diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-11-01 12:19:03 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-11-01 12:19:03 +0100 |
| commit | bbb74d4f60033899cd5cdd36aa70f157bc52209e (patch) | |
| tree | ca0f620ba0ffd59ff242071260d2346e4ca254ff | |
| parent | 70e48e8360875f22970174d409c46cb3f076fa99 (diff) | |
Fix bug in yesterdays release, add methods for BIC
94 files changed, 362 insertions, 2282 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index 13ccdb0d..d204bdd3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data -Version: 0.9.49.6 -Date: 2019-10-31 +Version: 0.9.49.7 +Date: 2019-11-01 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de", comment = c(ORCID = "0000-0003-4371-6538")), @@ -2,11 +2,13 @@ S3method("[",mmkin) S3method(AIC,mmkin) +S3method(BIC,mmkin) S3method(confint,mkinfit) S3method(logLik,mkinfit) S3method(lrtest,mkinfit) S3method(mkinpredict,mkinfit) S3method(mkinpredict,mkinmod) +S3method(nobs,mkinfit) S3method(parms,mkinfit) S3method(plot,mkinfit) S3method(plot,mmkin) @@ -68,11 +70,14 @@ importFrom(methods,signature) importFrom(parallel,detectCores) importFrom(parallel,mclapply) importFrom(parallel,parLapply) +importFrom(stats,AIC) +importFrom(stats,BIC) importFrom(stats,aggregate) importFrom(stats,cov2cor) importFrom(stats,dist) importFrom(stats,logLik) importFrom(stats,nlminb) +importFrom(stats,nobs) importFrom(stats,optimize) importFrom(stats,pt) importFrom(stats,qchisq) @@ -1,4 +1,10 @@ -# mkin 0.9.49.6 (unreleased) +# mkin 0.9.49.7 (2019-11-01) + +- Fix a bug introduced in 0.9.49.6 that occurred if the direct optimisation yielded a higher likelihood than the three-step optimisation in the d_3 algorithm, which caused the fitted parameters of the three-step optimisation to be returned instead of the parameters of the direct optimisation + +- Add an 'nobs' method for mkinfit methods, enabling the default 'BIC' method from the stats package. Also, add a 'BIC' method for mmkin column objects. + +# mkin 0.9.49.6 (2019-10-31) - Implement a likelihood ratio test as a method for 'lrtest' from the lmtest package diff --git a/R/AIC.mmkin.R b/R/AIC.mmkin.R index ab17f0a0..7d405c4a 100644 --- a/R/AIC.mmkin.R +++ b/R/AIC.mmkin.R @@ -1,8 +1,9 @@ -#' Calculated the AIC for a column of an mmkin object -#' +#' Calculate the AIC for a column of an mmkin object +#' #' Provides a convenient way to compare different kinetic models fitted to the #' same dataset. -#' +#' +#' @importFrom stats AIC BIC #' @param object An object of class \code{\link{mmkin}}, containing only one #' column. #' @param \dots For compatibility with the generic method @@ -11,22 +12,22 @@ #' dataframe if there are several fits in the column). #' @author Johannes Ranke #' @examples -#' +#' #' \dontrun{ # skip, as it takes > 10 s on winbuilder #' f <- mmkin(c("SFO", "FOMC", "DFOP"), #' list("FOCUS A" = FOCUS_2006_A, #' "FOCUS C" = FOCUS_2006_C), cores = 1, quiet = TRUE) #' AIC(f[1, "FOCUS A"]) # We get a single number for a single fit -#' +#' #' # For FOCUS A, the models fit almost equally well, so the higher the number #' # of parameters, the higher (worse) the AIC #' AIC(f[, "FOCUS A"]) #' AIC(f[, "FOCUS A"], k = 0) # If we do not penalize additional parameters, we get nearly the same -#' +#' #' # For FOCUS C, the more complex models fit better #' AIC(f[, "FOCUS C"]) #' } -#' +#' #' @export AIC.mmkin <- function(object, ..., k = 2) { @@ -42,3 +43,20 @@ AIC.mmkin <- function(object, ..., k = 2) if (n.fits > 1) rownames(res) <- model_names return(res) } + +#' @rdname AIC.mmkin +#' @export +BIC.mmkin <- function(object, ...) +{ + # We can only handle a single column + if (ncol(object) != 1) stop("Please provide a single column object") + n.fits <- length(object) + model_names <- rownames(object) + + code <- paste0("BIC(", + paste0("object[[", 1:n.fits, "]]", collapse = ", "), + ")") + res <- eval(parse(text = code)) + if (n.fits > 1) rownames(res) <- model_names + return(res) +} diff --git a/R/mkinfit.R b/R/mkinfit.R index 27c769db..1c409569 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -781,6 +781,8 @@ mkinfit <- function(mkinmod, observed, if (!quiet) message(d_3_messages["direct"]) fit <- fit_direct fit$d_3_message <- d_3_messages["direct"] + degparms <- fit$par[degparms_index] + errparms <- fit$par[errparms_index] } } } diff --git a/R/nobs.mkinfit.R b/R/nobs.mkinfit.R new file mode 100644 index 00000000..0e0dbbbb --- /dev/null +++ b/R/nobs.mkinfit.R @@ -0,0 +1,8 @@ +#' Number of observations on which an mkinfit object was fitted +#' +#' @importFrom stats nobs +#' @param object An mkinfit object +#' @param \dots For compatibility with the generic method +#' @return The number of rows in the data included in the mkinfit object +#' @export +nobs.mkinfit <- function(object, ...) nrow(object$data) diff --git a/_pkgdown.yml b/_pkgdown.yml index 2409bc85..c222a817 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -65,6 +65,7 @@ reference: - sigma_twocomp - logLik.mkinfit - residuals.mkinfit + - nobs.mkinfit - mkinresplot - mkinparplot - mkinerrplot @@ -6,5 +6,5 @@ * checking for LF line-endings in source and make files and shell scripts * checking for empty or unneeded directories * looking to see if a ‘data/datalist’ file should be added -* building ‘mkin_0.9.49.6.tar.gz’ +* building ‘mkin_0.9.49.7.tar.gz’ @@ -5,7 +5,7 @@ * using options ‘--no-tests --as-cran’ * checking for file ‘mkin/DESCRIPTION’ ... OK * checking extension type ... Package -* this is package ‘mkin’ version ‘0.9.49.6’ +* this is package ‘mkin’ version ‘0.9.49.7’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’ diff --git a/docs/404.html b/docs/404.html index ecb80807..f10cadb9 100644 --- a/docs/404.html +++ b/docs/404.html @@ -67,7 +67,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="https://pkgdown.jrwb.de/mkin/index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.7</span> </span> </div> diff --git a/docs/NEWS.html b/docs/NEWS.html deleted file mode 100644 index 744b8db4..00000000 --- a/docs/NEWS.html +++ /dev/null @@ -1,610 +0,0 @@ -<!-- 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-0-9-47-1-2018-02-06" class="section level1"> -<h1 class="hasAnchor"> -<a href="#mkin-0-9-47-1-2018-02-06" class="anchor"></a>mkin 0.9.47.1 (2018-02-06)</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 deleted file mode 100644 index 98d42ebc..00000000 --- a/docs/README.html +++ /dev/null @@ -1,200 +0,0 @@ -<!-- 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 f8c51e2d..42361b92 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -90,7 +90,7 @@ <h1>Example evaluation of FOCUS Example Dataset D</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-09-19</h4> + <h4 class="date">2019-11-01</h4> <div class="hidden name"><code>FOCUS_D.Rmd</code></div> @@ -170,8 +170,8 @@ <div class="sourceCode" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(fit)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.49.6 ## R version used for fitting: 3.6.1 -## Date of fit: Thu Sep 19 09:52:55 2019 -## Date of summary: Thu Sep 19 09:52:56 2019 +## Date of fit: Fri Nov 1 10:10:44 2019 +## Date of summary: Fri Nov 1 10:10:44 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -179,19 +179,18 @@ ## ## Model predictions using solution type deSolve ## -## Fitted using 389 model solutions performed in 1.001 s +## Fitted using 389 model solutions performed in 1.015 s ## ## Error model: Constant variance ## ## Error model algorithm: OLS ## ## Starting values for parameters to be optimised: -## value type -## parent_0 100.750000 state -## k_parent_sink 0.100000 deparm -## k_parent_m1 0.100100 deparm -## k_m1_sink 0.100200 deparm -## sigma 3.125504 error +## value type +## parent_0 100.7500 state +## k_parent_sink 0.1000 deparm +## k_parent_m1 0.1001 deparm +## k_m1_sink 0.1002 deparm ## ## Starting values for the transformed parameters actually optimised: ## value lower upper @@ -199,7 +198,6 @@ ## log_k_parent_sink -2.302585 -Inf Inf ## log_k_parent_m1 -2.301586 -Inf Inf ## log_k_m1_sink -2.300587 -Inf Inf -## sigma 3.125504 0 Inf ## ## Fixed parameter values: ## value type @@ -298,6 +296,7 @@ </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + </div> </div> diff --git a/docs/articles/FOCUS_D_files/figure-html/plot-1.png b/docs/articles/FOCUS_D_files/figure-html/plot-1.png Binary files differindex fc1142ab..6f4fa093 100644 --- a/docs/articles/FOCUS_D_files/figure-html/plot-1.png +++ b/docs/articles/FOCUS_D_files/figure-html/plot-1.png diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 7b35beeb..4033beba 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -90,7 +90,7 @@ <h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-09-19</h4> + <h4 class="date">2019-11-01</h4> <div class="hidden name"><code>FOCUS_L.Rmd</code></div> @@ -116,8 +116,8 @@ <a class="sourceLine" id="cb2-2" title="2"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(m.L1.SFO)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.49.6 ## R version used for fitting: 3.6.1 -## Date of fit: Thu Sep 19 09:52:57 2019 -## Date of summary: Thu Sep 19 09:52:57 2019 +## Date of fit: Fri Nov 1 10:10:46 2019 +## Date of summary: Fri Nov 1 10:10:46 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent @@ -131,16 +131,14 @@ ## Error model algorithm: OLS ## ## Starting values for parameters to be optimised: -## value type -## parent_0 89.850000 state -## k_parent_sink 0.100000 deparm -## sigma 2.779827 error +## value type +## parent_0 89.85 state +## k_parent_sink 0.10 deparm ## ## Starting values for the transformed parameters actually optimised: ## value lower upper ## parent_0 89.850000 -Inf Inf ## log_k_parent_sink -2.302585 -Inf Inf -## sigma 2.779827 0 Inf ## ## Fixed parameter values: ## None @@ -214,12 +212,12 @@ <div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(m.L1.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- -## finite result is doubtful</code></pre> +<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite +## result is doubtful</code></pre> <pre><code>## mkin version used for fitting: 0.9.49.6 ## R version used for fitting: 3.6.1 -## Date of fit: Thu Sep 19 09:52:59 2019 -## Date of summary: Thu Sep 19 09:52:59 2019 +## Date of fit: Fri Nov 1 10:10:48 2019 +## Date of summary: Fri Nov 1 10:10:48 2019 ## ## ## Warning: Optimisation did not converge: @@ -231,25 +229,23 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 899 model solutions performed in 1.908 s +## Fitted using 899 model solutions performed in 1.91 s ## ## Error model: Constant variance ## ## Error model algorithm: OLS ## ## Starting values for parameters to be optimised: -## value type -## parent_0 89.850000 state -## alpha 1.000000 deparm -## beta 10.000000 deparm -## sigma 2.779871 error +## value type +## parent_0 89.85 state +## alpha 1.00 deparm +## beta 10.00 deparm ## ## Starting values for the transformed parameters actually optimised: ## value lower upper ## parent_0 89.850000 -Inf Inf ## log_alpha 0.000000 -Inf Inf ## log_beta 2.302585 -Inf Inf -## sigma 2.779871 0 Inf ## ## Fixed parameter values: ## None @@ -323,33 +319,31 @@ <div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(m.L2.FOMC, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.49.6 ## R version used for fitting: 3.6.1 -## Date of fit: Thu Sep 19 09:53:00 2019 -## Date of summary: Thu Sep 19 09:53:00 2019 +## Date of fit: Fri Nov 1 10:10:49 2019 +## Date of summary: Fri Nov 1 10:10:49 2019 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted using 239 model solutions performed in 0.49 s +## Fitted using 239 model solutions performed in 0.489 s ## ## Error model: Constant variance ## ## Error model algorithm: OLS ## ## Starting values for parameters to be optimised: -## value type -## parent_0 93.950000 state -## alpha 1.000000 deparm -## beta 10.000000 deparm -## sigma 2.275722 error +## value type +## parent_0 93.95 state +## alpha 1.00 deparm +## beta 10.00 deparm ## ## Starting values for the transformed parameters actually optimised: ## value lower upper ## parent_0 93.950000 -Inf Inf ## log_alpha 0.000000 -Inf Inf ## log_beta 2.302585 -Inf Inf -## sigma 2.275722 0 Inf ## ## Fixed parameter values: ## None @@ -399,8 +393,8 @@ <div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(m.L2.DFOP, <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.49.6 ## R version used for fitting: 3.6.1 -## Date of fit: Thu Sep 19 09:53:02 2019 -## Date of summary: Thu Sep 19 09:53:02 2019 +## Date of fit: Fri Nov 1 10:10:51 2019 +## Date of summary: Fri Nov 1 10:10:51 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -409,19 +403,18 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 572 model solutions performed in 1.204 s +## Fitted using 572 model solutions performed in 1.218 s ## ## Error model: Constant variance ## ## Error model algorithm: OLS ## ## Starting values for parameters to be optimised: -## value type -## parent_0 93.950000 state -## k1 0.100000 deparm -## k2 0.010000 deparm -## g 0.500000 deparm -## sigma 1.413899 error +## value type +## parent_0 93.95 state +## k1 0.10 deparm +## k2 0.01 deparm +## g 0.50 deparm ## ## Starting values for the transformed parameters actually optimised: ## value lower upper @@ -429,7 +422,6 @@ ## log_k1 -2.302585 -Inf Inf ## log_k2 -4.605170 -Inf Inf ## g_ilr 0.000000 -Inf Inf -## sigma 1.413899 0 Inf ## ## Fixed parameter values: ## None @@ -499,8 +491,8 @@ <div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(mm.L3[[<span class="st">"DFOP"</span>, <span class="dv">1</span>]])</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.49.6 ## R version used for fitting: 3.6.1 -## Date of fit: Thu Sep 19 09:53:04 2019 -## Date of summary: Thu Sep 19 09:53:04 2019 +## Date of fit: Fri Nov 1 10:10:53 2019 +## Date of summary: Fri Nov 1 10:10:53 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -509,19 +501,18 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 373 model solutions performed in 0.799 s +## Fitted using 373 model solutions performed in 0.784 s ## ## Error model: Constant variance ## ## Error model algorithm: OLS ## ## Starting values for parameters to be optimised: -## value type -## parent_0 97.800000 state -## k1 0.100000 deparm -## k2 0.010000 deparm -## g 0.500000 deparm -## sigma 1.017292 error +## value type +## parent_0 97.80 state +## k1 0.10 deparm +## k2 0.01 deparm +## g 0.50 deparm ## ## Starting values for the transformed parameters actually optimised: ## value lower upper @@ -529,7 +520,6 @@ ## log_k1 -2.302585 -Inf Inf ## log_k2 -4.605170 -Inf Inf ## g_ilr 0.000000 -Inf Inf -## sigma 1.017292 0 Inf ## ## Fixed parameter values: ## None @@ -605,31 +595,29 @@ <div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(mm.L4[[<span class="st">"SFO"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.49.6 ## R version used for fitting: 3.6.1 -## Date of fit: Thu Sep 19 09:53:04 2019 -## Date of summary: Thu Sep 19 09:53:05 2019 +## Date of fit: Fri Nov 1 10:10:53 2019 +## Date of summary: Fri Nov 1 10:10:54 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted using 142 model solutions performed in 0.287 s +## Fitted using 142 model solutions performed in 0.292 s ## ## Error model: Constant variance ## ## Error model algorithm: OLS ## ## Starting values for parameters to be optimised: -## value type -## parent_0 96.60000 state -## k_parent_sink 0.10000 deparm -## sigma 3.16181 error +## value type +## parent_0 96.6 state +## k_parent_sink 0.1 deparm ## ## Starting values for the transformed parameters actually optimised: ## value lower upper ## parent_0 96.600000 -Inf Inf ## log_k_parent_sink -2.302585 -Inf Inf -## sigma 3.161810 0 Inf ## ## Fixed parameter values: ## None @@ -670,33 +658,31 @@ <div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(mm.L4[[<span class="st">"FOMC"</span>, <span class="dv">1</span>]], <span class="dt">data =</span> <span class="ot">FALSE</span>)</a></code></pre></div> <pre><code>## mkin version used for fitting: 0.9.49.6 ## R version used for fitting: 3.6.1 -## Date of fit: Thu Sep 19 09:53:05 2019 -## Date of summary: Thu Sep 19 09:53:05 2019 +## Date of fit: Fri Nov 1 10:10:54 2019 +## Date of summary: Fri Nov 1 10:10:54 2019 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted using 224 model solutions performed in 0.48 s +## Fitted using 224 model solutions performed in 0.455 s ## ## Error model: Constant variance ## ## Error model algorithm: OLS ## ## Starting values for parameters to be optimised: -## value type -## parent_0 96.600000 state -## alpha 1.000000 deparm -## beta 10.000000 deparm -## sigma 1.830055 error +## value type +## parent_0 96.6 state +## alpha 1.0 deparm +## beta 10.0 deparm ## ## Starting values for the transformed parameters actually optimised: ## value lower upper ## parent_0 96.600000 -Inf Inf ## log_alpha 0.000000 -Inf Inf ## log_beta 2.302585 -Inf Inf -## sigma 1.830055 0 Inf ## ## Fixed parameter values: ## None @@ -746,6 +732,7 @@ </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <div id="tocnav"> <h2 class="hasAnchor"> <a href="#tocnav" class="anchor"></a>Contents</h2> diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png Binary files differindex 32fef506..88d03d24 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-10-1.png diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png Binary files differindex 0bfac9e2..8b39f0fc 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-8-1.png diff --git a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png Binary files differindex d194c676..13019224 100644 --- a/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png +++ b/docs/articles/FOCUS_L_files/figure-html/unnamed-chunk-9-1.png diff --git a/docs/articles/FOCUS_Z.html b/docs/articles/FOCUS_Z.html deleted file mode 100644 index ff0bd537..00000000 --- a/docs/articles/FOCUS_Z.html +++ /dev/null @@ -1,332 +0,0 @@ -<!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html> -<head> -<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> -<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>Example evaluation of FOCUS dataset Z • 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><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> -<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]--> -</head> -<body> - <div class="container template-article"> - <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> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> - </span> - </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="col-md-9 contents"> - <div class="page-header toc-ignore"> - <h1>Example evaluation of FOCUS dataset Z</h1> - <h4 class="author">Johannes Ranke</h4> - - <h4 class="date">2018-09-14</h4> - - - <div class="hidden name"><code>FOCUS_Z.Rmd</code></div> - - </div> - - - -<p><a href="http://www.jrwb.de">Wissenschaftlicher Berater, Kronacher Str. 12, 79639 Grenzach-Wyhlen, Germany</a><br><a href="http://chem.uft.uni-bremen.de/ranke">Privatdozent at the University of Bremen</a></p> -<div id="the-data" class="section level1"> -<h1 class="hasAnchor"> -<a href="#the-data" class="anchor"></a>The data</h1> -<p>The following code defines the example dataset from Appendix 7 to the FOCUS kinetics report <span class="citation">(FOCUS Work Group on Degradation Kinetics 2014, 354)</span>.</p> -<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw">library</span>(mkin, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb1-2" data-line-number="2">LOD =<span class="st"> </span><span class="fl">0.5</span></a> -<a class="sourceLine" id="cb1-3" data-line-number="3">FOCUS_<span class="dv">2006</span>_Z =<span class="st"> </span><span class="kw">data.frame</span>(</a> -<a class="sourceLine" id="cb1-4" data-line-number="4"> <span class="dt">t =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="fl">0.04</span>, <span class="fl">0.125</span>, <span class="fl">0.29</span>, <span class="fl">0.54</span>, <span class="dv">1</span>, <span class="dv">2</span>, <span class="dv">3</span>, <span class="dv">4</span>, <span class="dv">7</span>, <span class="dv">10</span>, <span class="dv">14</span>, <span class="dv">21</span>,</a> -<a class="sourceLine" id="cb1-5" data-line-number="5"> <span class="dv">42</span>, <span class="dv">61</span>, <span class="dv">96</span>, <span class="dv">124</span>),</a> -<a class="sourceLine" id="cb1-6" data-line-number="6"> <span class="dt">Z0 =</span> <span class="kw">c</span>(<span class="dv">100</span>, <span class="fl">81.7</span>, <span class="fl">70.4</span>, <span class="fl">51.1</span>, <span class="fl">41.2</span>, <span class="fl">6.6</span>, <span class="fl">4.6</span>, <span class="fl">3.9</span>, <span class="fl">4.6</span>, <span class="fl">4.3</span>, <span class="fl">6.8</span>,</a> -<a class="sourceLine" id="cb1-7" data-line-number="7"> <span class="fl">2.9</span>, <span class="fl">3.5</span>, <span class="fl">5.3</span>, <span class="fl">4.4</span>, <span class="fl">1.2</span>, <span class="fl">0.7</span>),</a> -<a class="sourceLine" id="cb1-8" data-line-number="8"> <span class="dt">Z1 =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="fl">18.3</span>, <span class="fl">29.6</span>, <span class="fl">46.3</span>, <span class="fl">55.1</span>, <span class="fl">65.7</span>, <span class="fl">39.1</span>, <span class="dv">36</span>, <span class="fl">15.3</span>, <span class="fl">5.6</span>, <span class="fl">1.1</span>,</a> -<a class="sourceLine" id="cb1-9" data-line-number="9"> <span class="fl">1.6</span>, <span class="fl">0.6</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>),</a> -<a class="sourceLine" id="cb1-10" data-line-number="10"> <span class="dt">Z2 =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="ot">NA</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="fl">2.6</span>, <span class="fl">3.8</span>, <span class="fl">15.3</span>, <span class="fl">37.2</span>, <span class="fl">31.7</span>, <span class="fl">35.6</span>, <span class="fl">14.5</span>,</a> -<a class="sourceLine" id="cb1-11" data-line-number="11"> <span class="fl">0.8</span>, <span class="fl">2.1</span>, <span class="fl">1.9</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>),</a> -<a class="sourceLine" id="cb1-12" data-line-number="12"> <span class="dt">Z3 =</span> <span class="kw">c</span>(<span class="dv">0</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="ot">NA</span>, <span class="fl">0.5</span> <span class="op">*</span><span class="st"> </span>LOD, <span class="fl">9.2</span>, <span class="fl">13.1</span>, <span class="fl">22.3</span>, <span class="fl">28.4</span>, <span class="fl">32.5</span>,</a> -<a class="sourceLine" id="cb1-13" data-line-number="13"> <span class="fl">25.2</span>, <span class="fl">17.2</span>, <span class="fl">4.8</span>, <span class="fl">4.5</span>, <span class="fl">2.8</span>, <span class="fl">4.4</span>))</a> -<a class="sourceLine" id="cb1-14" data-line-number="14"></a> -<a class="sourceLine" id="cb1-15" data-line-number="15">FOCUS_<span class="dv">2006</span>_Z_mkin <-<span class="st"> </span><span class="kw"><a href="../reference/mkin_wide_to_long.html">mkin_wide_to_long</a></span>(FOCUS_<span class="dv">2006</span>_Z)</a></code></pre></div> -</div> -<div id="parent-and-one-metabolite" class="section level1"> -<h1 class="hasAnchor"> -<a href="#parent-and-one-metabolite" class="anchor"></a>Parent and one metabolite</h1> -<p>The next step is to set up the models used for the kinetic analysis. As the simultaneous fit of parent and the first metabolite is usually straightforward, Step 1 (SFO for parent only) is skipped here. We start with the model 2a, with formation and decline of metabolite Z1 and the pathway from parent directly to sink included (default in mkin).</p> -<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1">Z<span class="fl">.2</span>a <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>),</a> -<a class="sourceLine" id="cb2-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> -<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">m.Z<span class="fl">.2</span>a <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.2</span>a, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb4-2" data-line-number="2"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.2</span>a)</a></code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png" width="700"></p> -<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="kw">summary</span>(m.Z<span class="fl">.2</span>a, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> -<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper -## Z0_0 9.7015e+01 3.553140 2.7304e+01 1.6793e-21 NA NA -## k_Z0_sink 1.2790e-11 0.226895 5.6368e-11 5.0000e-01 NA NA -## k_Z0_Z1 2.2360e+00 0.165073 1.3546e+01 7.3938e-14 NA NA -## k_Z1_sink 4.8212e-01 0.065854 7.3212e+00 3.5520e-08 NA NA</code></pre> -<p>As obvious from the parameter summary (the component of the summary), the kinetic rate constant from parent compound Z to sink is very small and the t-test for this parameter suggests that it is not significantly different from zero. This suggests, in agreement with the analysis in the FOCUS kinetics report, to simplify the model by removing the pathway to sink.</p> -<p>A similar result can be obtained when formation fractions are used in the model formulation:</p> -<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">Z<span class="fl">.2</span>a.ff <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>),</a> -<a class="sourceLine" id="cb7-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> -<a class="sourceLine" id="cb7-3" data-line-number="3"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> -<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" data-line-number="1">m.Z<span class="fl">.2</span>a.ff <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.2</span>a.ff, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb9-2" data-line-number="2"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.2</span>a.ff)</a></code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png" width="700"></p> -<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" data-line-number="1"><span class="kw">summary</span>(m.Z<span class="fl">.2</span>a.ff, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> -<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper -## Z0_0 97.01488 3.553145 27.3039 1.6793e-21 NA NA -## k_Z0 2.23601 0.216849 10.3114 3.6623e-11 NA NA -## k_Z1 0.48212 0.065854 7.3211 3.5520e-08 NA NA -## f_Z0_to_Z1 1.00000 0.101473 9.8548 9.7068e-11 NA NA</code></pre> -<p>Here, the ilr transformed formation fraction fitted in the model takes a very large value, and the backtransformed formation fraction from parent Z to Z1 is practically unity. Here, the covariance matrix used for the calculation of confidence intervals is not returned as the model is overparameterised.</p> -<p>A simplified model is obtained by removing the pathway to the sink. </p> -<p>In the following, we use the parameterisation with formation fractions in order to be able to compare with the results in the FOCUS guidance, and as it makes it easier to use parameters obtained in a previous fit when adding a further metabolite.</p> -<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" data-line-number="1">Z<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb12-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>), <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> -<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb14"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb14-1" data-line-number="1">m.Z<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.3</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb14-2" data-line-number="2"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.3</span>)</a></code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png" width="700"></p> -<div class="sourceCode" id="cb15"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb15-1" data-line-number="1"><span class="kw">summary</span>(m.Z<span class="fl">.3</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> -<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper -## Z0_0 97.01488 2.681772 36.176 2.3636e-25 91.52152 102.508 -## k_Z0 2.23601 0.146861 15.225 2.2464e-15 1.95453 2.558 -## k_Z1 0.48212 0.042687 11.294 3.0686e-12 0.40216 0.578</code></pre> -<p>As there is only one transformation product for Z0 and no pathway to sink, the formation fraction is internally fixed to unity.</p> -</div> -<div id="metabolites-z2-and-z3" class="section level1"> -<h1 class="hasAnchor"> -<a href="#metabolites-z2-and-z3" class="anchor"></a>Metabolites Z2 and Z3</h1> -<p>As suggested in the FOCUS report, the pathway to sink was removed for metabolite Z1 as well in the next step. While this step appears questionable on the basis of the above results, it is followed here for the purpose of comparison. Also, in the FOCUS report, it is assumed that there is additional empirical evidence that Z1 quickly and exclusively hydrolyses to Z2.</p> -<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" data-line-number="1">Z<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb17-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb17-3" data-line-number="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>), <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> -<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" data-line-number="1">m.Z<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(Z<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb19-2" data-line-number="2"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z<span class="fl">.5</span>)</a></code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png" width="700"></p> -<p>Finally, metabolite Z3 is added to the model. We use the optimised differential equation parameter values from the previous fit in order to accelerate the optimization.</p> -<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" data-line-number="1">Z.FOCUS <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb20-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb20-3" data-line-number="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> -<a class="sourceLine" id="cb20-4" data-line-number="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>),</a> -<a class="sourceLine" id="cb20-5" data-line-number="5"> <span class="dt">use_of_ff =</span> <span class="st">"max"</span>)</a></code></pre></div> -<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1">m.Z.FOCUS <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(Z.FOCUS, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> -<a class="sourceLine" id="cb22-2" data-line-number="2"> <span class="dt">parms.ini =</span> m.Z<span class="fl">.5</span><span class="op">$</span>bparms.ode,</a> -<a class="sourceLine" id="cb22-3" data-line-number="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a></code></pre></div> -<pre><code>## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : Optimisation by method Port did not converge: -## false convergence (8)</code></pre> -<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" data-line-number="1"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.FOCUS)</a></code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png" width="700"></p> -<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1"><span class="kw">summary</span>(m.Z.FOCUS, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>bpar</a></code></pre></div> -<pre><code>## Estimate se_notrans t value Pr(>t) Lower Upper -## Z0_0 96.837112 2.058861 47.0343 5.5877e-44 92.703779 100.970445 -## k_Z0 2.215368 0.118098 18.7587 7.6563e-25 1.990525 2.465609 -## k_Z1 0.478302 0.029289 16.3302 3.3408e-22 0.422977 0.540864 -## k_Z2 0.451617 0.044214 10.2144 3.1133e-14 0.371034 0.549702 -## k_Z3 0.058693 0.014296 4.1056 7.2924e-05 0.035994 0.095705 -## f_Z2_to_Z3 0.471516 0.057057 8.2639 2.8156e-11 0.360381 0.585548</code></pre> -<div class="sourceCode" id="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" data-line-number="1"><span class="kw"><a href="../reference/endpoints.html">endpoints</a></span>(m.Z.FOCUS)</a></code></pre></div> -<pre><code>## $ff -## Z2_Z3 Z2_sink -## 0.47152 0.52848 -## -## $SFORB -## logical(0) -## -## $distimes -## DT50 DT90 -## Z0 0.31288 1.0394 -## Z1 1.44918 4.8141 -## Z2 1.53481 5.0985 -## Z3 11.80973 39.2311</code></pre> -<p>This fit corresponds to the final result chosen in Appendix 7 of the FOCUS report. Confidence intervals returned by mkin are based on internally transformed parameters, however.</p> -</div> -<div id="using-the-sforb-model" class="section level1"> -<h1 class="hasAnchor"> -<a href="#using-the-sforb-model" class="anchor"></a>Using the SFORB model</h1> -<p>As the FOCUS report states, there is a certain tailing of the time course of metabolite Z3. Also, the time course of the parent compound is not fitted very well using the SFO model, as residues at a certain low level remain.</p> -<p>Therefore, an additional model is offered here, using the single first-order reversible binding (SFORB) model for metabolite Z3. As expected, the <span class="math inline">\(\chi^2\)</span> error level is lower for metabolite Z3 using this model and the graphical fit for Z3 is improved. However, the covariance matrix is not returned.</p> -<div class="sourceCode" id="cb29"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb29-1" data-line-number="1">Z.mkin<span class="fl">.1</span> <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb29-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb29-3" data-line-number="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> -<a class="sourceLine" id="cb29-4" data-line-number="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</a></code></pre></div> -<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb31"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb31-1" data-line-number="1">m.Z.mkin<span class="fl">.1</span> <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.1</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb31-2" data-line-number="2"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.1</span>)</a></code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png" width="700"></p> -<div class="sourceCode" id="cb32"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb32-1" data-line-number="1"><span class="kw">summary</span>(m.Z.mkin<span class="fl">.1</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>cov.unscaled</a></code></pre></div> -<pre><code>## NULL</code></pre> -<p>Therefore, a further stepwise model building is performed starting from the stage of parent and two metabolites, starting from the assumption that the model fit for the parent compound can be improved by using the SFORB model.</p> -<div class="sourceCode" id="cb34"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb34-1" data-line-number="1">Z.mkin<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb34-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb34-3" data-line-number="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> -<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb36"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb36-1" data-line-number="1">m.Z.mkin<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.3</span>, FOCUS_<span class="dv">2006</span>_Z_mkin, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb36-2" data-line-number="2"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.3</span>)</a></code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png" width="700"></p> -<p>This results in a much better representation of the behaviour of the parent compound Z0.</p> -<p>Finally, Z3 is added as well. These models appear overparameterised (no covariance matrix returned) if the sink for Z1 is left in the models.</p> -<div class="sourceCode" id="cb37"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb37-1" data-line-number="1">Z.mkin<span class="fl">.4</span> <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb37-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb37-3" data-line-number="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> -<a class="sourceLine" id="cb37-4" data-line-number="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> -<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb39"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb39-1" data-line-number="1">m.Z.mkin<span class="fl">.4</span> <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.4</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> -<a class="sourceLine" id="cb39-2" data-line-number="2"> <span class="dt">parms.ini =</span> m.Z.mkin<span class="fl">.3</span><span class="op">$</span>bparms.ode,</a> -<a class="sourceLine" id="cb39-3" data-line-number="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb39-4" data-line-number="4"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.4</span>)</a></code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png" width="700"></p> -<p>The error level of the fit, but especially of metabolite Z3, can be improved if the SFORB model is chosen for this metabolite, as this model is capable of representing the tailing of the metabolite decline phase.</p> -<div class="sourceCode" id="cb40"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb40-1" data-line-number="1">Z.mkin<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb40-2" data-line-number="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> -<a class="sourceLine" id="cb40-3" data-line-number="3"> <span class="dt">Z2 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z3"</span>),</a> -<a class="sourceLine" id="cb40-4" data-line-number="4"> <span class="dt">Z3 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>))</a></code></pre></div> -<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<div class="sourceCode" id="cb42"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb42-1" data-line-number="1">m.Z.mkin<span class="fl">.5</span> <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> -<a class="sourceLine" id="cb42-2" data-line-number="2"> <span class="dt">parms.ini =</span> m.Z.mkin<span class="fl">.4</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">4</span>],</a> -<a class="sourceLine" id="cb42-3" data-line-number="3"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb42-4" data-line-number="4"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.5</span>)</a></code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png" width="700"></p> -<p>The summary view of the backtransformed parameters shows that we get no confidence intervals due to overparameterisation. As the optimized is excessively small, it seems reasonable to fix it to zero.</p> -<div class="sourceCode" id="cb43"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb43-1" data-line-number="1">m.Z.mkin<span class="fl">.5</span>a <-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(Z.mkin<span class="fl">.5</span>, FOCUS_<span class="dv">2006</span>_Z_mkin,</a> -<a class="sourceLine" id="cb43-2" data-line-number="2"> <span class="dt">parms.ini =</span> <span class="kw">c</span>(m.Z.mkin<span class="fl">.5</span><span class="op">$</span>bparms.ode[<span class="dv">1</span><span class="op">:</span><span class="dv">7</span>],</a> -<a class="sourceLine" id="cb43-3" data-line-number="3"> <span class="dt">k_Z3_bound_free =</span> <span class="dv">0</span>),</a> -<a class="sourceLine" id="cb43-4" data-line-number="4"> <span class="dt">fixed_parms =</span> <span class="st">"k_Z3_bound_free"</span>,</a> -<a class="sourceLine" id="cb43-5" data-line-number="5"> <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb43-6" data-line-number="6"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png" width="700"></p> -<p>As expected, the residual plots for Z0 and Z3 are more random than in the case of the all SFO model for which they were shown above. In conclusion, the model is proposed as the best-fit model for the dataset from Appendix 7 of the FOCUS report.</p> -<p>A graphical representation of the confidence intervals can finally be obtained.</p> -<div class="sourceCode" id="cb44"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb44-1" data-line-number="1"><span class="kw"><a href="../reference/mkinparplot.html">mkinparplot</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div> -<p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png" width="700"></p> -<p>The endpoints obtained with this model are</p> -<div class="sourceCode" id="cb45"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb45-1" data-line-number="1"><span class="kw"><a href="../reference/endpoints.html">endpoints</a></span>(m.Z.mkin<span class="fl">.5</span>a)</a></code></pre></div> -<pre><code>## $ff -## Z0_free_Z1 Z1_Z2 Z2_sink Z2_Z3_free Z3_free_sink -## 1.00000 1.00000 0.46344 0.53656 1.00000 -## -## $SFORB -## Z0_b1 Z0_b2 Z3_b1 Z3_b2 -## 2.4471382 0.0075127 0.0800075 0.0000000 -## -## $distimes -## DT50 DT90 DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2 -## Z0 0.3043 1.1848 0.28325 92.264 NA NA -## Z1 1.5148 5.0320 NA NA NA NA -## Z2 1.6414 5.4526 NA NA NA NA -## Z3 NA NA NA NA 8.6635 Inf</code></pre> -<p>It is clear the degradation rate of Z3 towards the end of the experiment is very low as DT50_Z3_b2 (the second Eigenvalue of the system of two differential equations representing the SFORB system for Z3, corresponding to the slower rate constant of the DFOP model) is reported to be infinity. However, this appears to be a feature of the data.</p> -</div> -<div id="references" class="section level1"> -<h1 class="hasAnchor"> -<a href="#references" class="anchor"></a>References</h1> -<!-- vim: set foldmethod=syntax: --> -<div id="refs" class="references"> -<div id="ref-FOCUSkinetics2014"> -<p>FOCUS Work Group on Degradation Kinetics. 2014. <em>Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="uri">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>.</p> -</div> -</div> -</div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <div id="tocnav"> - <h2 class="hasAnchor"> -<a href="#tocnav" class="anchor"></a>Contents</h2> - <ul class="nav nav-pills nav-stacked"> -<li><a href="#the-data">The data</a></li> - <li><a href="#parent-and-one-metabolite">Parent and one metabolite</a></li> - <li><a href="#metabolites-z2-and-z3">Metabolites Z2 and Z3</a></li> - <li><a href="#using-the-sforb-model">Using the SFORB model</a></li> - <li><a href="#references">References</a></li> - </ul> -</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_Z.pdf b/docs/articles/FOCUS_Z.pdf Binary files differdeleted file mode 100644 index 975ad17f..00000000 --- a/docs/articles/FOCUS_Z.pdf +++ /dev/null diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png Binary files differdeleted file mode 100644 index 53f2ce85..00000000 --- a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png +++ /dev/null diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png Binary files differdeleted file mode 100644 index 90eab945..00000000 --- a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png +++ /dev/null diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png Binary files differdeleted file mode 100644 index f44737ad..00000000 --- a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png +++ /dev/null diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png Binary files differdeleted file mode 100644 index 98562168..00000000 --- a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png +++ /dev/null diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png Binary files differdeleted file mode 100644 index 27e7eb52..00000000 --- a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png +++ /dev/null diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png Binary files differdeleted file mode 100644 index 236cdbfe..00000000 --- a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png +++ /dev/null diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png Binary files differdeleted file mode 100644 index 693c9c2c..00000000 --- a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png +++ /dev/null diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png Binary files differdeleted file mode 100644 index 180f44f9..00000000 --- a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png +++ /dev/null diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png Binary files differdeleted file mode 100644 index a67e9c1d..00000000 --- a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png +++ /dev/null diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png Binary files differdeleted file mode 100644 index 80452f9f..00000000 --- a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png +++ /dev/null diff --git a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png b/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png Binary files differdeleted file mode 100644 index e6ce97cd..00000000 --- a/docs/articles/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png +++ /dev/null diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html deleted file mode 100644 index a6598fd4..00000000 --- a/docs/articles/compiled_models.html +++ /dev/null @@ -1,201 +0,0 @@ -<!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html> -<head> -<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> -<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>Performance benefit by using compiled model definitions in mkin • 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><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"> -<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]--> -</head> -<body> - <div class="container template-article"> - <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> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> - </span> - </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="col-md-9 contents"> - <div class="page-header toc-ignore"> - <h1>Performance benefit by using compiled model definitions in mkin</h1> - <h4 class="author">Johannes Ranke</h4> - - <h4 class="date">2018-09-14</h4> - - - <div class="hidden name"><code>compiled_models.Rmd</code></div> - - </div> - - - -<div id="model-that-can-also-be-solved-with-eigenvalues" class="section level2"> -<h2 class="hasAnchor"> -<a href="#model-that-can-also-be-solved-with-eigenvalues" class="anchor"></a>Model that can also be solved with Eigenvalues</h2> -<p>This evaluation is taken from the example section of mkinfit. When using an mkin version equal to or greater than 0.9-36 and a C compiler (gcc) is available, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod. The <code><a href="../reference/mkinmod.html">mkinmod()</a></code> function checks for presence of the gcc compiler using</p> -<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw">Sys.which</span>(<span class="st">"gcc"</span>)</a></code></pre></div> -<pre><code>## gcc -## "/usr/bin/gcc"</code></pre> -<p>First, we build a simple degradation model for a parent compound with one metabolite.</p> -<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw">library</span>(<span class="st">"mkin"</span>, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a> -<a class="sourceLine" id="cb3-2" data-line-number="2">SFO_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(</a> -<a class="sourceLine" id="cb3-3" data-line-number="3"> <span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>),</a> -<a class="sourceLine" id="cb3-4" data-line-number="4"> <span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div> -<pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre> -<p>We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the benchmark package.</p> -<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" data-line-number="1"><span class="cf">if</span> (<span class="kw">require</span>(rbenchmark)) {</a> -<a class="sourceLine" id="cb5-2" data-line-number="2"> b<span class="fl">.1</span> <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></span>(</a> -<a class="sourceLine" id="cb5-3" data-line-number="3"> <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D,</a> -<a class="sourceLine" id="cb5-4" data-line-number="4"> <span class="dt">solution_type =</span> <span class="st">"deSolve"</span>,</a> -<a class="sourceLine" id="cb5-5" data-line-number="5"> <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> -<a class="sourceLine" id="cb5-6" data-line-number="6"> <span class="st">"Eigenvalue based"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D,</a> -<a class="sourceLine" id="cb5-7" data-line-number="7"> <span class="dt">solution_type =</span> <span class="st">"eigen"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> -<a class="sourceLine" id="cb5-8" data-line-number="8"> <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D,</a> -<a class="sourceLine" id="cb5-9" data-line-number="9"> <span class="dt">solution_type =</span> <span class="st">"deSolve"</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> -<a class="sourceLine" id="cb5-10" data-line-number="10"> <span class="dt">replications =</span> <span class="dv">3</span>)</a> -<a class="sourceLine" id="cb5-11" data-line-number="11"> <span class="kw">print</span>(b<span class="fl">.1</span>)</a> -<a class="sourceLine" id="cb5-12" data-line-number="12"> factor_SFO_SFO <-<span class="st"> </span><span class="kw">round</span>(b<span class="fl">.1</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>])</a> -<a class="sourceLine" id="cb5-13" data-line-number="13">} <span class="cf">else</span> {</a> -<a class="sourceLine" id="cb5-14" data-line-number="14"> factor_SFO_SFO <-<span class="st"> </span><span class="ot">NA</span></a> -<a class="sourceLine" id="cb5-15" data-line-number="15"> <span class="kw">print</span>(<span class="st">"R package benchmark is not available"</span>)</a> -<a class="sourceLine" id="cb5-16" data-line-number="16">}</a></code></pre></div> -<pre><code>## Lade nötiges Paket: rbenchmark</code></pre> -<pre><code>## test replications elapsed relative user.self sys.self -## 3 deSolve, compiled 3 2.205 1.000 2.203 0 -## 1 deSolve, not compiled 3 17.206 7.803 17.196 0 -## 2 Eigenvalue based 3 2.829 1.283 2.828 0 -## user.child sys.child -## 3 0 0 -## 1 0 0 -## 2 0 0</code></pre> -<p>We see that using the compiled model is by a factor of around 8 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs.</p> -</div> -<div id="model-that-can-not-be-solved-with-eigenvalues" class="section level2"> -<h2 class="hasAnchor"> -<a href="#model-that-can-not-be-solved-with-eigenvalues" class="anchor"></a>Model that can not be solved with Eigenvalues</h2> -<p>This evaluation is also taken from the example section of mkinfit.</p> -<div class="sourceCode" id="cb8"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb8-1" data-line-number="1"><span class="cf">if</span> (<span class="kw">require</span>(rbenchmark)) {</a> -<a class="sourceLine" id="cb8-2" data-line-number="2"> FOMC_SFO <-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(</a> -<a class="sourceLine" id="cb8-3" data-line-number="3"> <span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"FOMC"</span>, <span class="st">"m1"</span>),</a> -<a class="sourceLine" id="cb8-4" data-line-number="4"> <span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>( <span class="st">"SFO"</span>))</a> -<a class="sourceLine" id="cb8-5" data-line-number="5"></a> -<a class="sourceLine" id="cb8-6" data-line-number="6"> b<span class="fl">.2</span> <-<span class="st"> </span><span class="kw"><a href="http://www.rdocumentation.org/packages/rbenchmark/topics/benchmark">benchmark</a></span>(</a> -<a class="sourceLine" id="cb8-7" data-line-number="7"> <span class="st">"deSolve, not compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D,</a> -<a class="sourceLine" id="cb8-8" data-line-number="8"> <span class="dt">use_compiled =</span> <span class="ot">FALSE</span>, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> -<a class="sourceLine" id="cb8-9" data-line-number="9"> <span class="st">"deSolve, compiled"</span> =<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(FOMC_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>),</a> -<a class="sourceLine" id="cb8-10" data-line-number="10"> <span class="dt">replications =</span> <span class="dv">3</span>)</a> -<a class="sourceLine" id="cb8-11" data-line-number="11"> <span class="kw">print</span>(b<span class="fl">.2</span>)</a> -<a class="sourceLine" id="cb8-12" data-line-number="12"> factor_FOMC_SFO <-<span class="st"> </span><span class="kw">round</span>(b<span class="fl">.2</span>[<span class="st">"1"</span>, <span class="st">"relative"</span>])</a> -<a class="sourceLine" id="cb8-13" data-line-number="13">} <span class="cf">else</span> {</a> -<a class="sourceLine" id="cb8-14" data-line-number="14"> factor_FOMC_SFO <-<span class="st"> </span><span class="ot">NA</span></a> -<a class="sourceLine" id="cb8-15" data-line-number="15"> <span class="kw">print</span>(<span class="st">"R package benchmark is not available"</span>)</a> -<a class="sourceLine" id="cb8-16" data-line-number="16">}</a></code></pre></div> -<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 3.874 1.000 3.866 0.004 -## 1 deSolve, not compiled 3 35.712 9.218 35.692 0.000 -## user.child sys.child -## 2 0 0 -## 1 0 0</code></pre> -<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 0.9.47.3 on</p> -<pre><code>## R version 3.5.1 (2018-07-02) -## Platform: x86_64-pc-linux-gnu (64-bit) -## Running under: Debian GNU/Linux 9 (stretch)</code></pre> -<pre><code>## CPU model: AMD Ryzen 7 1700 Eight-Core Processor</code></pre> -</div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <div id="tocnav"> - <h2 class="hasAnchor"> -<a href="#tocnav" class="anchor"></a>Contents</h2> - <ul class="nav nav-pills nav-stacked"> -<li><a href="#model-that-can-also-be-solved-with-eigenvalues">Model that can also be solved with Eigenvalues</a></li> - <li><a href="#model-that-can-not-be-solved-with-eigenvalues">Model that can not be solved with Eigenvalues</a></li> - </ul> -</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/index.html b/docs/articles/index.html index babe3137..76d7bc69 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -67,7 +67,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.7</span> </span> </div> diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index 9caabec8..42eb6c0a 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -90,7 +90,7 @@ <h1>Introduction to mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-10-25</h4> + <h4 class="date">2019-11-01</h4> <div class="hidden name"><code>mkin.Rmd</code></div> diff --git a/docs/articles/mkin_vignettes.css b/docs/articles/mkin_vignettes.css deleted file mode 100644 index 3bd91ab1..00000000 --- a/docs/articles/mkin_vignettes.css +++ /dev/null @@ -1,16 +0,0 @@ -/* Thanks to Steve Powell for http://rpubs.com/stevepowell99/floating-css */ -#TOC { - position: fixed; - left: 0; - top: 0; - width: 200px; - height: 100%; - overflow:auto; -} - -body { - max-width: 800px; - margin: auto; - margin-left:210px; - line-height: 20px; -} diff --git a/docs/articles/references.bib b/docs/articles/references.bib deleted file mode 100644 index efccb362..00000000 --- a/docs/articles/references.bib +++ /dev/null @@ -1,112 +0,0 @@ -% This file was originally created with JabRef 2.7b. -% Encoding: ISO8859_1 - -@BOOK{bates1988, - title = {Nonlinear regression and its applications}, - publisher = {Wiley-Interscience}, - year = {1988}, - author = {D. Bates and D. Watts} -} - -@MANUAL{FOCUSkinetics2011, - title = {Generic guidance for estimating persistence and degradation kinetics - from environmental fate studies on pesticides in EU registration}, - author = {{FOCUS Work Group on Degradation Kinetics}}, - edition = {1.0}, - month = {November}, - year = {2011}, - file = {FOCUS kinetics 2011 Generic guidance:/home/ranke/dok/orgs/focus/FOCUSkineticsvc_1_0_Nov23.pdf:PDF}, - url = {http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} -} - -@MANUAL{FOCUSkinetics2014, - title = {Generic guidance for estimating persistence and degradation kinetics - from environmental fate studies on pesticides in EU registration}, - author = {{FOCUS Work Group on Degradation Kinetics}}, - edition = {1.1}, - month = {December}, - year = {2014}, - file = {FOCUS kinetics 2011 Generic guidance:/home/ranke/dok/orgs/focus/dk/FOCUSkineticsvc1.1Dec2014.pdf:PDF}, - url = {http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} -} - -@MANUAL{FOCUS2006, - title = {Guidance Document on Estimating Persistence and Degradation Kinetics - from Environmental Fate Studies on Pesticides in EU Registration. - Report of the FOCUS Work Group on Degradation Kinetics}, - author = {{FOCUS Work Group on Degradation Kinetics}}, - year = {2006}, - note = {EC Document Reference Sanco/10058/2005 version 2.0}, - url = {http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} -} - -@MANUAL{rcore2016, - title = {\textsf{R}: A Language and Environment for Statistical Computing}, - author = {{R Development Core Team}}, - organization = {R Foundation for Statistical Computing}, - address = {Vienna, Austria}, - year = {2016}, - note = {{ISBN} 3-900051-07-0}, - url = {https://www.R-project.org} -} - -@MANUAL{pkg:kinfit, - title = {`kinfit`: {R}outines for fitting simple kinetic models to chemical - degradation data}, - author = {J. Ranke}, - year = {2015}, - url = {https://CRAN.R-project.org/package=kinfit} -} - -@MANUAL{pkg:mkin, - title = {`mkin`: {K}inetic evaluation of chemical degradation data}, - author = {J. Ranke}, - year = {2016}, - url = {https://CRAN.R-project.org/package=mkin} -} - -@Inproceedings{ schaefer2007, - title = {{KinGUI}: a new kinetic software tool for evaluations according to {FOCUS} degradation kinetics}, - author = {D. Sch\"{a}fer and B. Mikolasch and P. Rainbird and B. Harvey}, - booktitle = {Proceedings of the XIII Symposium Pesticide Chemistry}, - editor = {Del Re A. A. M. and Capri E. and Fragoulis G. and Trevisan M.}, - year = {2007}, - address = {Piacenza}, - pages = {916--923} -} - -@ARTICLE{soetaert2010, - author = {Karline Soetaert and Thomas Petzoldt}, - title = {Inverse Modelling, Sensitivity and Monte Carlo Analysis in {R} Using - Package {FME}}, - journal = {Journal of Statistical Software}, - year = {2010}, - volume = {33}, - pages = {1--28}, - number = {3}, - url = {http://www.jstatsoft.org/v33/i03/} -} - -@Inproceedings{ ranke2012, - title = {Parameter reliability in kinetic evaluation of environmental metabolism data - Assessment and the influence of model specification}, - author = {J. Ranke and R. Lehmann}, - booktitle = {SETAC World 20-24 May}, - year = {2012}, - address = {Berlin} -} -@Inproceedings{ ranke2015, - title = {To t-test or not to t-test, that is the question}, - author = {J. Ranke and R. Lehmann}, - booktitle = {XV Symposium on Pesticide Chemistry 2-4 September 2015}, - year = {2015}, - address = {Piacenza}, - url = {http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf} -} -@Techreport{ranke2014, - title = {{Prüfung und Validierung von Modellierungssoftware als Alternative zu - ModelMaker 4.0}}, - author = {J. Ranke}, - year = 2014, - institution = {Umweltbundesamt}, - volume = {Projektnummer 27452} -} diff --git a/docs/articles/twa.html b/docs/articles/twa.html index 9cb5873a..8d8bac0e 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -90,7 +90,7 @@ <h1>Calculation of time weighted average concentrations with mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-09-19</h4> + <h4 class="date">2019-11-01</h4> <div class="hidden name"><code>twa.Rmd</code></div> @@ -139,6 +139,7 @@ </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + </div> </div> diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index 5ea0b256..14234785 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -90,7 +90,7 @@ <h1>Example evaluation of FOCUS dataset Z</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-09-19</h4> + <h4 class="date">2019-11-01</h4> <div class="hidden name"><code>FOCUS_Z.Rmd</code></div> @@ -244,36 +244,7 @@ <div class="sourceCode" id="cb41"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb41-1" title="1"><span class="kw"><a href="../../reference/plot.mkinfit.html">plot_sep</a></span>(m.Z.mkin<span class="fl">.1</span>)</a></code></pre></div> <p><img src="FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png" width="700"></p> <div class="sourceCode" id="cb42"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb42-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(m.Z.mkin<span class="fl">.1</span>, <span class="dt">data =</span> <span class="ot">FALSE</span>)<span class="op">$</span>cov.unscaled</a></code></pre></div> -<pre><code>## Z0_0 log_k_Z0_Z1 log_k_Z1_Z2 log_k_Z2_sink -## Z0_0 3.8375e+00 5.4918e-03 3.0584e-02 1.2969e-01 -## log_k_Z0_Z1 5.4918e-03 2.7613e-03 -1.8820e-04 2.6634e-04 -## log_k_Z1_Z2 3.0584e-02 -1.8820e-04 3.3807e-03 3.2177e-03 -## log_k_Z2_sink 1.2969e-01 2.6634e-04 3.2177e-03 3.4256e-02 -## log_k_Z2_Z3_free -2.4223e-02 -2.6169e-04 -1.1845e-03 -8.1134e-03 -## log_k_Z3_free_sink -6.5467e-02 -4.0815e-04 -3.2978e-03 -3.6010e-02 -## log_k_Z3_free_bound -6.0659e-02 -4.4768e-04 -3.0588e-03 -3.9074e-02 -## log_k_Z3_bound_free 5.2844e-01 4.5458e-03 7.9800e-03 4.6274e-02 -## sigma 2.0366e-10 -3.4658e-10 8.9910e-11 -2.5946e-10 -## log_k_Z2_Z3_free log_k_Z3_free_sink -## Z0_0 -2.4223e-02 -6.5467e-02 -## log_k_Z0_Z1 -2.6169e-04 -4.0815e-04 -## log_k_Z1_Z2 -1.1845e-03 -3.2978e-03 -## log_k_Z2_sink -8.1134e-03 -3.6010e-02 -## log_k_Z2_Z3_free 1.5500e-02 2.1583e-02 -## log_k_Z3_free_sink 2.1583e-02 7.5705e-02 -## log_k_Z3_free_bound 2.5836e-02 1.1964e-01 -## log_k_Z3_bound_free 5.2534e-02 2.9441e-01 -## sigma 1.3063e-10 3.4170e-10 -## log_k_Z3_free_bound log_k_Z3_bound_free sigma -## Z0_0 -6.0659e-02 5.2844e-01 2.0366e-10 -## log_k_Z0_Z1 -4.4768e-04 4.5458e-03 -3.4658e-10 -## log_k_Z1_Z2 -3.0588e-03 7.9800e-03 8.9910e-11 -## log_k_Z2_sink -3.9074e-02 4.6274e-02 -2.5946e-10 -## log_k_Z2_Z3_free 2.5836e-02 5.2534e-02 1.3063e-10 -## log_k_Z3_free_sink 1.1964e-01 2.9441e-01 3.4170e-10 -## log_k_Z3_free_bound 6.5902e-01 5.4737e+00 -6.7704e-10 -## log_k_Z3_bound_free 5.4737e+00 2.8722e+08 7.2421e-02 -## sigma -6.7704e-10 7.2421e-02 1.4170e-01</code></pre> +<pre><code>## NULL</code></pre> <p>Therefore, a further stepwise model building is performed starting from the stage of parent and two metabolites, starting from the assumption that the model fit for the parent compound can be improved by using the SFORB model.</p> <div class="sourceCode" id="cb44"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb44-1" title="1">Z.mkin<span class="fl">.3</span> <-<span class="st"> </span><span class="kw"><a href="../../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">Z0 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFORB"</span>, <span class="st">"Z1"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> <a class="sourceLine" id="cb44-2" title="2"> <span class="dt">Z1 =</span> <span class="kw"><a href="../../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"Z2"</span>, <span class="dt">sink =</span> <span class="ot">FALSE</span>),</a> @@ -358,6 +329,7 @@ </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <div id="tocnav"> <h2 class="hasAnchor"> <a href="#tocnav" class="anchor"></a>Contents</h2> diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png Binary files differindex 471db177..76826836 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png Binary files differindex 3c983f21..25249a9a 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png Binary files differindex 0e0a78a9..f9c28e5a 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png Binary files differindex d7dd85a5..6926c367 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png Binary files differindex d24b8a40..c84e21f1 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_2-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png Binary files differindex dd8c1e0a..38805220 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_3-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png Binary files differindex 45a32027..e1cbf084 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_5-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png Binary files differindex 18832ed2..30f6a0b7 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png Binary files differindex 0d3b4d1a..891d95e1 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_7-1.png diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png Binary files differindex 898e6190..ea4f89e6 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png +++ b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index 0476acf8..fecbe3b1 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -90,7 +90,7 @@ <h1>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-09-19</h4> + <h4 class="date">2019-11-01</h4> <div class="hidden name"><code>NAFTA_examples.Rmd</code></div> @@ -414,8 +414,8 @@ <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- -## finite result is doubtful</code></pre> +<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite +## result is doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> <div class="sourceCode" id="cb44"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb44-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p9b)</a></code></pre></div> @@ -628,8 +628,8 @@ <pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- -## finite result is doubtful</code></pre> +<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite +## result is doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> <div class="sourceCode" id="cb76"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb76-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p12b)</a></code></pre></div> @@ -680,8 +680,8 @@ <div class="sourceCode" id="cb79"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb79-1" title="1">p13 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p13"</span>]])</a></code></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- -## finite result is doubtful</code></pre> +<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite +## result is doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> <div class="sourceCode" id="cb85"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb85-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p13)</a></code></pre></div> @@ -733,8 +733,8 @@ <div class="sourceCode" id="cb88"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb88-1" title="1">p14 <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p14"</span>]])</a></code></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- -## finite result is doubtful</code></pre> +<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite +## result is doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> <div class="sourceCode" id="cb94"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb94-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p14)</a></code></pre></div> @@ -787,8 +787,8 @@ <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- -## finite result is doubtful</code></pre> +<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite +## result is doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> <div class="sourceCode" id="cb104"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb104-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p15a)</a></code></pre></div> @@ -835,8 +835,8 @@ <div class="sourceCode" id="cb107"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb107-1" title="1">p15b <-<span class="st"> </span><span class="kw"><a href="../../reference/nafta.html">nafta</a></span>(NAFTA_SOP_Attachment[[<span class="st">"p15b"</span>]])</a></code></pre></div> <pre><code>## Warning in sqrt(diag(covar)): NaNs wurden erzeugt</code></pre> <pre><code>## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt</code></pre> -<pre><code>## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non- -## finite result is doubtful</code></pre> +<pre><code>## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite +## result is doubtful</code></pre> <pre><code>## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</code></pre> <pre><code>## The half-life obtained from the IORE model may be used</code></pre> <div class="sourceCode" id="cb113"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb113-1" title="1"><span class="kw"><a href="https://rdrr.io/r/graphics/plot.html">plot</a></span>(p15b)</a></code></pre></div> @@ -951,6 +951,7 @@ </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <div id="tocnav"> <h2 class="hasAnchor"> <a href="#tocnav" class="anchor"></a>Contents</h2> diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html index c0682cb0..4fb76fa2 100644 --- a/docs/articles/web_only/benchmarks.html +++ b/docs/articles/web_only/benchmarks.html @@ -90,7 +90,7 @@ <h1>Benchmark timings for mkin on various systems</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-09-19</h4> + <h4 class="date">2019-11-01</h4> <div class="hidden name"><code>benchmarks.Rmd</code></div> @@ -204,82 +204,83 @@ ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.064 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.296 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.936 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 6.005 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 5.901 ## t2 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 11.019 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 22.889 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 12.558 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 21.239 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.545 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 37.266 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 36.164 ## t3 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.764 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.649 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.786 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.510 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.446 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.559 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.510 ## t4 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 14.347 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 13.789 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 8.461 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 13.805 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 15.335 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 31.574 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 30.849 ## t5 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 9.495 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 6.002 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 10.659 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 10.545 ## t6 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 2.623 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 2.542 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 2.723 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 2.643 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.635 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 2.634 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 2.563 ## t7 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.259 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.324 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.252 ## t8 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 7.525 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.632 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.862 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.02 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.737 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 8.233 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 7.865 ## t9 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 16.621 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.171 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.618 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 11.124 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 7.763 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 16.376 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 16.195 ## t10 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 8.576 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 3.676 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 3.579 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 5.388 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.427 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 8.058 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 7.729 ## t11 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 31.267 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 5.636 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.574 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.365 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.626 -## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 11.133</code></pre> +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 10.787</code></pre> <div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/save.html">save</a></span>(mkin_benchmarks, <span class="dt">file =</span> <span class="st">"~/git/mkin/vignettes/mkin_benchmarks.rda"</span>)</a></code></pre></div> </div> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <div id="tocnav"> <h2 class="hasAnchor"> <a href="#tocnav" class="anchor"></a>Contents</h2> diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 6df504ed..363f0c38 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -90,7 +90,7 @@ <h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 class="author">Johannes Ranke</h4> - <h4 class="date">2019-09-19</h4> + <h4 class="date">2019-11-01</h4> <div class="hidden name"><code>compiled_models.Rmd</code></div> @@ -165,9 +165,9 @@ ## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet ## = TRUE): Observations with value of zero were removed from the data</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 3 deSolve, compiled 3 3.171 1.000 3.170 0 -## 1 deSolve, not compiled 3 29.012 9.149 28.996 0 -## 2 Eigenvalue based 3 4.473 1.411 4.470 0 +## 3 deSolve, compiled 3 3.143 1.000 3.142 0 +## 1 deSolve, not compiled 3 29.169 9.281 29.154 0 +## 2 Eigenvalue based 3 4.358 1.387 4.356 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 @@ -216,8 +216,8 @@ ## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with ## value of zero were removed from the data</code></pre> <pre><code>## test replications elapsed relative user.self sys.self -## 2 deSolve, compiled 3 4.913 1.000 4.909 0 -## 1 deSolve, not compiled 3 53.418 10.873 53.393 0 +## 2 deSolve, compiled 3 4.840 1.000 4.837 0 +## 1 deSolve, not compiled 3 54.338 11.227 54.309 0 ## user.child sys.child ## 2 0 0 ## 1 0 0</code></pre> @@ -231,6 +231,7 @@ </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> + <div id="tocnav"> <h2 class="hasAnchor"> <a href="#tocnav" class="anchor"></a>Contents</h2> diff --git a/docs/authors.html b/docs/authors.html index 30c81ddf..cb970788 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -67,7 +67,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.7</span> </span> </div> diff --git a/docs/index.html b/docs/index.html index 2b8e0303..a745a7ac 100644 --- a/docs/index.html +++ b/docs/index.html @@ -38,7 +38,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.7</span> </span> </div> diff --git a/docs/jquery.sticky-kit.min.js b/docs/jquery.sticky-kit.min.js deleted file mode 100644 index e2a3c6de..00000000 --- a/docs/jquery.sticky-kit.min.js +++ /dev/null @@ -1,9 +0,0 @@ -/* - Sticky-kit v1.1.2 | WTFPL | Leaf Corcoran 2015 | http://leafo.net -*/ -(function(){var b,f;b=this.jQuery||window.jQuery;f=b(window);b.fn.stick_in_parent=function(d){var A,w,J,n,B,K,p,q,k,E,t;null==d&&(d={});t=d.sticky_class;B=d.inner_scrolling;E=d.recalc_every;k=d.parent;q=d.offset_top;p=d.spacer;w=d.bottoming;null==q&&(q=0);null==k&&(k=void 0);null==B&&(B=!0);null==t&&(t="is_stuck");A=b(document);null==w&&(w=!0);J=function(a,d,n,C,F,u,r,G){var v,H,m,D,I,c,g,x,y,z,h,l;if(!a.data("sticky_kit")){a.data("sticky_kit",!0);I=A.height();g=a.parent();null!=k&&(g=g.closest(k)); -if(!g.length)throw"failed to find stick parent";v=m=!1;(h=null!=p?p&&a.closest(p):b("<div />"))&&h.css("position",a.css("position"));x=function(){var c,f,e;if(!G&&(I=A.height(),c=parseInt(g.css("border-top-width"),10),f=parseInt(g.css("padding-top"),10),d=parseInt(g.css("padding-bottom"),10),n=g.offset().top+c+f,C=g.height(),m&&(v=m=!1,null==p&&(a.insertAfter(h),h.detach()),a.css({position:"",top:"",width:"",bottom:""}).removeClass(t),e=!0),F=a.offset().top-(parseInt(a.css("margin-top"),10)||0)-q, -u=a.outerHeight(!0),r=a.css("float"),h&&h.css({width:a.outerWidth(!0),height:u,display:a.css("display"),"vertical-align":a.css("vertical-align"),"float":r}),e))return l()};x();if(u!==C)return D=void 0,c=q,z=E,l=function(){var b,l,e,k;if(!G&&(e=!1,null!=z&&(--z,0>=z&&(z=E,x(),e=!0)),e||A.height()===I||x(),e=f.scrollTop(),null!=D&&(l=e-D),D=e,m?(w&&(k=e+u+c>C+n,v&&!k&&(v=!1,a.css({position:"fixed",bottom:"",top:c}).trigger("sticky_kit:unbottom"))),e<F&&(m=!1,c=q,null==p&&("left"!==r&&"right"!==r||a.insertAfter(h), -h.detach()),b={position:"",width:"",top:""},a.css(b).removeClass(t).trigger("sticky_kit:unstick")),B&&(b=f.height(),u+q>b&&!v&&(c-=l,c=Math.max(b-u,c),c=Math.min(q,c),m&&a.css({top:c+"px"})))):e>F&&(m=!0,b={position:"fixed",top:c},b.width="border-box"===a.css("box-sizing")?a.outerWidth()+"px":a.width()+"px",a.css(b).addClass(t),null==p&&(a.after(h),"left"!==r&&"right"!==r||h.append(a)),a.trigger("sticky_kit:stick")),m&&w&&(null==k&&(k=e+u+c>C+n),!v&&k)))return v=!0,"static"===g.css("position")&&g.css({position:"relative"}), -a.css({position:"absolute",bottom:d,top:"auto"}).trigger("sticky_kit:bottom")},y=function(){x();return l()},H=function(){G=!0;f.off("touchmove",l);f.off("scroll",l);f.off("resize",y);b(document.body).off("sticky_kit:recalc",y);a.off("sticky_kit:detach",H);a.removeData("sticky_kit");a.css({position:"",bottom:"",top:"",width:""});g.position("position","");if(m)return null==p&&("left"!==r&&"right"!==r||a.insertAfter(h),h.remove()),a.removeClass(t)},f.on("touchmove",l),f.on("scroll",l),f.on("resize", -y),b(document.body).on("sticky_kit:recalc",y),a.on("sticky_kit:detach",H),setTimeout(l,0)}};n=0;for(K=this.length;n<K;n++)d=this[n],J(b(d));return this}}).call(this); diff --git a/docs/news/index.html b/docs/news/index.html index 52bc3458..5d1fc00f 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -67,7 +67,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.7</span> </span> </div> @@ -129,9 +129,18 @@ </div> - <div id="mkin-0-9-49-6-unreleased" class="section level1"> + <div id="mkin-0-9-49-7-2019-11-01" class="section level1"> <h1 class="page-header"> -<a href="#mkin-0-9-49-6-unreleased" class="anchor"></a>mkin 0.9.49.6 (unreleased)<small> Unreleased </small> +<a href="#mkin-0-9-49-7-2019-11-01" class="anchor"></a>mkin 0.9.49.7 (2019-11-01)<small> Unreleased </small> +</h1> +<ul> +<li><p>Fix a bug introduced in 0.9.49.6 that occurred if the direct optimisation yielded a higher likelihood than the three-step optimisation in the d_3 algorithm, which caused the fitted parameters of the three-step optimisation to be returned instead of the parameters of the direct optimisation</p></li> +<li><p>Add an ‘nobs’ method for mkinfit methods, enabling the default ‘BIC’ method from the stats package. Also, add a ‘BIC’ method for mmkin column objects.</p></li> +</ul> +</div> + <div id="mkin-0-9-49-6-2019-10-31" class="section level1"> +<h1 class="page-header"> +<a href="#mkin-0-9-49-6-2019-10-31" class="anchor"></a>mkin 0.9.49.6 (2019-10-31)<small> 2019-10-31 </small> </h1> <ul> <li><p>Implement a likelihood ratio test as a method for ‘lrtest’ from the lmtest package</p></li> @@ -726,7 +735,8 @@ <div id="tocnav"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#mkin-0-9-49-6-unreleased">0.9.49.6</a></li> + <li><a href="#mkin-0-9-49-7-2019-11-01">0.9.49.7</a></li> + <li><a href="#mkin-0-9-49-6-2019-10-31">0.9.49.6</a></li> <li><a href="#mkin-0-9-49-5-2019-07-04">0.9.49.5</a></li> <li><a href="#mkin-0-9-48-1-2019-03-04">0.9.48.1</a></li> <li><a href="#mkin-0-9-47-5-2018-09-14">0.9.47.5</a></li> diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index 103bcb4a..7ca12302 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -6,7 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Calculated the AIC for a column of an mmkin object — AIC.mmkin • mkin</title> +<title>Calculate the AIC for a column of an mmkin object — AIC.mmkin • mkin</title> <!-- jquery --> @@ -35,7 +35,7 @@ -<meta property="og:title" content="Calculated the AIC for a column of an mmkin object — AIC.mmkin" /> +<meta property="og:title" content="Calculate the AIC for a column of an mmkin object — AIC.mmkin" /> <meta property="og:description" content="Provides a convenient way to compare different kinetic models fitted to the same dataset." /> <meta name="twitter:card" content="summary" /> @@ -70,7 +70,7 @@ same dataset." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.7</span> </span> </div> @@ -128,7 +128,7 @@ same dataset." /> <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Calculated the AIC for a column of an mmkin object</h1> + <h1>Calculate the AIC for a column of an mmkin object</h1> <div class="hidden name"><code>AIC.mmkin.Rd</code></div> </div> @@ -139,7 +139,10 @@ same dataset.</p> </div> <pre class="usage"><span class='co'># S3 method for mmkin</span> -<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span>(<span class='no'>object</span>, <span class='no'>...</span>, <span class='kw'>k</span> <span class='kw'>=</span> <span class='fl'>2</span>)</pre> +<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>AIC</a></span>(<span class='no'>object</span>, <span class='no'>...</span>, <span class='kw'>k</span> <span class='kw'>=</span> <span class='fl'>2</span>) + +<span class='co'># S3 method for mmkin</span> +<span class='fu'><a href='https://rdrr.io/r/stats/AIC.html'>BIC</a></span>(<span class='no'>object</span>, <span class='no'>...</span>)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 879c1444..7273b5de 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -176,16 +176,16 @@ either a list of mkinfit objects or a single mkinfit object.</p></td> <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ]</div><div class='output co'>#> dataset #> model B C -#> FOMC List,40 List,40 +#> FOMC List,41 List,41 #> attr(,"class") #> [1] "mmkin"</div><div class='input'> <span class='no'>fits</span>[, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset #> model B -#> SFO List,40 -#> FOMC List,40 +#> SFO List,41 +#> FOMC List,41 #> attr(,"class") #> [1] "mmkin"</div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset #> model B -#> SFO List,40 +#> SFO List,41 #> attr(,"class") #> [1] "mmkin"</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/utils/head.html'>head</a></span>( 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 8f418b75..83d624bb 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -8,11 +8,13 @@ <title>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,8 +34,8 @@ -<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: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 @@ -43,6 +45,7 @@ in this fit." /> + <!-- mathjax --> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> @@ -113,7 +116,6 @@ in this fit." /> <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -135,17 +137,16 @@ in this fit." /> </div> <div class="ref-description"> - <p>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.</p> - </div> <pre class="usage"><span class='no'>FOCUS_2006_DFOP_ref_A_to_B</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A data frame containing the following variables.</p><dl class='dl-horizontal'> @@ -160,7 +161,6 @@ in this fit.</p> </dl> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and @@ -168,7 +168,6 @@ in this fit.</p> Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>FOCUS_2006_DFOP_ref_A_to_B</span>)</div></pre> @@ -176,11 +175,8 @@ in this fit.</p> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#format">Format</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> </ul> 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 a457a4a2..75a0da96 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -8,11 +8,13 @@ <title>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,8 +34,8 @@ -<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: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 @@ -43,6 +45,7 @@ in this fit." /> + <!-- mathjax --> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> @@ -113,7 +116,6 @@ in this fit." /> <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -135,17 +137,16 @@ in this fit." /> </div> <div class="ref-description"> - <p>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.</p> - </div> <pre class="usage"><span class='no'>FOCUS_2006_FOMC_ref_A_to_F</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A data frame containing the following variables.</p><dl class='dl-horizontal'> @@ -159,7 +160,6 @@ in this fit.</p> </dl> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and @@ -167,7 +167,6 @@ in this fit.</p> Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>FOCUS_2006_FOMC_ref_A_to_F</span>)</div></pre> @@ -175,11 +174,8 @@ in this fit.</p> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#format">Format</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> </ul> 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 4285c70c..d9d24bdf 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -8,11 +8,13 @@ <title>Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,8 +34,8 @@ -<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: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 @@ -43,6 +45,7 @@ in this fit." /> + <!-- mathjax --> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> @@ -113,7 +116,6 @@ in this fit." /> <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -135,17 +137,16 @@ in this fit." /> </div> <div class="ref-description"> - <p>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.</p> - </div> <pre class="usage"><span class='no'>FOCUS_2006_HS_ref_A_to_F</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A data frame containing the following variables.</p><dl class='dl-horizontal'> @@ -160,7 +161,6 @@ in this fit.</p> </dl> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and @@ -168,7 +168,6 @@ in this fit.</p> Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>FOCUS_2006_HS_ref_A_to_F</span>)</div></pre> @@ -176,11 +175,8 @@ in this fit.</p> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#format">Format</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> </ul> 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 d1dab9a9..8c0f5bc9 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -8,11 +8,13 @@ <title>Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,8 +34,8 @@ -<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: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 @@ -43,6 +45,7 @@ in this fit." /> + <!-- mathjax --> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> @@ -113,7 +116,6 @@ in this fit." /> <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -135,17 +137,16 @@ in this fit." /> </div> <div class="ref-description"> - <p>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.</p> - </div> <pre class="usage"><span class='no'>FOCUS_2006_SFO_ref_A_to_F</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A data frame containing the following variables.</p><dl class='dl-horizontal'> @@ -158,7 +159,6 @@ in this fit.</p> </dl> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and @@ -166,7 +166,6 @@ in this fit.</p> Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>FOCUS_2006_SFO_ref_A_to_F</span>)</div></pre> @@ -174,11 +173,8 @@ in this fit.</p> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#format">Format</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 2f183654..8ccf363e 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -8,11 +8,13 @@ <title>Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,13 +34,14 @@ -<meta property="og:title" content="Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets" /> +<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://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> @@ -109,7 +112,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -131,9 +133,7 @@ </div> <div class="ref-description"> - <p>Data taken from FOCUS (2006), p. 258.</p> - </div> <pre class="usage"><span class='no'>FOCUS_2006_A</span> @@ -142,7 +142,8 @@ <span class='no'>FOCUS_2006_D</span> <span class='no'>FOCUS_2006_E</span> <span class='no'>FOCUS_2006_F</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>6 datasets with observations on the following variables.</p><dl class='dl-horizontal'> @@ -152,7 +153,6 @@ </dl> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and @@ -160,7 +160,6 @@ Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>FOCUS_2006_C</span></div><div class='output co'>#> name time value @@ -177,11 +176,8 @@ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#format">Format</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/NAFTA_2015_datasets-1.png b/docs/reference/NAFTA_2015_datasets-1.png Binary files differdeleted file mode 100644 index c4f9f048..00000000 --- a/docs/reference/NAFTA_2015_datasets-1.png +++ /dev/null diff --git a/docs/reference/NAFTA_2015_datasets.html b/docs/reference/NAFTA_2015_datasets.html deleted file mode 100644 index be080428..00000000 --- a/docs/reference/NAFTA_2015_datasets.html +++ /dev/null @@ -1,218 +0,0 @@ -<!-- Generated by pkgdown: do not edit by hand --> -<!DOCTYPE html> -<html lang="en"> - <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>Example datasets from the NAFTA guidance published 2015 — NAFTA_2015_datasets • mkin</title> - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> - -<!-- Font Awesome icons --> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous" /> - -<!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> - -<!-- sticky kit --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> - -<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<script src="../pkgdown.js"></script> - - - -<meta property="og:title" content="Example datasets from the NAFTA guidance published 2015 — NAFTA_2015_datasets" /> - -<meta property="og:description" content="Data taken from US EPA (2015), p. 23." /> -<meta name="twitter:card" content="summary" /> - - - -<!-- mathjax --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></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-reference-topic"> - <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" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.48.1</span> - </span> - </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/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> - </li> - <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> - </li> - <li> - <a href="../articles/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="col-md-9 contents"> - <div class="page-header"> - <h1>Example datasets from the NAFTA guidance published 2015</h1> - - <div class="hidden name"><code>NAFTA_2015_datasets.Rd</code></div> - </div> - - <div class="ref-description"> - - <p>Data taken from US EPA (2015), p. 23.</p> - - </div> - - <pre class="usage"><span class='no'>NAFTA_2015_datasets</span></pre> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - - <p>1 dataset with observations on the following variables.</p><dl class='dl-horizontal'> - <dt><code>name</code></dt><dd><p>a factor containing the name of the observed variable</p></dd> - <dt><code>time</code></dt><dd><p>a numeric vector containing time points</p></dd> - <dt><code>value</code></dt><dd><p>a numeric vector containing concentrations</p></dd> - </dl> - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - - <p>NAFTA (2011) Guidance for evaluating and calculating degradation kinetics - in environmental media. NAFTA Technical Working Group on Pesticides - <a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation</a> - accessed 2019-02-22</p> -<p>US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to - Calculate Representative Half-life Values and Characterizing Pesticide - Degradation - <a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='no'>nafta_evaluation</span> <span class='kw'><-</span> <span class='fu'><a href='nafta.html'>nafta</a></span>(<span class='no'>MRID_555555</span>)</div><div class='output co'>#> <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#> <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#> <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#> <span class='message'>The representative half-life obtained from the DFOP model may be used</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='output co'>#> Sums of squares: -#> SFO IORE DFOP -#> 1378.6832 615.7730 517.8836 -#> [1] 717.4598 -#> -#> Parameters: -#> $SFO -#> Estimate Pr(>t) Lower Upper -#> parent_0 83.755751519 8.076390e-15 76.928220975 90.583282063 -#> k_parent_sink 0.001703321 7.452357e-05 0.001108568 0.002617164 -#> -#> $IORE -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.685291e+01 NA 8.752855e+01 1.061773e+02 -#> k__iore_parent_sink 8.403374e-14 NA 1.092054e-19 6.466412e-08 -#> N_parent 6.684458e+00 NA 3.538511e+00 9.830405e+00 -#> -#> $DFOP -#> Estimate Pr(>t) Lower Upper -#> parent_0 9.755655e+01 4.439930e-13 8.884447e+01 1.062686e+02 -#> k1 4.240633e-02 3.554769e-02 1.414189e-02 1.271610e-01 -#> k2 8.237928e-04 2.060933e-02 3.172784e-04 2.138925e-03 -#> g 2.881037e-01 1.313715e-04 1.783967e-01 4.299694e-01 -#> -#> -#> DTx values: -#> DT50 DT90 DT50_rep -#> SFO 407 1352 407 -#> IORE 541 5192066 1562968 -#> DFOP 429 2383 841 -#> -#> Representative half-life: -#> [1] 841.4096</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='img'><img src='NAFTA_2015_datasets-1.png' alt='' width='700' height='433' /></div></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - - <li><a href="#format">Format</a></li> - - <li><a href="#source">Source</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> - - </div> -</div> - - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p> -</div> - </footer> - </div> - - - - </body> -</html> - diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html index 84d5508a..5ad02bf9 100644 --- a/docs/reference/NAFTA_SOP_2015.html +++ b/docs/reference/NAFTA_SOP_2015.html @@ -8,11 +8,13 @@ <title>Example datasets from the NAFTA SOP published 2015 — NAFTA_SOP_2015 • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,13 +34,14 @@ -<meta property="og:title" content="Example datasets from the NAFTA SOP published 2015 — NAFTA_SOP_2015" /> +<meta property="og:title" content="Example datasets from the NAFTA SOP published 2015 — NAFTA_SOP_2015" /> <meta property="og:description" content="Data taken from US EPA (2015), p. 19 and 23." /> <meta name="twitter:card" content="summary" /> + <!-- mathjax --> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> @@ -109,7 +112,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -131,14 +133,13 @@ </div> <div class="ref-description"> - <p>Data taken from US EPA (2015), p. 19 and 23.</p> - </div> <pre class="usage"><span class='no'>NAFTA_SOP_Appendix_B</span> <span class='no'>NAFTA_SOP_Appendix_D</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>2 datasets with observations on the following variables.</p><dl class='dl-horizontal'> @@ -148,7 +149,6 @@ </dl> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <p>NAFTA (2011) Guidance for evaluating and calculating degradation kinetics @@ -159,7 +159,6 @@ Calculate Representative Half-life Values and Characterizing Pesticide Degradation <a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='no'>nafta_evaluation</span> <span class='kw'><-</span> <span class='fu'><a href='nafta.html'>nafta</a></span>(<span class='no'>NAFTA_SOP_Appendix_D</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#> <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#> <span class='message'>The representative half-life of the IORE model is longer than the one corresponding</span></div><div class='output co'>#> <span class='message'>to the terminal degradation rate found with the DFOP model.</span></div><div class='output co'>#> <span class='message'>The representative half-life obtained from the DFOP model may be used</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>nafta_evaluation</span>)</div><div class='output co'>#> Sums of squares: @@ -204,11 +203,8 @@ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#format">Format</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/NAFTA_SOP_Attachment.html b/docs/reference/NAFTA_SOP_Attachment.html index a0498a31..110ccc86 100644 --- a/docs/reference/NAFTA_SOP_Attachment.html +++ b/docs/reference/NAFTA_SOP_Attachment.html @@ -8,11 +8,13 @@ <title>Example datasets from Attachment 1 to the NAFTA SOP published 2015 — NAFTA_SOP_Attachment • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,13 +34,14 @@ -<meta property="og:title" content="Example datasets from Attachment 1 to the NAFTA SOP published 2015 — NAFTA_SOP_Attachment" /> +<meta property="og:title" content="Example datasets from Attachment 1 to the NAFTA SOP published 2015 — NAFTA_SOP_Attachment" /> <meta property="og:description" content="Data taken from from Attachment 1 of the SOP." /> <meta name="twitter:card" content="summary" /> + <!-- mathjax --> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> @@ -109,7 +112,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -131,18 +133,16 @@ </div> <div class="ref-description"> - <p>Data taken from from Attachment 1 of the SOP.</p> - </div> <pre class="usage"><span class='no'>NAFTA_SOP_Attachment</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A list (NAFTA_SOP_Attachment) containing 16 datasets suitable for the evaluation with <code><a href='nafta.html'>nafta</a></code></p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <p>NAFTA (2011) Guidance for evaluating and calculating degradation kinetics @@ -153,7 +153,6 @@ Calculate Representative Half-life Values and Characterizing Pesticide Degradation <a href='https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance'>https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='no'>nafta_att_p5a</span> <span class='kw'><-</span> <span class='fu'><a href='nafta.html'>nafta</a></span>(<span class='no'>NAFTA_SOP_Attachment</span><span class='kw'>[[</span><span class='st'>"p5a"</span>]], <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#> <span class='message'>The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span></div><div class='output co'>#> <span class='message'>The half-life obtained from the IORE model may be used</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>nafta_att_p5a</span>)</div><div class='output co'>#> Sums of squares: @@ -198,11 +197,8 @@ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#format">Format</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index 6fb806fc..54696ff5 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -236,7 +236,7 @@ machines, cores > 1 is not supported.</p></td> <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='no'>f_d_1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>ci_profile</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f_d_1</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> User System verstrichen -#> 50.987 0.008 51.023 </div><div class='input'><span class='co'># The following does not save much time, as parent_0 takes up most of the time</span> +#> 51.646 0.000 51.673 </div><div class='input'><span class='co'># The following does not save much time, as parent_0 takes up most of the time</span> <span class='co'># system.time(ci_profile <- confint(f_d_1, cores = 5))</span> <span class='co'># system.time(ci_profile <- confint(f_d_1,</span> <span class='co'># c("k_parent_sink", "k_parent_m1", "k_m1_sink", "sigma"), cores = 1))</span> diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html index f35aee5f..18e11261 100644 --- a/docs/reference/experimental_data_for_UBA.html +++ b/docs/reference/experimental_data_for_UBA.html @@ -8,11 +8,13 @@ <title>Experimental datasets used for development and testing of error models — experimental_data_for_UBA_2019 • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,8 +34,8 @@ -<meta property="og:title" content="Experimental datasets used for development and testing of error models — experimental_data_for_UBA_2019" /> +<meta property="og:title" content="Experimental datasets used for development and testing of error models — experimental_data_for_UBA_2019" /> <meta property="og:description" content="The 12 datasets were extracted from active substance evaluation dossiers published by EFSA. Kinetic evaluations shown for these datasets are intended to illustrate and advance error model specifications. The fact that these data and some @@ -67,6 +69,7 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl + <!-- mathjax --> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> @@ -137,7 +140,6 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -159,7 +161,6 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl </div> <div class="ref-description"> - <p>The 12 datasets were extracted from active substance evaluation dossiers published by EFSA. Kinetic evaluations shown for these datasets are intended to illustrate and advance error model specifications. The fact that these data and some @@ -189,11 +190,11 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl to one half of the LOD reported to be 1% AR.</p> <p>Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl (United Kingdom, 2014, p. 81).</p> - </div> <pre class="usage"><span class='no'>experimental_data_for_UBA_2019</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A list containing twelve datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>, @@ -203,7 +204,6 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl </dl> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> @@ -225,7 +225,6 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl <p>United Kingdom (2014). Thifensulfuron-methyl - Annex B.8 (Volume 3) to the Report and Proposed Decision of the United Kingdom made to the European Commission under Regulation (EC) No. 1141/2010 for renewal of an active substance</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> @@ -264,11 +263,8 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#format">Format</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/index.html b/docs/reference/index.html index 8987db96..4279f6de 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -67,7 +67,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.7</span> </span> </div> @@ -255,9 +255,9 @@ of an mmkin object</p></td> </tr><tr> <td> - <p><code><a href="AIC.mmkin.html">AIC(<i><mmkin></i>)</a></code> </p> + <p><code><a href="AIC.mmkin.html">AIC(<i><mmkin></i>)</a></code> <code><a href="AIC.mmkin.html">BIC(<i><mmkin></i>)</a></code> </p> </td> - <td><p>Calculated the AIC for a column of an mmkin object</p></td> + <td><p>Calculate the AIC for a column of an mmkin object</p></td> </tr> </tbody><tbody> <tr> @@ -448,6 +448,12 @@ kinetic models fitted with mkinfit</p></td> </tr><tr> <td> + <p><code><a href="nobs.mkinfit.html">nobs(<i><mkinfit></i>)</a></code> </p> + </td> + <td><p>Number of observations on which an mkinfit object was fitted</p></td> + </tr><tr> + + <td> <p><code><a href="mkinresplot.html">mkinresplot()</a></code> </p> </td> <td><p>Function to plot residuals stored in an mkin object</p></td> diff --git a/docs/reference/mccall81_245T-1.png b/docs/reference/mccall81_245T-1.png Binary files differindex b9a42571..5b70455c 100644 --- a/docs/reference/mccall81_245T-1.png +++ b/docs/reference/mccall81_245T-1.png diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 91c55a6a..ce2d40cd 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -8,11 +8,13 @@ <title>Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,8 +34,8 @@ -<meta property="og:title" content="Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T" /> +<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." /> @@ -41,6 +43,7 @@ + <!-- mathjax --> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> @@ -111,7 +114,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -133,15 +135,14 @@ </div> <div class="ref-description"> - <p>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.</p> - </div> <pre class="usage"><span class='no'>mccall81_245T</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A dataframe containing the following variables.</p><dl class='dl-horizontal'> @@ -156,12 +157,10 @@ </dl> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <p>McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labeled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107 <a href='http://dx.doi.org/10.1021/jf00103a026'>http://dx.doi.org/10.1021/jf00103a026</a></p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"phenol"</span>), @@ -228,11 +227,8 @@ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#format">Format</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index c72d1cd0..7ee73f15 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -402,15 +402,15 @@ estimators.</p> <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Thu Oct 31 01:48:29 2019 -#> Date of summary: Thu Oct 31 01:48:29 2019 +#> Date of fit: Fri Nov 1 10:08:21 2019 +#> Date of summary: Fri Nov 1 10:08:21 2019 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 222 model solutions performed in 0.455 s +#> Fitted using 222 model solutions performed in 0.456 s #> #> Error model: Constant variance #> @@ -482,7 +482,7 @@ estimators.</p> <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> User System verstrichen -#> 1.464 0.000 1.465 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> NULL</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 +#> 1.488 0.000 1.491 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> NULL</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 #> @@ -555,7 +555,7 @@ estimators.</p> #> Sum of squared residuals at call 126: 371.2134 #> Sum of squared residuals at call 135: 371.2134 #> Negative log-likelihood at call 145: 97.22429</div><div class='output co'>#> <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#> User System verstrichen -#> 1.047 0.000 1.047 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> $ff +#> 1.058 0.000 1.059 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/stats/coef.html'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> NULL</div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -591,8 +591,8 @@ estimators.</p> <span class='no'>SFO_SFO.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Thu Oct 31 01:48:44 2019 -#> Date of summary: Thu Oct 31 01:48:44 2019 +#> Date of fit: Fri Nov 1 10:08:36 2019 +#> Date of summary: Fri Nov 1 10:08:36 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -600,7 +600,7 @@ estimators.</p> #> #> Model predictions using solution type deSolve #> -#> Fitted using 421 model solutions performed in 1.136 s +#> Fitted using 421 model solutions performed in 1.083 s #> #> Error model: Constant variance #> @@ -708,8 +708,8 @@ estimators.</p> #> 120 m1 25.15 28.78984 -3.640e+00 #> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Thu Oct 31 01:48:47 2019 -#> Date of summary: Thu Oct 31 01:48:47 2019 +#> Date of fit: Fri Nov 1 10:08:39 2019 +#> Date of summary: Fri Nov 1 10:08:39 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -717,7 +717,7 @@ estimators.</p> #> #> Model predictions using solution type deSolve #> -#> Fitted using 978 model solutions performed in 2.512 s +#> Fitted using 978 model solutions performed in 2.553 s #> #> Error model: Variance unique to each observed variable #> @@ -840,8 +840,8 @@ estimators.</p> #> 120 m1 25.15 28.80429 -3.654e+00 #> 120 m1 33.31 28.80429 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Thu Oct 31 01:48:56 2019 -#> Date of summary: Thu Oct 31 01:48:56 2019 +#> Date of fit: Fri Nov 1 10:08:48 2019 +#> Date of summary: Fri Nov 1 10:08:48 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -849,7 +849,7 @@ estimators.</p> #> #> Model predictions using solution type deSolve #> -#> Fitted using 2289 model solutions performed in 9.124 s +#> Fitted using 2289 model solutions performed in 9.253 s #> #> Error model: Two-component variance function #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 2eefdc2e..317ffe5f 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -239,7 +239,7 @@ in the FOCUS and NAFTA guidance documents are used.</p> <span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> Compilation argument: -#> /usr/lib/R/bin/R CMD SHLIB file59d942b9ac06.c 2> file59d942b9ac06.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file12cd48616f1.c 2> file12cd48616f1.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index f7d543ad..0eca973c 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -350,7 +350,7 @@ solver is used.</p></td> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 #> 201 20 4.978707 27.46227</div><div class='output co'>#> User System verstrichen -#> 0.004 0.000 0.004 </div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>( +#> 0.004 0.000 0.003 </div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>( <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 @@ -360,7 +360,7 @@ solver is used.</p></td> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='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 verstrichen -#> 0.021 0.000 0.021 </div><div class='input'> +#> 0.021 0.000 0.022 </div><div class='input'> <span class='co'># \dontrun{</span> <span class='co'># Predict from a fitted model</span> <span class='no'>f</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_C</span>)</div><div class='output co'>#> <span class='message'>Ordinary least squares optimisation</span></div><div class='output co'>#> Sum of squared residuals at call 1: 552.5739 diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 8312c17c..d1ea7a52 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -202,8 +202,8 @@ for parallel execution.</p></td> <span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fits.4</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='no'>time_default</span></div><div class='output co'>#> User System verstrichen -#> 0.011 0.032 4.774 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen -#> 18.676 0.000 18.687 </div><div class='input'> +#> 0.014 0.024 4.895 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen +#> 19.047 0.004 19.063 </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340481 0.2659519 0.7505684 0.2494316 diff --git a/docs/reference/print.nafta.html b/docs/reference/nobs.mkinfit.html index fa8223ad..1bd97732 100644 --- a/docs/reference/print.nafta.html +++ b/docs/reference/nobs.mkinfit.html @@ -6,13 +6,15 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Print nafta objects — print.nafta • mkin</title> +<title>Number of observations on which an mkinfit object was fitted — nobs.mkinfit • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,15 +34,14 @@ -<meta property="og:title" content="Print nafta objects — print.nafta" /> -<meta property="og:description" content="Print nafta objects. The results for the three models - are printed in the order of increasing model complexity, - i.e. SFO, then IORE, and finally DFOP." /> +<meta property="og:title" content="Number of observations on which an mkinfit object was fitted — nobs.mkinfit" /> +<meta property="og:description" content="Number of observations on which an mkinfit object was fitted" /> <meta name="twitter:card" content="summary" /> + <!-- mathjax --> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> @@ -68,7 +69,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.7</span> </span> </div> @@ -111,7 +112,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -127,50 +127,42 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Print nafta objects</h1> + <h1>Number of observations on which an mkinfit object was fitted</h1> - <div class="hidden name"><code>print.nafta.Rd</code></div> + <div class="hidden name"><code>nobs.mkinfit.Rd</code></div> </div> <div class="ref-description"> - - <p>Print nafta objects. The results for the three models - are printed in the order of increasing model complexity, - i.e. SFO, then IORE, and finally DFOP.</p> - + <p>Number of observations on which an mkinfit object was fitted</p> </div> - <pre class="usage"><span class='co'># S3 method for nafta</span> -<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>x</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='no'>...</span>)</pre> - + <pre class="usage"><span class='co'># S3 method for mkinfit</span> +<span class='fu'><a href='https://rdrr.io/r/stats/nobs.html'>nobs</a></span>(<span class='no'>object</span>, <span class='no'>...</span>)</pre> + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> <colgroup><col class="name" /><col class="desc" /></colgroup> <tr> - <th>x</th> - <td><p>An <code><a href='nafta.html'>nafta</a></code> object.</p></td> - </tr> - <tr> - <th>quiet</th> - <td><p>Should the evaluation text be shown?</p></td> - </tr> - <tr> - <th>digits</th> - <td><p>Number of digits to be used for printing parameters and dissipation times.</p></td> + <th>object</th> + <td><p>An mkinfit object</p></td> </tr> <tr> <th>...</th> - <td><p>Not used.</p></td> + <td><p>For compatibility with the generic method</p></td> </tr> </table> - + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>The number of rows in the data included in the mkinfit object</p> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - </ul> + <li><a href="#value">Value</a></li> + </ul> </div> </div> diff --git a/docs/reference/plot.mkinfit-6.png b/docs/reference/plot.mkinfit-6.png Binary files differdeleted file mode 100644 index ad2ffa8c..00000000 --- a/docs/reference/plot.mkinfit-6.png +++ /dev/null diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png Binary files differindex 13d96256..44037bb4 100644 --- a/docs/reference/plot.mmkin-4.png +++ b/docs/reference/plot.mmkin-4.png diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index c6635409..27b19430 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -8,11 +8,13 @@ <title>Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,8 +34,8 @@ -<meta property="og:title" content="Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case" /> +<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." /> @@ -41,6 +43,7 @@ + <!-- mathjax --> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> @@ -111,7 +114,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -133,15 +135,14 @@ </div> <div class="ref-description"> - <p>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.</p> - </div> <pre class="usage"><span class='no'>schaefer07_complex_case</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>The data set is a data frame with 8 observations on the following 6 variables.</p><dl class='dl-horizontal'> @@ -153,14 +154,12 @@ <dt><code>A2</code></dt><dd><p>a numeric vector</p></dd> </dl><p>The results are a data frame with 14 results for different parameter values</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> <p>Schäfer D, Mikolasch B, Rainbird P and Harvey B (2007). KinGUI: a new kinetic software tool for evaluations according to FOCUS degradation kinetics. In: Del Re AAM, Capri E, Fragoulis G and Trevisan M (Eds.). Proceedings of the XIII Symposium Pesticide Chemistry, Piacenza, 2007, p. 916-923.</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>data</span> <span class='kw'><-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span>(<span class='no'>schaefer07_complex_case</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>) @@ -206,11 +205,8 @@ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#format">Format</a></li> - <li><a href="#references">References</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 65bc6326..fb3c43ef 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -225,15 +225,15 @@ distribution</p></td> <pre class="examples"><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version used for fitting: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Fri Oct 25 02:09:45 2019 -#> Date of summary: Fri Oct 25 02:09:45 2019 +#> Date of fit: Fri Nov 1 10:10:07 2019 +#> Date of summary: Fri Nov 1 10:10:07 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 131 model solutions performed in 0.274 s +#> Fitted using 131 model solutions performed in 0.265 s #> #> Error model: Constant variance #> diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html deleted file mode 100644 index b3da0016..00000000 --- a/docs/reference/synthetic_data_for_UBA.html +++ /dev/null @@ -1,225 +0,0 @@ -<!-- Generated by pkgdown: do not edit by hand --> -<!DOCTYPE html> -<html lang="en"> - <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>Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014 • mkin</title> - -<!-- jquery --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> -<!-- Bootstrap --> - -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> -<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> - -<!-- Font Awesome icons --> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> -<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> - -<!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> - -<!-- headroom.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> - -<!-- pkgdown --> -<link href="../pkgdown.css" rel="stylesheet"> -<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. Note that this is a simplified version - of the error model proposed by Rocke and Lorenzato (1995), as in their model the error of the - measured values approximates lognormal distribution for high values, whereas we are using - normally distributed error components all along. -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://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> -<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></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-reference-topic"> - <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" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span> - </span> - </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/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> - </li> - <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> - </li> - <li> - <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> - </li> - <li> - <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> - </li> - </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="col-md-9 contents"> - <div class="page-header"> - <h1>Synthetic datasets for one parent compound with two metabolites</h1> - - <div class="hidden name"><code>synthetic_data_for_UBA.Rd</code></div> - </div> - - <div class="ref-description"> - - <p>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.</p> -<p>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. Note that this is a simplified version - of the error model proposed by Rocke and Lorenzato (1995), as in their model the error of the - measured values approximates lognormal distribution for high values, whereas we are using - normally distributed error components all along.</p> -<p>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 <code>NA</code>.</p> -<p>As an example, the first dataset has the title <code>SFO_lin_a</code> and is based on the SFO model - with two sequential metabolites (linear pathway), with added variance component 'a'.</p> -<p>Compare also the code in the example section to see the degradation models.</p> - - </div> - - <pre class="usage"><span class='no'>synthetic_data_for_UBA_2014</span></pre> - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> - - <p>A list containing twelve datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>, - each containing, among others, the following components</p><dl class='dl-horizontal'> - <dt><code>title</code></dt><dd><p>The name of the dataset, e.g. <code>SFO_lin_a</code></p></dd> - <dt><code>data</code></dt><dd><p>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></p></dd> - -</dl> - - - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - - <p>Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative - zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452</p> -<p>Rocke, David M. und Lorenzato, Stefan (1995) A two-component model for - measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p> - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"></pre> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> - <h2>Contents</h2> - <ul class="nav nav-pills nav-stacked"> - - <li><a href="#format">Format</a></li> - - <li><a href="#source">Source</a></li> - - <li><a href="#examples">Examples</a></li> - </ul> - - </div> -</div> - - - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> -</div> - -<div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> -</div> - - </footer> - </div> - - - - - </body> -</html> - - diff --git a/docs/reference/synthetic_data_for_UBA_2014.html b/docs/reference/synthetic_data_for_UBA_2014.html index eb5b8c65..6ac7403a 100644 --- a/docs/reference/synthetic_data_for_UBA_2014.html +++ b/docs/reference/synthetic_data_for_UBA_2014.html @@ -282,8 +282,8 @@ Compare also the code in the example section to see the degradation models." /> <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='synthetic_data_for_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Mon Oct 21 22:49:25 2019 -#> Date of summary: Mon Oct 21 22:49:25 2019 +#> Date of fit: Fri Nov 1 10:10:17 2019 +#> Date of summary: Fri Nov 1 10:10:17 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -292,7 +292,7 @@ Compare also the code in the example section to see the degradation models." /> #> #> Model predictions using solution type deSolve #> -#> Fitted using 847 model solutions performed in 2.43 s +#> Fitted using 847 model solutions performed in 2.468 s #> #> Error model: Constant variance #> diff --git a/docs/reference/test_data_from_UBA_2014-1.png b/docs/reference/test_data_from_UBA_2014-1.png Binary files differindex fc05f896..51b38eda 100644 --- a/docs/reference/test_data_from_UBA_2014-1.png +++ b/docs/reference/test_data_from_UBA_2014-1.png diff --git a/docs/reference/test_data_from_UBA_2014-2.png b/docs/reference/test_data_from_UBA_2014-2.png Binary files differindex b0dfdd5a..a40f7553 100644 --- a/docs/reference/test_data_from_UBA_2014-2.png +++ b/docs/reference/test_data_from_UBA_2014-2.png diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index 5c1a3bed..0040c331 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -8,11 +8,13 @@ <title>Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014 • mkin</title> + <!-- jquery --> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <!-- Bootstrap --> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + <script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script> <!-- Font Awesome icons --> @@ -32,14 +34,15 @@ -<meta property="og:title" content="Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014" /> +<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://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> @@ -110,7 +113,6 @@ <a href="../news/index.html">News</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -132,14 +134,13 @@ </div> <div class="ref-description"> - <p>The datasets were used for the comparative validation of several kinetic evaluation software packages (Ranke, 2014).</p> - </div> <pre class="usage"><span class='no'>test_data_from_UBA_2014</span></pre> - + + <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> <p>A list containing three datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>. @@ -149,12 +150,10 @@ </dl> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <p>Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452</p> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='co'># \dontrun{</span> @@ -222,11 +221,8 @@ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> <ul class="nav nav-pills nav-stacked"> - <li><a href="#format">Format</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> </ul> diff --git a/docs/reference/update.mkinfit.html b/docs/reference/update.mkinfit.html index b4040a1b..b9f6f9a9 100644 --- a/docs/reference/update.mkinfit.html +++ b/docs/reference/update.mkinfit.html @@ -264,7 +264,7 @@ remove arguments given in the original call</p></td> #> #> $time #> User System verstrichen -#> 10.314 0.000 10.320 +#> 10.251 0.000 10.257 #> #> $mkinmod #> <mkinmod> model generated with @@ -413,8 +413,8 @@ remove arguments given in the original call</p></td> #> $rss #> function (P) #> cost_function(P, OLS = TRUE, update_data = FALSE) -#> <bytecode: 0x555557c557c8> -#> <environment: 0x55555bb0e330> +#> <bytecode: 0x555558e48258> +#> <environment: 0x55555caa08e0> #> #> $ll #> function (P, fixed_degparms = FALSE, fixed_errparms = FALSE) @@ -422,8 +422,8 @@ remove arguments given in the original call</p></td> #> -cost_function(P, trans = FALSE, fixed_degparms = fixed_degparms, #> fixed_errparms = fixed_errparms, OLS = FALSE, update_data = FALSE) #> } -#> <bytecode: 0x555557c55bf0> -#> <environment: 0x55555bb0e330> +#> <bytecode: 0x555558e47e30> +#> <environment: 0x55555caa08e0> #> #> $start #> value type @@ -500,7 +500,7 @@ remove arguments given in the original call</p></td> #> [1] 12 #> #> $date -#> [1] "Thu Oct 31 01:49:09 2019" +#> [1] "Fri Nov 1 10:10:42 2019" #> #> $version #> [1] "0.9.49.6" diff --git a/docs/sitemap.xml b/docs/sitemap.xml index 3767bdda..3a56fe49 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -124,6 +124,9 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/nafta.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/reference/nobs.mkinfit.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/reference/parms.html</loc> </url> <url> diff --git a/man/AIC.mmkin.Rd b/man/AIC.mmkin.Rd index 42c9a73b..a49b69b8 100644 --- a/man/AIC.mmkin.Rd +++ b/man/AIC.mmkin.Rd @@ -2,9 +2,12 @@ % Please edit documentation in R/AIC.mmkin.R \name{AIC.mmkin} \alias{AIC.mmkin} -\title{Calculated the AIC for a column of an mmkin object} +\alias{BIC.mmkin} +\title{Calculate the AIC for a column of an mmkin object} \usage{ \method{AIC}{mmkin}(object, ..., k = 2) + +\method{BIC}{mmkin}(object, ...) } \arguments{ \item{object}{An object of class \code{\link{mmkin}}, containing only one diff --git a/man/nobs.mkinfit.Rd b/man/nobs.mkinfit.Rd new file mode 100644 index 00000000..200a450f --- /dev/null +++ b/man/nobs.mkinfit.Rd @@ -0,0 +1,19 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/nobs.mkinfit.R +\name{nobs.mkinfit} +\alias{nobs.mkinfit} +\title{Number of observations on which an mkinfit object was fitted} +\usage{ +\method{nobs}{mkinfit}(object, ...) +} +\arguments{ +\item{object}{An mkinfit object} + +\item{\dots}{For compatibility with the generic method} +} +\value{ +The number of rows in the data included in the mkinfit object +} +\description{ +Number of observations on which an mkinfit object was fitted +} @@ -2,32 +2,32 @@ Loading mkin Testing mkin ✔ | OK F W S | Context ✔ | 2 | Export dataset for reading into CAKE -✔ | 10 | Confidence intervals and p-values [9.7 s] -✔ | 10 | Error model fitting [37.4 s] -✔ | 4 | Calculation of FOCUS chi2 error levels [2.2 s] -✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.4 s] -✔ | 6 | Test fitting the decline of metabolites from their maximum [0.7 s] +✔ | 10 | Confidence intervals and p-values [9.8 s] +✔ | 14 | Error model fitting [38.8 s] +✔ | 4 | Calculation of FOCUS chi2 error levels [2.3 s] +✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.5 s] +✔ | 6 | Test fitting the decline of metabolites from their maximum [0.8 s] ✔ | 1 | Fitting the logistic model [0.9 s] ✔ | 1 | Test dataset class mkinds used in gmkin ✔ | 12 | Special cases of mkinfit calls [2.4 s] ✔ | 9 | mkinmod model generation and printing [0.2 s] ✔ | 3 | Model predictions with mkinpredict [0.3 s] -✔ | 16 | Evaluations according to 2015 NAFTA guidance [4.1 s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [4.2 s] ✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.3 s] ✔ | 3 | Summary ✔ | 11 | Plotting [0.6 s] -✔ | 3 | AIC calculation +✔ | 4 | AIC calculation ✔ | 2 | Residuals extracted from mkinfit models -✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.3 s] +✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.5 s] ✔ | 4 | Fitting the SFORB model [1.7 s] ✔ | 1 | Summaries of old mkinfit objects -✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.1 s] -✔ | 6 | Hypothesis tests [31.3 s] +✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.3 s] +✔ | 6 | Hypothesis tests [32.5 s] ══ Results ═════════════════════════════════════════════════════════════════════ -Duration: 109.7 s +Duration: 113.3 s -OK: 127 +OK: 132 Failed: 0 Warnings: 0 Skipped: 0 diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf index 942d56e1..a28aafec 100644 --- a/tests/testthat/FOCUS_2006_D.csf +++ b/tests/testthat/FOCUS_2006_D.csf @@ -5,7 +5,7 @@ Description: MeasurementUnits: % AR TimeUnits: days Comments: Created using mkin::CAKE_export -Date: 2019-10-31 +Date: 2019-11-01 Optimiser: IRLS [Data] diff --git a/tests/testthat/test_error_models.R b/tests/testthat/test_error_models.R index 12a8b7e5..83cff2e5 100644 --- a/tests/testthat/test_error_models.R +++ b/tests/testthat/test_error_models.R @@ -36,30 +36,36 @@ test_that("The different error model fitting methods work for parent fits", { f_9_OLS <- mkinfit("SFO", experimental_data_for_UBA_2019[[9]]$data, quiet = TRUE) expect_equivalent(round(AIC(f_9_OLS), 2), 137.43) + f_9_parms_const <- parms(f_9_OLS) f_9_direct <- mkinfit("SFO", experimental_data_for_UBA_2019[[9]]$data, error_model = "tc", error_model_algorithm = "direct", quiet = TRUE) expect_equivalent(round(AIC(f_9_direct), 2), 134.94) + f_9_parms_tc_direct <- parms(f_9_direct) f_9_twostep <- mkinfit("SFO", experimental_data_for_UBA_2019[[9]]$data, error_model = "tc", error_model_algorithm = "twostep", quiet = TRUE) - expect_equivalent(round(AIC(f_9_twostep), 2), 134.94) + expect_equivalent(parms(f_9_twostep), f_9_parms_tc_direct) f_9_threestep <- mkinfit("SFO", experimental_data_for_UBA_2019[[9]]$data, error_model = "tc", error_model_algorithm = "threestep", quiet = TRUE) expect_equivalent(round(AIC(f_9_threestep), 2), 139.43) + expect_equivalent(parms(f_9_threestep)[1:3], f_9_parms_const) f_9_fourstep <- mkinfit("SFO", experimental_data_for_UBA_2019[[9]]$data, error_model = "tc", error_model_algorithm = "fourstep", quiet = TRUE) expect_equivalent(round(AIC(f_9_fourstep), 2), 139.43) + expect_equivalent(parms(f_9_fourstep)[1:3], f_9_parms_const) f_9_IRLS <- mkinfit("SFO", experimental_data_for_UBA_2019[[9]]$data, error_model = "tc", error_model_algorithm = "IRLS", quiet = TRUE) expect_equivalent(round(AIC(f_9_IRLS), 2), 139.43) + expect_equivalent(parms(f_9_IRLS)[1:3], f_9_parms_const) f_9_d_3 <- mkinfit("SFO", experimental_data_for_UBA_2019[[9]]$data, error_model = "tc", error_model_algorithm = "d_3", quiet = TRUE) expect_equivalent(round(AIC(f_9_d_3), 2), 134.94) + expect_equivalent(parms(f_9_d_3), f_9_parms_tc_direct) }) test_that("The default error model algorithm finds the best known AIC values for parent fits", { diff --git a/tests/testthat/test_plots_summary_twa.R b/tests/testthat/test_plots_summary_twa.R index 28c569b6..5917dd6e 100644 --- a/tests/testthat/test_plots_summary_twa.R +++ b/tests/testthat/test_plots_summary_twa.R @@ -126,4 +126,7 @@ test_that("The AIC is reproducible", { data.frame(df = c(3, 4, 5, 5), AIC = c(59.3, 44.7, 29.0, 39.2)), scale = 1, tolerance = 0.1) expect_error(AIC(fits["SFO", ]), "column object") + expect_equivalent(BIC(fits[, "FOCUS_C"]), + data.frame(df = c(3, 4, 5, 5), AIC = c(59.9, 45.5, 30.0, 40.2)), + scale = 1, tolerance = 0.1) }) diff --git a/vignettes/mkin_benchmarks.rda b/vignettes/mkin_benchmarks.rda Binary files differindex bf9aec62..1190d924 100644 --- a/vignettes/mkin_benchmarks.rda +++ b/vignettes/mkin_benchmarks.rda |
