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authorJohannes Ranke <jranke@uni-bremen.de>2020-11-09 09:24:34 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2020-11-09 09:24:34 +0100
commit82c8b014c537c0634615c3c007aa4a3fa672307f (patch)
treefbf193fb210a72954d7c925b35992a44222cbdc2
parenta3e058f8bceca903e7952e66abb4744f66115921 (diff)
Doc improvements
-rw-r--r--R/summary.saem.mmkin.R1
-rw-r--r--docs/dev/pkgdown.yml2
-rw-r--r--docs/dev/reference/summary.saem.mmkin.html11
-rw-r--r--man/summary.saem.mmkin.Rd1
4 files changed, 9 insertions, 6 deletions
diff --git a/R/summary.saem.mmkin.R b/R/summary.saem.mmkin.R
index a8917144..75fdb045 100644
--- a/R/summary.saem.mmkin.R
+++ b/R/summary.saem.mmkin.R
@@ -25,6 +25,7 @@
#' \item{data}{The data}
#' \item{confint_trans}{Transformed parameters as used in the optimisation, with confidence intervals}
#' \item{confint_back}{Backtransformed parameters, with confidence intervals if available}
+#' \item{confint_errmod}{Error model parameters with confidence intervals}
#' \item{ff}{The estimated formation fractions derived from the fitted
#' model.}
#' \item{distimes}{The DT50 and DT90 values for each observed variable.}
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index 0b40dd02..a8bb6144 100644
--- a/docs/dev/pkgdown.yml
+++ b/docs/dev/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
web_only/NAFTA_examples: NAFTA_examples.html
web_only/benchmarks: benchmarks.html
web_only/compiled_models: compiled_models.html
-last_built: 2020-11-09T08:10Z
+last_built: 2020-11-09T08:23Z
urls:
reference: https://pkgdown.jrwb.de/mkin/reference
article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html
index 75ede09f..e718806e 100644
--- a/docs/dev/reference/summary.saem.mmkin.html
+++ b/docs/dev/reference/summary.saem.mmkin.html
@@ -208,6 +208,7 @@ produced</p></dd>
<dt>data</dt><dd><p>The data</p></dd>
<dt>confint_trans</dt><dd><p>Transformed parameters as used in the optimisation, with confidence intervals</p></dd>
<dt>confint_back</dt><dd><p>Backtransformed parameters, with confidence intervals if available</p></dd>
+<dt>confint_errmod</dt><dd><p>Error model parameters with confidence intervals</p></dd>
<dt>ff</dt><dd><p>The estimated formation fractions derived from the fitted
model.</p></dd>
<dt>distimes</dt><dd><p>The DT50 and DT90 values for each observed variable.</p></dd>
@@ -258,15 +259,15 @@ saemix authors for the parts inherited from saemix.</p>
<span class='va'>f_mmkin_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds_syn_dfop_sfo</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span>, cores <span class='op'>=</span> <span class='fl'>5</span><span class='op'>)</span>
<span class='va'>f_saem_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f_mmkin_dfop_sfo</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Mon Nov 9 09:11:04 2020"
+#&gt; [1] "Mon Nov 9 09:24:08 2020"
#&gt; ....
#&gt; Minimisation finished
-#&gt; [1] "Mon Nov 9 09:11:16 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
+#&gt; [1] "Mon Nov 9 09:24:21 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
</div><div class='output co'>#&gt; saemix version used for fitting: 3.1.9000
#&gt; mkin version used for pre-fitting: 0.9.50.4
#&gt; R version used for fitting: 4.0.3
-#&gt; Date of fit: Mon Nov 9 09:11:17 2020
-#&gt; Date of summary: Mon Nov 9 09:11:17 2020
+#&gt; Date of fit: Mon Nov 9 09:24:22 2020
+#&gt; Date of summary: Mon Nov 9 09:24:22 2020
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -281,7 +282,7 @@ saemix authors for the parts inherited from saemix.</p>
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted in 13.497 s using 300, 100 iterations
+#&gt; Fitted in 13.457 s using 300, 100 iterations
#&gt;
#&gt; Variance model: Two-component variance function
#&gt;
diff --git a/man/summary.saem.mmkin.Rd b/man/summary.saem.mmkin.Rd
index 828691e6..f3e3fde3 100644
--- a/man/summary.saem.mmkin.Rd
+++ b/man/summary.saem.mmkin.Rd
@@ -37,6 +37,7 @@ produced}
\item{data}{The data}
\item{confint_trans}{Transformed parameters as used in the optimisation, with confidence intervals}
\item{confint_back}{Backtransformed parameters, with confidence intervals if available}
+\item{confint_errmod}{Error model parameters with confidence intervals}
\item{ff}{The estimated formation fractions derived from the fitted
model.}
\item{distimes}{The DT50 and DT90 values for each observed variable.}

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