diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2016-07-30 11:29:09 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2016-07-30 11:29:09 +0200 |
| commit | 2f618da8cfbeb0379f4d38af6f608a69c6d54bd5 (patch) | |
| tree | a968ed591c8b400ec11d5d2d8561481201cfbda0 /pkg | |
| parent | 3b8730a58f7846b5261922ec90e582e0158a54c7 (diff) | |
Update static documentation
Diffstat (limited to 'pkg')
| -rw-r--r-- | pkg/inst/web/FOCUS_GW_scenarios_2012.html | 6 | ||||
| -rw-r--r-- | pkg/inst/web/GUS.html | 4 | ||||
| -rw-r--r-- | pkg/inst/web/PEC_soil.html | 4 | ||||
| -rw-r--r-- | pkg/inst/web/PEC_sw_drainage_UK.html | 4 | ||||
| -rw-r--r-- | pkg/inst/web/PEC_sw_drift.html | 9 | ||||
| -rw-r--r-- | pkg/inst/web/PEC_sw_sed.html | 4 | ||||
| -rw-r--r-- | pkg/inst/web/SFO_actual_twa.html | 4 | ||||
| -rw-r--r-- | pkg/inst/web/SSLRC_mobility_classification.html | 4 | ||||
| -rw-r--r-- | pkg/inst/web/TOXSWA_cwa.html | 4 | ||||
| -rw-r--r-- | pkg/inst/web/drift_data_JKI.html | 4 | ||||
| -rw-r--r-- | pkg/inst/web/endpoint.html | 6 | ||||
| -rw-r--r-- | pkg/inst/web/geomean.html | 4 | ||||
| -rw-r--r-- | pkg/inst/web/index.html | 6 | ||||
| -rw-r--r-- | pkg/inst/web/pfm_degradation.html | 4 | ||||
| -rw-r--r-- | pkg/inst/web/plot.TOXSWA_cwa.html | 4 | ||||
| -rw-r--r-- | pkg/inst/web/read.TOXSWA_cwa.html | 21 | ||||
| -rw-r--r-- | pkg/inst/web/soil_scenario_data_EFSA_2015.html | 4 |
17 files changed, 55 insertions, 41 deletions
diff --git a/pkg/inst/web/FOCUS_GW_scenarios_2012.html b/pkg/inst/web/FOCUS_GW_scenarios_2012.html index 43fc3a3..43ac090 100644 --- a/pkg/inst/web/FOCUS_GW_scenarios_2012.html +++ b/pkg/inst/web/FOCUS_GW_scenarios_2012.html @@ -2,7 +2,7 @@ <html lang="en"> <head> <meta charset="utf-8"> -<title>FOCUS_GW_scenarios_2012. pfm 0.3-1</title> +<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=""> @@ -32,7 +32,7 @@ <div class="navbar"> <div class="navbar-inner"> <div class="container"> - <a class="brand" href="#">pfm 0.3-1</a> + <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> @@ -73,7 +73,7 @@ </div> <div class='output'>$names Cha Ham Jok Kre Oke - "Châteadun" "Hamburg" "Jokioinen" "Kremsmünster" "Okehampton" + "Châteaudun" "Hamburg" "Jokioinen" "Kremsmünster" "Okehampton" Pia Por Sev Thi "Piacenza" "Porto" "Sevilla" "Thiva" diff --git a/pkg/inst/web/GUS.html b/pkg/inst/web/GUS.html index dae2e5f..a330be2 100644 --- a/pkg/inst/web/GUS.html +++ b/pkg/inst/web/GUS.html @@ -2,7 +2,7 @@ <html lang="en"> <head> <meta charset="utf-8"> -<title>GUS. pfm 0.3-1</title> +<title>GUS. pfm 0.3-7</title> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="author" content=" Johannes Ranke @@ -34,7 +34,7 @@ Johannes Ranke <div class="navbar"> <div class="navbar-inner"> <div class="container"> - <a class="brand" href="#">pfm 0.3-1</a> + <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> diff --git a/pkg/inst/web/PEC_soil.html b/pkg/inst/web/PEC_soil.html index d74a49f..1304d19 100644 --- a/pkg/inst/web/PEC_soil.html +++ b/pkg/inst/web/PEC_soil.html @@ -2,7 +2,7 @@ <html lang="en"> <head> <meta charset="utf-8"> -<title>PEC_soil. pfm 0.3-1</title> +<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 @@ -34,7 +34,7 @@ Johannes Ranke <div class="navbar"> <div class="navbar-inner"> <div class="container"> - <a class="brand" href="#">pfm 0.3-1</a> + <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> diff --git a/pkg/inst/web/PEC_sw_drainage_UK.html b/pkg/inst/web/PEC_sw_drainage_UK.html index 1cbac88..bf97fea 100644 --- a/pkg/inst/web/PEC_sw_drainage_UK.html +++ b/pkg/inst/web/PEC_sw_drainage_UK.html @@ -2,7 +2,7 @@ <html lang="en"> <head> <meta charset="utf-8"> -<title>PEC_sw_drainage_UK. pfm 0.3-1</title> +<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 @@ -34,7 +34,7 @@ Johannes Ranke <div class="navbar"> <div class="navbar-inner"> <div class="container"> - <a class="brand" href="#">pfm 0.3-1</a> + <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> diff --git a/pkg/inst/web/PEC_sw_drift.html b/pkg/inst/web/PEC_sw_drift.html index 4a097fc..5d4bb47 100644 --- a/pkg/inst/web/PEC_sw_drift.html +++ b/pkg/inst/web/PEC_sw_drift.html @@ -2,7 +2,7 @@ <html lang="en"> <head> <meta charset="utf-8"> -<title>PEC_sw_drift. pfm 0.3-1</title> +<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 @@ -34,7 +34,7 @@ Johannes Ranke <div class="navbar"> <div class="navbar-inner"> <div class="container"> - <a class="brand" href="#">pfm 0.3-1</a> + <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> @@ -54,7 +54,7 @@ Johannes Ranke <div class="row"> <div class="span8"> <h2>Usage</h2> - <pre><div>PEC_sw_drift(rate, applications = 1, water_depth = 30, drift_data = "JKI", crop = "Ackerbau", distances = c(1, 5, 10, 20), rate_units = "g/ha", PEC_units = "µg/L")</div></pre> + <pre><div>PEC_sw_drift(rate, applications = 1, water_depth = 30, drift_percentages = NULL, drift_data = "JKI", crop = "Ackerbau", distances = c(1, 5, 10, 20), rate_units = "g/ha", PEC_units = "µg/L")</div></pre> <h2>Arguments</h2> <dl> @@ -64,6 +64,9 @@ Johannes Ranke <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> diff --git a/pkg/inst/web/PEC_sw_sed.html b/pkg/inst/web/PEC_sw_sed.html index 231c48f..4eda1d7 100644 --- a/pkg/inst/web/PEC_sw_sed.html +++ b/pkg/inst/web/PEC_sw_sed.html @@ -2,7 +2,7 @@ <html lang="en"> <head> <meta charset="utf-8"> -<title>PEC_sw_sed. pfm 0.3-1</title> +<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 @@ -34,7 +34,7 @@ Johannes Ranke <div class="navbar"> <div class="navbar-inner"> <div class="container"> - <a class="brand" href="#">pfm 0.3-1</a> + <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> diff --git a/pkg/inst/web/SFO_actual_twa.html b/pkg/inst/web/SFO_actual_twa.html index e132828..3ce9220 100644 --- a/pkg/inst/web/SFO_actual_twa.html +++ b/pkg/inst/web/SFO_actual_twa.html @@ -2,7 +2,7 @@ <html lang="en"> <head> <meta charset="utf-8"> -<title>SFO_actual_twa. pfm 0.3-1</title> +<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 @@ -34,7 +34,7 @@ Johannes Ranke <div class="navbar"> <div class="navbar-inner"> <div class="container"> - <a class="brand" href="#">pfm 0.3-1</a> + <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> diff --git a/pkg/inst/web/SSLRC_mobility_classification.html b/pkg/inst/web/SSLRC_mobility_classification.html index 06c6119..43d701e 100644 --- a/pkg/inst/web/SSLRC_mobility_classification.html +++ b/pkg/inst/web/SSLRC_mobility_classification.html @@ -2,7 +2,7 @@ <html lang="en"> <head> <meta charset="utf-8"> -<title>SSLRC_mobility_classification. pfm 0.3-1</title> +<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 @@ -34,7 +34,7 @@ Johannes Ranke <div class="navbar"> <div class="navbar-inner"> <div class="container"> - <a class="brand" href="#">pfm 0.3-1</a> + <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> diff --git a/pkg/inst/web/TOXSWA_cwa.html b/pkg/inst/web/TOXSWA_cwa.html index 8edb15a..0d8ae17 100644 --- a/pkg/inst/web/TOXSWA_cwa.html +++ b/pkg/inst/web/TOXSWA_cwa.html @@ -2,7 +2,7 @@ <html lang="en"> <head> <meta charset="utf-8"> -<title>TOXSWA_cwa. pfm 0.3-1</title> +<title>TOXSWA_cwa. pfm 0.3-7</title> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="author" content=""> @@ -32,7 +32,7 @@ <div class="navbar"> <div class="navbar-inner"> <div class="container"> - <a class="brand" href="#">pfm 0.3-1</a> + <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> diff --git a/pkg/inst/web/drift_data_JKI.html b/pkg/inst/web/drift_data_JKI.html index 865e7fa..c3471c9 100644 --- a/pkg/inst/web/drift_data_JKI.html +++ b/pkg/inst/web/drift_data_JKI.html @@ -2,7 +2,7 @@ <html lang="en"> <head> <meta charset="utf-8"> -<title>drift_data_JKI. pfm 0.3-1</title> +<title>drift_data_JKI. pfm 0.3-7</title> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="author" content=""> @@ -32,7 +32,7 @@ <div class="navbar"> <div class="navbar-inner"> <div class="container"> - <a class="brand" href="#">pfm 0.3-1</a> + <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> diff --git a/pkg/inst/web/endpoint.html b/pkg/inst/web/endpoint.html index 0789d95..521f7f4 100644 --- a/pkg/inst/web/endpoint.html +++ b/pkg/inst/web/endpoint.html @@ -2,7 +2,7 @@ <html lang="en"> <head> <meta charset="utf-8"> -<title>endpoint. pfm 0.3-1</title> +<title>endpoint. pfm 0.3-7</title> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="author" content=""> @@ -32,7 +32,7 @@ <div class="navbar"> <div class="navbar-inner"> <div class="container"> - <a class="brand" href="#">pfm 0.3-1</a> + <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> @@ -56,7 +56,7 @@ <div>soil_DT50(chent, aggregator = geomean, signif = 3, lab_field = "laboratory", value = "DT50ref", redox = "aerobic", raw = FALSE)</div> <div>soil_Kfoc(chent, aggregator = geomean, signif = 3, value = "Kfoc", raw = FALSE)</div> <div>soil_N(chent, aggregator = mean, signif = 3, raw = FALSE)</div> -<div>soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc = geomean, Koc = geomean, N = mean), signif = rep(3, length(values)), raw = FALSE)</div></pre> +<div>soil_sorption(chent, values = c("Kfoc", "N"), aggregators = c(Kfoc = geomean, Koc = geomean, N = mean), signif = c(Kfoc = 3, N = 3), raw = FALSE)</div></pre> <h2>Arguments</h2> <dl> diff --git a/pkg/inst/web/geomean.html b/pkg/inst/web/geomean.html index fb859fa..672e9b5 100644 --- a/pkg/inst/web/geomean.html +++ b/pkg/inst/web/geomean.html @@ -2,7 +2,7 @@ <html lang="en"> <head> <meta charset="utf-8"> -<title>geomean. pfm 0.3-1</title> +<title>geomean. pfm 0.3-7</title> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="author" content=" Johannes Ranke @@ -34,7 +34,7 @@ Johannes Ranke <div class="navbar"> <div class="navbar-inner"> <div class="container"> - <a class="brand" href="#">pfm 0.3-1</a> + <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> diff --git a/pkg/inst/web/index.html b/pkg/inst/web/index.html index 3eb1ad1..54f0f35 100644 --- a/pkg/inst/web/index.html +++ b/pkg/inst/web/index.html @@ -2,7 +2,7 @@ <html lang="en"> <head> <meta charset="utf-8"> -<title>Index. pfm 0.3-1</title> +<title>Index. pfm 0.3-7</title> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="author" content=""> @@ -32,7 +32,7 @@ <div class="navbar"> <div class="navbar-inner"> <div class="container"> - <a class="brand" href="#">pfm 0.3-1</a> + <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> @@ -161,7 +161,7 @@ fate modelling software packages. <h2>Dependencies</h2> <ul> <li><strong>Depends</strong>: R6, mkin</li> - <li><strong>Imports</strong>: graphics, chents</li> + <li><strong>Imports</strong>: graphics, chents, readr, methods</li> <li><strong>Suggests</strong>: testthat</li> </ul> diff --git a/pkg/inst/web/pfm_degradation.html b/pkg/inst/web/pfm_degradation.html index 68e8859..fad64be 100644 --- a/pkg/inst/web/pfm_degradation.html +++ b/pkg/inst/web/pfm_degradation.html @@ -2,7 +2,7 @@ <html lang="en"> <head> <meta charset="utf-8"> -<title>pfm_degradation. pfm 0.3-1</title> +<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 @@ -34,7 +34,7 @@ Johannes Ranke <div class="navbar"> <div class="navbar-inner"> <div class="container"> - <a class="brand" href="#">pfm 0.3-1</a> + <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> diff --git a/pkg/inst/web/plot.TOXSWA_cwa.html b/pkg/inst/web/plot.TOXSWA_cwa.html index 184c4f6..a6118df 100644 --- a/pkg/inst/web/plot.TOXSWA_cwa.html +++ b/pkg/inst/web/plot.TOXSWA_cwa.html @@ -2,7 +2,7 @@ <html lang="en"> <head> <meta charset="utf-8"> -<title>plot.TOXSWA_cwa. pfm 0.3-1</title> +<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 @@ -34,7 +34,7 @@ Johannes Ranke <div class="navbar"> <div class="navbar-inner"> <div class="container"> - <a class="brand" href="#">pfm 0.3-1</a> + <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> diff --git a/pkg/inst/web/read.TOXSWA_cwa.html b/pkg/inst/web/read.TOXSWA_cwa.html index 5542fca..3f2d997 100644 --- a/pkg/inst/web/read.TOXSWA_cwa.html +++ b/pkg/inst/web/read.TOXSWA_cwa.html @@ -2,7 +2,7 @@ <html lang="en"> <head> <meta charset="utf-8"> -<title>read.TOXSWA_cwa. pfm 0.3-1</title> +<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 @@ -34,7 +34,7 @@ Johannes Ranke <div class="navbar"> <div class="navbar-inner"> <div class="container"> - <a class="brand" href="#">pfm 0.3-1</a> + <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> @@ -54,12 +54,13 @@ Johannes Ranke <div class="row"> <div class="span8"> <h2>Usage</h2> - <pre><div>read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL, segment = "last", windows = NULL, thresholds = NULL)</div></pre> + <pre><div>read.TOXSWA_cwa(filename, basedir = ".", zipfile = NULL, segment = "last", substance = "parent", total = FALSE, windows = NULL, thresholds = NULL)</div></pre> <h2>Arguments</h2> <dl> <dt>filename</dt> - <dd>The filename of the cwa file.</dd> + <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> @@ -67,6 +68,14 @@ Johannes Ranke <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> @@ -90,7 +99,9 @@ An instance of an R6 object of class <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.</p> +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> diff --git a/pkg/inst/web/soil_scenario_data_EFSA_2015.html b/pkg/inst/web/soil_scenario_data_EFSA_2015.html index 1d4328f..0230afb 100644 --- a/pkg/inst/web/soil_scenario_data_EFSA_2015.html +++ b/pkg/inst/web/soil_scenario_data_EFSA_2015.html @@ -2,7 +2,7 @@ <html lang="en"> <head> <meta charset="utf-8"> -<title>soil_scenario_data_EFSA_2015. pfm 0.3-1</title> +<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=""> @@ -32,7 +32,7 @@ <div class="navbar"> <div class="navbar-inner"> <div class="container"> - <a class="brand" href="#">pfm 0.3-1</a> + <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> |