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authorJohannes Ranke <jranke@uni-bremen.de>2018-09-18 10:14:40 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2018-09-18 10:14:40 +0200
commit39b6d8b8569801c2957b22d0973b5ad0c9405e7d (patch)
tree97d0580eec85d9ab4196338ec742ba407ccfa7f8
parent9a793d0d39c8239ebcc76390f227596cef9b9be1 (diff)
Support maximum twa for HS, test, docs
-rw-r--r--DESCRIPTION2
-rw-r--r--NEWS.md4
-rw-r--r--R/max_twa_parent.R18
-rw-r--r--build.log2
-rw-r--r--docs/articles/FOCUS_D.html4
-rw-r--r--docs/articles/FOCUS_L.html46
-rw-r--r--docs/articles/index.html2
-rw-r--r--docs/articles/mkin.html4
-rw-r--r--docs/articles/twa.html4
-rw-r--r--docs/articles/web_only/FOCUS_Z.html4
-rw-r--r--docs/articles/web_only/compiled_models.html14
-rw-r--r--docs/authors.html2
-rw-r--r--docs/index.html3
-rw-r--r--docs/news/index.html14
-rw-r--r--docs/reference/DFOP.solution.html2
-rw-r--r--docs/reference/Extract.mmkin.html16
-rw-r--r--docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html2
-rw-r--r--docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html2
-rw-r--r--docs/reference/FOCUS_2006_HS_ref_A_to_F.html2
-rw-r--r--docs/reference/FOCUS_2006_SFO_ref_A_to_F.html2
-rw-r--r--docs/reference/FOCUS_2006_datasets.html2
-rw-r--r--docs/reference/FOMC.solution.html2
-rw-r--r--docs/reference/HS.solution.html2
-rw-r--r--docs/reference/IORE.solution.html2
-rw-r--r--docs/reference/SFO.solution.html2
-rw-r--r--docs/reference/SFORB.solution.html2
-rw-r--r--docs/reference/add_err.html2
-rw-r--r--docs/reference/endpoints.html2
-rw-r--r--docs/reference/geometric_mean.html2
-rw-r--r--docs/reference/ilr.html2
-rw-r--r--docs/reference/index.html2
-rw-r--r--docs/reference/max_twa_parent.html6
-rw-r--r--docs/reference/mccall81_245T.html18
-rw-r--r--docs/reference/mkin_long_to_wide.html2
-rw-r--r--docs/reference/mkin_wide_to_long.html2
-rw-r--r--docs/reference/mkinds.html2
-rw-r--r--docs/reference/mkinerrmin.html2
-rw-r--r--docs/reference/mkinfit.html62
-rw-r--r--docs/reference/mkinmod.html4
-rw-r--r--docs/reference/mkinparplot.html2
-rw-r--r--docs/reference/mkinplot.html2
-rw-r--r--docs/reference/mkinpredict.html8
-rw-r--r--docs/reference/mkinresplot.html2
-rw-r--r--docs/reference/mkinsub.html2
-rw-r--r--docs/reference/mmkin.html6
-rw-r--r--docs/reference/plot.mkinfit.html2
-rw-r--r--docs/reference/plot.mmkin.html2
-rw-r--r--docs/reference/print.mkinds.html2
-rw-r--r--docs/reference/print.mkinmod.html2
-rw-r--r--docs/reference/schaefer07_complex_case.html2
-rw-r--r--docs/reference/sigma_twocomp.html2
-rw-r--r--docs/reference/summary.mkinfit.html10
-rw-r--r--docs/reference/synthetic_data_for_UBA.html2
-rw-r--r--docs/reference/test_data_from_UBA_2014.html2
-rw-r--r--docs/reference/transform_odeparms.html34
-rw-r--r--man/max_twa_parent.Rd2
-rw-r--r--test.log20
-rw-r--r--tests/testthat/test_twa.R42
58 files changed, 225 insertions, 190 deletions
diff --git a/DESCRIPTION b/DESCRIPTION
index 1b5b399d..53285036 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: mkin
Type: Package
Title: Kinetic Evaluation of Chemical Degradation Data
Version: 0.9.47.6
-Date: 2018-09-14
+Date: 2018-09-18
Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"),
email = "jranke@uni-bremen.de",
comment = c(ORCID = "0000-0003-4371-6538")),
diff --git a/NEWS.md b/NEWS.md
index 43146df9..780ee5ac 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,7 +1,9 @@
-# mkin 0.9.47.6 (2018-09-15)
+# mkin 0.9.47.6 (2018-09-18)
- 'add_err': Respect the argument giving the number of replicates in the synthetic dataset
+- 'max_twa_parent': Support maximum time weighted average concentration calculations for the hockey stick (HS) model
+
# mkin 0.9.47.5 (2018-09-14)
- Make the two-component error model stop in cases where it is inadequate to avoid nls crashes on windows
diff --git a/R/max_twa_parent.R b/R/max_twa_parent.R
index 8d8b77f8..946a9b3d 100644
--- a/R/max_twa_parent.R
+++ b/R/max_twa_parent.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2016,2017 Johannes Ranke
+# Copyright (C) 2016,2017,2018 Johannes Ranke
# Contact: jranke@uni-bremen.de
# This file is part of the R package mkin
@@ -55,7 +55,21 @@ max_twa_parent <- function(fit, windows) {
M0/t * ((g/k1) * (1 - exp(- k1 * t)) + ((1 - g)/k2) * (1 - exp(- k2 * t)))
}
}
- if (type %in% c("HS", "IORE", "SFORB")) {
+ if (type == "HS") {
+ k1 <- parms.all["k1"]
+ k2 <- parms.all["k2"]
+ tb <- parms.all["tb"]
+ twafunc <- function(t) {
+ ifelse(t <= tb,
+ M0 * (1 - exp(- k1 * t)) / (k1 * t),
+ (M0 / t) * (
+ (1/k1) * (1 - exp(- k1 * tb)) +
+ (exp(- k1 * tb) / k2) * (1 - exp(- k2 * (t - tb)))
+ )
+ )
+ }
+ }
+ if (type %in% c("IORE", "SFORB")) {
stop("Calculation of maximum time weighted average concentrations is currently ",
"not implemented for the ", type, " model.")
}
diff --git a/build.log b/build.log
index ca1c6f50..79c00855 100644
--- a/build.log
+++ b/build.log
@@ -6,5 +6,5 @@
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
-* building ‘mkin_0.9.47.5.tar.gz’
+* building ‘mkin_0.9.47.6.tar.gz’
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index a90cb7fb..b44462aa 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -29,7 +29,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
@@ -84,7 +84,7 @@
<h1>Example evaluation of FOCUS Example Dataset D</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-09-14</h4>
+ <h4 class="date">2018-09-18</h4>
<div class="hidden name"><code>FOCUS_D.Rmd</code></div>
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 2a99a609..8ef55b81 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -29,7 +29,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
@@ -84,7 +84,7 @@
<h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-09-14</h4>
+ <h4 class="date">2018-09-18</h4>
<div class="hidden name"><code>FOCUS_L.Rmd</code></div>
@@ -110,15 +110,15 @@
<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw">summary</span>(m.L1.SFO)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.5
## R version used for fitting: 3.5.1
-## Date of fit: Fri Sep 14 21:00:22 2018
-## Date of summary: Fri Sep 14 21:00:22 2018
+## Date of fit: Tue Sep 18 09:50:45 2018
+## Date of summary: Tue Sep 18 09:50:45 2018
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 37 model solutions performed in 0.087 s
+## Fitted with method Port using 37 model solutions performed in 0.081 s
##
## Weighting: none
##
@@ -201,15 +201,15 @@
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="kw">summary</span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.5
## R version used for fitting: 3.5.1
-## Date of fit: Fri Sep 14 21:00:23 2018
-## Date of summary: Fri Sep 14 21:00:23 2018
+## Date of fit: Tue Sep 18 09:50:47 2018
+## Date of summary: Tue Sep 18 09:50:47 2018
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 611 model solutions performed in 1.352 s
+## Fitted with method Port using 611 model solutions performed in 1.294 s
##
## Weighting: none
##
@@ -296,15 +296,15 @@
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1"><span class="kw">summary</span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.5
## R version used for fitting: 3.5.1
-## Date of fit: Fri Sep 14 21:00:24 2018
-## Date of summary: Fri Sep 14 21:00:24 2018
+## Date of fit: Tue Sep 18 09:50:47 2018
+## Date of summary: Tue Sep 18 09:50:47 2018
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 81 model solutions performed in 0.175 s
+## Fitted with method Port using 81 model solutions performed in 0.166 s
##
## Weighting: none
##
@@ -367,8 +367,8 @@
<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="kw">summary</span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.5
## R version used for fitting: 3.5.1
-## Date of fit: Fri Sep 14 21:00:25 2018
-## Date of summary: Fri Sep 14 21:00:25 2018
+## Date of fit: Tue Sep 18 09:50:48 2018
+## Date of summary: Tue Sep 18 09:50:48 2018
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -377,7 +377,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 336 model solutions performed in 0.758 s
+## Fitted with method Port using 336 model solutions performed in 0.714 s
##
## Weighting: none
##
@@ -459,8 +459,8 @@
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1"><span class="kw">summary</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.5
## R version used for fitting: 3.5.1
-## Date of fit: Fri Sep 14 21:00:26 2018
-## Date of summary: Fri Sep 14 21:00:26 2018
+## Date of fit: Tue Sep 18 09:50:49 2018
+## Date of summary: Tue Sep 18 09:50:49 2018
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -469,7 +469,7 @@
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 137 model solutions performed in 0.31 s
+## Fitted with method Port using 137 model solutions performed in 0.299 s
##
## Weighting: none
##
@@ -560,15 +560,15 @@
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1"><span class="kw">summary</span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.5
## R version used for fitting: 3.5.1
-## Date of fit: Fri Sep 14 21:00:26 2018
-## Date of summary: Fri Sep 14 21:00:27 2018
+## Date of fit: Tue Sep 18 09:50:50 2018
+## Date of summary: Tue Sep 18 09:50:50 2018
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 46 model solutions performed in 0.102 s
+## Fitted with method Port using 46 model solutions performed in 0.093 s
##
## Weighting: none
##
@@ -620,15 +620,15 @@
<div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" data-line-number="1"><span class="kw">summary</span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.47.5
## R version used for fitting: 3.5.1
-## Date of fit: Fri Sep 14 21:00:26 2018
-## Date of summary: Fri Sep 14 21:00:27 2018
+## Date of fit: Tue Sep 18 09:50:50 2018
+## Date of summary: Tue Sep 18 09:50:50 2018
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 66 model solutions performed in 0.151 s
+## Fitted with method Port using 66 model solutions performed in 0.138 s
##
## Weighting: none
##
diff --git a/docs/articles/index.html b/docs/articles/index.html
index ad0ab46e..c48dfec7 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -58,7 +58,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 3ae09165..e483043b 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -29,7 +29,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
@@ -84,7 +84,7 @@
<h1>Introduction to mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-09-14</h4>
+ <h4 class="date">2018-09-18</h4>
<div class="hidden name"><code>mkin.Rmd</code></div>
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 4d516ff1..d9249f9d 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -29,7 +29,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
@@ -84,7 +84,7 @@
<h1>Calculation of time weighted average concentrations with mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-09-14</h4>
+ <h4 class="date">2018-09-18</h4>
<div class="hidden name"><code>twa.Rmd</code></div>
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index 381c9e4f..a3e743d1 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -29,7 +29,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
@@ -84,7 +84,7 @@
<h1>Example evaluation of FOCUS dataset Z</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-09-14</h4>
+ <h4 class="date">2018-09-18</h4>
<div class="hidden name"><code>FOCUS_Z.Rmd</code></div>
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 9aac1ab2..3b3e9150 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -29,7 +29,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
@@ -84,7 +84,7 @@
<h1>Performance benefit by using compiled model definitions in mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2018-09-14</h4>
+ <h4 class="date">2018-09-18</h4>
<div class="hidden name"><code>compiled_models.Rmd</code></div>
@@ -125,9 +125,9 @@
<a class="sourceLine" id="cb5-16" data-line-number="16">}</a></code></pre></div>
<pre><code>## Lade nötiges Paket: rbenchmark</code></pre>
<pre><code>## test replications elapsed relative user.self sys.self
-## 3 deSolve, compiled 3 2.134 1.000 2.132 0
-## 1 deSolve, not compiled 3 16.165 7.575 16.157 0
-## 2 Eigenvalue based 3 2.597 1.217 2.595 0
+## 3 deSolve, compiled 3 2.001 1.000 1.999 0
+## 1 deSolve, not compiled 3 15.374 7.683 15.368 0
+## 2 Eigenvalue based 3 2.439 1.219 2.438 0
## user.child sys.child
## 3 0 0
## 1 0 0
@@ -156,8 +156,8 @@
<a class="sourceLine" id="cb8-16" data-line-number="16">}</a></code></pre></div>
<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
<pre><code>## test replications elapsed relative user.self sys.self
-## 2 deSolve, compiled 3 3.717 1.000 3.715 0
-## 1 deSolve, not compiled 3 34.646 9.321 34.630 0
+## 2 deSolve, compiled 3 3.608 1.000 3.607 0
+## 1 deSolve, not compiled 3 33.150 9.188 33.135 0
## user.child sys.child
## 2 0 0
## 1 0 0</code></pre>
diff --git a/docs/authors.html b/docs/authors.html
index fddc66c9..d80afb2e 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -58,7 +58,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/index.html b/docs/index.html
index 60787c81..10b75279 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -36,7 +36,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
@@ -189,6 +189,7 @@
<h2>Dev status</h2>
<ul class="list-unstyled">
<li><a href="https://cran.r-project.org/package=mkin"><img src="https://www.r-pkg.org/badges/version/mkin"></a></li>
+<li><a href="https://travis-ci.com/jranke/mkin"><img src="https://travis-ci.com/jranke/mkin.svg?branch=master" alt="Build Status"></a></li>
</ul>
</div>
</div>
diff --git a/docs/news/index.html b/docs/news/index.html
index 73eb7aa2..2636b8b0 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -58,7 +58,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
@@ -117,9 +117,18 @@
</div>
+ <div id="mkin-0-9-47-6-2018-09-18" class="section level1">
+<h1 class="page-header">
+<a href="#mkin-0-9-47-6-2018-09-18" class="anchor"></a>mkin 0.9.47.6 (2018-09-18)<small> Unreleased </small>
+</h1>
+<ul>
+<li><p>‘add_err’: Respect the argument giving the number of replicates in the synthetic dataset</p></li>
+<li><p>‘max_twa_parent’: Support maximum time weighted average concentration calculations for the hockey stick (HS) model</p></li>
+</ul>
+</div>
<div id="mkin-0-9-47-5-2018-09-14" class="section level1">
<h1 class="page-header">
-<a href="#mkin-0-9-47-5-2018-09-14" class="anchor"></a>mkin 0.9.47.5 (2018-09-14)<small> Unreleased </small>
+<a href="#mkin-0-9-47-5-2018-09-14" class="anchor"></a>mkin 0.9.47.5 (2018-09-14)<small> 2018-09-14 </small>
</h1>
<ul>
<li><p>Make the two-component error model stop in cases where it is inadequate to avoid nls crashes on windows</p></li>
@@ -658,6 +667,7 @@
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
+ <li><a href="#mkin-0-9-47-6-2018-09-18">0.9.47.6</a></li>
<li><a href="#mkin-0-9-47-5-2018-09-14">0.9.47.5</a></li>
<li><a href="#mkin-0-9-47-3">0.9.47.3</a></li>
<li><a href="#mkin-0-9-47-2-2018-07-19">0.9.47.2</a></li>
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index f3ee0099..ad0ff22a 100644
--- a/docs/reference/DFOP.solution.html
+++ b/docs/reference/DFOP.solution.html
@@ -62,7 +62,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 97562d44..39a8bb84 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -61,7 +61,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
@@ -278,7 +278,7 @@
#&gt;
#&gt; $time
#&gt; User System verstrichen
-#&gt; 0.177 0.000 0.176
+#&gt; 0.161 0.000 0.162
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -467,8 +467,8 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555bd7f230&gt;
-#&gt; &lt;environment: 0x55555bc85178&gt;
+#&gt; &lt;bytecode: 0x55555bd56848&gt;
+#&gt; &lt;environment: 0x55555bd53cb0&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -490,8 +490,8 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;bytecode: 0x55555ca9fca8&gt;
-#&gt; &lt;environment: 0x55555bc85178&gt;
+#&gt; &lt;bytecode: 0x55555c9bc2c0&gt;
+#&gt; &lt;environment: 0x55555bd53cb0&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -558,10 +558,10 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] "Fri Sep 14 20:58:46 2018"
+#&gt; [1] "Tue Sep 18 09:49:15 2018"
#&gt;
#&gt; $version
-#&gt; [1] "0.9.47.5"
+#&gt; [1] "0.9.47.6"
#&gt;
#&gt; $Rversion
#&gt; [1] "3.5.1"
diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
index d5354c28..6923f19a 100644
--- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
+++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
@@ -65,7 +65,7 @@ in this fit." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
index f5c36792..90f6eb49 100644
--- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
@@ -65,7 +65,7 @@ in this fit." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
index fb2cd7de..85a72047 100644
--- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
@@ -65,7 +65,7 @@ in this fit." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
index dfccea5c..f2fb835b 100644
--- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
@@ -65,7 +65,7 @@ in this fit." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html
index 7f89e33e..9023aee0 100644
--- a/docs/reference/FOCUS_2006_datasets.html
+++ b/docs/reference/FOCUS_2006_datasets.html
@@ -61,7 +61,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html
index abda4d81..1d3e4dd3 100644
--- a/docs/reference/FOMC.solution.html
+++ b/docs/reference/FOMC.solution.html
@@ -65,7 +65,7 @@ The form given here differs slightly from the original reference by Gustafson
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html
index bb3768ba..99f537cf 100644
--- a/docs/reference/HS.solution.html
+++ b/docs/reference/HS.solution.html
@@ -62,7 +62,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html
index d86ee0c3..8394cd52 100644
--- a/docs/reference/IORE.solution.html
+++ b/docs/reference/IORE.solution.html
@@ -62,7 +62,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index 17f1920c..e123d358 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.html
@@ -61,7 +61,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
index 050d19cf..75449616 100644
--- a/docs/reference/SFORB.solution.html
+++ b/docs/reference/SFORB.solution.html
@@ -65,7 +65,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html
index cea1e03c..db910f82 100644
--- a/docs/reference/add_err.html
+++ b/docs/reference/add_err.html
@@ -63,7 +63,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
index a54fb71e..6a505e9f 100644
--- a/docs/reference/endpoints.html
+++ b/docs/reference/endpoints.html
@@ -64,7 +64,7 @@ with the advantage that the SFORB model can also be used for metabolites." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html
index 41ccbbfd..6e154149 100644
--- a/docs/reference/geometric_mean.html
+++ b/docs/reference/geometric_mean.html
@@ -61,7 +61,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html
index 601ab1a2..722bb0e9 100644
--- a/docs/reference/ilr.html
+++ b/docs/reference/ilr.html
@@ -61,7 +61,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 615f6777..a7806970 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -58,7 +58,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html
index 3a19c754..c760960f 100644
--- a/docs/reference/max_twa_parent.html
+++ b/docs/reference/max_twa_parent.html
@@ -34,7 +34,7 @@
<meta property="og:description" content="This function calculates maximum moving window time weighted average concentrations
(TWAs) for kinetic models fitted with mkinfit. Currently, only
-calculations for the parent are implemented for the SFO, FOMC and DFOP models,
+calculations for the parent are implemented for the SFO, FOMC, DFOP and HS models,
using the analytical formulas given in the PEC soil section of the FOCUS
guidance." />
<meta name="twitter:card" content="summary" />
@@ -65,7 +65,7 @@ guidance." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
@@ -129,7 +129,7 @@ guidance." />
<p>This function calculates maximum moving window time weighted average concentrations
(TWAs) for kinetic models fitted with <code><a href='mkinfit.html'>mkinfit</a></code>. Currently, only
-calculations for the parent are implemented for the SFO, FOMC and DFOP models,
+calculations for the parent are implemented for the SFO, FOMC, DFOP and HS models,
using the analytical formulas given in the PEC soil section of the FOCUS
guidance.</p>
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 52c09969..042073f2 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -63,7 +63,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
@@ -156,10 +156,10 @@
<pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"phenol"</span>),
<span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"anisole"</span>),
<span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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'> </div><div class='input'> <span class='no'>fit.1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
- <span class='fu'>summary</span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.5
+ <span class='fu'>summary</span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 20:58:58 2018
-#&gt; Date of summary: Fri Sep 14 20:58:58 2018
+#&gt; Date of fit: Tue Sep 18 09:49:26 2018
+#&gt; Date of summary: Tue Sep 18 09:49:26 2018
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -169,7 +169,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 574 model solutions performed in 3.393 s
+#&gt; Fitted with method Port using 574 model solutions performed in 3.213 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -245,10 +245,10 @@
<span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>),
<span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>),
<span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
- <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.5
+ <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 20:58:59 2018
-#&gt; Date of summary: Fri Sep 14 20:59:00 2018
+#&gt; Date of fit: Tue Sep 18 09:49:27 2018
+#&gt; Date of summary: Tue Sep 18 09:49:27 2018
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -258,7 +258,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.451 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.363 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html
index ea74ff47..36a7e0ae 100644
--- a/docs/reference/mkin_long_to_wide.html
+++ b/docs/reference/mkin_long_to_wide.html
@@ -63,7 +63,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html
index 369649e3..f09f5102 100644
--- a/docs/reference/mkin_wide_to_long.html
+++ b/docs/reference/mkin_wide_to_long.html
@@ -62,7 +62,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
index d356fdab..357370ad 100644
--- a/docs/reference/mkinds.html
+++ b/docs/reference/mkinds.html
@@ -61,7 +61,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html
index 4f70a274..dd947e65 100644
--- a/docs/reference/mkinerrmin.html
+++ b/docs/reference/mkinerrmin.html
@@ -62,7 +62,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index f3c6d595..1ae53f8a 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -71,7 +71,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
@@ -432,17 +432,17 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='co'># Use shorthand notation for parent only degradation</span>
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.5
+<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 20:59:02 2018
-#&gt; Date of summary: Fri Sep 14 20:59:02 2018
+#&gt; Date of fit: Tue Sep 18 09:49:30 2018
+#&gt; Date of summary: Tue Sep 18 09:49:30 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted with method Port using 64 model solutions performed in 0.141 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.14 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -511,7 +511,7 @@
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>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='co'># Fit the model to the FOCUS example dataset D using defaults</span>
<span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.895 0.000 0.897 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 0.872 0.001 0.874 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
@@ -586,7 +586,7 @@
#&gt; Model cost at call 146 : 371.2134
#&gt; Optimisation by method Port successfully terminated.
#&gt; User System verstrichen
-#&gt; 0.726 0.000 0.726 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 0.690 0.000 0.689 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
@@ -622,10 +622,10 @@
</div><div class='input'><span class='co'># Weighted fits, including IRLS</span>
<span class='no'>SFO_SFO.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>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='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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'>f.noweight</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.5
+<span class='fu'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 20:59:13 2018
-#&gt; Date of summary: Fri Sep 14 20:59:13 2018
+#&gt; Date of fit: Tue Sep 18 09:49:40 2018
+#&gt; Date of summary: Tue Sep 18 09:49:40 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -633,7 +633,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 186 model solutions performed in 0.757 s
+#&gt; Fitted with method Port using 186 model solutions performed in 0.725 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -739,10 +739,10 @@
#&gt; 100 m1 33.13 31.98163 1.148e+00
#&gt; 120 m1 25.15 28.78984 -3.640e+00
#&gt; 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.irls</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.5
+<span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 20:59:15 2018
-#&gt; Date of summary: Fri Sep 14 20:59:16 2018
+#&gt; Date of fit: Tue Sep 18 09:49:42 2018
+#&gt; Date of summary: Tue Sep 18 09:49:42 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -750,7 +750,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 551 model solutions performed in 2.329 s
+#&gt; Fitted with method Port using 551 model solutions performed in 2.147 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -861,10 +861,10 @@
#&gt; 100 m1 33.13 31.98971 1.140e+00 2.722
#&gt; 120 m1 25.15 28.80898 -3.659e+00 2.722
#&gt; 120 m1 33.31 28.80898 4.501e+00 2.722</div><div class='input'><span class='no'>f.w.mean</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.5
+<span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 20:59:16 2018
-#&gt; Date of summary: Fri Sep 14 20:59:16 2018
+#&gt; Date of fit: Tue Sep 18 09:49:43 2018
+#&gt; Date of summary: Tue Sep 18 09:49:43 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -872,7 +872,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 155 model solutions performed in 0.628 s
+#&gt; Fitted with method Port using 155 model solutions performed in 0.603 s
#&gt;
#&gt; Weighting: mean
#&gt;
@@ -979,10 +979,10 @@
#&gt; 120 m1 25.15 28.82413 -3.674128
#&gt; 120 m1 33.31 28.82413 4.485872</div><div class='input'><span class='no'>f.w.value</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='fu'>subset</span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"value"</span>,
<span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.5
+<span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 20:59:17 2018
-#&gt; Date of summary: Fri Sep 14 20:59:17 2018
+#&gt; Date of fit: Tue Sep 18 09:49:44 2018
+#&gt; Date of summary: Tue Sep 18 09:49:44 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -990,7 +990,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 174 model solutions performed in 0.713 s
+#&gt; Fitted with method Port using 174 model solutions performed in 0.69 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1099,10 +1099,10 @@
<span class='no'>errors</span> <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>1</span>)
<span class='no'>dw</span>$<span class='no'>err.man</span> <span class='kw'>&lt;-</span> <span class='no'>errors</span>[<span class='no'>FOCUS_2006_D</span>$<span class='no'>name</span>]
<span class='no'>f.w.man</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.5
+<span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 20:59:18 2018
-#&gt; Date of summary: Fri Sep 14 20:59:18 2018
+#&gt; Date of fit: Tue Sep 18 09:49:45 2018
+#&gt; Date of summary: Tue Sep 18 09:49:45 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1110,7 +1110,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 270 model solutions performed in 1.119 s
+#&gt; Fitted with method Port using 270 model solutions performed in 1.133 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1217,10 +1217,10 @@
#&gt; 120 m1 25.15 28.76062 -3.610621 2
#&gt; 120 m1 33.31 28.76062 4.549379 2</div><div class='input'><span class='no'>f.w.man.irls</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>)
-<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.5
+<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 20:59:21 2018
-#&gt; Date of summary: Fri Sep 14 20:59:21 2018
+#&gt; Date of fit: Tue Sep 18 09:49:48 2018
+#&gt; Date of summary: Tue Sep 18 09:49:48 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1228,7 +1228,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 692 model solutions performed in 2.955 s
+#&gt; Fitted with method Port using 692 model solutions performed in 2.77 s
#&gt;
#&gt; Weighting: manual
#&gt;
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 464178bc..c1e7b840 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -66,7 +66,7 @@ For the definition of model types and their parameters, the equations given
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
@@ -229,7 +229,7 @@ For the definition of model types and their parameters, the equations given
<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>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='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; Compilation argument:
-#&gt; /usr/lib/R/bin/R CMD SHLIB file7aee6cc2a6d.c 2&gt; file7aee6cc2a6d.c.err.txt
+#&gt; /usr/lib/R/bin/R CMD SHLIB file73da22034c44.c 2&gt; file73da22034c44.c.err.txt
#&gt; Program source:
#&gt; 1: #include &lt;R.h&gt;
#&gt; 2:
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index 6ed32315..a57a439c 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -62,7 +62,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html
index 72ff93f6..18da0660 100644
--- a/docs/reference/mkinplot.html
+++ b/docs/reference/mkinplot.html
@@ -61,7 +61,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index dfcd08a8..5fad64de 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -63,7 +63,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
@@ -321,17 +321,17 @@
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.004 0.000 0.003 </div><div class='input'> <span class='fu'>system.time</span>(
+#&gt; 0.003 0.000 0.003 </div><div class='input'> <span class='fu'>system.time</span>(
<span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.001 0.000 0.002 </div><div class='input'> <span class='fu'>system.time</span>(
+#&gt; 0.002 0.000 0.001 </div><div class='input'> <span class='fu'>system.time</span>(
<span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
<span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#&gt; time parent m1
#&gt; 201 20 4.978707 27.46227</div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.036 0.000 0.036 </div></pre>
+#&gt; 0.033 0.000 0.034 </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html
index 306b7400..b57af4d3 100644
--- a/docs/reference/mkinresplot.html
+++ b/docs/reference/mkinresplot.html
@@ -64,7 +64,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html
index 0a2bf41a..3f2d2f86 100644
--- a/docs/reference/mkinsub.html
+++ b/docs/reference/mkinsub.html
@@ -62,7 +62,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 383e5928..13cdedff 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -62,7 +62,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
@@ -189,8 +189,8 @@
<span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'>system.time</span>(<span class='no'>fits.4</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))
<span class='no'>time_default</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 0.056 0.024 6.712 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 20.446 0.000 20.459 </div><div class='input'>
+#&gt; 0.043 0.040 6.475 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
+#&gt; 19.165 0.000 19.179 </div><div class='input'>
<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#&gt; $ff
#&gt; parent_M1 parent_sink M1_M2 M1_sink
#&gt; 0.7340480 0.2659520 0.7505686 0.2494314
diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index e88c2025..c082f125 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -66,7 +66,7 @@ If the current plot device is a tikz device,
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index d67d87d9..3f155473 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -65,7 +65,7 @@ If the current plot device is a tikz device,
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html
index 2489269c..022efe67 100644
--- a/docs/reference/print.mkinds.html
+++ b/docs/reference/print.mkinds.html
@@ -61,7 +61,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html
index b6cbad61..efa3272e 100644
--- a/docs/reference/print.mkinmod.html
+++ b/docs/reference/print.mkinmod.html
@@ -61,7 +61,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index 4ceba867..b22c67fa 100644
--- a/docs/reference/schaefer07_complex_case.html
+++ b/docs/reference/schaefer07_complex_case.html
@@ -63,7 +63,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html
index e74707ff..36612f18 100644
--- a/docs/reference/sigma_twocomp.html
+++ b/docs/reference/sigma_twocomp.html
@@ -66,7 +66,7 @@ This is the error model used for example by Werner et al. (1978). The model
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 317c7a87..0af65ed8 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -64,7 +64,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
@@ -204,17 +204,17 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.5
+ <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 21:00:08 2018
-#&gt; Date of summary: Fri Sep 14 21:00:08 2018
+#&gt; Date of fit: Tue Sep 18 09:50:32 2018
+#&gt; Date of summary: Tue Sep 18 09:50:32 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted with method Port using 35 model solutions performed in 0.081 s
+#&gt; Fitted with method Port using 35 model solutions performed in 0.071 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index 384d628d..94397ddf 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -76,7 +76,7 @@ Compare also the code in the example section to see the degradation models." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index 094e003d..b8c4a76b 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -62,7 +62,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 6f7ec4a4..ce6f6c8d 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -69,7 +69,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.5</span>
+ <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.6</span>
</span>
</div>
@@ -198,10 +198,10 @@ The transformation of sets of formation fractions is fragile, as it supposes
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</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='co'># Fit the model to the FOCUS example dataset D using defaults</span>
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.5
+<span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 21:00:16 2018
-#&gt; Date of summary: Fri Sep 14 21:00:16 2018
+#&gt; Date of fit: Tue Sep 18 09:50:39 2018
+#&gt; Date of summary: Tue Sep 18 09:50:39 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -209,7 +209,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 153 model solutions performed in 0.71 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.586 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -274,10 +274,10 @@ The transformation of sets of formation fractions is fragile, as it supposes
#&gt; parent 7.023 23.33
#&gt; m1 131.761 437.70</div><div class='input'>
</div><div class='input'><span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.5
+<span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 21:00:17 2018
-#&gt; Date of summary: Fri Sep 14 21:00:17 2018
+#&gt; Date of fit: Tue Sep 18 09:50:41 2018
+#&gt; Date of summary: Tue Sep 18 09:50:41 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -285,7 +285,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 350 model solutions performed in 1.417 s
+#&gt; Fitted with method Port using 350 model solutions performed in 1.341 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -362,10 +362,10 @@ The transformation of sets of formation fractions is fragile, as it supposes
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
<span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'>summary</span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.5
+<span class='fu'>summary</span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 21:00:18 2018
-#&gt; Date of summary: Fri Sep 14 21:00:18 2018
+#&gt; Date of fit: Tue Sep 18 09:50:42 2018
+#&gt; Date of summary: Tue Sep 18 09:50:42 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -373,7 +373,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 186 model solutions performed in 0.755 s
+#&gt; Fitted with method Port using 186 model solutions performed in 0.73 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -446,10 +446,10 @@ The transformation of sets of formation fractions is fragile, as it supposes
<span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</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.ff.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.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='fu'>summary</span>(<span class='no'>fit.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.5
+<span class='fu'>summary</span>(<span class='no'>fit.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.47.6
#&gt; R version used for fitting: 3.5.1
-#&gt; Date of fit: Fri Sep 14 21:00:19 2018
-#&gt; Date of summary: Fri Sep 14 21:00:19 2018
+#&gt; Date of fit: Tue Sep 18 09:50:42 2018
+#&gt; Date of summary: Tue Sep 18 09:50:42 2018
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -457,7 +457,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 104 model solutions performed in 0.416 s
+#&gt; Fitted with method Port using 104 model solutions performed in 0.401 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/man/max_twa_parent.Rd b/man/max_twa_parent.Rd
index b8c820bc..f599eb1c 100644
--- a/man/max_twa_parent.Rd
+++ b/man/max_twa_parent.Rd
@@ -6,7 +6,7 @@
\description{
This function calculates maximum moving window time weighted average concentrations
(TWAs) for kinetic models fitted with \code{\link{mkinfit}}. Currently, only
-calculations for the parent are implemented for the SFO, FOMC and DFOP models,
+calculations for the parent are implemented for the SFO, FOMC, DFOP and HS models,
using the analytical formulas given in the PEC soil section of the FOCUS
guidance.}
\usage{
diff --git a/test.log b/test.log
index c4ced344..cd3ffc7c 100644
--- a/test.log
+++ b/test.log
@@ -2,19 +2,21 @@ Loading mkin
Loading required package: testthat
Testing mkin
✔ | OK F W S | Context
- ⠏ | 0 | Calculation of FOCUS chi2 error levels ⠋ | 1 | Calculation of FOCUS chi2 error levels ⠙ | 2 | Calculation of FOCUS chi2 error levels ✔ | 2 | Calculation of FOCUS chi2 error levels [2.2 s]
- ⠏ | 0 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠋ | 1 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠙ | 2 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠹ | 3 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠸ | 4 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠼ | 5 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠴ | 6 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠦ | 7 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠧ | 8 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ✔ | 8 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [6.5 s]
- ⠏ | 0 | Iteratively reweighted least squares (IRLS) fitting ⠋ | 1 | Iteratively reweighted least squares (IRLS) fitting ⠙ | 2 | Iteratively reweighted least squares (IRLS) fitting ⠹ | 3 | Iteratively reweighted least squares (IRLS) fitting ✔ | 3 | Iteratively reweighted least squares (IRLS) fitting [36.6 s]
+ ⠏ | 0 | Calculation of FOCUS chi2 error levels ⠋ | 1 | Calculation of FOCUS chi2 error levels ⠙ | 2 | Calculation of FOCUS chi2 error levels ✔ | 2 | Calculation of FOCUS chi2 error levels [2.1 s]
+ ⠏ | 0 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠋ | 1 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠙ | 2 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠹ | 3 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠸ | 4 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠼ | 5 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠴ | 6 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠦ | 7 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ⠧ | 8 | Results for FOCUS D established in expertise for UBA (Ranke 2014) ✔ | 8 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [6.1 s]
+ ⠏ | 0 | Iteratively reweighted least squares (IRLS) fitting ⠋ | 1 | Iteratively reweighted least squares (IRLS) fitting ⠙ | 2 | Iteratively reweighted least squares (IRLS) fitting ⠹ | 3 | Iteratively reweighted least squares (IRLS) fitting ✔ | 3 | Iteratively reweighted least squares (IRLS) fitting [35.8 s]
⠏ | 0 | Model predictions with mkinpredict ⠋ | 1 | Model predictions with mkinpredict ⠙ | 2 | Model predictions with mkinpredict ⠹ | 3 | Model predictions with mkinpredict ✔ | 3 | Model predictions with mkinpredict [0.3 s]
- ⠏ | 0 | Fitting of parent only models ⠋ | 1 | Fitting of parent only models ⠙ | 2 | Fitting of parent only models ⠹ | 3 | Fitting of parent only models ⠸ | 4 | Fitting of parent only models ⠼ | 5 | Fitting of parent only models ⠴ | 6 | Fitting of parent only models ⠦ | 7 | Fitting of parent only models ⠧ | 8 | Fitting of parent only models ⠇ | 9 | Fitting of parent only models ⠏ | 10 | Fitting of parent only models ⠋ | 11 | Fitting of parent only models ⠙ | 12 | Fitting of parent only models ⠹ | 13 | Fitting of parent only models ⠸ | 14 | Fitting of parent only models ⠼ | 15 | Fitting of parent only models ⠴ | 16 | Fitting of parent only models ⠦ | 17 | Fitting of parent only models ⠧ | 18 | Fitting of parent only models ⠇ | 19 | Fitting of parent only models ⠏ | 20 | Fitting of parent only models ⠋ | 21 | Fitting of parent only models ✔ | 21 | Fitting of parent only models [22.6 s]
- ⠏ | 0 | Complex test case from Schaefer et al. (2007) Piacenza paper ⠋ | 1 | Complex test case from Schaefer et al. (2007) Piacenza paper ⠙ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.5 s]
- ⠏ | 0 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠋ | 1 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠙ | 2 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠹ | 3 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠸ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [6.7 s]
- ⠏ | 0 | Calculation of maximum time weighted average concentrations (TWAs) ⠋ | 1 | Calculation of maximum time weighted average concentrations (TWAs) ⠙ | 2 | Calculation of maximum time weighted average concentrations (TWAs) ⠹ | 3 | Calculation of maximum time weighted average concentrations (TWAs) ✔ | 3 | Calculation of maximum time weighted average concentrations (TWAs) [3.8 s]
+ ⠏ | 0 | Fitting of parent only models ⠋ | 1 | Fitting of parent only models ⠙ | 2 | Fitting of parent only models ⠹ | 3 | Fitting of parent only models ⠸ | 4 | Fitting of parent only models ⠼ | 5 | Fitting of parent only models ⠴ | 6 | Fitting of parent only models ⠦ | 7 | Fitting of parent only models ⠧ | 8 | Fitting of parent only models ⠇ | 9 | Fitting of parent only models ⠏ | 10 | Fitting of parent only models ⠋ | 11 | Fitting of parent only models ⠙ | 12 | Fitting of parent only models ⠹ | 13 | Fitting of parent only models ⠸ | 14 | Fitting of parent only models ⠼ | 15 | Fitting of parent only models ⠴ | 16 | Fitting of parent only models ⠦ | 17 | Fitting of parent only models ⠧ | 18 | Fitting of parent only models ⠇ | 19 | Fitting of parent only models ⠏ | 20 | Fitting of parent only models ⠋ | 21 | Fitting of parent only models ✔ | 21 | Fitting of parent only models [22.0 s]
+ ⠏ | 0 | Complex test case from Schaefer et al. (2007) Piacenza paper ⠋ | 1 | Complex test case from Schaefer et al. (2007) Piacenza paper ⠙ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper ✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.1 s]
+ ⠏ | 0 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠋ | 1 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠙ | 2 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠹ | 3 | Results for synthetic data established in expertise for UBA (Ranke 2014) ⠸ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) ✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [6.4 s]
+ ⠏ | 0 | Calculation of maximum time weighted average concentrations (TWAs) ⠋ | 1 | Calculation of maximum time weighted average concentrations (TWAs) ⠙ | 2 | Calculation of maximum time weighted average concentrations (TWAs) ⠹ | 3 | Calculation of maximum time weighted average concentrations (TWAs) ⠸ | 4 | Calculation of maximum time weighted average concentrations (TWAs) ⠼ | 5 | Calculation of maximum time weighted average concentrations (TWAs) ⠴ | 6 | Calculation of maximum time weighted average concentrations (TWAs) ⠦ | 7 | Calculation of maximum time weighted average concentrations (TWAs) ⠧ | 8 | Calculation of maximum time weighted average concentrations (TWAs) ✔ | 8 | Calculation of maximum time weighted average concentrations (TWAs) [7.5 s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 84.2 s
+Duration: 85.3 s
-OK: 46
+OK: 51
Failed: 0
Warnings: 0
Skipped: 0
+
+Keep up the good work.
diff --git a/tests/testthat/test_twa.R b/tests/testthat/test_twa.R
index a84b2c4e..758c42c3 100644
--- a/tests/testthat/test_twa.R
+++ b/tests/testthat/test_twa.R
@@ -21,23 +21,29 @@ context("Calculation of maximum time weighted average concentrations (TWAs)")
test_that("Time weighted average concentrations are correct", {
skip_on_cran()
- twa_models <- c("SFO", "FOMC", "DFOP")
- fits <- mmkin(twa_models, list(FOCUS_D = FOCUS_2006_D),
- quiet = TRUE, cores = 1)
-
- outtimes_7 <- seq(0, 7, length.out = 10000)
- for (model in twa_models) {
- fit <- fits[[model, 1]]
- bpar <- summary(fit)$bpar[, "Estimate"]
- pred_7 <- mkinpredict(fit$mkinmod,
- odeparms = bpar[2:length(bpar)],
- odeini = c(parent = bpar[[1]]),
- outtimes = outtimes_7)
- twa_num <- mean(pred_7$parent)
- names(twa_num) <- 7
- twa_ana <- max_twa_parent(fit, 7)
-
- # Test for absolute difference (scale = 1)
- expect_equal(twa_num, twa_ana, tolerance = 0.001, scale = 1)
+ twa_models <- c("SFO", "FOMC", "DFOP", "HS")
+ fits <- mmkin(twa_models,
+ list(FOCUS_C = FOCUS_2006_C, FOCUS_D = FOCUS_2006_D),
+ quiet = TRUE, cores = 8)
+
+ outtimes_10 <- seq(0, 10, length.out = 10000)
+
+ for (ds in c("FOCUS_C", "FOCUS_D")) {
+ for (model in twa_models) {
+ fit <- fits[[model, ds]]
+ bpar <- summary(fit)$bpar[, "Estimate"]
+ pred_10 <- mkinpredict(fit$mkinmod,
+ odeparms = bpar[2:length(bpar)],
+ odeini = c(parent = bpar[[1]]),
+ outtimes = outtimes_10)
+ twa_num <- mean(pred_10$parent)
+ names(twa_num) <- 10
+ twa_ana <- max_twa_parent(fit, 10)
+
+ # Test for absolute difference (scale = 1)
+ # The tolerance can be reduced if the length of outtimes is increased,
+ # but this needs more computing time so we stay with lenght.out = 10k
+ expect_equal(twa_num, twa_ana, tolerance = 0.003, scale = 1)
+ }
}
})

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