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-rw-r--r--DESCRIPTION3
-rw-r--r--NAMESPACE1
-rw-r--r--R/confint.mkinfit.R4
-rw-r--r--R/parms.mkinfit.R1
-rw-r--r--_pkgdown.yml12
-rw-r--r--docs/news/index.html1
-rw-r--r--docs/reference/confint.mkinfit.html252
-rw-r--r--docs/reference/index.html24
-rw-r--r--docs/reference/parms.html200
-rw-r--r--docs/sitemap.xml6
-rw-r--r--man/confint.mkinfit.Rd6
-rw-r--r--man/parms.Rd4
-rw-r--r--test.log18
-rw-r--r--tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg12
-rw-r--r--tests/testthat/FOCUS_2006_D.csf2
15 files changed, 513 insertions, 33 deletions
diff --git a/DESCRIPTION b/DESCRIPTION
index 9efa2b89..88412fa8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -17,8 +17,7 @@ Description: Calculation routines based on the FOCUS Kinetics Report (2006,
equation models are solved using compiled C functions. Please note that no
warranty is implied for correctness of results or fitness for a particular
purpose.
-Imports: stats, graphics, methods, deSolve, R6, inline, parallel, plyr,
- numDeriv
+Imports: stats, graphics, methods, deSolve, R6, inline, parallel, numDeriv
Suggests: knitr, rbenchmark, tikzDevice, testthat, rmarkdown, covr, vdiffr,
benchmarkme, tibble
License: GPL
diff --git a/NAMESPACE b/NAMESPACE
index b4b781ac..3718f45f 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -71,6 +71,7 @@ importFrom(stats,optimize)
importFrom(stats,pt)
importFrom(stats,qchisq)
importFrom(stats,qf)
+importFrom(stats,qnorm)
importFrom(stats,qt)
importFrom(stats,rnorm)
importFrom(utils,write.table)
diff --git a/R/confint.mkinfit.R b/R/confint.mkinfit.R
index 58918321..58a3c8db 100644
--- a/R/confint.mkinfit.R
+++ b/R/confint.mkinfit.R
@@ -28,7 +28,9 @@
#' @examples
#' f <- mkinfit("SFO", FOCUS_2006_C, quiet = TRUE)
#' confint(f, method = "quadratic")
-#' confint(f, method = "profile")
+#' \dontrun{
+#' confint(f, method = "profile")
+#' }
#' @export
confint.mkinfit <- function(object, parm,
level = 0.95, alpha = 1 - level,
diff --git a/R/parms.mkinfit.R b/R/parms.mkinfit.R
index 8f9b4136..0628cb92 100644
--- a/R/parms.mkinfit.R
+++ b/R/parms.mkinfit.R
@@ -5,6 +5,7 @@
#' considering the error structure that was assumed for the fit.
#'
#' @param object A fitted model object
+#' @param \dots Not used
#' @return A numeric vector of fitted model parameters
#' @export
parms <- function(object, ...)
diff --git a/_pkgdown.yml b/_pkgdown.yml
index d51a7f27..bbf63301 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -17,13 +17,15 @@ reference:
desc: Functions working with mkinfit objects
contents:
- plot.mkinfit
+ - parms.mkinfit
+ - confint.mkinfit
- summary.mkinfit
- - mkinresplot
- - mkinparplot
- - mkinerrplot
- - endpoints
- - mkinerrmin
- logLik.mkinfit
+ - mkinresplot
+ - mkinparplot
+ - mkinerrplot
+ - endpoints
+ - mkinerrmin
- title: Work with mmkin objects
desc: Functions working with aggregated results
contents:
diff --git a/docs/news/index.html b/docs/news/index.html
index 67f64150..1322f75d 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -134,6 +134,7 @@
<a href="#mkin-0-9-49-6-unreleased" class="anchor"></a>mkin 0.9.49.6 (unreleased)<small> Unreleased </small>
</h1>
<ul>
+<li><p>Add ‘parms’ and ‘confint’ methods for mkinfit objects. Confidence intervals based on the quadratic approximation as in the summary, and based on the profile likelihood</p></li>
<li><p>Move long-running tests to tests/testthat/slow with a separate test log. They currently take around 7 minutes on my system</p></li>
<li><p>‘mkinfit’: Clean the code and return functions to calculate the log-likelihood and the sum of squared residuals</p></li>
<li><p>Vignette ‘twa.html’: Add the maximum time weighted average formulas for the hockey stick model</p></li>
diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html
new file mode 100644
index 00000000..64ea0d4c
--- /dev/null
+++ b/docs/reference/confint.mkinfit.html
@@ -0,0 +1,252 @@
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+ <a class="navbar-link" href="../index.html">mkin</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span>
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+ <li>
+ <a href="../articles/mkin.html">Introduction to mkin</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+ </li>
+ <li>
+ <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
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+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Confidence intervals for parameters of mkinfit objects</h1>
+
+ <div class="hidden name"><code>confint.mkinfit.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Confidence intervals for parameters of mkinfit objects</p>
+ </div>
+
+ <pre class="usage"><span class='co'># S3 method for mkinfit</span>
+<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>object</span>, <span class='no'>parm</span>, <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0.95</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1</span> -
+ <span class='no'>level</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"profile"</span>, <span class='st'>"quadratic"</span>), <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='kw'>backtransform</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>distribution</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"student_t"</span>, <span class='st'>"normal"</span>),
+ <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>object</th>
+ <td><p>An <code><a href='mkinfit.html'>mkinfit</a></code> object</p></td>
+ </tr>
+ <tr>
+ <th>parm</th>
+ <td><p>A vector of names of the parameters which are to be given
+confidence intervals. If missing, all parameters are considered.</p></td>
+ </tr>
+ <tr>
+ <th>level</th>
+ <td><p>The confidence level required</p></td>
+ </tr>
+ <tr>
+ <th>alpha</th>
+ <td><p>The allowed error probability, overrides 'level' if specified.</p></td>
+ </tr>
+ <tr>
+ <th>method</th>
+ <td><p>The 'profile' method searches the parameter space for the
+cutoff of the confidence intervals by means of a likelihood ratio test.
+The 'quadratic' method approximates the likelihood function at the
+optimised parameters using the second term of the Taylor expansion, using
+a second derivative (hessian) contained in the object.</p></td>
+ </tr>
+ <tr>
+ <th>transformed</th>
+ <td><p>If the quadratic approximation is used, should it be
+applied to the likelihood based on the transformed parameters?</p></td>
+ </tr>
+ <tr>
+ <th>backtransform</th>
+ <td><p>If we approximate the likelihood in terms of the
+transformed parameters, should we backtransform the parameters with
+their confidence intervals?</p></td>
+ </tr>
+ <tr>
+ <th>distribution</th>
+ <td><p>For the quadratic approximation, should we use
+the student t distribution or assume normal distribution for
+the parameter estimate</p></td>
+ </tr>
+ <tr>
+ <th>quiet</th>
+ <td><p>Should we suppress messages?</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>Not used</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>A matrix with columns giving lower and upper confidence limits for
+ each parameter.</p>
+ <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+ <p>Pawitan Y (2013) In all likelihood - Statistical modelling and
+ inference using likelihood. Clarendon Press, Oxford.</p>
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='no'>f</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFO"</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://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 71.8242430 93.1600766
+#&gt; k_parent_sink 0.2109541 0.4440528
+#&gt; sigma 1.9778868 7.3681380</div><div class='input'><span class='co'># \dontrun{</span>
+ <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>)</div><div class='output co'>#&gt; <span class='message'>Profiling the likelihood</span></div><div class='output co'>#&gt; 2.5% 97.5%
+#&gt; parent_0 71.3471007 93.9447024
+#&gt; k_parent_sink 0.2030765 0.4491067
+#&gt; sigma 2.9810656 8.8633278</div><div class='input'># }
+</div></pre>
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ <li><a href="#value">Value</a></li>
+ <li><a href="#references">References</a></li>
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
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diff --git a/docs/reference/index.html b/docs/reference/index.html
index 328f5aca..fa424060 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -185,12 +185,30 @@ more datasets</p></td>
</tr><tr>
<td>
+ <p><code><a href="parms.html">parms()</a></code> </p>
+ </td>
+ <td><p>Extract model parameters from mkinfit models</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="confint.mkinfit.html">confint(<i>&lt;mkinfit&gt;</i>)</a></code> </p>
+ </td>
+ <td><p>Confidence intervals for parameters of mkinfit objects</p></td>
+ </tr><tr>
+
+ <td>
<p><code><a href="summary.mkinfit.html">summary(<i>&lt;mkinfit&gt;</i>)</a></code> <code><a href="summary.mkinfit.html">print(<i>&lt;summary.mkinfit&gt;</i>)</a></code> </p>
</td>
<td><p>Summary method for class "mkinfit"</p></td>
</tr><tr>
<td>
+ <p><code><a href="logLik.mkinfit.html">logLik(<i>&lt;mkinfit&gt;</i>)</a></code> </p>
+ </td>
+ <td><p>Calculated the log-likelihood of a fitted mkinfit object</p></td>
+ </tr><tr>
+
+ <td>
<p><code><a href="mkinresplot.html">mkinresplot()</a></code> </p>
</td>
<td><p>Function to plot residuals stored in an mkin object</p></td>
@@ -219,12 +237,6 @@ with mkinfit</p></td>
<p><code><a href="mkinerrmin.html">mkinerrmin()</a></code> </p>
</td>
<td><p>Calculate the minimum error to assume in order to pass the variance test</p></td>
- </tr><tr>
-
- <td>
- <p><code><a href="logLik.mkinfit.html">logLik(<i>&lt;mkinfit&gt;</i>)</a></code> </p>
- </td>
- <td><p>Calculated the log-likelihood of a fitted mkinfit object</p></td>
</tr>
</tbody><tbody>
<tr>
diff --git a/docs/reference/parms.html b/docs/reference/parms.html
new file mode 100644
index 00000000..8ab26240
--- /dev/null
+++ b/docs/reference/parms.html
@@ -0,0 +1,200 @@
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+model parameters, in order to avoid working with a fitted model without
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+ <a class="navbar-link" href="../index.html">mkin</a>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span>
+ </span>
+ </div>
+
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Functions and data</a>
+</li>
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+
+ <span class="caret"></span>
+ </a>
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+ <li>
+ <a href="../articles/mkin.html">Introduction to mkin</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+ </li>
+ <li>
+ <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+ </li>
+ <li>
+ <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+ </li>
+ <li>
+ <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
+ </li>
+ </ul>
+</li>
+<li>
+ <a href="../news/index.html">News</a>
+</li>
+ </ul>
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+
+ </header>
+
+<div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Extract model parameters from mkinfit models</h1>
+
+ <div class="hidden name"><code>parms.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>This function always returns degradation model parameters as well as error
+model parameters, in order to avoid working with a fitted model without
+considering the error structure that was assumed for the fit.</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>parms</span>(<span class='no'>object</span>, <span class='no'>...</span>)
+
+<span class='co'># S3 method for mkinfit</span>
+<span class='fu'>parms</span>(<span class='no'>object</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre>
+
+ <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+ <table class="ref-arguments">
+ <colgroup><col class="name" /><col class="desc" /></colgroup>
+ <tr>
+ <th>object</th>
+ <td><p>A fitted model object</p></td>
+ </tr>
+ <tr>
+ <th>...</th>
+ <td><p>Not used</p></td>
+ </tr>
+ <tr>
+ <th>transformed</th>
+ <td><p>Should the parameters be returned
+as used internally during the optimisation?</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>A numeric vector of fitted model parameters</p>
+
+ </div>
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+ <li><a href="#arguments">Arguments</a></li>
+ <li><a href="#value">Value</a></li>
+ </ul>
+
+ </div>
+</div>
+
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+</div>
+
+ </footer>
+ </div>
+
+
+
+
+ </body>
+</html>
+
+
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index b62b9a44..9e3363ba 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -55,6 +55,9 @@
<loc>https://pkgdown.jrwb.de/mkin/reference/add_err.html</loc>
</url>
<url>
+ <loc>https://pkgdown.jrwb.de/mkin/reference/confint.mkinfit.html</loc>
+ </url>
+ <url>
<loc>https://pkgdown.jrwb.de/mkin/reference/endpoints.html</loc>
</url>
<url>
@@ -118,6 +121,9 @@
<loc>https://pkgdown.jrwb.de/mkin/reference/nafta.html</loc>
</url>
<url>
+ <loc>https://pkgdown.jrwb.de/mkin/reference/parms.html</loc>
+ </url>
+ <url>
<loc>https://pkgdown.jrwb.de/mkin/reference/plot.mkinfit.html</loc>
</url>
<url>
diff --git a/man/confint.mkinfit.Rd b/man/confint.mkinfit.Rd
index 94f55d14..943904b9 100644
--- a/man/confint.mkinfit.Rd
+++ b/man/confint.mkinfit.Rd
@@ -37,6 +37,8 @@ the student t distribution or assume normal distribution for
the parameter estimate}
\item{quiet}{Should we suppress messages?}
+
+\item{\dots}{Not used}
}
\value{
A matrix with columns giving lower and upper confidence limits for
@@ -48,7 +50,9 @@ Confidence intervals for parameters of mkinfit objects
\examples{
f <- mkinfit("SFO", FOCUS_2006_C, quiet = TRUE)
confint(f, method = "quadratic")
-confint(f, method = "profile")
+\dontrun{
+ confint(f, method = "profile")
+}
}
\references{
Pawitan Y (2013) In all likelihood - Statistical modelling and
diff --git a/man/parms.Rd b/man/parms.Rd
index 6de52557..73cb23cd 100644
--- a/man/parms.Rd
+++ b/man/parms.Rd
@@ -12,10 +12,10 @@ parms(object, ...)
\arguments{
\item{object}{A fitted model object}
+\item{\dots}{Not used}
+
\item{transformed}{Should the parameters be returned
as used internally during the optimisation?}
-
-\item{complete}{Unused argument for compatibility with the generic coef function from base R}
}
\value{
A numeric vector of fitted model parameters
diff --git a/test.log b/test.log
index 7e3f1c4e..bc3b3c8c 100644
--- a/test.log
+++ b/test.log
@@ -2,30 +2,30 @@ Loading mkin
Testing mkin
✔ | OK F W S | Context
✔ | 2 | Export dataset for reading into CAKE
-✔ | 3 | Confidence intervals and p-values
-✔ | 10 | Error model fitting [37.1 s]
+✔ | 9 | Confidence intervals and p-values [2.3 s]
+✔ | 10 | Error model fitting [37.2 s]
✔ | 5 | Calculation of FOCUS chi2 error levels [3.5 s]
-✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.5 s]
+✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.3 s]
✔ | 6 | Test fitting the decline of metabolites from their maximum [0.9 s]
✔ | 1 | Fitting the logistic model [0.9 s]
✔ | 1 | Test dataset class mkinds used in gmkin
✔ | 12 | Special cases of mkinfit calls [2.7 s]
✔ | 9 | mkinmod model generation and printing [0.2 s]
✔ | 3 | Model predictions with mkinpredict [0.3 s]
-✔ | 16 | Evaluations according to 2015 NAFTA guidance [4.1 s]
-✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2 s]
+✔ | 16 | Evaluations according to 2015 NAFTA guidance [4.0 s]
+✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.3 s]
✔ | 3 | Summary
✔ | 11 | Plotting [0.6 s]
✔ | 3 | AIC calculation
-✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.3 s]
+✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.2 s]
✔ | 4 | Fitting the SFORB model [1.7 s]
✔ | 1 | Summaries of old mkinfit objects
-✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.2 s]
+✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.0 s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 70.2 s
+Duration: 72.1 s
-OK: 113
+OK: 119
Failed: 0
Warnings: 0
Skipped: 0
diff --git a/tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg b/tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg
index 920f70cd..2b4930ba 100644
--- a/tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg
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@@ -223,7 +223,7 @@
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diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index e3d2a303..22a4b125 100644
--- a/tests/testthat/FOCUS_2006_D.csf
+++ b/tests/testthat/FOCUS_2006_D.csf
@@ -5,7 +5,7 @@ Description:
MeasurementUnits: % AR
TimeUnits: days
Comments: Created using mkin::CAKE_export
-Date: 2019-10-25
+Date: 2019-10-26
Optimiser: IRLS
[Data]

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