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Diffstat (limited to 'docs/reference/plot.mmkin.html')
| -rw-r--r-- | docs/reference/plot.mmkin.html | 113 |
1 files changed, 73 insertions, 40 deletions
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 3dd0203b..30d0406e 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -21,7 +21,7 @@ the fit of at least one model to the same dataset is shown."><!-- mathjax --><sc </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.1.0</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.0</span> </span> </div> @@ -48,19 +48,25 @@ the fit of at least one model to the same dataset is shown."><!-- mathjax --><sc <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a> </li> <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> </li> <li> <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> </li> <li> + <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> </li> <li> <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> </li> <li> - <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a> + <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + </li> + <li> + <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> </li> </ul></li> <li> @@ -94,22 +100,22 @@ the fit of at least one model to the same dataset is shown.</p> </div> <div id="ref-usage"> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for mmkin</span> -<span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span> - <span class="va">x</span>, - main <span class="op">=</span> <span class="st">"auto"</span>, - legends <span class="op">=</span> <span class="fl">1</span>, - resplot <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"time"</span>, <span class="st">"errmod"</span><span class="op">)</span>, - ylab <span class="op">=</span> <span class="st">"Residue"</span>, - standardized <span class="op">=</span> <span class="cn">FALSE</span>, - show_errmin <span class="op">=</span> <span class="cn">TRUE</span>, - errmin_var <span class="op">=</span> <span class="st">"All data"</span>, - errmin_digits <span class="op">=</span> <span class="fl">3</span>, - cex <span class="op">=</span> <span class="fl">0.7</span>, - rel.height.middle <span class="op">=</span> <span class="fl">0.9</span>, - ymax <span class="op">=</span> <span class="st">"auto"</span>, - <span class="va">...</span> -<span class="op">)</span></code></pre></div> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mmkin</span></span> +<span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span></span> +<span> <span class="va">x</span>,</span> +<span> main <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> legends <span class="op">=</span> <span class="fl">1</span>,</span> +<span> resplot <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"time"</span>, <span class="st">"errmod"</span><span class="op">)</span>,</span> +<span> ylab <span class="op">=</span> <span class="st">"Residue"</span>,</span> +<span> standardized <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> show_errmin <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<span> errmin_var <span class="op">=</span> <span class="st">"All data"</span>,</span> +<span> errmin_digits <span class="op">=</span> <span class="fl">3</span>,</span> +<span> cex <span class="op">=</span> <span class="fl">0.7</span>,</span> +<span> rel.height.middle <span class="op">=</span> <span class="fl">0.9</span>,</span> +<span> ymax <span class="op">=</span> <span class="st">"auto"</span>,</span> +<span> <span class="va">...</span></span> +<span><span class="op">)</span></span></code></pre></div> </div> <div id="arguments"> @@ -117,43 +123,70 @@ the fit of at least one model to the same dataset is shown.</p> <dl><dt>x</dt> <dd><p>An object of class <code><a href="mmkin.html">mmkin</a></code>, with either one row or one column.</p></dd> + + <dt>main</dt> <dd><p>The main title placed on the outer margin of the plot.</p></dd> + + <dt>legends</dt> <dd><p>An index for the fits for which legends should be shown.</p></dd> + + <dt>resplot</dt> <dd><p>Should the residuals plotted against time, using <code><a href="mkinresplot.html">mkinresplot</a></code>, or as squared residuals against predicted values, with the error model, using <code><a href="mkinerrplot.html">mkinerrplot</a></code>.</p></dd> + + <dt>ylab</dt> <dd><p>Label for the y axis.</p></dd> + + <dt>standardized</dt> <dd><p>Should the residuals be standardized? This option is passed to <code><a href="mkinresplot.html">mkinresplot</a></code>, it only takes effect if <code>resplot = "time"</code>.</p></dd> + + <dt>show_errmin</dt> <dd><p>Should the chi2 error level be shown on top of the plots to the left?</p></dd> + + <dt>errmin_var</dt> <dd><p>The variable for which the FOCUS chi2 error value should be shown.</p></dd> + + <dt>errmin_digits</dt> <dd><p>The number of significant digits for rounding the FOCUS chi2 error percentage.</p></dd> + + <dt>cex</dt> <dd><p>Passed to the plot functions and <code><a href="https://rdrr.io/r/graphics/mtext.html" class="external-link">mtext</a></code>.</p></dd> + + <dt>rel.height.middle</dt> <dd><p>The relative height of the middle plot, if more than two rows of plots are shown.</p></dd> + + <dt>ymax</dt> <dd><p>Maximum y axis value for <code><a href="plot.mkinfit.html">plot.mkinfit</a></code>.</p></dd> + + <dt>...</dt> <dd><p>Further arguments passed to <code><a href="plot.mkinfit.html">plot.mkinfit</a></code> and <code><a href="mkinresplot.html">mkinresplot</a></code>.</p></dd> + </dl></div> <div id="value"> <h2>Value</h2> - <p>The function is called for its side effect.</p> + + +<p>The function is called for its side effect.</p> </div> <div id="details"> <h2>Details</h2> @@ -167,32 +200,32 @@ latex is being used for the formatting of the chi2 error level.</p> <div id="ref-examples"> <h2>Examples</h2> - <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span> -<span class="r-in"> <span class="co"># \dontrun{</span></span> -<span class="r-in"> <span class="co"># Only use one core not to offend CRAN checks</span></span> -<span class="r-in"> <span class="va">fits</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"HS"</span><span class="op">)</span>,</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS B"</span> <span class="op">=</span> <span class="va">FOCUS_2006_B</span>, <span class="st">"FOCUS C"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>, <span class="co"># named list for titles</span></span> -<span class="r-in"> cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># \dontrun{</span></span></span> +<span class="r-in"><span> <span class="co"># Only use one core not to offend CRAN checks</span></span></span> +<span class="r-in"><span> <span class="va">fits</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="st">"HS"</span><span class="op">)</span>,</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS B"</span> <span class="op">=</span> <span class="va">FOCUS_2006_B</span>, <span class="st">"FOCUS C"</span> <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>, <span class="co"># named list for titles</span></span></span> +<span class="r-in"><span> cores <span class="op">=</span> <span class="fl">1</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span><span class="op">)</span></span></span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Optimisation did not converge:</span> <span class="r-wrn co"><span class="r-pr">#></span> iteration limit reached without convergence (10)</span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="plot.mmkin-1.png" alt="" width="700" height="433"></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="plot.mmkin-2.png" alt="" width="700" height="433"></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span>, show_errmin <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span>, show_errmin <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="plot.mmkin-3.png" alt="" width="700" height="433"></span> -<span class="r-in"></span> -<span class="r-in"> <span class="co"># We can also plot a single fit, if we like the way plot.mmkin works, but then the plot</span></span> -<span class="r-in"> <span class="co"># height should be smaller than the plot width (this is not possible for the html pages</span></span> -<span class="r-in"> <span class="co"># generated by pkgdown, as far as I know).</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span> <span class="co"># same as plot(fits[1, 2])</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># We can also plot a single fit, if we like the way plot.mmkin works, but then the plot</span></span></span> +<span class="r-in"><span> <span class="co"># height should be smaller than the plot width (this is not possible for the html pages</span></span></span> +<span class="r-in"><span> <span class="co"># generated by pkgdown, as far as I know).</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="st">"FOCUS C"</span><span class="op">]</span><span class="op">)</span> <span class="co"># same as plot(fits[1, 2])</span></span></span> <span class="r-plt img"><img src="plot.mmkin-4.png" alt="" width="700" height="433"></span> -<span class="r-in"></span> -<span class="r-in"> <span class="co"># Show the error models</span></span> -<span class="r-in"> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span>, resplot <span class="op">=</span> <span class="st">"errmod"</span><span class="op">)</span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># Show the error models</span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits</span><span class="op">[</span><span class="st">"FOMC"</span>, <span class="op">]</span>, resplot <span class="op">=</span> <span class="st">"errmod"</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="plot.mmkin-5.png" alt="" width="700" height="433"></span> -<span class="r-in"> <span class="co"># }</span></span> -<span class="r-in"></span> +<span class="r-in"><span> <span class="co"># }</span></span></span> +<span class="r-in"><span></span></span> </code></pre></div> </div> </div> @@ -207,7 +240,7 @@ latex is being used for the formatting of the chi2 error level.</p> </div> <div class="pkgdown"> - <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p> </div> 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