Add a parms method for mmkin objects

7 files changed, 143 insertions, 8 deletions

diff --git a/NAMESPACE b/NAMESPACE
index ef1ddca5..72a60dea 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -16,6 +16,7 @@ S3method(mkinpredict,mkinmod)
 S3method(nlme,mmkin)
 S3method(nobs,mkinfit)
 S3method(parms,mkinfit)
+S3method(parms,mmkin)
 S3method(plot,mkinfit)
 S3method(plot,mmkin)
 S3method(plot,nafta)
diff --git a/NEWS.md b/NEWS.md
index 3867320e..37cb5072 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,7 @@
+# mkin 0.9.50.3 (unreleased)
+
+- 'parms': Add a method for mmkin objects
+
 # mkin 0.9.50.2 (2020-05-12)
 
 - Increase tolerance for a platform specific test results on the Solaris test machine on CRAN
diff --git a/R/parms.mkinfit.R b/R/parms.mkinfit.R
index 281d06de..f173ef51 100644
--- a/R/parms.mkinfit.R
+++ b/R/parms.mkinfit.R
@@ -4,9 +4,13 @@
 #' model parameters, in order to avoid working with a fitted model without
 #' considering the error structure that was assumed for the fit.
 #'
-#' @param object A fitted model object
+#' @param object A fitted model object. Methods are implemented for
+#'  [mkinfit()] objects and for [mmkin()] objects.
 #' @param \dots Not used
-#' @return A numeric vector of fitted model parameters
+#' @return For mkinfit objects, a numeric vector of fitted model parameters.
+#'  For mmkin row objects, a matrix with the parameters with a
+#'  row for each dataset. If the mmkin object has more than one row, a list of
+#'  such matrices is returned.
 #' @export
 parms <- function(object, ...)
 {
@@ -26,3 +30,29 @@ parms.mkinfit <- function(object, transformed = FALSE, ...)
   if (transformed) object$par
   else c(object$bparms.optim, object$errparms)
 }
+
+#' @rdname parms
+#' @examples
+#' ds <- lapply(experimental_data_for_UBA_2019[6:10],
+#'  function(x) subset(x$data[c("name", "time", "value")]))
+#' names(ds) <- paste("Dataset", 6:10)
+#' fits <- mmkin(c("SFO", "FOMC", "DFOP"), ds, quiet = TRUE)
+#' parms(fits["SFO", ])
+#' parms(fits[, 2])
+#' parms(fits)
+#' parms(fits, transformed = TRUE)
+#' @export
+parms.mmkin <- function(object, transformed = FALSE, ...)
+{
+  if (nrow(object) == 1) {
+    res <- sapply(object, parms, transformed = transformed, ...)
+    colnames(res) <- colnames(object)
+  } else {
+    res <- list()
+    for (i in 1:nrow(object)) {
+      res[[i]] <- parms(object[i, ], transformed = transformed, ...)
+    }
+    names(res) <- rownames(object)
+  }
+  return(res)
+}
diff --git a/docs/news/index.html b/docs/news/index.html
index 20f532ab..c3713a94 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -141,6 +141,14 @@
       <small>Source: <a href='http://github.com/jranke/mkin/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
+    <div id="mkin-0-9-50-3-unreleased" class="section level1">
+<h1 class="page-header" data-toc-text="0.9.50.3">
+<a href="#mkin-0-9-50-3-unreleased" class="anchor"></a>mkin 0.9.50.3 (unreleased)<small> Unreleased </small>
+</h1>
+<ul>
+<li>‘parms’: Add a method for mmkin objects</li>
+</ul>
+</div>
     <div id="mkin-0-9-50-2-2020-05-12" class="section level1">
 <h1 class="page-header" data-toc-text="0.9.50.2">
 <a href="#mkin-0-9-50-2-2020-05-12" class="anchor"></a>mkin 0.9.50.2 (2020-05-12)<small> 2020-05-12 </small>
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index eb3f0f6e..77d13196 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
   NAFTA_examples: web_only/NAFTA_examples.html
   benchmarks: web_only/benchmarks.html
   compiled_models: web_only/compiled_models.html
-last_built: 2020-05-14T15:07Z
+last_built: 2020-05-14T16:37Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/reference/parms.html b/docs/reference/parms.html
index f62b3898..cb705d2c 100644
--- a/docs/reference/parms.html
+++ b/docs/reference/parms.html
@@ -111,6 +111,9 @@ considering the error structure that was assumed for the fit." />
     <li>
       <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
+    <li>
+      <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
+    </li>
   </ul>
 </li>
 <li>
@@ -151,6 +154,9 @@ considering the error structure that was assumed for the fit.</p>
     <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>)
+
+<span class='co'># S3 method for mmkin</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>
@@ -158,7 +164,8 @@ considering the error structure that was assumed for the fit.</p>
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>object</th>
-      <td><p>A fitted model object</p></td>
+      <td><p>A fitted model object. Methods are implemented for
+<code><a href='mkinfit.html'>mkinfit()</a></code> objects and for <code><a href='mmkin.html'>mmkin()</a></code> objects.</p></td>
     </tr>
     <tr>
       <th>...</th>
@@ -173,7 +180,10 @@ as used internally during the optimisation?</p></td>
 
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>A numeric vector of fitted model parameters</p>
+    <p>For mkinfit objects, a numeric vector of fitted model parameters.
+For mmkin row objects, a matrix with the parameters with a
+row for each dataset. If the mmkin object has more than one row, a list of
+such matrices is returned.</p>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='no'>fit</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>)</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: 2388.077
@@ -190,7 +200,74 @@ as used internally during the optimisation?</p></td>
 #&gt; Sum of squared residuals at call 25: 196.5334
 #&gt; Negative log-likelihood at call 31: 26.64668</div><div class='output co'>#&gt; <span class='message'>Optimisation successfully terminated.</span></div><div class='input'><span class='fu'>parms</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt;      parent_0 k_parent_sink         sigma 
 #&gt;    82.4921598     0.3060633     4.6730124 </div><div class='input'><span class='fu'>parms</span>(<span class='no'>fit</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt;          parent_0 log_k_parent_sink             sigma 
-#&gt;         82.492160         -1.183963          4.673012 </div></pre>
+#&gt;         82.492160         -1.183963          4.673012 </div><div class='input'><span class='no'>ds</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>6</span>:<span class='fl'>10</span>],
+ <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>x</span>$<span class='no'>data</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span>)]))
+<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span>(<span class='no'>ds</span>) <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span>(<span class='st'>"Dataset"</span>, <span class='fl'>6</span>:<span class='fl'>10</span>)
+<span class='no'>fits</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span>), <span class='no'>ds</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'>parms</span>(<span class='no'>fits</span>[<span class='st'>"SFO"</span>, ])</div><div class='output co'>#&gt;                 Dataset 6    Dataset 7  Dataset 8  Dataset 9  Dataset 10
+#&gt; parent_0      88.52275400 82.666781678 86.8547308 91.7779306 82.14809450
+#&gt; k_parent_sink  0.05794659  0.009647805  0.2102974  0.1232258  0.00720421
+#&gt; sigma          5.15274487  7.040168584  3.6769645  6.4669234  6.50457673</div><div class='input'><span class='fu'>parms</span>(<span class='no'>fits</span>[, <span class='fl'>2</span>])</div><div class='output co'>#&gt; $SFO
+#&gt;                  Dataset 7
+#&gt; parent_0      82.666781678
+#&gt; k_parent_sink  0.009647805
+#&gt; sigma          7.040168584
+#&gt; 
+#&gt; $FOMC
+#&gt;           Dataset 7
+#&gt; parent_0 92.6837649
+#&gt; alpha     0.4967832
+#&gt; beta     14.1451255
+#&gt; sigma     1.9167519
+#&gt; 
+#&gt; $DFOP
+#&gt;             Dataset 7
+#&gt; parent_0 91.058971503
+#&gt; k1        0.044946770
+#&gt; k2        0.002868336
+#&gt; g         0.526942415
+#&gt; sigma     2.221302196
+#&gt; </div><div class='input'><span class='fu'>parms</span>(<span class='no'>fits</span>)</div><div class='output co'>#&gt; $SFO
+#&gt;                 Dataset 6    Dataset 7  Dataset 8  Dataset 9  Dataset 10
+#&gt; parent_0      88.52275400 82.666781678 86.8547308 91.7779306 82.14809450
+#&gt; k_parent_sink  0.05794659  0.009647805  0.2102974  0.1232258  0.00720421
+#&gt; sigma          5.15274487  7.040168584  3.6769645  6.4669234  6.50457673
+#&gt; 
+#&gt; $FOMC
+#&gt;          Dataset 6  Dataset 7 Dataset 8 Dataset 9 Dataset 10
+#&gt; parent_0 95.558575 92.6837649 90.719787 98.383939 94.8481458
+#&gt; alpha     1.338667  0.4967832  1.639099  1.074460  0.2805272
+#&gt; beta     13.033315 14.1451255  5.007077  4.397126  6.9052224
+#&gt; sigma     1.847671  1.9167519  1.066063  3.146056  1.6222778
+#&gt; 
+#&gt; $DFOP
+#&gt;            Dataset 6    Dataset 7   Dataset 8   Dataset 9   Dataset 10
+#&gt; parent_0 96.55213663 91.058971503 90.34509469 98.14858850 94.311323409
+#&gt; k1        0.21954589  0.044946770  0.41232289  0.31697588  0.080663853
+#&gt; k2        0.02957934  0.002868336  0.07581767  0.03260384  0.003425417
+#&gt; g         0.44845068  0.526942415  0.66091965  0.65322767  0.342652880
+#&gt; sigma     1.35690468  2.221302196  1.34169076  2.87159846  1.942067831
+#&gt; </div><div class='input'><span class='fu'>parms</span>(<span class='no'>fits</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; $SFO
+#&gt;                   Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10
+#&gt; parent_0          88.522754 82.666782 86.854731 91.777931  82.148094
+#&gt; log_k_parent_sink -2.848234 -4.641025 -1.559232 -2.093737  -4.933090
+#&gt; sigma              5.152745  7.040169  3.676964  6.466923   6.504577
+#&gt; 
+#&gt; $FOMC
+#&gt;            Dataset 6  Dataset 7  Dataset 8   Dataset 9 Dataset 10
+#&gt; parent_0  95.5585751 92.6837649 90.7197870 98.38393897  94.848146
+#&gt; log_alpha  0.2916741 -0.6996015  0.4941466  0.07181816  -1.271085
+#&gt; log_beta   2.5675088  2.6493701  1.6108523  1.48095106   1.932278
+#&gt; sigma      1.8476712  1.9167519  1.0660627  3.14605557   1.622278
+#&gt; 
+#&gt; $DFOP
+#&gt;           Dataset 6   Dataset 7  Dataset 8  Dataset 9 Dataset 10
+#&gt; parent_0 96.5521366 91.05897150 90.3450947 98.1485885  94.311323
+#&gt; log_k1   -1.5161940 -3.10227638 -0.8859485 -1.1489296  -2.517465
+#&gt; log_k2   -3.5206791 -5.85402317 -2.5794240 -3.4233253  -5.676532
+#&gt; g_ilr    -0.1463234  0.07627854  0.4719196  0.4477805  -0.460676
+#&gt; sigma     1.3569047  2.22130220  1.3416908  2.8715985   1.942068
+#&gt; </div></pre>
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   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
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diff --git a/man/parms.Rd b/man/parms.Rd
index 5752de0b..87e23781 100644
--- a/man/parms.Rd
+++ b/man/parms.Rd
@@ -3,14 +3,18 @@
 \name{parms}
 \alias{parms}
 \alias{parms.mkinfit}
+\alias{parms.mmkin}
 \title{Extract model parameters from mkinfit models}
 \usage{
 parms(object, ...)
 
 \method{parms}{mkinfit}(object, transformed = FALSE, ...)
+
+\method{parms}{mmkin}(object, transformed = FALSE, ...)
 }
 \arguments{
-\item{object}{A fitted model object}
+\item{object}{A fitted model object. Methods are implemented for
+\code{\link[=mkinfit]{mkinfit()}} objects and for \code{\link[=mmkin]{mmkin()}} objects.}
 
 \item{\dots}{Not used}
 
@@ -18,7 +22,10 @@ parms(object, ...)
 as used internally during the optimisation?}
 }
 \value{
-A numeric vector of fitted model parameters
+For mkinfit objects, a numeric vector of fitted model parameters.
+For mmkin row objects, a matrix with the parameters with a
+row for each dataset. If the mmkin object has more than one row, a list of
+such matrices is returned.
 }
 \description{
 This function always returns degradation model parameters as well as error
@@ -29,4 +36,12 @@ considering the error structure that was assumed for the fit.
 fit <- mkinfit("SFO", FOCUS_2006_C)
 parms(fit)
 parms(fit, transformed = TRUE)
+ds <- lapply(experimental_data_for_UBA_2019[6:10],
+ function(x) subset(x$data[c("name", "time", "value")]))
+names(ds) <- paste("Dataset", 6:10)
+fits <- mmkin(c("SFO", "FOMC", "DFOP"), ds, quiet = TRUE)
+parms(fits["SFO", ])
+parms(fits[, 2])
+parms(fits)
+parms(fits, transformed = TRUE)
 }