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diff --git a/pkg/inst/web/FOCUS_GW_scenarios_2012.html b/pkg/inst/web/FOCUS_GW_scenarios_2012.html deleted file mode 100644 index 43ac090..0000000 --- a/pkg/inst/web/FOCUS_GW_scenarios_2012.html +++ /dev/null @@ -1,154 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>FOCUS_GW_scenarios_2012. pfm 0.3-7</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="#">pfm 0.3-7</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html"><i class="icon-home icon-white"></i> Index</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'>FOCUS_GW_scenarios_2012 -</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"> - <!-- <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="http://twitter.github.com/bootstrap">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/pkg/inst/web/GUS.html b/pkg/inst/web/GUS.html deleted file mode 100644 index a330be2..0000000 --- a/pkg/inst/web/GUS.html +++ /dev/null @@ -1,160 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>GUS. pfm 0.3-7</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="#">pfm 0.3-7</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html"><i class="icon-home icon-white"></i> Index</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><div>GUS(...)</div> -<div>"GUS"(DT50, Koc, ...)</div> -<div>"GUS"(chent, degradation_value = "DT50ref", lab_field = "laboratory", redox = "aerobic", sorption_value = "Kfoc", degradation_aggregator = geomean, sorption_aggregator = geomean, ...)</div> -<div>"print"(x, ..., digits = 1)</div></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"> - <!-- <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="http://twitter.github.com/bootstrap">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/pkg/inst/web/PEC_soil.html b/pkg/inst/web/PEC_soil.html deleted file mode 100644 index 1304d19..0000000 --- a/pkg/inst/web/PEC_soil.html +++ /dev/null @@ -1,228 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>PEC_soil. pfm 0.3-7</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="#">pfm 0.3-7</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html"><i class="icon-home icon-white"></i> Index</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><div>PEC_soil(rate, rate_units = "g/ha", interception = 0, mixing_depth = 5, PEC_units = "mg/kg", PEC_pw_units = "mg/L", interval = NA, n_periods = Inf, tillage_depth = 20, chent = NA, DT50 = NA, Koc = NA, Kom = Koc/1.724, t_avg = 0, scenarios = c("default", "EFSA_2015"), porewater = FALSE)</div></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'>PEC_soil(100, interception = 0.25) -</div> -<div class='output'> scenario -t_avg default - 0 0.1 -</div> -<div class='input'> -# This is example 1 starting at p. 79 of the EFSA guidance (2015) -PEC_soil(1000, interval = 365, DT50 = 250, t_avg = c(0, 21), - scenarios = "EFSA_2015") -</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'>PEC_soil(1000, interval = 365, DT50 = 250, t_av = c(0, 21), - Kom = 1000, scenarios = "EFSA_2015", porewater = TRUE) -</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'> -# The following is from example 4 starting at p. 85 of the EFSA guidance (2015) -# Metabolite M2 -# Calculate total and porewater soil concentrations for tier 1 scenarios -# Relative molar mass is 100/300, formation fraction is 0.7 * 1 -results_pfm <- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_avg = c(0, 21), - scenarios = "EFSA_2015") -results_pfm_pw <- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_av = c(0, 21), - Kom = 100, scenarios = "EFSA_2015", porewater = TRUE) -</div></pre> - </div> - <div class="span4"> - <!-- <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="http://twitter.github.com/bootstrap">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/pkg/inst/web/PEC_soil_product.html b/pkg/inst/web/PEC_soil_product.html deleted file mode 100644 index 9704de2..0000000 --- a/pkg/inst/web/PEC_soil_product.html +++ /dev/null @@ -1,141 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>PEC_soil_product. pfm 0.2-4</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="#">pfm 0.2-4</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html"><i class="icon-home icon-white"></i> Index</a></li> - </ul> - </div> - </div> - </div> -</div> - - <div class="container"> - <header> - - </header> - - <h1>Calculate predicted environmental concentrations in soil for a product</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><div>PEC_soil_product(product, rate, rate_units = "L/ha", interception = 0, mixing_depth = 5, tillage_depth = 20, interval = 365, PEC_units = "mg/kg", scenarios = "EFSA_2015")</div></pre> - - <h2>Arguments</h2> - <dl> - <dt>product</dt> - <dd>An object of class pp</dd> - <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>tillage_depth</dt> - <dd>Periodic (see interval) deeper mixing in cm</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>PEC_units</dt> - <dd>Requested units for the calculated PEC. Only mg/kg currently supported</dd> - </dl> - - <div class="Source"> - <h2>Source</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> - - <div class="Value"> - <h2>Value</h2> - - <p><dl> -A data frame with compound names, and initial, background (plateau minimum) - and long term maximum predicted concentrations in soil -</dl></p> - - </div> - - <div class="Description"> - <h2>Description</h2> - - <p>Calculates long term accumulation PEC values. 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. -By default, PEC values for the scenarios as defined in the EFSA guidance -(2015, p. 13) are calculated.</p> - - </div> - </div> - <div class="span4"> - <!-- <ul> - <li>PEC_soil_product</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="http://twitter.github.com/bootstrap">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/pkg/inst/web/PEC_sw_drainage_UK.html b/pkg/inst/web/PEC_sw_drainage_UK.html deleted file mode 100644 index bf97fea..0000000 --- a/pkg/inst/web/PEC_sw_drainage_UK.html +++ /dev/null @@ -1,124 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>PEC_sw_drainage_UK. pfm 0.3-7</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="#">pfm 0.3-7</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html"><i class="icon-home icon-white"></i> Index</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><div>PEC_sw_drainage_UK(rate, interception = 0, Koc, latest_application = NULL, soil_DT50 = NULL, model = NULL, model_parms = NULL)</div></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'>PEC_sw_drainage_UK(150, Koc = 100) -</div> -<div class='output'>[1] 8.076923 -</div></pre> - </div> - <div class="span4"> - <!-- <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="http://twitter.github.com/bootstrap">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/pkg/inst/web/PEC_sw_drainage_UK_ini.html b/pkg/inst/web/PEC_sw_drainage_UK_ini.html deleted file mode 100644 index 0d55bd9..0000000 --- a/pkg/inst/web/PEC_sw_drainage_UK_ini.html +++ /dev/null @@ -1,124 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>PEC_sw_drainage_UK_ini. pfm 0.2-4</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="#">pfm 0.2-4</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html"><i class="icon-home icon-white"></i> Index</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><div>PEC_sw_drainage_UK_ini(rate, interception = 0, Koc, latest_application = NULL, soil_DT50 = NULL, model = NULL, model_parms = NULL)</div></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 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'>PEC_sw_drainage_UK_ini(150, Koc = 100) -</div> -<div class='output'>[1] 8.076923 -</div></pre> - </div> - <div class="span4"> - <!-- <ul> - <li>PEC_sw_drainage_UK_ini</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="http://twitter.github.com/bootstrap">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/pkg/inst/web/PEC_sw_drift.html b/pkg/inst/web/PEC_sw_drift.html deleted file mode 100644 index 5d4bb47..0000000 --- a/pkg/inst/web/PEC_sw_drift.html +++ /dev/null @@ -1,130 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>PEC_sw_drift. pfm 0.3-7</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="#">pfm 0.3-7</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html"><i class="icon-home icon-white"></i> Index</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><div>PEC_sw_drift(rate, applications = 1, water_depth = 30, drift_percentages = NULL, drift_data = "JKI", crop = "Ackerbau", distances = c(1, 5, 10, 20), rate_units = "g/ha", PEC_units = "µg/L")</div></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'>PEC_sw_drift(100) -</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"> - <!-- <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="http://twitter.github.com/bootstrap">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/pkg/inst/web/PEC_sw_drift_ini.html b/pkg/inst/web/PEC_sw_drift_ini.html deleted file mode 100644 index bc7eed5..0000000 --- a/pkg/inst/web/PEC_sw_drift_ini.html +++ /dev/null @@ -1,127 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>PEC_sw_drift_ini. pfm 0.2-4</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="#">pfm 0.2-4</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html"><i class="icon-home icon-white"></i> Index</a></li> - </ul> - </div> - </div> - </div> -</div> - - <div class="container"> - <header> - - </header> - - <h1>Calculate initial predicted environmental concentrations in surface water due to drift</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><div>PEC_sw_drift_ini(rate, applications = 1, water_depth = 30, drift_data = "JKI", crop = "Ackerbau", distances = c(1, 5, 10, 20), rate_units = "g/ha", PEC_units = "µg/L")</div></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_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'>PEC_sw_drift_ini(100) -</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"> - <!-- <ul> - <li>PEC_sw_drift_ini</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="http://twitter.github.com/bootstrap">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/pkg/inst/web/PEC_sw_sed.html b/pkg/inst/web/PEC_sw_sed.html deleted file mode 100644 index 4eda1d7..0000000 --- a/pkg/inst/web/PEC_sw_sed.html +++ /dev/null @@ -1,127 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>PEC_sw_sed. pfm 0.3-7</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="#">pfm 0.3-7</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html"><i class="icon-home icon-white"></i> Index</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><div>PEC_sw_sed(PEC_sw, percentage = 100, method = "percentage", sediment_depth = 5, water_depth = 30, sediment_density = 1.3, PEC_sed_units = c("µg/kg", "mg/kg"))</div></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'>PEC_sw_sed(PEC_sw_drift(100, distances = 1), percentage = 50) -</div> -<div class='output'> 1 m -2.130769 -</div></pre> - </div> - <div class="span4"> - <!-- <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="http://twitter.github.com/bootstrap">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/pkg/inst/web/SFO_actual_twa.html b/pkg/inst/web/SFO_actual_twa.html deleted file mode 100644 index 3ce9220..0000000 --- a/pkg/inst/web/SFO_actual_twa.html +++ /dev/null @@ -1,123 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>SFO_actual_twa. pfm 0.3-7</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="#">pfm 0.3-7</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html"><i class="icon-home icon-white"></i> Index</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><div>SFO_actual_twa(DT50 = 1000, times = c(0, 1, 2, 4, 7, 14, 21, 28, 42, 50, 100))</div></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'>SFO_actual_twa(10) -</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"> - <!-- <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="http://twitter.github.com/bootstrap">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/pkg/inst/web/SSLRC_mobility_classification.html b/pkg/inst/web/SSLRC_mobility_classification.html deleted file mode 100644 index 43d701e..0000000 --- a/pkg/inst/web/SSLRC_mobility_classification.html +++ /dev/null @@ -1,117 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>SSLRC_mobility_classification. pfm 0.3-7</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="#">pfm 0.3-7</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html"><i class="icon-home icon-white"></i> Index</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><div>SSLRC_mobility_classification(Koc)</div></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'>SSLRC_mobility_classification(100) -</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"> - <!-- <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="http://twitter.github.com/bootstrap">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/pkg/inst/web/TOXSWA_cwa.html b/pkg/inst/web/TOXSWA_cwa.html deleted file mode 100644 index 0d8ae17..0000000 --- a/pkg/inst/web/TOXSWA_cwa.html +++ /dev/null @@ -1,176 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>TOXSWA_cwa. pfm 0.3-7</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="#">pfm 0.3-7</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html"><i class="icon-home icon-white"></i> Index</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><div>TOXSWA_cwa</div></pre> - - <div class="Format"> - <h2>Format</h2> - - <p>An <code><a href='http://www.inside-r.org/packages/cran/R6/docs/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'>H_sw_R1_stream <- read.TOXSWA_cwa("00003s_pa.cwa", - basedir = "SwashProjects/project_H_sw/TOXSWA", - zipfile = system.file("testdata/SwashProjects.zip", - package = "pfm")) -H_sw_R1_stream$get_events(c(2, 10)) -H_sw_R1_stream$moving_windows(c(7, 21)) -print(H_sw_R1_stream) -</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"> - <!-- <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="http://twitter.github.com/bootstrap">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
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a/pkg/inst/web/css/highlight.css +++ /dev/null @@ -1,28 +0,0 @@ -/* Syntax highlighting ---------------------------------------------------- */ - -pre .input { - border-left: 3px solid #ccc; - padding-left: 0.5em; -} -pre .output { - background-color: #eee; -} - -.number {color:rgb(21,20,181);} -.functioncall {color:#264D66 ;} -.string {color:#375D81 ;} -.keyword {font-weight:bolder ;color:black;} -.argument {color:#264D66 ;} -.comment {color: #333;} -.formalargs {color: #264D66;} -.eqformalargs {color:#264D66;} -.slot {font-style:italic;} -.symbol {color:black ;} -.prompt {color:black ;} - -pre img { - background-color: #fff; - border: 1px solid #ccc; - display: block; - margin: 0.5em auto 0.5em auto; -} diff --git a/pkg/inst/web/css/staticdocs.css b/pkg/inst/web/css/staticdocs.css deleted file mode 100644 index 9fee28b..0000000 --- a/pkg/inst/web/css/staticdocs.css +++ /dev/null @@ -1,18 +0,0 @@ -h2 {padding-top: 20px} - -.icon img { - float: right; - border: 1px solid #ccc; -} -.index .internal {display: none;} -ul.index li {margin-bottom: 0.5em; clear: both;} - -footer { - margin-top: 45px; - padding: 35px 0 36px; - border-top: 1px solid #e5e5e5; -} -footer p { - margin-bottom: 0; - color: #555; -} diff --git a/pkg/inst/web/drift_data_JKI.html b/pkg/inst/web/drift_data_JKI.html deleted file mode 100644 index c3471c9..0000000 --- a/pkg/inst/web/drift_data_JKI.html +++ /dev/null @@ -1,239 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>drift_data_JKI. pfm 0.3-7</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="#">pfm 0.3-7</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html"><i class="icon-home icon-white"></i> Index</a></li> - </ul> - </div> - </div> - </div> -</div> - - <div class="container"> - <header> - - </header> - - <h1>Deposition from spray drift expressed as percent of the applied dose as -published by the JKI</h1> - -<div class="row"> - <div class="span8"> - - <div class="Format"> - <h2>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> - - </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'> -## Not run: -# # This is the code that was used to extract the data -# library(readxl) -# abdrift_path <- "inst/extdata/Tabelle der Abdrifteckwerte.xls" -# JKI_crops <- c("Ackerbau", "Obstbau frueh", "Obstbau spaet") -# names(JKI_crops) <- c("Field crops", "Pome/stone fruit, early", "Pome/stone fruit, late") -# drift_data_JKI <- list() -# -# for (n in 1:8) { -# drift_data_raw <- read_excel(abdrift_path, sheet = n + 1, skip = 2) -# drift_data <- as.matrix(drift_data_raw[1:9, 2:4]) -# dimnames(drift_data) <- list(distance = as.integer(drift_data_raw[1:9, 1]), -# crop = JKI_crops) -# drift_data_JKI[[n]] <- drift_data -# } -# save(drift_data_JKI, file = "data/drift_data_JKI.RData") -# ## End(Not run) - -# And this is the resulting data -drift_data_JKI -</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"> - <!-- <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/pkg/inst/web/endpoint.html b/pkg/inst/web/endpoint.html deleted file mode 100644 index 521f7f4..0000000 --- a/pkg/inst/web/endpoint.html +++ /dev/null @@ -1,142 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>endpoint. pfm 0.3-7</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="#">pfm 0.3-7</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html"><i class="icon-home icon-white"></i> Index</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><div>endpoint(chent, medium = "soil", type = c("degradation", "sorption"), lab_field = c(NA, "laboratory", "field"), redox = c(NA, "aerobic", "anaerobic"), value = c("DT50ref", "Kfoc", "N"), aggregator = geomean, raw = FALSE, signif = 3)</div> -<div>soil_DT50(chent, aggregator = geomean, signif = 3, lab_field = "laboratory", value = "DT50ref", redox = "aerobic", raw = FALSE)</div> -<div>soil_Kfoc(chent, aggregator = geomean, signif = 3, value = "Kfoc", raw = FALSE)</div> -<div>soil_N(chent, aggregator = mean, signif = 3, raw = FALSE)</div> -<div>soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc = geomean, Koc = geomean, N = mean), signif = c(Kfoc = 3, N = 3), raw = FALSE)</div></pre> - - <h2>Arguments</h2> - <dl> - <dt>chent</dt> - <dd>The <code><a href='http://www.inside-r.org/packages/cran/chents/docs/chent'>chent</a></code> 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 <code><a href='http://www.inside-r.org/packages/cran/chents/docs/chent'>chent</a></code> 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"> - <!-- <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="http://twitter.github.com/bootstrap">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/pkg/inst/web/geomean.html b/pkg/inst/web/geomean.html deleted file mode 100644 index 672e9b5..0000000 --- a/pkg/inst/web/geomean.html +++ /dev/null @@ -1,121 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>geomean. pfm 0.3-7</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="#">pfm 0.3-7</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html"><i class="icon-home icon-white"></i> Index</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><div>geomean(x, na.rm = TRUE)</div></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'>geomean(c(1, 3, 9)) -</div> -<div class='output'>[1] 3 -</div> -<div class='input'>geomean(c(1, 3, NA, 9)) -</div> -<div class='output'>[1] 3 -</div> -<div class='input'>## Not run: geomean(c(1, -3, 9)) # returns an error -</div></pre> - </div> - <div class="span4"> - <!-- <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="http://twitter.github.com/bootstrap">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/pkg/inst/web/img/glyphicons-halflings-white.png b/pkg/inst/web/img/glyphicons-halflings-white.png Binary files differdeleted file mode 100644 index 3bf6484..0000000 --- a/pkg/inst/web/img/glyphicons-halflings-white.png +++ /dev/null diff --git a/pkg/inst/web/img/glyphicons-halflings.png b/pkg/inst/web/img/glyphicons-halflings.png Binary files differdeleted file mode 100644 index 79bc568..0000000 --- a/pkg/inst/web/img/glyphicons-halflings.png +++ /dev/null diff --git a/pkg/inst/web/index.html b/pkg/inst/web/index.html deleted file mode 100644 index 54f0f35..0000000 --- a/pkg/inst/web/index.html +++ /dev/null @@ -1,182 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>Index. pfm 0.3-7</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="#">pfm 0.3-7</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html"><i class="icon-home icon-white"></i> Index</a></li> - </ul> - </div> - </div> - </div> -</div> - - <div class="container"> - <header> - - </header> - - <div class="row"> - <div class="span8"> - Utilities for simple calculations of predicted environmental -concentrations (PECs) and for dealing with data from some FOCUS pesticide -fate modelling software packages. - - <h2>Help topics</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 -</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 -</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 class="span3 offset1"> - - <h2>Dependencies</h2> - <ul> - <li><strong>Depends</strong>: R6, mkin</li> - <li><strong>Imports</strong>: graphics, chents, readr, methods</li> - <li><strong>Suggests</strong>: testthat</li> - - </ul> - <h2>Authors</h2> - <ul> - <li><a href="mailto:jranke@uni-bremen.de">Johannes Ranke</a> [aut, cre, cph]</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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'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') - 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* ==================== */ - - 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 $active = container.find('> .active') - , transition = callback - 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- - /* TYPEAHEAD PUBLIC CLASS DEFINITION - * ================================= */ - - var Typeahead = function (element, options) { - this.$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 - 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\ No newline at end of file diff --git a/pkg/inst/web/pfm_degradation.html b/pkg/inst/web/pfm_degradation.html deleted file mode 100644 index fad64be..0000000 --- a/pkg/inst/web/pfm_degradation.html +++ /dev/null @@ -1,119 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>pfm_degradation. pfm 0.3-7</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="#">pfm 0.3-7</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html"><i class="icon-home icon-white"></i> Index</a></li> - </ul> - </div> - </div> - </div> -</div> - - <div class="container"> - <header> - - </header> - - <h1>Calculate a time course of relative concentrations based on an mkinmod model</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><div>pfm_degradation(model = "SFO", DT50 = 1000, parms = c(k_parent_sink = log(2)/DT50), years = 1, step_days = 1, times = seq(0, years * 365, by = step_days))</div></pre> - - <h2>Arguments</h2> - <dl> - <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> - - <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'>head(pfm_degradation("SFO", DT50 = 10)) -</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"> - <!-- <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="http://twitter.github.com/bootstrap">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/pkg/inst/web/plot.TOXSWA_cwa-2.png b/pkg/inst/web/plot.TOXSWA_cwa-2.png Binary files differdeleted file mode 100644 index 764c7f4..0000000 --- a/pkg/inst/web/plot.TOXSWA_cwa-2.png +++ /dev/null diff --git a/pkg/inst/web/plot.TOXSWA_cwa-4.png b/pkg/inst/web/plot.TOXSWA_cwa-4.png Binary files differdeleted file mode 100644 index 764c7f4..0000000 --- a/pkg/inst/web/plot.TOXSWA_cwa-4.png +++ /dev/null diff --git a/pkg/inst/web/plot.TOXSWA_cwa.html b/pkg/inst/web/plot.TOXSWA_cwa.html deleted file mode 100644 index a6118df..0000000 --- a/pkg/inst/web/plot.TOXSWA_cwa.html +++ /dev/null @@ -1,119 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>plot.TOXSWA_cwa. pfm 0.3-7</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="#">pfm 0.3-7</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html"><i class="icon-home icon-white"></i> Index</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><div>"plot"(x, time_column = c("datetime", "t", "t_firstjan", "t_rel_to_max"), xlab = "default", ylab = "default", add = FALSE, total = FALSE, LC_TIME = "C", ...)</div></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'>H_sw_D4_pond <- read.TOXSWA_cwa("00001p_pa.cwa", - basedir = "SwashProjects/project_H_sw/TOXSWA", - zipfile = system.file("testdata/SwashProjects.zip", - package = "pfm")) -plot(H_sw_D4_pond) -</div> -<p><img src='plot.TOXSWA_cwa-2.png' alt='' width='540' height='400' /></p></pre> - </div> - <div class="span4"> - <!-- <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="http://twitter.github.com/bootstrap">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/pkg/inst/web/read.TOXSWA_cwa.html b/pkg/inst/web/read.TOXSWA_cwa.html deleted file mode 100644 index 3f2d997..0000000 --- a/pkg/inst/web/read.TOXSWA_cwa.html +++ /dev/null @@ -1,138 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>read.TOXSWA_cwa. pfm 0.3-7</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="#">pfm 0.3-7</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html"><i class="icon-home icon-white"></i> Index</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><div>read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL, segment = "last", substance = "parent", total = FALSE, windows = NULL, thresholds = NULL)</div></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'>H_sw_D4_pond <- read.TOXSWA_cwa("00001p_pa.cwa", - basedir = "SwashProjects/project_H_sw/TOXSWA", - zipfile = system.file("testdata/SwashProjects.zip", - package = "pfm")) -</div></pre> - </div> - <div class="span4"> - <!-- <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="http://twitter.github.com/bootstrap">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/pkg/inst/web/soil_DT50.html b/pkg/inst/web/soil_DT50.html deleted file mode 100644 index 0e142ae..0000000 --- a/pkg/inst/web/soil_DT50.html +++ /dev/null @@ -1,104 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>soil_DT50. pfm 0.2-4</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="#">pfm 0.2-4</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html"><i class="icon-home icon-white"></i> Index</a></li> - </ul> - </div> - </div> - </div> -</div> - - <div class="container"> - <header> - - </header> - - <h1>Obtain soil DT50</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><div>soil_DT50(chent, aggregator = geomean, signif = 3, lab_field = "laboratory", value = "DT50ref", redox = "aerobic", raw = FALSE)</div></pre> - - <h2>Arguments</h2> - <dl> - <dt>chent</dt> - <dd>The <code><a href='http://www.inside-r.org/packages/cran/chents/docs/chent'>chent</a></code> object to get the information from</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>signif</dt> - <dd>How many significant digits do we want</dd> - <dt>lab_field</dt> - <dd>If not NA, do we want laboratory or field endpoints</dd> - <dt>value</dt> - <dd>The name of the value we want. The list given in the -usage section is not exclusive</dd> - <dt>redox</dt> - <dd>If not NA, are we looking for aerobic or anaerobic data</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> - </dl> - - <div class="Description"> - <h2>Description</h2> - - <p>Obtain soil DT50</p> - - </div> - </div> - <div class="span4"> - <!-- <ul> - <li>soil_DT50</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="http://twitter.github.com/bootstrap">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/pkg/inst/web/soil_Kfoc.html b/pkg/inst/web/soil_Kfoc.html deleted file mode 100644 index ace5f4b..0000000 --- a/pkg/inst/web/soil_Kfoc.html +++ /dev/null @@ -1,100 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>soil_Kfoc. pfm 0.2-4</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="#">pfm 0.2-4</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html"><i class="icon-home icon-white"></i> Index</a></li> - </ul> - </div> - </div> - </div> -</div> - - <div class="container"> - <header> - - </header> - - <h1>Obtain soil Kfoc</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><div>soil_Kfoc(chent, aggregator = geomean, signif = 3, value = "Kfoc", raw = FALSE)</div></pre> - - <h2>Arguments</h2> - <dl> - <dt>chent</dt> - <dd>The <code><a href='http://www.inside-r.org/packages/cran/chents/docs/chent'>chent</a></code> object to get the information from</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>signif</dt> - <dd>How many significant digits do we want</dd> - <dt>value</dt> - <dd>The name of the value we want. The list given in the -usage section is not exclusive</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> - </dl> - - <div class="Description"> - <h2>Description</h2> - - <p>Obtain soil Kfoc</p> - - </div> - </div> - <div class="span4"> - <!-- <ul> - <li>soil_Kfoc</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="http://twitter.github.com/bootstrap">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/pkg/inst/web/soil_N.html b/pkg/inst/web/soil_N.html deleted file mode 100644 index 886bbc7..0000000 --- a/pkg/inst/web/soil_N.html +++ /dev/null @@ -1,98 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>soil_N. pfm 0.2-4</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="#">pfm 0.2-4</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html"><i class="icon-home icon-white"></i> Index</a></li> - </ul> - </div> - </div> - </div> -</div> - - <div class="container"> - <header> - - </header> - - <h1>Obtain soil Freundlich exponent</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><div>soil_N(chent, aggregator = mean, signif = 3, raw = FALSE)</div></pre> - - <h2>Arguments</h2> - <dl> - <dt>chent</dt> - <dd>The <code><a href='http://www.inside-r.org/packages/cran/chents/docs/chent'>chent</a></code> object to get the information from</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>signif</dt> - <dd>How many significant digits do we want</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> - </dl> - - <div class="Description"> - <h2>Description</h2> - - <p>In pesticide fate modelling, this exponent is often called 1/n. Here, in -order to facilitate dealing with such data in R, it is called N.</p> - - </div> - </div> - <div class="span4"> - <!-- <ul> - <li>soil_N</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="http://twitter.github.com/bootstrap">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/pkg/inst/web/soil_scenario_data_EFSA_2015.html b/pkg/inst/web/soil_scenario_data_EFSA_2015.html deleted file mode 100644 index 0230afb..0000000 --- a/pkg/inst/web/soil_scenario_data_EFSA_2015.html +++ /dev/null @@ -1,141 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>soil_scenario_data_EFSA_2015. pfm 0.3-7</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="#">pfm 0.3-7</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html"><i class="icon-home icon-white"></i> Index</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'>## Not run: -# # This is the code that was used to define the data -# soil_scenario_data_EFSA_2015 <- data.frame( -# Zone = rep(c("North", "Central", "South"), 2), -# Country = c("Estonia", "Germany", "France", "Denmark", "Czech Republik", "Spain"), -# T_arit = c(4.7, 8.0, 11.0, 8.2, 9.1, 12.8), -# T_arr = c(7.0, 10.1, 12.3, 9.8, 11.2, 14.7), -# Texture = c("Coarse", "Coarse", "Medium fine", "Medium", "Medium", "Medium"), -# f_om = c(0.118, 0.086, 0.048, 0.023, 0.018, 0.011), -# theta_fc = c(0.244, 0.244, 0.385, 0.347, 0.347, 0.347), -# rho = c(0.95, 1.05, 1.22, 1.39, 1.43, 1.51), -# f_sce = c(3, 2, 2, 2, 1.5, 1.5), -# f_mod = c(2, 2, 2, 4, 4, 4), -# stringsAsFactors = FALSE, -# row.names = c("CTN", "CTC", "CTS", "CLN", "CLC", "CLS") -# ) -# save(soil_scenario_data_EFSA_2015, file = '../data/soil_scenario_data_EFSA_2015.RData') -# ## End(Not run) - -# And this is the resulting dataframe -soil_scenario_data_EFSA_2015 -</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"> - <!-- <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>. Styled with <a href="http://twitter.github.com/bootstrap">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
\ No newline at end of file diff --git a/pkg/inst/web/soil_sorption.html b/pkg/inst/web/soil_sorption.html deleted file mode 100644 index 152fc5e..0000000 --- a/pkg/inst/web/soil_sorption.html +++ /dev/null @@ -1,98 +0,0 @@ -<!DOCTYPE html> -<html lang="en"> - <head> - <meta charset="utf-8"> -<title>soil_sorption. pfm 0.2-4</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="#">pfm 0.2-4</a> - <div class="nav"> - <ul class="nav"> - <li><a href="index.html"><i class="icon-home icon-white"></i> Index</a></li> - </ul> - </div> - </div> - </div> -</div> - - <div class="container"> - <header> - - </header> - - <h1>Obtain soil sorption data</h1> - -<div class="row"> - <div class="span8"> - <h2>Usage</h2> - <pre><div>soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc = geomean, Koc = geomean, N = mean), signif = rep(3, length(values)), raw = FALSE)</div></pre> - - <h2>Arguments</h2> - <dl> - <dt>chent</dt> - <dd>The <code><a href='http://www.inside-r.org/packages/cran/chents/docs/chent'>chent</a></code> object to get the information from</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> - <dt>signif</dt> - <dd>How many significant digits do we want</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> - </dl> - - <div class="Description"> - <h2>Description</h2> - - <p>Obtain soil sorption data</p> - - </div> - </div> - <div class="span4"> - <!-- <ul> - <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="http://twitter.github.com/bootstrap">bootstrap</a>.</p> - </footer> - </div> - </body> -</html>
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