aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
-rw-r--r--R/mkinfit.R27
-rw-r--r--docs/articles/FOCUS_D.html13
-rw-r--r--docs/articles/FOCUS_L.html77
-rw-r--r--docs/articles/mkin.html2
-rw-r--r--docs/articles/twa.html2
-rw-r--r--docs/articles/web_only/FOCUS_Z.html2
-rw-r--r--docs/articles/web_only/NAFTA_examples.html2
-rw-r--r--docs/articles/web_only/benchmarks.html24
-rw-r--r--docs/articles/web_only/compiled_models.html12
-rw-r--r--docs/reference/Extract.mmkin.html8
-rw-r--r--docs/reference/experimental_data_for_UBA.html66
-rw-r--r--docs/reference/mkinfit.html50
-rw-r--r--docs/reference/mkinmod.html2
-rw-r--r--docs/reference/mkinpredict.html6
-rw-r--r--docs/reference/mmkin.html4
-rw-r--r--docs/reference/summary.mkinfit.html11
-rw-r--r--vignettes/mkin_benchmarks.rdabin874 -> 876 bytes
17 files changed, 198 insertions, 110 deletions
diff --git a/R/mkinfit.R b/R/mkinfit.R
index 60697cb1..2af4e493 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -506,18 +506,23 @@ mkinfit <- function(mkinmod, observed,
control = control, ...)
fit$logLik <- - nlogLik.current
+ d_3_messages = c(
+ same = "Direct fitting and three-step fitting yield approximately the same likelihood",
+ threestep = "Three-step fitting yielded a higher likelihood than direct fitting",
+ direct = "Direct fitting yielded a higher likelihood than three-step fitting")
if (error_model_algorithm == "d_3") {
rel_diff <- abs((fit_direct$logLik - fit$logLik))/-mean(c(fit_direct$logLik, fit$logLik))
if (rel_diff < 0.0001) {
- if (!quiet) {
- message("Direct fitting and three-step fitting yield approximately the same likelihood")
- }
+ if (!quiet) message(d_3_messages["same"])
+ fit$d_3_message <- d_3_messages["same"]
} else {
if (fit$logLik > fit_direct$logLik) {
- if (!quiet) message("Three-step fitting yielded a higher likelihood than direct fitting")
+ if (!quiet) message(d_3_messages["threestep"])
+ fit$d_3_message <- d_3_messages["threestep"]
} else {
- if (!quiet) message("Direct fitting yielded a higher likelihood than three-step fitting")
+ if (!quiet) message(d_3_messages["direct"])
fit <- fit_direct
+ fit$d_3_message <- d_3_messages["direct"]
}
}
}
@@ -553,6 +558,7 @@ mkinfit <- function(mkinmod, observed,
}
}
}
+ fit$error_model_algorithm <- error_model_algorithm
# We include the error model in the parameter uncertainty analysis, also
# for constant variance, to get a confidence interval for it
@@ -725,6 +731,7 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, alpha = 0.05,
solution_type = object$solution_type,
warning = object$warning,
use_of_ff = object$mkinmod$use_of_ff,
+ error_model_algorithm = object$error_model_algorithm,
df = c(p, rdf),
cov.unscaled = covar,
err_mod = object$err_mod,
@@ -763,8 +770,9 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, alpha = 0.05,
ep <- endpoints(object)
if (length(ep$ff) != 0)
ans$ff <- ep$ff
- if(distimes) ans$distimes <- ep$distimes
- if(length(ep$SFORB) != 0) ans$SFORB <- ep$SFORB
+ if (distimes) ans$distimes <- ep$distimes
+ if (length(ep$SFORB) != 0) ans$SFORB <- ep$SFORB
+ if (!is.null(object$d_3_message)) ans$d_3_message <- object$d_3_message
class(ans) <- c("summary.mkinfit", "summary.modFit")
return(ans)
}
@@ -794,12 +802,15 @@ print.summary.mkinfit <- function(x, digits = max(3, getOption("digits") - 3), .
cat("\nFitted using", x$calls, "model solutions performed in", x$time[["elapsed"]], "s\n")
- cat("\nError model:\n")
+ cat("\nError model: ")
cat(switch(x$err_mod,
const = "Constant variance",
obs = "Variance unique to each observed variable",
tc = "Two-component variance function"), "\n")
+ cat("\nError model algorithm:", x$error_model_algorithm, "\n")
+ if (!is.null(x$d_3_message)) cat(x$d_3_message, "\n")
+
cat("\nStarting values for parameters to be optimised:\n")
print(x$start)
diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index 698ccebc..be1f40f5 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -88,7 +88,7 @@
<h1>Example evaluation of FOCUS Example Dataset D</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-06-04</h4>
+ <h4 class="date">2019-06-05</h4>
<div class="hidden name"><code>FOCUS_D.Rmd</code></div>
@@ -168,8 +168,8 @@
<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(fit)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.49.5
## R version used for fitting: 3.6.0
-## Date of fit: Tue Jun 4 15:03:18 2019
-## Date of summary: Tue Jun 4 15:03:18 2019
+## Date of fit: Wed Jun 5 15:10:49 2019
+## Date of summary: Wed Jun 5 15:10:50 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -177,10 +177,11 @@
##
## Model predictions using solution type deSolve
##
-## Fitted using 389 model solutions performed in 0.978 s
+## Fitted using 389 model solutions performed in 0.984 s
##
-## Error model:
-## Constant variance
+## Error model: Constant variance
+##
+## Error model algorithm: d_3
##
## Starting values for parameters to be optimised:
## value type
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 75b2cf10..4388edd2 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -88,7 +88,7 @@
<h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-06-04</h4>
+ <h4 class="date">2019-06-05</h4>
<div class="hidden name"><code>FOCUS_L.Rmd</code></div>
@@ -114,18 +114,19 @@
<a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.SFO)</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.49.5
## R version used for fitting: 3.6.0
-## Date of fit: Tue Jun 4 15:03:20 2019
-## Date of summary: Tue Jun 4 15:03:20 2019
+## Date of fit: Wed Jun 5 15:10:52 2019
+## Date of summary: Wed Jun 5 15:10:52 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 133 model solutions performed in 0.28 s
+## Fitted using 133 model solutions performed in 0.277 s
##
-## Error model:
-## Constant variance
+## Error model: Constant variance
+##
+## Error model algorithm: d_3
##
## Starting values for parameters to be optimised:
## value type
@@ -215,8 +216,8 @@
## finite result is doubtful</code></pre>
<pre><code>## mkin version used for fitting: 0.9.49.5
## R version used for fitting: 3.6.0
-## Date of fit: Tue Jun 4 15:03:22 2019
-## Date of summary: Tue Jun 4 15:03:22 2019
+## Date of fit: Wed Jun 5 15:10:54 2019
+## Date of summary: Wed Jun 5 15:10:54 2019
##
##
## Warning: Optimisation did not converge:
@@ -228,10 +229,11 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 899 model solutions performed in 1.868 s
+## Fitted using 899 model solutions performed in 1.877 s
+##
+## Error model: Constant variance
##
-## Error model:
-## Constant variance
+## Error model algorithm: d_3
##
## Starting values for parameters to be optimised:
## value type
@@ -319,18 +321,19 @@
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 0.9.49.5
## R version used for fitting: 3.6.0
-## Date of fit: Tue Jun 4 15:03:23 2019
-## Date of summary: Tue Jun 4 15:03:23 2019
+## Date of fit: Wed Jun 5 15:10:55 2019
+## Date of summary: Wed Jun 5 15:10:55 2019
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 239 model solutions performed in 0.484 s
+## Fitted using 239 model solutions performed in 0.492 s
##
-## Error model:
-## Constant variance
+## Error model: Constant variance
+##
+## Error model algorithm: d_3
##
## Starting values for parameters to be optimised:
## value type
@@ -394,8 +397,8 @@
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 0.9.49.5
## R version used for fitting: 3.6.0
-## Date of fit: Tue Jun 4 15:03:25 2019
-## Date of summary: Tue Jun 4 15:03:25 2019
+## Date of fit: Wed Jun 5 15:10:56 2019
+## Date of summary: Wed Jun 5 15:10:56 2019
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -404,10 +407,11 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 572 model solutions performed in 1.193 s
+## Fitted using 572 model solutions performed in 1.183 s
+##
+## Error model: Constant variance
##
-## Error model:
-## Constant variance
+## Error model algorithm: d_3
##
## Starting values for parameters to be optimised:
## value type
@@ -493,8 +497,8 @@
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div>
<pre><code>## mkin version used for fitting: 0.9.49.5
## R version used for fitting: 3.6.0
-## Date of fit: Tue Jun 4 15:03:26 2019
-## Date of summary: Tue Jun 4 15:03:27 2019
+## Date of fit: Wed Jun 5 15:10:58 2019
+## Date of summary: Wed Jun 5 15:10:58 2019
##
## Equations:
## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -503,10 +507,11 @@
##
## Model predictions using solution type analytical
##
-## Fitted using 373 model solutions performed in 0.767 s
+## Fitted using 373 model solutions performed in 0.773 s
##
-## Error model:
-## Constant variance
+## Error model: Constant variance
+##
+## Error model algorithm: d_3
##
## Starting values for parameters to be optimised:
## value type
@@ -598,8 +603,8 @@
<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 0.9.49.5
## R version used for fitting: 3.6.0
-## Date of fit: Tue Jun 4 15:03:27 2019
-## Date of summary: Tue Jun 4 15:03:28 2019
+## Date of fit: Wed Jun 5 15:10:59 2019
+## Date of summary: Wed Jun 5 15:10:59 2019
##
## Equations:
## d_parent/dt = - k_parent_sink * parent
@@ -608,8 +613,9 @@
##
## Fitted using 142 model solutions performed in 0.288 s
##
-## Error model:
-## Constant variance
+## Error model: Constant variance
+##
+## Error model algorithm: d_3
##
## Starting values for parameters to be optimised:
## value type
@@ -662,18 +668,19 @@
<div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></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: 0.9.49.5
## R version used for fitting: 3.6.0
-## Date of fit: Tue Jun 4 15:03:28 2019
-## Date of summary: Tue Jun 4 15:03:28 2019
+## Date of fit: Wed Jun 5 15:10:59 2019
+## Date of summary: Wed Jun 5 15:10:59 2019
##
## Equations:
## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted using 224 model solutions performed in 0.449 s
+## Fitted using 224 model solutions performed in 0.453 s
+##
+## Error model: Constant variance
##
-## Error model:
-## Constant variance
+## Error model algorithm: d_3
##
## Starting values for parameters to be optimised:
## value type
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 09b1b8ea..5977d642 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -88,7 +88,7 @@
<h1>Introduction to mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-06-04</h4>
+ <h4 class="date">2019-06-05</h4>
<div class="hidden name"><code>mkin.Rmd</code></div>
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index ede27942..f98026e7 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -88,7 +88,7 @@
<h1>Calculation of time weighted average concentrations with mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-06-04</h4>
+ <h4 class="date">2019-06-05</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 555400df..542deb14 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -88,7 +88,7 @@
<h1>Example evaluation of FOCUS dataset Z</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-06-04</h4>
+ <h4 class="date">2019-06-05</h4>
<div class="hidden name"><code>FOCUS_Z.Rmd</code></div>
diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html
index 7f3cc76b..4cd16437 100644
--- a/docs/articles/web_only/NAFTA_examples.html
+++ b/docs/articles/web_only/NAFTA_examples.html
@@ -88,7 +88,7 @@
<h1>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-06-04</h4>
+ <h4 class="date">2019-06-05</h4>
<div class="hidden name"><code>NAFTA_examples.Rmd</code></div>
diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index 43f8d238..507bdb61 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -88,7 +88,7 @@
<h1>Benchmark timings for mkin on various systems</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-06-04</h4>
+ <h4 class="date">2019-06-05</h4>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
@@ -202,77 +202,77 @@
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.064
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.296
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.936
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 5.805
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 5.828
## t2
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 11.019
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 22.889
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 12.558
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 21.239
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.545
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 35.748
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 35.869
## t3
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.764
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.649
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.786
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.510
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.446
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.403
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.412
## t4
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 14.347
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 13.789
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 8.461
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 13.805
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 15.335
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 30.613
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 30.497
## t5
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 9.495
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 6.002
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.309
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.329
## t6
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 2.623
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 2.542
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 2.723
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 2.643
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.635
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 2.546
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 2.548
## t7
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.259
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.214
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.192
## t8
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 7.525
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.632
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.862
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.02
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.737
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.871
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.827
## t9
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 16.621
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.171
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.618
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 11.124
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.763
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 15.738
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 15.653
## t10
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 8.576
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 3.676
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 3.579
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 5.388
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.427
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.763
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.762
## t11
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 31.267
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 5.636
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.574
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.365
## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.626
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.527</code></pre>
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.512</code></pre>
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/save">save</a></span>(mkin_benchmarks, <span class="dt">file =</span> <span class="st">"~/git/mkin/vignettes/mkin_benchmarks.rda"</span>)</a></code></pre></div>
</div>
</div>
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index f3062c66..5f0301fc 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -88,7 +88,7 @@
<h1>Performance benefit by using compiled model definitions in mkin</h1>
<h4 class="author">Johannes Ranke</h4>
- <h4 class="date">2019-06-04</h4>
+ <h4 class="date">2019-06-05</h4>
<div class="hidden name"><code>compiled_models.Rmd</code></div>
@@ -163,9 +163,9 @@
## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet
## = TRUE): Observations with value of zero were removed from the data</code></pre>
<pre><code>## test replications elapsed relative user.self sys.self
-## 3 deSolve, compiled 3 3.053 1.000 3.052 0
-## 1 deSolve, not compiled 3 28.457 9.321 28.442 0
-## 2 Eigenvalue based 3 4.296 1.407 4.293 0
+## 3 deSolve, compiled 3 3.041 1.000 3.039 0
+## 1 deSolve, not compiled 3 28.429 9.349 28.415 0
+## 2 Eigenvalue based 3 4.291 1.411 4.288 0
## user.child sys.child
## 3 0 0
## 1 0 0
@@ -214,8 +214,8 @@
## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
## value of zero were removed from the data</code></pre>
<pre><code>## test replications elapsed relative user.self sys.self
-## 2 deSolve, compiled 3 4.828 1.000 4.825 0
-## 1 deSolve, not compiled 3 53.153 11.009 53.125 0
+## 2 deSolve, compiled 3 4.927 1.000 4.924 0
+## 1 deSolve, not compiled 3 53.138 10.785 53.108 0
## user.child sys.child
## 2 0 0
## 1 0 0</code></pre>
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 1d1da50e..37c0b361 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -172,16 +172,16 @@
<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'>fits</span>[<span class='st'>"FOMC"</span>, ]</div><div class='output co'>#&gt; dataset
#&gt; model B C
-#&gt; FOMC List,36 List,36
+#&gt; FOMC List,37 List,37
#&gt; attr(,"class")
#&gt; [1] "mmkin"</div><div class='input'> <span class='no'>fits</span>[, <span class='st'>"B"</span>]</div><div class='output co'>#&gt; dataset
#&gt; model B
-#&gt; SFO List,36
-#&gt; FOMC List,36
+#&gt; SFO List,37
+#&gt; FOMC List,37
#&gt; attr(,"class")
#&gt; [1] "mmkin"</div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#&gt; dataset
#&gt; model B
-#&gt; SFO List,36
+#&gt; SFO List,37
#&gt; attr(,"class")
#&gt; [1] "mmkin"</div><div class='input'>
<span class='fu'><a href='https://www.rdocumentation.org/packages/utils/topics/head'>head</a></span>(
diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html
index 3e8d20ef..bb94fd11 100644
--- a/docs/reference/experimental_data_for_UBA.html
+++ b/docs/reference/experimental_data_for_UBA.html
@@ -37,7 +37,30 @@
and advance error model specifications. The fact that these data and some
results are shown here do not imply a license to use them in the context of
pesticide registrations, as the use of the data may be constrained by
- data protection regulations." />
+ data protection regulations.
+Preprocessing of data was performed based on the recommendations of the FOCUS
+ kinetics workgroup (FOCUS, 2014) as described below.
+Datasets 1 and 2 are from the Renewal Assessment Report (RAR) for imazamox
+ (France, 2015, p. 15). For setting values reported as zero, an LOQ of 0.1
+ was assumed. Metabolite residues reported for day zero were added to the
+ parent compound residues.
+Datasets 3 and 4 are from the Renewal Assessment Report (RAR) for isofetamid
+ (Belgium, 2014, p. 8) and show the data for two different radiolabels. For
+ dataset 4, the value given for the metabolite in the day zero sampling
+ in replicate B was added to the parent compound, following the respective
+ FOCUS recommendation.
+Dataset 5 is from the Renewal Assessment Report (RAR) for ethofumesate
+ (Austria, 2015, p. 16).
+Datasets 6 to 10 are from the Renewal Assessment Report (RAR) for glyphosate
+ (Germany, 2013a, pages 8, 28, 50, 51). For the initial sampling,
+ the residues given for the metabolite were added to the parent
+ value, following the recommendation of the FOCUS kinetics workgroup.
+Dataset 11 is from the Renewal Assessment Report (RAR) for 2,4-D
+ (Germany, 2013b, p. 644). Values reported as zero were set to NA, with
+ the exception of the day three sampling of metabolite A2, which was set
+ to one half of the LOD reported to be 1% AR.
+Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
+ (United Kingdom, 2014, p. 81)." />
<meta name="twitter:card" content="summary" />
@@ -139,6 +162,29 @@
results are shown here do not imply a license to use them in the context of
pesticide registrations, as the use of the data may be constrained by
data protection regulations.</p>
+<p>Preprocessing of data was performed based on the recommendations of the FOCUS
+ kinetics workgroup (FOCUS, 2014) as described below.</p>
+<p>Datasets 1 and 2 are from the Renewal Assessment Report (RAR) for imazamox
+ (France, 2015, p. 15). For setting values reported as zero, an LOQ of 0.1
+ was assumed. Metabolite residues reported for day zero were added to the
+ parent compound residues.</p>
+<p>Datasets 3 and 4 are from the Renewal Assessment Report (RAR) for isofetamid
+ (Belgium, 2014, p. 8) and show the data for two different radiolabels. For
+ dataset 4, the value given for the metabolite in the day zero sampling
+ in replicate B was added to the parent compound, following the respective
+ FOCUS recommendation.</p>
+<p>Dataset 5 is from the Renewal Assessment Report (RAR) for ethofumesate
+ (Austria, 2015, p. 16).</p>
+<p>Datasets 6 to 10 are from the Renewal Assessment Report (RAR) for glyphosate
+ (Germany, 2013a, pages 8, 28, 50, 51). For the initial sampling,
+ the residues given for the metabolite were added to the parent
+ value, following the recommendation of the FOCUS kinetics workgroup.</p>
+<p>Dataset 11 is from the Renewal Assessment Report (RAR) for 2,4-D
+ (Germany, 2013b, p. 644). Values reported as zero were set to NA, with
+ the exception of the day three sampling of metabolite A2, which was set
+ to one half of the LOD reported to be 1% AR.</p>
+<p>Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl
+ (United Kingdom, 2014, p. 81).</p>
</div>
@@ -154,8 +200,24 @@
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
- <p>Ranke (2019) Documentation of results obtained for the error model expertise
+
+ <p>Austria (2015). Ethofumesate Renewal Assessment Report Volume 3 Annex B.8 (AS)</p>
+<p>Belgium (2014). Isofetamid (IKF-5411) Draft Assessment Report Volume 3 Annex B.8 (AS)</p>
+<p>France (2015). Imazamox Draft Renewal Assessment Report Volume 3 Annex B.8 (AS)</p>
+<p>FOCUS (2014) &#8220;Generic guidance for Estimating Persistence and
+ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
+ Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+ Version 1.1, 18 December 2014
+ <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
+<p>Germany (2013a). Renewal Assessment Report Glyphosate Volume 3 Annex B.8: Environmental Fate
+ and Behaviour</p>
+<p>Germany (2013b). Renewal Assessment Report 2,4-D Volume 3 Annex B.8: Fate and behaviour in the
+ environment</p>
+<p>Ranke (2019) Documentation of results obtained for the error model expertise
written for the German Umweltbundesamt.</p>
+<p>United Kingdom (2014). Thifensulfuron-methyl - Annex B.8 (Volume 3) to the Report and Proposed
+ Decision of the United Kingdom made to the European Commission under Regulation (EC) No.
+ 1141/2010 for renewal of an active substance</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 8cabcb21..700b6805 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -399,18 +399,19 @@ Per default, parameters in the kinetic models are internally transformed in
<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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.5
#&gt; R version used for fitting: 3.6.0
-#&gt; Date of fit: Tue Jun 4 15:01:15 2019
-#&gt; Date of summary: Tue Jun 4 15:01:15 2019
+#&gt; Date of fit: Wed Jun 5 15:08:20 2019
+#&gt; Date of summary: Wed Jun 5 15:08:20 2019
#&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 using 222 model solutions performed in 0.461 s
+#&gt; Fitted using 222 model solutions performed in 0.469 s
#&gt;
-#&gt; Error model:
-#&gt; Constant variance
+#&gt; Error model: Constant variance
+#&gt;
+#&gt; Error model algorithm: d_3
#&gt;
#&gt; Starting values for parameters to be optimised:
#&gt; value type
@@ -480,7 +481,7 @@ Per default, parameters in the kinetic models are internally transformed in
<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'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></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; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 1.521 0.000 1.526 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; NULL</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; 1.579 0.000 1.581 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; NULL</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
#&gt;
@@ -552,7 +553,7 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; Sum of squared residuals at call 126: 371.2134
#&gt; Sum of squared residuals at call 135: 371.2134
#&gt; Negative log-likelihood at call 145: 97.22429</div><div class='output co'>#&gt; <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 1.093 0.000 1.093 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; NULL</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; 1.159 0.000 1.160 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; NULL</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
#&gt;
@@ -584,8 +585,8 @@ Per default, parameters in the kinetic models are internally transformed in
<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>)</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='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.5
#&gt; R version used for fitting: 3.6.0
-#&gt; Date of fit: Tue Jun 4 15:01:31 2019
-#&gt; Date of summary: Tue Jun 4 15:01:31 2019
+#&gt; Date of fit: Wed Jun 5 15:08:36 2019
+#&gt; Date of summary: Wed Jun 5 15:08:36 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -593,10 +594,11 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 421 model solutions performed in 1.096 s
+#&gt; Fitted using 421 model solutions performed in 1.181 s
+#&gt;
+#&gt; Error model: Constant variance
#&gt;
-#&gt; Error model:
-#&gt; Constant variance
+#&gt; Error model algorithm: d_3
#&gt;
#&gt; Starting values for parameters to be optimised:
#&gt; value type
@@ -702,8 +704,8 @@ Per default, parameters in the kinetic models are internally transformed in
#&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.obs</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'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</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='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.5
#&gt; R version used for fitting: 3.6.0
-#&gt; Date of fit: Tue Jun 4 15:01:34 2019
-#&gt; Date of summary: Tue Jun 4 15:01:34 2019
+#&gt; Date of fit: Wed Jun 5 15:08:39 2019
+#&gt; Date of summary: Wed Jun 5 15:08:39 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -711,10 +713,12 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 979 model solutions performed in 2.603 s
+#&gt; Fitted using 979 model solutions performed in 2.672 s
#&gt;
-#&gt; Error model:
-#&gt; Variance unique to each observed variable
+#&gt; Error model: Variance unique to each observed variable
+#&gt;
+#&gt; Error model algorithm: d_3
+#&gt; Direct fitting and three-step fitting yield approximately the same likelihood
#&gt;
#&gt; Starting values for parameters to be optimised:
#&gt; value type
@@ -832,8 +836,8 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; 120 m1 25.15 28.80429 -3.654e+00
#&gt; 120 m1 33.31 28.80429 4.506e+00</div><div class='input'><span class='no'>f.tc</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'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</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='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.5
#&gt; R version used for fitting: 3.6.0
-#&gt; Date of fit: Tue Jun 4 15:01:43 2019
-#&gt; Date of summary: Tue Jun 4 15:01:43 2019
+#&gt; Date of fit: Wed Jun 5 15:08:50 2019
+#&gt; Date of summary: Wed Jun 5 15:08:50 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -841,10 +845,12 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 2289 model solutions performed in 9.499 s
+#&gt; Fitted using 2289 model solutions performed in 10.959 s
+#&gt;
+#&gt; Error model: Two-component variance function
#&gt;
-#&gt; Error model:
-#&gt; Two-component variance function
+#&gt; Error model algorithm: d_3
+#&gt; Direct fitting and three-step fitting yield approximately the same likelihood
#&gt;
#&gt; Starting values for parameters to be optimised:
#&gt; value type
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 2c5f056e..ddab656c 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -234,7 +234,7 @@ 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 filebbe6b539c4f.c 2&gt; filebbe6b539c4f.c.err.txt
+#&gt; /usr/lib/R/bin/R CMD SHLIB file50a55c3108b2.c 2&gt; file50a55c3108b2.c.err.txt
#&gt; Program source:
#&gt; 1: #include &lt;R.h&gt;
#&gt; 2:
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index f339b26a..7e71ec27 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -328,17 +328,17 @@
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></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; 0.003 0.000 0.003 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
+#&gt; 0.004 0.000 0.004 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></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; 0.002 0.000 0.002 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
+#&gt; 0.003 0.000 0.002 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(
<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></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; 0.021 0.000 0.022 </div><div class='input'>
+#&gt; 0.022 0.000 0.022 </div><div class='input'>
</div><div class='input'> <span class='co'># Predict from a fitted model</span>
<span class='no'>f</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_C</span>)</div><div class='output co'>#&gt; <span class='message'>Ordinary least squares optimisation</span></div><div class='output co'>#&gt; Sum of squared residuals at call 1: 552.5739
#&gt; Sum of squared residuals at call 3: 552.5739
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index a830646f..61a029fc 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -194,8 +194,8 @@
<span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></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; 0.046 0.032 5.094 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
-#&gt; 19.798 0.004 19.814 </div><div class='input'>
+#&gt; 0.038 0.050 6.779 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; User System verstrichen
+#&gt; 27.209 0.004 27.278 </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; 0.7340481 0.2659519 0.7505684 0.2494316
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index ffe1edb1..68b36542 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -211,18 +211,19 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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: 0.9.49.5
#&gt; R version used for fitting: 3.6.0
-#&gt; Date of fit: Tue Jun 4 15:03:02 2019
-#&gt; Date of summary: Tue Jun 4 15:03:02 2019
+#&gt; Date of fit: Wed Jun 5 15:10:34 2019
+#&gt; Date of summary: Wed Jun 5 15:10:34 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted using 131 model solutions performed in 0.266 s
+#&gt; Fitted using 131 model solutions performed in 0.268 s
#&gt;
-#&gt; Error model:
-#&gt; Constant variance
+#&gt; Error model: Constant variance
+#&gt;
+#&gt; Error model algorithm: d_3
#&gt;
#&gt; Starting values for parameters to be optimised:
#&gt; value type
diff --git a/vignettes/mkin_benchmarks.rda b/vignettes/mkin_benchmarks.rda
index 3e160a06..17cf86ce 100644
--- a/vignettes/mkin_benchmarks.rda
+++ b/vignettes/mkin_benchmarks.rda
Binary files differ

Contact - Imprint