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-rw-r--r--docs/authors.html2
-rw-r--r--docs/index.html2
-rw-r--r--docs/pkgdown.yml2
-rw-r--r--docs/reference/FOCUS_GW_scenarios_2012.html2
-rw-r--r--docs/reference/FOCUS_Step_12_scenarios.html2
-rw-r--r--docs/reference/FOMC_actual_twa.html2
-rw-r--r--docs/reference/GUS.html2
-rw-r--r--docs/reference/PEC_FOMC_accu_rel.html2
-rw-r--r--docs/reference/PEC_soil.html2
-rw-r--r--docs/reference/PEC_soil_mets.html2
-rw-r--r--docs/reference/PEC_sw_drainage_UK.html2
-rw-r--r--docs/reference/PEC_sw_drift.html2
-rw-r--r--docs/reference/PEC_sw_exposit_drainage.html2
-rw-r--r--docs/reference/PEC_sw_exposit_runoff.html2
-rw-r--r--docs/reference/PEC_sw_focus.html2
-rw-r--r--docs/reference/PEC_sw_sed.html2
-rw-r--r--docs/reference/SFO_actual_twa.html2
-rw-r--r--docs/reference/SSLRC_mobility_classification.html2
-rw-r--r--docs/reference/TOXSWA_cwa.html2
-rw-r--r--docs/reference/chent_focus_sw.html2
-rw-r--r--docs/reference/drift_data_JKI.html2
-rw-r--r--docs/reference/endpoint.html2
-rw-r--r--docs/reference/geomean.html2
-rw-r--r--docs/reference/get_vertex.html2
-rw-r--r--docs/reference/index.html2
-rw-r--r--docs/reference/max_twa.html2
-rw-r--r--docs/reference/one_box-1.pngbin15900 -> 15801 bytes
-rw-r--r--docs/reference/one_box-2.pngbin15306 -> 15228 bytes
-rw-r--r--docs/reference/one_box-3.pngbin30090 -> 30063 bytes
-rw-r--r--docs/reference/one_box.html5
-rw-r--r--docs/reference/perc_runoff_exposit.html2
-rw-r--r--docs/reference/perc_runoff_reduction_exposit.html2
-rw-r--r--docs/reference/pfm_degradation.html2
-rw-r--r--docs/reference/plot.TOXSWA_cwa-1.pngbin21899 -> 21821 bytes
-rw-r--r--docs/reference/plot.TOXSWA_cwa-2.pngbin21097 -> 21005 bytes
-rw-r--r--docs/reference/plot.TOXSWA_cwa-3.pngbin22377 -> 22278 bytes
-rw-r--r--docs/reference/plot.TOXSWA_cwa-4.pngbin22788 -> 22682 bytes
-rw-r--r--docs/reference/plot.TOXSWA_cwa-5.pngbin16346 -> 16209 bytes
-rw-r--r--docs/reference/plot.TOXSWA_cwa.html2
-rw-r--r--docs/reference/plot.one_box-1.pngbin16217 -> 16135 bytes
-rw-r--r--docs/reference/plot.one_box-2.pngbin32580 -> 32593 bytes
-rw-r--r--docs/reference/plot.one_box-3.pngbin37322 -> 37285 bytes
-rw-r--r--docs/reference/plot.one_box.html5
-rw-r--r--docs/reference/read.TOXSWA_cwa.html2
-rw-r--r--docs/reference/sawtooth-1.pngbin16254 -> 16202 bytes
-rw-r--r--docs/reference/sawtooth-2.pngbin37322 -> 37285 bytes
-rw-r--r--docs/reference/sawtooth.html15
-rw-r--r--docs/reference/soil_scenario_data_EFSA_2015.html2
-rw-r--r--docs/reference/soil_scenario_data_EFSA_2017.html2
-rw-r--r--docs/reference/twa.html2
50 files changed, 47 insertions, 46 deletions
diff --git a/docs/authors.html b/docs/authors.html
index fbdd9e7..beacee0 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -117,7 +117,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/index.html b/docs/index.html
index ee8a376..8fb855a 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -131,7 +131,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 354fdca..1dc6ec1 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,5 +1,5 @@
pandoc: 2.2.1
-pkgdown: 1.3.0.9000
+pkgdown: 1.3.0
pkgdown_sha: ~
articles: []
diff --git a/docs/reference/FOCUS_GW_scenarios_2012.html b/docs/reference/FOCUS_GW_scenarios_2012.html
index 4fbb601..a70e56e 100644
--- a/docs/reference/FOCUS_GW_scenarios_2012.html
+++ b/docs/reference/FOCUS_GW_scenarios_2012.html
@@ -207,7 +207,7 @@ soil definitions are from page 46ff. from FOCUS (2012).</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/FOCUS_Step_12_scenarios.html b/docs/reference/FOCUS_Step_12_scenarios.html
index e9bc762..8f58610 100644
--- a/docs/reference/FOCUS_Step_12_scenarios.html
+++ b/docs/reference/FOCUS_Step_12_scenarios.html
@@ -310,7 +310,7 @@ The text file is not included in the package as its licence is not clear.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/FOMC_actual_twa.html b/docs/reference/FOMC_actual_twa.html
index d0e9df8..7dde9fb 100644
--- a/docs/reference/FOMC_actual_twa.html
+++ b/docs/reference/FOMC_actual_twa.html
@@ -172,7 +172,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/GUS.html b/docs/reference/GUS.html
index b2691ec..7f22c59 100644
--- a/docs/reference/GUS.html
+++ b/docs/reference/GUS.html
@@ -234,7 +234,7 @@ toxicology and chemistry</em> <b>8</b>(4) 339–57.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/PEC_FOMC_accu_rel.html b/docs/reference/PEC_FOMC_accu_rel.html
index cce464c..be189bd 100644
--- a/docs/reference/PEC_FOMC_accu_rel.html
+++ b/docs/reference/PEC_FOMC_accu_rel.html
@@ -152,7 +152,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/PEC_soil.html b/docs/reference/PEC_soil.html
index 13b2209..b1cc84c 100644
--- a/docs/reference/PEC_soil.html
+++ b/docs/reference/PEC_soil.html
@@ -358,7 +358,7 @@ from 2017 (p. 92).</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/PEC_soil_mets.html b/docs/reference/PEC_soil_mets.html
index b83bb31..fe59070 100644
--- a/docs/reference/PEC_soil_mets.html
+++ b/docs/reference/PEC_soil_mets.html
@@ -156,7 +156,7 @@ maximum occurrence in soil and their soil DT50</p></td>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/PEC_sw_drainage_UK.html b/docs/reference/PEC_sw_drainage_UK.html
index 813ac59..5e96f42 100644
--- a/docs/reference/PEC_sw_drainage_UK.html
+++ b/docs/reference/PEC_sw_drainage_UK.html
@@ -179,7 +179,7 @@ published on the CRC website</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/PEC_sw_drift.html b/docs/reference/PEC_sw_drift.html
index fd36cac..3ce87e4 100644
--- a/docs/reference/PEC_sw_drift.html
+++ b/docs/reference/PEC_sw_drift.html
@@ -191,7 +191,7 @@ with input via spray drift.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/PEC_sw_exposit_drainage.html b/docs/reference/PEC_sw_exposit_drainage.html
index 7e1ff1b..1187559 100644
--- a/docs/reference/PEC_sw_exposit_drainage.html
+++ b/docs/reference/PEC_sw_exposit_drainage.html
@@ -227,7 +227,7 @@ autumn/winter/early spring.</p></td>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/PEC_sw_exposit_runoff.html b/docs/reference/PEC_sw_exposit_runoff.html
index 28e2f89..f8b0d8d 100644
--- a/docs/reference/PEC_sw_exposit_runoff.html
+++ b/docs/reference/PEC_sw_exposit_runoff.html
@@ -245,7 +245,7 @@ and the bound fraction.</p></td>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/PEC_sw_focus.html b/docs/reference/PEC_sw_focus.html
index aba76e5..3e8223b 100644
--- a/docs/reference/PEC_sw_focus.html
+++ b/docs/reference/PEC_sw_focus.html
@@ -355,7 +355,7 @@ should be written</p></td>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/PEC_sw_sed.html b/docs/reference/PEC_sw_sed.html
index 5c03e8f..2d09a97 100644
--- a/docs/reference/PEC_sw_sed.html
+++ b/docs/reference/PEC_sw_sed.html
@@ -184,7 +184,7 @@ g/cm3)</p></td>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/SFO_actual_twa.html b/docs/reference/SFO_actual_twa.html
index 59e759b..c290ade 100644
--- a/docs/reference/SFO_actual_twa.html
+++ b/docs/reference/SFO_actual_twa.html
@@ -168,7 +168,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/SSLRC_mobility_classification.html b/docs/reference/SSLRC_mobility_classification.html
index a41b289..9cfa9c8 100644
--- a/docs/reference/SSLRC_mobility_classification.html
+++ b/docs/reference/SSLRC_mobility_classification.html
@@ -158,7 +158,7 @@ checked against the spreadsheet published on the CRC website</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/TOXSWA_cwa.html b/docs/reference/TOXSWA_cwa.html
index f430cba..d840e52 100644
--- a/docs/reference/TOXSWA_cwa.html
+++ b/docs/reference/TOXSWA_cwa.html
@@ -202,7 +202,7 @@ for the requested moving window sizes in days.</p></dd>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/chent_focus_sw.html b/docs/reference/chent_focus_sw.html
index 0ba53be..2579c47 100644
--- a/docs/reference/chent_focus_sw.html
+++ b/docs/reference/chent_focus_sw.html
@@ -184,7 +184,7 @@ systems</p></td>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/drift_data_JKI.html b/docs/reference/drift_data_JKI.html
index be24f42..9c14f54 100644
--- a/docs/reference/drift_data_JKI.html
+++ b/docs/reference/drift_data_JKI.html
@@ -411,7 +411,7 @@ included.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/endpoint.html b/docs/reference/endpoint.html
index d55daeb..f5520f6 100644
--- a/docs/reference/endpoint.html
+++ b/docs/reference/endpoint.html
@@ -223,7 +223,7 @@ exponent is often called 1/n.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/geomean.html b/docs/reference/geomean.html
index 1e106e0..c52e3e8 100644
--- a/docs/reference/geomean.html
+++ b/docs/reference/geomean.html
@@ -162,7 +162,7 @@ returns 0 if at least one element of the vector is 0.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/get_vertex.html b/docs/reference/get_vertex.html
index 10957ce..73c0b22 100644
--- a/docs/reference/get_vertex.html
+++ b/docs/reference/get_vertex.html
@@ -144,7 +144,7 @@ https://stackoverflow.com/a/717791</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 556cb67..c24f7cc 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -372,7 +372,7 @@ water concentrations</p></td>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/max_twa.html b/docs/reference/max_twa.html
index 07060af..fee0ceb 100644
--- a/docs/reference/max_twa.html
+++ b/docs/reference/max_twa.html
@@ -193,7 +193,7 @@ SFO, FOMC and DFOP models and to the parent compound</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/one_box-1.png b/docs/reference/one_box-1.png
index 5015348..10bc9f7 100644
--- a/docs/reference/one_box-1.png
+++ b/docs/reference/one_box-1.png
Binary files differ
diff --git a/docs/reference/one_box-2.png b/docs/reference/one_box-2.png
index eb60bd6..9cbb045 100644
--- a/docs/reference/one_box-2.png
+++ b/docs/reference/one_box-2.png
Binary files differ
diff --git a/docs/reference/one_box-3.png b/docs/reference/one_box-3.png
index fcb308b..ec1cc0c 100644
--- a/docs/reference/one_box-3.png
+++ b/docs/reference/one_box-3.png
Binary files differ
diff --git a/docs/reference/one_box.html b/docs/reference/one_box.html
index 8fd10ba..e7379e2 100644
--- a/docs/reference/one_box.html
+++ b/docs/reference/one_box.html
@@ -175,7 +175,8 @@ all observed variables.</p></td>
<span class='no'>pred_1</span> <span class='kw'>&lt;-</span> <span class='fu'>one_box</span>(<span class='no'>fit</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>pred_1</span>)</div><div class='img'><img src='one_box-2.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='co'># Use a model with more than one observed variable</span>
-<span class='no'>m_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/mkin/topics/mkinmod'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/mkin/topics/mkinsub'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/mkin/topics/mkinsub'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/mkin/topics/mkinfit'>mkinfit</a></span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='no'>pred_2</span> <span class='kw'>&lt;-</span> <span class='fu'>one_box</span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='st'>"model"</span>)
+<span class='no'>m_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/mkin/topics/mkinmod'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/mkin/topics/mkinsub'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/mkin/topics/mkinsub'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/mkin/topics/mkinfit'>mkinfit</a></span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='no'>pred_2</span> <span class='kw'>&lt;-</span> <span class='fu'>one_box</span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='st'>"model"</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>pred_2</span>)</div><div class='img'><img src='one_box-3.png' alt='' width='700' height='433' /></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
@@ -197,7 +198,7 @@ all observed variables.</p></td>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/perc_runoff_exposit.html b/docs/reference/perc_runoff_exposit.html
index 8bb9c42..4473907 100644
--- a/docs/reference/perc_runoff_exposit.html
+++ b/docs/reference/perc_runoff_exposit.html
@@ -163,7 +163,7 @@
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/perc_runoff_reduction_exposit.html b/docs/reference/perc_runoff_reduction_exposit.html
index a4f7857..ff71d24 100644
--- a/docs/reference/perc_runoff_reduction_exposit.html
+++ b/docs/reference/perc_runoff_reduction_exposit.html
@@ -178,7 +178,7 @@ from which the values were taken.</p><dl class='dl-horizontal'>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/pfm_degradation.html b/docs/reference/pfm_degradation.html
index 9d3a2ac..79fbfe1 100644
--- a/docs/reference/pfm_degradation.html
+++ b/docs/reference/pfm_degradation.html
@@ -174,7 +174,7 @@ is calculated (SFO model).</p></td>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/plot.TOXSWA_cwa-1.png b/docs/reference/plot.TOXSWA_cwa-1.png
index 79f5bfd..c6a278a 100644
--- a/docs/reference/plot.TOXSWA_cwa-1.png
+++ b/docs/reference/plot.TOXSWA_cwa-1.png
Binary files differ
diff --git a/docs/reference/plot.TOXSWA_cwa-2.png b/docs/reference/plot.TOXSWA_cwa-2.png
index d306e0f..869c43c 100644
--- a/docs/reference/plot.TOXSWA_cwa-2.png
+++ b/docs/reference/plot.TOXSWA_cwa-2.png
Binary files differ
diff --git a/docs/reference/plot.TOXSWA_cwa-3.png b/docs/reference/plot.TOXSWA_cwa-3.png
index e347b3f..315c741 100644
--- a/docs/reference/plot.TOXSWA_cwa-3.png
+++ b/docs/reference/plot.TOXSWA_cwa-3.png
Binary files differ
diff --git a/docs/reference/plot.TOXSWA_cwa-4.png b/docs/reference/plot.TOXSWA_cwa-4.png
index 0cb99f8..a0a88f9 100644
--- a/docs/reference/plot.TOXSWA_cwa-4.png
+++ b/docs/reference/plot.TOXSWA_cwa-4.png
Binary files differ
diff --git a/docs/reference/plot.TOXSWA_cwa-5.png b/docs/reference/plot.TOXSWA_cwa-5.png
index 44eb28f..3ac506d 100644
--- a/docs/reference/plot.TOXSWA_cwa-5.png
+++ b/docs/reference/plot.TOXSWA_cwa-5.png
Binary files differ
diff --git a/docs/reference/plot.TOXSWA_cwa.html b/docs/reference/plot.TOXSWA_cwa.html
index 896080e..78a29ae 100644
--- a/docs/reference/plot.TOXSWA_cwa.html
+++ b/docs/reference/plot.TOXSWA_cwa.html
@@ -194,7 +194,7 @@ to suspended matter?</p></td>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/plot.one_box-1.png b/docs/reference/plot.one_box-1.png
index 6179195..cf3f132 100644
--- a/docs/reference/plot.one_box-1.png
+++ b/docs/reference/plot.one_box-1.png
Binary files differ
diff --git a/docs/reference/plot.one_box-2.png b/docs/reference/plot.one_box-2.png
index 56f1454..0e152d6 100644
--- a/docs/reference/plot.one_box-2.png
+++ b/docs/reference/plot.one_box-2.png
Binary files differ
diff --git a/docs/reference/plot.one_box-3.png b/docs/reference/plot.one_box-3.png
index b2c339b..ad93165 100644
--- a/docs/reference/plot.one_box-3.png
+++ b/docs/reference/plot.one_box-3.png
Binary files differ
diff --git a/docs/reference/plot.one_box.html b/docs/reference/plot.one_box.html
index 6fcec65..6b8fdbb 100644
--- a/docs/reference/plot.one_box.html
+++ b/docs/reference/plot.one_box.html
@@ -163,7 +163,8 @@ be shown if max_twa is not NULL.</p></td>
<pre class="examples"><div class='input'><span class='no'>dfop_pred</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='st'>"DFOP"</span>, <span class='kw'>parms</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k1</span> <span class='kw'>=</span> <span class='fl'>0.2</span>, <span class='kw'>k2</span> <span class='kw'>=</span> <span class='fl'>0.02</span>, <span class='kw'>g</span> <span class='kw'>=</span> <span class='fl'>0.7</span>))
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>dfop_pred</span>)</div><div class='img'><img src='plot.one_box-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='no'>dfop_pred</span>, <span class='fl'>3</span>, <span class='fl'>7</span>), <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>)</div><div class='img'><img src='plot.one_box-2.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='co'># Use a fitted mkinfit model</span>
-<span class='no'>m_2</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='no'>pred_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>)
+<span class='no'>m_2</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='no'>pred_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>)
<span class='no'>pred_2_saw</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='sawtooth.html'>sawtooth</a></span>(<span class='no'>pred_2</span>, <span class='fl'>2</span>, <span class='fl'>7</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><div class='img'><img src='plot.one_box-3.png' alt='' width='700' height='433' /></div></pre>
</div>
@@ -186,7 +187,7 @@ be shown if max_twa is not NULL.</p></td>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/read.TOXSWA_cwa.html b/docs/reference/read.TOXSWA_cwa.html
index d7bb0be..f081162 100644
--- a/docs/reference/read.TOXSWA_cwa.html
+++ b/docs/reference/read.TOXSWA_cwa.html
@@ -202,7 +202,7 @@ generating event statistics.</p></td>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/sawtooth-1.png b/docs/reference/sawtooth-1.png
index 02a6b7c..2952433 100644
--- a/docs/reference/sawtooth-1.png
+++ b/docs/reference/sawtooth-1.png
Binary files differ
diff --git a/docs/reference/sawtooth-2.png b/docs/reference/sawtooth-2.png
index b2c339b..ad93165 100644
--- a/docs/reference/sawtooth-2.png
+++ b/docs/reference/sawtooth-2.png
Binary files differ
diff --git a/docs/reference/sawtooth.html b/docs/reference/sawtooth.html
index 93085e2..a94833c 100644
--- a/docs/reference/sawtooth.html
+++ b/docs/reference/sawtooth.html
@@ -32,9 +32,8 @@
<meta property="og:title" content="Create decline time series for multiple applications — sawtooth" />
-<meta property="og:description" content="If the number of application cycles n is greater than 1, the
-application pattern specified in applications is repeated n
-times, with an interval i." />
+<meta property="og:description" content="If the application pattern is specified in applications,
+n and i are disregarded." />
<meta name="twitter:card" content="summary" />
@@ -108,9 +107,8 @@ times, with an interval i." />
<div class="ref-description">
- <p>If the number of application cycles <code>n</code> is greater than 1, the
-application pattern specified in <code>applications</code> is repeated <code>n</code>
-times, with an interval <code>i</code>.</p>
+ <p>If the application pattern is specified in <code>applications</code>,
+<code>n</code> and <code>i</code> are disregarded.</p>
</div>
@@ -145,7 +143,8 @@ the corresponding amounts applied in the second column.</p></td>
<pre class="examples"><div class='input'><span class='no'>applications</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></span>(<span class='kw'>time</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>14</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>7</span>), <span class='kw'>amount</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>1</span>, <span class='fl'>2</span>, <span class='fl'>3</span>))
<span class='no'>pred</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='fl'>10</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='fu'>sawtooth</span>(<span class='no'>pred</span>, <span class='kw'>applications</span> <span class='kw'>=</span> <span class='no'>applications</span>))</div><div class='img'><img src='sawtooth-1.png' alt='' width='700' height='433' /></div><div class='input'>
-<span class='no'>m_2</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='no'>pred_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>)
+<span class='no'>m_2</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit_2</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>m_2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='no'>pred_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='one_box.html'>one_box</a></span>(<span class='no'>fit_2</span>, <span class='kw'>ini</span> <span class='kw'>=</span> <span class='fl'>1</span>)
<span class='no'>pred_2_saw</span> <span class='kw'>&lt;-</span> <span class='fu'>sawtooth</span>(<span class='no'>pred_2</span>, <span class='fl'>2</span>, <span class='fl'>7</span>)
<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>pred_2_saw</span>, <span class='kw'>max_twa</span> <span class='kw'>=</span> <span class='fl'>21</span>, <span class='kw'>max_twa_var</span> <span class='kw'>=</span> <span class='st'>"m1"</span>)</div><div class='img'><img src='sawtooth-2.png' alt='' width='700' height='433' /></div><div class='input'>
<span class='fu'><a href='max_twa.html'>max_twa</a></span>(<span class='no'>pred_2_saw</span>)</div><div class='output co'>#&gt; $max
@@ -178,7 +177,7 @@ the corresponding amounts applied in the second column.</p></td>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/soil_scenario_data_EFSA_2015.html b/docs/reference/soil_scenario_data_EFSA_2015.html
index 93d1a42..cb2e1fa 100644
--- a/docs/reference/soil_scenario_data_EFSA_2015.html
+++ b/docs/reference/soil_scenario_data_EFSA_2015.html
@@ -185,7 +185,7 @@ scenario and model adjustment factors from p. 15 and p. 17 are included.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/soil_scenario_data_EFSA_2017.html b/docs/reference/soil_scenario_data_EFSA_2017.html
index e87663b..21f69a2 100644
--- a/docs/reference/soil_scenario_data_EFSA_2017.html
+++ b/docs/reference/soil_scenario_data_EFSA_2017.html
@@ -166,7 +166,7 @@ scenario and model adjustment factors from p. 16 and p. 18 are included.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>
diff --git a/docs/reference/twa.html b/docs/reference/twa.html
index 1ca31c1..86c0f9b 100644
--- a/docs/reference/twa.html
+++ b/docs/reference/twa.html
@@ -172,7 +172,7 @@ is after one window has passed.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.</p>
</div>
</footer>
</div>

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