SwashProjects.zip"</span>, + <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>)) +<span class='fu'>plot</span>(<span class='no'>H_sw_D4_pond</span>)</div><img src='plot.TOXSWA_cwa-2.png' alt='' width='540' height='400' /></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + <h2>Author</h2> + +Johannes Ranke + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/plot.one_box-2.png b/docs/reference/plot.one_box-2.png Binary files differnew file mode 100644 index 0000000..4007876 --- /dev/null +++ b/docs/reference/plot.one_box-2.png diff --git a/docs/reference/plot.one_box.html b/docs/reference/plot.one_box.html new file mode 100644 index 0000000..1870a55 --- /dev/null +++ b/docs/reference/plot.one_box.html @@ -0,0 +1,131 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Plot time series of decline data — plot.one_box • pfm</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" 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src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">pfm</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Plot time series of decline data</h1> + </div> + + + <p>Plot time series of decline data</p> + + + <pre><span class='co'># S3 method for one_box</span> +<span class='fu'>plot</span>(<span class='no'>x</span>, <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'>range</span>(<span class='fu'>time</span>(<span class='no'>x</span>)), <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fu'>max</span>(<span class='no'>x</span>)), + <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Fraction of initial"</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, + <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='fu'>dimnames</span>(<span class='no'>x</span>)<span class='kw'>[[</span><span class='fl'>2</span>]][<span class='fl'>1</span>], <span class='no'>...</span>)</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <dl class="dl-horizontal"> + <dt>x</dt> + <dd>The object of type <code><a href='one_box.html'>one_box</a></code> to be plotted</dd> + <dt>xlim</dt> + <dd>Limits for the x axis</dd> + <dt>ylim</dt> + <dd>Limits for the y axis</dd> + <dt>xlab</dt> + <dd>Label for the x axis</dd> + <dt>ylab</dt> + <dd>Label for the y axis</dd> + <dt>max_twa</dt> + <dd>If a numeric value is given, the maximum time weighted +average concentration(s) is/are shown in the graph.</dd> + <dt>max_twa_var</dt> + <dd>Variable for which the maximum time weighted average should +be shown if max_twa is not NULL.</dd> + <dt>...</dt> + <dd>Further arguments passed to methods</dd> + </dl> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='fu'>plot</span>(<span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='fl'>10</span>), <span class='fl'>3</span>, <span class='fl'>7</span>), <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>)</div><img src='plot.one_box-2.png' alt='' width='540' height='400' /></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html new file mode 100644 index 0000000..3afec9c --- /dev/null +++ b/docs/reference/read.TOXSWA_cwa.html @@ -0,0 +1,154 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Read TOXSWA surface water concentrations — read.TOXSWA_cwa • pfm</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">pfm</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Read TOXSWA surface water concentrations</h1> + </div> + + + <p>Read TOXSWA hourly concentrations of a chemical substance in a specific +segment of a TOXSWA surface water body. Per default, the data for the last +segment are imported. As TOXSWA 4 reports the values at the end of the hour +(ConLiqWatLayCur) in its summary file, we use this value as well instead +of the hourly averages (ConLiqWatLay).</p> + + + <pre><span class='fu'>read.TOXSWA_cwa</span>(<span class='no'>filename</span>, <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"."</span>, <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>segment</span> <span class='kw'>=</span> <span class='st'>"last"</span>, + <span class='kw'>substance</span> <span class='kw'>=</span> <span class='st'>"parent"</span>, <span class='kw'>total</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>windows</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, + <span class='kw'>thresholds</span> <span class='kw'>=</span> <span class='kw'>NULL</span>)</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <dl class="dl-horizontal"> + <dt>filename</dt> + <dd>The filename of the cwa file (TOXSWA 2.x.y or similar) or the +out file (FOCUS TOXSWA 4, i.e. TOXSWA 4.4.2 or similar).</dd> + <dt>basedir</dt> + <dd>The path to the directory where the cwa file resides.</dd> + <dt>zipfile</dt> + <dd>Optional path to a zip file containing the cwa file.</dd> + <dt>segment</dt> + <dd>The segment for which the data should be read. Either "last", or +the segment number.</dd> + <dt>substance</dt> + <dd>For TOXSWA 4 .out files, the default value "parent" leads +to reading concentrations of the parent compound. Alternatively, the substance +of interested can be selected by its code name.</dd> + <dt>total</dt> + <dd>Set this to TRUE in order to read total concentrations as well. This is +only necessary for .out files as generated by TOXSWA 4.4.2 or similar, not for .cwa +files. For .cwa files, the total concentration is always read as well.</dd> + <dt>windows</dt> + <dd>Numeric vector of width of moving windows in days, for calculating +maximum time weighted average concentrations and areas under the curve.</dd> + <dt>thresholds</dt> + <dd>Numeric vector of threshold concentrations in µg/L for +generating event statistics.</dd> + </dl> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>An instance of an R6 object of class +<code><a href='TOXSWA_cwa.html'>TOXSWA_cwa</a></code>.</p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='no'>H_sw_D4_pond</span> <span class='kw'><-</span> <span class='fu'>read.TOXSWA_cwa</span>(<span class='st'>"00001p_pa.cwa"</span>, + <span class='kw'>basedir</span> <span class='kw'>=</span> <span class='st'>"SwashProjects/project_H_sw/TOXSWA"</span>, + <span class='kw'>zipfile</span> <span class='kw'>=</span> <span class='fu'>system.file</span>(<span class='st'>"testdata/SwashProjects.zip"</span>, + <span class='kw'>package</span> <span class='kw'>=</span> <span class='st'>"pfm"</span>))</div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#value">Value</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + <h2>Author</h2> + +Johannes Ranke + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/sawtooth-2.png b/docs/reference/sawtooth-2.png Binary files differnew file mode 100644 index 0000000..e6ff97d --- /dev/null +++ b/docs/reference/sawtooth-2.png diff --git a/docs/reference/sawtooth-6.png b/docs/reference/sawtooth-6.png Binary files differnew file mode 100644 index 0000000..161ecb4 --- /dev/null +++ b/docs/reference/sawtooth-6.png diff --git a/docs/reference/sawtooth-8.png b/docs/reference/sawtooth-8.png Binary files differnew file mode 100644 index 0000000..161ecb4 --- /dev/null +++ b/docs/reference/sawtooth-8.png diff --git a/docs/reference/sawtooth.html b/docs/reference/sawtooth.html new file mode 100644 index 0000000..e24186e --- /dev/null +++ b/docs/reference/sawtooth.html @@ -0,0 +1,142 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Create decline time series for multiple applications — sawtooth • pfm</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">pfm</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Create decline time series for multiple applications</h1> + </div> + + + <p>If the number of application cycles <code>n</code> is greater than 1, the +application pattern specified in <code>applications</code> is repeated <code>n</code> +times, with an interval <code>i</code>.</p> + + + <pre><span class='fu'>sawtooth</span>(<span class='no'>x</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>365</span>, <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fu'>data.frame</span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>0</span> + <span class='no'>n</span> + * <span class='no'>i</span>, <span class='kw'>length.out</span> <span class='kw'>=</span> <span class='no'>n</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fl'>1</span>))</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <dl class="dl-horizontal"> + <dt>x</dt> + <dd>A <code><a href='one_box.html'>one_box</a></code> object</dd> + <dt>n</dt> + <dd>The number of applications. If <code>applications</code> is specified, <code>n</code> is not used</dd> + <dt>i</dt> + <dd>The interval between applications. If <code>applications</code> is specified, <code>i</code> +is not used</dd> + <dt>applications</dt> + <dd>A data frame holding the application times in the first column and +the corresponding amounts applied in the second column for each application cycle. +If <code>n</code> is one, the application pattern specified here is used only once.</dd> + </dl> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='no'>applications</span> <span class='kw'>=</span> <span class='fu'>data.frame</span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>14</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>7</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>3</span>)) +<span class='no'>pred</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='fl'>10</span>) +<span class='fu'>plot</span>(<span class='fu'>sawtooth</span>(<span class='no'>pred</span>, <span class='kw'>applications</span> <span class='kw'>=</span> <span class='no'>applications</span>))</div><img src='sawtooth-2.png' alt='' width='540' height='400' /><div class='input'> +<span class='no'>m_2</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='no'>pred_2</span> <span class='kw'><-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='no'>fit_2</span>) +<span class='no'>pred_2_saw</span> <span class='kw'><-</span> <span class='fu'>sawtooth</span>(<span class='no'>pred_2</span>, <span class='fl'>2</span>, <span class='fl'>7</span>) +<span class='fu'>plot</span>(<span class='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><img src='sawtooth-6.png' alt='' width='540' height='400' /><div class='input'> +<span class='fu'><a href='max_twa.html'>max_twa</a></span>(<span class='no'>pred_2_saw</span>)</div><div class='output co'>#> $max +#> parent m1 +#> 0.6627707 0.8542785 +#> +#> $window_start +#> parent m1 +#> 0.00 32.09 +#> +#> $window_end +#> parent m1 +#> 21.00 53.09 +#> </div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/soil_scenario_data_EFSA_2015.html b/docs/reference/soil_scenario_data_EFSA_2015.html new file mode 100644 index 0000000..f842d08 --- /dev/null +++ b/docs/reference/soil_scenario_data_EFSA_2015.html @@ -0,0 +1,157 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Properties of the predefined scenarios from the EFSA guidance from 2015 — soil_scenario_data_EFSA_2015 • pfm</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">pfm</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Properties of the predefined scenarios from the EFSA guidance from 2015</h1> + </div> + + + <p>Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the +concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the +scenario and model adjustment factors from p. 15 and p. 17 are included.</p> + + + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + + <p>A data frame with one row for each scenario. Row names are the scenario codes, + e.g. CTN for the Northern scenario for the total concentration in soil. Columns are + mostly self-explanatory. <code>rho</code> is the dry bulk density of the top soil.</p> + + <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> + + <p>EFSA (European Food Safety Authority) (2015) +EFSA guidance document for predicting environmental concentrations +of active substances of plant protection products and transformation products of these +active substances in soil. <em>EFSA Journal</em> <b>13</b>(4) 4093 +doi:10.2903/j.efsa.2015.4093</p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='co'>## Not run: ------------------------------------</span> +<span class='co'># # This is the code that was used to define the data</span> +<span class='co'># soil_scenario_data_EFSA_2015 <- data.frame(</span> +<span class='co'># Zone = rep(c("North", "Central", "South"), 2),</span> +<span class='co'># Country = c("Estonia", "Germany", "France", "Denmark", "Czech Republik", "Spain"),</span> +<span class='co'># T_arit = c(4.7, 8.0, 11.0, 8.2, 9.1, 12.8),</span> +<span class='co'># T_arr = c(7.0, 10.1, 12.3, 9.8, 11.2, 14.7),</span> +<span class='co'># Texture = c("Coarse", "Coarse", "Medium fine", "Medium", "Medium", "Medium"),</span> +<span class='co'># f_om = c(0.118, 0.086, 0.048, 0.023, 0.018, 0.011),</span> +<span class='co'># theta_fc = c(0.244, 0.244, 0.385, 0.347, 0.347, 0.347),</span> +<span class='co'># rho = c(0.95, 1.05, 1.22, 1.39, 1.43, 1.51),</span> +<span class='co'># f_sce = c(3, 2, 2, 2, 1.5, 1.5),</span> +<span class='co'># f_mod = c(2, 2, 2, 4, 4, 4),</span> +<span class='co'># stringsAsFactors = FALSE,</span> +<span class='co'># row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS")</span> +<span class='co'># )</span> +<span class='co'># save(soil_scenario_data_EFSA_2015, file = '../data/soil_scenario_data_EFSA_2015.RData')</span> +<span class='co'>## ---------------------------------------------</span> + +<span class='co'># And this is the resulting dataframe</span> +<span class='no'>soil_scenario_data_EFSA_2015</span></div><div class='output co'>#> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce +#> CTN North Estonia 4.7 7.0 Coarse 0.118 0.244 0.95 3.0 +#> CTC Central Germany 8.0 10.1 Coarse 0.086 0.244 1.05 2.0 +#> CTS South France 11.0 12.3 Medium fine 0.048 0.385 1.22 2.0 +#> CLN North Denmark 8.2 9.8 Medium 0.023 0.347 1.39 2.0 +#> CLC Central Czech Republik 9.1 11.2 Medium 0.018 0.347 1.43 1.5 +#> CLS South Spain 12.8 14.7 Medium 0.011 0.347 1.51 1.5 +#> f_mod +#> CTN 2 +#> CTC 2 +#> CTS 2 +#> CLN 4 +#> CLC 4 +#> CLS 4</div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + + <li><a href="#format">Format</a></li> + + <li><a href="#source">Source</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/twa.html b/docs/reference/twa.html new file mode 100644 index 0000000..414b372 --- /dev/null +++ b/docs/reference/twa.html @@ -0,0 +1,138 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Calculate a time weighted average concentration — twa • pfm</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container template-reference-topic"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">pfm</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="col-md-9 contents"> + <div class="page-header"> + <h1>Calculate a time weighted average concentration</h1> + </div> + + + <p>The moving average is built only using the values in the past, so +the earliest possible time for the maximum in the time series returned +is after one window has passed.</p> + + + <pre><span class='fu'>twa</span>(<span class='no'>x</span>, <span class='kw'>window</span> <span class='kw'>=</span> <span class='fl'>21</span>) + +<span class='co'># S3 method for one_box</span> +<span class='fu'>twa</span>(<span class='no'>x</span>, <span class='kw'>window</span> <span class='kw'>=</span> <span class='fl'>21</span>)</pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> + <dl class="dl-horizontal"> + <dt>x</dt> + <dd>An object of type <code><a href='one_box.html'>one_box</a></code></dd> + <dt>window</dt> + <dd>The size of the moving window</dd> + </dl> + + <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> + + <p><code><a href='max_twa.html'>max_twa</a></code></p> + + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='no'>pred</span> <span class='kw'><-</span> <span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='fl'>10</span>), + <span class='kw'>applications</span> <span class='kw'>=</span> <span class='fu'>data.frame</span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>7</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>, <span class='fl'>1</span>))) +<span class='fu'><a href='max_twa.html'>max_twa</a></span>(<span class='no'>pred</span>)</div><div class='output co'>#> $max +#> parent +#> 0.9537545 +#> +#> $window_start +#> parent +#> 0 +#> +#> $window_end +#> parent +#> 21 +#> </div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <h2>Contents</h2> + <ul class="nav nav-pills nav-stacked"> + <li><a href="#arguments">Arguments</a></li> + + <li><a href="#see-also">See also</a></li> + + <li><a href="#examples">Examples</a></li> + </ul> + + </div> +</div> + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> diff --git a/docs/soil_scenario_data_EFSA_2015.html b/docs/soil_scenario_data_EFSA_2015.html deleted file mode 100644 index 405e5b0..0000000 --- a/docs/soil_scenario_data_EFSA_2015.html +++ /dev/null @@ -1,144 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>soil_scenario_data_EFSA_2015. pfm 0.3-8</title> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> -<meta name="author" content=""> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <body> - <div class="navbar"> - <div class="navbar-inner"> - <div class="container"> - <a class="brand" href="index.html">pfm 0.3-8</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html">Home</a></li> - <li><a href="reference.html">Reference</a></li> - </ul> - </div> - </div> - </div> -</div> - - - <div class="container"> - <header> - - </header> - - <h1>Properties of the predefined scenarios from the EFSA guidance from 2015</h1> - -<div class="row"> - <div class="span8"> - - <div class="Format"> - <h2>Format</h2> - - <p>A data frame with one row for each scenario. Row names are the scenario codes, - e.g. CTN for the Northern scenario for the total concentration in soil. Columns are - mostly self-explanatory. <code>rho</code> is the dry bulk density of the top soil.</p> - - </div> - - <div class="Source"> - <h2>Source</h2> - - <p>EFSA (European Food Safety Authority) (2015) -EFSA guidance document for predicting environmental concentrations -of active substances of plant protection products and transformation products of these -active substances in soil. <em>EFSA Journal</em> <b>13</b>(4) 4093 -doi:10.2903/j.efsa.2015.4093</p> - - </div> - - <div class="Description"> - <h2>Description</h2> - - <p>Properties of the predefined scenarios used at Tier 1, Tier 2A and Tier 3A for the -concentration in soil as given in the EFSA guidance (2015, p. 13/14). Also, the -scenario and model adjustment factors from p. 15 and p. 17 are included.</p> - - </div> - - <h2 id="examples">Examples</h2> - <pre class="examples"><div class='input'><span class="comment">## Not run: ------------------------------------</span> -<span class="comment"># # This is the code that was used to define the data</span> -<span class="comment"># soil_scenario_data_EFSA_2015 <- data.frame(</span> -<span class="comment"># Zone = rep(c("North", "Central", "South"), 2),</span> -<span class="comment"># Country = c("Estonia", "Germany", "France", "Denmark", "Czech Republik", "Spain"),</span> -<span class="comment"># T_arit = c(4.7, 8.0, 11.0, 8.2, 9.1, 12.8),</span> -<span class="comment"># T_arr = c(7.0, 10.1, 12.3, 9.8, 11.2, 14.7),</span> -<span class="comment"># Texture = c("Coarse", "Coarse", "Medium fine", "Medium", "Medium", "Medium"),</span> -<span class="comment"># f_om = c(0.118, 0.086, 0.048, 0.023, 0.018, 0.011),</span> -<span class="comment"># theta_fc = c(0.244, 0.244, 0.385, 0.347, 0.347, 0.347),</span> -<span class="comment"># rho = c(0.95, 1.05, 1.22, 1.39, 1.43, 1.51),</span> -<span class="comment"># f_sce = c(3, 2, 2, 2, 1.5, 1.5),</span> -<span class="comment"># f_mod = c(2, 2, 2, 4, 4, 4),</span> -<span class="comment"># stringsAsFactors = FALSE,</span> -<span class="comment"># row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS")</span> -<span class="comment"># )</span> -<span class="comment"># save(soil_scenario_data_EFSA_2015, file = '../data/soil_scenario_data_EFSA_2015.RData')</span> -<span class="comment">## ---------------------------------------------</span> - -<span class="comment"># And this is the resulting dataframe</span> -<span class="symbol">soil_scenario_data_EFSA_2015</span></div> -<div class='output'> Zone Country T_arit T_arr Texture f_om theta_fc rho f_sce -CTN North Estonia 4.7 7.0 Coarse 0.118 0.244 0.95 3.0 -CTC Central Germany 8.0 10.1 Coarse 0.086 0.244 1.05 2.0 -CTS South France 11.0 12.3 Medium fine 0.048 0.385 1.22 2.0 -CLN North Denmark 8.2 9.8 Medium 0.023 0.347 1.39 2.0 -CLC Central Czech Republik 9.1 11.2 Medium 0.018 0.347 1.43 1.5 -CLS South Spain 12.8 14.7 Medium 0.011 0.347 1.51 1.5 - f_mod -CTN 2 -CTC 2 -CTS 2 -CLN 4 -CLC 4 -CLS 4 -</div></pre> - </div> - <div class="span4 sidebar"> - <!-- <ul> - <li>soil_scenario_data_EFSA_2015</li> - </ul> - <ul> - <li>datasets</li> - </ul> --> - - - - - </div> -</div> - - <footer> - <p class="pull-right"><a href="#">Back to top</a></p> -<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. 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\ No newline at end of file diff --git a/man/max_twa.Rd b/man/max_twa.Rd index 13e7bbf..86cc174 100644 --- a/man/max_twa.Rd +++ b/man/max_twa.Rd @@ -15,5 +15,5 @@ max_twa(x, window = 21) The maximum time weighted average concentration for a moving window } \seealso{ -twa +\code{\link{twa}} } diff --git a/man/one_box.Rd b/man/one_box.Rd index 86440ce..0085f3f 100644 --- a/man/one_box.Rd +++ b/man/one_box.Rd @@ -33,13 +33,13 @@ plot(pred_0) # Use a fitted mkinfit model require(mkin) -fit <- mkinfit("FOMC", FOCUS_2006_C) +fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) pred_1 <- one_box(fit) plot(pred_1) # Use a model with more than one observed variable m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")) -fit_2 <- mkinfit(m_2, FOCUS_2006_D) +fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) pred_2 <- one_box(fit_2) plot(pred_2) } diff --git a/man/sawtooth.Rd b/man/sawtooth.Rd index 4576c8b..d26c0bf 100644 --- a/man/sawtooth.Rd +++ b/man/sawtooth.Rd @@ -30,7 +30,7 @@ pred <- one_box(10) plot(sawtooth(pred, applications = applications)) m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")) -fit_2 <- mkinfit(m_2, FOCUS_2006_D) +fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE) pred_2 <- one_box(fit_2) pred_2_saw <- sawtooth(pred_2, 2, 7) plot(pred_2_saw, max_twa = 21, max_twa_var = "m1") @@ -25,5 +25,5 @@ pred <- sawtooth(one_box(10), max_twa(pred) } \seealso{ -max_twa +\code{\link{max_twa}} } |
