diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2018-03-11 22:12:51 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2018-03-11 22:12:51 +0100 |
| commit | d185c26e4909efbae9dc4210ed9eac4b2600910e (patch) | |
| tree | 7ac9660d439a6de997dac800d09c82404027ef9a | |
| parent | a0bbfd3291aaa1a55438b8746c1e3cfb58ce4172 (diff) | |
Static docs rebuilt again, with current pkgdown
58 files changed, 1256 insertions, 162 deletions
@@ -1,5 +1,4 @@ docs/articles/*_cache/ -docs/articles/*.R install.log mkin*.tar.gz mkin.tar diff --git a/GNUmakefile b/GNUmakefile index 4955a3e2..d56eee90 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -59,6 +59,7 @@ quickcheck: build-no-vignettes clean: $(RM) -r vignettes/*_cache $(RM) -r vignettes/*_files + $(RM) -r vignettes/*.R $(RM) Rplots.pdf test: quickinstall @@ -73,9 +74,7 @@ vignettes/%.html: vignettes/mkin_vignettes.css vignettes/references.bib vignette vignettes: vignettes/mkin.html vignettes/FOCUS_D.html vignettes/FOCUS_L.html vignettes/FOCUS_Z.html vignettes/compiled_models.html pd: - "$(RBIN)/Rscript" -e "pkgdown::build_news()" - "$(RBIN)/Rscript" -e "pkgdown::build_reference(run_dont_run = TRUE)" - "$(RBIN)/Rscript" -e "pkgdown::build_home()" + "$(RBIN)/Rscript" -e "pkgdown::build_site()" git add -A git commit -m 'Static documentation except articles rebuilt by pkgdown' -e diff --git a/docs/NEWS.html b/docs/NEWS.html new file mode 100644 index 00000000..8ea2aff9 --- /dev/null +++ b/docs/NEWS.html @@ -0,0 +1,610 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>/home/jranke/git/mkin/NEWS.md • mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> + +<!-- pkgdown --> +<link href="pkgdown.css" rel="stylesheet"> +<script src="jquery.sticky-kit.min.js"></script> +<script src="pkgdown.js"></script> + + +<meta property="og:title" content="/home/jranke/git/mkin/NEWS.md" /> +<!-- mathjax --> +<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + + + </head> + + <body> + <div class="container template-title-body"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + </ul> +</li> +<li> + <a href="news/index.html">News</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="contents col-md-12"> + <div class="page-header"> + <h1>/home/jranke/git/mkin/NEWS.md</h1> + </div> + + +<div id="mkin-0-9-47-1-2017-02-06" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-47-1-2017-02-06" class="anchor"></a>mkin 0.9.47.1 (2017-02-06)</h1> +<ul> +<li><p>Skip some test on CRAN and winbuilder to avoid timeouts</p></li> +<li><p>‘test_data_from_UBA_2014’: Added this list of datasets containing experimental data used in the expertise from 2014</p></li> +<li><p>‘mkinfit’: Added the iterative reweighting method ‘tc’ using the two-component error model from Rocke and Lorenzato. NA values in the data are not returned any more.</p></li> +<li><p>‘mkinfit’: Work around a bug in the current FME version that prevented the convergence message to be returned in the case of non-convergence.</p></li> +<li><p>‘summary.mkinfit’: Improved output regarding weighting method. No predictions are returned for NA values in the model (see above).</p></li> +<li><p>‘summary.mkinfit’: Show versions of mkin and R used for fitting (not the ones used for the summary) if the fit was generated with mkin >= 0.9.47.1</p></li> +</ul> +</div> +<div id="mkin-0-9-46-3-2017-11-16" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-46-3-2017-11-16" class="anchor"></a>mkin 0.9.46.3 (2017-11-16)</h1> +<ul> +<li><p><code>README.md</code>, <code>vignettes/mkin.Rmd</code>: URLs were updated</p></li> +<li><p><code>synthetic_data_for_UBA</code>: Add the code used to generate the data in the interest of reproducibility</p></li> +</ul> +</div> +<div id="mkin-0-9-46-2-2017-10-10" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-46-2-2017-10-10" class="anchor"></a>mkin 0.9.46.2 (2017-10-10)</h1> +<ul> +<li><p>Converted the vignette FOCUS_Z from tex/pdf to markdown/html</p></li> +<li><p><code>DESCRIPTION</code>: Add ORCID</p></li> +</ul> +</div> +<div id="mkin-0-9-46-1-2017-09-14" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-46-1-2017-09-14" class="anchor"></a>mkin 0.9.46.1 (2017-09-14)</h1> +<ul> +<li><p><code>plot.mkinfit</code>: Fix scaling of residual plots for the case of separate plots for each observed variable</p></li> +<li><p><code>plot.mkinfit</code>: Use all data points of the fitted curve for y axis scaling for the case of separate plots for each observed variable</p></li> +<li><p>Documentation updates</p></li> +</ul> +</div> +<div id="mkin-0-9-46-2017-07-24" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-46-2017-07-24" class="anchor"></a>mkin 0.9.46 (2017-07-24)</h1> +<ul> +<li>Remove <code>test_FOMC_ill-defined.R</code> as it is too platform dependent</li> +</ul> +</div> +<div id="mkin-0-9-45-2-2017-07-24" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-45-2-2017-07-24" class="anchor"></a>mkin 0.9.45.2 (2017-07-24)</h1> +<ul> +<li><p>Rename <code>twa</code> to <code>max_twa_parent</code> to avoid conflict with <code>twa</code> from my <code>pfm</code> package</p></li> +<li><p>Update URLs in documentation</p></li> +<li><p>Limit test code to one core to pass on windows</p></li> +<li><p>Switch from <code>microbenchmark</code> to <code>rbenchmark</code> as the former is not supported on all platforms</p></li> +</ul> +</div> +<div id="mkin-0-9-45-1-2016-12-20" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-45-1-2016-12-20" class="anchor"></a>mkin 0.9.45.1 (2016-12-20)</h1> +<div id="new-features" class="section level2"> +<h2 class="hasAnchor"> +<a href="#new-features" class="anchor"></a>New features</h2> +<ul> +<li>A <code>twa</code> function, calculating maximum time weighted average concentrations for the parent (SFO, FOMC and DFOP).</li> +</ul> +</div> +</div> +<div id="mkin-0-9-45-2016-12-08" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-45-2016-12-08" class="anchor"></a>mkin 0.9.45 (2016-12-08)</h1> +<div id="minor-changes" class="section level2"> +<h2 class="hasAnchor"> +<a href="#minor-changes" class="anchor"></a>Minor changes</h2> +<ul> +<li><p><code>plot.mkinfit</code> and <code>plot.mmkin</code>: If the plotting device is <code>tikz</code>, LaTeX markup is being used for the chi2 error in the graphs.</p></li> +<li><p>Use <code>pkgdown</code>, the successor of <code>staticdocs</code> for generating static HTML documentation. Include example output and graphs also for <code>dontrun</code> sections.</p></li> +<li><p><code>plot.mkinfit</code>: Plotting does not fail any more when the compiled model is not available, e.g. because it was removed from the temporary directory. In this case, the uncompiled model is now used for plotting</p></li> +</ul> +</div> +</div> +<div id="mkin-0-9-44-2016-06-29" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-44-2016-06-29" class="anchor"></a>mkin 0.9.44 (2016-06-29)</h1> +<div id="bug-fixes" class="section level2"> +<h2 class="hasAnchor"> +<a href="#bug-fixes" class="anchor"></a>Bug fixes</h2> +<ul> +<li>The test <code>test_FOMC_ill-defined</code> failed on several architectures, so the test is now skipped</li> +</ul> +</div> +</div> +<div id="mkin-0-9-43-2016-06-28" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-43-2016-06-28" class="anchor"></a>mkin 0.9.43 (2016-06-28)</h1> +<div id="major-changes" class="section level2"> +<h2 class="hasAnchor"> +<a href="#major-changes" class="anchor"></a>Major changes</h2> +<ul> +<li><p>The title was changed to <code>Kinetic evaluations of chemical degradation data</code></p></li> +<li><p><code>plot.mkinfit</code>: Add the possibility to show fits (and residual plots if requested) separately for the observed variables</p></li> +<li><p><code>plot.mkinfit</code>: Add the possibility to show the chi2 error levels in the plot, similar to the way they are shown in <code>plot.mmkin</code></p></li> +<li><p><code>plot_sep</code>: Add this function as a convenience wrapper for plotting observed variables of mkinfit objects separately, with chi2 error values and residual plots.</p></li> +<li><p>Vignettes: The main vignette <code>mkin</code> was converted to R markdown and updated. The other vignettes were also updated to show current improved functionality.</p></li> +<li><p>The function <code>add_err</code> was added to the package, making it easy to generate simulated data using an error model based on the normal distribution</p></li> +</ul> +</div> +<div id="minor-changes-1" class="section level2"> +<h2 class="hasAnchor"> +<a href="#minor-changes-1" class="anchor"></a>Minor changes</h2> +<ul> +<li><p>Remove an outdated reference to the inline package in the <code>compiled_models</code> vignette</p></li> +<li><p><code>mkinfit</code>: Do not error out in cases where the fit converges, but the Jacobian for the untransformed model cost can not be estimated. Give a warning instead and return NA for the t-test results.</p></li> +<li><p><code>summary.mkinfit</code>: Give a warning message when the covariance matrix can not be obtained.</p></li> +<li><p>A test has been added to containing a corresponding edge case to check that the warnings are correctly issued and the fit does not terminate.</p></li> +<li><p><code>plot.mmkin</code>: Round the chi2 error value to three significant digits, instead of two decimal digits.</p></li> +<li><p><code>mkinfit</code>: Return the <code>err</code> values used on weighted fits as a column named <code>err</code>. Also include these inverse weights when the column <code>value</code> in the observed data is used, which is returned as <code>observed</code> in the data component of the mkinfit object.</p></li> +</ul> +</div> +<div id="bug-fixes-1" class="section level2"> +<h2 class="hasAnchor"> +<a href="#bug-fixes-1" class="anchor"></a>Bug fixes</h2> +<ul> +<li><p><code>endpoints</code>: When the name of a substance degrading to a metabolite (e.g. a parent compound) used in the model formulation ended in the letter <code>f</code>, some rate parameters could be listed as formation fractions with mixed up names. These would also appear in the summary.</p></li> +<li><p><code>mkinfit</code>: Check for all observed variables when checking if the user tried to fix formation fractions when fitting them using ilr transformation.</p></li> +<li><p><code>plot.mmkin</code>: Set the plot margins correctly, also in the case of a single fit to be plotted, so the main title is placed in a reasonable way.</p></li> +<li><p><code>plot.mkinfit</code>: Correct default values for <code>col_obs</code>, <code>pch_obs</code> and <code>lty_obs</code> for the case that <code>obs_vars</code> is specified.</p></li> +</ul> +</div> +</div> +<div id="mkin-0-9-42-2016-03-25" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-42-2016-03-25" class="anchor"></a>mkin 0.9.42 (2016-03-25)</h1> +<div id="major-changes-1" class="section level2"> +<h2 class="hasAnchor"> +<a href="#major-changes-1" class="anchor"></a>Major changes</h2> +<ul> +<li>Add the argument <code>from_max_mean</code> to <code>mkinfit</code>, for fitting only the decline from the maximum observed value for models with a single observed variable</li> +</ul> +</div> +<div id="minor-changes-2" class="section level2"> +<h2 class="hasAnchor"> +<a href="#minor-changes-2" class="anchor"></a>Minor changes</h2> +<ul> +<li><p>Add plots to <code>compiled_models</code> vignette</p></li> +<li><p>Give an explanatory error message when mkinmod fails due to a missing definition of a target variable</p></li> +<li><p><code><a href="reference/print.mkinmod.html">print.mkinmod()</a></code>: Improve formatting when printing mkinmod model definitions</p></li> +</ul> +</div> +</div> +<div id="mkin-0-9-41-2015-11-09" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-41-2015-11-09" class="anchor"></a>mkin 0.9-41 (2015-11-09)</h1> +<div id="minor-changes-3" class="section level2"> +<h2 class="hasAnchor"> +<a href="#minor-changes-3" class="anchor"></a>Minor changes</h2> +<ul> +<li><p>Add an R6 class <code>mkinds</code> representing datasets with a printing method</p></li> +<li><p>Add a printing method for mkinmod objects</p></li> +<li><p>Make it possible to specify arbitrary strings as names for the compounds in <code>mkinmod</code>, and show them in the plot</p></li> +<li><p>Use an index.r file to group help topics in static documentation</p></li> +</ul> +</div> +<div id="bug-fixes-2" class="section level2"> +<h2 class="hasAnchor"> +<a href="#bug-fixes-2" class="anchor"></a>Bug fixes</h2> +<ul> +<li> +<code><a href="reference/summary.mkinfit.html">print.summary.mkinfit()</a></code>: Avoid an error that occurred when printing summaries generated with mkin versions before 0.9-36</li> +</ul> +</div> +</div> +<div id="mkin-0-9-40-2015-07-21" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-40-2015-07-21" class="anchor"></a>mkin 0.9-40 (2015-07-21)</h1> +<div id="bug-fixes-3" class="section level2"> +<h2 class="hasAnchor"> +<a href="#bug-fixes-3" class="anchor"></a>Bug fixes</h2> +<ul> +<li> +<code><a href="reference/endpoints.html">endpoints()</a></code>: For DFOP and SFORB models, where <code>optimize()</code> is used, make use of the fact that the DT50 must be between DT50_k1 and DT50_k2 (DFOP) or DT50_b1 and DT50_b2 (SFORB), as <code>optimize()</code> sometimes did not find the minimum. Likewise for finding DT90 values. Also fit on the log scale to make the function more efficient.</li> +</ul> +</div> +<div id="internal-changes" class="section level2"> +<h2 class="hasAnchor"> +<a href="#internal-changes" class="anchor"></a>Internal changes</h2> +<ul> +<li> +<code>DESCRIPTION</code>, <code>NAMESPACE</code>, <code>R/*.R</code>: Import (from) stats, graphics and methods packages, and qualify some function calls for non-base packages installed with R to avoid NOTES made by R CMD check –as-cran with upcoming R versions.</li> +</ul> +</div> +</div> +<div id="mkin-0-9-39-2015-06-26" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-39-2015-06-26" class="anchor"></a>mkin 0.9-39 (2015-06-26)</h1> +<div id="major-changes-2" class="section level2"> +<h2 class="hasAnchor"> +<a href="#major-changes-2" class="anchor"></a>Major changes</h2> +<ul> +<li><p>New function <code><a href="reference/mmkin.html">mmkin()</a></code>: This function takes a character vector of model shorthand names, or alternatively a list of mkinmod models, as well as a list of dataset as main arguments. It returns a matrix of mkinfit objects, with a row for each model and a column for each dataset. A subsetting method with single brackets is available. Fitting the models in parallel using the <code>parallel</code> package is supported.</p></li> +<li><p>New function <code><a href="reference/plot.mmkin.html">plot.mmkin()</a></code>: Plots single-row or single-column <code>mmkin</code> objects including residual plots.</p></li> +</ul> +</div> +<div id="bug-fixes-4" class="section level2"> +<h2 class="hasAnchor"> +<a href="#bug-fixes-4" class="anchor"></a>Bug fixes</h2> +<ul> +<li> +<code><a href="reference/mkinparplot.html">mkinparplot()</a></code>: Fix the x axis scaling for rate constants and formation fractions that got confused by the introduction of the t-values of transformed parameters.</li> +</ul> +</div> +</div> +<div id="mkin-0-9-38-2015-06-24" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-38-2015-06-24" class="anchor"></a>mkin 0.9-38 (2015-06-24)</h1> +<div id="minor-changes-4" class="section level2"> +<h2 class="hasAnchor"> +<a href="#minor-changes-4" class="anchor"></a>Minor changes</h2> +<ul> +<li><p><code>vignettes/compiled_models.html</code>: Show the performance improvement factor actually obtained when building the vignette, as well as mkin version, some system info and the CPU model used for building the vignette.</p></li> +<li><p><code>GNUMakefile</code>,<code>vignettes/*</code>: Clean up vignette generation and include table of contents in HTML vignettes.</p></li> +</ul> +</div> +<div id="bug-fixes-5" class="section level2"> +<h2 class="hasAnchor"> +<a href="#bug-fixes-5" class="anchor"></a>Bug fixes</h2> +<ul> +<li> +<code><a href="reference/mkinmod.html">mkinmod()</a></code>: When generating the C code for the derivatives, only declare the time variable when it is needed and remove the ‘-W-no-unused-variable’ compiler flag as the C compiler used in the CRAN checks on Solaris does not know it.</li> +</ul> +</div> +</div> +<div id="mkin-0-9-36-2015-06-21" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-36-2015-06-21" class="anchor"></a>mkin 0.9-36 (2015-06-21)</h1> +<div id="major-changes-3" class="section level2"> +<h2 class="hasAnchor"> +<a href="#major-changes-3" class="anchor"></a>Major changes</h2> +<ul> +<li><p><code><a href="reference/summary.mkinfit.html">summary.mkinfit()</a></code>: A one-sided t-test for significant difference of untransformed parameters from zero is now always shown, based on the assumption of normal distribution for estimators of all untransformed parameters. Use with caution, as this assumption is unrealistic e.g. for rate constants in these nonlinear kinetic models.</p></li> +<li><p>If a compiler (gcc) is installed, use a version of the differential equation model compiled from C code, which is a huge performance boost for models where only the deSolve method works.</p></li> +<li><p><code><a href="reference/mkinmod.html">mkinmod()</a></code>: Create a list component $cf (of class CFuncList) in the list returned by mkinmod, if a version can be compiled from autogenerated C code (see above).</p></li> +<li><p><code><a href="reference/mkinfit.html">mkinfit()</a></code>: Set the default <code>solution_type</code> to <code>deSolve</code> when a compiled version of the model is present, except when an analytical solution is possible.</p></li> +</ul> +</div> +<div id="minor-changes-5" class="section level2"> +<h2 class="hasAnchor"> +<a href="#minor-changes-5" class="anchor"></a>Minor changes</h2> +<ul> +<li>Added a simple showcase vignette with an evaluation of FOCUS example dataset D</li> +</ul> +</div> +</div> +<div id="mkin-0-9-35-2015-05-15" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-35-2015-05-15" class="anchor"></a>mkin 0.9-35 (2015-05-15)</h1> +<div id="major-changes-4" class="section level2"> +<h2 class="hasAnchor"> +<a href="#major-changes-4" class="anchor"></a>Major changes</h2> +<ul> +<li>Switch from RUnit to testthat for testing</li> +</ul> +</div> +<div id="bug-fixes-6" class="section level2"> +<h2 class="hasAnchor"> +<a href="#bug-fixes-6" class="anchor"></a>Bug fixes</h2> +<ul> +<li><p><code><a href="reference/mkinparplot.html">mkinparplot()</a></code>: Avoid warnings that occurred when not all confidence intervals were available in the summary of the fit</p></li> +<li><p><code><a href="reference/summary.mkinfit.html">print.summary.mkinfit()</a></code>: Fix printing the summary for the case that the number of iterations is not available</p></li> +<li><p>NAMESPACE: export S3 methods plot.mkinfit, summary.mkinfit and print.summary.mkinfit to satisfy R CMD check on R-devel</p></li> +<li><p><code><a href="reference/mkinparplot.html">mkinparplot()</a></code>: Avoid warning in R CMD check about undeclared global variable <code>Lower</code></p></li> +</ul> +</div> +<div id="new-features-1" class="section level2"> +<h2 class="hasAnchor"> +<a href="#new-features-1" class="anchor"></a>New features</h2> +<ul> +<li><p><code><a href="reference/mkinfit.html">mkinfit()</a></code>: Report successful termination when quiet = FALSE. This is helpful for more difficult problems fitted with reweight.method = obs, as no progress is often indicated during the reweighting.</p></li> +<li><p>A first test using results established in the expertise written for the German Federal Environmental Agency (UBA) was added.</p></li> +<li><p>Add synthetic datasets generated for expertise written for the German Federal Environmental Agency UBA</p></li> +<li><p>Add tests based on these datasets</p></li> +</ul> +</div> +</div> +<div id="mkin-0-9-34-2014-11-22" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-34-2014-11-22" class="anchor"></a>mkin 0.9-34 (2014-11-22)</h1> +<div id="new-features-2" class="section level2"> +<h2 class="hasAnchor"> +<a href="#new-features-2" class="anchor"></a>New features</h2> +<ul> +<li><p>Add the convenience function <code><a href="reference/mkinsub.html">mkinsub()</a></code> for creating the lists used in <code><a href="reference/mkinmod.html">mkinmod()</a></code></p></li> +<li><p>Add the possibility to fit indeterminate order rate equation (IORE) models using an analytical solution (parent only) or a numeric solution. Paths from IORE compounds to metabolites are supported when using formation fractions (use_of_ff = ‘max’). Note that the numerical solution (method.ode = ‘deSolve’) of the IORE differential equations sometimes fails due to numerical problems.</p></li> +<li><p>Switch to using the Port algorithm (using a model/trust region approach) per default. While needing more iterations than the Levenberg-Marquardt algorithm previously used per default, it is less sensitive to starting parameters.</p></li> +</ul> +</div> +<div id="minor-changes-6" class="section level2"> +<h2 class="hasAnchor"> +<a href="#minor-changes-6" class="anchor"></a>Minor changes</h2> +<ul> +<li><p>The formatting of differential equations in the summary was further improved</p></li> +<li><p>Always include 0 on y axis when plotting during the fit</p></li> +</ul> +</div> +</div> +<div id="mkin-0-9-33-2014-10-22" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-33-2014-10-22" class="anchor"></a>mkin 0.9-33 (2014-10-22)</h1> +<div id="new-features-3" class="section level2"> +<h2 class="hasAnchor"> +<a href="#new-features-3" class="anchor"></a>New features</h2> +<ul> +<li><p>The initial value (state.ini) for the observed variable with the highest observed residue is set to 100 in case it has no time zero observation and <code>state.ini = "auto"</code></p></li> +<li><p>A basic unit test for <code><a href="reference/mkinerrmin.html">mkinerrmin()</a></code> was written</p></li> +</ul> +</div> +<div id="bug-fixes-7" class="section level2"> +<h2 class="hasAnchor"> +<a href="#bug-fixes-7" class="anchor"></a>Bug fixes</h2> +<ul> +<li><p><code><a href="reference/mkinfit.html">mkinfit()</a></code>: The internally fitted parameter for <code>g</code> was named <code>g_ilr</code> even when <code>transform_fractions=FALSE</code></p></li> +<li><p><code><a href="reference/mkinfit.html">mkinfit()</a></code>: The initial value (state.ini) for the parent compound was not set when the parent was not the (only) variable with the highest value in the observed data.</p></li> +<li><p><code><a href="reference/mkinerrmin.html">mkinerrmin()</a></code>: When checking for degrees of freedom for metabolites, check if their time zero value is fixed instead of checking if the observed value is zero. This ensures correct calculation of degrees of freedom also in cases where the metabolite residue at time zero is greater zero.</p></li> +<li><p><code><a href="reference/plot.mkinfit.html">plot.mkinfit()</a></code>: Avoid a warning message about only using the first component of ylim that occurred when ylim was specified explicitly</p></li> +</ul> +</div> +<div id="minor-changes-7" class="section level2"> +<h2 class="hasAnchor"> +<a href="#minor-changes-7" class="anchor"></a>Minor changes</h2> +<ul> +<li><p>The formatting of differential equations in the summary was improved by wrapping overly long lines</p></li> +<li><p>The FOCUS_Z vignette was rebuilt with the above improvement and using a width of 70 to avoid output outside of the grey area</p></li> +<li><p><code><a href="reference/summary.mkinfit.html">print.summary.mkinfit()</a></code>: Avoid a warning that occurred when gmkin showed summaries ofinitial fits without iterations</p></li> +<li><p><code><a href="reference/mkinfit.html">mkinfit()</a></code>: Avoid a warning that occurred when summarising a fit that was performed with maxitmodFit = 0 as done in gmkin for configuring new fits.</p></li> +</ul> +</div> +</div> +<div id="mkin-0-9-32-2014-07-24" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-32-2014-07-24" class="anchor"></a>mkin 0.9-32 (2014-07-24)</h1> +<div id="new-features-4" class="section level2"> +<h2 class="hasAnchor"> +<a href="#new-features-4" class="anchor"></a>New features</h2> +<ul> +<li><p>The number of degrees of freedom is difficult to define in the case of ilr transformation of formation fractions. Now for each source compartment the number of ilr parameters (=number of optimised parameters) is divided by the number of pathways to metabolites (=number of affected data series) which leads to fractional degrees of freedom in some cases.</p></li> +<li><p>The default for the initial value for the first state value is now taken from the mean of the observations at time zero, if available.</p></li> +<li><p>The kinetic model can alternatively be specified with a shorthand name for parent only degradation models, e.g. <code>SFO</code>, or <code>DFOP</code>.</p></li> +<li><p>Optimisation method, number of model evaluations and time elapsed during optimisation are given in the summary of mkinfit objects.</p></li> +<li><p>The maximum number of iterations in the optimisation algorithm can be specified using the argument <code>maxit.modFit</code> to the mkinfit function.</p></li> +<li><p>mkinfit gives a warning when the fit does not converge (does not apply to SANN method). This warning is included in the summary.</p></li> +</ul> +</div> +<div id="bug-fixes-8" class="section level2"> +<h2 class="hasAnchor"> +<a href="#bug-fixes-8" class="anchor"></a>Bug fixes</h2> +<ul> +<li><p>Avoid plotting an artifical 0 residual at time zero in <code>mkinresplot</code></p></li> +<li><p>In the determination of the degrees of freedom in <code>mkinerrmin</code>, formation fractions were accounted for multiple times in the case of parallel formation of metabolites. See the new feature described above for the solution.</p></li> +<li><p><code>transform_rates=FALSE</code> in <code>mkinfit</code> now also works for FOMC and HS models.</p></li> +<li><p>Initial values for formation fractions were not set in all cases.</p></li> +<li><p>No warning was given when the fit did not converge when a method other than the default Levenberg-Marquardt method <code>Marq</code> was used.</p></li> +</ul> +</div> +<div id="minor-changes-8" class="section level2"> +<h2 class="hasAnchor"> +<a href="#minor-changes-8" class="anchor"></a>Minor changes</h2> +<ul> +<li><p>Vignettes were rebuilt to reflect the changes in the summary method.</p></li> +<li><p>Algorithm <code>Pseudo</code> was excluded because it needs user-defined parameter limits which are not supported.</p></li> +<li><p>Algorithm <code>Newton</code> was excluded because of its different way to specify the maximum number of iterations and because it does not appear to provide additional benefits.</p></li> +</ul> +</div> +</div> +<div id="mkin-0-9-31-2014-07-14" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-31-2014-07-14" class="anchor"></a>mkin 0.9-31 (2014-07-14)</h1> +<div id="bug-fixes-9" class="section level2"> +<h2 class="hasAnchor"> +<a href="#bug-fixes-9" class="anchor"></a>Bug fixes</h2> +<ul> +<li>The internal renaming of optimised parameters in Version 0.9-30 led to errors in the determination of the degrees of freedom for the chi2 error level calulations in <code><a href="reference/mkinerrmin.html">mkinerrmin()</a></code> used by the summary function.</li> +</ul> +</div> +</div> +<div id="mkin-0-9-30-2014-07-11" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-30-2014-07-11" class="anchor"></a>mkin 0.9-30 (2014-07-11)</h1> +<div id="new-features-5" class="section level2"> +<h2 class="hasAnchor"> +<a href="#new-features-5" class="anchor"></a>New features</h2> +<ul> +<li>It is now possible to use formation fractions in combination with turning off the sink in <code><a href="reference/mkinmod.html">mkinmod()</a></code>.</li> +</ul> +</div> +<div id="major-changes-5" class="section level2"> +<h2 class="hasAnchor"> +<a href="#major-changes-5" class="anchor"></a>Major changes</h2> +<ul> +<li><p>The original and the transformed parameters now have different names (e.g. <code>k_parent</code> and <code>log_k_parent</code>. They also differ in how many they are when we have formation fractions but no pathway to sink.</p></li> +<li><p>The order of some of the information blocks in <code>print.summary.mkinfit.R()</code> has been ordered in a more logical way.</p></li> +</ul> +</div> +<div id="minor-changes-9" class="section level2"> +<h2 class="hasAnchor"> +<a href="#minor-changes-9" class="anchor"></a>Minor changes</h2> +<ul> +<li><p>The vignette FOCUS_Z has been simplified to use formation fractions with turning off the sink, and slightly amended to use the new versions of DT50 values calculated since mkin 0.9-29.</p></li> +<li><p>All vignettes have been rebuilt so they reflect all changes.</p></li> +<li><p>The ChangeLog was renamed to NEWS.md and the entries were converted to markdown syntax compatible with the <code>tools::news()</code> function built into R.</p></li> +<li><p>The test suite was overhauled. Tests of the DFOP and SFORB models with dataset FOCUS_2006_A were removed, as they were too much dependent on the optimisation algorithm and/or starting parameters, because the dataset is SFO (compare kinfit vignette).</p></li> +<li><p>Also, the Schaefer complex case can now be fitted using formation fractions, and with the ‘Port’ optimisation method we also fit A2 in the same way as published in the Piacenza paper.</p></li> +<li><p>Some more checks were introduced to <code><a href="reference/mkinfit.html">mkinfit()</a></code>, leading to warnings or stopping execution if unsupported combinations of methods and parameters are requested.</p></li> +</ul> +</div> +</div> +<div id="mkin-0-9-29-2014-06-27" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-29-2014-06-27" class="anchor"></a>mkin 0.9-29 (2014-06-27)</h1> +<ul> +<li><p>R/mkinresplot.R: Make it possible to specify <code>xlim</code></p></li> +<li><p>R/geometric_mean.R, man/geometric_mean.Rd: Add geometric mean function</p></li> +<li><p>R/endpoints.R, man/endpoints.Rd: Calculate additional (pseudo)-DT50 values for FOMC, DFOP, HS and SFORB. Avoid calculation of formation fractions from rate constants when they are directly fitted</p></li> +</ul> +</div> +<div id="mkin-0-9-28-2014-05-20" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-28-2014-05-20" class="anchor"></a>mkin 0.9-28 (2014-05-20)</h1> +<ul> +<li><p>Do not backtransform confidence intervals for formation fractions if more than one compound is formed, as such parameters only define the pathways as a set</p></li> +<li><p>Add historical remarks and some background to the main package vignette</p></li> +<li><p>Correct ‘isotropic’ into ‘isometric’ for the ilr transformation</p></li> +</ul> +</div> +<div id="mkin-0-9-27-2014-05-10" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-27-2014-05-10" class="anchor"></a>mkin 0.9-27 (2014-05-10)</h1> +<ul> +<li><p>Fork the GUI into a separate package <a href="http://github.com/jranke/gmkin">gmkin</a></p></li> +<li><p>DESCRIPTION, NAMESPACE, TODO: Adapt and add copyright information</p></li> +<li><p>Remove files belonging to the GUI</p></li> +<li><p>Possibility to fit without parameter transformations, using bounds as implemented in FME</p></li> +<li><p>Add McCall 2,4,5-T dataset</p></li> +<li><p>Enable selection of observed variables in plotting</p></li> +<li><p>Add possibility to show residual plot in <code>plot.mkinfit</code></p></li> +<li><p>R/mkinparplot.R, man/mkinparplot.Rd: plot parameters with confidence intervals</p></li> +<li><p>Change vignette format from Sweave to knitr</p></li> +<li><p>Split examples vignette to FOCUS_L and FOCUS_Z</p></li> +<li><p>Remove warning about constant formation fractions in mkinmod as it was based on a misconception</p></li> +<li><p>Restrict the unit test with the Schaefer data to parent and primary metabolites as formation fraction and DT50 for A2 are higly correlated and passing the test is platform dependent. For example, the test fails in 1 out of 14 platforms on CRAN as of today.</p></li> +<li><p>Add Eurofins Regulatory AG copyright notices</p></li> +<li><p>Import FME and deSolve instead of depending on them to have clean startup</p></li> +<li><p>Add a starter function for the GUI: <code>gmkin()</code></p></li> +<li><p>Change the format of the workspace files of gmkin so they can be distributed and documented in the package</p></li> +<li><p>Add gmkin workspace datasets FOCUS_2006_gmkin and FOCUS_2006_Z_gmkin</p></li> +</ul> +</div> +<div id="mkin-0-9-24-2013-11-06" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-24-2013-11-06" class="anchor"></a>mkin 0.9-24 (2013-11-06)</h1> +<ul> +<li><p>Bugfix re-enabling the fixing of any combination of initial values for state variables</p></li> +<li><p>Default values for kinetic rate constants are not all 0.1 any more but are “salted” with a small increment to avoid numeric artefacts with the eigenvalue based solutions</p></li> +<li><p>Backtransform fixed ODE parameters for the summary</p></li> +</ul> +</div> +<div id="mkin-0-9-22-2013-10-26" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin-0-9-22-2013-10-26" class="anchor"></a>mkin 0.9-22 (2013-10-26)</h1> +<ul> +<li><p>Get rid of the optimisation step in <code>mkinerrmin</code> - this was unnecessary. Thanks to KinGUII for the inspiration - actually this is equation 6-2 in FOCUS kinetics p. 91 that I had overlooked originally</p></li> +<li><p>Fix <code>plot.mkinfit</code> as it passed graphical arguments like main to the solver</p></li> +<li><p>Do not use <code>plot=TRUE</code> in <code><a href="reference/mkinfit.html">mkinfit()</a></code> example</p></li> +<li><p>The first successful fits in the not so simple GUI</p></li> +<li><p>Fix iteratively reweighted least squares for the case of many metabolites</p></li> +<li><p>Unify naming of initial values of state variables</p></li> +<li><p>Unify naming in dataframes of optimised and fixed parameters in the summary</p></li> +<li><p>Show the weighting method for residuals in the summary</p></li> +<li><p>Correct the output of the data in the case of manual weighting</p></li> +<li><p>Implement IRLS assuming different variances for observed variables</p></li> +<li><p>Do not use 0 values at time zero for chi2 error level calculations. This is the way it is done in KinGUII and it makes sense. It does impact the chi2 error levels in the output. Generally they seem to be lower for metabolites now, presumably because the mean of the observed values is higher</p></li> +</ul> +<p>For a detailed list of changes to the mkin source please consult the commit history on <a href="http://github.com/jranke/mkin" class="uri">http://github.com/jranke/mkin</a></p> +</div> + + + </div> + +</div> + + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> + diff --git a/docs/README.html b/docs/README.html new file mode 100644 index 00000000..98d42ebc --- /dev/null +++ b/docs/README.html @@ -0,0 +1,200 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>/home/jranke/git/mkin/README.md • mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + +<!-- clipboard.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> + +<!-- pkgdown --> +<link href="pkgdown.css" rel="stylesheet"> +<script src="jquery.sticky-kit.min.js"></script> +<script src="pkgdown.js"></script> + + +<meta property="og:title" content="/home/jranke/git/mkin/README.md" /> +<!-- mathjax --> +<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + + + </head> + + <body> + <div class="container template-title-body"> + <header> + <div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="reference/index.html">Functions and data</a> +</li> +<li class="dropdown"> + <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> + Articles + + <span class="caret"></span> + </a> + <ul class="dropdown-menu" role="menu"> + <li> + <a href="articles/mkin.html">Introduction to mkin</a> + </li> + <li> + <a href="articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + </li> + <li> + <a href="articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + </li> + <li> + <a href="articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + </li> + <li> + <a href="articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + </li> + <li> + <a href="articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + </li> + </ul> +</li> +<li> + <a href="news/index.html">News</a> +</li> + </ul> + + <ul class="nav navbar-nav navbar-right"> + + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + + </header> + + <div class="row"> + <div class="contents col-md-12"> + <div class="page-header"> + <h1>/home/jranke/git/mkin/README.md</h1> + </div> + +<div id="mkin" class="section level1"> +<h1 class="hasAnchor"> +<a href="#mkin" class="anchor"></a>mkin</h1> +<p><a href="https://cran.r-project.org/package=mkin"><img src="https://www.r-pkg.org/badges/version/mkin"></a></p> +<p>The R package <strong>mkin</strong> provides calculation routines for the analysis of chemical degradation data, including <b>m</b>ulticompartment <b>kin</b>etics as needed for modelling the formation and decline of transformation products, or if several compartments are involved.</p> +<div id="installation" class="section level2"> +<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"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">install.packages</span>(<span class="st">"mkin"</span>)</code></pre></div> +</div> +<div id="background" class="section level2"> +<h2 class="hasAnchor"> +<a href="#background" class="anchor"></a>Background</h2> +<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 and helpful tools have been developed as detailed in ‘Credits and historical remarks’ below.</p> +</div> +<div id="usage" class="section level2"> +<h2 class="hasAnchor"> +<a href="#usage" class="anchor"></a>Usage</h2> +<p>For a start, have a look a the code examples provided for <a href="https://pkgdown.jrwb.de/mkin/reference/plot.mkinfit.html"><code>plot.mkinfit</code></a> and <a href="https://pkgdown.jrwb.de/mkin/reference/plot.mmkin.html"><code>plot.mmkin</code></a>, and at the package vignettes <a href="https://pkgdown.jrwb.de/mkin/articles/FOCUS_L.html"><code>FOCUS L</code></a> and <a href="https://pkgdown.jrwb.de/mkin/articles/FOCUS_D.html"><code>FOCUS D</code></a>.</p> +</div> +<div id="documentation" class="section level2"> +<h2 class="hasAnchor"> +<a href="#documentation" class="anchor"></a>Documentation</h2> +<p>The HTML documentation is available at <a href="https://pkgdown.jrwb.de/mkin">jrwb.de</a>, at <a href="http://jranke.github.io/mkin">github</a> and at <a href="http://kinfit.r-forge.r-project.org/mkin_static/index.html">R-Forge</a>.</p> +</div> +<div id="features" class="section level2"> +<h2 class="hasAnchor"> +<a href="#features" class="anchor"></a>Features</h2> +<ul> +<li>Highly flexible model specification using <a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html"><code>mkinmod</code></a>, including equilibrium reactions and using the single first-order reversible binding (SFORB) model, which will automatically create two latent state variables for the observed variable.</li> +<li>As of version 0.9-39, fitting of several models to several datasets, optionally in parallel, is supported, see for example <a href="https://pkgdown.jrwb.de/mkin/reference/plot.mmkin.html"><code>plot.mmkin</code></a>.</li> +<li>Model solution (forward modelling) in the function <a href="https://pkgdown.jrwb.de/mkin/reference/mkinpredict.html"><code>mkinpredict</code></a> is performed either using the analytical solution for the case of parent only degradation, an eigenvalue based solution if only simple first-order (SFO) or SFORB kinetics are used in the model, or using a numeric solver from the <code>deSolve</code> package (default is <code>lsoda</code>).</li> +<li>If a C compiler is installed, the kinetic models are compiled from automatically generated C code, see <a href="https://pkgdown.jrwb.de/mkin/articles/compiled_models.html">vignette <code>compiled_models</code></a>. The autogeneration of C code was inspired by the <a href="https://github.com/karlines/ccSolve"><code>ccSolve</code></a> package. Thanks to Karline Soetaert for her work on that.</li> +<li>By default, kinetic rate constants and kinetic formation fractions are transformed internally using <a href="https://pkgdown.jrwb.de/mkin/reference/transform_odeparms.html"><code>transform_odeparms</code></a> so their estimators can more reasonably be expected to follow a normal distribution. This has the side effect that no constraints are needed in the optimisation. Thanks to René Lehmann for the nice cooperation on this, especially the isometric logration transformation that is now used for the formation fractions.</li> +<li>A side effect of this is that when parameter estimates are backtransformed to match the model definition, confidence intervals calculated from standard errors are also backtransformed to the correct scale, and will not include meaningless values like negative rate constants or formation fractions adding up to more than 1, which can not occur in a single experiment with a single defined radiolabel position.</li> +<li>The usual one-sided t-test for significant difference from zero is nevertheless shown based on estimators for the untransformed parameters.</li> +<li>Summary and plotting functions. The <code>summary</code> of an <code>mkinfit</code> object is in fact a full report that should give enough information to be able to approximately reproduce the fit with other tools.</li> +<li>The chi-squared error level as defined in the FOCUS kinetics guidance (see below) is calculated for each observed variable.</li> +<li>Iteratively reweighted least squares fitting is implemented in a similar way as in KinGUII and CAKE (see below). Simply add the argument <code>reweight.method = "obs"</code> to your call to <code>mkinfit</code> and a separate variance componenent for each of the observed variables will be optimised in a second stage after the primary optimisation algorithm has converged.</li> +<li>Iterative reweighting is also possible using the two-component error model for analytical data of <a href="https://pkgdown.jrwb.de/mkin/reference/sigma_rl.html">Rocke and Lorenzato</a> using the argument <code>reweight.method = "tc"</code>.</li> +<li>When a metabolite decline phase is not described well by SFO kinetics, SFORB kinetics can be used for the metabolite.</li> +</ul> +</div> +<div id="gui" class="section level2"> +<h2 class="hasAnchor"> +<a href="#gui" class="anchor"></a>GUI</h2> +<p>There is a graphical user interface that I consider useful for real work. Please refer to its <a href="http://kinfit.r-forge.r-project.org/gmkin_static">documentation page</a> for installation instructions and a manual.</p> +</div> +<div id="news" class="section level2"> +<h2 class="hasAnchor"> +<a href="#news" class="anchor"></a>News</h2> +<p>There is a ChangeLog, for the latest <a href="https://cran.r-project.org/package=mkin/news.html">CRAN release</a> and one for the <a href="https://github.com/jranke/mkin/blob/master/NEWS.md">github master branch</a>.</p> +</div> +<div id="credits-and-historical-remarks" class="section level2"> +<h2 class="hasAnchor"> +<a href="#credits-and-historical-remarks" class="anchor"></a>Credits and historical remarks</h2> +<p><code>mkin</code> would not be possible without the underlying software stack consisting of R and the packages <a href="https://cran.r-project.org/package=deSolve">deSolve</a> and <a href="https://cran.r-project.org/package=FME">FME</a>, to say the least.</p> +<p>It could not have been written without me being introduced to regulatory fate modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories Ltd (formerly RCC Ltd). <code>mkin</code> greatly profits from and largely follows the work done by the <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics">FOCUS Degradation Kinetics Workgroup</a>, as detailed in their guidance document from 2006, slightly updated in 2011 and in 2014.</p> +<p>Also, it was inspired by the first version of KinGUI developed by BayerCropScience, which is based on the MatLab runtime environment.</p> +<p>The companion package <a href="http://kinfit.r-forge.r-project.org/kinfit_static/index.html">kinfit</a> (now deprecated) was <a href="https://r-forge.r-project.org/scm/viewvc.php?view=rev&root=kinfit&revision=2">started in 2008</a> and <a href="https://cran.r-project.org/src/contrib/Archive/kinfit/">first published</a> on CRAN on 01 May 2010.</p> +<p>The first <code>mkin</code> code was <a href="https://r-forge.r-project.org/scm/viewvc.php?view=rev&root=kinfit&revision=8">published on 11 May 2010</a> and the <a href="https://cran.r-project.org/src/contrib/Archive/mkin">first CRAN version</a> on 18 May 2010.</p> +<p>In 2011, Bayer Crop Science started to distribute an R based successor to KinGUI named KinGUII whose R code is based on <code>mkin</code>, but which added, amongst other refinements, a closed source graphical user interface (GUI), iteratively reweighted least squares (IRLS) optimisation of the variance for each of the observed variables, and Markov Chain Monte Carlo (MCMC) simulation functionality, similar to what is available e.g. in the <code>FME</code> package.</p> +<p>Somewhat in parallel, Syngenta has sponsored the development of an <code>mkin</code> and KinGUII based GUI application called CAKE, which also adds IRLS and MCMC, is more limited in the model formulation, but puts more weight on usability. CAKE is available for download from the <a href="http://showcase.tessella.com/products/cake">CAKE website</a>, where you can also find a zip archive of the R scripts derived from <code>mkin</code>, published under the GPL license.</p> +<p>Finally, there is <a href="http://github.com/zhenglei-gao/KineticEval">KineticEval</a>, which contains a further development of the scripts used for KinGUII, so the different tools will hopefully be able to learn from each other in the future as well.</p> +</div> +<div id="development" class="section level2"> +<h2 class="hasAnchor"> +<a href="#development" class="anchor"></a>Development</h2> +<p>Contributions are welcome! Your <a href="https://help.github.com/articles/fork-a-repo">mkin fork</a> is just a mouse click away… The master branch on github should always be in good shape, I implement new features in separate branches now. If you prefer subversion, project members for the <a href="http://r-forge.r-project.org/R/?group_id=615">r-forge project</a> are welcome as well. Generally, the source code of the latest CRAN version should be available there. You can also browse the source code at <a href="http://cgit.jrwb.de/mkin">cgit.jrwb.de/mkin</a>.</p> +</div> +</div> + + </div> + +</div> + + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> +</div> + + </footer> + </div> + + </body> +</html> + diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index d85246f8..a8002acd 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -9,7 +9,10 @@ <!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> <!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Example evaluation of FOCUS Example Dataset D"> +<meta property="og:description" content=""> +<meta name="twitter:card" content="summary"> +<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--> @@ -77,7 +80,7 @@ <h1>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-09</h4> + <h4 class="date">2018-03-11</h4> </div> @@ -152,8 +155,8 @@ <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(fit)</code></pre></div> <pre><code>## mkin version: 0.9.46.3 ## R version: 3.4.3 -## Date of fit: Fri Mar 9 23:09:48 2018 -## Date of summary: Fri Mar 9 23:09:48 2018 +## Date of fit: Sun Mar 11 22:11:56 2018 +## Date of summary: Sun Mar 11 22:11:57 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -161,7 +164,7 @@ ## ## Model predictions using solution type deSolve ## -## Fitted with method Port using 153 model solutions performed in 0.99 s +## Fitted with method Port using 153 model solutions performed in 0.984 s ## ## Weighting: none ## diff --git a/docs/articles/FOCUS_L.R b/docs/articles/FOCUS_L.R deleted file mode 100644 index 063e3d57..00000000 --- a/docs/articles/FOCUS_L.R +++ /dev/null @@ -1,86 +0,0 @@ -## ---- include = FALSE---------------------------------------------------- -library(knitr) -opts_chunk$set(tidy = FALSE, cache = FALSE) - -## ------------------------------------------------------------------------ -library("mkin", quietly = TRUE) -FOCUS_2006_L1 = data.frame( - t = rep(c(0, 1, 2, 3, 5, 7, 14, 21, 30), each = 2), - parent = c(88.3, 91.4, 85.6, 84.5, 78.9, 77.6, - 72.0, 71.9, 50.3, 59.4, 47.0, 45.1, - 27.7, 27.3, 10.0, 10.4, 2.9, 4.0)) -FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1) - -## ------------------------------------------------------------------------ -m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet = TRUE) -summary(m.L1.SFO) - -## ----fig.width = 6, fig.height = 5--------------------------------------- -plot(m.L1.SFO, show_errmin = TRUE, main = "FOCUS L1 - SFO") - -## ----fig.width = 6, fig.height = 5--------------------------------------- -mkinresplot(m.L1.SFO, ylab = "Observed", xlab = "Time") - -## ----fig.width = 6, fig.height = 5--------------------------------------- -m.L1.FOMC <- mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet=TRUE) -plot(m.L1.FOMC, show_errmin = TRUE, main = "FOCUS L1 - FOMC") -summary(m.L1.FOMC, data = FALSE) - -## ------------------------------------------------------------------------ -FOCUS_2006_L2 = data.frame( - t = rep(c(0, 1, 3, 7, 14, 28), each = 2), - parent = c(96.1, 91.8, 41.4, 38.7, - 19.3, 22.3, 4.6, 4.6, - 2.6, 1.2, 0.3, 0.6)) -FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2) - -## ----fig.width = 7, fig.height = 6--------------------------------------- -m.L2.SFO <- mkinfit("SFO", FOCUS_2006_L2_mkin, quiet=TRUE) -plot(m.L2.SFO, show_residuals = TRUE, show_errmin = TRUE, - main = "FOCUS L2 - SFO") - -## ----fig.width = 7, fig.height = 6--------------------------------------- -m.L2.FOMC <- mkinfit("FOMC", FOCUS_2006_L2_mkin, quiet = TRUE) -plot(m.L2.FOMC, show_residuals = TRUE, - main = "FOCUS L2 - FOMC") -summary(m.L2.FOMC, data = FALSE) - -## ----fig.width = 7, fig.height = 6--------------------------------------- -m.L2.DFOP <- mkinfit("DFOP", FOCUS_2006_L2_mkin, quiet = TRUE) -plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE, - main = "FOCUS L2 - DFOP") -summary(m.L2.DFOP, data = FALSE) - -## ------------------------------------------------------------------------ -FOCUS_2006_L3 = data.frame( - t = c(0, 3, 7, 14, 30, 60, 91, 120), - parent = c(97.8, 60, 51, 43, 35, 22, 15, 12)) -FOCUS_2006_L3_mkin <- mkin_wide_to_long(FOCUS_2006_L3) - -## ----fig.height = 8------------------------------------------------------ -# Only use one core here, not to offend the CRAN checks -mm.L3 <- mmkin(c("SFO", "FOMC", "DFOP"), cores = 1, - list("FOCUS L3" = FOCUS_2006_L3_mkin), quiet = TRUE) -plot(mm.L3) - -## ----fig.height = 5------------------------------------------------------ -summary(mm.L3[["DFOP", 1]]) -plot(mm.L3[["DFOP", 1]], show_errmin = TRUE) - -## ------------------------------------------------------------------------ -FOCUS_2006_L4 = data.frame( - t = c(0, 3, 7, 14, 30, 60, 91, 120), - parent = c(96.6, 96.3, 94.3, 88.8, 74.9, 59.9, 53.5, 49.0)) -FOCUS_2006_L4_mkin <- mkin_wide_to_long(FOCUS_2006_L4) - -## ----fig.height = 6------------------------------------------------------ -# Only use one core here, not to offend the CRAN checks -mm.L4 <- mmkin(c("SFO", "FOMC"), cores = 1, - list("FOCUS L4" = FOCUS_2006_L4_mkin), - quiet = TRUE) -plot(mm.L4) - -## ----fig.height = 8------------------------------------------------------ -summary(mm.L4[["SFO", 1]], data = FALSE) -summary(mm.L4[["FOMC", 1]], data = FALSE) - diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 196a0c4f..a23876ec 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -9,7 +9,10 @@ <!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> <!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Example evaluation of FOCUS Laboratory Data L1 to L3"> +<meta property="og:description" content=""> +<meta name="twitter:card" content="summary"> +<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--> @@ -77,7 +80,7 @@ <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-09</h4> + <h4 class="date">2018-03-11</h4> </div> @@ -100,15 +103,15 @@ FOCUS_<span class="dv">2006</span>_L1_mkin <-<span class="st"> </span><span c <span class="kw">summary</span>(m.L1.SFO)</code></pre></div> <pre><code>## mkin version: 0.9.46.3 ## R version: 3.4.3 -## Date of fit: Fri Mar 9 23:09:50 2018 -## Date of summary: Fri Mar 9 23:09:50 2018 +## Date of fit: Sun Mar 11 22:11:58 2018 +## Date of summary: Sun Mar 11 22:11:58 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 37 model solutions performed in 0.264 s +## Fitted with method Port using 37 model solutions performed in 0.235 s ## ## Weighting: none ## @@ -191,15 +194,15 @@ FOCUS_<span class="dv">2006</span>_L1_mkin <-<span class="st"> </span><span c <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> <pre><code>## mkin version: 0.9.46.3 ## R version: 3.4.3 -## Date of fit: Fri Mar 9 23:09:52 2018 -## Date of summary: Fri Mar 9 23:09:52 2018 +## Date of fit: Sun Mar 11 22:12:01 2018 +## Date of summary: Sun Mar 11 22:12:01 2018 ## ## 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 1.451 s +## Fitted with method Port using 611 model solutions performed in 1.458 s ## ## Weighting: none ## @@ -286,15 +289,15 @@ FOCUS_<span class="dv">2006</span>_L2_mkin <-<span class="st"> </span><span c <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> <pre><code>## mkin version: 0.9.46.3 ## R version: 3.4.3 -## Date of fit: Fri Mar 9 23:09:53 2018 -## Date of summary: Fri Mar 9 23:09:53 2018 +## Date of fit: Sun Mar 11 22:12:01 2018 +## Date of summary: Sun Mar 11 22:12:01 2018 ## ## 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 0.175 s +## Fitted with method Port using 81 model solutions performed in 0.158 s ## ## Weighting: none ## @@ -357,8 +360,8 @@ FOCUS_<span class="dv">2006</span>_L2_mkin <-<span class="st"> </span><span c <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> <pre><code>## mkin version: 0.9.46.3 ## R version: 3.4.3 -## Date of fit: Fri Mar 9 23:09:54 2018 -## Date of summary: Fri Mar 9 23:09:54 2018 +## Date of fit: Sun Mar 11 22:12:02 2018 +## Date of summary: Sun Mar 11 22:12:02 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -367,7 +370,7 @@ FOCUS_<span class="dv">2006</span>_L2_mkin <-<span class="st"> </span><span c ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 336 model solutions performed in 0.739 s +## Fitted with method Port using 336 model solutions performed in 0.681 s ## ## Weighting: none ## @@ -449,8 +452,8 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</code></pre></div> <pre><code>## mkin version: 0.9.46.3 ## R version: 3.4.3 -## Date of fit: Fri Mar 9 23:09:55 2018 -## Date of summary: Fri Mar 9 23:09:55 2018 +## Date of fit: Sun Mar 11 22:12:03 2018 +## Date of summary: Sun Mar 11 22:12:03 2018 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -459,7 +462,7 @@ mm.L3 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 137 model solutions performed in 0.293 s +## Fitted with method Port using 137 model solutions performed in 0.272 s ## ## Weighting: none ## @@ -550,15 +553,15 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> <pre><code>## mkin version: 0.9.46.3 ## R version: 3.4.3 -## Date of fit: Fri Mar 9 23:09:55 2018 -## Date of summary: Fri Mar 9 23:09:56 2018 +## Date of fit: Sun Mar 11 22:12:04 2018 +## Date of summary: Sun Mar 11 22:12:04 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.09 s +## Fitted with method Port using 46 model solutions performed in 0.092 s ## ## Weighting: none ## @@ -610,15 +613,15 @@ mm.L4 <-<span class="st"> </span><span class="kw"><a href="../reference/mmkin <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</code></pre></div> <pre><code>## mkin version: 0.9.46.3 ## R version: 3.4.3 -## Date of fit: Fri Mar 9 23:09:56 2018 -## Date of summary: Fri Mar 9 23:09:56 2018 +## Date of fit: Sun Mar 11 22:12:04 2018 +## Date of summary: Sun Mar 11 22:12:04 2018 ## ## 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 0.134 s +## Fitted with method Port using 66 model solutions performed in 0.13 s ## ## Weighting: none ## diff --git a/docs/articles/FOCUS_Z.html b/docs/articles/FOCUS_Z.html index 606121ff..78a00062 100644 --- a/docs/articles/FOCUS_Z.html +++ b/docs/articles/FOCUS_Z.html @@ -9,7 +9,10 @@ <!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> <!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Example evaluation of FOCUS dataset Z"> +<meta property="og:description" content=""> +<meta name="twitter:card" content="summary"> +<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--> @@ -77,7 +80,7 @@ <h1>Example evaluation of FOCUS dataset Z</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-09</h4> + <h4 class="date">2018-03-11</h4> </div> diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html index 915e5474..8923acac 100644 --- a/docs/articles/compiled_models.html +++ b/docs/articles/compiled_models.html @@ -9,7 +9,10 @@ <!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> <!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Performance benefit by using compiled model definitions in mkin"> +<meta property="og:description" content=""> +<meta name="twitter:card" content="summary"> +<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--> @@ -77,7 +80,7 @@ <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-09</h4> + <h4 class="date">2018-03-11</h4> </div> @@ -115,9 +118,9 @@ SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mki }</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 2.044 1.000 2.042 0 -## 1 deSolve, not compiled 3 14.198 6.946 14.185 0 -## 2 Eigenvalue based 3 2.751 1.346 2.747 0 +## 3 deSolve, compiled 3 1.978 1.000 1.976 0 +## 1 deSolve, not compiled 3 13.541 6.846 13.531 0 +## 2 Eigenvalue based 3 2.332 1.179 2.330 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 @@ -146,12 +149,12 @@ SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mki }</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 3.695 1.000 3.692 0 -## 1 deSolve, not compiled 3 31.143 8.428 31.114 0 +## 2 deSolve, compiled 3 3.334 1.000 3.331 0 +## 1 deSolve, not compiled 3 29.917 8.973 29.888 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> -<p>Here we get a performance benefit of a factor of 8 using the version of the differential equation model compiled from C code!</p> +<p>Here we get a performance benefit of a factor of 9 using the version of the differential equation model compiled from C code!</p> <p>This vignette was built with mkin 0.9.46.3 on</p> <pre><code>## R version 3.4.3 (2017-11-30) ## Platform: x86_64-pc-linux-gnu (64-bit) diff --git a/docs/articles/index.html b/docs/articles/index.html index c0c5864b..f338f1b2 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -27,6 +27,7 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Articles" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -134,3 +135,4 @@ </body> </html> + diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index f668b500..7b26b3f1 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -9,7 +9,10 @@ <!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> <!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Introduction to mkin"> +<meta property="og:description" content=""> +<meta name="twitter:card" content="summary"> +<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--> @@ -77,7 +80,7 @@ <h1>Introduction to mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-09</h4> + <h4 class="date">2018-03-11</h4> </div> diff --git a/docs/articles/twa.html b/docs/articles/twa.html index e5b68cfe..7f4c941e 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -9,7 +9,10 @@ <!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> <!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> -<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Calculation of time weighted average concentrations with mkin"> +<meta property="og:description" content=""> +<meta name="twitter:card" content="summary"> +<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--> @@ -77,7 +80,7 @@ <h1>Calculation of time weighted average concentrations with mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2018-03-09</h4> + <h4 class="date">2018-03-11</h4> </div> diff --git a/docs/authors.html b/docs/authors.html index af022eab..a9712678 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -27,6 +27,7 @@ <script src="pkgdown.js"></script> +<meta property="og:title" content="Authors" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -106,19 +107,19 @@ <ul class="list-unstyled"> <li> - <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder. - <br /><small>0000-0003-4371-6538</small></p> + <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder. <a href='https://orcid.org/0000-0003-4371-6538' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid'></a> + </p> </li> <li> - <p><strong>Katrin Lindenberger</strong>. Contributor. + <p><strong>Katrin Lindenberger</strong>. Contributor. </p> </li> <li> - <p><strong>René Lehmann</strong>. Contributor. + <p><strong>René Lehmann</strong>. Contributor. </p> </li> <li> - <p><strong>Eurofins Regulatory AG</strong>. Copyright holder. + <p><strong>Eurofins Regulatory AG</strong>. Copyright holder. </p> </li> </ul> @@ -142,3 +143,4 @@ </body> </html> + diff --git a/docs/index.html b/docs/index.html index 88fd4f6d..9caba262 100644 --- a/docs/index.html +++ b/docs/index.html @@ -9,7 +9,17 @@ <!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> <!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet"> -<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> +<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><meta property="og:title" content="Kinetic Evaluation of Chemical Degradation Data"> +<meta property="og:description" content="Calculation routines based on the FOCUS Kinetics Report (2006, + 2014). Includes a function for conveniently defining differential equation + models, model solution based on eigenvalues if possible or using numerical + solvers and a choice of the optimisation methods made available by the 'FME' + package. If a C compiler (on windows: 'Rtools') is installed, differential + equation models are solved using compiled C functions. Please note that no + warranty is implied for correctness of results or fitness for a particular + purpose."> +<meta name="twitter:card" content="summary"> +<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--> @@ -159,8 +169,7 @@ <p>GPL</p> <h2>Developers</h2> <ul class="list-unstyled"> -<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> <br><small>(0000-0003-4371-6538)</small> -</li> +<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> <a href="https://orcid.org/0000-0003-4371-6538" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid"></a> </li> <li><a href="authors.html">All authors...</a></li> </ul> <h2>Dev status</h2> diff --git a/docs/news/index.html b/docs/news/index.html index 39b21d12..f311efe5 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -27,6 +27,7 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="All news" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -640,3 +641,4 @@ </body> </html> + diff --git a/docs/pkgdown.css b/docs/pkgdown.css index 59b659f2..181fe639 100644 --- a/docs/pkgdown.css +++ b/docs/pkgdown.css @@ -100,6 +100,11 @@ a.anchor { margin-bottom: 0.5em; } +.orcid { + height: 16px; + vertical-align: middle; +} + /* Reference index & topics ----------------------------------------------- */ .ref-index th {font-weight: normal;} @@ -137,6 +142,12 @@ pre, code { color: #333; } +pre code { + overflow: auto; + word-wrap: normal; + white-space: pre; +} + pre .img { margin: 5px 0; } @@ -151,6 +162,10 @@ code a, pre a { color: #375f84; } +a.sourceLine:hover { + text-decoration: none; +} + .fl {color: #1514b5;} .fu {color: #000000;} /* function */ .ch,.st {color: #036a07;} /* string */ diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml new file mode 100644 index 00000000..974e3585 --- /dev/null +++ b/docs/pkgdown.yml @@ -0,0 +1,20 @@ +pandoc: 1.19.2.4 +pkgdown: 0.1.0.9000 +pkgdown_sha: ~ +articles: + FOCUS_D: FOCUS_D.html + FOCUS_D.html: FOCUS_D.html + FOCUS_L: FOCUS_L.html + FOCUS_L.html: FOCUS_L.html + FOCUS_Z: FOCUS_Z.html + FOCUS_Z.html: FOCUS_Z.html + FOCUS_Z.pdf: FOCUS_Z.pdf + compiled_models: compiled_models.html + compiled_models.html: compiled_models.html + mkin: mkin.html + mkin.html: mkin.html + mkin_vignettes.css: mkin_vignettes.css + references.bib: references.bib + twa: twa.html + twa.html: twa.html + diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index f89a66e2..b1b3cf50 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -27,6 +27,11 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Double First-Order in Parallel kinetics — DFOP.solution" /> + +<meta property="og:description" content="Function describing decline from a defined starting value using the sum + of two exponential decline functions." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -182,3 +187,4 @@ </body> </html> + diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 3b96f9ae..e554432f 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -27,6 +27,10 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Subsetting method for mmkin objects — [.mmkin" /> + +<meta property="og:description" content="Subsetting method for mmkin objects." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -259,7 +263,7 @@ #> #> $time #> user system elapsed -#> 0.06 0.00 0.06 +#> 0.234 0.000 0.234 #> #> $mkinmod #> <mkinmod> model generated with @@ -448,8 +452,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x5555599fd348> -#> <environment: 0x555557684190> +#> <bytecode: 0x5555578e66e0> +#> <environment: 0x555559cd9780> #> #> $cost_notrans #> function (P) @@ -471,8 +475,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x555559feb960> -#> <environment: 0x555557684190> +#> <bytecode: 0x55555acf3f50> +#> <environment: 0x555559cd9780> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -539,7 +543,7 @@ #> 99.17407 #> #> $date -#> [1] "Fri Mar 9 23:08:11 2018" +#> [1] "Sun Mar 11 22:10:21 2018" #> #> $version #> [1] "0.9.47.1" @@ -582,3 +586,4 @@ </body> </html> + diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html index ed5f29b3..f392bf64 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -27,6 +27,14 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B" /> + +<meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values +generated with different software packages. Taken directly from FOCUS (2006). +The results from fitting the data with the Topfit software was removed, as +the initial concentration of the parent compound was fixed to a value of 100 +in this fit." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -167,3 +175,4 @@ in this fit.</p> </body> </html> + diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html index e3e0d238..6e4c8d64 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -27,6 +27,14 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F" /> + +<meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values +generated with different software packages. Taken directly from FOCUS (2006). +The results from fitting the data with the Topfit software was removed, as +the initial concentration of the parent compound was fixed to a value of 100 +in this fit." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -166,3 +174,4 @@ in this fit.</p> </body> </html> + diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html index be785b0b..ed38ccae 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -27,6 +27,14 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F" /> + +<meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values +generated with different software packages. Taken directly from FOCUS (2006). +The results from fitting the data with the Topfit software was removed, as +the initial concentration of the parent compound was fixed to a value of 100 +in this fit." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -167,3 +175,4 @@ in this fit.</p> </body> </html> + diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html index 6ca8e78e..107f3e5f 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -27,6 +27,14 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F" /> + +<meta property="og:description" content="A table with the fitted parameters and the resulting DT50 and DT90 values +generated with different software packages. Taken directly from FOCUS (2006). +The results from fitting the data with the Topfit software was removed, as +the initial concentration of the parent compound was fixed to a value of 100 +in this fit." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -165,3 +173,4 @@ in this fit.</p> </body> </html> + diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 9ea69f23..cc310ee3 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -27,6 +27,10 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets" /> + +<meta property="og:description" content="Data taken from FOCUS (2006), p. 258." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -167,3 +171,4 @@ </body> </html> + diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index b5b4c87c..397dc82d 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -27,6 +27,14 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="First-Order Multi-Compartment kinetics — FOMC.solution" /> + +<meta property="og:description" content="Function describing exponential decline from a defined starting value, with + a decreasing rate constant. +The form given here differs slightly from the original reference by Gustafson + and Holden (1990). The parameter beta corresponds to 1/beta in the + original equation." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -193,3 +201,4 @@ </body> </html> + diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 0dc432ef..f633aa67 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -27,6 +27,11 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Hockey-Stick kinetics — HS.solution" /> + +<meta property="og:description" content="Function describing two exponential decline functions with a break point + between them." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -183,3 +188,4 @@ </body> </html> + diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index b055534a..687dee5a 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -27,6 +27,11 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Indeterminate order rate equation kinetics — IORE.solution" /> + +<meta property="og:description" content="Function describing exponential decline from a defined starting value, with + a concentration dependent rate constant." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -197,3 +202,4 @@ </body> </html> + diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index eda43e4d..1156c16f 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -27,6 +27,10 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Single First-Order kinetics — SFO.solution" /> + +<meta property="og:description" content="Function describing exponential decline from a defined starting value." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -174,3 +178,4 @@ </body> </html> + diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 2b6b2bc6..6901c435 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -27,6 +27,14 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Single First-Order Reversible Binding kinetics — SFORB.solution" /> + +<meta property="og:description" content="Function describing the solution of the differential equations describing + the kinetic model with first-order terms for a two-way transfer from a free + to a bound fraction, and a first-order degradation term for the free + fraction. The initial condition is a defined amount in the free fraction and + no substance in the bound fraction." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -187,3 +195,4 @@ </body> </html> + diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 407e1a3e..6d830113 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -27,6 +27,12 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Add normally distributed errors to simulated kinetic degradation data — add_err" /> + +<meta property="og:description" content="Normally distributed errors are added to data predicted for a specific + degradation model using mkinpredict. The variance of the error + may depend on the predicted value and is specified as a standard deviation." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -241,3 +247,4 @@ </body> </html> + diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 4ab395cb..0f5ba0a4 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -27,6 +27,13 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Function to calculate endpoints for further use from kinetic models fitted with mkinfit — endpoints" /> + +<meta property="og:description" content="This function calculates DT50 and DT90 values as well as formation fractions from kinetic models +fitted with mkinfit. If the SFORB model was specified for one of the parents or metabolites, +the Eigenvalues are returned. These are equivalent to the rate constantes of the DFOP model, but +with the advantage that the SFORB model can also be used for metabolites." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -177,3 +184,4 @@ with the advantage that the SFORB model can also be used for metabolites.</p> </body> </html> + diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 7e27c1dc..9d91b5a8 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -27,6 +27,10 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Calculate the geometric mean — geometric_mean" /> + +<meta property="og:description" content="Function calculating the geometric mean of numeric vectors" /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -158,3 +162,4 @@ </body> </html> + diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 7ed15db5..33d749ce 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -27,6 +27,10 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Function to perform isometric log-ratio transformation — ilr" /> + +<meta property="og:description" content="This implementation is a special case of the class of isometric log-ratio transformations." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -182,3 +186,4 @@ </body> </html> + diff --git a/docs/reference/index.html b/docs/reference/index.html index 157eaad3..6c05941d 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -27,6 +27,7 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Function reference" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -453,3 +454,4 @@ </body> </html> + diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 9e1e3974..696ca729 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -27,6 +27,14 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Function to calculate maximum time weighted average concentrations from kinetic models fitted with mkinfit — max_twa_parent" /> + +<meta property="og:description" content="This function calculates maximum moving window time weighted average concentrations +(TWAs) for kinetic models fitted with mkinfit. Currently, only +calculations for the parent are implemented for the SFO, FOMC and DFOP models, +using the analytical formulas given in the PEC soil section of the FOCUS +guidance." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -178,3 +186,4 @@ guidance.</p> </body> </html> + diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 30aa894e..80cac442 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -27,6 +27,12 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T" /> + +<meta property="og:description" content="Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding + 2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether + extracts." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -145,8 +151,8 @@ <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'>summary</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: 0.9.47.1 #> R version used for fitting: 3.4.3 -#> Date of fit: Fri Mar 9 23:08:18 2018 -#> Date of summary: Fri Mar 9 23:08:18 2018 +#> Date of fit: Sun Mar 11 22:10:30 2018 +#> Date of summary: Sun Mar 11 22:10:30 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -156,7 +162,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.359 s +#> Fitted with method Port using 246 model solutions performed in 1.318 s #> #> Weighting: none #> @@ -266,3 +272,4 @@ </body> </html> + diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index dc781aaf..3c498a76 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -27,6 +27,12 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Convert a dataframe from long to wide format — mkin_long_to_wide" /> + +<meta property="og:description" content="This function takes a dataframe in the long form as required by modCost + and converts it into a dataframe with one independent variable and several + dependent variables as columns." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -192,3 +198,4 @@ </body> </html> + diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 2a8d20a3..f40cb7cf 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -27,6 +27,11 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Convert a dataframe with observations over time into long format — mkin_wide_to_long" /> + +<meta property="og:description" content="This function simply takes a dataframe with one independent variable and several + dependent variable and converts it into the long form as required by modCost." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -171,3 +176,4 @@ </body> </html> + diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index fd707cfd..7f5ec78e 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -27,6 +27,10 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="A dataset class for mkin — mkinds" /> + +<meta property="og:description" content="A dataset class for mkin" /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -160,3 +164,4 @@ in order to be compatible with mkinfit</p></dd> </body> </html> + diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 045e5805..f172cba1 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -27,6 +27,11 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Calculate the minimum error to assume in order to pass the variance test — mkinerrmin" /> + +<meta property="og:description" content="This function finds the smallest relative error still resulting in passing the +chi-squared test as defined in the FOCUS kinetics report from 2006." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -195,3 +200,4 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.</p> </body> </html> + diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 10052053..991df1cc 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -27,6 +27,20 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Fit a kinetic model to data with one or more state variables — mkinfit" /> + +<meta property="og:description" content="This function uses the Flexible Modelling Environment package + FME to create a function calculating the model cost, i.e. the + deviation between the kinetic model and the observed data. This model cost is + then minimised using the Port algorithm nlminb, + using the specified initial or fixed parameters and starting values. + Per default, parameters in the kinetic models are internally transformed in order + to better satisfy the assumption of a normal distribution of their estimators. + In each step of the optimsation, the kinetic model is solved using the + function mkinpredict. The variance of the residuals for each + observed variable can optionally be iteratively reweighted until convergence + using the argument reweight.method = "obs"." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -400,15 +414,15 @@ <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'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.1 #> R version used for fitting: 3.4.3 -#> Date of fit: Fri Mar 9 23:08:20 2018 -#> Date of summary: Fri Mar 9 23:08:20 2018 +#> Date of fit: Sun Mar 11 22:10:32 2018 +#> Date of summary: Sun Mar 11 22:10:32 2018 #> #> 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 0.148 s +#> Fitted with method Port using 64 model solutions performed in 0.135 s #> #> Weighting: none #> @@ -477,7 +491,7 @@ <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'>print</span>(<span class='fu'>system.time</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 elapsed -#> 0.839 0.000 0.840 </div><div class='input'><span class='fu'>coef</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 +#> 0.829 0.000 0.829 </div><div class='input'><span class='fu'>coef</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 @@ -585,3 +599,4 @@ </body> </html> + diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 032fcbb6..7d3c0f94 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -27,6 +27,15 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Function to set up a kinetic model with one or more state variables — mkinmod" /> + +<meta property="og:description" content="The function usually takes several expressions, each assigning a compound name to + a list, specifying the kinetic model type and reaction or transfer to other + observed compartments. Instead of specifying several expressions, a list + of lists can be given in the speclist argument. +For the definition of model types and their parameters, the equations given + in the FOCUS and NAFTA guidance documents are used." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -255,3 +264,4 @@ </body> </html> + diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index e416d67c..81f52fc3 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -27,6 +27,11 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Function to plot the confidence intervals obtained using mkinfit — mkinparplot" /> + +<meta property="og:description" content="This function plots the confidence intervals for the parameters + fitted using mkinfit." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -163,3 +168,4 @@ </body> </html> + diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index e1ee1607..cfd72521 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -27,6 +27,10 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Plot the observed data and the fitted model of an mkinfit object — mkinplot" /> + +<meta property="og:description" content="Deprecated function. It now only calls the plot method plot.mkinfit." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -158,3 +162,4 @@ </body> </html> + diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 7354c496..044b2d92 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -27,6 +27,12 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Produce predictions from a kinetic model using specific parameters — mkinpredict" /> + +<meta property="og:description" content="This function produces a time series for all the observed variables in a + kinetic model as specified by mkinmod, using a specific set of + kinetic parameters and initial values for the state variables." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -300,17 +306,17 @@ <span class='fu'>c</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'>seq</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 elapsed -#> 0.003 0.000 0.003 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.002 0.000 0.003 </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</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'>c</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'>seq</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 #> 201 20 4.978707 27.46227</div><div class='output co'>#> user system elapsed -#> 0.002 0.000 0.002 </div><div class='input'> <span class='fu'>system.time</span>( +#> 0.002 0.000 0.001 </div><div class='input'> <span class='fu'>system.time</span>( <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</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'>c</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'>seq</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='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</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 elapsed -#> 0.031 0.000 0.031 </div></pre> +#> 0.029 0.000 0.029 </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> @@ -343,3 +349,4 @@ </body> </html> + diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index b4b6b116..df83f693 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -27,6 +27,13 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Function to plot residuals stored in an mkin object — mkinresplot" /> + +<meta property="og:description" content="This function plots the residuals for the specified subset of the + observed variables from an mkinfit object. A combined plot of the fitted + model and the residuals can be obtained using plot.mkinfit + using the argument show_residuals = TRUE." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -208,3 +215,4 @@ </body> </html> + diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index b4915112..db727427 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -27,6 +27,11 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Function to set up a kinetic submodel for one state variable — mkinsub" /> + +<meta property="og:description" content="This is a convenience function to set up the lists used as arguments for + mkinmod." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -188,3 +193,4 @@ </body> </html> + diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 78033dd2..65c37898 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -27,6 +27,11 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Fit one or more kinetic models with one or more state variables to one or more datasets — mmkin" /> + +<meta property="og:description" content="This function calls mkinfit on all combinations of models and datasets + specified in its first two arguments." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -220,3 +225,4 @@ </body> </html> + diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index b6dd1525..319ba75b 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -27,6 +27,15 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit" /> + +<meta property="og:description" content="Solves the differential equations with the optimised and fixed parameters + from a previous successful call to mkinfit and plots + the observed data together with the solution of the fitted model. +If the current plot device is a tikz device, + then latex is being used for the formatting of the chi2 error level, + if show_errmin = TRUE." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -275,3 +284,4 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … </body> </html> + diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 8b80273c..f1aa789f 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -27,6 +27,14 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object — plot.mmkin" /> + +<meta property="og:description" content="When x is a row selected from an mmkin object ([.mmkin), the same model + fitted for at least one dataset is shown. When it is a column, the fit of at least one model + to the same dataset is shown. +If the current plot device is a tikz device, + then latex is being used for the formatting of the chi2 error level." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -200,3 +208,4 @@ </body> </html> + diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index 02882776..2a469fc2 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -27,6 +27,10 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Print mkinds objects — print.mkinds" /> + +<meta property="og:description" content="Print mkinds objects." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -149,3 +153,4 @@ </body> </html> + diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index cd6678a6..30703dfd 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -27,6 +27,10 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Print mkinmod objects — print.mkinmod" /> + +<meta property="og:description" content="Print mkinmod objects in a way that the user finds his way to get to its components." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -170,3 +174,4 @@ </body> </html> + diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 15c23fd3..2c06b1dd 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -27,6 +27,12 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case" /> + +<meta property="og:description" content="This dataset was used for a comparison of KinGUI and ModelMaker to check the + software quality of KinGUI in the original publication (Schäfer et al., 2007). + The results from the fitting are also included." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -188,3 +194,4 @@ </body> </html> + diff --git a/docs/reference/sigma_rl.html b/docs/reference/sigma_rl.html index 4b287e55..fd714224 100644 --- a/docs/reference/sigma_rl.html +++ b/docs/reference/sigma_rl.html @@ -27,6 +27,12 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Two component error model of Rocke and Lorenzato — sigma_rl" /> + +<meta property="og:description" content="Function describing the standard deviation of the measurement error + in dependence of the measured value \(y\): +$$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$" /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -168,3 +174,4 @@ </body> </html> + diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index f34736b3..e462fd17 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -27,6 +27,13 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Summary method for class "mkinfit" — summary.mkinfit" /> + +<meta property="og:description" content="Lists model equations, the summary as returned by summary.modFit, + the chi2 error levels calculated according to FOCUS guidance (2006) as far + as defined therein, and optionally the data, consisting of observed, predicted + and residual values." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -184,15 +191,15 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'>summary</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: 0.9.47.1 #> R version used for fitting: 3.4.3 -#> Date of fit: Fri Mar 9 23:08:29 2018 -#> Date of summary: Fri Mar 9 23:08:29 2018 +#> Date of fit: Sun Mar 11 22:10:41 2018 +#> Date of summary: Sun Mar 11 22:10:41 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.075 s +#> Fitted with method Port using 35 model solutions performed in 0.07 s #> #> Weighting: none #> @@ -286,3 +293,4 @@ </body> </html> + diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index 396a6e2b..18da9ff6 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -27,6 +27,22 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014" /> + +<meta property="og:description" content="The 12 datasets were generated using four different models and three different + variance components. The four models are either the SFO or the DFOP model with either + two sequential or two parallel metabolites. +Variance component 'a' is based on a normal distribution with standard deviation of 3, + Variance component 'b' is also based on a normal distribution, but with a standard deviation of 7. + Variance component 'c' is based on the error model from Rocke and Lorenzato (1995), with the + minimum standard deviation (for small y values) of 0.5, and a proportionality constant of 0.07 + for the increase of the standard deviation with y. +Initial concentrations for metabolites and all values where adding the variance component resulted + in a value below the assumed limit of detection of 0.1 were set to NA. +As an example, the first dataset has the title SFO_lin_a and is based on the SFO model + with two sequential metabolites (linear pathway), with added variance component 'a'. +Compare also the code in the example section to see the degradation models." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -269,3 +285,4 @@ summary(fit) </body> </html> + diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index 13e072c6..b1b5e617 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -27,6 +27,11 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014" /> + +<meta property="og:description" content="The datasets were used for the comparative validation of several kinetic evaluation + software packages (Ranke, 2014)." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -184,3 +189,4 @@ </body> </html> + diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 266db603..5c89f8e2 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -27,6 +27,18 @@ <script src="../pkgdown.js"></script> +<meta property="og:title" content="Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms" /> + +<meta property="og:description" content="The transformations are intended to map parameters that should only take + on restricted values to the full scale of real numbers. For kinetic rate + constants and other paramters that can only take on positive values, a + simple log transformation is used. For compositional parameters, such as + the formations fractions that should always sum up to 1 and can not be + negative, the ilr transformation is used. +The transformation of sets of formation fractions is fragile, as it supposes + the same ordering of the components in forward and backward transformation. + This is no problem for the internal use in mkinfit." /> +<meta name="twitter:card" content="summary" /> <!-- mathjax --> <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> @@ -173,8 +185,8 @@ <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'>summary</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: 0.9.47.1 #> R version used for fitting: 3.4.3 -#> Date of fit: Fri Mar 9 23:08:30 2018 -#> Date of summary: Fri Mar 9 23:08:30 2018 +#> Date of fit: Sun Mar 11 22:10:42 2018 +#> Date of summary: Sun Mar 11 22:10:42 2018 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -182,7 +194,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.657 s +#> Fitted with method Port using 153 model solutions performed in 0.564 s #> #> Weighting: none #> @@ -312,3 +324,4 @@ </body> </html> + |