diff options
| -rw-r--r-- | ChangeLog | 13 | ||||
| -rw-r--r-- | DESCRIPTION | 2 | ||||
| -rw-r--r-- | R/PEC_sw_focus.R | 3 | ||||
| -rw-r--r-- | docs/reference/PEC_sw_focus.html | 67 | ||||
| -rw-r--r-- | docs/reference/PELMO_runs.html | 2 | ||||
| -rw-r--r-- | docs/reference/chent_focus_sw.html | 22 | ||||
| -rw-r--r-- | docs/reference/index.html | 2 | ||||
| -rw-r--r-- | docs/reference/pesticide.txt | 3 | ||||
| -rw-r--r-- | man/PEC_sw_focus.Rd | 11 |
9 files changed, 103 insertions, 22 deletions
@@ -1,8 +1,17 @@ -commit 7df0f45b785841e9e490a945a9f6091a68e6333c +commit dffa31a5ad5026d4d67327da622f45c00be40584 Author: Johannes Ranke <jranke@uni-bremen.de> Date: 2017-06-22 08:23:13 +0200 - Add region and season to run name + Add scenario, region and season to run name + +commit 0607a619d92d582ba40f9c0c3b32a1d0a8791655 +Author: Johannes Ranke <jranke@uni-bremen.de> +Date: 2017-06-20 16:40:21 +0200 + + Possibility to turn off formation in water + + This makes it possible to compare the Step 1 output with earlier + versions of the Steps 12 tool. commit 0d60c88ba7e0693a832056ea3db5cc0eaf3b0819 Author: Johannes Ranke <jranke@uni-bremen.de> diff --git a/DESCRIPTION b/DESCRIPTION index 379f8a8..714a2ac 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: pfm Type: Package Title: Utilities for Pesticide Fate Modelling Version: 0.4-3 -Date: 2017-06-22 +Date: 2017-07-21 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de", role = c("aut", "cre", "cph")) Description: Utilities for simple calculations of predicted environmental diff --git a/R/PEC_sw_focus.R b/R/PEC_sw_focus.R index 0536341..3f67be8 100644 --- a/R/PEC_sw_focus.R +++ b/R/PEC_sw_focus.R @@ -64,7 +64,8 @@ #' #' # Metabolite #' new_dummy <- chent_focus_sw("New Dummy", mw = 250, Koc = 100) -#' M1 <- chent_focus_sw(mw = 100, cwsat = 100, DT50_ws = 100, Koc = 50, max_ws = 0, max_soil = 0.5) +#' M1 <- chent_focus_sw("M1", mw = 100, cwsat = 100, DT50_ws = 100, Koc = 50, +#' max_ws = 0, max_soil = 0.5) #' PEC_sw_focus(new_dummy, 1000, scenario = "cereals, winter", met = M1) PEC_sw_focus <- function(parent, rate, n = 1, i = NA, comment = "", diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html index 7331d42..50651ae 100644 --- a/docs/reference/PEC_sw_focus.html +++ b/docs/reference/PEC_sw_focus.html @@ -6,7 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Calculate FOCUS Step 1 PEC surface water — PEC_sw_focus • pfm</title> +<title>Calculate PEC surface water at FOCUS Step 1 — PEC_sw_focus • pfm</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -68,19 +68,25 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Calculate FOCUS Step 1 PEC surface water</h1> + <h1>Calculate PEC surface water at FOCUS Step 1</h1> </div> - <p>This is reimplementation of Step 1 of the FOCUS Step 1 and 2 calculator -version 3.2, authored by Michael Klein. Note that results for multiple + <p>This is reimplementation of the FOCUS Step 1 and 2 calculator version 3.2, +authored by Michael Klein, in R. Note that results for multiple applications should be compared to the corresponding results for a single application. At current, this is not done automatically in -this implementation.</p> +this implementation. Only Step 1 PECs are calculated. However, +input files are generated that are suitable as input also for Step 2 +to be used with the FOCUS calculator.</p> - <pre class="usage"><span class='fu'>PEC_sw_focus</span>(<span class='no'>parent</span>, <span class='no'>rate</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>met</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>f_drift</span> <span class='kw'>=</span> <span class='fl'>NA</span>, - <span class='kw'>f_rd</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>scenario</span> <span class='kw'>=</span> <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>names</span>)</pre> + <pre class="usage"><span class='fu'>PEC_sw_focus</span>(<span class='no'>parent</span>, <span class='no'>rate</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>i</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>comment</span> <span class='kw'>=</span> <span class='st'>""</span>, <span class='kw'>met</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, + <span class='kw'>f_drift</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>f_rd</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>scenario</span> <span class='kw'>=</span> <span class='no'>FOCUS_Step_12_scenarios</span>$<span class='no'>names</span>, + <span class='kw'>region</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"n"</span>, <span class='st'>"s"</span>), <span class='kw'>season</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>NA</span>, <span class='st'>"of"</span>, <span class='st'>"mm"</span>, <span class='st'>"js"</span>), + <span class='kw'>interception</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"no interception"</span>, <span class='st'>"minimal crop cover"</span>, + <span class='st'>"average crop cover"</span>, <span class='st'>"full canopy"</span>), <span class='kw'>met_form_water</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>txt_file</span> <span class='kw'>=</span> <span class='st'>"pesticide.txt"</span>, <span class='kw'>overwrite</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>append</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <table class="ref-arguments"> @@ -104,6 +110,10 @@ applications are given explicitly</p></td> <td><p>The application interval</p></td> </tr> <tr> + <th>comment</th> + <td><p>A comment for the input file</p></td> + </tr> + <tr> <th>met</th> <td><p>A list containing metabolite specific parameters. e.g. conveniently generated by <code><a href='chent_focus_sw.html'>chent_focus_sw</a></code>. If not NULL, @@ -127,6 +137,42 @@ parent or a metabolite</p></td> <td><p>The name of the scenario. Must be one of the scenario names given in <code><a href='FOCUS_Step_12_scenarios.html'>FOCUS_Step_12_scenarios</a></code></p></td> </tr> + <tr> + <th>region</th> + <td><p>'n' for Northern Europe or 's' for Southern Europe. If NA, only +Step 1 PECsw are calculated</p></td> + </tr> + <tr> + <th>season</th> + <td><p>'of' for October to February, 'mm' for March to May, and 'js' +for June to September. If NA, only step 1 PECsw are calculated</p></td> + </tr> + <tr> + <th>interception</th> + <td><p>One of 'no interception' (default), 'minimal crop cover', +'average crop cover' or 'full canopy'</p></td> + </tr> + <tr> + <th>met_form_water</th> + <td><p>Should the metabolite formation in water be taken into +account? This can be switched off to check the influence and to compare +with previous versions of the Steps 12 calculator</p></td> + </tr> + <tr> + <th>txt_file</th> + <td><p>the name, and potentially the full path to the +Steps.12 input text file to which the specification of the run(s) +should be written</p></td> + </tr> + <tr> + <th>overwrite</th> + <td><p>Should an existing file a the location specified in +<code>txt_file</code> be overwritten?</p></td> + </tr> + <tr> + <th>append</th> + <td><p>Should the input text file be appended?</p></td> + </tr> </table> <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> @@ -151,7 +197,7 @@ names given in <code><a href='FOCUS_Step_12_scenarios.html'>FOCUS_Step_12_scenar <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># Parent only</span> -<span class='no'>dummy_1</span> <span class='kw'><-</span> <span class='fu'><a href='chent_focus_sw.html'>chent_focus_sw</a></span>(<span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>6000</span>, <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>6</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>344.8</span>) +<span class='no'>dummy_1</span> <span class='kw'><-</span> <span class='fu'><a href='chent_focus_sw.html'>chent_focus_sw</a></span>(<span class='st'>"Dummy 1"</span>, <span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>6000</span>, <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>6</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>344.8</span>) <span class='fu'>PEC_sw_focus</span>(<span class='no'>dummy_1</span>, <span class='fl'>3000</span>, <span class='kw'>f_drift</span> <span class='kw'>=</span> <span class='fl'>0</span>)</div><div class='output co'>#> $f_drift #> [1] 0 #> @@ -198,8 +244,9 @@ names given in <code><a href='FOCUS_Step_12_scenarios.html'>FOCUS_Step_12_scenar #> [1] 2362.075 #> </div><div class='input'> <span class='co'># Metabolite</span> -<span class='no'>new_dummy</span> <span class='kw'><-</span> <span class='fu'><a href='chent_focus_sw.html'>chent_focus_sw</a></span>(<span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>100</span>) -<span class='no'>M1</span> <span class='kw'><-</span> <span class='fu'><a href='chent_focus_sw.html'>chent_focus_sw</a></span>(<span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>50</span>, <span class='kw'>max_ws</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>max_soil</span> <span class='kw'>=</span> <span class='fl'>0.5</span>) +<span class='no'>new_dummy</span> <span class='kw'><-</span> <span class='fu'><a href='chent_focus_sw.html'>chent_focus_sw</a></span>(<span class='st'>"New Dummy"</span>, <span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>250</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>100</span>) +<span class='no'>M1</span> <span class='kw'><-</span> <span class='fu'><a href='chent_focus_sw.html'>chent_focus_sw</a></span>(<span class='st'>"M1"</span>, <span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>Koc</span> <span class='kw'>=</span> <span class='fl'>50</span>, + <span class='kw'>max_ws</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>max_soil</span> <span class='kw'>=</span> <span class='fl'>0.5</span>) <span class='fu'>PEC_sw_focus</span>(<span class='no'>new_dummy</span>, <span class='fl'>1000</span>, <span class='kw'>scenario</span> <span class='kw'>=</span> <span class='st'>"cereals, winter"</span>, <span class='kw'>met</span> <span class='kw'>=</span> <span class='no'>M1</span>)</div><div class='output co'>#> $f_drift #> [1] 0.02759 #> diff --git a/docs/reference/PELMO_runs.html b/docs/reference/PELMO_runs.html index 25afcf0..f2df73a 100644 --- a/docs/reference/PELMO_runs.html +++ b/docs/reference/PELMO_runs.html @@ -190,7 +190,7 @@ the period.plm file generated by the FOCUS PELMO GUI.</p> #> #> </div><div class='input'><span class='co'># We get exactly the same PECgw values (on Linux, calling PELMO using Wine).</span> <span class='fu'>print</span>(<span class='no'>time_1</span>)</div><div class='output co'>#> User System verstrichen -#> 218.736 0.940 54.948 </div><div class='input'> +#> 218.452 0.788 55.054 </div><div class='input'> <span class='co'># Demonstrate some results with metabolites.</span> <span class='no'>runs_2</span> <span class='kw'><-</span> <span class='fu'>list</span>(<span class='fu'>list</span>(<span class='kw'>psm</span> <span class='kw'>=</span> <span class='st'>'Pesticide_D_1_May_every_other_year_mets'</span>, <span class='kw'>win</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Cha"</span>, <span class='st'>"Ham"</span>, <span class='st'>"Kre"</span>))) diff --git a/docs/reference/chent_focus_sw.html b/docs/reference/chent_focus_sw.html index bd3d084..8e95618 100644 --- a/docs/reference/chent_focus_sw.html +++ b/docs/reference/chent_focus_sw.html @@ -75,13 +75,17 @@ <p>Create a chemical compound object for FOCUS Step 1 calculations</p> - <pre class="usage"><span class='fu'>chent_focus_sw</span>(<span class='no'>Koc</span>, <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>max_soil</span> <span class='kw'>=</span> <span class='fl'>1</span>, - <span class='kw'>max_ws</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre> + <pre class="usage"><span class='fu'>chent_focus_sw</span>(<span class='no'>name</span>, <span class='no'>Koc</span>, <span class='kw'>DT50_ws</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>DT50_soil</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>DT50_water</span> <span class='kw'>=</span> <span class='fl'>NA</span>, + <span class='kw'>DT50_sediment</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>cwsat</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>mw</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>max_soil</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>max_ws</span> <span class='kw'>=</span> <span class='fl'>1</span>)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> + <th>name</th> + <td><p>Length one character vector containing the name</p></td> + </tr> + <tr> <th>Koc</th> <td><p>Partition coefficient between organic carbon and water in L/kg.</p></td> @@ -91,12 +95,24 @@ in L/kg.</p></td> <td><p>Half-life in water/sediment systems in days</p></td> </tr> <tr> + <th>DT50_soil</th> + <td><p>Half-life in soil in days</p></td> + </tr> + <tr> + <th>DT50_water</th> + <td><p>Half-life in water in days (Step 2)</p></td> + </tr> + <tr> + <th>DT50_sediment</th> + <td><p>Half-life in sediment in days (Step 2)</p></td> + </tr> + <tr> <th>cwsat</th> <td><p>Water solubility in mg/L</p></td> </tr> <tr> <th>mw</th> - <td><p>Molar weight in g/mol</p></td> + <td><p>Molar weight in g/mol.</p></td> </tr> <tr> <th>max_soil</th> diff --git a/docs/reference/index.html b/docs/reference/index.html index a6ae657..9973635 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -191,7 +191,7 @@ published by the JKI</p></td> <td> <p><code><a href="PEC_sw_focus.html">PEC_sw_focus</a></code> </p> </td> - <td><p>Calculate FOCUS Step 1 PEC surface water</p></td> + <td><p>Calculate PEC surface water at FOCUS Step 1</p></td> </tr><tr> <!-- --> <td> diff --git a/docs/reference/pesticide.txt b/docs/reference/pesticide.txt new file mode 100644 index 0000000..e4c6dac --- /dev/null +++ b/docs/reference/pesticide.txt @@ -0,0 +1,3 @@ +Active Substance Compound Comment Mol mass a.i. Mol mass met. Water solubility KOC assessed compound KOC parent compound DT50 Max. in Water Max. in Soil asessed compound App. Rate Number of App. Time between app. App. Type DT50 soil parent compound DT50 soil DT50 water DT50 sediment Region / Season Interception class +Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA Dummy 1 cereals, spring n NA Dummy 1 cereals, winter s of Dummy 1 citrus n mm Dummy 1 cotton s js Dummy 1 field beans n NA Dummy 1 grass / alfalfa s of Dummy 1 hops n mm Dummy 1 legumes s js Dummy 1 maize n NA Dummy 1 oil seed rape, spring s of Dummy 1 oil seed rape, winter n mm Dummy 1 olives s js Dummy 1 pome / stone fruit, early applns n NA Dummy 1 pome / stone fruit, late applns s of Dummy 1 potatoes n mm Dummy 1 soybeans s js Dummy 1 sugar beets n NA Dummy 1 sunflowers s of Dummy 1 tobacco n mm Dummy 1 vegetables, bulb s js Dummy 1 vegetables, fruiting n NA Dummy 1 vegetables, leafy s of Dummy 1 vegetables, root n mm Dummy 1 vines, early applns s js Dummy 1 vines, late applns n NA Dummy 1 appln, aerial s of Dummy 1 appln, hand (crop < 50 cm) n mm Dummy 1 appln, hand (crop > 50 cm) s js Dummy 1 no drift (incorp or seed trtmt) n NA -99.00 -99.00 6000.00 344.80 0.00E+00 6.00 0.00E+00 0.00E+00 3000.00 1.00 0.00E+00 0.00E+00 1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00 13.00 14.00 15.00 16.00 17.00 18.00 19.00 20.00 21.00 22.00 23.00 24.00 25.00 26.00 27.00 28.00 0.00E+00 -99.00 -99.00 -99.00 0.00E+00 1.00 +M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js M1 cereals, winter n NA M1 cereals, winter s of M1 cereals, winter n mm M1 cereals, winter s js 250.00 100.00 100.00 50.00 100.00 100.00 0.00E+00 50.00 1000.00 1.00 0.00E+00 1.00 -99.00 -99.00 -99.00 -99.00 0.00E+00 1.00 diff --git a/man/PEC_sw_focus.Rd b/man/PEC_sw_focus.Rd index f55fccc..00975a2 100644 --- a/man/PEC_sw_focus.Rd +++ b/man/PEC_sw_focus.Rd @@ -8,8 +8,8 @@ PEC_sw_focus(parent, rate, n = 1, i = NA, comment = "", met = NULL, f_drift = NA, f_rd = 0.1, scenario = FOCUS_Step_12_scenarios$names, region = c("n", "s"), season = c(NA, "of", "mm", "js"), interception = c("no interception", "minimal crop cover", - "average crop cover", "full canopy"), txt_file = "pesticide.txt", - overwrite = FALSE, append = TRUE) + "average crop cover", "full canopy"), met_form_water = TRUE, + txt_file = "pesticide.txt", overwrite = FALSE, append = TRUE) } \arguments{ \item{parent}{A list containing substance specific parameters, e.g. @@ -49,6 +49,10 @@ for June to September. If NA, only step 1 PECsw are calculated} \item{interception}{One of 'no interception' (default), 'minimal crop cover', 'average crop cover' or 'full canopy'} +\item{met_form_water}{Should the metabolite formation in water be taken into +account? This can be switched off to check the influence and to compare +with previous versions of the Steps 12 calculator} + \item{txt_file}{the name, and potentially the full path to the Steps.12 input text file to which the specification of the run(s) should be written} @@ -84,7 +88,8 @@ PEC_sw_focus(dummy_1, 3000, f_drift = 0) # Metabolite new_dummy <- chent_focus_sw("New Dummy", mw = 250, Koc = 100) -M1 <- chent_focus_sw(mw = 100, cwsat = 100, DT50_ws = 100, Koc = 50, max_ws = 0, max_soil = 0.5) +M1 <- chent_focus_sw("M1", mw = 100, cwsat = 100, DT50_ws = 100, Koc = 50, + max_ws = 0, max_soil = 0.5) PEC_sw_focus(new_dummy, 1000, scenario = "cereals, winter", met = M1) } \references{ |