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-rw-r--r--inst/web/FOCUS_GW_scenarios_2012.html154
-rw-r--r--inst/web/GUS.html160
-rw-r--r--inst/web/PEC_soil.html228
-rw-r--r--inst/web/PEC_soil_product.html141
-rw-r--r--inst/web/PEC_sw_drainage_UK.html124
-rw-r--r--inst/web/PEC_sw_drainage_UK_ini.html124
-rw-r--r--inst/web/PEC_sw_drift.html130
-rw-r--r--inst/web/PEC_sw_drift_ini.html127
-rw-r--r--inst/web/PEC_sw_sed.html127
-rw-r--r--inst/web/SFO_actual_twa.html123
-rw-r--r--inst/web/SSLRC_mobility_classification.html117
-rw-r--r--inst/web/TOXSWA_cwa.html176
-rw-r--r--inst/web/css/bootstrap-responsive.css815
-rw-r--r--inst/web/css/bootstrap-responsive.min.css9
-rw-r--r--inst/web/css/bootstrap.css4983
-rw-r--r--inst/web/css/bootstrap.min.css9
-rw-r--r--inst/web/css/highlight.css28
-rw-r--r--inst/web/css/staticdocs.css18
-rw-r--r--inst/web/drift_data_JKI.html239
-rw-r--r--inst/web/endpoint.html142
-rw-r--r--inst/web/geomean.html121
-rw-r--r--inst/web/img/glyphicons-halflings-white.pngbin8777 -> 0 bytes
-rw-r--r--inst/web/img/glyphicons-halflings.pngbin13826 -> 0 bytes
-rw-r--r--inst/web/index.html182
-rw-r--r--inst/web/js/bootstrap.js1825
-rw-r--r--inst/web/js/bootstrap.min.js6
-rw-r--r--inst/web/pfm_degradation.html119
-rw-r--r--inst/web/plot.TOXSWA_cwa-2.pngbin7409 -> 0 bytes
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-rw-r--r--inst/web/plot.TOXSWA_cwa.html119
-rw-r--r--inst/web/read.TOXSWA_cwa.html138
-rw-r--r--inst/web/soil_DT50.html104
-rw-r--r--inst/web/soil_Kfoc.html100
-rw-r--r--inst/web/soil_N.html98
-rw-r--r--inst/web/soil_scenario_data_EFSA_2015.html141
-rw-r--r--inst/web/soil_sorption.html98
36 files changed, 0 insertions, 11025 deletions
diff --git a/inst/web/FOCUS_GW_scenarios_2012.html b/inst/web/FOCUS_GW_scenarios_2012.html
deleted file mode 100644
index 43ac090..0000000
--- a/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'>$names
- Cha Ham Jok Kre Oke
- &quot;Châteaudun&quot; &quot;Hamburg&quot; &quot;Jokioinen&quot; &quot;Kremsmünster&quot; &quot;Okehampton&quot;
- Pia Por Sev Thi
- &quot;Piacenza&quot; &quot;Porto&quot; &quot;Sevilla&quot; &quot;Thiva&quot;
-
-$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 &lt;NA&gt; 1 7.7 14.0 3.60 1.0
-21 Kre &lt;NA&gt; 2 7.0 25.0 1.00 0.5
-22 Kre &lt;NA&gt; 3 7.1 27.0 0.50 0.5
-23 Kre &lt;NA&gt; 4 7.1 27.0 0.50 0.3
-24 Kre &lt;NA&gt; 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 &lt;NA&gt; 1 4.9 10.0 1.42 1.0
-37 Por &lt;NA&gt; 2 4.8 8.0 0.78 0.5
-38 Por &lt;NA&gt; 3 4.8 8.0 0.78 0.3
-39 Por &lt;NA&gt; 4 4.8 8.0 0.78 0.0
-40 Sev &lt;NA&gt; 1 7.3 14.0 0.93 1.0
-41 Sev &lt;NA&gt; 2 7.3 13.0 0.93 1.0
-42 Sev &lt;NA&gt; 3 7.8 15.0 0.70 0.5
-43 Sev &lt;NA&gt; 4 8.1 16.0 0.58 0.3
-44 Sev &lt;NA&gt; 5 8.1 16.0 0.58 0.0
-45 Sev &lt;NA&gt; 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/inst/web/GUS.html b/inst/web/GUS.html
deleted file mode 100644
index a330be2..0000000
--- a/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&nbsp;=&nbsp;"DT50ref", lab_field&nbsp;=&nbsp;"laboratory", redox&nbsp;=&nbsp;"aerobic", sorption_value&nbsp;=&nbsp;"Kfoc", degradation_aggregator&nbsp;=&nbsp;geomean, sorption_aggregator&nbsp;=&nbsp;geomean, ...)</div>
-<div>"print"(x, ..., digits&nbsp;=&nbsp;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/inst/web/PEC_soil.html b/inst/web/PEC_soil.html
deleted file mode 100644
index 1304d19..0000000
--- a/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&nbsp;=&nbsp;"g/ha", interception&nbsp;=&nbsp;0, mixing_depth&nbsp;=&nbsp;5, PEC_units&nbsp;=&nbsp;"mg/kg", PEC_pw_units&nbsp;=&nbsp;"mg/L", interval&nbsp;=&nbsp;NA, n_periods&nbsp;=&nbsp;Inf, tillage_depth&nbsp;=&nbsp;20, chent&nbsp;=&nbsp;NA, DT50&nbsp;=&nbsp;NA, Koc&nbsp;=&nbsp;NA, Kom&nbsp;=&nbsp;Koc/1.724, t_avg&nbsp;=&nbsp;0, scenarios&nbsp;=&nbsp;c("default", "EFSA_2015"), porewater&nbsp;=&nbsp;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 = &quot;EFSA_2015&quot;)
-</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 = &quot;EFSA_2015&quot;, 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 &lt;- PEC_soil(100/300 * 0.7 * 1 * 1000, interval = 365, DT50 = 250, t_avg = c(0, 21),
- scenarios = &quot;EFSA_2015&quot;)
-results_pfm_pw &lt;- PEC_soil(100/300 * 0.7 * 1000, interval = 365, DT50 = 250, t_av = c(0, 21),
- Kom = 100, scenarios = &quot;EFSA_2015&quot;, 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/inst/web/PEC_soil_product.html b/inst/web/PEC_soil_product.html
deleted file mode 100644
index 9704de2..0000000
--- a/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&nbsp;=&nbsp;"L/ha", interception&nbsp;=&nbsp;0, mixing_depth&nbsp;=&nbsp;5, tillage_depth&nbsp;=&nbsp;20, interval&nbsp;=&nbsp;365, PEC_units&nbsp;=&nbsp;"mg/kg", scenarios&nbsp;=&nbsp;"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/inst/web/PEC_sw_drainage_UK.html b/inst/web/PEC_sw_drainage_UK.html
deleted file mode 100644
index bf97fea..0000000
--- a/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&nbsp;=&nbsp;0, Koc, latest_application&nbsp;=&nbsp;NULL, soil_DT50&nbsp;=&nbsp;NULL, model&nbsp;=&nbsp;NULL, model_parms&nbsp;=&nbsp;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/inst/web/PEC_sw_drainage_UK_ini.html b/inst/web/PEC_sw_drainage_UK_ini.html
deleted file mode 100644
index 0d55bd9..0000000
--- a/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&nbsp;=&nbsp;0, Koc, latest_application&nbsp;=&nbsp;NULL, soil_DT50&nbsp;=&nbsp;NULL, model&nbsp;=&nbsp;NULL, model_parms&nbsp;=&nbsp;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/inst/web/PEC_sw_drift.html b/inst/web/PEC_sw_drift.html
deleted file mode 100644
index 5d4bb47..0000000
--- a/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&nbsp;=&nbsp;1, water_depth&nbsp;=&nbsp;30, drift_percentages&nbsp;=&nbsp;NULL, drift_data&nbsp;=&nbsp;"JKI", crop&nbsp;=&nbsp;"Ackerbau", distances&nbsp;=&nbsp;c(1, 5, 10, 20), rate_units&nbsp;=&nbsp;"g/ha", PEC_units&nbsp;=&nbsp;"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/inst/web/PEC_sw_drift_ini.html b/inst/web/PEC_sw_drift_ini.html
deleted file mode 100644
index bc7eed5..0000000
--- a/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&nbsp;=&nbsp;1, water_depth&nbsp;=&nbsp;30, drift_data&nbsp;=&nbsp;"JKI", crop&nbsp;=&nbsp;"Ackerbau", distances&nbsp;=&nbsp;c(1, 5, 10, 20), rate_units&nbsp;=&nbsp;"g/ha", PEC_units&nbsp;=&nbsp;"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/inst/web/PEC_sw_sed.html b/inst/web/PEC_sw_sed.html
deleted file mode 100644
index 4eda1d7..0000000
--- a/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&nbsp;=&nbsp;100, method&nbsp;=&nbsp;"percentage", sediment_depth&nbsp;=&nbsp;5, water_depth&nbsp;=&nbsp;30, sediment_density&nbsp;=&nbsp;1.3, PEC_sed_units&nbsp;=&nbsp;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/inst/web/SFO_actual_twa.html b/inst/web/SFO_actual_twa.html
deleted file mode 100644
index 3ce9220..0000000
--- a/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&nbsp;=&nbsp;1000, times&nbsp;=&nbsp;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/inst/web/SSLRC_mobility_classification.html b/inst/web/SSLRC_mobility_classification.html
deleted file mode 100644
index 43d701e..0000000
--- a/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'>$`Mobility classification`
-[1] &quot;Moderately mobile&quot;
-
-$`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/inst/web/TOXSWA_cwa.html b/inst/web/TOXSWA_cwa.html
deleted file mode 100644
index 0d8ae17..0000000
--- a/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 &lt;- read.TOXSWA_cwa(&quot;00003s_pa.cwa&quot;,
- basedir = &quot;SwashProjects/project_H_sw/TOXSWA&quot;,
- zipfile = system.file(&quot;testdata/SwashProjects.zip&quot;,
- package = &quot;pfm&quot;))
-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'>&lt;TOXSWA_cwa&gt; 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> \ No newline at end of file
diff --git a/inst/web/css/bootstrap-responsive.css b/inst/web/css/bootstrap-responsive.css
deleted file mode 100644
index 06e55c0..0000000
--- a/inst/web/css/bootstrap-responsive.css
+++ /dev/null
@@ -1,815 +0,0 @@
-/*!
- * Bootstrap Responsive v2.0.4
- *
- * Copyright 2012 Twitter, Inc
- * Licensed under the Apache License v2.0
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Designed and built with all the love in the world @twitter by @mdo and @fat.
- */
-
-.clearfix {
- *zoom: 1;
-}
-
-.clearfix:before,
-.clearfix:after {
- display: table;
- content: "";
-}
-
-.clearfix:after {
- clear: both;
-}
-
-.hide-text {
- font: 0/0 a;
- color: transparent;
- text-shadow: none;
- background-color: transparent;
- border: 0;
-}
-
-.input-block-level {
- display: block;
- width: 100%;
- min-height: 28px;
- -webkit-box-sizing: border-box;
- -moz-box-sizing: border-box;
- -ms-box-sizing: border-box;
- box-sizing: border-box;
-}
-
-.hidden {
- display: none;
- visibility: hidden;
-}
-
-.visible-phone {
- display: none !important;
-}
-
-.visible-tablet {
- display: none !important;
-}
-
-.hidden-desktop {
- display: none !important;
-}
-
-@media (max-width: 767px) {
- .visible-phone {
- display: inherit !important;
- }
- .hidden-phone {
- display: none !important;
- }
- .hidden-desktop {
- display: inherit !important;
- }
- .visible-desktop {
- display: none !important;
- }
-}
-
-@media (min-width: 768px) and (max-width: 979px) {
- .visible-tablet {
- display: inherit !important;
- }
- .hidden-tablet {
- display: none !important;
- }
- .hidden-desktop {
- display: inherit !important;
- }
- .visible-desktop {
- display: none !important ;
- }
-}
-
-@media (max-width: 480px) {
- .nav-collapse {
- -webkit-transform: translate3d(0, 0, 0);
- }
- .page-header h1 small {
- display: block;
- line-height: 18px;
- }
- input[type="checkbox"],
- input[type="radio"] {
- border: 1px solid #ccc;
- }
- .form-horizontal .control-group > label {
- float: none;
- width: auto;
- padding-top: 0;
- text-align: left;
- }
- .form-horizontal .controls {
- margin-left: 0;
- }
- .form-horizontal .control-list {
- padding-top: 0;
- }
- .form-horizontal .form-actions {
- padding-right: 10px;
- padding-left: 10px;
- }
- .modal {
- position: absolute;
- top: 10px;
- right: 10px;
- left: 10px;
- width: auto;
- margin: 0;
- }
- .modal.fade.in {
- top: auto;
- }
- .modal-header .close {
- padding: 10px;
- margin: -10px;
- }
- .carousel-caption {
- position: static;
- }
-}
-
-@media (max-width: 767px) {
- body {
- padding-right: 20px;
- padding-left: 20px;
- }
- .navbar-fixed-top,
- .navbar-fixed-bottom {
- margin-right: -20px;
- margin-left: -20px;
- }
- .container-fluid {
- padding: 0;
- }
- .dl-horizontal dt {
- float: none;
- width: auto;
- clear: none;
- text-align: left;
- }
- .dl-horizontal dd {
- margin-left: 0;
- }
- .container {
- width: auto;
- }
- .row-fluid {
- width: 100%;
- }
- .row,
- .thumbnails {
- margin-left: 0;
- }
- [class*="span"],
- .row-fluid [class*="span"] {
- display: block;
- float: none;
- width: auto;
- margin-left: 0;
- }
- .input-large,
- .input-xlarge,
- .input-xxlarge,
- input[class*="span"],
- select[class*="span"],
- textarea[class*="span"],
- .uneditable-input {
- display: block;
- width: 100%;
- min-height: 28px;
- -webkit-box-sizing: border-box;
- -moz-box-sizing: border-box;
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diff --git a/inst/web/css/bootstrap-responsive.min.css b/inst/web/css/bootstrap-responsive.min.css
deleted file mode 100644
index 1f55036..0000000
--- a/inst/web/css/bootstrap-responsive.min.css
+++ /dev/null
@@ -1,9 +0,0 @@
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diff --git a/inst/web/css/bootstrap.css b/inst/web/css/bootstrap.css
deleted file mode 100644
index bb40c85..0000000
--- a/inst/web/css/bootstrap.css
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#e5e5e5}.carousel{position:relative;margin-bottom:18px;line-height:1}.carousel-inner{position:relative;width:100%;overflow:hidden}.carousel .item{position:relative;display:none;-webkit-transition:.6s ease-in-out left;-moz-transition:.6s ease-in-out left;-ms-transition:.6s ease-in-out left;-o-transition:.6s ease-in-out left;transition:.6s ease-in-out left}.carousel .item>img{display:block;line-height:1}.carousel .active,.carousel .next,.carousel .prev{display:block}.carousel .active{left:0}.carousel .next,.carousel .prev{position:absolute;top:0;width:100%}.carousel .next{left:100%}.carousel .prev{left:-100%}.carousel .next.left,.carousel .prev.right{left:0}.carousel .active.left{left:-100%}.carousel .active.right{left:100%}.carousel-control{position:absolute;top:40%;left:15px;width:40px;height:40px;margin-top:-20px;font-size:60px;font-weight:100;line-height:30px;color:#fff;text-align:center;background:#222;border:3px solid 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diff --git a/inst/web/css/highlight.css b/inst/web/css/highlight.css
deleted file mode 100644
index 4b85237..0000000
--- a/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/inst/web/css/staticdocs.css b/inst/web/css/staticdocs.css
deleted file mode 100644
index 9fee28b..0000000
--- a/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/inst/web/drift_data_JKI.html b/inst/web/drift_data_JKI.html
deleted file mode 100644
index c3471c9..0000000
--- a/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 &lt;- &quot;inst/extdata/Tabelle der Abdrifteckwerte.xls&quot;
-# JKI_crops &lt;- c(&quot;Ackerbau&quot;, &quot;Obstbau frueh&quot;, &quot;Obstbau spaet&quot;)
-# names(JKI_crops) &lt;- c(&quot;Field crops&quot;, &quot;Pome/stone fruit, early&quot;, &quot;Pome/stone fruit, late&quot;)
-# drift_data_JKI &lt;- list()
-#
-# for (n in 1:8) {
-# drift_data_raw &lt;- read_excel(abdrift_path, sheet = n + 1, skip = 2)
-# drift_data &lt;- as.matrix(drift_data_raw[1:9, 2:4])
-# dimnames(drift_data) &lt;- list(distance = as.integer(drift_data_raw[1:9, 1]),
-# crop = JKI_crops)
-# drift_data_JKI[[n]] &lt;- drift_data
-# }
-# save(drift_data_JKI, file = &quot;data/drift_data_JKI.RData&quot;)
-# ## 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>. 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/inst/web/endpoint.html b/inst/web/endpoint.html
deleted file mode 100644
index 521f7f4..0000000
--- a/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&nbsp;=&nbsp;"soil", type&nbsp;=&nbsp;c("degradation", "sorption"), lab_field&nbsp;=&nbsp;c(NA, "laboratory", "field"), redox&nbsp;=&nbsp;c(NA, "aerobic", "anaerobic"), value&nbsp;=&nbsp;c("DT50ref", "Kfoc", "N"), aggregator&nbsp;=&nbsp;geomean, raw&nbsp;=&nbsp;FALSE, signif&nbsp;=&nbsp;3)</div>
-<div>soil_DT50(chent, aggregator&nbsp;=&nbsp;geomean, signif&nbsp;=&nbsp;3, lab_field&nbsp;=&nbsp;"laboratory", value&nbsp;=&nbsp;"DT50ref", redox&nbsp;=&nbsp;"aerobic", raw&nbsp;=&nbsp;FALSE)</div>
-<div>soil_Kfoc(chent, aggregator&nbsp;=&nbsp;geomean, signif&nbsp;=&nbsp;3, value&nbsp;=&nbsp;"Kfoc", raw&nbsp;=&nbsp;FALSE)</div>
-<div>soil_N(chent, aggregator&nbsp;=&nbsp;mean, signif&nbsp;=&nbsp;3, raw&nbsp;=&nbsp;FALSE)</div>
-<div>soil_sorption(chent, values&nbsp;=&nbsp;c("Kfoc", "N"), aggregators&nbsp;=&nbsp;c(Kfoc = geomean, Koc&nbsp;=&nbsp;geomean, N&nbsp;=&nbsp;mean), signif&nbsp;=&nbsp;c(Kfoc&nbsp;=&nbsp;3, N&nbsp;=&nbsp;3), raw&nbsp;=&nbsp;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/inst/web/geomean.html b/inst/web/geomean.html
deleted file mode 100644
index 672e9b5..0000000
--- a/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&nbsp;=&nbsp;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/inst/web/img/glyphicons-halflings-white.png b/inst/web/img/glyphicons-halflings-white.png
deleted file mode 100644
index 3bf6484..0000000
--- a/inst/web/img/glyphicons-halflings-white.png
+++ /dev/null
Binary files differ
diff --git a/inst/web/img/glyphicons-halflings.png b/inst/web/img/glyphicons-halflings.png
deleted file mode 100644
index 79bc568..0000000
--- a/inst/web/img/glyphicons-halflings.png
+++ /dev/null
Binary files differ
diff --git a/inst/web/index.html b/inst/web/index.html
deleted file mode 100644
index 54f0f35..0000000
--- a/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>. 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/inst/web/js/bootstrap.js b/inst/web/js/bootstrap.js
deleted file mode 100644
index 5d6e65b..0000000
--- a/inst/web/js/bootstrap.js
+++ /dev/null
@@ -1,1825 +0,0 @@
-/* ===================================================
- * bootstrap-transition.js v2.0.4
- * http://twitter.github.com/bootstrap/javascript.html#transitions
- * ===================================================
- * Copyright 2012 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * ========================================================== */
-
-
-!function ($) {
-
- $(function () {
-
- "use strict"; // jshint ;_;
-
-
- /* CSS TRANSITION SUPPORT (http://www.modernizr.com/)
- * ======================================================= */
-
- $.support.transition = (function () {
-
- var transitionEnd = (function () {
-
- var el = document.createElement('bootstrap')
- , transEndEventNames = {
- 'WebkitTransition' : 'webkitTransitionEnd'
- , 'MozTransition' : 'transitionend'
- , 'OTransition' : 'oTransitionEnd'
- , 'msTransition' : 'MSTransitionEnd'
- , 'transition' : 'transitionend'
- }
- , name
-
- for (name in transEndEventNames){
- if (el.style[name] !== undefined) {
- return transEndEventNames[name]
- }
- }
-
- }())
-
- return transitionEnd && {
- end: transitionEnd
- }
-
- })()
-
- })
-
-}(window.jQuery);/* ==========================================================
- * bootstrap-alert.js v2.0.4
- * http://twitter.github.com/bootstrap/javascript.html#alerts
- * ==========================================================
- * Copyright 2012 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * ========================================================== */
-
-
-!function ($) {
-
- "use strict"; // jshint ;_;
-
-
- /* ALERT CLASS DEFINITION
- * ====================== */
-
- var dismiss = '[data-dismiss="alert"]'
- , Alert = function (el) {
- $(el).on('click', dismiss, this.close)
- }
-
- Alert.prototype.close = function (e) {
- var $this = $(this)
- , selector = $this.attr('data-target')
- , $parent
-
- if (!selector) {
- selector = $this.attr('href')
- selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7
- }
-
- $parent = $(selector)
-
- e && e.preventDefault()
-
- $parent.length || ($parent = $this.hasClass('alert') ? $this : $this.parent())
-
- $parent.trigger(e = $.Event('close'))
-
- if (e.isDefaultPrevented()) return
-
- $parent.removeClass('in')
-
- function removeElement() {
- $parent
- .trigger('closed')
- .remove()
- }
-
- $.support.transition && $parent.hasClass('fade') ?
- $parent.on($.support.transition.end, removeElement) :
- removeElement()
- }
-
-
- /* ALERT PLUGIN DEFINITION
- * ======================= */
-
- $.fn.alert = function (option) {
- return this.each(function () {
- var $this = $(this)
- , data = $this.data('alert')
- if (!data) $this.data('alert', (data = new Alert(this)))
- if (typeof option == 'string') data[option].call($this)
- })
- }
-
- $.fn.alert.Constructor = Alert
-
-
- /* ALERT DATA-API
- * ============== */
-
- $(function () {
- $('body').on('click.alert.data-api', dismiss, Alert.prototype.close)
- })
-
-}(window.jQuery);/* ============================================================
- * bootstrap-button.js v2.0.4
- * http://twitter.github.com/bootstrap/javascript.html#buttons
- * ============================================================
- * Copyright 2012 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * ============================================================ */
-
-
-!function ($) {
-
- "use strict"; // jshint ;_;
-
-
- /* BUTTON PUBLIC CLASS DEFINITION
- * ============================== */
-
- var Button = function (element, options) {
- this.$element = $(element)
- this.options = $.extend({}, $.fn.button.defaults, options)
- }
-
- Button.prototype.setState = function (state) {
- var d = 'disabled'
- , $el = this.$element
- , data = $el.data()
- , val = $el.is('input') ? 'val' : 'html'
-
- state = state + 'Text'
- data.resetText || $el.data('resetText', $el[val]())
-
- $el[val](data[state] || this.options[state])
-
- // push to event loop to allow forms to submit
- setTimeout(function () {
- state == 'loadingText' ?
- $el.addClass(d).attr(d, d) :
- $el.removeClass(d).removeAttr(d)
- }, 0)
- }
-
- Button.prototype.toggle = function () {
- var $parent = this.$element.parent('[data-toggle="buttons-radio"]')
-
- $parent && $parent
- .find('.active')
- .removeClass('active')
-
- this.$element.toggleClass('active')
- }
-
-
- /* BUTTON PLUGIN DEFINITION
- * ======================== */
-
- $.fn.button = function (option) {
- return this.each(function () {
- var $this = $(this)
- , data = $this.data('button')
- , options = typeof option == 'object' && option
- if (!data) $this.data('button', (data = new Button(this, options)))
- if (option == 'toggle') data.toggle()
- else if (option) data.setState(option)
- })
- }
-
- $.fn.button.defaults = {
- loadingText: 'loading...'
- }
-
- $.fn.button.Constructor = Button
-
-
- /* BUTTON DATA-API
- * =============== */
-
- $(function () {
- $('body').on('click.button.data-api', '[data-toggle^=button]', function ( e ) {
- var $btn = $(e.target)
- if (!$btn.hasClass('btn')) $btn = $btn.closest('.btn')
- $btn.button('toggle')
- })
- })
-
-}(window.jQuery);/* ==========================================================
- * bootstrap-carousel.js v2.0.4
- * http://twitter.github.com/bootstrap/javascript.html#carousel
- * ==========================================================
- * Copyright 2012 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * ========================================================== */
-
-
-!function ($) {
-
- "use strict"; // jshint ;_;
-
-
- /* CAROUSEL CLASS DEFINITION
- * ========================= */
-
- var Carousel = function (element, options) {
- this.$element = $(element)
- this.options = options
- this.options.slide && this.slide(this.options.slide)
- this.options.pause == 'hover' && this.$element
- .on('mouseenter', $.proxy(this.pause, this))
- .on('mouseleave', $.proxy(this.cycle, this))
- }
-
- Carousel.prototype = {
-
- cycle: function (e) {
- if (!e) this.paused = false
- this.options.interval
- && !this.paused
- && (this.interval = setInterval($.proxy(this.next, this), this.options.interval))
- return this
- }
-
- , to: function (pos) {
- var $active = this.$element.find('.active')
- , children = $active.parent().children()
- , activePos = children.index($active)
- , that = this
-
- if (pos > (children.length - 1) || pos < 0) return
-
- if (this.sliding) {
- return this.$element.one('slid', function () {
- that.to(pos)
- })
- }
-
- if (activePos == pos) {
- return this.pause().cycle()
- }
-
- return this.slide(pos > activePos ? 'next' : 'prev', $(children[pos]))
- }
-
- , pause: function (e) {
- if (!e) this.paused = true
- clearInterval(this.interval)
- this.interval = null
- return this
- }
-
- , next: function () {
- if (this.sliding) return
- return this.slide('next')
- }
-
- , prev: function () {
- if (this.sliding) return
- return this.slide('prev')
- }
-
- , slide: function (type, next) {
- var $active = this.$element.find('.active')
- , $next = next || $active[type]()
- , isCycling = this.interval
- , direction = type == 'next' ? 'left' : 'right'
- , fallback = type == 'next' ? 'first' : 'last'
- , that = this
- , e = $.Event('slide')
-
- this.sliding = true
-
- isCycling && this.pause()
-
- $next = $next.length ? $next : this.$element.find('.item')[fallback]()
-
- if ($next.hasClass('active')) return
-
- if ($.support.transition && this.$element.hasClass('slide')) {
- this.$element.trigger(e)
- if (e.isDefaultPrevented()) return
- $next.addClass(type)
- $next[0].offsetWidth // force reflow
- $active.addClass(direction)
- $next.addClass(direction)
- this.$element.one($.support.transition.end, function () {
- $next.removeClass([type, direction].join(' ')).addClass('active')
- $active.removeClass(['active', direction].join(' '))
- that.sliding = false
- setTimeout(function () { that.$element.trigger('slid') }, 0)
- })
- } else {
- this.$element.trigger(e)
- if (e.isDefaultPrevented()) return
- $active.removeClass('active')
- $next.addClass('active')
- this.sliding = false
- this.$element.trigger('slid')
- }
-
- isCycling && this.cycle()
-
- return this
- }
-
- }
-
-
- /* CAROUSEL PLUGIN DEFINITION
- * ========================== */
-
- $.fn.carousel = function (option) {
- return this.each(function () {
- var $this = $(this)
- , data = $this.data('carousel')
- , options = $.extend({}, $.fn.carousel.defaults, typeof option == 'object' && option)
- if (!data) $this.data('carousel', (data = new Carousel(this, options)))
- if (typeof option == 'number') data.to(option)
- else if (typeof option == 'string' || (option = options.slide)) data[option]()
- else if (options.interval) data.cycle()
- })
- }
-
- $.fn.carousel.defaults = {
- interval: 5000
- , pause: 'hover'
- }
-
- $.fn.carousel.Constructor = Carousel
-
-
- /* CAROUSEL DATA-API
- * ================= */
-
- $(function () {
- $('body').on('click.carousel.data-api', '[data-slide]', function ( e ) {
- var $this = $(this), href
- , $target = $($this.attr('data-target') || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7
- , options = !$target.data('modal') && $.extend({}, $target.data(), $this.data())
- $target.carousel(options)
- e.preventDefault()
- })
- })
-
-}(window.jQuery);/* =============================================================
- * bootstrap-collapse.js v2.0.4
- * http://twitter.github.com/bootstrap/javascript.html#collapse
- * =============================================================
- * Copyright 2012 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * ============================================================ */
-
-
-!function ($) {
-
- "use strict"; // jshint ;_;
-
-
- /* COLLAPSE PUBLIC CLASS DEFINITION
- * ================================ */
-
- var Collapse = function (element, options) {
- this.$element = $(element)
- this.options = $.extend({}, $.fn.collapse.defaults, options)
-
- if (this.options.parent) {
- this.$parent = $(this.options.parent)
- }
-
- this.options.toggle && this.toggle()
- }
-
- Collapse.prototype = {
-
- constructor: Collapse
-
- , dimension: function () {
- var hasWidth = this.$element.hasClass('width')
- return hasWidth ? 'width' : 'height'
- }
-
- , show: function () {
- var dimension
- , scroll
- , actives
- , hasData
-
- if (this.transitioning) return
-
- dimension = this.dimension()
- scroll = $.camelCase(['scroll', dimension].join('-'))
- actives = this.$parent && this.$parent.find('> .accordion-group > .in')
-
- if (actives && actives.length) {
- hasData = actives.data('collapse')
- if (hasData && hasData.transitioning) return
- actives.collapse('hide')
- hasData || actives.data('collapse', null)
- }
-
- this.$element[dimension](0)
- this.transition('addClass', $.Event('show'), 'shown')
- this.$element[dimension](this.$element[0][scroll])
- }
-
- , hide: function () {
- var dimension
- if (this.transitioning) return
- dimension = this.dimension()
- this.reset(this.$element[dimension]())
- this.transition('removeClass', $.Event('hide'), 'hidden')
- this.$element[dimension](0)
- }
-
- , reset: function (size) {
- var dimension = this.dimension()
-
- this.$element
- .removeClass('collapse')
- [dimension](size || 'auto')
- [0].offsetWidth
-
- this.$element[size !== null ? 'addClass' : 'removeClass']('collapse')
-
- return this
- }
-
- , transition: function (method, startEvent, completeEvent) {
- var that = this
- , complete = function () {
- if (startEvent.type == 'show') that.reset()
- that.transitioning = 0
- that.$element.trigger(completeEvent)
- }
-
- this.$element.trigger(startEvent)
-
- if (startEvent.isDefaultPrevented()) return
-
- this.transitioning = 1
-
- this.$element[method]('in')
-
- $.support.transition && this.$element.hasClass('collapse') ?
- this.$element.one($.support.transition.end, complete) :
- complete()
- }
-
- , toggle: function () {
- this[this.$element.hasClass('in') ? 'hide' : 'show']()
- }
-
- }
-
-
- /* COLLAPSIBLE PLUGIN DEFINITION
- * ============================== */
-
- $.fn.collapse = function (option) {
- return this.each(function () {
- var $this = $(this)
- , data = $this.data('collapse')
- , options = typeof option == 'object' && option
- if (!data) $this.data('collapse', (data = new Collapse(this, options)))
- if (typeof option == 'string') data[option]()
- })
- }
-
- $.fn.collapse.defaults = {
- toggle: true
- }
-
- $.fn.collapse.Constructor = Collapse
-
-
- /* COLLAPSIBLE DATA-API
- * ==================== */
-
- $(function () {
- $('body').on('click.collapse.data-api', '[data-toggle=collapse]', function ( e ) {
- var $this = $(this), href
- , target = $this.attr('data-target')
- || e.preventDefault()
- || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '') //strip for ie7
- , option = $(target).data('collapse') ? 'toggle' : $this.data()
- $(target).collapse(option)
- })
- })
-
-}(window.jQuery);/* ============================================================
- * bootstrap-dropdown.js v2.0.4
- * http://twitter.github.com/bootstrap/javascript.html#dropdowns
- * ============================================================
- * Copyright 2012 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * ============================================================ */
-
-
-!function ($) {
-
- "use strict"; // jshint ;_;
-
-
- /* DROPDOWN CLASS DEFINITION
- * ========================= */
-
- var toggle = '[data-toggle="dropdown"]'
- , Dropdown = function (element) {
- var $el = $(element).on('click.dropdown.data-api', this.toggle)
- $('html').on('click.dropdown.data-api', function () {
- $el.parent().removeClass('open')
- })
- }
-
- Dropdown.prototype = {
-
- constructor: Dropdown
-
- , toggle: function (e) {
- var $this = $(this)
- , $parent
- , selector
- , isActive
-
- if ($this.is('.disabled, :disabled')) return
-
- selector = $this.attr('data-target')
-
- if (!selector) {
- selector = $this.attr('href')
- selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7
- }
-
- $parent = $(selector)
- $parent.length || ($parent = $this.parent())
-
- isActive = $parent.hasClass('open')
-
- clearMenus()
-
- if (!isActive) $parent.toggleClass('open')
-
- return false
- }
-
- }
-
- function clearMenus() {
- $(toggle).parent().removeClass('open')
- }
-
-
- /* DROPDOWN PLUGIN DEFINITION
- * ========================== */
-
- $.fn.dropdown = function (option) {
- return this.each(function () {
- var $this = $(this)
- , data = $this.data('dropdown')
- if (!data) $this.data('dropdown', (data = new Dropdown(this)))
- if (typeof option == 'string') data[option].call($this)
- })
- }
-
- $.fn.dropdown.Constructor = Dropdown
-
-
- /* APPLY TO STANDARD DROPDOWN ELEMENTS
- * =================================== */
-
- $(function () {
- $('html').on('click.dropdown.data-api', clearMenus)
- $('body')
- .on('click.dropdown', '.dropdown form', function (e) { e.stopPropagation() })
- .on('click.dropdown.data-api', toggle, Dropdown.prototype.toggle)
- })
-
-}(window.jQuery);/* =========================================================
- * bootstrap-modal.js v2.0.4
- * http://twitter.github.com/bootstrap/javascript.html#modals
- * =========================================================
- * Copyright 2012 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * ========================================================= */
-
-
-!function ($) {
-
- "use strict"; // jshint ;_;
-
-
- /* MODAL CLASS DEFINITION
- * ====================== */
-
- var Modal = function (content, options) {
- this.options = options
- this.$element = $(content)
- .delegate('[data-dismiss="modal"]', 'click.dismiss.modal', $.proxy(this.hide, this))
- }
-
- Modal.prototype = {
-
- constructor: Modal
-
- , toggle: function () {
- return this[!this.isShown ? 'show' : 'hide']()
- }
-
- , show: function () {
- var that = this
- , e = $.Event('show')
-
- this.$element.trigger(e)
-
- if (this.isShown || e.isDefaultPrevented()) return
-
- $('body').addClass('modal-open')
-
- this.isShown = true
-
- escape.call(this)
- backdrop.call(this, function () {
- var transition = $.support.transition && that.$element.hasClass('fade')
-
- if (!that.$element.parent().length) {
- that.$element.appendTo(document.body) //don't move modals dom position
- }
-
- that.$element
- .show()
-
- if (transition) {
- that.$element[0].offsetWidth // force reflow
- }
-
- that.$element.addClass('in')
-
- transition ?
- that.$element.one($.support.transition.end, function () { that.$element.trigger('shown') }) :
- that.$element.trigger('shown')
-
- })
- }
-
- , hide: function (e) {
- e && e.preventDefault()
-
- var that = this
-
- e = $.Event('hide')
-
- this.$element.trigger(e)
-
- if (!this.isShown || e.isDefaultPrevented()) return
-
- this.isShown = false
-
- $('body').removeClass('modal-open')
-
- escape.call(this)
-
- this.$element.removeClass('in')
-
- $.support.transition && this.$element.hasClass('fade') ?
- hideWithTransition.call(this) :
- hideModal.call(this)
- }
-
- }
-
-
- /* MODAL PRIVATE METHODS
- * ===================== */
-
- function hideWithTransition() {
- var that = this
- , timeout = setTimeout(function () {
- that.$element.off($.support.transition.end)
- hideModal.call(that)
- }, 500)
-
- this.$element.one($.support.transition.end, function () {
- clearTimeout(timeout)
- hideModal.call(that)
- })
- }
-
- function hideModal(that) {
- this.$element
- .hide()
- .trigger('hidden')
-
- backdrop.call(this)
- }
-
- function backdrop(callback) {
- var that = this
- , animate = this.$element.hasClass('fade') ? 'fade' : ''
-
- if (this.isShown && this.options.backdrop) {
- var doAnimate = $.support.transition && animate
-
- this.$backdrop = $('<div class="modal-backdrop ' + animate + '" />')
- .appendTo(document.body)
-
- if (this.options.backdrop != 'static') {
- this.$backdrop.click($.proxy(this.hide, this))
- }
-
- if (doAnimate) this.$backdrop[0].offsetWidth // force reflow
-
- this.$backdrop.addClass('in')
-
- doAnimate ?
- this.$backdrop.one($.support.transition.end, callback) :
- callback()
-
- } else if (!this.isShown && this.$backdrop) {
- this.$backdrop.removeClass('in')
-
- $.support.transition && this.$element.hasClass('fade')?
- this.$backdrop.one($.support.transition.end, $.proxy(removeBackdrop, this)) :
- removeBackdrop.call(this)
-
- } else if (callback) {
- callback()
- }
- }
-
- function removeBackdrop() {
- this.$backdrop.remove()
- this.$backdrop = null
- }
-
- function escape() {
- var that = this
- if (this.isShown && this.options.keyboard) {
- $(document).on('keyup.dismiss.modal', function ( e ) {
- e.which == 27 && that.hide()
- })
- } else if (!this.isShown) {
- $(document).off('keyup.dismiss.modal')
- }
- }
-
-
- /* MODAL PLUGIN DEFINITION
- * ======================= */
-
- $.fn.modal = function (option) {
- return this.each(function () {
- var $this = $(this)
- , data = $this.data('modal')
- , options = $.extend({}, $.fn.modal.defaults, $this.data(), typeof option == 'object' && option)
- if (!data) $this.data('modal', (data = new Modal(this, options)))
- if (typeof option == 'string') data[option]()
- else if (options.show) data.show()
- })
- }
-
- $.fn.modal.defaults = {
- backdrop: true
- , keyboard: true
- , show: true
- }
-
- $.fn.modal.Constructor = Modal
-
-
- /* MODAL DATA-API
- * ============== */
-
- $(function () {
- $('body').on('click.modal.data-api', '[data-toggle="modal"]', function ( e ) {
- var $this = $(this), href
- , $target = $($this.attr('data-target') || (href = $this.attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7
- , option = $target.data('modal') ? 'toggle' : $.extend({}, $target.data(), $this.data())
-
- e.preventDefault()
- $target.modal(option)
- })
- })
-
-}(window.jQuery);/* ===========================================================
- * bootstrap-tooltip.js v2.0.4
- * http://twitter.github.com/bootstrap/javascript.html#tooltips
- * Inspired by the original jQuery.tipsy by Jason Frame
- * ===========================================================
- * Copyright 2012 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * ========================================================== */
-
-
-!function ($) {
-
- "use strict"; // jshint ;_;
-
-
- /* TOOLTIP PUBLIC CLASS DEFINITION
- * =============================== */
-
- var Tooltip = function (element, options) {
- this.init('tooltip', element, options)
- }
-
- Tooltip.prototype = {
-
- constructor: Tooltip
-
- , init: function (type, element, options) {
- var eventIn
- , eventOut
-
- this.type = type
- this.$element = $(element)
- this.options = this.getOptions(options)
- this.enabled = true
-
- if (this.options.trigger != 'manual') {
- eventIn = this.options.trigger == 'hover' ? 'mouseenter' : 'focus'
- eventOut = this.options.trigger == 'hover' ? 'mouseleave' : 'blur'
- this.$element.on(eventIn, this.options.selector, $.proxy(this.enter, this))
- this.$element.on(eventOut, this.options.selector, $.proxy(this.leave, this))
- }
-
- this.options.selector ?
- (this._options = $.extend({}, this.options, { trigger: 'manual', selector: '' })) :
- this.fixTitle()
- }
-
- , getOptions: function (options) {
- options = $.extend({}, $.fn[this.type].defaults, options, this.$element.data())
-
- if (options.delay && typeof options.delay == 'number') {
- options.delay = {
- show: options.delay
- , hide: options.delay
- }
- }
-
- return options
- }
-
- , enter: function (e) {
- var self = $(e.currentTarget)[this.type](this._options).data(this.type)
-
- if (!self.options.delay || !self.options.delay.show) return self.show()
-
- clearTimeout(this.timeout)
- self.hoverState = 'in'
- this.timeout = setTimeout(function() {
- if (self.hoverState == 'in') self.show()
- }, self.options.delay.show)
- }
-
- , leave: function (e) {
- var self = $(e.currentTarget)[this.type](this._options).data(this.type)
-
- if (this.timeout) clearTimeout(this.timeout)
- if (!self.options.delay || !self.options.delay.hide) return self.hide()
-
- self.hoverState = 'out'
- this.timeout = setTimeout(function() {
- if (self.hoverState == 'out') self.hide()
- }, self.options.delay.hide)
- }
-
- , show: function () {
- var $tip
- , inside
- , pos
- , actualWidth
- , actualHeight
- , placement
- , tp
-
- if (this.hasContent() && this.enabled) {
- $tip = this.tip()
- this.setContent()
-
- if (this.options.animation) {
- $tip.addClass('fade')
- }
-
- placement = typeof this.options.placement == 'function' ?
- this.options.placement.call(this, $tip[0], this.$element[0]) :
- this.options.placement
-
- inside = /in/.test(placement)
-
- $tip
- .remove()
- .css({ top: 0, left: 0, display: 'block' })
- .appendTo(inside ? this.$element : document.body)
-
- pos = this.getPosition(inside)
-
- actualWidth = $tip[0].offsetWidth
- actualHeight = $tip[0].offsetHeight
-
- switch (inside ? placement.split(' ')[1] : placement) {
- case 'bottom':
- tp = {top: pos.top + pos.height, left: pos.left + pos.width / 2 - actualWidth / 2}
- break
- case 'top':
- tp = {top: pos.top - actualHeight, left: pos.left + pos.width / 2 - actualWidth / 2}
- break
- case 'left':
- tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left - actualWidth}
- break
- case 'right':
- tp = {top: pos.top + pos.height / 2 - actualHeight / 2, left: pos.left + pos.width}
- break
- }
-
- $tip
- .css(tp)
- .addClass(placement)
- .addClass('in')
- }
- }
-
- , isHTML: function(text) {
- // html string detection logic adapted from jQuery
- return typeof text != 'string'
- || ( text.charAt(0) === "<"
- && text.charAt( text.length - 1 ) === ">"
- && text.length >= 3
- ) || /^(?:[^<]*<[\w\W]+>[^>]*$)/.exec(text)
- }
-
- , setContent: function () {
- var $tip = this.tip()
- , title = this.getTitle()
-
- $tip.find('.tooltip-inner')[this.isHTML(title) ? 'html' : 'text'](title)
- $tip.removeClass('fade in top bottom left right')
- }
-
- , hide: function () {
- var that = this
- , $tip = this.tip()
-
- $tip.removeClass('in')
-
- function removeWithAnimation() {
- var timeout = setTimeout(function () {
- $tip.off($.support.transition.end).remove()
- }, 500)
-
- $tip.one($.support.transition.end, function () {
- clearTimeout(timeout)
- $tip.remove()
- })
- }
-
- $.support.transition && this.$tip.hasClass('fade') ?
- removeWithAnimation() :
- $tip.remove()
- }
-
- , fixTitle: function () {
- var $e = this.$element
- if ($e.attr('title') || typeof($e.attr('data-original-title')) != 'string') {
- $e.attr('data-original-title', $e.attr('title') || '').removeAttr('title')
- }
- }
-
- , hasContent: function () {
- return this.getTitle()
- }
-
- , getPosition: function (inside) {
- return $.extend({}, (inside ? {top: 0, left: 0} : this.$element.offset()), {
- width: this.$element[0].offsetWidth
- , height: this.$element[0].offsetHeight
- })
- }
-
- , getTitle: function () {
- var title
- , $e = this.$element
- , o = this.options
-
- title = $e.attr('data-original-title')
- || (typeof o.title == 'function' ? o.title.call($e[0]) : o.title)
-
- return title
- }
-
- , tip: function () {
- return this.$tip = this.$tip || $(this.options.template)
- }
-
- , validate: function () {
- if (!this.$element[0].parentNode) {
- this.hide()
- this.$element = null
- this.options = null
- }
- }
-
- , enable: function () {
- this.enabled = true
- }
-
- , disable: function () {
- this.enabled = false
- }
-
- , toggleEnabled: function () {
- this.enabled = !this.enabled
- }
-
- , toggle: function () {
- this[this.tip().hasClass('in') ? 'hide' : 'show']()
- }
-
- }
-
-
- /* TOOLTIP PLUGIN DEFINITION
- * ========================= */
-
- $.fn.tooltip = function ( option ) {
- return this.each(function () {
- var $this = $(this)
- , data = $this.data('tooltip')
- , options = typeof option == 'object' && option
- if (!data) $this.data('tooltip', (data = new Tooltip(this, options)))
- if (typeof option == 'string') data[option]()
- })
- }
-
- $.fn.tooltip.Constructor = Tooltip
-
- $.fn.tooltip.defaults = {
- animation: true
- , placement: 'top'
- , selector: false
- , template: '<div class="tooltip"><div class="tooltip-arrow"></div><div class="tooltip-inner"></div></div>'
- , trigger: 'hover'
- , title: ''
- , delay: 0
- }
-
-}(window.jQuery);
-/* ===========================================================
- * bootstrap-popover.js v2.0.4
- * http://twitter.github.com/bootstrap/javascript.html#popovers
- * ===========================================================
- * Copyright 2012 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * =========================================================== */
-
-
-!function ($) {
-
- "use strict"; // jshint ;_;
-
-
- /* POPOVER PUBLIC CLASS DEFINITION
- * =============================== */
-
- var Popover = function ( element, options ) {
- this.init('popover', element, options)
- }
-
-
- /* NOTE: POPOVER EXTENDS BOOTSTRAP-TOOLTIP.js
- ========================================== */
-
- Popover.prototype = $.extend({}, $.fn.tooltip.Constructor.prototype, {
-
- constructor: Popover
-
- , setContent: function () {
- var $tip = this.tip()
- , title = this.getTitle()
- , content = this.getContent()
-
- $tip.find('.popover-title')[this.isHTML(title) ? 'html' : 'text'](title)
- $tip.find('.popover-content > *')[this.isHTML(content) ? 'html' : 'text'](content)
-
- $tip.removeClass('fade top bottom left right in')
- }
-
- , hasContent: function () {
- return this.getTitle() || this.getContent()
- }
-
- , getContent: function () {
- var content
- , $e = this.$element
- , o = this.options
-
- content = $e.attr('data-content')
- || (typeof o.content == 'function' ? o.content.call($e[0]) : o.content)
-
- return content
- }
-
- , tip: function () {
- if (!this.$tip) {
- this.$tip = $(this.options.template)
- }
- return this.$tip
- }
-
- })
-
-
- /* POPOVER PLUGIN DEFINITION
- * ======================= */
-
- $.fn.popover = function (option) {
- return this.each(function () {
- var $this = $(this)
- , data = $this.data('popover')
- , options = typeof option == 'object' && option
- if (!data) $this.data('popover', (data = new Popover(this, options)))
- if (typeof option == 'string') data[option]()
- })
- }
-
- $.fn.popover.Constructor = Popover
-
- $.fn.popover.defaults = $.extend({} , $.fn.tooltip.defaults, {
- placement: 'right'
- , content: ''
- , template: '<div class="popover"><div class="arrow"></div><div class="popover-inner"><h3 class="popover-title"></h3><div class="popover-content"><p></p></div></div></div>'
- })
-
-}(window.jQuery);/* =============================================================
- * bootstrap-scrollspy.js v2.0.4
- * http://twitter.github.com/bootstrap/javascript.html#scrollspy
- * =============================================================
- * Copyright 2012 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * ============================================================== */
-
-
-!function ($) {
-
- "use strict"; // jshint ;_;
-
-
- /* SCROLLSPY CLASS DEFINITION
- * ========================== */
-
- function ScrollSpy( element, options) {
- var process = $.proxy(this.process, this)
- , $element = $(element).is('body') ? $(window) : $(element)
- , href
- this.options = $.extend({}, $.fn.scrollspy.defaults, options)
- this.$scrollElement = $element.on('scroll.scroll.data-api', process)
- this.selector = (this.options.target
- || ((href = $(element).attr('href')) && href.replace(/.*(?=#[^\s]+$)/, '')) //strip for ie7
- || '') + ' .nav li > a'
- this.$body = $('body')
- this.refresh()
- this.process()
- }
-
- ScrollSpy.prototype = {
-
- constructor: ScrollSpy
-
- , refresh: function () {
- var self = this
- , $targets
-
- this.offsets = $([])
- this.targets = $([])
-
- $targets = this.$body
- .find(this.selector)
- .map(function () {
- var $el = $(this)
- , href = $el.data('target') || $el.attr('href')
- , $href = /^#\w/.test(href) && $(href)
- return ( $href
- && href.length
- && [[ $href.position().top, href ]] ) || null
- })
- .sort(function (a, b) { return a[0] - b[0] })
- .each(function () {
- self.offsets.push(this[0])
- self.targets.push(this[1])
- })
- }
-
- , process: function () {
- var scrollTop = this.$scrollElement.scrollTop() + this.options.offset
- , scrollHeight = this.$scrollElement[0].scrollHeight || this.$body[0].scrollHeight
- , maxScroll = scrollHeight - this.$scrollElement.height()
- , offsets = this.offsets
- , targets = this.targets
- , activeTarget = this.activeTarget
- , i
-
- if (scrollTop >= maxScroll) {
- return activeTarget != (i = targets.last()[0])
- && this.activate ( i )
- }
-
- for (i = offsets.length; i--;) {
- activeTarget != targets[i]
- && scrollTop >= offsets[i]
- && (!offsets[i + 1] || scrollTop <= offsets[i + 1])
- && this.activate( targets[i] )
- }
- }
-
- , activate: function (target) {
- var active
- , selector
-
- this.activeTarget = target
-
- $(this.selector)
- .parent('.active')
- .removeClass('active')
-
- selector = this.selector
- + '[data-target="' + target + '"],'
- + this.selector + '[href="' + target + '"]'
-
- active = $(selector)
- .parent('li')
- .addClass('active')
-
- if (active.parent('.dropdown-menu')) {
- active = active.closest('li.dropdown').addClass('active')
- }
-
- active.trigger('activate')
- }
-
- }
-
-
- /* SCROLLSPY PLUGIN DEFINITION
- * =========================== */
-
- $.fn.scrollspy = function ( option ) {
- return this.each(function () {
- var $this = $(this)
- , data = $this.data('scrollspy')
- , options = typeof option == 'object' && option
- if (!data) $this.data('scrollspy', (data = new ScrollSpy(this, options)))
- if (typeof option == 'string') data[option]()
- })
- }
-
- $.fn.scrollspy.Constructor = ScrollSpy
-
- $.fn.scrollspy.defaults = {
- offset: 10
- }
-
-
- /* SCROLLSPY DATA-API
- * ================== */
-
- $(function () {
- $('[data-spy="scroll"]').each(function () {
- var $spy = $(this)
- $spy.scrollspy($spy.data())
- })
- })
-
-}(window.jQuery);/* ========================================================
- * bootstrap-tab.js v2.0.4
- * http://twitter.github.com/bootstrap/javascript.html#tabs
- * ========================================================
- * Copyright 2012 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * ======================================================== */
-
-
-!function ($) {
-
- "use strict"; // jshint ;_;
-
-
- /* TAB CLASS DEFINITION
- * ==================== */
-
- var Tab = function ( element ) {
- this.element = $(element)
- }
-
- Tab.prototype = {
-
- constructor: Tab
-
- , show: function () {
- var $this = this.element
- , $ul = $this.closest('ul:not(.dropdown-menu)')
- , selector = $this.attr('data-target')
- , previous
- , $target
- , e
-
- if (!selector) {
- selector = $this.attr('href')
- selector = selector && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7
- }
-
- if ( $this.parent('li').hasClass('active') ) return
-
- previous = $ul.find('.active a').last()[0]
-
- e = $.Event('show', {
- relatedTarget: previous
- })
-
- $this.trigger(e)
-
- if (e.isDefaultPrevented()) return
-
- $target = $(selector)
-
- this.activate($this.parent('li'), $ul)
- this.activate($target, $target.parent(), function () {
- $this.trigger({
- type: 'shown'
- , relatedTarget: previous
- })
- })
- }
-
- , activate: function ( element, container, callback) {
- var $active = container.find('> .active')
- , transition = callback
- && $.support.transition
- && $active.hasClass('fade')
-
- function next() {
- $active
- .removeClass('active')
- .find('> .dropdown-menu > .active')
- .removeClass('active')
-
- element.addClass('active')
-
- if (transition) {
- element[0].offsetWidth // reflow for transition
- element.addClass('in')
- } else {
- element.removeClass('fade')
- }
-
- if ( element.parent('.dropdown-menu') ) {
- element.closest('li.dropdown').addClass('active')
- }
-
- callback && callback()
- }
-
- transition ?
- $active.one($.support.transition.end, next) :
- next()
-
- $active.removeClass('in')
- }
- }
-
-
- /* TAB PLUGIN DEFINITION
- * ===================== */
-
- $.fn.tab = function ( option ) {
- return this.each(function () {
- var $this = $(this)
- , data = $this.data('tab')
- if (!data) $this.data('tab', (data = new Tab(this)))
- if (typeof option == 'string') data[option]()
- })
- }
-
- $.fn.tab.Constructor = Tab
-
-
- /* TAB DATA-API
- * ============ */
-
- $(function () {
- $('body').on('click.tab.data-api', '[data-toggle="tab"], [data-toggle="pill"]', function (e) {
- e.preventDefault()
- $(this).tab('show')
- })
- })
-
-}(window.jQuery);/* =============================================================
- * bootstrap-typeahead.js v2.0.4
- * http://twitter.github.com/bootstrap/javascript.html#typeahead
- * =============================================================
- * Copyright 2012 Twitter, Inc.
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- * ============================================================ */
-
-
-!function($){
-
- "use strict"; // jshint ;_;
-
-
- /* TYPEAHEAD PUBLIC CLASS DEFINITION
- * ================================= */
-
- var Typeahead = function (element, options) {
- this.$element = $(element)
- this.options = $.extend({}, $.fn.typeahead.defaults, options)
- this.matcher = this.options.matcher || this.matcher
- this.sorter = this.options.sorter || this.sorter
- this.highlighter = this.options.highlighter || this.highlighter
- this.updater = this.options.updater || this.updater
- this.$menu = $(this.options.menu).appendTo('body')
- this.source = this.options.source
- this.shown = false
- this.listen()
- }
-
- Typeahead.prototype = {
-
- constructor: Typeahead
-
- , select: function () {
- var val = this.$menu.find('.active').attr('data-value')
- this.$element
- .val(this.updater(val))
- .change()
- return this.hide()
- }
-
- , updater: function (item) {
- return item
- }
-
- , show: function () {
- var pos = $.extend({}, this.$element.offset(), {
- height: this.$element[0].offsetHeight
- })
-
- this.$menu.css({
- top: pos.top + pos.height
- , left: pos.left
- })
-
- this.$menu.show()
- this.shown = true
- return this
- }
-
- , hide: function () {
- this.$menu.hide()
- this.shown = false
- return this
- }
-
- , lookup: function (event) {
- var that = this
- , items
- , q
-
- this.query = this.$element.val()
-
- if (!this.query) {
- return this.shown ? this.hide() : this
- }
-
- items = $.grep(this.source, function (item) {
- return that.matcher(item)
- })
-
- items = this.sorter(items)
-
- if (!items.length) {
- return this.shown ? this.hide() : this
- }
-
- return this.render(items.slice(0, this.options.items)).show()
- }
-
- , matcher: function (item) {
- return ~item.toLowerCase().indexOf(this.query.toLowerCase())
- }
-
- , sorter: function (items) {
- var beginswith = []
- , caseSensitive = []
- , caseInsensitive = []
- , item
-
- while (item = items.shift()) {
- if (!item.toLowerCase().indexOf(this.query.toLowerCase())) beginswith.push(item)
- else if (~item.indexOf(this.query)) caseSensitive.push(item)
- else caseInsensitive.push(item)
- }
-
- return beginswith.concat(caseSensitive, caseInsensitive)
- }
-
- , highlighter: function (item) {
- var query = this.query.replace(/[\-\[\]{}()*+?.,\\\^$|#\s]/g, '\\$&')
- return item.replace(new RegExp('(' + query + ')', 'ig'), function ($1, match) {
- return '<strong>' + match + '</strong>'
- })
- }
-
- , render: function (items) {
- var that = this
-
- items = $(items).map(function (i, item) {
- i = $(that.options.item).attr('data-value', item)
- i.find('a').html(that.highlighter(item))
- return i[0]
- })
-
- items.first().addClass('active')
- this.$menu.html(items)
- return this
- }
-
- , next: function (event) {
- var active = this.$menu.find('.active').removeClass('active')
- , next = active.next()
-
- if (!next.length) {
- next = $(this.$menu.find('li')[0])
- }
-
- next.addClass('active')
- }
-
- , prev: function (event) {
- var active = this.$menu.find('.active').removeClass('active')
- , prev = active.prev()
-
- if (!prev.length) {
- prev = this.$menu.find('li').last()
- }
-
- prev.addClass('active')
- }
-
- , listen: function () {
- this.$element
- .on('blur', $.proxy(this.blur, this))
- .on('keypress', $.proxy(this.keypress, this))
- .on('keyup', $.proxy(this.keyup, this))
-
- if ($.browser.webkit || $.browser.msie) {
- this.$element.on('keydown', $.proxy(this.keypress, this))
- }
-
- this.$menu
- .on('click', $.proxy(this.click, this))
- .on('mouseenter', 'li', $.proxy(this.mouseenter, this))
- }
-
- , keyup: function (e) {
- switch(e.keyCode) {
- case 40: // down arrow
- case 38: // up arrow
- break
-
- case 9: // tab
- case 13: // enter
- if (!this.shown) return
- this.select()
- break
-
- case 27: // escape
- if (!this.shown) return
- this.hide()
- break
-
- default:
- this.lookup()
- }
-
- e.stopPropagation()
- e.preventDefault()
- }
-
- , keypress: function (e) {
- if (!this.shown) return
-
- switch(e.keyCode) {
- case 9: // tab
- case 13: // enter
- case 27: // escape
- e.preventDefault()
- break
-
- case 38: // up arrow
- if (e.type != 'keydown') break
- e.preventDefault()
- this.prev()
- break
-
- case 40: // down arrow
- if (e.type != 'keydown') break
- e.preventDefault()
- this.next()
- break
- }
-
- e.stopPropagation()
- }
-
- , blur: function (e) {
- var that = this
- setTimeout(function () { that.hide() }, 150)
- }
-
- , click: function (e) {
- e.stopPropagation()
- e.preventDefault()
- this.select()
- }
-
- , mouseenter: function (e) {
- this.$menu.find('.active').removeClass('active')
- $(e.currentTarget).addClass('active')
- }
-
- }
-
-
- /* TYPEAHEAD PLUGIN DEFINITION
- * =========================== */
-
- $.fn.typeahead = function (option) {
- return this.each(function () {
- var $this = $(this)
- , data = $this.data('typeahead')
- , options = typeof option == 'object' && option
- if (!data) $this.data('typeahead', (data = new Typeahead(this, options)))
- if (typeof option == 'string') data[option]()
- })
- }
-
- $.fn.typeahead.defaults = {
- source: []
- , items: 8
- , menu: '<ul class="typeahead dropdown-menu"></ul>'
- , item: '<li><a href="#"></a></li>'
- }
-
- $.fn.typeahead.Constructor = Typeahead
-
-
- /* TYPEAHEAD DATA-API
- * ================== */
-
- $(function () {
- $('body').on('focus.typeahead.data-api', '[data-provide="typeahead"]', function (e) {
- var $this = $(this)
- if ($this.data('typeahead')) return
- e.preventDefault()
- $this.typeahead($this.data())
- })
- })
-
-}(window.jQuery); \ No newline at end of file
diff --git a/inst/web/js/bootstrap.min.js b/inst/web/js/bootstrap.min.js
deleted file mode 100644
index 1435698..0000000
--- a/inst/web/js/bootstrap.min.js
+++ /dev/null
@@ -1,6 +0,0 @@
-/*!
-* Bootstrap.js by @fat & @mdo
-* Copyright 2012 Twitter, Inc.
-* http://www.apache.org/licenses/LICENSE-2.0.txt
-*/
-!function(a){a(function(){"use strict",a.support.transition=function(){var a=function(){var a=document.createElement("bootstrap"),b={WebkitTransition:"webkitTransitionEnd",MozTransition:"transitionend",OTransition:"oTransitionEnd",msTransition:"MSTransitionEnd",transition:"transitionend"},c;for(c in b)if(a.style[c]!==undefined)return b[c]}();return a&&{end:a}}()})}(window.jQuery),!function(a){"use strict";var b='[data-dismiss="alert"]',c=function(c){a(c).on("click",b,this.close)};c.prototype.close=function(b){function f(){e.trigger("closed").remove()}var c=a(this),d=c.attr("data-target"),e;d||(d=c.attr("href"),d=d&&d.replace(/.*(?=#[^\s]*$)/,"")),e=a(d),b&&b.preventDefault(),e.length||(e=c.hasClass("alert")?c:c.parent()),e.trigger(b=a.Event("close"));if(b.isDefaultPrevented())return;e.removeClass("in"),a.support.transition&&e.hasClass("fade")?e.on(a.support.transition.end,f):f()},a.fn.alert=function(b){return this.each(function(){var d=a(this),e=d.data("alert");e||d.data("alert",e=new 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diff --git a/inst/web/pfm_degradation.html b/inst/web/pfm_degradation.html
deleted file mode 100644
index fad64be..0000000
--- a/inst/web/pfm_degradation.html
+++ /dev/null
@@ -1,119 +0,0 @@
-<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="utf-8">
-<title>pfm_degradation. pfm 0.3-7</title>
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<meta name="author" content="
-Johannes Ranke
-">
-
-<link href="css/bootstrap.css" rel="stylesheet">
-<link href="css/bootstrap-responsive.css" rel="stylesheet">
-<link href="css/highlight.css" rel="stylesheet">
-<link href="css/staticdocs.css" rel="stylesheet">
-
-<!--[if lt IE 9]>
- <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
-<![endif]-->
-
-<script type="text/x-mathjax-config">
- MathJax.Hub.Config({
- tex2jax: {
- inlineMath: [ ['$','$'], ["\\(","\\)"] ],
- 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&nbsp;=&nbsp;"SFO", DT50&nbsp;=&nbsp;1000, parms&nbsp;=&nbsp;c(k_parent_sink = log(2)/DT50), years&nbsp;=&nbsp;1, step_days&nbsp;=&nbsp;1, times&nbsp;=&nbsp;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(&quot;SFO&quot;, 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/inst/web/plot.TOXSWA_cwa-2.png b/inst/web/plot.TOXSWA_cwa-2.png
deleted file mode 100644
index 764c7f4..0000000
--- a/inst/web/plot.TOXSWA_cwa-2.png
+++ /dev/null
Binary files differ
diff --git a/inst/web/plot.TOXSWA_cwa-4.png b/inst/web/plot.TOXSWA_cwa-4.png
deleted file mode 100644
index 764c7f4..0000000
--- a/inst/web/plot.TOXSWA_cwa-4.png
+++ /dev/null
Binary files differ
diff --git a/inst/web/plot.TOXSWA_cwa.html b/inst/web/plot.TOXSWA_cwa.html
deleted file mode 100644
index a6118df..0000000
--- a/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&nbsp;=&nbsp;c("datetime", "t", "t_firstjan", "t_rel_to_max"), xlab&nbsp;=&nbsp;"default", ylab&nbsp;=&nbsp;"default", add&nbsp;=&nbsp;FALSE, total&nbsp;=&nbsp;FALSE, LC_TIME&nbsp;=&nbsp;"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 &lt;- read.TOXSWA_cwa(&quot;00001p_pa.cwa&quot;,
- basedir = &quot;SwashProjects/project_H_sw/TOXSWA&quot;,
- zipfile = system.file(&quot;testdata/SwashProjects.zip&quot;,
- package = &quot;pfm&quot;))
-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/inst/web/read.TOXSWA_cwa.html b/inst/web/read.TOXSWA_cwa.html
deleted file mode 100644
index 3f2d997..0000000
--- a/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&nbsp;=&nbsp;".", zipfile&nbsp;=&nbsp;NULL, segment&nbsp;=&nbsp;"last", substance&nbsp;=&nbsp;"parent", total&nbsp;=&nbsp;FALSE, windows&nbsp;=&nbsp;NULL, thresholds&nbsp;=&nbsp;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 &lt;- read.TOXSWA_cwa(&quot;00001p_pa.cwa&quot;,
- basedir = &quot;SwashProjects/project_H_sw/TOXSWA&quot;,
- zipfile = system.file(&quot;testdata/SwashProjects.zip&quot;,
- package = &quot;pfm&quot;))
-</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/inst/web/soil_DT50.html b/inst/web/soil_DT50.html
deleted file mode 100644
index 0e142ae..0000000
--- a/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&nbsp;=&nbsp;geomean, signif&nbsp;=&nbsp;3, lab_field&nbsp;=&nbsp;"laboratory", value&nbsp;=&nbsp;"DT50ref", redox&nbsp;=&nbsp;"aerobic", raw&nbsp;=&nbsp;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/inst/web/soil_Kfoc.html b/inst/web/soil_Kfoc.html
deleted file mode 100644
index ace5f4b..0000000
--- a/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&nbsp;=&nbsp;geomean, signif&nbsp;=&nbsp;3, value&nbsp;=&nbsp;"Kfoc", raw&nbsp;=&nbsp;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/inst/web/soil_N.html b/inst/web/soil_N.html
deleted file mode 100644
index 886bbc7..0000000
--- a/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&nbsp;=&nbsp;mean, signif&nbsp;=&nbsp;3, raw&nbsp;=&nbsp;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/inst/web/soil_scenario_data_EFSA_2015.html b/inst/web/soil_scenario_data_EFSA_2015.html
deleted file mode 100644
index 0230afb..0000000
--- a/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 &lt;- data.frame(
-# Zone = rep(c(&quot;North&quot;, &quot;Central&quot;, &quot;South&quot;), 2),
-# Country = c(&quot;Estonia&quot;, &quot;Germany&quot;, &quot;France&quot;, &quot;Denmark&quot;, &quot;Czech Republik&quot;, &quot;Spain&quot;),
-# 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(&quot;Coarse&quot;, &quot;Coarse&quot;, &quot;Medium fine&quot;, &quot;Medium&quot;, &quot;Medium&quot;, &quot;Medium&quot;),
-# 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(&quot;CTN&quot;, &quot;CTC&quot;, &quot;CTS&quot;, &quot;CLN&quot;, &quot;CLC&quot;, &quot;CLS&quot;)
-# )
-# save(soil_scenario_data_EFSA_2015, file = &#39;../data/soil_scenario_data_EFSA_2015.RData&#39;)
-# ## 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/inst/web/soil_sorption.html b/inst/web/soil_sorption.html
deleted file mode 100644
index 152fc5e..0000000
--- a/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&nbsp;=&nbsp;c("Kfoc", "N"), aggregators&nbsp;=&nbsp;c(Kfoc = geomean, Koc&nbsp;=&nbsp;geomean, N&nbsp;=&nbsp;mean), signif&nbsp;=&nbsp;rep(3, length(values)), raw&nbsp;=&nbsp;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>
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