diff options
| -rw-r--r-- | DESCRIPTION | 3 | ||||
| -rw-r--r-- | NAMESPACE | 1 | ||||
| -rw-r--r-- | R/confint.mkinfit.R | 4 | ||||
| -rw-r--r-- | R/parms.mkinfit.R | 1 | ||||
| -rw-r--r-- | _pkgdown.yml | 12 | ||||
| -rw-r--r-- | docs/news/index.html | 1 | ||||
| -rw-r--r-- | docs/reference/confint.mkinfit.html | 252 | ||||
| -rw-r--r-- | docs/reference/index.html | 24 | ||||
| -rw-r--r-- | docs/reference/parms.html | 200 | ||||
| -rw-r--r-- | docs/sitemap.xml | 6 | ||||
| -rw-r--r-- | man/confint.mkinfit.Rd | 6 | ||||
| -rw-r--r-- | man/parms.Rd | 4 | ||||
| -rw-r--r-- | test.log | 18 | ||||
| -rw-r--r-- | tests/figs/plotting/plot-errmod-with-sfo-lin-a-obs.svg | 12 | ||||
| -rw-r--r-- | tests/testthat/FOCUS_2006_D.csf | 2 |
15 files changed, 513 insertions, 33 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index 9efa2b89..88412fa8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -17,8 +17,7 @@ Description: Calculation routines based on the FOCUS Kinetics Report (2006, equation models are solved using compiled C functions. Please note that no warranty is implied for correctness of results or fitness for a particular purpose. -Imports: stats, graphics, methods, deSolve, R6, inline, parallel, plyr, - numDeriv +Imports: stats, graphics, methods, deSolve, R6, inline, parallel, numDeriv Suggests: knitr, rbenchmark, tikzDevice, testthat, rmarkdown, covr, vdiffr, benchmarkme, tibble License: GPL @@ -71,6 +71,7 @@ importFrom(stats,optimize) importFrom(stats,pt) importFrom(stats,qchisq) importFrom(stats,qf) +importFrom(stats,qnorm) importFrom(stats,qt) importFrom(stats,rnorm) importFrom(utils,write.table) diff --git a/R/confint.mkinfit.R b/R/confint.mkinfit.R index 58918321..58a3c8db 100644 --- a/R/confint.mkinfit.R +++ b/R/confint.mkinfit.R @@ -28,7 +28,9 @@ #' @examples #' f <- mkinfit("SFO", FOCUS_2006_C, quiet = TRUE) #' confint(f, method = "quadratic") -#' confint(f, method = "profile") +#' \dontrun{ +#' confint(f, method = "profile") +#' } #' @export confint.mkinfit <- function(object, parm, level = 0.95, alpha = 1 - level, diff --git a/R/parms.mkinfit.R b/R/parms.mkinfit.R index 8f9b4136..0628cb92 100644 --- a/R/parms.mkinfit.R +++ b/R/parms.mkinfit.R @@ -5,6 +5,7 @@ #' considering the error structure that was assumed for the fit. #' #' @param object A fitted model object +#' @param \dots Not used #' @return A numeric vector of fitted model parameters #' @export parms <- function(object, ...) diff --git a/_pkgdown.yml b/_pkgdown.yml index d51a7f27..bbf63301 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -17,13 +17,15 @@ reference: desc: Functions working with mkinfit objects contents: - plot.mkinfit + - parms.mkinfit + - confint.mkinfit - summary.mkinfit - - mkinresplot - - mkinparplot - - mkinerrplot - - endpoints - - mkinerrmin - logLik.mkinfit + - mkinresplot + - mkinparplot + - mkinerrplot + - endpoints + - mkinerrmin - title: Work with mmkin objects desc: Functions working with aggregated results contents: diff --git a/docs/news/index.html b/docs/news/index.html index 67f64150..1322f75d 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -134,6 +134,7 @@ <a href="#mkin-0-9-49-6-unreleased" class="anchor"></a>mkin 0.9.49.6 (unreleased)<small> Unreleased </small> </h1> <ul> +<li><p>Add ‘parms’ and ‘confint’ methods for mkinfit objects. Confidence intervals based on the quadratic approximation as in the summary, and based on the profile likelihood</p></li> <li><p>Move long-running tests to tests/testthat/slow with a separate test log. They currently take around 7 minutes on my system</p></li> <li><p>‘mkinfit’: Clean the code and return functions to calculate the log-likelihood and the sum of squared residuals</p></li> <li><p>Vignette ‘twa.html’: Add the maximum time weighted average formulas for the hockey stick model</p></li> diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html new file mode 100644 index 00000000..64ea0d4c --- /dev/null +++ b/docs/reference/confint.mkinfit.html @@ -0,0 +1,252 @@ +<!-- 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>Confidence intervals for parameters of mkinfit objects — confint.mkinfit • mkin</title> + + +<!-- jquery --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" 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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>Confidence intervals for parameters of mkinfit objects</h1> + + <div class="hidden name"><code>confint.mkinfit.Rd</code></div> + </div> + + <div class="ref-description"> + <p>Confidence intervals for parameters of mkinfit objects</p> + </div> + + <pre class="usage"><span class='co'># S3 method for mkinfit</span> +<span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>object</span>, <span class='no'>parm</span>, <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0.95</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>1</span> - + <span class='no'>level</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"profile"</span>, <span class='st'>"quadratic"</span>), <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>backtransform</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>distribution</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"student_t"</span>, <span class='st'>"normal"</span>), + <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</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>object</th> + <td><p>An <code><a href='mkinfit.html'>mkinfit</a></code> object</p></td> + </tr> + <tr> + <th>parm</th> + <td><p>A vector of names of the parameters which are to be given +confidence intervals. If missing, all parameters are considered.</p></td> + </tr> + <tr> + <th>level</th> + <td><p>The confidence level required</p></td> + </tr> + <tr> + <th>alpha</th> + <td><p>The allowed error probability, overrides 'level' if specified.</p></td> + </tr> + <tr> + <th>method</th> + <td><p>The 'profile' method searches the parameter space for the +cutoff of the confidence intervals by means of a likelihood ratio test. +The 'quadratic' method approximates the likelihood function at the +optimised parameters using the second term of the Taylor expansion, using +a second derivative (hessian) contained in the object.</p></td> + </tr> + <tr> + <th>transformed</th> + <td><p>If the quadratic approximation is used, should it be +applied to the likelihood based on the transformed parameters?</p></td> + </tr> + <tr> + <th>backtransform</th> + <td><p>If we approximate the likelihood in terms of the +transformed parameters, should we backtransform the parameters with +their confidence intervals?</p></td> + </tr> + <tr> + <th>distribution</th> + <td><p>For the quadratic approximation, should we use +the student t distribution or assume normal distribution for +the parameter estimate</p></td> + </tr> + <tr> + <th>quiet</th> + <td><p>Should we suppress messages?</p></td> + </tr> + <tr> + <th>...</th> + <td><p>Not used</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>A matrix with columns giving lower and upper confidence limits for + each parameter.</p> + <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> + + <p>Pawitan Y (2013) In all likelihood - Statistical modelling and + inference using likelihood. Clarendon Press, Oxford.</p> + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='no'>f</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFO"</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/stats/confint.html'>confint</a></span>(<span class='no'>f</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"quadratic"</span>)</div><div class='output co'>#> 2.5% 97.5% +#> parent_0 71.8242430 93.1600766 +#> k_parent_sink 0.2109541 0.4440528 +#> sigma 1.9778868 7.3681380</div><div class='input'><span class='co'># \dontrun{</span> + <span class='fu'><a href='https://rdrr.io/r/stats/confint.html'>confint</a></span>(<span class='no'>f</span>, <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"profile"</span>)</div><div class='output co'>#> <span class='message'>Profiling the likelihood</span></div><div class='output co'>#> 2.5% 97.5% +#> parent_0 71.3471007 93.9447024 +#> k_parent_sink 0.2030765 0.4491067 +#> sigma 2.9810656 8.8633278</div><div class='input'># } +</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="#arguments">Arguments</a></li> + <li><a href="#value">Value</a></li> + <li><a href="#references">References</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/index.html b/docs/reference/index.html index 328f5aca..fa424060 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -185,12 +185,30 @@ more datasets</p></td> </tr><tr> <td> + <p><code><a href="parms.html">parms()</a></code> </p> + </td> + <td><p>Extract model parameters from mkinfit models</p></td> + </tr><tr> + + <td> + <p><code><a href="confint.mkinfit.html">confint(<i><mkinfit></i>)</a></code> </p> + </td> + <td><p>Confidence intervals for parameters of mkinfit objects</p></td> + </tr><tr> + + <td> <p><code><a href="summary.mkinfit.html">summary(<i><mkinfit></i>)</a></code> <code><a href="summary.mkinfit.html">print(<i><summary.mkinfit></i>)</a></code> </p> </td> <td><p>Summary method for class "mkinfit"</p></td> </tr><tr> <td> + <p><code><a href="logLik.mkinfit.html">logLik(<i><mkinfit></i>)</a></code> </p> + </td> + <td><p>Calculated the log-likelihood of a fitted mkinfit object</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> @@ -219,12 +237,6 @@ with mkinfit</p></td> <p><code><a href="mkinerrmin.html">mkinerrmin()</a></code> </p> </td> <td><p>Calculate the minimum error to assume in order to pass the variance test</p></td> - </tr><tr> - - <td> - <p><code><a href="logLik.mkinfit.html">logLik(<i><mkinfit></i>)</a></code> </p> - </td> - <td><p>Calculated the log-likelihood of a fitted mkinfit object</p></td> </tr> </tbody><tbody> <tr> diff --git a/docs/reference/parms.html b/docs/reference/parms.html new file mode 100644 index 00000000..8ab26240 --- /dev/null +++ b/docs/reference/parms.html @@ -0,0 +1,200 @@ +<!-- 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>Extract model parameters from mkinfit models — parms • mkin</title> + + +<!-- jquery --> +<script 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working with a fitted model without +considering the error structure that was assumed for the fit." /> +<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" 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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>Extract model parameters from mkinfit models</h1> + + <div class="hidden name"><code>parms.Rd</code></div> + </div> + + <div class="ref-description"> + <p>This function always returns degradation model parameters as well as error +model parameters, in order to avoid working with a fitted model without +considering the error structure that was assumed for the fit.</p> + </div> + + <pre class="usage"><span class='fu'>parms</span>(<span class='no'>object</span>, <span class='no'>...</span>) + +<span class='co'># S3 method for mkinfit</span> +<span class='fu'>parms</span>(<span class='no'>object</span>, <span class='kw'>transformed</span> <span class='kw'>=</span> <span class='fl'>FALSE</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>object</th> + <td><p>A fitted model object</p></td> + </tr> + <tr> + <th>...</th> + <td><p>Not used</p></td> + </tr> + <tr> + <th>transformed</th> + <td><p>Should the parameters be returned +as used internally during the optimisation?</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>A numeric vector of fitted model parameters</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> + <li><a href="#value">Value</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/sitemap.xml b/docs/sitemap.xml index b62b9a44..9e3363ba 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -55,6 +55,9 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/add_err.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/reference/confint.mkinfit.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/reference/endpoints.html</loc> </url> <url> @@ -118,6 +121,9 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/nafta.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/reference/parms.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/reference/plot.mkinfit.html</loc> </url> <url> diff --git a/man/confint.mkinfit.Rd b/man/confint.mkinfit.Rd index 94f55d14..943904b9 100644 --- a/man/confint.mkinfit.Rd +++ b/man/confint.mkinfit.Rd @@ -37,6 +37,8 @@ the student t distribution or assume normal distribution for the parameter estimate} \item{quiet}{Should we suppress messages?} + +\item{\dots}{Not used} } \value{ A matrix with columns giving lower and upper confidence limits for @@ -48,7 +50,9 @@ Confidence intervals for parameters of mkinfit objects \examples{ f <- mkinfit("SFO", FOCUS_2006_C, quiet = TRUE) confint(f, method = "quadratic") -confint(f, method = "profile") +\dontrun{ + confint(f, method = "profile") +} } \references{ Pawitan Y (2013) In all likelihood - Statistical modelling and diff --git a/man/parms.Rd b/man/parms.Rd index 6de52557..73cb23cd 100644 --- a/man/parms.Rd +++ b/man/parms.Rd @@ -12,10 +12,10 @@ parms(object, ...) \arguments{ \item{object}{A fitted model object} +\item{\dots}{Not used} + \item{transformed}{Should the parameters be returned as used internally during the optimisation?} - -\item{complete}{Unused argument for compatibility with the generic coef function from base R} } \value{ A numeric vector of fitted model parameters @@ -2,30 +2,30 @@ Loading mkin Testing mkin ✔ | OK F W S | Context ✔ | 2 | Export dataset for reading into CAKE -✔ | 3 | Confidence intervals and p-values -✔ | 10 | Error model fitting [37.1 s] +✔ | 9 | Confidence intervals and p-values [2.3 s] +✔ | 10 | Error model fitting [37.2 s] ✔ | 5 | Calculation of FOCUS chi2 error levels [3.5 s] -✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.5 s] +✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.3 s] ✔ | 6 | Test fitting the decline of metabolites from their maximum [0.9 s] ✔ | 1 | Fitting the logistic model [0.9 s] ✔ | 1 | Test dataset class mkinds used in gmkin ✔ | 12 | Special cases of mkinfit calls [2.7 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] -✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2 s] +✔ | 16 | Evaluations according to 2015 NAFTA guidance [4.0 s] +✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.3 s] ✔ | 3 | Summary ✔ | 11 | Plotting [0.6 s] ✔ | 3 | AIC calculation -✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.3 s] +✔ | 2 | Complex test case from Schaefer et al. 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