Fix checks and tests

Static documentation rebuilt by pkgdown
author: Johannes Ranke <jranke@uni-bremen.de> 2019-10-26 22:52:53 +0200
committer: Johannes Ranke <jranke@uni-bremen.de> 2019-10-26 22:52:53 +0200
commit: 6e5630a0df7e857697ff2ce4730a5f7f45b67377 (patch)
tree: 1d65d0b5c0540b1ae1ab160ed3c6cd1c50a4446f
parent: cb03bf1fb1e6326f06029969663f3399af96b05d (diff)
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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+
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+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
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+      <a href="../articles/mkin.html">Introduction to mkin</a>
+    </li>
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+      <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>
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+      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+    </li>
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+      <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
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+
+      
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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>
+
+
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+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
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+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
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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 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
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+        <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>
+    <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>
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+</li>
+      </ul>
+      <ul class="nav navbar-nav navbar-right">
+        
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+    </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
+++ b/tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg
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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]
author	Johannes Ranke <jranke@uni-bremen.de>	2019-10-26 22:52:53 +0200
committer	Johannes Ranke <jranke@uni-bremen.de>	2019-10-26 22:52:53 +0200
commit	6e5630a0df7e857697ff2ce4730a5f7f45b67377 (patch)
tree	1d65d0b5c0540b1ae1ab160ed3c6cd1c50a4446f
parent	cb03bf1fb1e6326f06029969663f3399af96b05d (diff)