diff options
38 files changed, 715 insertions, 668 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index 03346bad..23e65ba1 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data Version: 0.9.48.1 -Date: 2019-02-27 +Date: 2019-03-04 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de", comment = c(ORCID = "0000-0003-4371-6538")), @@ -20,7 +20,6 @@ Description: Calculation routines based on the FOCUS Kinetics Report (2006, Imports: stats, graphics, methods, FME, deSolve, R6, minpack.lm, rootSolve, inline, parallel, plyr Suggests: knitr, rbenchmark, tikzDevice, testthat, rmarkdown, covr, vdiffr -Remotes: r-lib/vdiffr License: GPL LazyLoad: yes LazyData: yes diff --git a/GNUmakefile b/GNUmakefile index 20a9c723..a900ce5c 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -32,6 +32,11 @@ pkgfiles = \ all: build $(TGZ): $(pkgfiles) vignettes + $(RM) -r vignettes/*_cache + $(RM) -r vignettes/*_files + $(RM) -r vignettes/*.R + $(RM) -r vignettes/web_only/*.R + $(RM) Rplots.pdf "$(RBIN)/R" CMD build . 2>&1 | tee build.log $(TGZVNR): $(pkgfiles) @@ -66,6 +71,8 @@ clean: test: install "$(RBIN)/Rscript" -e 'devtools::test()' 2>&1 | tee test.log +testcheck: test check + README.html: README.md "$(RBIN)/Rscript" -e "rmarkdown::render('README.md', output_format = 'html_document', output_options = list(mathjax = NULL))" @@ -1,4 +1,4 @@ -# mkin 0.9.48.1 (2019-02-22) +# mkin 0.9.48.1 (2019-03-04) - Add the function 'logLik.mkinfit' which makes it possible to calculate an AIC for mkinfit objects @@ -64,16 +64,16 @@ plot.nafta <- function(x, legend = FALSE, main = "auto", ...) { plot(x$mmkin, ..., legend = legend, main = main) } -print.nafta <- function(x, quiet = TRUE, ...) { +print.nafta <- function(x, quiet = TRUE, digits = 3, ...) { cat("Sums of squares:\n") print(x$S) cat("\nCritical sum of squares for checking the SFO model:\n") print(x$S_c) cat("\nParameters:\n") - print(x$parameters) + print(x$parameters, digits = digits) t_rep <- .evaluate_nafta_results(x$S, x$S_c, x$distimes, quiet = quiet) cat("\nDTx values:\n") - print(signif((x$distimes), 3)) + print(x$distimes, digits = digits) cat("\nRepresentative half-life:\n") print(t_rep) } @@ -7,11 +7,8 @@ * checking extension type ... Package * this is package ‘mkin’ version ‘0.9.48.1’ * package encoding: UTF-8 -* checking CRAN incoming feasibility ... NOTE +* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’ - -Unknown, possibly mis-spelled, fields in DESCRIPTION: - ‘Remotes’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK @@ -58,10 +55,7 @@ Unknown, possibly mis-spelled, fields in DESCRIPTION: * checking data for ASCII and uncompressed saves ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK -* checking examples ... NOTE -Examples with CPU or elapsed time > 5s - user system elapsed -logLik.mkinfit 6.66 0.075 6.737 +* checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... SKIPPED * checking for unstated dependencies in vignettes ... OK @@ -70,9 +64,5 @@ logLik.mkinfit 6.66 0.075 6.737 * checking PDF version of manual ... OK * DONE -Status: 2 NOTEs -See - ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’ -for details. - +Status: OK diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index e01fd46d..fabb567a 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">2019-02-26</h4> + <h4 class="date">2019-03-04</h4> <div class="hidden name"><code>FOCUS_D.Rmd</code></div> @@ -98,8 +98,8 @@ <p>This is just a very simple vignette showing how to fit a degradation model for a parent compound with one transformation product using <code>mkin</code>. After loading the library we look at the data. We have observed concentrations in the column named <code>value</code> at the times specified in column <code>time</code> for the two observed variables named <code>parent</code> and <code>m1</code>.</p> -<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(mkin, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(FOCUS_<span class="dv">2006</span>_D)</a></code></pre></div> +<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(mkin, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb1-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(FOCUS_<span class="dv">2006</span>_D)</a></code></pre></div> <pre><code>## name time value ## 1 parent 0 99.46 ## 2 parent 0 102.04 @@ -147,27 +147,27 @@ ## 44 m1 120 33.31</code></pre> <p>Next we specify the degradation model: The parent compound degrades with simple first-order kinetics (SFO) to one metabolite named m1, which also degrades with SFO kinetics.</p> <p>The call to mkinmod returns a degradation model. The differential equations represented in R code can be found in the character vector <code>$diffs</code> of the <code>mkinmod</code> object. If a C compiler (gcc) is installed and functional, the differential equation model will be compiled from auto-generated C code.</p> -<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1">SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>), <span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>), <span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(SFO_SFO<span class="op">$</span>diffs)</a></code></pre></div> +<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(SFO_SFO<span class="op">$</span>diffs)</a></code></pre></div> <pre><code>## parent ## "d_parent = - k_parent_sink * parent - k_parent_m1 * parent" ## m1 ## "d_m1 = + k_parent_m1 * parent - k_m1_sink * m1"</code></pre> <p>We do the fitting without progress report (<code>quiet = TRUE</code>).</p> -<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">fit <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">fit <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> <p>A plot of the fit including a residual plot for both observed variables is obtained using the <code>plot_sep</code> method for <code>mkinfit</code> objects, which shows separate graphs for all compounds and their residuals.</p> -<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(fit, <span class="dt">lpos =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(fit, <span class="dt">lpos =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>))</a></code></pre></div> <p><img src="FOCUS_D_files/figure-html/plot-1.png" width="768"></p> <p>Confidence intervals for the parameter estimates are obtained using the <code>mkinparplot</code> function.</p> -<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1"><span class="kw"><a href="../reference/mkinparplot.html">mkinparplot</a></span>(fit)</a></code></pre></div> +<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1"><span class="kw"><a href="../reference/mkinparplot.html">mkinparplot</a></span>(fit)</a></code></pre></div> <p><img src="FOCUS_D_files/figure-html/plot_2-1.png" width="768"></p> <p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code> objects.</p> -<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(fit)</a></code></pre></div> +<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" 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: 0.9.48.1 ## R version used for fitting: 3.5.2 -## Date of fit: Tue Feb 26 21:09:15 2019 -## Date of summary: Tue Feb 26 21:09:15 2019 +## Date of fit: Mon Mar 4 10:09:33 2019 +## Date of summary: Mon Mar 4 10:09:33 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -175,7 +175,7 @@ ## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 0.712 s +## Fitted with method Port using 153 model solutions performed in 0.687 s ## ## Weighting: none ## diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index aeded526..7157f973 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">2019-02-26</h4> + <h4 class="date">2019-03-04</h4> <div class="hidden name"><code>FOCUS_L.Rmd</code></div> @@ -101,28 +101,28 @@ <h1 class="hasAnchor"> <a href="#laboratory-data-l1" class="anchor"></a>Laboratory Data L1</h1> <p>The following code defines example dataset L1 from the FOCUS kinetics report, p. 284:</p> -<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(<span class="st">"mkin"</span>, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb1-2" data-line-number="2">FOCUS_<span class="dv">2006</span>_L1 =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(</a> -<a class="sourceLine" id="cb1-3" data-line-number="3"> <span class="dt">t =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="dv">1</span>, <span class="dv">2</span>, <span class="dv">3</span>, <span class="dv">5</span>, <span class="dv">7</span>, <span class="dv">14</span>, <span class="dv">21</span>, <span class="dv">30</span>), <span class="dt">each =</span> <span class="dv">2</span>),</a> -<a class="sourceLine" id="cb1-4" data-line-number="4"> <span class="dt">parent =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="fl">88.3</span>, <span class="fl">91.4</span>, <span class="fl">85.6</span>, <span class="fl">84.5</span>, <span class="fl">78.9</span>, <span class="fl">77.6</span>,</a> -<a class="sourceLine" id="cb1-5" data-line-number="5"> <span class="fl">72.0</span>, <span class="fl">71.9</span>, <span class="fl">50.3</span>, <span class="fl">59.4</span>, <span class="fl">47.0</span>, <span class="fl">45.1</span>,</a> -<a class="sourceLine" id="cb1-6" data-line-number="6"> <span class="fl">27.7</span>, <span class="fl">27.3</span>, <span class="fl">10.0</span>, <span class="fl">10.4</span>, <span class="fl">2.9</span>, <span class="fl">4.0</span>))</a> -<a class="sourceLine" id="cb1-7" data-line-number="7">FOCUS_<span class="dv">2006</span>_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_<span class="dv">2006</span>_L1)</a></code></pre></div> +<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(<span class="st">"mkin"</span>, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb1-2" title="2">FOCUS_<span class="dv">2006</span>_L1 =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(</a> +<a class="sourceLine" id="cb1-3" title="3"> <span class="dt">t =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="dv">1</span>, <span class="dv">2</span>, <span class="dv">3</span>, <span class="dv">5</span>, <span class="dv">7</span>, <span class="dv">14</span>, <span class="dv">21</span>, <span class="dv">30</span>), <span class="dt">each =</span> <span class="dv">2</span>),</a> +<a class="sourceLine" id="cb1-4" title="4"> <span class="dt">parent =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="fl">88.3</span>, <span class="fl">91.4</span>, <span class="fl">85.6</span>, <span class="fl">84.5</span>, <span class="fl">78.9</span>, <span class="fl">77.6</span>,</a> +<a class="sourceLine" id="cb1-5" title="5"> <span class="fl">72.0</span>, <span class="fl">71.9</span>, <span class="fl">50.3</span>, <span class="fl">59.4</span>, <span class="fl">47.0</span>, <span class="fl">45.1</span>,</a> +<a class="sourceLine" id="cb1-6" title="6"> <span class="fl">27.7</span>, <span class="fl">27.3</span>, <span class="fl">10.0</span>, <span class="fl">10.4</span>, <span class="fl">2.9</span>, <span class="fl">4.0</span>))</a> +<a class="sourceLine" id="cb1-7" title="7">FOCUS_<span class="dv">2006</span>_L1_mkin <-<span class="st"> </span><span class="kw"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_<span class="dv">2006</span>_L1)</a></code></pre></div> <p>Here we use the assumptions of simple first order (SFO), the case of declining rate constant over time (FOMC) and the case of two different phases of the kinetics (DFOP). For a more detailed discussion of the models, please see the FOCUS kinetics report.</p> <p>Since mkin version 0.9-32 (July 2014), we can use shorthand notation like <code>"SFO"</code> for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.</p> -<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">m.L1.SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"SFO"</span>, FOCUS_<span class="dv">2006</span>_L1_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.SFO)</a></code></pre></div> +<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1">m.L1.SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"SFO"</span>, FOCUS_<span class="dv">2006</span>_L1_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<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: 0.9.48.1 ## R version used for fitting: 3.5.2 -## Date of fit: Tue Feb 26 21:09:17 2019 -## Date of summary: Tue Feb 26 21:09:17 2019 +## Date of fit: Mon Mar 4 10:09:35 2019 +## Date of summary: Mon Mar 4 10:09:35 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.096 s +## Fitted with method Port using 37 model solutions performed in 0.102 s ## ## Weighting: none ## @@ -193,27 +193,27 @@ ## 30 parent 2.9 5.251 -2.3513 ## 30 parent 4.0 5.251 -1.2513</code></pre> <p>A plot of the fit is obtained with the plot function for mkinfit objects.</p> -<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(m.L1.SFO, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L1 - SFO"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(m.L1.SFO, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L1 - SFO"</span>)</a></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-4-1.png" width="576"></p> <p>The residual plot can be easily obtained by</p> -<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw"><a href="../reference/mkinresplot.html">mkinresplot</a></span>(m.L1.SFO, <span class="dt">ylab =</span> <span class="st">"Observed"</span>, <span class="dt">xlab =</span> <span class="st">"Time"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="../reference/mkinresplot.html">mkinresplot</a></span>(m.L1.SFO, <span class="dt">ylab =</span> <span class="st">"Observed"</span>, <span class="dt">xlab =</span> <span class="st">"Time"</span>)</a></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-5-1.png" width="576"></p> <p>For comparison, the FOMC model is fitted as well, and the <span class="math inline">\(\chi^2\)</span> error level is checked.</p> -<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" data-line-number="1">m.L1.FOMC <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"FOMC"</span>, FOCUS_<span class="dv">2006</span>_L1_mkin, <span class="dt">quiet=</span><span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb6-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(m.L1.FOMC, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L1 - FOMC"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1">m.L1.FOMC <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"FOMC"</span>, FOCUS_<span class="dv">2006</span>_L1_mkin, <span class="dt">quiet=</span><span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb6-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(m.L1.FOMC, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>, <span class="dt">main =</span> <span class="st">"FOCUS L1 - FOMC"</span>)</a></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-6-1.png" width="576"></p> -<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> +<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.48.1 ## R version used for fitting: 3.5.2 -## Date of fit: Tue Feb 26 21:09:19 2019 -## Date of summary: Tue Feb 26 21:09:19 2019 +## Date of fit: Mon Mar 4 10:09:36 2019 +## Date of summary: Mon Mar 4 10:09:36 2019 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 611 model solutions performed in 1.539 s +## Fitted with method Port using 611 model solutions performed in 1.508 s ## ## Weighting: none ## @@ -271,19 +271,19 @@ <h1 class="hasAnchor"> <a href="#laboratory-data-l2" class="anchor"></a>Laboratory Data L2</h1> <p>The following code defines example dataset L2 from the FOCUS kinetics report, p. 287:</p> -<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1">FOCUS_<span class="dv">2006</span>_L2 =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(</a> -<a class="sourceLine" id="cb9-2" data-line-number="2"> <span class="dt">t =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="dv">1</span>, <span class="dv">3</span>, <span class="dv">7</span>, <span class="dv">14</span>, <span class="dv">28</span>), <span class="dt">each =</span> <span class="dv">2</span>),</a> -<a class="sourceLine" id="cb9-3" data-line-number="3"> <span class="dt">parent =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="fl">96.1</span>, <span class="fl">91.8</span>, <span class="fl">41.4</span>, <span class="fl">38.7</span>,</a> -<a class="sourceLine" id="cb9-4" data-line-number="4"> <span class="fl">19.3</span>, <span class="fl">22.3</span>, <span class="fl">4.6</span>, <span class="fl">4.6</span>,</a> -<a class="sourceLine" id="cb9-5" data-line-number="5"> <span class="fl">2.6</span>, <span class="fl">1.2</span>, <span class="fl">0.3</span>, <span class="fl">0.6</span>))</a> -<a class="sourceLine" id="cb9-6" data-line-number="6">FOCUS_<span class="dv">2006</span>_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_<span class="dv">2006</span>_L2)</a></code></pre></div> +<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1">FOCUS_<span class="dv">2006</span>_L2 =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(</a> +<a class="sourceLine" id="cb9-2" title="2"> <span class="dt">t =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/rep">rep</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="dv">1</span>, <span class="dv">3</span>, <span class="dv">7</span>, <span class="dv">14</span>, <span class="dv">28</span>), <span class="dt">each =</span> <span class="dv">2</span>),</a> +<a class="sourceLine" id="cb9-3" title="3"> <span class="dt">parent =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="fl">96.1</span>, <span class="fl">91.8</span>, <span class="fl">41.4</span>, <span class="fl">38.7</span>,</a> +<a class="sourceLine" id="cb9-4" title="4"> <span class="fl">19.3</span>, <span class="fl">22.3</span>, <span class="fl">4.6</span>, <span class="fl">4.6</span>,</a> +<a class="sourceLine" id="cb9-5" title="5"> <span class="fl">2.6</span>, <span class="fl">1.2</span>, <span class="fl">0.3</span>, <span class="fl">0.6</span>))</a> +<a class="sourceLine" id="cb9-6" title="6">FOCUS_<span class="dv">2006</span>_L2_mkin <-<span class="st"> </span><span class="kw"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_<span class="dv">2006</span>_L2)</a></code></pre></div> <div id="sfo-fit-for-l2" class="section level2"> <h2 class="hasAnchor"> <a href="#sfo-fit-for-l2" class="anchor"></a>SFO fit for L2</h2> <p>Again, the SFO model is fitted and the result is plotted. The residual plot can be obtained simply by adding the argument <code>show_residuals</code> to the plot command.</p> -<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1">m.L2.SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"SFO"</span>, FOCUS_<span class="dv">2006</span>_L2_mkin, <span class="dt">quiet=</span><span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb10-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(m.L2.SFO, <span class="dt">show_residuals =</span> <span class="ot">TRUE</span>, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>,</a> -<a class="sourceLine" id="cb10-3" data-line-number="3"> <span class="dt">main =</span> <span class="st">"FOCUS L2 - SFO"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1">m.L2.SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"SFO"</span>, FOCUS_<span class="dv">2006</span>_L2_mkin, <span class="dt">quiet=</span><span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb10-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(m.L2.SFO, <span class="dt">show_residuals =</span> <span class="ot">TRUE</span>, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>,</a> +<a class="sourceLine" id="cb10-3" title="3"> <span class="dt">main =</span> <span class="st">"FOCUS L2 - SFO"</span>)</a></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-8-1.png" width="672"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 14% suggests that the model does not fit very well. This is also obvious from the plots of the fit, in which we have included the residual plot.</p> <p>In the FOCUS kinetics report, it is stated that there is no apparent systematic error observed from the residual plot up to the measured DT90 (approximately at day 5), and there is an underestimation beyond that point.</p> @@ -293,22 +293,22 @@ <h2 class="hasAnchor"> <a href="#fomc-fit-for-l2" class="anchor"></a>FOMC fit for L2</h2> <p>For comparison, the FOMC model is fitted as well, and the <span class="math inline">\(\chi^2\)</span> error level is checked.</p> -<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" data-line-number="1">m.L2.FOMC <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"FOMC"</span>, FOCUS_<span class="dv">2006</span>_L2_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb11-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(m.L2.FOMC, <span class="dt">show_residuals =</span> <span class="ot">TRUE</span>,</a> -<a class="sourceLine" id="cb11-3" data-line-number="3"> <span class="dt">main =</span> <span class="st">"FOCUS L2 - FOMC"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1">m.L2.FOMC <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"FOMC"</span>, FOCUS_<span class="dv">2006</span>_L2_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb11-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(m.L2.FOMC, <span class="dt">show_residuals =</span> <span class="ot">TRUE</span>,</a> +<a class="sourceLine" id="cb11-3" title="3"> <span class="dt">main =</span> <span class="st">"FOCUS L2 - FOMC"</span>)</a></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-9-1.png" width="672"></p> -<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="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> +<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" 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: 0.9.48.1 ## R version used for fitting: 3.5.2 -## Date of fit: Tue Feb 26 21:09:19 2019 -## Date of summary: Tue Feb 26 21:09:19 2019 +## Date of fit: Mon Mar 4 10:09:37 2019 +## Date of summary: Mon Mar 4 10:09:37 2019 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 81 model solutions performed in 0.199 s +## Fitted with method Port using 81 model solutions performed in 0.196 s ## ## Weighting: none ## @@ -364,15 +364,17 @@ <h2 class="hasAnchor"> <a href="#dfop-fit-for-l2" class="anchor"></a>DFOP fit for L2</h2> <p>Fitting the four parameter DFOP model further reduces the <span class="math inline">\(\chi^2\)</span> error level.</p> -<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" data-line-number="1">m.L2.DFOP <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"DFOP"</span>, FOCUS_<span class="dv">2006</span>_L2_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb14-2" data-line-number="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(m.L2.DFOP, <span class="dt">show_residuals =</span> <span class="ot">TRUE</span>, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>,</a> -<a class="sourceLine" id="cb14-3" data-line-number="3"> <span class="dt">main =</span> <span class="st">"FOCUS L2 - DFOP"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1">m.L2.DFOP <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="st">"DFOP"</span>, FOCUS_<span class="dv">2006</span>_L2_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb14-2" title="2"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(m.L2.DFOP, <span class="dt">show_residuals =</span> <span class="ot">TRUE</span>, <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>,</a> +<a class="sourceLine" id="cb14-3" title="3"> <span class="dt">main =</span> <span class="st">"FOCUS L2 - DFOP"</span>)</a></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-10-1.png" width="672"></p> -<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="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> +<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" 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>## Warning in summary.mkinfit(m.L2.DFOP, data = FALSE): Could not estimate +## covariance matrix; singular system.</code></pre> <pre><code>## mkin version used for fitting: 0.9.48.1 ## R version used for fitting: 3.5.2 -## Date of fit: Tue Feb 26 21:09:20 2019 -## Date of summary: Tue Feb 26 21:09:20 2019 +## Date of fit: Mon Mar 4 10:09:38 2019 +## Date of summary: Mon Mar 4 10:09:38 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -381,7 +383,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.844 s +## Fitted with method Port using 336 model solutions performed in 0.841 s ## ## Weighting: none ## @@ -409,10 +411,8 @@ ## log_k2 -1.0880 NA NA NA ## g_ilr -0.2821 NA NA NA ## -## Parameter correlation:</code></pre> -<pre><code>## Warning in print.summary.mkinfit(x): Could not estimate covariance matrix; singular system:</code></pre> -<pre><code>## Could not estimate covariance matrix; singular system: -## +## Parameter correlation: +## Could not estimate covariance matrix; singular system. ## Residual standard error: 1.732 on 8 degrees of freedom ## ## Backtransformed parameters: @@ -440,18 +440,18 @@ <h1 class="hasAnchor"> <a href="#laboratory-data-l3" class="anchor"></a>Laboratory Data L3</h1> <p>The following code defines example dataset L3 from the FOCUS kinetics report, p. 290.</p> -<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" data-line-number="1">FOCUS_<span class="dv">2006</span>_L3 =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(</a> -<a class="sourceLine" id="cb19-2" data-line-number="2"> <span class="dt">t =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="dv">3</span>, <span class="dv">7</span>, <span class="dv">14</span>, <span class="dv">30</span>, <span class="dv">60</span>, <span class="dv">91</span>, <span class="dv">120</span>),</a> -<a class="sourceLine" id="cb19-3" data-line-number="3"> <span class="dt">parent =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="fl">97.8</span>, <span class="dv">60</span>, <span class="dv">51</span>, <span class="dv">43</span>, <span class="dv">35</span>, <span class="dv">22</span>, <span class="dv">15</span>, <span class="dv">12</span>))</a> -<a class="sourceLine" id="cb19-4" data-line-number="4">FOCUS_<span class="dv">2006</span>_L3_mkin <-<span class="st"> </span><span class="kw"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_<span class="dv">2006</span>_L3)</a></code></pre></div> +<div class="sourceCode" id="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" title="1">FOCUS_<span class="dv">2006</span>_L3 =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(</a> +<a class="sourceLine" id="cb18-2" title="2"> <span class="dt">t =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="dv">3</span>, <span class="dv">7</span>, <span class="dv">14</span>, <span class="dv">30</span>, <span class="dv">60</span>, <span class="dv">91</span>, <span class="dv">120</span>),</a> +<a class="sourceLine" id="cb18-3" title="3"> <span class="dt">parent =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="fl">97.8</span>, <span class="dv">60</span>, <span class="dv">51</span>, <span class="dv">43</span>, <span class="dv">35</span>, <span class="dv">22</span>, <span class="dv">15</span>, <span class="dv">12</span>))</a> +<a class="sourceLine" id="cb18-4" title="4">FOCUS_<span class="dv">2006</span>_L3_mkin <-<span class="st"> </span><span class="kw"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_<span class="dv">2006</span>_L3)</a></code></pre></div> <div id="fit-multiple-models" class="section level2"> <h2 class="hasAnchor"> <a href="#fit-multiple-models" class="anchor"></a>Fit multiple models</h2> <p>As of mkin version 0.9-39 (June 2015), we can fit several models to one or more datasets in one call to the function <code>mmkin</code>. The datasets have to be passed in a list, in this case a named list holding only the L3 dataset prepared above.</p> -<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" data-line-number="1"><span class="co"># Only use one core here, not to offend the CRAN checks</span></a> -<a class="sourceLine" id="cb20-2" data-line-number="2">mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin.html">mmkin</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>), <span class="dt">cores =</span> <span class="dv">1</span>,</a> -<a class="sourceLine" id="cb20-3" data-line-number="3"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="st">"FOCUS L3"</span> =<span class="st"> </span>FOCUS_<span class="dv">2006</span>_L3_mkin), <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb20-4" data-line-number="4"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(mm.L3)</a></code></pre></div> +<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1"><span class="co"># Only use one core here, not to offend the CRAN checks</span></a> +<a class="sourceLine" id="cb19-2" title="2">mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin.html">mmkin</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span>), <span class="dt">cores =</span> <span class="dv">1</span>,</a> +<a class="sourceLine" id="cb19-3" title="3"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="st">"FOCUS L3"</span> =<span class="st"> </span>FOCUS_<span class="dv">2006</span>_L3_mkin), <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb19-4" title="4"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(mm.L3)</a></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-12-1.png" width="700"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 21% as well as the plot suggest that the SFO model does not fit very well. The FOMC model performs better, with an error level at which the <span class="math inline">\(\chi^2\)</span> test passes of 7%. Fitting the four parameter DFOP model further reduces the <span class="math inline">\(\chi^2\)</span> error level considerably.</p> </div> @@ -460,11 +460,11 @@ <a href="#accessing-mmkin-objects" class="anchor"></a>Accessing mmkin objects</h2> <p>The objects returned by mmkin are arranged like a matrix, with models as a row index and datasets as a column index.</p> <p>We can extract the summary and plot for <em>e.g.</em> the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.</p> -<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="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> +<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>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.48.1 ## R version used for fitting: 3.5.2 -## Date of fit: Tue Feb 26 21:09:21 2019 -## Date of summary: Tue Feb 26 21:09:22 2019 +## Date of fit: Mon Mar 4 10:09:39 2019 +## Date of summary: Mon Mar 4 10:09:39 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -473,7 +473,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 137 model solutions performed in 0.344 s +## Fitted with method Port using 137 model solutions performed in 0.343 s ## ## Weighting: none ## @@ -539,7 +539,7 @@ ## 60 parent 22.0 23.26 -1.25919 ## 91 parent 15.0 15.18 -0.18181 ## 120 parent 12.0 10.19 1.81395</code></pre> -<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]], <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]], <span class="dt">show_errmin =</span> <span class="ot">TRUE</span>)</a></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-13-1.png" width="700"></p> <p>Here, a look to the model plot, the confidence intervals of the parameters and the correlation matrix suggest that the parameter estimates are reliable, and the DFOP model can be used as the best-fit model based on the <span class="math inline">\(\chi^2\)</span> error level criterion for laboratory data L3.</p> <p>This is also an example where the standard t-test for the parameter <code>g_ilr</code> is misleading, as it tests for a significant difference from zero. In this case, zero appears to be the correct value for this parameter, and the confidence interval for the backtransformed parameter <code>g</code> is quite narrow.</p> @@ -549,23 +549,23 @@ <h1 class="hasAnchor"> <a href="#laboratory-data-l4" class="anchor"></a>Laboratory Data L4</h1> <p>The following code defines example dataset L4 from the FOCUS kinetics report, p. 293:</p> -<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" data-line-number="1">FOCUS_<span class="dv">2006</span>_L4 =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(</a> -<a class="sourceLine" id="cb24-2" data-line-number="2"> <span class="dt">t =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="dv">3</span>, <span class="dv">7</span>, <span class="dv">14</span>, <span class="dv">30</span>, <span class="dv">60</span>, <span class="dv">91</span>, <span class="dv">120</span>),</a> -<a class="sourceLine" id="cb24-3" data-line-number="3"> <span class="dt">parent =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="fl">96.6</span>, <span class="fl">96.3</span>, <span class="fl">94.3</span>, <span class="fl">88.8</span>, <span class="fl">74.9</span>, <span class="fl">59.9</span>, <span class="fl">53.5</span>, <span class="fl">49.0</span>))</a> -<a class="sourceLine" id="cb24-4" data-line-number="4">FOCUS_<span class="dv">2006</span>_L4_mkin <-<span class="st"> </span><span class="kw"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_<span class="dv">2006</span>_L4)</a></code></pre></div> +<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" title="1">FOCUS_<span class="dv">2006</span>_L4 =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(</a> +<a class="sourceLine" id="cb23-2" title="2"> <span class="dt">t =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="dv">3</span>, <span class="dv">7</span>, <span class="dv">14</span>, <span class="dv">30</span>, <span class="dv">60</span>, <span class="dv">91</span>, <span class="dv">120</span>),</a> +<a class="sourceLine" id="cb23-3" title="3"> <span class="dt">parent =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="fl">96.6</span>, <span class="fl">96.3</span>, <span class="fl">94.3</span>, <span class="fl">88.8</span>, <span class="fl">74.9</span>, <span class="fl">59.9</span>, <span class="fl">53.5</span>, <span class="fl">49.0</span>))</a> +<a class="sourceLine" id="cb23-4" title="4">FOCUS_<span class="dv">2006</span>_L4_mkin <-<span class="st"> </span><span class="kw"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_<span class="dv">2006</span>_L4)</a></code></pre></div> <p>Fits of the SFO and FOMC models, plots and summaries are produced below:</p> -<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1"><span class="co"># Only use one core here, not to offend the CRAN checks</span></a> -<a class="sourceLine" id="cb25-2" data-line-number="2">mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin.html">mmkin</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>), <span class="dt">cores =</span> <span class="dv">1</span>,</a> -<a class="sourceLine" id="cb25-3" data-line-number="3"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="st">"FOCUS L4"</span> =<span class="st"> </span>FOCUS_<span class="dv">2006</span>_L4_mkin),</a> -<a class="sourceLine" id="cb25-4" data-line-number="4"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb25-5" data-line-number="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(mm.L4)</a></code></pre></div> +<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" title="1"><span class="co"># Only use one core here, not to offend the CRAN checks</span></a> +<a class="sourceLine" id="cb24-2" title="2">mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin.html">mmkin</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"SFO"</span>, <span class="st">"FOMC"</span>), <span class="dt">cores =</span> <span class="dv">1</span>,</a> +<a class="sourceLine" id="cb24-3" title="3"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/list">list</a></span>(<span class="st">"FOCUS L4"</span> =<span class="st"> </span>FOCUS_<span class="dv">2006</span>_L4_mkin),</a> +<a class="sourceLine" id="cb24-4" title="4"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb24-5" title="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(mm.L4)</a></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-15-1.png" width="700"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the <span class="math inline">\(\chi^2\)</span> test passes is slightly lower for the FOMC model. However, the difference appears negligible.</p> -<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="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> +<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" 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: 0.9.48.1 ## R version used for fitting: 3.5.2 -## Date of fit: Tue Feb 26 21:09:22 2019 -## Date of summary: Tue Feb 26 21:09:22 2019 +## Date of fit: Mon Mar 4 10:09:40 2019 +## Date of summary: Mon Mar 4 10:09:40 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent @@ -621,18 +621,18 @@ ## Estimated disappearance times: ## DT50 DT90 ## parent 106 352</code></pre> -<div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" data-line-number="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> +<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" 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: 0.9.48.1 ## R version used for fitting: 3.5.2 -## Date of fit: Tue Feb 26 21:09:22 2019 -## Date of summary: Tue Feb 26 21:09:22 2019 +## Date of fit: Mon Mar 4 10:09:40 2019 +## Date of summary: Mon Mar 4 10:09:40 2019 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 66 model solutions performed in 0.163 s +## Fitted with method Port using 66 model solutions performed in 0.162 s ## ## Weighting: none ## diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index d5d5e3bf..93ad4b56 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">2019-02-26</h4> + <h4 class="date">2019-03-04</h4> <div class="hidden name"><code>mkin.Rmd</code></div> @@ -102,41 +102,41 @@ <h1 class="hasAnchor"> <a href="#abstract" class="anchor"></a>Abstract</h1> <p>In the regulatory evaluation of chemical substances like plant protection products (pesticides), biocides and other chemicals, degradation data play an important role. For the evaluation of pesticide degradation experiments, detailed guidance has been developed, based on nonlinear optimisation. The <code>R</code> add-on package <code>mkin</code> <span class="citation">(Ranke 2016)</span> implements fitting some of the models recommended in this guidance from within R and calculates some statistical measures for data series within one or more compartments, for parent and metabolites.</p> -<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(<span class="st">"mkin"</span>, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb1-2" data-line-number="2"><span class="co"># Define the kinetic model</span></a> -<a class="sourceLine" id="cb1-3" data-line-number="3">m_SFO_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M1"</span>),</a> -<a class="sourceLine" id="cb1-4" data-line-number="4"> <span class="dt">M1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M2"</span>),</a> -<a class="sourceLine" id="cb1-5" data-line-number="5"> <span class="dt">M2 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> -<a class="sourceLine" id="cb1-6" data-line-number="6"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb1-7" data-line-number="7"></a> -<a class="sourceLine" id="cb1-8" data-line-number="8"></a> -<a class="sourceLine" id="cb1-9" data-line-number="9"><span class="co"># Produce model predictions using some arbitrary parameters</span></a> -<a class="sourceLine" id="cb1-10" data-line-number="10">sampling_times =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="dv">1</span>, <span class="dv">3</span>, <span class="dv">7</span>, <span class="dv">14</span>, <span class="dv">28</span>, <span class="dv">60</span>, <span class="dv">90</span>, <span class="dv">120</span>)</a> -<a class="sourceLine" id="cb1-11" data-line-number="11">d_SFO_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinpredict.html">mkinpredict</a></span>(m_SFO_SFO_SFO,</a> -<a class="sourceLine" id="cb1-12" data-line-number="12"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dt">k_parent =</span> <span class="fl">0.03</span>,</a> -<a class="sourceLine" id="cb1-13" data-line-number="13"> <span class="dt">f_parent_to_M1 =</span> <span class="fl">0.5</span>, <span class="dt">k_M1 =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/Log">log</a></span>(<span class="dv">2</span>)<span class="op">/</span><span class="dv">100</span>,</a> -<a class="sourceLine" id="cb1-14" data-line-number="14"> <span class="dt">f_M1_to_M2 =</span> <span class="fl">0.9</span>, <span class="dt">k_M2 =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/Log">log</a></span>(<span class="dv">2</span>)<span class="op">/</span><span class="dv">50</span>),</a> -<a class="sourceLine" id="cb1-15" data-line-number="15"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dt">parent =</span> <span class="dv">100</span>, <span class="dt">M1 =</span> <span class="dv">0</span>, <span class="dt">M2 =</span> <span class="dv">0</span>),</a> -<a class="sourceLine" id="cb1-16" data-line-number="16"> sampling_times)</a> -<a class="sourceLine" id="cb1-17" data-line-number="17"></a> -<a class="sourceLine" id="cb1-18" data-line-number="18"><span class="co"># Generate a dataset by adding normally distributed errors with</span></a> -<a class="sourceLine" id="cb1-19" data-line-number="19"><span class="co"># standard deviation 3, for two replicates at each sampling time</span></a> -<a class="sourceLine" id="cb1-20" data-line-number="20">d_SFO_SFO_SFO_err <-<span class="st"> </span><span class="kw"><a href="../reference/add_err.html">add_err</a></span>(d_SFO_SFO_SFO, <span class="dt">reps =</span> <span class="dv">2</span>,</a> -<a class="sourceLine" id="cb1-21" data-line-number="21"> <span class="dt">sdfunc =</span> <span class="cf">function</span>(x) <span class="dv">3</span>,</a> -<a class="sourceLine" id="cb1-22" data-line-number="22"> <span class="dt">n =</span> <span class="dv">1</span>, <span class="dt">seed =</span> <span class="dv">123456789</span> )</a> -<a class="sourceLine" id="cb1-23" data-line-number="23"></a> -<a class="sourceLine" id="cb1-24" data-line-number="24"><span class="co"># Fit the model to the dataset</span></a> -<a class="sourceLine" id="cb1-25" data-line-number="25">f_SFO_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(m_SFO_SFO_SFO, d_SFO_SFO_SFO_err[[<span class="dv">1</span>]], <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb1-26" data-line-number="26"></a> -<a class="sourceLine" id="cb1-27" data-line-number="27"><span class="co"># Plot the results separately for parent and metabolites</span></a> -<a class="sourceLine" id="cb1-28" data-line-number="28"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(f_SFO_SFO_SFO, <span class="dt">lpos =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>, <span class="st">"bottomright"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(<span class="st">"mkin"</span>, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb1-2" title="2"><span class="co"># Define the kinetic model</span></a> +<a class="sourceLine" id="cb1-3" title="3">m_SFO_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M1"</span>),</a> +<a class="sourceLine" id="cb1-4" title="4"> <span class="dt">M1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"M2"</span>),</a> +<a class="sourceLine" id="cb1-5" title="5"> <span class="dt">M2 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> +<a class="sourceLine" id="cb1-6" title="6"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb1-7" title="7"></a> +<a class="sourceLine" id="cb1-8" title="8"></a> +<a class="sourceLine" id="cb1-9" title="9"><span class="co"># Produce model predictions using some arbitrary parameters</span></a> +<a class="sourceLine" id="cb1-10" title="10">sampling_times =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="dv">1</span>, <span class="dv">3</span>, <span class="dv">7</span>, <span class="dv">14</span>, <span class="dv">28</span>, <span class="dv">60</span>, <span class="dv">90</span>, <span class="dv">120</span>)</a> +<a class="sourceLine" id="cb1-11" title="11">d_SFO_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinpredict.html">mkinpredict</a></span>(m_SFO_SFO_SFO,</a> +<a class="sourceLine" id="cb1-12" title="12"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dt">k_parent =</span> <span class="fl">0.03</span>,</a> +<a class="sourceLine" id="cb1-13" title="13"> <span class="dt">f_parent_to_M1 =</span> <span class="fl">0.5</span>, <span class="dt">k_M1 =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/Log">log</a></span>(<span class="dv">2</span>)<span class="op">/</span><span class="dv">100</span>,</a> +<a class="sourceLine" id="cb1-14" title="14"> <span class="dt">f_M1_to_M2 =</span> <span class="fl">0.9</span>, <span class="dt">k_M2 =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/Log">log</a></span>(<span class="dv">2</span>)<span class="op">/</span><span class="dv">50</span>),</a> +<a class="sourceLine" id="cb1-15" title="15"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dt">parent =</span> <span class="dv">100</span>, <span class="dt">M1 =</span> <span class="dv">0</span>, <span class="dt">M2 =</span> <span class="dv">0</span>),</a> +<a class="sourceLine" id="cb1-16" title="16"> sampling_times)</a> +<a class="sourceLine" id="cb1-17" title="17"></a> +<a class="sourceLine" id="cb1-18" title="18"><span class="co"># Generate a dataset by adding normally distributed errors with</span></a> +<a class="sourceLine" id="cb1-19" title="19"><span class="co"># standard deviation 3, for two replicates at each sampling time</span></a> +<a class="sourceLine" id="cb1-20" title="20">d_SFO_SFO_SFO_err <-<span class="st"> </span><span class="kw"><a href="../reference/add_err.html">add_err</a></span>(d_SFO_SFO_SFO, <span class="dt">reps =</span> <span class="dv">2</span>,</a> +<a class="sourceLine" id="cb1-21" title="21"> <span class="dt">sdfunc =</span> <span class="cf">function</span>(x) <span class="dv">3</span>,</a> +<a class="sourceLine" id="cb1-22" title="22"> <span class="dt">n =</span> <span class="dv">1</span>, <span class="dt">seed =</span> <span class="dv">123456789</span> )</a> +<a class="sourceLine" id="cb1-23" title="23"></a> +<a class="sourceLine" id="cb1-24" title="24"><span class="co"># Fit the model to the dataset</span></a> +<a class="sourceLine" id="cb1-25" title="25">f_SFO_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(m_SFO_SFO_SFO, d_SFO_SFO_SFO_err[[<span class="dv">1</span>]], <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb1-26" title="26"></a> +<a class="sourceLine" id="cb1-27" title="27"><span class="co"># Plot the results separately for parent and metabolites</span></a> +<a class="sourceLine" id="cb1-28" title="28"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(f_SFO_SFO_SFO, <span class="dt">lpos =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>, <span class="st">"bottomright"</span>))</a></code></pre></div> <p><img src="mkin_files/figure-html/unnamed-chunk-2-1.png" width="768"></p> </div> <div id="background" class="section level1"> <h1 class="hasAnchor"> <a href="#background" class="anchor"></a>Background</h1> <p>Many approaches are possible regarding the evaluation of chemical degradation data.</p> -<p>The now deprecated <code>kinfit</code> package <span class="citation">(Ranke 2015)</span> in <code>R</code> <span class="citation">(R Development Core Team 2016)</span> implements the approach recommended in the kinetics report provided by the FOrum for Co-ordination of pesticide fate models and their USe <span class="citation">(FOCUS Work Group on Degradation Kinetics 2006; 2014)</span> for simple data series for one parent compound in one compartment.</p> +<p>The now deprecated <code>kinfit</code> package <span class="citation">(Ranke 2015)</span> in <code>R</code> <span class="citation">(R Development Core Team 2016)</span> implements the approach recommended in the kinetics report provided by the FOrum for Co-ordination of pesticide fate models and their USe <span class="citation">(FOCUS Work Group on Degradation Kinetics 2006, 2014)</span> for simple data series for one parent compound in one compartment.</p> <p>The <code>mkin</code> package <span class="citation">(Ranke 2016)</span> extends this approach to data series with transformation products, commonly termed metabolites, and to more than one compartment. It is also possible to include back reactions, so equilibrium reactions and equilibrium partitioning can be specified, although this oftentimes leads to an overparameterisation of the model.</p> <p>When the first <code>mkin</code> code was published in 2010, the most commonly used tools for fitting more complex kinetic degradation models to experimental data were KinGUI <span class="citation">(Schäfer et al. 2007)</span>, a MATLAB based tool with a graphical user interface that was specifically tailored to the task and included some output as proposed by the FOCUS Kinetics Workgroup, and ModelMaker, a general purpose compartment based tool providing infrastructure for fitting dynamic simulation models based on differential equations to data.</p> <p>The code was first uploaded to the BerliOS platform. When this was taken down, the version control history was imported into the R-Forge site, where the code is still mirrored today (see <em>e.g.</em> <a href="http://cgit.jrwb.de/mkin/commit/?id=30cbb4092f6d2d3beff5800603374a0d009ad770">the initial commit on 11 May 2010</a>).</p> @@ -194,9 +194,6 @@ <div id="ref-FOCUSkinetics2014"> <p>———. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="uri">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p> </div> -<div id="ref-rcore2016"> -<p>R Development Core Team. 2016. <em>R: A Language and Environment for Statistical Computing</em>. Vienna, Austria: R Foundation for Statistical Computing. <a href="https://www.R-project.org" class="uri">https://www.R-project.org</a>.</p> -</div> <div id="ref-pkg:kinfit"> <p>Ranke, J. 2015. <em>‘Kinfit‘: Routines for Fitting Simple Kinetic Models to Chemical Degradation Data</em>. <a href="https://CRAN.R-project.org/package=kinfit" class="uri">https://CRAN.R-project.org/package=kinfit</a>.</p> </div> @@ -209,6 +206,9 @@ <div id="ref-ranke2015"> <p>———. 2015. “To T-Test or Not to T-Test, That Is the Question.” In <em>XV Symposium on Pesticide Chemistry 2-4 September 2015</em>. Piacenza. <a href="http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf" class="uri">http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf</a>.</p> </div> +<div id="ref-rcore2016"> +<p>R Development Core Team. 2016. <em><span class="sans-serif">R</span>: A Language and Environment for Statistical Computing</em>. Vienna, Austria: R Foundation for Statistical Computing. <a href="https://www.R-project.org" class="uri">https://www.R-project.org</a>.</p> +</div> <div id="ref-schaefer2007"> <p>Schäfer, D., B. Mikolasch, P. Rainbird, and B. Harvey. 2007. “KinGUI: A New Kinetic Software Tool for Evaluations According to FOCUS Degradation Kinetics.” In <em>Proceedings of the Xiii Symposium Pesticide Chemistry</em>, edited by Del Re A. A. M., Capri E., Fragoulis G., and Trevisan M., 916–23. Piacenza.</p> </div> diff --git a/docs/articles/twa.html b/docs/articles/twa.html index af8dbd4e..f58814e3 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">2019-02-26</h4> + <h4 class="date">2019-03-04</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 1926662a..79e39e55 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">2019-02-26</h4> + <h4 class="date">2019-03-04</h4> <div class="hidden name"><code>FOCUS_Z.Rmd</code></div> @@ -102,33 +102,35 @@ <h1 class="hasAnchor"> <a href="#the-data" class="anchor"></a>The data</h1> <p>The following code defines the example dataset from Appendix 7 to the FOCUS kinetics report <span class="citation">(FOCUS Work Group on Degradation Kinetics 2014, 354)</span>.</p> -<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(mkin, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb1-2" data-line-number="2">LOD =<span class="st"> </span><span class="fl">0.5</span></a> -<a class="sourceLine" id="cb1-3" data-line-number="3">FOCUS_<span class="dv">2006</span>_Z =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(</a> -<a class="sourceLine" id="cb1-4" data-line-number="4"> <span class="dt">t =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="fl">0.04</span>, <span class="fl">0.125</span>, <span class="fl">0.29</span>, <span class="fl">0.54</span>, <span class="dv">1</span>, <span class="dv">2</span>, <span class="dv">3</span>, <span class="dv">4</span>, <span class="dv">7</span>, <span class="dv">10</span>, <span class="dv">14</span>, <span class="dv">21</span>,</a> -<a class="sourceLine" id="cb1-5" data-line-number="5"> <span class="dv">42</span>, <span class="dv">61</span>, <span class="dv">96</span>, <span class="dv">124</span>),</a> -<a class="sourceLine" id="cb1-6" data-line-number="6"> <span class="dt">Z0 =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">100</span>, <span class="fl">81.7</span>, <span class="fl">70.4</span>, <span class="fl">51.1</span>, <span class="fl">41.2</span>, <span class="fl">6.6</span>, <span class="fl">4.6</span>, <span class="fl">3.9</span>, <span class="fl">4.6</span>, <span class="fl">4.3</span>, <span class="fl">6.8</span>,</a> -<a class="sourceLine" id="cb1-7" data-line-number="7"> <span class="fl">2.9</span>, <span class="fl">3.5</span>, <span class="fl">5.3</span>, <span class="fl">4.4</span>, <span class="fl">1.2</span>, <span class="fl">0.7</span>),</a> -<a class="sourceLine" id="cb1-8" data-line-number="8"> <span class="dt">Z1 =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="fl">18.3</span>, <span class="fl">29.6</span>, <span class="fl">46.3</span>, <span class="fl">55.1</span>, <span class="fl">65.7</span>, <span class="fl">39.1</span>, <span class="dv">36</span>, <span class="fl">15.3</span>, <span class="fl">5.6</span>, <span class="fl">1.1</span>,</a> -<a class="sourceLine" id="cb1-9" data-line-number="9"> <span class="fl">1.6</span>, <span class="fl">0.6</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>),</a> -<a class="sourceLine" id="cb1-10" data-line-number="10"> <span class="dt">Z2 =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="ot">NA</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="fl">2.6</span>, <span class="fl">3.8</span>, <span class="fl">15.3</span>, <span class="fl">37.2</span>, <span class="fl">31.7</span>, <span class="fl">35.6</span>, <span class="fl">14.5</span>,</a> -<a class="sourceLine" id="cb1-11" data-line-number="11"> <span class="fl">0.8</span>, <span class="fl">2.1</span>, <span class="fl">1.9</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>),</a> -<a class="sourceLine" id="cb1-12" data-line-number="12"> <span class="dt">Z3 =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="fl">9.2</span>, <span class="fl">13.1</span>, <span class="fl">22.3</span>, <span class="fl">28.4</span>, <span class="fl">32.5</span>,</a> -<a class="sourceLine" id="cb1-13" data-line-number="13"> <span class="fl">25.2</span>, <span class="fl">17.2</span>, <span class="fl">4.8</span>, <span class="fl">4.5</span>, <span class="fl">2.8</span>, <span class="fl">4.4</span>))</a> -<a class="sourceLine" id="cb1-14" data-line-number="14"></a> -<a class="sourceLine" id="cb1-15" data-line-number="15">FOCUS_<span class="dv">2006</span>_Z_mkin <-<span class="st"> </span><span class="kw"><a href="../../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_<span class="dv">2006</span>_Z)</a></code></pre></div> +<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(mkin, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb1-2" title="2">LOD =<span class="st"> </span><span class="fl">0.5</span></a> +<a class="sourceLine" id="cb1-3" title="3">FOCUS_<span class="dv">2006</span>_Z =<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/data.frame">data.frame</a></span>(</a> +<a class="sourceLine" id="cb1-4" title="4"> <span class="dt">t =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="fl">0.04</span>, <span class="fl">0.125</span>, <span class="fl">0.29</span>, <span class="fl">0.54</span>, <span class="dv">1</span>, <span class="dv">2</span>, <span class="dv">3</span>, <span class="dv">4</span>, <span class="dv">7</span>, <span class="dv">10</span>, <span class="dv">14</span>, <span class="dv">21</span>,</a> +<a class="sourceLine" id="cb1-5" title="5"> <span class="dv">42</span>, <span class="dv">61</span>, <span class="dv">96</span>, <span class="dv">124</span>),</a> +<a class="sourceLine" id="cb1-6" title="6"> <span class="dt">Z0 =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">100</span>, <span class="fl">81.7</span>, <span class="fl">70.4</span>, <span class="fl">51.1</span>, <span class="fl">41.2</span>, <span class="fl">6.6</span>, <span class="fl">4.6</span>, <span class="fl">3.9</span>, <span class="fl">4.6</span>, <span class="fl">4.3</span>, <span class="fl">6.8</span>,</a> +<a class="sourceLine" id="cb1-7" title="7"> <span class="fl">2.9</span>, <span class="fl">3.5</span>, <span class="fl">5.3</span>, <span class="fl">4.4</span>, <span class="fl">1.2</span>, <span class="fl">0.7</span>),</a> +<a class="sourceLine" id="cb1-8" title="8"> <span class="dt">Z1 =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="fl">18.3</span>, <span class="fl">29.6</span>, <span class="fl">46.3</span>, <span class="fl">55.1</span>, <span class="fl">65.7</span>, <span class="fl">39.1</span>, <span class="dv">36</span>, <span class="fl">15.3</span>, <span class="fl">5.6</span>, <span class="fl">1.1</span>,</a> +<a class="sourceLine" id="cb1-9" title="9"> <span class="fl">1.6</span>, <span class="fl">0.6</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>),</a> +<a class="sourceLine" id="cb1-10" title="10"> <span class="dt">Z2 =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="ot">NA</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="fl">2.6</span>, <span class="fl">3.8</span>, <span class="fl">15.3</span>, <span class="fl">37.2</span>, <span class="fl">31.7</span>, <span class="fl">35.6</span>, <span class="fl">14.5</span>,</a> +<a class="sourceLine" id="cb1-11" title="11"> <span class="fl">0.8</span>, <span class="fl">2.1</span>, <span class="fl">1.9</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>),</a> +<a class="sourceLine" id="cb1-12" title="12"> <span class="dt">Z3 =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">0</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="fl">9.2</span>, <span class="fl">13.1</span>, <span class="fl">22.3</span>, <span class="fl">28.4</span>, <span class="fl">32.5</span>,</a> +<a class="sourceLine" id="cb1-13" title="13"> <span class="fl">25.2</span>, <span class="fl">17.2</span>, <span class="fl">4.8</span>, <span class="fl">4.5</span>, <span class="fl">2.8</span>, <span class="fl">4.4</span>))</a> +<a class="sourceLine" id="cb1-14" title="14"></a> +<a class="sourceLine" id="cb1-15" title="15">FOCUS_<span class="dv">2006</span>_Z_mkin <-<span class="st"> </span><span class="kw"><a href="../../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_<span class="dv">2006</span>_Z)</a></code></pre></div> </div> <div id="parent-and-one-metabolite" class="section level1"> <h1 class="hasAnchor"> <a href="#parent-and-one-metabolite" class="anchor"></a>Parent and one metabolite</h1> <p>The next step is to set up the models used for the kinetic analysis. As the simultaneous fit of parent and the first metabolite is usually straightforward, Step 1 (SFO for parent only) is skipped here. We start with the model 2a, with formation and decline of metabolite Z1 and the pathway from parent directly to sink included (default in mkin).</p> -<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">Z<span class="fl">.2</span>a <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>),</a> -<a class="sourceLine" id="cb2-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1">Z<span class="fl">.2</span>a <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>),</a> +<a class="sourceLine" id="cb2-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">m.Z<span class="fl">.2</span>a <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.2</span>a, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb4-2" data-line-number="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.2</span>a)</a></code></pre></div> +<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">m.Z<span class="fl">.2</span>a <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.2</span>a, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb4-2" title="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.2</span>a)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png" width="700"></p> -<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.2</span>a, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> +<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.2</span>a, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(m.Z.2a, data = FALSE): Could not estimate +## covariance matrix; singular system.</code></pre> <pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper ## Z0_0 9.7015e+01 3.553140 2.7304e+01 1.6793e-21 NA NA ## k_Z0_sink 1.2790e-11 0.226895 5.6368e-11 5.0000e-01 NA NA @@ -136,14 +138,16 @@ ## k_Z1_sink 4.8212e-01 0.065854 7.3212e+00 3.5520e-08 NA NA</code></pre> <p>As obvious from the parameter summary (the component of the summary), the kinetic rate constant from parent compound Z to sink is very small and the t-test for this parameter suggests that it is not significantly different from zero. This suggests, in agreement with the analysis in the FOCUS kinetics report, to simplify the model by removing the pathway to sink.</p> <p>A similar result can be obtained when formation fractions are used in the model formulation:</p> -<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">Z<span class="fl">.2</span>a.ff <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>),</a> -<a class="sourceLine" id="cb7-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> -<a class="sourceLine" id="cb7-3" data-line-number="3"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">Z<span class="fl">.2</span>a.ff <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>),</a> +<a class="sourceLine" id="cb8-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> +<a class="sourceLine" id="cb8-3" title="3"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1">m.Z<span class="fl">.2</span>a.ff <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.2</span>a.ff, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb9-2" data-line-number="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.2</span>a.ff)</a></code></pre></div> +<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1">m.Z<span class="fl">.2</span>a.ff <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.2</span>a.ff, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb10-2" title="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.2</span>a.ff)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png" width="700"></p> -<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.2</span>a.ff, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> +<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.2</span>a.ff, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(m.Z.2a.ff, data = FALSE): Could not estimate +## covariance matrix; singular system.</code></pre> <pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper ## Z0_0 97.01488 3.553145 27.3039 1.6793e-21 NA NA ## k_Z0 2.23601 0.216849 10.3114 3.6623e-11 NA NA @@ -152,13 +156,13 @@ <p>Here, the ilr transformed formation fraction fitted in the model takes a very large value, and the backtransformed formation fraction from parent Z to Z1 is practically unity. Here, the covariance matrix used for the calculation of confidence intervals is not returned as the model is overparameterised.</p> <p>A simplified model is obtained by removing the pathway to the sink. </p> <p>In the following, we use the parameterisation with formation fractions in order to be able to compare with the results in the FOCUS guidance, and as it makes it easier to use parameters obtained in a previous fit when adding a further metabolite.</p> -<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1">Z<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb12-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>), <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" title="1">Z<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb14-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>), <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" data-line-number="1">m.Z<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.3</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb14-2" data-line-number="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.3</span>)</a></code></pre></div> +<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" title="1">m.Z<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.3</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb16-2" title="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.3</span>)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png" width="700"></p> -<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.3</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> +<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z<span class="fl">.3</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> <pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper ## Z0_0 97.01488 2.681772 36.176 2.3636e-25 91.52152 102.508 ## k_Z0 2.23601 0.146861 15.225 2.2464e-15 1.95453 2.558 @@ -169,28 +173,28 @@ <h1 class="hasAnchor"> <a href="#metabolites-z2-and-z3" class="anchor"></a>Metabolites Z2 and Z3</h1> <p>As suggested in the FOCUS report, the pathway to sink was removed for metabolite Z1 as well in the next step. While this step appears questionable on the basis of the above results, it is followed here for the purpose of comparison. Also, in the FOCUS report, it is assumed that there is additional empirical evidence that Z1 quickly and exclusively hydrolyses to Z2.</p> -<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" data-line-number="1">Z<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb17-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb17-3" data-line-number="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>), <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1">Z<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb19-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb19-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>), <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" data-line-number="1">m.Z<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb19-2" data-line-number="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.5</span>)</a></code></pre></div> +<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" title="1">m.Z<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb21-2" title="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.5</span>)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png" width="700"></p> <p>Finally, metabolite Z3 is added to the model. We use the optimised differential equation parameter values from the previous fit in order to accelerate the optimization.</p> -<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" data-line-number="1">Z.FOCUS <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb20-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb20-3" data-line-number="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> -<a class="sourceLine" id="cb20-4" data-line-number="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> -<a class="sourceLine" id="cb20-5" data-line-number="5"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1">Z.FOCUS <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb22-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb22-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> +<a class="sourceLine" id="cb22-4" title="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> +<a class="sourceLine" id="cb22-5" title="5"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1">m.Z.FOCUS <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.FOCUS, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> -<a class="sourceLine" id="cb22-2" data-line-number="2"> <span class="dt">parms.ini =</span> m.Z<span class="fl">.5</span><span class="op">$</span>bparms.ode,</a> -<a class="sourceLine" id="cb22-3" data-line-number="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> +<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" title="1">m.Z.FOCUS <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.FOCUS, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> +<a class="sourceLine" id="cb24-2" title="2"> <span class="dt">parms.ini =</span> m.Z<span class="fl">.5</span><span class="op">$</span>bparms.ode,</a> +<a class="sourceLine" id="cb24-3" title="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> <pre><code>## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : Optimisation by method Port did not converge: ## false convergence (8)</code></pre> -<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" data-line-number="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.FOCUS)</a></code></pre></div> +<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.FOCUS)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png" width="700"></p> -<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z.FOCUS, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> +<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z.FOCUS, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> <pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper ## Z0_0 96.837112 2.058861 47.0343 5.5877e-44 92.703779 100.970445 ## k_Z0 2.215368 0.118098 18.7587 7.6563e-25 1.990525 2.465609 @@ -198,7 +202,7 @@ ## k_Z2 0.451617 0.044214 10.2144 3.1133e-14 0.371034 0.549702 ## k_Z3 0.058693 0.014296 4.1056 7.2924e-05 0.035994 0.095705 ## f_Z2_to_Z3 0.471516 0.057057 8.2639 2.8156e-11 0.360381 0.585548</code></pre> -<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" data-line-number="1"><span class="kw"><a href="../../reference/endpoints.html">endpoints</a></span>(m.Z.FOCUS)</a></code></pre></div> +<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="../../reference/endpoints.html">endpoints</a></span>(m.Z.FOCUS)</a></code></pre></div> <pre><code>## $ff ## Z2_Z3 Z2_sink ## 0.47152 0.52848 @@ -219,61 +223,63 @@ <a href="#using-the-sforb-model" class="anchor"></a>Using the SFORB model</h1> <p>As the FOCUS report states, there is a certain tailing of the time course of metabolite Z3. Also, the time course of the parent compound is not fitted very well using the SFO model, as residues at a certain low level remain.</p> <p>Therefore, an additional model is offered here, using the single first-order reversible binding (SFORB) model for metabolite Z3. As expected, the <span class="math inline">\(\chi^2\)</span> error level is lower for metabolite Z3 using this model and the graphical fit for Z3 is improved. However, the covariance matrix is not returned.</p> -<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" data-line-number="1">Z.mkin<span class="fl">.1</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb29-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb29-3" data-line-number="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> -<a class="sourceLine" id="cb29-4" data-line-number="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" title="1">Z.mkin<span class="fl">.1</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb31-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb31-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> +<a class="sourceLine" id="cb31-4" title="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" data-line-number="1">m.Z.mkin<span class="fl">.1</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.1</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb31-2" data-line-number="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.1</span>)</a></code></pre></div> +<div class="sourceCode" id="cb33"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb33-1" title="1">m.Z.mkin<span class="fl">.1</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.1</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb33-2" title="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.1</span>)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png" width="700"></p> -<div class="sourceCode" id="cb32"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb32-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z.mkin<span class="fl">.1</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>cov.unscaled</a></code></pre></div> +<div class="sourceCode" id="cb34"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb34-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/summary">summary</a></span>(m.Z.mkin<span class="fl">.1</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>cov.unscaled</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(m.Z.mkin.1, data = FALSE): Could not estimate +## covariance matrix; singular system.</code></pre> <pre><code>## NULL</code></pre> <p>Therefore, a further stepwise model building is performed starting from the stage of parent and two metabolites, starting from the assumption that the model fit for the parent compound can be improved by using the SFORB model.</p> -<div class="sourceCode" id="cb34"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb34-1" data-line-number="1">Z.mkin<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb34-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb34-3" data-line-number="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb37"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb37-1" title="1">Z.mkin<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb37-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb37-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb36"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb36-1" data-line-number="1">m.Z.mkin<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.3</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb36-2" data-line-number="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.3</span>)</a></code></pre></div> +<div class="sourceCode" id="cb39"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb39-1" title="1">m.Z.mkin<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.3</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb39-2" title="2"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.3</span>)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png" width="700"></p> <p>This results in a much better representation of the behaviour of the parent compound Z0.</p> <p>Finally, Z3 is added as well. These models appear overparameterised (no covariance matrix returned) if the sink for Z1 is left in the models.</p> -<div class="sourceCode" id="cb37"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb37-1" data-line-number="1">Z.mkin<span class="fl">.4</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb37-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb37-3" data-line-number="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> -<a class="sourceLine" id="cb37-4" data-line-number="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb40"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb40-1" title="1">Z.mkin<span class="fl">.4</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb40-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb40-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> +<a class="sourceLine" id="cb40-4" title="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb39"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb39-1" data-line-number="1">m.Z.mkin<span class="fl">.4</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.4</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> -<a class="sourceLine" id="cb39-2" data-line-number="2"> <span class="dt">parms.ini =</span> m.Z.mkin<span class="fl">.3</span><span class="op">$</span>bparms.ode,</a> -<a class="sourceLine" id="cb39-3" data-line-number="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb39-4" data-line-number="4"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.4</span>)</a></code></pre></div> +<div class="sourceCode" id="cb42"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb42-1" title="1">m.Z.mkin<span class="fl">.4</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.4</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> +<a class="sourceLine" id="cb42-2" title="2"> <span class="dt">parms.ini =</span> m.Z.mkin<span class="fl">.3</span><span class="op">$</span>bparms.ode,</a> +<a class="sourceLine" id="cb42-3" title="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb42-4" title="4"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.4</span>)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png" width="700"></p> <p>The error level of the fit, but especially of metabolite Z3, can be improved if the SFORB model is chosen for this metabolite, as this model is capable of representing the tailing of the metabolite decline phase.</p> -<div class="sourceCode" id="cb40"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb40-1" data-line-number="1">Z.mkin<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb40-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb40-3" data-line-number="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> -<a class="sourceLine" id="cb40-4" data-line-number="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb43"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb43-1" title="1">Z.mkin<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb43-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> +<a class="sourceLine" id="cb43-3" title="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> +<a class="sourceLine" id="cb43-4" title="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb42"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb42-1" data-line-number="1">m.Z.mkin<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> -<a class="sourceLine" id="cb42-2" data-line-number="2"> <span class="dt">parms.ini =</span> m.Z.mkin<span class="fl">.4</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>],</a> -<a class="sourceLine" id="cb42-3" data-line-number="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb42-4" data-line-number="4"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.5</span>)</a></code></pre></div> +<div class="sourceCode" id="cb45"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb45-1" title="1">m.Z.mkin<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> +<a class="sourceLine" id="cb45-2" title="2"> <span class="dt">parms.ini =</span> m.Z.mkin<span class="fl">.4</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>],</a> +<a class="sourceLine" id="cb45-3" title="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb45-4" title="4"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.5</span>)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png" width="700"></p> <p>The summary view of the backtransformed parameters shows that we get no confidence intervals due to overparameterisation. As the optimized is excessively small, it seems reasonable to fix it to zero.</p> -<div class="sourceCode" id="cb43"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb43-1" data-line-number="1">m.Z.mkin<span class="fl">.5</span>a <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> -<a class="sourceLine" id="cb43-2" data-line-number="2"> <span class="dt">parms.ini =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(m.Z.mkin<span class="fl">.5</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">7</span>],</a> -<a class="sourceLine" id="cb43-3" data-line-number="3"> <span class="dt">k_Z3_bound_free =</span> <span class="dv">0</span>),</a> -<a class="sourceLine" id="cb43-4" data-line-number="4"> <span class="dt">fixed_parms =</span> <span class="st">"k_Z3_bound_free"</span>,</a> -<a class="sourceLine" id="cb43-5" data-line-number="5"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb43-6" data-line-number="6"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div> +<div class="sourceCode" id="cb46"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb46-1" title="1">m.Z.mkin<span class="fl">.5</span>a <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> +<a class="sourceLine" id="cb46-2" title="2"> <span class="dt">parms.ini =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(m.Z.mkin<span class="fl">.5</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">7</span>],</a> +<a class="sourceLine" id="cb46-3" title="3"> <span class="dt">k_Z3_bound_free =</span> <span class="dv">0</span>),</a> +<a class="sourceLine" id="cb46-4" title="4"> <span class="dt">fixed_parms =</span> <span class="st">"k_Z3_bound_free"</span>,</a> +<a class="sourceLine" id="cb46-5" title="5"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb46-6" title="6"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png" width="700"></p> <p>As expected, the residual plots for Z0 and Z3 are more random than in the case of the all SFO model for which they were shown above. In conclusion, the model is proposed as the best-fit model for the dataset from Appendix 7 of the FOCUS report.</p> <p>A graphical representation of the confidence intervals can finally be obtained.</p> -<div class="sourceCode" id="cb44"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb44-1" data-line-number="1"><span class="kw"><a href="../../reference/mkinparplot.html">mkinparplot</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div> +<div class="sourceCode" id="cb47"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb47-1" title="1"><span class="kw"><a href="../../reference/mkinparplot.html">mkinparplot</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png" width="700"></p> <p>The endpoints obtained with this model are</p> -<div class="sourceCode" id="cb45"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb45-1" data-line-number="1"><span class="kw"><a href="../../reference/endpoints.html">endpoints</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div> +<div class="sourceCode" id="cb48"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb48-1" title="1"><span class="kw"><a href="../../reference/endpoints.html">endpoints</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div> <pre><code>## $ff ## Z0_free_Z1 Z1_Z2 Z2_sink Z2_Z3_free Z3_free_sink ## 1.00000 1.00000 0.46344 0.53656 1.00000 diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index cae0cd6b..db1fc478 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">2019-02-26</h4> + <h4 class="date">2019-03-04</h4> <div class="hidden name"><code>NAFTA_examples.Rmd</code></div> @@ -110,12 +110,14 @@ <div id="example-on-page-5-upper-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-5-upper-panel" class="anchor"></a>Example on page 5, upper panel</h2> -<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1">p5a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p5a"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1">p5a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p5a"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p5a)</a></code></pre></div> +<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p5a)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5a-1.png" width="700"></p> -<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p5a)</a></code></pre></div> +<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb6-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p5a)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 465.21753 56.27506 32.06401 @@ -125,22 +127,22 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 95.84012168 1.095639e-21 92.120517864 99.55972549 -## k_parent_sink 0.01024015 1.710227e-12 0.008996874 0.01165524 +## Estimate Pr(>t) Lower Upper +## parent_0 95.8401 1.10e-21 92.121 99.5597 +## k_parent_sink 0.0102 1.71e-12 0.009 0.0117 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 1.007532e+02 2.365797e-26 9.891170e+01 1.025947e+02 -## k__iore_parent_sink 1.544192e-05 8.733384e-02 3.482391e-06 6.847393e-05 -## N_parent 2.569877e+00 1.140446e-11 2.215298e+00 2.924456e+00 +## Estimate Pr(>t) Lower Upper +## parent_0 1.01e+02 2.37e-26 9.89e+01 1.03e+02 +## k__iore_parent_sink 1.54e-05 8.73e-02 3.48e-06 6.85e-05 +## N_parent 2.57e+00 1.14e-11 2.22e+00 2.92e+00 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.994630e+01 4.330861e-27 NA NA -## k1 2.674255e-02 3.171390e-05 NA NA -## k2 2.161318e-12 5.000000e-01 NA NA -## g 6.465276e-01 2.129114e-05 NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 9.99e+01 4.33e-27 NA NA +## k1 2.67e-02 3.17e-05 NA NA +## k2 2.16e-12 5.00e-01 NA NA +## g 6.47e-01 2.13e-05 NA NA ## ## ## DTx values: @@ -155,12 +157,14 @@ <div id="example-on-page-5-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-5-lower-panel" class="anchor"></a>Example on page 5, lower panel</h2> -<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">p5b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p5b"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1">p5b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p5b"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p5b)</a></code></pre></div> +<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p5b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p5b-1.png" width="700"></p> -<div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p5b)</a></code></pre></div> +<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p5b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 94.81123 10.10936 7.55871 @@ -170,22 +174,22 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 96.497133849 2.623748e-25 94.776528606 98.217739092 -## k_parent_sink 0.008002704 1.352275e-14 0.007356108 0.008706135 +## Estimate Pr(>t) Lower Upper +## parent_0 96.497 2.62e-25 94.77653 98.21774 +## k_parent_sink 0.008 1.35e-14 0.00736 0.00871 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 9.854518e+01 1.019174e-29 9.780760e+01 9.928276e+01 -## k__iore_parent_sink 1.532766e-04 1.152046e-02 6.603390e-05 3.557826e-04 -## N_parent 1.939125e+00 8.177751e-13 1.741616e+00 2.136633e+00 +## Estimate Pr(>t) Lower Upper +## parent_0 9.85e+01 1.02e-29 9.78e+01 9.93e+01 +## k__iore_parent_sink 1.53e-04 1.15e-02 6.60e-05 3.56e-04 +## N_parent 1.94e+00 8.18e-13 1.74e+00 2.14e+00 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.836323e+01 1.896304e-28 NA NA -## k1 1.546859e-02 2.833415e-03 NA NA -## k2 8.172408e-12 5.000000e-01 NA NA -## g 6.889941e-01 1.306276e-02 NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 9.84e+01 1.90e-28 NA NA +## k1 1.55e-02 2.83e-03 NA NA +## k2 8.17e-12 5.00e-01 NA NA +## g 6.89e-01 1.31e-02 NA NA ## ## ## DTx values: @@ -200,12 +204,14 @@ <div id="example-on-page-6" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-6" class="anchor"></a>Example on page 6</h2> -<div class="sourceCode" id="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1">p6 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p6"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" title="1">p6 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p6"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb16"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb16-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p6)</a></code></pre></div> +<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p6)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p6-1.png" width="700"></p> -<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p6)</a></code></pre></div> +<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/print">print</a></span>(p6)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 188.45361 51.00699 42.46931 @@ -215,22 +221,22 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 94.77587412 1.246335e-24 92.25575879 97.29598945 -## k_parent_sink 0.01794259 2.347664e-16 0.01660595 0.01938682 +## Estimate Pr(>t) Lower Upper +## parent_0 94.7759 1.25e-24 92.2558 97.2960 +## k_parent_sink 0.0179 2.35e-16 0.0166 0.0194 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 97.124460863 5.616271e-27 95.493434421 98.755487305 -## k__iore_parent_sink 0.002517728 3.535472e-03 0.001263771 0.005015906 -## N_parent 1.495871465 6.129227e-13 1.323799338 1.667943591 +## Estimate Pr(>t) Lower Upper +## parent_0 97.12446 5.62e-27 95.49343 98.75549 +## k__iore_parent_sink 0.00252 3.54e-03 0.00126 0.00502 +## N_parent 1.49587 6.13e-13 1.32380 1.66794 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.662275e+01 4.174516e-26 NA NA -## k1 2.547327e-02 2.115246e-05 NA NA -## k2 3.087623e-11 5.000000e-01 NA NA -## g 8.613785e-01 2.097173e-05 NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 9.66e+01 4.17e-26 NA NA +## k1 2.55e-02 2.12e-05 NA NA +## k2 3.09e-11 5.00e-01 NA NA +## g 8.61e-01 2.10e-05 NA NA ## ## ## DTx values: @@ -245,12 +251,14 @@ <div id="example-on-page-7" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-7" class="anchor"></a>Example on page 7</h2> -<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" data-line-number="1">p7 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p7"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" title="1">p7 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p7"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p7)</a></code></pre></div> +<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p7)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p7-1.png" width="700"></p> -<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p7)</a></code></pre></div> +<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p7)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 3661.661 3195.030 3174.145 @@ -260,22 +268,22 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 96.417960406 1.520951e-53 93.295541980 99.540378832 -## k_parent_sink 0.007350054 3.592731e-21 0.006413446 0.008423441 +## Estimate Pr(>t) Lower Upper +## parent_0 96.41796 1.52e-53 93.29554 99.54038 +## k_parent_sink 0.00735 3.59e-21 0.00641 0.00842 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 9.915322e+01 7.332574e-49 9.534934e+01 1.029571e+02 -## k__iore_parent_sink 1.600884e-05 3.472978e-01 9.982484e-08 2.567328e-03 -## N_parent 2.446000e+00 6.141482e-05 1.260173e+00 3.631827e+00 +## Estimate Pr(>t) Lower Upper +## parent_0 9.92e+01 7.33e-49 9.53e+01 1.03e+02 +## k__iore_parent_sink 1.60e-05 3.47e-01 9.98e-08 2.57e-03 +## N_parent 2.45e+00 6.14e-05 1.26e+00 3.63e+00 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.886065e+01 8.134302e-48 NA NA -## k1 1.805928e-02 2.198367e-01 NA NA -## k2 3.279731e-10 5.000000e-01 NA NA -## g 6.063177e-01 2.601365e-01 NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 9.89e+01 8.13e-48 NA NA +## k1 1.81e-02 2.20e-01 NA NA +## k2 3.28e-10 5.00e-01 NA NA +## g 6.06e-01 2.60e-01 NA NA ## ## ## DTx values: @@ -295,12 +303,17 @@ <h2 class="hasAnchor"> <a href="#example-on-page-8" class="anchor"></a>Example on page 8</h2> <p>For this dataset, the IORE fit does not converge when the default starting values used by mkin for the IORE model are used. Therefore, a lower value for the rate constant is used here.</p> -<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1">p8 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p8"</span>]], <span class="dt">parms.ini =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dt">k__iore_parent_sink =</span> <span class="fl">1e-3</span>))</a></code></pre></div> +<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" title="1">p8 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p8"</span>]], <span class="dt">parms.ini =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dt">k__iore_parent_sink =</span> <span class="fl">1e-3</span>))</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system. + +## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb28"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb28-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p8)</a></code></pre></div> +<div class="sourceCode" id="cb33"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb33-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p8)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p8-1.png" width="700"></p> -<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p8)</a></code></pre></div> +<div class="sourceCode" id="cb34"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb34-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p8)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 1996.9408 444.9237 547.5616 @@ -310,31 +323,31 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 88.165489334 NA NA NA -## k__iore_parent_sink 0.001000000 NA NA NA -## k_parent_sink 0.008032303 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 88.16549 NA NA NA +## k__iore_parent_sink 0.00100 NA NA NA +## k_parent_sink 0.00803 NA NA NA ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 9.771060e+01 1.048016e-35 9.442778e+01 1.009934e+02 -## k__iore_parent_sink 6.141041e-05 2.763666e-02 2.205805e-05 1.709688e-04 -## N_parent 2.271648e+00 5.996684e-19 2.015215e+00 2.528080e+00 +## Estimate Pr(>t) Lower Upper +## parent_0 9.77e+01 1.05e-35 9.44e+01 1.01e+02 +## k__iore_parent_sink 6.14e-05 2.76e-02 2.21e-05 1.71e-04 +## N_parent 2.27e+00 6.00e-19 2.02e+00 2.53e+00 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 95.706193520 NA NA NA -## k__iore_parent_sink 0.001000000 NA NA NA -## k1 0.024995243 NA NA NA -## k2 0.002734623 NA NA NA -## g 0.588349874 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 95.70619 NA NA NA +## k__iore_parent_sink 0.00100 NA NA NA +## k1 0.02500 NA NA NA +## k2 0.00273 NA NA NA +## g 0.58835 NA NA NA ## ## ## DTx values: ## DT50 DT90 DT50_rep ## SFO 86.3 287 86.3 ## IORE 53.4 668 201.0 -## DFOP 55.6 517 253.0 +## DFOP 55.6 517 253.5 ## ## Representative half-life: ## [1] 201.0316</code></pre> @@ -346,12 +359,14 @@ <div id="example-on-page-9-upper-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-9-upper-panel" class="anchor"></a>Example on page 9, upper panel</h2> -<div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" data-line-number="1">p9a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9a"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb36"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb36-1" title="1">p9a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9a"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb34"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb34-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9a)</a></code></pre></div> +<div class="sourceCode" id="cb40"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb40-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9a)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9a-1.png" width="700"></p> -<div class="sourceCode" id="cb35"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb35-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9a)</a></code></pre></div> +<div class="sourceCode" id="cb41"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb41-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9a)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 839.35238 88.57064 9.93363 @@ -361,22 +376,22 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 88.1933161 1.117569e-12 79.76708923 96.61954288 -## k_parent_sink 0.0409019 9.501453e-08 0.03258829 0.05133639 +## Estimate Pr(>t) Lower Upper +## parent_0 88.1933 1.12e-12 79.7671 96.6195 +## k_parent_sink 0.0409 9.50e-08 0.0326 0.0513 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 9.891481e+01 5.163566e-17 9.497891e+01 1.028507e+02 -## k__iore_parent_sink 1.927824e-05 1.480158e-01 2.650455e-06 1.402214e-04 -## N_parent 2.910027e+00 3.738041e-09 2.428904e+00 3.391151e+00 +## Estimate Pr(>t) Lower Upper +## parent_0 9.89e+01 5.16e-17 9.50e+01 1.03e+02 +## k__iore_parent_sink 1.93e-05 1.48e-01 2.65e-06 1.40e-04 +## N_parent 2.91e+00 3.74e-09 2.43e+00 3.39e+00 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 9.853112e+01 1.308505e-21 NA NA -## k1 1.382145e-01 3.630589e-09 NA NA -## k2 6.019228e-13 5.000000e-01 NA NA -## g 6.518659e-01 1.502543e-10 NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 9.85e+01 1.31e-21 NA NA +## k1 1.38e-01 3.63e-09 NA NA +## k2 6.02e-13 5.00e-01 NA NA +## g 6.52e-01 1.50e-10 NA NA ## ## ## DTx values: @@ -392,12 +407,14 @@ <div id="example-on-page-9-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-9-lower-panel" class="anchor"></a>Example on page 9, lower panel</h2> -<div class="sourceCode" id="cb37"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb37-1" data-line-number="1">p9b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9b"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb43"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb43-1" title="1">p9b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p9b"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb40"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb40-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9b)</a></code></pre></div> +<div class="sourceCode" id="cb47"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb47-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p9b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p9b-1.png" width="700"></p> -<div class="sourceCode" id="cb41"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb41-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9b)</a></code></pre></div> +<div class="sourceCode" id="cb48"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb48-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p9b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 35.64867 23.22334 35.64867 @@ -407,22 +424,22 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 94.71226787 2.207090e-20 93.0673253 96.35721040 -## k_parent_sink 0.03887215 1.482921e-14 0.0368549 0.04099981 +## Estimate Pr(>t) Lower Upper +## parent_0 94.7123 2.21e-20 93.0673 96.357 +## k_parent_sink 0.0389 1.48e-14 0.0369 0.041 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 93.8626223 2.911881e-19 92.29955547 95.4256890 -## k__iore_parent_sink 0.1271399 2.725876e-02 0.04570569 0.3536663 -## N_parent 0.7108771 3.130915e-05 0.46052920 0.9612249 +## Estimate Pr(>t) Lower Upper +## parent_0 93.863 2.91e-19 92.2996 95.426 +## k__iore_parent_sink 0.127 2.73e-02 0.0457 0.354 +## N_parent 0.711 3.13e-05 0.4605 0.961 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 94.71226786 NA NA NA -## k1 0.03887215 NA NA NA -## k2 0.03887215 NA NA NA -## g 0.77417779 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 94.7123 NA NA NA +## k1 0.0389 NA NA NA +## k2 0.0389 NA NA NA +## g 0.7742 NA NA NA ## ## ## DTx values: @@ -438,12 +455,14 @@ <div id="example-on-page-10" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-10" class="anchor"></a>Example on page 10</h2> -<div class="sourceCode" id="cb43"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb43-1" data-line-number="1">p10 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p10"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb50"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb50-1" title="1">p10 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p10"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb46"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb46-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p10)</a></code></pre></div> +<div class="sourceCode" id="cb54"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb54-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p10)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p10-1.png" width="700"></p> -<div class="sourceCode" id="cb47"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb47-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p10)</a></code></pre></div> +<div class="sourceCode" id="cb55"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb55-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p10)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 899.4089 336.4348 899.4089 @@ -453,29 +472,29 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 101.73153064 4.954950e-11 90.96832870 112.49473259 -## k_parent_sink 0.04952864 3.398569e-07 0.03930194 0.06241642 +## Estimate Pr(>t) Lower Upper +## parent_0 101.7315 4.95e-11 90.9683 112.4947 +## k_parent_sink 0.0495 3.40e-07 0.0393 0.0624 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 96.855416 2.706118e-12 89.8843855 103.8264461 -## k__iore_parent_sink 2.960977 1.308097e-01 0.4609504 19.0202303 -## N_parent 0.000000 5.000000e-01 -0.4728922 0.4728922 +## Estimate Pr(>t) Lower Upper +## parent_0 96.86 2.71e-12 89.884 103.826 +## k__iore_parent_sink 2.96 1.31e-01 0.461 19.020 +## N_parent 0.00 5.00e-01 -0.473 0.473 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 101.73153022 NA NA NA -## k1 0.04952864 NA NA NA -## k2 0.04952864 NA NA NA -## g 0.66344649 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 101.7315 NA NA NA +## k1 0.0495 NA NA NA +## k2 0.0495 NA NA NA +## g 0.6634 NA NA NA ## ## ## DTx values: ## DT50 DT90 DT50_rep -## SFO 14.0 46.5 14.00 +## SFO 14.0 46.5 13.99 ## IORE 16.4 29.4 8.86 -## DFOP 14.0 46.5 14.00 +## DFOP 14.0 46.5 13.99 ## ## Representative half-life: ## [1] 8.862193</code></pre> @@ -488,12 +507,14 @@ <div id="example-on-page-11" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-11" class="anchor"></a>Example on page 11</h2> -<div class="sourceCode" id="cb49"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb49-1" data-line-number="1">p11 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p11"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb57"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb57-1" title="1">p11 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p11"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb52"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb52-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p11)</a></code></pre></div> +<div class="sourceCode" id="cb61"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb61-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p11)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p11-1.png" width="700"></p> -<div class="sourceCode" id="cb53"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb53-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p11)</a></code></pre></div> +<div class="sourceCode" id="cb62"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb62-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p11)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 579.6805 204.7932 144.7783 @@ -503,22 +524,22 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 96.158200840 1.560217e-13 89.913728706 1.024027e+02 -## k_parent_sink 0.003208498 5.266271e-05 0.002183575 4.714497e-03 +## Estimate Pr(>t) Lower Upper +## parent_0 96.15820 1.56e-13 89.91373 1.02e+02 +## k_parent_sink 0.00321 5.27e-05 0.00218 4.71e-03 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 1.045981e+02 NA 9.798102e+01 1.112151e+02 -## k__iore_parent_sink 3.110367e-17 NA 6.875825e-25 1.407014e-09 -## N_parent 8.360812e+00 NA 4.397006e+00 1.232462e+01 +## Estimate Pr(>t) Lower Upper +## parent_0 1.05e+02 NA 9.80e+01 1.11e+02 +## k__iore_parent_sink 3.11e-17 NA 6.88e-25 1.41e-09 +## N_parent 8.36e+00 NA 4.40e+00 1.23e+01 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 1.045607e+02 7.502642e-13 NA NA -## k1 4.414526e-02 3.343950e-02 NA NA -## k2 7.246905e-13 5.000000e-01 NA NA -## g 3.217737e-01 7.868540e-03 NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 1.05e+02 7.50e-13 NA NA +## k1 4.41e-02 3.34e-02 NA NA +## k2 7.25e-13 5.00e-01 NA NA +## g 3.22e-01 7.87e-03 NA NA ## ## ## DTx values: @@ -539,12 +560,14 @@ <div id="example-on-page-12-upper-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-12-upper-panel" class="anchor"></a>Example on page 12, upper panel</h2> -<div class="sourceCode" id="cb55"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb55-1" data-line-number="1">p12a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12a"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb64"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb64-1" title="1">p12a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12a"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb58"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb58-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12a)</a></code></pre></div> +<div class="sourceCode" id="cb68"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb68-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12a)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12a-1.png" width="700"></p> -<div class="sourceCode" id="cb59"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb59-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12a)</a></code></pre></div> +<div class="sourceCode" id="cb69"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb69-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12a)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 695.4440 220.0685 695.4440 @@ -554,22 +577,22 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 100.5206988 5.606929e-12 91.6867692 109.3546284 -## k_parent_sink 0.1243142 7.235485e-08 0.1017305 0.1519113 +## Estimate Pr(>t) Lower Upper +## parent_0 100.521 5.61e-12 91.687 109.355 +## k_parent_sink 0.124 7.24e-08 0.102 0.152 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 96.8234045 1.242894e-13 91.56908085 102.0777281 -## k__iore_parent_sink 2.4360714 3.893118e-02 0.78536982 7.5562415 -## N_parent 0.2627157 3.639503e-02 -0.02875633 0.5541876 +## Estimate Pr(>t) Lower Upper +## parent_0 96.823 1.24e-13 91.5691 102.078 +## k__iore_parent_sink 2.436 3.89e-02 0.7854 7.556 +## N_parent 0.263 3.64e-02 -0.0288 0.554 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 100.5206988 NA NA NA -## k1 0.1243142 NA NA NA -## k2 0.1243142 NA NA NA -## g 0.8772377 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 100.521 NA NA NA +## k1 0.124 NA NA NA +## k2 0.124 NA NA NA +## g 0.877 NA NA NA ## ## ## DTx values: @@ -584,12 +607,14 @@ <div id="example-on-page-12-lower-panel" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-12-lower-panel" class="anchor"></a>Example on page 12, lower panel</h2> -<div class="sourceCode" id="cb61"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb61-1" data-line-number="1">p12b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12b"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb71"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb71-1" title="1">p12b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p12b"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb64"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb64-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12b)</a></code></pre></div> +<div class="sourceCode" id="cb75"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb75-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p12b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p12b-1.png" width="700"></p> -<div class="sourceCode" id="cb65"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb65-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12b)</a></code></pre></div> +<div class="sourceCode" id="cb76"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb76-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p12b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 58.90242 19.06353 58.90242 @@ -599,29 +624,29 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 97.6840211 0.0000535970 86.32050115 109.04754103 -## k_parent_sink 0.0589177 0.0009869932 0.04320553 0.08034377 +## Estimate Pr(>t) Lower Upper +## parent_0 97.6840 5.36e-05 86.3205 109.0475 +## k_parent_sink 0.0589 9.87e-04 0.0432 0.0803 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 95.5232270 0.0003860431 84.09629121 106.950163 -## k__iore_parent_sink 0.3329365 0.1708863327 0.01026046 10.803285 -## N_parent 0.5677771 0.0548808046 -0.31606833 1.451622 +## Estimate Pr(>t) Lower Upper +## parent_0 95.523 0.000386 84.0963 106.95 +## k__iore_parent_sink 0.333 0.170886 0.0103 10.80 +## N_parent 0.568 0.054881 -0.3161 1.45 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 97.6840212 NA NA NA -## k1 0.0589177 NA NA NA -## k2 0.0589177 NA NA NA -## g 0.6901929 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 97.6840 NA NA NA +## k1 0.0589 NA NA NA +## k2 0.0589 NA NA NA +## g 0.6902 NA NA NA ## ## ## DTx values: ## DT50 DT90 DT50_rep -## SFO 11.8 39.1 11.80 +## SFO 11.8 39.1 11.76 ## IORE 12.9 31.4 9.46 -## DFOP 11.8 39.1 11.80 +## DFOP 11.8 39.1 11.76 ## ## Representative half-life: ## [1] 9.461912</code></pre> @@ -629,12 +654,14 @@ <div id="example-on-page-13" class="section level2"> <h2 class="hasAnchor"> <a href="#example-on-page-13" class="anchor"></a>Example on page 13</h2> -<div class="sourceCode" id="cb67"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb67-1" data-line-number="1">p13 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p13"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb78"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb78-1" title="1">p13 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p13"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb70"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb70-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p13)</a></code></pre></div> +<div class="sourceCode" id="cb82"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb82-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p13)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p13-1.png" width="700"></p> -<div class="sourceCode" id="cb71"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb71-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p13)</a></code></pre></div> +<div class="sourceCode" id="cb83"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb83-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p13)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 174.5971 142.3951 174.5971 @@ -644,22 +671,22 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 92.735003006 1.453426e-17 89.389064698 96.080941315 -## k_parent_sink 0.002581189 2.630396e-09 0.002198171 0.003030945 +## Estimate Pr(>t) Lower Upper +## parent_0 92.73500 1.45e-17 89.3891 96.08094 +## k_parent_sink 0.00258 2.63e-09 0.0022 0.00303 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 91.60158658 2.932498e-16 88.08710837 95.116065 -## k__iore_parent_sink 0.03960674 2.810573e-01 0.00102485 1.530656 -## N_parent 0.35408757 1.972378e-01 -0.51942545 1.227601 +## Estimate Pr(>t) Lower Upper +## parent_0 91.6016 2.93e-16 88.08711 95.12 +## k__iore_parent_sink 0.0396 2.81e-01 0.00102 1.53 +## N_parent 0.3541 1.97e-01 -0.51943 1.23 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 92.735003208 NA NA NA -## k1 0.002581186 NA NA NA -## k2 0.002581188 NA NA NA -## g 0.004422859 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 92.73500 NA NA NA +## k1 0.00258 NA NA NA +## k2 0.00258 NA NA NA +## g 0.00442 NA NA NA ## ## ## DTx values: @@ -675,12 +702,14 @@ <div id="dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="section level1"> <h1 class="hasAnchor"> <a href="#dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf" class="anchor"></a>DT50 not observed in the study and DFOP problems in PestDF</h1> -<div class="sourceCode" id="cb73"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb73-1" data-line-number="1">p14 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p14"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb85"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb85-1" title="1">p14 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p14"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb76"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb76-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p14)</a></code></pre></div> +<div class="sourceCode" id="cb89"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb89-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p14)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p14-1.png" width="700"></p> -<div class="sourceCode" id="cb77"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb77-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p14)</a></code></pre></div> +<div class="sourceCode" id="cb90"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb90-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p14)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 48.43249 28.67746 27.26248 @@ -690,22 +719,22 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 99.471243637 1.708290e-31 98.373131052 1.005694e+02 -## k_parent_sink 0.002789581 2.222078e-15 0.002554583 3.046197e-03 +## Estimate Pr(>t) Lower Upper +## parent_0 99.47124 1.71e-31 98.37313 1.01e+02 +## k_parent_sink 0.00279 2.22e-15 0.00255 3.05e-03 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 1.003522e+02 NA 9.926773e+01 1.014366e+02 -## k__iore_parent_sink 9.443770e-08 NA 6.810412e-11 1.309536e-04 -## N_parent 3.308552e+00 NA 1.690051e+00 4.927053e+00 +## Estimate Pr(>t) Lower Upper +## parent_0 1.00e+02 NA 9.93e+01 1.01e+02 +## k__iore_parent_sink 9.44e-08 NA 6.81e-11 1.31e-04 +## N_parent 3.31e+00 NA 1.69e+00 4.93e+00 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 1.003398e+02 2.698790e-28 NA NA -## k1 9.532677e-03 3.394353e-01 NA NA -## k2 9.189935e-12 5.000000e-01 NA NA -## g 3.982564e-01 3.920847e-01 NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 1.00e+02 2.70e-28 NA NA +## k1 9.53e-03 3.39e-01 NA NA +## k2 9.19e-12 5.00e-01 NA NA +## g 3.98e-01 3.92e-01 NA NA ## ## ## DTx values: @@ -721,12 +750,14 @@ <div id="n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="section level1"> <h1 class="hasAnchor"> <a href="#n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero" class="anchor"></a>N is less than 1 and DFOP fraction parameter is below zero</h1> -<div class="sourceCode" id="cb79"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb79-1" data-line-number="1">p15a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15a"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb92"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb92-1" title="1">p15a <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15a"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb82"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb82-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15a)</a></code></pre></div> +<div class="sourceCode" id="cb96"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb96-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15a)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15a-1.png" width="700"></p> -<div class="sourceCode" id="cb83"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb83-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15a)</a></code></pre></div> +<div class="sourceCode" id="cb97"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb97-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15a)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 245.5248 135.0132 245.5248 @@ -736,22 +767,22 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 97.967511635 4.984358e-16 94.038286642 101.8967366 -## k_parent_sink 0.009522227 5.239115e-09 0.008126698 0.0111574 +## Estimate Pr(>t) Lower Upper +## parent_0 97.96751 4.98e-16 94.03829 101.8967 +## k_parent_sink 0.00952 5.24e-09 0.00813 0.0112 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 95.8736780 8.295860e-16 92.58018331 99.1671726 -## k__iore_parent_sink 0.6285106 2.386496e-01 0.03155477 12.5187302 -## N_parent 0.0000000 5.000000e-01 -0.72189225 0.7218923 +## Estimate Pr(>t) Lower Upper +## parent_0 95.874 8.30e-16 92.5802 99.167 +## k__iore_parent_sink 0.629 2.39e-01 0.0316 12.519 +## N_parent 0.000 5.00e-01 -0.7219 0.722 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 97.967516468 NA NA NA -## k1 0.009522243 NA NA NA -## k2 0.009522223 NA NA NA -## g 0.172466840 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 97.96752 NA NA NA +## k1 0.00952 NA NA NA +## k2 0.00952 NA NA NA +## g 0.17247 NA NA NA ## ## ## DTx values: @@ -762,12 +793,14 @@ ## ## Representative half-life: ## [1] 41.32749</code></pre> -<div class="sourceCode" id="cb85"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb85-1" data-line-number="1">p15b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15b"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb99"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb99-1" title="1">p15b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15b"</span>]])</a></code></pre></div> +<pre><code>## Warning in summary.mkinfit(x): Could not estimate covariance matrix; +## singular system.</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> -<div class="sourceCode" id="cb88"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb88-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15b)</a></code></pre></div> +<div class="sourceCode" id="cb103"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb103-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p15b)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p15b-1.png" width="700"></p> -<div class="sourceCode" id="cb89"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb89-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15b)</a></code></pre></div> +<div class="sourceCode" id="cb104"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb104-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p15b)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 106.91629 68.55574 106.91629 @@ -777,29 +810,29 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 1.008816e+02 4.987925e-18 98.127607367 1.036355e+02 -## k_parent_sink 4.856586e-03 1.756208e-10 0.004316334 5.464459e-03 +## Estimate Pr(>t) Lower Upper +## parent_0 1.01e+02 4.99e-18 98.12761 1.04e+02 +## k_parent_sink 4.86e-03 1.76e-10 0.00432 5.46e-03 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 99.8268283 4.490292e-17 97.19753163 102.45613 -## k__iore_parent_sink 0.3799625 3.406003e-01 0.00206198 70.01593 -## N_parent 0.0000000 5.000000e-01 -1.20105017 1.20105 +## Estimate Pr(>t) Lower Upper +## parent_0 99.83 4.49e-17 97.19753 102.5 +## k__iore_parent_sink 0.38 3.41e-01 0.00206 70.0 +## N_parent 0.00 5.00e-01 -1.20105 1.2 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 1.008816e+02 NA NA NA -## k1 4.856586e-03 NA NA NA -## k2 4.856586e-03 NA NA NA -## g 1.496838e-01 NA NA NA +## Estimate Pr(>t) Lower Upper +## parent_0 1.01e+02 NA NA NA +## k1 4.86e-03 NA NA NA +## k2 4.86e-03 NA NA NA +## g 1.50e-01 NA NA NA ## ## ## DTx values: ## DT50 DT90 DT50_rep -## SFO 143 474 143.0 +## SFO 143 474 142.7 ## IORE 131 236 71.2 -## DFOP 143 474 143.0 +## DFOP 143 474 142.7 ## ## Representative half-life: ## [1] 71.18014</code></pre> @@ -808,14 +841,14 @@ <div id="the-dfop-fraction-parameter-is-greater-than-1" class="section level1"> <h1 class="hasAnchor"> <a href="#the-dfop-fraction-parameter-is-greater-than-1" class="anchor"></a>The DFOP fraction parameter is greater than 1</h1> -<div class="sourceCode" id="cb91"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb91-1" data-line-number="1">p16 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p16"</span>]])</a></code></pre></div> +<div class="sourceCode" id="cb106"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb106-1" title="1">p16 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p16"</span>]])</a></code></pre></div> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The representative half-life of the IORE model is longer than the one corresponding</code></pre> <pre><code>## to the terminal degradation rate found with the DFOP model.</code></pre> <pre><code>## The representative half-life obtained from the DFOP model may be used</code></pre> -<div class="sourceCode" id="cb96"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb96-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p16)</a></code></pre></div> +<div class="sourceCode" id="cb111"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb111-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/plot">plot</a></span>(p16)</a></code></pre></div> <p><img src="NAFTA_examples_files/figure-html/p16-1.png" width="700"></p> -<div class="sourceCode" id="cb97"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb97-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p16)</a></code></pre></div> +<div class="sourceCode" id="cb112"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb112-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(p16)</a></code></pre></div> <pre><code>## Sums of squares: ## SFO IORE DFOP ## 3831.804 2062.008 1550.980 @@ -825,22 +858,22 @@ ## ## Parameters: ## $SFO -## Estimate Pr(>t) Lower Upper -## parent_0 71.9528227 3.923531e-14 61.0870510 82.8185944 -## k_parent_sink 0.1594518 2.271601e-06 0.1110583 0.2289327 +## Estimate Pr(>t) Lower Upper +## parent_0 71.953 3.92e-14 61.087 82.819 +## k_parent_sink 0.159 2.27e-06 0.111 0.229 ## ## $IORE -## Estimate Pr(>t) Lower Upper -## parent_0 8.738846e+01 1.739390e-16 7.706991e+01 97.707005461 -## k__iore_parent_sink 4.549683e-04 2.282721e-01 3.008533e-05 0.006880303 -## N_parent 2.696278e+00 1.869479e-08 1.966442e+00 3.426114200 +## Estimate Pr(>t) Lower Upper +## parent_0 8.74e+01 1.74e-16 7.71e+01 97.70701 +## k__iore_parent_sink 4.55e-04 2.28e-01 3.01e-05 0.00688 +## N_parent 2.70e+00 1.87e-08 1.97e+00 3.42611 ## ## $DFOP -## Estimate Pr(>t) Lower Upper -## parent_0 88.53333334 NA 79.36733990 97.6993268 -## k1 18.55624337 NA 0.00000000 Inf -## k2 0.07759679 NA 0.04709945 0.1278414 -## g 0.47333008 NA 0.31375096 0.6385506 +## Estimate Pr(>t) Lower Upper +## parent_0 88.5333 NA 79.3673 97.699 +## k1 18.5562 NA 0.0000 Inf +## k2 0.0776 NA 0.0471 0.128 +## g 0.4733 NA 0.3138 0.639 ## ## ## DTx values: diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 3d49d262..1d96ea76 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">2019-02-26</h4> + <h4 class="date">2019-03-04</h4> <div class="hidden name"><code>compiled_models.Rmd</code></div> @@ -101,37 +101,37 @@ <h2 class="hasAnchor"> <a href="#model-that-can-also-be-solved-with-eigenvalues" class="anchor"></a>Model that can also be solved with Eigenvalues</h2> <p>This evaluation is taken from the example section of mkinfit. When using an mkin version equal to or greater than 0.9-36 and a C compiler (gcc) is available, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod. The <code><a href="../../reference/mkinmod.html">mkinmod()</a></code> function checks for presence of the gcc compiler using</p> -<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/Sys.which">Sys.which</a></span>(<span class="st">"gcc"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/Sys.which">Sys.which</a></span>(<span class="st">"gcc"</span>)</a></code></pre></div> <pre><code>## gcc ## "/usr/bin/gcc"</code></pre> <p>First, we build a simple degradation model for a parent compound with one metabolite.</p> -<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(<span class="st">"mkin"</span>, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb3-2" data-line-number="2">SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> -<a class="sourceLine" id="cb3-3" data-line-number="3"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>),</a> -<a class="sourceLine" id="cb3-4" data-line-number="4"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> +<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(<span class="st">"mkin"</span>, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a> +<a class="sourceLine" id="cb3-2" title="2">SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> +<a class="sourceLine" id="cb3-3" title="3"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>),</a> +<a class="sourceLine" id="cb3-4" title="4"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <p>We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the benchmark package.</p> -<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="cf">if</span> (<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">require</a></span>(rbenchmark)) {</a> -<a class="sourceLine" id="cb5-2" data-line-number="2"> b<span class="fl">.1</span> <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></span>(</a> -<a class="sourceLine" id="cb5-3" data-line-number="3"> <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D,</a> -<a class="sourceLine" id="cb5-4" data-line-number="4"> <span class="dt">solution_type =</span> <span class="st">"deSolve"</span>,</a> -<a class="sourceLine" id="cb5-5" data-line-number="5"> <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> -<a class="sourceLine" id="cb5-6" data-line-number="6"> <span class="st">"Eigenvalue based"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D,</a> -<a class="sourceLine" id="cb5-7" data-line-number="7"> <span class="dt">solution_type =</span> <span class="st">"eigen"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> -<a class="sourceLine" id="cb5-8" data-line-number="8"> <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D,</a> -<a class="sourceLine" id="cb5-9" data-line-number="9"> <span class="dt">solution_type =</span> <span class="st">"deSolve"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> -<a class="sourceLine" id="cb5-10" data-line-number="10"> <span class="dt">replications =</span> <span class="dv">3</span>)</a> -<a class="sourceLine" id="cb5-11" data-line-number="11"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(b<span class="fl">.1</span>)</a> -<a class="sourceLine" id="cb5-12" data-line-number="12"> factor_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/Round">round</a></span>(b<span class="fl">.1</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>])</a> -<a class="sourceLine" id="cb5-13" data-line-number="13">} <span class="cf">else</span> {</a> -<a class="sourceLine" id="cb5-14" data-line-number="14"> factor_SFO_SFO <-<span class="st"> </span><span class="ot">NA</span></a> -<a class="sourceLine" id="cb5-15" data-line-number="15"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(<span class="st">"R package benchmark is not available"</span>)</a> -<a class="sourceLine" id="cb5-16" data-line-number="16">}</a></code></pre></div> +<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="cf">if</span> (<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">require</a></span>(rbenchmark)) {</a> +<a class="sourceLine" id="cb5-2" title="2"> b<span class="fl">.1</span> <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></span>(</a> +<a class="sourceLine" id="cb5-3" title="3"> <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D,</a> +<a class="sourceLine" id="cb5-4" title="4"> <span class="dt">solution_type =</span> <span class="st">"deSolve"</span>,</a> +<a class="sourceLine" id="cb5-5" title="5"> <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> +<a class="sourceLine" id="cb5-6" title="6"> <span class="st">"Eigenvalue based"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D,</a> +<a class="sourceLine" id="cb5-7" title="7"> <span class="dt">solution_type =</span> <span class="st">"eigen"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> +<a class="sourceLine" id="cb5-8" title="8"> <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D,</a> +<a class="sourceLine" id="cb5-9" title="9"> <span class="dt">solution_type =</span> <span class="st">"deSolve"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> +<a class="sourceLine" id="cb5-10" title="10"> <span class="dt">replications =</span> <span class="dv">3</span>)</a> +<a class="sourceLine" id="cb5-11" title="11"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(b<span class="fl">.1</span>)</a> +<a class="sourceLine" id="cb5-12" title="12"> factor_SFO_SFO <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/Round">round</a></span>(b<span class="fl">.1</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>])</a> +<a class="sourceLine" id="cb5-13" title="13">} <span class="cf">else</span> {</a> +<a class="sourceLine" id="cb5-14" title="14"> factor_SFO_SFO <-<span class="st"> </span><span class="ot">NA</span></a> +<a class="sourceLine" id="cb5-15" title="15"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(<span class="st">"R package benchmark is not available"</span>)</a> +<a class="sourceLine" id="cb5-16" title="16">}</a></code></pre></div> <pre><code>## Lade nötiges Paket: rbenchmark</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 3 deSolve, compiled 3 2.309 1.000 2.307 0 -## 1 deSolve, not compiled 3 17.535 7.594 17.527 0 -## 2 Eigenvalue based 3 2.846 1.233 2.844 0 +## 3 deSolve, compiled 3 2.313 1.000 2.312 0 +## 1 deSolve, not compiled 3 17.602 7.610 17.595 0 +## 2 Eigenvalue based 3 2.853 1.233 2.851 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 @@ -142,26 +142,26 @@ <h2 class="hasAnchor"> <a href="#model-that-can-not-be-solved-with-eigenvalues" class="anchor"></a>Model that can not be solved with Eigenvalues</h2> <p>This evaluation is also taken from the example section of mkinfit.</p> -<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1"><span class="cf">if</span> (<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">require</a></span>(rbenchmark)) {</a> -<a class="sourceLine" id="cb8-2" data-line-number="2"> FOMC_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> -<a class="sourceLine" id="cb8-3" data-line-number="3"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),</a> -<a class="sourceLine" id="cb8-4" data-line-number="4"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>( <span class="st">"SFO"</span>))</a> -<a class="sourceLine" id="cb8-5" data-line-number="5"></a> -<a class="sourceLine" id="cb8-6" data-line-number="6"> b<span class="fl">.2</span> <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></span>(</a> -<a class="sourceLine" id="cb8-7" data-line-number="7"> <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D,</a> -<a class="sourceLine" id="cb8-8" data-line-number="8"> <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> -<a class="sourceLine" id="cb8-9" data-line-number="9"> <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> -<a class="sourceLine" id="cb8-10" data-line-number="10"> <span class="dt">replications =</span> <span class="dv">3</span>)</a> -<a class="sourceLine" id="cb8-11" data-line-number="11"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(b<span class="fl">.2</span>)</a> -<a class="sourceLine" id="cb8-12" data-line-number="12"> factor_FOMC_SFO <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/Round">round</a></span>(b<span class="fl">.2</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>])</a> -<a class="sourceLine" id="cb8-13" data-line-number="13">} <span class="cf">else</span> {</a> -<a class="sourceLine" id="cb8-14" data-line-number="14"> factor_FOMC_SFO <-<span class="st"> </span><span class="ot">NA</span></a> -<a class="sourceLine" id="cb8-15" data-line-number="15"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(<span class="st">"R package benchmark is not available"</span>)</a> -<a class="sourceLine" id="cb8-16" data-line-number="16">}</a></code></pre></div> +<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" title="1"><span class="cf">if</span> (<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">require</a></span>(rbenchmark)) {</a> +<a class="sourceLine" id="cb8-2" title="2"> FOMC_SFO <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(</a> +<a class="sourceLine" id="cb8-3" title="3"> <span class="dt">parent =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),</a> +<a class="sourceLine" id="cb8-4" title="4"> <span class="dt">m1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>( <span class="st">"SFO"</span>))</a> +<a class="sourceLine" id="cb8-5" title="5"></a> +<a class="sourceLine" id="cb8-6" title="6"> b<span class="fl">.2</span> <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></span>(</a> +<a class="sourceLine" id="cb8-7" title="7"> <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D,</a> +<a class="sourceLine" id="cb8-8" title="8"> <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> +<a class="sourceLine" id="cb8-9" title="9"> <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw"><a href="../../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> +<a class="sourceLine" id="cb8-10" title="10"> <span class="dt">replications =</span> <span class="dv">3</span>)</a> +<a class="sourceLine" id="cb8-11" title="11"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(b<span class="fl">.2</span>)</a> +<a class="sourceLine" id="cb8-12" title="12"> factor_FOMC_SFO <-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/Round">round</a></span>(b<span class="fl">.2</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>])</a> +<a class="sourceLine" id="cb8-13" title="13">} <span class="cf">else</span> {</a> +<a class="sourceLine" id="cb8-14" title="14"> factor_FOMC_SFO <-<span class="st"> </span><span class="ot">NA</span></a> +<a class="sourceLine" id="cb8-15" title="15"> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(<span class="st">"R package benchmark is not available"</span>)</a> +<a class="sourceLine" id="cb8-16" title="16">}</a></code></pre></div> <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 2 deSolve, compiled 3 4.071 1.000 4.069 0 -## 1 deSolve, not compiled 3 37.139 9.123 37.123 0 +## 2 deSolve, compiled 3 4.049 1.000 4.047 0 +## 1 deSolve, not compiled 3 37.135 9.171 37.119 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> diff --git a/docs/index.html b/docs/index.html index 47bc7464..f7e4c6c8 100644 --- a/docs/index.html +++ b/docs/index.html @@ -100,7 +100,7 @@ <h2 class="hasAnchor"> <a href="#installation" class="anchor"></a>Installation</h2> <p>You can install the latest released version from <a href="https://cran.r-project.org/package=mkin">CRAN</a> from within R:</p> -<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"mkin"</span>)</a></code></pre></div> +<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/install.packages">install.packages</a></span>(<span class="st">"mkin"</span>)</a></code></pre></div> </div> <div id="background" class="section level2"> <h2 class="hasAnchor"> diff --git a/docs/news/index.html b/docs/news/index.html index c1644a00..cb56adf5 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -122,9 +122,9 @@ </div> - <div id="mkin-0-9-48-1-2019-02-22" class="section level1"> + <div id="mkin-0-9-48-1-2019-03-04" class="section level1"> <h1 class="page-header"> -<a href="#mkin-0-9-48-1-2019-02-22" class="anchor"></a>mkin 0.9.48.1 (2019-02-22)<small> Unreleased </small> +<a href="#mkin-0-9-48-1-2019-03-04" class="anchor"></a>mkin 0.9.48.1 (2019-03-04)<small> Unreleased </small> </h1> <ul> <li><p>Add the function ‘logLik.mkinfit’ which makes it possible to calculate an AIC for mkinfit objects</p></li> @@ -680,7 +680,7 @@ <div id="tocnav"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#mkin-0-9-48-1-2019-02-22">0.9.48.1</a></li> + <li><a href="#mkin-0-9-48-1-2019-03-04">0.9.48.1</a></li> <li><a href="#mkin-0-9-47-5-2018-09-14">0.9.47.5</a></li> <li><a href="#mkin-0-9-47-3">0.9.47.3</a></li> <li><a href="#mkin-0-9-47-2-2018-07-19">0.9.47.2</a></li> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 93be7412..96b9f218 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -283,7 +283,7 @@ #> #> $time #> User System verstrichen -#> 0.071 0.000 0.071 +#> 0.069 0.000 0.069 #> #> $mkinmod #> <mkinmod> model generated with @@ -472,8 +472,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555c80a350> -#> <environment: 0x55555b478bb8> +#> <bytecode: 0x55555c1f3208> +#> <environment: 0x555555c27dc0> #> #> $cost_notrans #> function (P) @@ -495,8 +495,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555c522e40> -#> <environment: 0x55555b478bb8> +#> <bytecode: 0x55555b84fce8> +#> <environment: 0x555555c27dc0> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -563,7 +563,7 @@ #> 99.17407 #> #> $date -#> [1] "Tue Feb 26 21:07:19 2019" +#> [1] "Mon Mar 4 10:07:37 2019" #> #> $version #> [1] "0.9.48.1" diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index c8b97493..d56c0ca3 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -165,29 +165,29 @@ #> #> Parameters: #> $SFO -#> Estimate Pr(>t) Lower Upper -#> parent_0 83.755751519 8.076390e-15 76.928220975 90.583282063 -#> k_parent_sink 0.001703321 7.452357e-05 0.001108568 0.002617164 +#> Estimate Pr(>t) Lower Upper +#> parent_0 83.7558 8.08e-15 76.92822 90.58328 +#> k_parent_sink 0.0017 7.45e-05 0.00111 0.00262 #> #> $IORE -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.685291e+01 NA 8.752855e+01 1.061773e+02 -#> k__iore_parent_sink 8.403401e-14 NA 1.092058e-19 6.466429e-08 -#> N_parent 6.684457e+00 NA 3.538510e+00 9.830404e+00 +#> Estimate Pr(>t) Lower Upper +#> parent_0 9.69e+01 NA 8.75e+01 1.06e+02 +#> k__iore_parent_sink 8.40e-14 NA 1.09e-19 6.47e-08 +#> N_parent 6.68e+00 NA 3.54e+00 9.83e+00 #> #> $DFOP -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.755655e+01 4.439930e-13 8.884447e+01 1.062686e+02 -#> k1 4.240633e-02 3.554769e-02 1.414189e-02 1.271610e-01 -#> k2 8.237928e-04 2.060933e-02 3.172784e-04 2.138925e-03 -#> g 2.881037e-01 1.313715e-04 1.783967e-01 4.299694e-01 +#> Estimate Pr(>t) Lower Upper +#> parent_0 9.76e+01 4.44e-13 8.88e+01 1.06e+02 +#> k1 4.24e-02 3.55e-02 1.41e-02 1.27e-01 +#> k2 8.24e-04 2.06e-02 3.17e-04 2.14e-03 +#> g 2.88e-01 1.31e-04 1.78e-01 4.30e-01 #> #> #> DTx values: #> DT50 DT90 DT50_rep -#> SFO 407 1350 407 -#> IORE 541 5190000 1560000 -#> DFOP 429 2380 841 +#> SFO 407 1352 407 +#> IORE 541 5192060 1562966 +#> DFOP 429 2383 841 #> #> Representative half-life: #> [1] 841.4096</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='NAFTA_SOP_2015-1.png' alt='' width='700' height='433' /></div></pre> diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html index 373da052..22d9c9fd 100644 --- a/docs/reference/NAFTA_SOP_Attachment.html +++ b/docs/reference/NAFTA_SOP_Attachment.html @@ -152,7 +152,7 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='no'>nafta_att_p5a</span> <span class='kw'><-</span> <span class='fu'><a href='nafta.html'>nafta</a></span>(<span class='no'>NAFTA_SOP_Attachment</span><span class='kw'>[[</span><span class='st'>"p5a"</span>]], <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#> <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#> <span class='message'>The half-life obtained from the IORE model may be used</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>nafta_att_p5a</span>)</div><div class='output co'>#> Sums of squares: + <pre class="examples"><div class='input'> <span class='no'>nafta_att_p5a</span> <span class='kw'><-</span> <span class='fu'><a href='nafta.html'>nafta</a></span>(<span class='no'>NAFTA_SOP_Attachment</span><span class='kw'>[[</span><span class='st'>"p5a"</span>]], <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#> <span class='warning'>Warning: Could not estimate covariance matrix; singular system.</span></div><div class='output co'>#> <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#> <span class='message'>The half-life obtained from the IORE model may be used</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>nafta_att_p5a</span>)</div><div class='output co'>#> Sums of squares: #> SFO IORE DFOP #> 465.21753 56.27506 32.06401 #> @@ -161,22 +161,22 @@ #> #> Parameters: #> $SFO -#> Estimate Pr(>t) Lower Upper -#> parent_0 95.84012168 1.095639e-21 92.120517864 99.55972549 -#> k_parent_sink 0.01024015 1.710227e-12 0.008996874 0.01165524 +#> Estimate Pr(>t) Lower Upper +#> parent_0 95.8401 1.10e-21 92.121 99.5597 +#> k_parent_sink 0.0102 1.71e-12 0.009 0.0117 #> #> $IORE -#> Estimate Pr(>t) Lower Upper -#> parent_0 1.007532e+02 2.365797e-26 9.891170e+01 1.025947e+02 -#> k__iore_parent_sink 1.544192e-05 8.733384e-02 3.482391e-06 6.847393e-05 -#> N_parent 2.569877e+00 1.140446e-11 2.215298e+00 2.924456e+00 +#> Estimate Pr(>t) Lower Upper +#> parent_0 1.01e+02 2.37e-26 9.89e+01 1.03e+02 +#> k__iore_parent_sink 1.54e-05 8.73e-02 3.48e-06 6.85e-05 +#> N_parent 2.57e+00 1.14e-11 2.22e+00 2.92e+00 #> #> $DFOP -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.994630e+01 4.330861e-27 NA NA -#> k1 2.674255e-02 3.171390e-05 NA NA -#> k2 2.161318e-12 5.000000e-01 NA NA -#> g 6.465276e-01 2.129114e-05 NA NA +#> Estimate Pr(>t) Lower Upper +#> parent_0 9.99e+01 4.33e-27 NA NA +#> k1 2.67e-02 3.17e-05 NA NA +#> k2 2.16e-12 5.00e-01 NA NA +#> g 6.47e-01 2.13e-05 NA NA #> #> #> DTx values: diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index 229f8b04..fc4193cb 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -195,7 +195,7 @@ In the case of iterative reweighting, the variances obtained by this <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='no'>sfo_sfo</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( + <pre class="examples"><div class='input'> </div><div class='input'> <span class='no'>sfo_sfo</span> <span class='kw'><-</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='kw'>to</span> <span class='kw'>=</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>) )</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='no'>d_t</span> <span class='kw'><-</span> <span class='no'>FOCUS_2006_D</span> @@ -209,7 +209,7 @@ In the case of iterative reweighting, the variances obtained by this #> f_nw 5 204.4619 #> f_obs 6 205.8727 #> f_tc 6 143.8773 -#> f_man 4 291.8000</div></pre> +#> f_man 4 291.8000</div><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index bfb34489..5fbbc962 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -161,10 +161,10 @@ <pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"phenol"</span>), <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"anisole"</span>), <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> </div><div class='input'> <span class='no'>fit.1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</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.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 + <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Could not estimate covariance matrix; singular system.</span></div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 21:07:42 2019 -#> Date of summary: Tue Feb 26 21:07:42 2019 +#> Date of fit: Mon Mar 4 10:08:00 2019 +#> Date of summary: Mon Mar 4 10:08:00 2019 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -174,7 +174,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 574 model solutions performed in 3.766 s +#> Fitted with method Port using 574 model solutions performed in 3.762 s #> #> Weighting: none #> @@ -210,8 +210,8 @@ #> log_k_phenol_anisole -0.9037 NA NA NA #> log_k_anisole_sink -5.0090 NA NA NA #> -#> Parameter correlation:</div><div class='output co'>#> <span class='warning'>Warning: Could not estimate covariance matrix; singular system:</span></div><div class='output co'>#> Could not estimate covariance matrix; singular system: -#> +#> Parameter correlation: +#> Could not estimate covariance matrix; singular system. #> Residual standard error: 2.78 on 18 degrees of freedom #> #> Backtransformed parameters: @@ -252,8 +252,8 @@ <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</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.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 21:07:44 2019 -#> Date of summary: Tue Feb 26 21:07:44 2019 +#> Date of fit: Mon Mar 4 10:08:02 2019 +#> Date of summary: Mon Mar 4 10:08:02 2019 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -263,7 +263,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.612 s +#> Fitted with method Port using 246 model solutions performed in 1.598 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 2494faf9..cd6ace43 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -441,15 +441,15 @@ <span class='no'>fit</span> <span class='kw'><-</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'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 21:07:47 2019 -#> Date of summary: Tue Feb 26 21:07:47 2019 +#> Date of fit: Mon Mar 4 10:08:05 2019 +#> Date of summary: Mon Mar 4 10:08:05 2019 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.161 s +#> Fitted with method Port using 64 model solutions performed in 0.159 s #> #> Weighting: none #> @@ -518,7 +518,7 @@ <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'>#> <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'><-</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'>#> User System verstrichen -#> 1.111 0.000 1.112 </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'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 1.026 0.000 1.035 </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'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -593,7 +593,7 @@ #> Model cost at call 146 : 371.2134 #> Optimisation by method Port successfully terminated. #> User System verstrichen -#> 0.826 0.000 0.827 </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'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.814 0.008 0.830 </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'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750 </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'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -631,8 +631,8 @@ <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'>#> <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'><-</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>) <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'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 21:07:59 2019 -#> Date of summary: Tue Feb 26 21:07:59 2019 +#> Date of fit: Mon Mar 4 10:08:17 2019 +#> Date of summary: Mon Mar 4 10:08:17 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -640,7 +640,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 186 model solutions performed in 0.841 s +#> Fitted with method Port using 186 model solutions performed in 0.853 s #> #> Weighting: none #> @@ -748,8 +748,8 @@ #> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.irls</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</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'>f.irls</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 21:08:02 2019 -#> Date of summary: Tue Feb 26 21:08:02 2019 +#> Date of fit: Mon Mar 4 10:08:20 2019 +#> Date of summary: Mon Mar 4 10:08:20 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -757,7 +757,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 551 model solutions performed in 2.596 s +#> Fitted with method Port using 551 model solutions performed in 2.525 s #> #> Weighting: none #> @@ -870,8 +870,8 @@ #> 120 m1 33.31 28.80898 4.501e+00 2.722</div><div class='input'><span class='no'>f.w.mean</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</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'>f.w.mean</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 21:08:03 2019 -#> Date of summary: Tue Feb 26 21:08:03 2019 +#> Date of fit: Mon Mar 4 10:08:21 2019 +#> Date of summary: Mon Mar 4 10:08:21 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -879,7 +879,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 155 model solutions performed in 0.701 s +#> Fitted with method Port using 155 model solutions performed in 0.706 s #> #> Weighting: mean #> @@ -988,8 +988,8 @@ <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'>f.w.value</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 21:08:03 2019 -#> Date of summary: Tue Feb 26 21:08:03 2019 +#> Date of fit: Mon Mar 4 10:08:22 2019 +#> Date of summary: Mon Mar 4 10:08:22 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -997,7 +997,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 174 model solutions performed in 0.795 s +#> Fitted with method Port using 174 model solutions performed in 0.875 s #> #> Weighting: manual #> @@ -1108,8 +1108,8 @@ <span class='no'>f.w.man</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</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'>f.w.man</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 21:08:05 2019 -#> Date of summary: Tue Feb 26 21:08:05 2019 +#> Date of fit: Mon Mar 4 10:08:23 2019 +#> Date of summary: Mon Mar 4 10:08:23 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1117,7 +1117,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 270 model solutions performed in 1.24 s +#> Fitted with method Port using 270 model solutions performed in 1.279 s #> #> Weighting: manual #> @@ -1226,8 +1226,8 @@ <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 21:08:08 2019 -#> Date of summary: Tue Feb 26 21:08:08 2019 +#> Date of fit: Mon Mar 4 10:08:26 2019 +#> Date of summary: Mon Mar 4 10:08:26 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1235,7 +1235,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 692 model solutions performed in 3.192 s +#> Fitted with method Port using 692 model solutions performed in 3.203 s #> #> Weighting: manual #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 8c2ec38c..ddb695e3 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'><-</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'>#> Compilation argument: -#> /usr/lib/R/bin/R CMD SHLIB file3dbe7c3499b.c 2> file3dbe7c3499b.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file135d360177d0.c 2> file135d360177d0.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index fb4afa9a..a0880959 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -328,7 +328,7 @@ <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'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen -#> 0.004 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>( +#> 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'>#> time parent m1 diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 44aaaa79..5f82f41f 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -194,8 +194,8 @@ <span class='no'>time_1</span> <span class='kw'><-</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'><-</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'>#> User System verstrichen -#> 0.041 0.032 6.955 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen -#> 22.625 0.004 22.646 </div><div class='input'> +#> 0.057 0.014 6.939 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen +#> 22.525 0.000 22.538 </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'>#> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340480 0.2659520 0.7505686 0.2494314 diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index c05ce4cb..38e642df 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -192,29 +192,29 @@ #> #> Parameters: #> $SFO -#> Estimate Pr(>t) Lower Upper -#> parent_0 83.755751519 8.076390e-15 76.928220975 90.583282063 -#> k_parent_sink 0.001703321 7.452357e-05 0.001108568 0.002617164 +#> Estimate Pr(>t) Lower Upper +#> parent_0 83.7558 8.08e-15 76.92822 90.58328 +#> k_parent_sink 0.0017 7.45e-05 0.00111 0.00262 #> #> $IORE -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.685291e+01 NA 8.752855e+01 1.061773e+02 -#> k__iore_parent_sink 8.403401e-14 NA 1.092058e-19 6.466429e-08 -#> N_parent 6.684457e+00 NA 3.538510e+00 9.830404e+00 +#> Estimate Pr(>t) Lower Upper +#> parent_0 9.69e+01 NA 8.75e+01 1.06e+02 +#> k__iore_parent_sink 8.40e-14 NA 1.09e-19 6.47e-08 +#> N_parent 6.68e+00 NA 3.54e+00 9.83e+00 #> #> $DFOP -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.755655e+01 4.439930e-13 8.884447e+01 1.062686e+02 -#> k1 4.240633e-02 3.554769e-02 1.414189e-02 1.271610e-01 -#> k2 8.237928e-04 2.060933e-02 3.172784e-04 2.138925e-03 -#> g 2.881037e-01 1.313715e-04 1.783967e-01 4.299694e-01 +#> Estimate Pr(>t) Lower Upper +#> parent_0 9.76e+01 4.44e-13 8.88e+01 1.06e+02 +#> k1 4.24e-02 3.55e-02 1.41e-02 1.27e-01 +#> k2 8.24e-04 2.06e-02 3.17e-04 2.14e-03 +#> g 2.88e-01 1.31e-04 1.78e-01 4.30e-01 #> #> #> DTx values: #> DT50 DT90 DT50_rep -#> SFO 407 1350 407 -#> IORE 541 5190000 1560000 -#> DFOP 429 2380 841 +#> SFO 407 1352 407 +#> IORE 541 5192060 1562966 +#> DFOP 429 2383 841 #> #> Representative half-life: #> [1] 841.4096</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='nafta-1.png' alt='' width='700' height='433' /></div></pre> diff --git a/docs/reference/print.nafta.html b/docs/reference/print.nafta.html index 31bd2956..1b35053f 100644 --- a/docs/reference/print.nafta.html +++ b/docs/reference/print.nafta.html @@ -137,7 +137,7 @@ </div> <pre class="usage"><span class='co'># S3 method for nafta</span> -<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>x</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre> +<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>x</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='no'>...</span>)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -151,6 +151,10 @@ <td><p>Should the evaluation text be shown?</p></td> </tr> <tr> + <th>digits</th> + <td><p>Number of digits to be used for printing parameters and dissipation times.</p></td> + </tr> + <tr> <th>…</th> <td><p>Not used.</p></td> </tr> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 8d9e0287..e2f4d2e2 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -211,15 +211,15 @@ <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'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 21:09:01 2019 -#> Date of summary: Tue Feb 26 21:09:01 2019 +#> Date of fit: Mon Mar 4 10:09:19 2019 +#> Date of summary: Mon Mar 4 10:09:19 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.084 s +#> Fitted with method Port using 35 model solutions performed in 0.086 s #> #> Weighting: none #> diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index 12904a1f..28e8b41c 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -160,7 +160,7 @@ <span class='no'>m_ws</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent_w</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_s"</span>), <span class='kw'>parent_s</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_w"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='no'>f_river</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_ws</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_river</span>)</div><div class='img'><img src='test_data_from_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'> - <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f_river</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower + <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f_river</span>)$<span class='no'>bpar</span></div><div class='output co'>#> <span class='warning'>Warning: Could not estimate covariance matrix; singular system.</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower #> parent_w_0 9.598567e+01 2.33959800 4.102657e+01 9.568967e-19 NA #> k_parent_w_sink 3.603743e-01 0.03497750 1.030303e+01 4.989002e-09 NA #> k_parent_w_parent_s 6.031371e-02 0.01746024 3.454346e+00 1.514723e-03 NA diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 115ee0ca..3148f00b 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -205,8 +205,8 @@ The transformation of sets of formation fractions is fragile, as it supposes <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</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>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 21:09:09 2019 -#> Date of summary: Tue Feb 26 21:09:09 2019 +#> Date of fit: Mon Mar 4 10:09:27 2019 +#> Date of summary: Mon Mar 4 10:09:27 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -214,7 +214,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.709 s +#> Fitted with method Port using 153 model solutions performed in 0.699 s #> #> Weighting: none #> @@ -281,8 +281,8 @@ The transformation of sets of formation fractions is fragile, as it supposes </div><div class='input'><span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</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.2</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 21:09:11 2019 -#> Date of summary: Tue Feb 26 21:09:11 2019 +#> Date of fit: Mon Mar 4 10:09:29 2019 +#> Date of summary: Mon Mar 4 10:09:29 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -290,7 +290,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 350 model solutions performed in 1.588 s +#> Fitted with method Port using 350 model solutions performed in 1.584 s #> #> Weighting: none #> @@ -369,8 +369,8 @@ The transformation of sets of formation fractions is fragile, as it supposes <span class='no'>fit.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></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>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 21:09:12 2019 -#> Date of summary: Tue Feb 26 21:09:12 2019 +#> Date of fit: Mon Mar 4 10:09:30 2019 +#> Date of summary: Mon Mar 4 10:09:30 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -378,7 +378,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 186 model solutions performed in 0.849 s +#> Fitted with method Port using 186 model solutions performed in 0.86 s #> #> Weighting: none #> @@ -453,8 +453,8 @@ The transformation of sets of formation fractions is fragile, as it supposes <span class='no'>fit.ff.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.2</span>, <span class='no'>FOCUS_2006_D</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.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Tue Feb 26 21:09:13 2019 -#> Date of summary: Tue Feb 26 21:09:13 2019 +#> Date of fit: Mon Mar 4 10:09:31 2019 +#> Date of summary: Mon Mar 4 10:09:31 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -462,7 +462,7 @@ The transformation of sets of formation fractions is fragile, as it supposes #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 104 model solutions performed in 0.47 s +#> Fitted with method Port using 104 model solutions performed in 0.476 s #> #> Weighting: none #> diff --git a/man/logLik.mkinfit.Rd b/man/logLik.mkinfit.Rd index fe517955..736ccd1e 100644 --- a/man/logLik.mkinfit.Rd +++ b/man/logLik.mkinfit.Rd @@ -48,6 +48,7 @@ \code{\link{AIC.mmkin}}. } \examples{ + \dontrun{ sfo_sfo <- mkinmod( parent = mkinsub("SFO", to = "m1"), m1 = mkinsub("SFO") @@ -60,6 +61,7 @@ d_t$err <- d_t$value # Manual weighting assuming sigma ~ y f_man <- mkinfit(sfo_sfo, d_t, err = "err", quiet = TRUE) AIC(f_nw, f_obs, f_tc, f_man) + } } \author{ Johannes Ranke diff --git a/man/print.nafta.Rd b/man/print.nafta.Rd index 78ece0ad..e42a619d 100644 --- a/man/print.nafta.Rd +++ b/man/print.nafta.Rd @@ -9,7 +9,7 @@ i.e. SFO, then IORE, and finally DFOP. } \usage{ - \method{print}{nafta}(x, quiet = TRUE, ...) + \method{print}{nafta}(x, quiet = TRUE, digits = 3, ...) } \arguments{ \item{x}{ @@ -18,6 +18,9 @@ \item{quiet}{ Should the evaluation text be shown? } + \item{digits}{ + Number of digits to be used for printing parameters and dissipation times. + } \item{\dots}{ Not used. } @@ -2,10 +2,10 @@ Loading mkin Testing mkin ✔ | OK F W S | Context
⠏ | 0 | Export dataset for reading into CAKE
⠋ | 1 | Export dataset for reading into CAKE
✔ | 1 | Export dataset for reading into CAKE -
⠏ | 0 | Calculation of FOCUS chi2 error levels
⠋ | 1 | Calculation of FOCUS chi2 error levels
⠙ | 2 | Calculation of FOCUS chi2 error levels
✔ | 2 | Calculation of FOCUS chi2 error levels [2.3 s] +
⠏ | 0 | Calculation of FOCUS chi2 error levels
⠋ | 1 | Calculation of FOCUS chi2 error levels
⠙ | 2 | Calculation of FOCUS chi2 error levels
✔ | 2 | Calculation of FOCUS chi2 error levels [2.4 s]
⠏ | 0 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠋ | 1 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠙ | 2 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠹ | 3 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠸ | 4 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠼ | 5 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠴ | 6 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠦ | 7 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠧ | 8 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠇ | 9 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠏ | 10 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠋ | 11 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠙ | 12 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
⠹ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014)
✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [8.0 s]
⠏ | 0 | Test fitting the decline of metabolites from their maximum
⠋ | 1 | Test fitting the decline of metabolites from their maximum
⠙ | 2 | Test fitting the decline of metabolites from their maximum
⠹ | 3 | Test fitting the decline of metabolites from their maximum
✔ | 3 | Test fitting the decline of metabolites from their maximum [0.6 s] -
⠏ | 0 | Iteratively reweighted least squares (IRLS) fitting
⠋ | 1 | Iteratively reweighted least squares (IRLS) fitting
⠙ | 2 | Iteratively reweighted least squares (IRLS) fitting
⠹ | 2 1 | Iteratively reweighted least squares (IRLS) fitting
✔ | 2 1 | Iteratively reweighted least squares (IRLS) fitting [15.9 s] +
⠏ | 0 | Iteratively reweighted least squares (IRLS) fitting
⠋ | 1 | Iteratively reweighted least squares (IRLS) fitting
⠙ | 2 | Iteratively reweighted least squares (IRLS) fitting
⠹ | 2 1 | Iteratively reweighted least squares (IRLS) fitting
✔ | 2 1 | Iteratively reweighted least squares (IRLS) fitting [16.0 s] ──────────────────────────────────────────────────────────────────────────────── test_irls.R:48: skip: Reweighting method 'tc' works Too much trouble with datasets that are randomly generated @@ -23,7 +23,7 @@ The SANN algorithm takes very long with the default maximum number of iterations ────────────────────────────────────────────────────────────────────────────────
⠏ | 0 | mkinmod model generation and printing
⠋ | 1 | mkinmod model generation and printing
⠙ | 2 | mkinmod model generation and printing
⠹ | 3 | mkinmod model generation and printing
⠸ | 4 | mkinmod model generation and printing
⠼ | 5 | mkinmod model generation and printing
⠴ | 6 | mkinmod model generation and printing
⠦ | 7 | mkinmod model generation and printing
⠧ | 8 | mkinmod model generation and printing
⠇ | 9 | mkinmod model generation and printing
✔ | 9 | mkinmod model generation and printing [0.2 s]
⠏ | 0 | Model predictions with mkinpredict
⠋ | 1 | Model predictions with mkinpredict
⠙ | 2 | Model predictions with mkinpredict
⠹ | 3 | Model predictions with mkinpredict
✔ | 3 | Model predictions with mkinpredict [0.3 s] -
⠏ | 0 | Evaluations according to 2015 NAFTA guidance
⠋ | 1 | Evaluations according to 2015 NAFTA guidance
⠙ | 2 | Evaluations according to 2015 NAFTA guidance
⠹ | 3 | Evaluations according to 2015 NAFTA guidance
⠸ | 4 | Evaluations according to 2015 NAFTA guidance
⠼ | 5 | Evaluations according to 2015 NAFTA guidance
⠴ | 6 | Evaluations according to 2015 NAFTA guidance
⠦ | 7 | Evaluations according to 2015 NAFTA guidance
⠧ | 8 | Evaluations according to 2015 NAFTA guidance
⠇ | 9 | Evaluations according to 2015 NAFTA guidance
⠏ | 9 1 | Evaluations according to 2015 NAFTA guidance
⠏ | 10 | Evaluations according to 2015 NAFTA guidance
⠋ | 11 | Evaluations according to 2015 NAFTA guidance
⠙ | 12 | Evaluations according to 2015 NAFTA guidance
⠹ | 13 | Evaluations according to 2015 NAFTA guidance
⠸ | 14 | Evaluations according to 2015 NAFTA guidance
⠼ | 15 | Evaluations according to 2015 NAFTA guidance
⠴ | 16 | Evaluations according to 2015 NAFTA guidance
⠦ | 17 | Evaluations according to 2015 NAFTA guidance
✔ | 17 | Evaluations according to 2015 NAFTA guidance [1.5 s] +
⠏ | 0 | Evaluations according to 2015 NAFTA guidance
⠋ | 1 | Evaluations according to 2015 NAFTA guidance
⠙ | 2 | Evaluations according to 2015 NAFTA guidance
⠹ | 3 | Evaluations according to 2015 NAFTA guidance
⠸ | 4 | Evaluations according to 2015 NAFTA guidance
⠼ | 5 | Evaluations according to 2015 NAFTA guidance
⠴ | 6 | Evaluations according to 2015 NAFTA guidance
⠦ | 7 | Evaluations according to 2015 NAFTA guidance
⠧ | 8 | Evaluations according to 2015 NAFTA guidance
⠇ | 9 | Evaluations according to 2015 NAFTA guidance
⠏ | 10 | Evaluations according to 2015 NAFTA guidance
⠋ | 11 | Evaluations according to 2015 NAFTA guidance
⠙ | 12 | Evaluations according to 2015 NAFTA guidance
⠹ | 13 | Evaluations according to 2015 NAFTA guidance
⠸ | 14 | Evaluations according to 2015 NAFTA guidance
⠼ | 15 | Evaluations according to 2015 NAFTA guidance
⠴ | 16 | Evaluations according to 2015 NAFTA guidance
⠦ | 17 | Evaluations according to 2015 NAFTA guidance
✔ | 17 | Evaluations according to 2015 NAFTA guidance [2.2 s]
⠏ | 0 | Fitting of parent only models
⠋ | 1 | Fitting of parent only models
⠙ | 2 | Fitting of parent only models
⠹ | 3 | Fitting of parent only models
⠸ | 4 | Fitting of parent only models
⠼ | 5 | Fitting of parent only models
⠴ | 6 | Fitting of parent only models
⠦ | 7 | Fitting of parent only models
⠧ | 8 | Fitting of parent only models
⠇ | 9 | Fitting of parent only models
⠏ | 10 | Fitting of parent only models
⠋ | 11 | Fitting of parent only models
⠙ | 12 | Fitting of parent only models
⠹ | 13 | Fitting of parent only models
⠸ | 14 | Fitting of parent only models
⠼ | 15 | Fitting of parent only models
⠴ | 16 | Fitting of parent only models
⠦ | 17 | Fitting of parent only models
⠧ | 18 | Fitting of parent only models
⠇ | 19 | Fitting of parent only models
⠏ | 20 | Fitting of parent only models
⠋ | 21 | Fitting of parent only models
✔ | 21 | Fitting of parent only models [23.8 s]
⠏ | 0 | Calculation of maximum time weighted average concentrations (TWAs)
⠋ | 1 | Calculation of maximum time weighted average concentrations (TWAs)
⠙ | 2 | Calculation of maximum time weighted average concentrations (TWAs)
⠹ | 3 | Calculation of maximum time weighted average concentrations (TWAs)
⠸ | 4 | Calculation of maximum time weighted average concentrations (TWAs)
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [3.7 s]
⠏ | 0 | Summary
⠋ | 1 | Summary
✔ | 1 | Summary @@ -33,7 +33,7 @@ The SANN algorithm takes very long with the default maximum number of iterations
⠏ | 0 | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠋ | 1 | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠙ | 2 | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠹ | 3 | Results for synthetic data established in expertise for UBA (Ranke 2014)
⠸ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014)
✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.4 s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 74.5 s +Duration: 75.3 s OK: 106 Failed: 0 diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf index ae524e01..c14aab4d 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: 2019-02-27 +Date: 2019-03-04 Optimiser: IRLS [Data] diff --git a/tests/testthat/NAFTA_SOP_Appendix_B.txt b/tests/testthat/NAFTA_SOP_Appendix_B.txt index 3842db91..e5479b88 100644 --- a/tests/testthat/NAFTA_SOP_Appendix_B.txt +++ b/tests/testthat/NAFTA_SOP_Appendix_B.txt @@ -7,29 +7,29 @@ Critical sum of squares for checking the SFO model: Parameters: $SFO - Estimate Pr(>t) Lower Upper -parent_0 51.2430312 1.178492e-10 45.4036817 57.0823806 -k_parent_sink 0.2531291 1.608492e-06 0.1935733 0.3310082 + Estimate Pr(>t) Lower Upper +parent_0 51.243 1.18e-10 45.404 57.082 +k_parent_sink 0.253 1.61e-06 0.194 0.331 $IORE - Estimate Pr(>t) Lower Upper -parent_0 51.710529483 8.522723e-15 4.951371e+01 53.907348241 -k__iore_parent_sink 0.001348359 6.841094e-02 3.421379e-04 0.005313859 -N_parent 2.661469429 3.975823e-08 2.191012e+00 3.131927092 + Estimate Pr(>t) Lower Upper +parent_0 51.71053 8.52e-15 4.95e+01 53.90735 +k__iore_parent_sink 0.00135 6.84e-02 3.42e-04 0.00531 +N_parent 2.66147 3.98e-08 2.19e+00 3.13193 $DFOP - Estimate Pr(>t) Lower Upper -parent_0 51.70546719 3.457982e-14 49.677926850 53.73300753 -k1 0.41569648 1.002119e-06 0.330769606 0.52242879 -k2 0.01273299 1.393989e-03 0.007230162 0.02242399 -g 0.83380396 5.718367e-12 0.771816175 0.88153694 + Estimate Pr(>t) Lower Upper +parent_0 51.7055 3.46e-14 49.67793 53.7330 +k1 0.4157 1.00e-06 0.33077 0.5224 +k2 0.0127 1.39e-03 0.00723 0.0224 +g 0.8338 5.72e-12 0.77182 0.8815 DTx values: DT50 DT90 DT50_rep SFO 2.74 9.1 2.74 IORE 1.37 28.5 8.57 -DFOP 2.17 39.9 54.40 +DFOP 2.17 39.9 54.44 Representative half-life: [1] 8.573302 diff --git a/tests/testthat/NAFTA_SOP_Appendix_D.txt b/tests/testthat/NAFTA_SOP_Appendix_D.txt index 8720a3b6..7ff2817c 100644 --- a/tests/testthat/NAFTA_SOP_Appendix_D.txt +++ b/tests/testthat/NAFTA_SOP_Appendix_D.txt @@ -7,29 +7,29 @@ Critical sum of squares for checking the SFO model: Parameters: $SFO - Estimate Pr(>t) Lower Upper -parent_0 83.755751519 8.076390e-15 76.928220975 90.583282063 -k_parent_sink 0.001703321 7.452357e-05 0.001108568 0.002617164 + Estimate Pr(>t) Lower Upper +parent_0 83.7558 8.08e-15 76.92822 90.58328 +k_parent_sink 0.0017 7.45e-05 0.00111 0.00262 $IORE - Estimate Pr(>t) Lower Upper -parent_0 9.685291e+01 NA 8.752855e+01 1.061773e+02 -k__iore_parent_sink 8.403401e-14 NA 1.092058e-19 6.466429e-08 -N_parent 6.684457e+00 NA 3.538510e+00 9.830404e+00 + Estimate Pr(>t) Lower Upper +parent_0 9.69e+01 NA 8.75e+01 1.06e+02 +k__iore_parent_sink 8.40e-14 NA 1.09e-19 6.47e-08 +N_parent 6.68e+00 NA 3.54e+00 9.83e+00 $DFOP - Estimate Pr(>t) Lower Upper -parent_0 9.755655e+01 4.439930e-13 8.884447e+01 1.062686e+02 -k1 4.240633e-02 3.554769e-02 1.414189e-02 1.271610e-01 -k2 8.237928e-04 2.060933e-02 3.172784e-04 2.138925e-03 -g 2.881037e-01 1.313715e-04 1.783967e-01 4.299694e-01 + Estimate Pr(>t) Lower Upper +parent_0 9.76e+01 4.44e-13 8.88e+01 1.06e+02 +k1 4.24e-02 3.55e-02 1.41e-02 1.27e-01 +k2 8.24e-04 2.06e-02 3.17e-04 2.14e-03 +g 2.88e-01 1.31e-04 1.78e-01 4.30e-01 DTx values: DT50 DT90 DT50_rep -SFO 407 1350 407 -IORE 541 5190000 1560000 -DFOP 429 2380 841 +SFO 407 1352 407 +IORE 541 5192060 1562966 +DFOP 429 2383 841 Representative half-life: [1] 841.4096 diff --git a/tests/testthat/SFO_SFO_printed.txt b/tests/testthat/SFO_SFO_printed.txt index 8a188152..d0402fc0 100644 --- a/tests/testthat/SFO_SFO_printed.txt +++ b/tests/testthat/SFO_SFO_printed.txt @@ -6,7 +6,6 @@ $type: SFO; $to: m1; $sink: TRUE $m1 $type: SFO; $sink: TRUE Coefficient matrix $coefmat available -Compiled model $cf available Differential equations: d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1 diff --git a/tests/testthat/test_mkinfit_errors.R b/tests/testthat/test_mkinfit_errors.R index 50d528e0..f1b4618c 100644 --- a/tests/testthat/test_mkinfit_errors.R +++ b/tests/testthat/test_mkinfit_errors.R @@ -81,6 +81,7 @@ test_that("We get reproducible output if quiet = FALSE", { }) test_that("We get warnings in case of overparameterisation", { + skip_on_cran() # On winbuilder the following fit does not give a warning expect_warning(f <- mkinfit("FOMC", FOCUS_2006_A, quiet = TRUE), "not converge") s2 <- expect_warning(summary(mkinfit("DFOP", FOCUS_2006_A, quiet = TRUE)), "singular system") }) diff --git a/tests/testthat/test_mkinmod.R b/tests/testthat/test_mkinmod.R index 430fad61..1f8ec166 100644 --- a/tests/testthat/test_mkinmod.R +++ b/tests/testthat/test_mkinmod.R @@ -45,8 +45,10 @@ test_that("mkinmod stops to prevent and/or explain user errors", { }) test_that("Printing mkinmod models is reproducible", { - expect_known_output(print(mkinmod(parent = mkinsub("SFO", "m1"), - m1 = mkinsub("SFO"), - quiet = TRUE)), + m_test <- mkinmod(parent = mkinsub("SFO", "m1"), + m1 = mkinsub("SFO"), + quiet = TRUE) + m_test$cf <- NULL # Remove to make test robust against missing gcc + expect_known_output(print(m_test), file = "SFO_SFO_printed.txt") }) diff --git a/tests/testthat/test_nafta.R b/tests/testthat/test_nafta.R index ad0f1d63..9528200d 100644 --- a/tests/testthat/test_nafta.R +++ b/tests/testthat/test_nafta.R @@ -19,10 +19,10 @@ context("Evaluations according to 2015 NAFTA guidance") test_that("Data for more than one compound are rejected", - expect_error(nafta(FOCUS_2006_D))) + expect_error(nafta(FOCUS_2006_D, cores = 1))) test_that("Test data from Appendix B are correctly evaluated", { - expect_message(res <- nafta(NAFTA_SOP_Appendix_B, "aerobic aquatic")) + expect_message(res <- nafta(NAFTA_SOP_Appendix_B, "aerobic aquatic", cores = 1)) # From Figure D.1 dtx_sop <- matrix(c(2.74, 1.37, 2.17, 9.1, 28.5, 39.9), nrow = 3, ncol = 2) @@ -43,7 +43,8 @@ test_that("Test data from Appendix B are correctly evaluated", { }) test_that("Test data from Appendix D are correctly evaluated", { - expect_message(res <- nafta(NAFTA_SOP_Appendix_D, "MRID 555555")) + expect_warning(res <- nafta(NAFTA_SOP_Appendix_D, "MRID 555555", + cores = 1, quiet = TRUE)) # From Figure D.1 dtx_sop <- matrix(c(407, 541, 429, 1352, 5192066, 2383), nrow = 3, ncol = 2) |