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authorJohannes Ranke <jranke@uni-bremen.de>2020-04-18 00:38:26 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-04-18 00:38:26 +0200
commit518a801a9a0f1aef36df1f201b6a3f0f3a84b779 (patch)
tree0e3bcbdc0f50df02c4249f49d52c65bd2537ed4b
parent49ecddeab52babb7388990b5dd0e15acd70c8b43 (diff)
Avoid assignment to .GlobalEnv for CRAN
-rw-r--r--NAMESPACE2
-rw-r--r--R/nlme.mmkin.R35
-rw-r--r--R/summary.mkinfit.R12
-rw-r--r--_pkgdown.yml1
-rw-r--r--check.log28
-rw-r--r--docs/reference/get_deg_func.html176
-rw-r--r--docs/reference/index.html6
-rw-r--r--docs/reference/nlme.mmkin.html12
-rw-r--r--docs/sitemap.xml3
-rw-r--r--man/get_deg_func.Rd15
-rw-r--r--man/nlme.mmkin.Rd4
-rw-r--r--test.log16
-rw-r--r--tests/testthat/FOCUS_2006_D.csf2
-rw-r--r--tests/testthat/summary_DFOP_FOCUS_C.txt5
-rw-r--r--tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt5
-rw-r--r--tests/testthat/summary_DFOP_FOCUS_D_eigen.txt5
16 files changed, 271 insertions, 56 deletions
diff --git a/NAMESPACE b/NAMESPACE
index ef610857..c5528662 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -40,6 +40,7 @@ export(add_err)
export(aw)
export(backtransform_odeparms)
export(endpoints)
+export(get_deg_func)
export(ilr)
export(invilr)
export(loftest)
@@ -109,4 +110,5 @@ importFrom(stats,qt)
importFrom(stats,residuals)
importFrom(stats,rnorm)
importFrom(stats,update)
+importFrom(utils,getFromNamespace)
importFrom(utils,write.table)
diff --git a/R/nlme.mmkin.R b/R/nlme.mmkin.R
index 1d6c2e75..e58f11cb 100644
--- a/R/nlme.mmkin.R
+++ b/R/nlme.mmkin.R
@@ -1,3 +1,21 @@
+# Code inspired by nlme::nlme.nlsList and R/nlme_fit.R from nlmixr
+
+# We need to assign the degradation function created in nlme.mmkin to an
+# environment that is always accessible, also e.g. when evaluation is done by
+# testthat or pkgdown. Therefore parent.frame() is not good enough. The
+# following environment will be in the mkin namespace.
+.nlme_env <- new.env(parent = emptyenv())
+
+#' Retrieve a degradation function from the mmkin namespace
+#'
+#' @importFrom utils getFromNamespace
+#' @return A function that was likely previously assigned from within
+#' nlme.mmkin
+#' @export
+get_deg_func <- function() {
+ return(get("deg_func", getFromNamespace(".nlme_env", "mkin")))
+}
+
#' Create an nlme model for an mmkin row object
#'
#' This functions sets up a nonlinear mixed effects model for an mmkin row
@@ -35,9 +53,9 @@
#' f_nlme <- nlme(f)
#' print(f_nlme)
#' endpoints(f_nlme)
-#' f_nlme_2 <- nlme(f, start = c(parent_0 = 100, log_k_parent_sink = 0.1))
-#' update(f_nlme_2, random = parent_0 ~ 1)
#' \dontrun{
+#' f_nlme_2 <- nlme(f, start = c(parent_0 = 100, log_k_parent_sink = 0.1))
+#' update(f_nlme_2, random = parent_0 ~ 1)
#' # Test on some real data
#' ds_2 <- lapply(experimental_data_for_UBA_2019[6:10],
#' function(x) x$data[c("name", "time", "value")])
@@ -83,7 +101,6 @@
#' endpoints(f_nlme_sfo_sfo)
#' endpoints(f_nlme_dfop_sfo)
#' }
-# Code inspired by nlme.nlsList
nlme.mmkin <- function(model, data = sys.frame(sys.parent()),
fixed, random = fixed,
groups, start, correlation = NULL, weights = NULL,
@@ -95,19 +112,21 @@ nlme.mmkin <- function(model, data = sys.frame(sys.parent()),
thisCall <- as.list(match.call())[-1]
- # warn in case of use of arguments that are overriden
+ # Warn in case arguments were used that are overriden
if (any(!is.na(match(names(thisCall),
c("fixed", "data"))))) {
warning("'nlme.mmkin' will redefine 'fixed' and 'data'")
}
deg_func <- nlme_function(model)
- assign("deg_func", deg_func, globalenv())
- # specify the model formula
- this_model_text <- paste0("value ~ deg_func(",
+ assign("deg_func", deg_func, getFromNamespace(".nlme_env", "mkin"))
+
+ # For the formula, get the degradation function from the mkin namespace
+ this_model_text <- paste0("value ~ mkin::get_deg_func()(",
paste(names(formals(deg_func)), collapse = ", "), ")")
- this_model <- eval(parse(text = this_model_text))
+ this_model <- as.formula(this_model_text)
+
thisCall[["model"]] <- this_model
mean_dp <- mean_degparms(model)
diff --git a/R/summary.mkinfit.R b/R/summary.mkinfit.R
index a67f17ee..2dc74bd7 100644
--- a/R/summary.mkinfit.R
+++ b/R/summary.mkinfit.R
@@ -138,13 +138,11 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, alpha = 0.05,
if (!is.null(object$version)) {
ans$fit_version <- object$version
ans$fit_Rversion <- object$Rversion
- }
-
- AIC <- try(AIC(object))
- if (!inherits(AIC, "try-error")) {
- ans$AIC = AIC(object)
- ans$BIC = BIC(object)
- ans$logLik = logLik(object)
+ if (ans$fit_version >= "0.9.49.6") {
+ ans$AIC = AIC(object)
+ ans$BIC = BIC(object)
+ ans$logLik = logLik(object)
+ }
}
ans$diffs <- object$mkinmod$diffs
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 2ede6857..0623c6ed 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -39,6 +39,7 @@ reference:
- nlme.mmkin
- plot.nlme.mmkin
- nlme_function
+ - get_deg_func
- title: Datasets and known results
contents:
- FOCUS_2006_A
diff --git a/check.log b/check.log
index 43cc5f64..a50286a5 100644
--- a/check.log
+++ b/check.log
@@ -41,12 +41,28 @@ Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
-* checking R code for possible problems ... OK
+* checking R code for possible problems ... NOTE
+get_deg_func: no visible global function definition for
+ ‘getFromNamespace’
+nlme.mmkin: no visible global function definition for
+ ‘getFromNamespace’
+nlme.mmkin: no visible global function definition for ‘as.formula’
+Undefined global functions or variables:
+ as.formula getFromNamespace
+Consider adding
+ importFrom("stats", "as.formula")
+ importFrom("utils", "getFromNamespace")
+to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
-* checking for missing documentation entries ... OK
+* checking for missing documentation entries ... WARNING
+Undocumented code objects:
+ ‘get_deg_func’
+All user-level objects in a package should have documentation entries.
+See chapter ‘Writing R documentation files’ in the ‘Writing R
+Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
@@ -56,11 +72,7 @@ Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
-* checking examples ... NOTE
-Examples with CPU or elapsed time > 5s
- user system elapsed
-nlme.mmkin 4.801 1.040 4.497
-plot.nlme.mmkin 4.751 0.285 4.680
+* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... SKIPPED
* checking for unstated dependencies in vignettes ... OK
@@ -70,7 +82,7 @@ plot.nlme.mmkin 4.751 0.285 4.680
* checking for detritus in the temp directory ... OK
* DONE
-Status: 1 NOTE
+Status: 1 WARNING, 1 NOTE
See
‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’
for details.
diff --git a/docs/reference/get_deg_func.html b/docs/reference/get_deg_func.html
new file mode 100644
index 00000000..c5b8e38c
--- /dev/null
+++ b/docs/reference/get_deg_func.html
@@ -0,0 +1,176 @@
+<!-- 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>Retrieve a degradation function from the mmkin namespace — get_deg_func • 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="Retrieve a degradation function from the mmkin namespace — get_deg_func" />
+<meta property="og:description" content="Retrieve a degradation function from the mmkin namespace" />
+<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">0.9.49.10</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>
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+ <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>Retrieve a degradation function from the mmkin namespace</h1>
+
+ <div class="hidden name"><code>get_deg_func.Rd</code></div>
+ </div>
+
+ <div class="ref-description">
+ <p>Retrieve a degradation function from the mmkin namespace</p>
+ </div>
+
+ <pre class="usage"><span class='fu'>get_deg_func</span>()</pre>
+
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>A function that was likely previously assigned from within
+ nlme.mmkin</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="#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/reference/index.html b/docs/reference/index.html
index f4de5bd8..04e3b8b9 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -296,6 +296,12 @@ of an mmkin object</p></td>
<p><code><a href="nlme.html">nlme_function()</a></code> <code><a href="nlme.html">mean_degparms()</a></code> <code><a href="nlme.html">nlme_data()</a></code> </p>
</td>
<td><p>Helper functions to create nlme models from mmkin row objects</p></td>
+ </tr><tr>
+
+ <td>
+ <p><code><a href="get_deg_func.html">get_deg_func()</a></code> </p>
+ </td>
+ <td><p>Retrieve a degradation function from the mmkin namespace</p></td>
</tr>
</tbody><tbody>
<tr>
diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html
index 9af9cbf7..33cc9164 100644
--- a/docs/reference/nlme.mmkin.html
+++ b/docs/reference/nlme.mmkin.html
@@ -258,7 +258,7 @@ parameters taken from the mmkin object are used</p></td>
#&gt; parent 11.96183 39.73634
#&gt; </div><div class='input'><span class='no'>f_nlme</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>)
<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>f_nlme</span>)</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by maximum likelihood
-#&gt; Model: value ~ deg_func(name, time, parent_0, log_k_parent_sink)
+#&gt; Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_parent_sink)
#&gt; Data: "Not shown"
#&gt; Log-likelihood: -307.5269
#&gt; Fixed: list(parent_0 ~ 1, log_k_parent_sink ~ 1)
@@ -276,9 +276,10 @@ parameters taken from the mmkin object are used</p></td>
#&gt; Number of Groups: 5 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>f_nlme</span>)</div><div class='output co'>#&gt; $distimes
#&gt; DT50 DT90
#&gt; parent 17.51545 58.18505
-#&gt; </div><div class='input'><span class='no'>f_nlme_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>, <span class='kw'>start</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent_0</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>log_k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>))
-<span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>f_nlme_2</span>, <span class='kw'>random</span> <span class='kw'>=</span> <span class='no'>parent_0</span> ~ <span class='fl'>1</span>)</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by maximum likelihood
-#&gt; Model: value ~ deg_func(name, time, parent_0, log_k_parent_sink)
+#&gt; </div><div class='input'><span class='co'># \dontrun{</span>
+ <span class='no'>f_nlme_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>f</span>, <span class='kw'>start</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent_0</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>log_k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>))
+ <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>f_nlme_2</span>, <span class='kw'>random</span> <span class='kw'>=</span> <span class='no'>parent_0</span> ~ <span class='fl'>1</span>)</div><div class='output co'>#&gt; Nonlinear mixed-effects model fit by maximum likelihood
+#&gt; Model: value ~ (mkin::get_deg_func())(name, time, parent_0, log_k_parent_sink)
#&gt; Data: "Not shown"
#&gt; Log-likelihood: -404.3729
#&gt; Fixed: list(parent_0 ~ 1, log_k_parent_sink ~ 1)
@@ -291,8 +292,7 @@ parameters taken from the mmkin object are used</p></td>
#&gt; StdDev: 0.002416792 21.63027
#&gt;
#&gt; Number of Observations: 90
-#&gt; Number of Groups: 5 </div><div class='input'><span class='co'># \dontrun{</span>
- <span class='co'># Test on some real data</span>
+#&gt; Number of Groups: 5 </div><div class='input'> <span class='co'># Test on some real data</span>
<span class='no'>ds_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>6</span>:<span class='fl'>10</span>],
<span class='kw'>function</span>(<span class='no'>x</span>) <span class='no'>x</span>$<span class='no'>data</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span>)])
<span class='no'>m_sfo_sfo</span> <span class='kw'>&lt;-</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'>"A1"</span>),
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index d1c86707..5abcc894 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -67,6 +67,9 @@
<loc>https://pkgdown.jrwb.de/mkin/reference/experimental_data_for_UBA.html</loc>
</url>
<url>
+ <loc>https://pkgdown.jrwb.de/mkin/reference/get_deg_func.html</loc>
+ </url>
+ <url>
<loc>https://pkgdown.jrwb.de/mkin/reference/ilr.html</loc>
</url>
<url>
diff --git a/man/get_deg_func.Rd b/man/get_deg_func.Rd
new file mode 100644
index 00000000..1d8a3de9
--- /dev/null
+++ b/man/get_deg_func.Rd
@@ -0,0 +1,15 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/nlme.mmkin.R
+\name{get_deg_func}
+\alias{get_deg_func}
+\title{Retrieve a degradation function from the mmkin namespace}
+\usage{
+get_deg_func()
+}
+\value{
+A function that was likely previously assigned from within
+ nlme.mmkin
+}
+\description{
+Retrieve a degradation function from the mmkin namespace
+}
diff --git a/man/nlme.mmkin.Rd b/man/nlme.mmkin.Rd
index 97d444e4..430dbda1 100644
--- a/man/nlme.mmkin.Rd
+++ b/man/nlme.mmkin.Rd
@@ -83,9 +83,9 @@ endpoints(f[[1]])
f_nlme <- nlme(f)
print(f_nlme)
endpoints(f_nlme)
-f_nlme_2 <- nlme(f, start = c(parent_0 = 100, log_k_parent_sink = 0.1))
-update(f_nlme_2, random = parent_0 ~ 1)
\dontrun{
+ f_nlme_2 <- nlme(f, start = c(parent_0 = 100, log_k_parent_sink = 0.1))
+ update(f_nlme_2, random = parent_0 ~ 1)
# Test on some real data
ds_2 <- lapply(experimental_data_for_UBA_2019[6:10],
function(x) x$data[c("name", "time", "value")])
diff --git a/test.log b/test.log
index dd1a1cc0..0a14c115 100644
--- a/test.log
+++ b/test.log
@@ -7,29 +7,27 @@ Testing mkin
✔ | 4 | Fitting the SFORB model [1.7 s]
✔ | 5 | Calculation of Akaike weights
✔ | 10 | Confidence intervals and p-values [9.4 s]
-✔ | 14 | Error model fitting [37.9 s]
+✔ | 14 | Error model fitting [37.6 s]
✔ | 6 | Test fitting the decline of metabolites from their maximum [0.8 s]
✔ | 1 | Fitting the logistic model [0.9 s]
✔ | 1 | Test dataset class mkinds used in gmkin
✔ | 12 | Special cases of mkinfit calls [2.3 s]
✔ | 9 | mkinmod model generation and printing [0.2 s]
-✔ | 3 | Model predictions with mkinpredict [0.3 s]
+✔ | 3 | Model predictions with mkinpredict [0.4 s]
✔ | 16 | Evaluations according to 2015 NAFTA guidance [4.1 s]
-✔ | 9 | Nonlinear mixed-effects models [12.0 s]
+✔ | 9 | Nonlinear mixed-effects models [11.9 s]
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2 s]
✔ | 3 | Summary
✔ | 14 | Plotting [4.9 s]
✔ | 4 | AIC calculation
✔ | 4 | Residuals extracted from mkinfit models
-✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.4 s]
- ⠏ | 0 | Summaries of old mkinfit objectsError in attr(val, "df") <- length(object$bparms.optim) + length(object$errparms) :
- Versuch ein Attribut von NULL zu setzen
- ✔ | 1 | Summaries of old mkinfit objects
-✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.1 s]
+✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [5.3 s]
+✔ | 1 | Summaries of old mkinfit objects
+✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.2 s]
✔ | 9 | Hypothesis tests [37.0 s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 132.2 s
+Duration: 131.8 s
OK: 154
Failed: 0
diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index c61b55c4..818c055a 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: 2020-04-17
+Date: 2020-04-18
Optimiser: IRLS
[Data]
diff --git a/tests/testthat/summary_DFOP_FOCUS_C.txt b/tests/testthat/summary_DFOP_FOCUS_C.txt
index 4f96c8d3..14e00f62 100644
--- a/tests/testthat/summary_DFOP_FOCUS_C.txt
+++ b/tests/testthat/summary_DFOP_FOCUS_C.txt
@@ -33,11 +33,6 @@ g_ilr 0.000000 -Inf Inf
Fixed parameter values:
None
-Results:
-
- AIC BIC logLik
- 29.02372 30.00984 -9.511861
-
Optimised, transformed parameters with symmetric confidence intervals:
Estimate Std. Error Lower Upper
parent_0 85.0000 0.66620 83.1500 86.8500
diff --git a/tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt b/tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt
index 5a9093c3..66ab9348 100644
--- a/tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt
+++ b/tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt
@@ -33,11 +33,6 @@ Fixed parameter values:
value type
m1_0 0 state
-Results:
-
- AIC BIC logLik
- 204.4486 212.6365 -97.22429
-
Optimised, transformed parameters with symmetric confidence intervals:
Estimate Std. Error Lower Upper
parent_0 99.600 1.57000 96.400 102.800
diff --git a/tests/testthat/summary_DFOP_FOCUS_D_eigen.txt b/tests/testthat/summary_DFOP_FOCUS_D_eigen.txt
index f597cad5..1626c5da 100644
--- a/tests/testthat/summary_DFOP_FOCUS_D_eigen.txt
+++ b/tests/testthat/summary_DFOP_FOCUS_D_eigen.txt
@@ -33,11 +33,6 @@ Fixed parameter values:
value type
m1_0 0 state
-Results:
-
- AIC BIC logLik
- 204.4486 212.6365 -97.22429
-
Optimised, transformed parameters with symmetric confidence intervals:
Estimate Std. Error Lower Upper
parent_0 99.600 1.57000 96.400 102.800

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