Reduce check time for CRAN, releasev1.1.0

author: Johannes Ranke <jranke@uni-bremen.de> 2022-03-14 15:41:56 +0100
committer: Johannes Ranke <jranke@uni-bremen.de> 2022-03-14 15:41:56 +0100
commit: 3cddc58e6fcdd5341b354dc5b5f784ec8190f62b (patch)
tree: 8303617316a207e3e4ed7c1b554abf0ed77e3d39
parent: 72ef221369df14a527c2751c002b5cf3db29520d (diff)
19 files changed, 83 insertions, 63 deletions
diff --git a/R/create_deg_func.R b/R/create_deg_func.R
index 4b4284db..5794c65c 100644
--- a/R/create_deg_func.R
+++ b/R/create_deg_func.R
@@ -10,8 +10,8 @@
 #'   m1 = mkinsub("SFO"))
 #' FOCUS_D <- subset(FOCUS_2006_D, value != 0) # to avoid warnings
 #' fit_1 <- mkinfit(SFO_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE)
-#' fit_2 <- mkinfit(SFO_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE)
 #' \dontrun{
+#' fit_2 <- mkinfit(SFO_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE)
 #' if (require(rbenchmark))
 #'   benchmark(
 #'     analytical = mkinfit(SFO_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE),
diff --git a/R/nlme.mmkin.R b/R/nlme.mmkin.R
index b6b6c830..09cb84b8 100644
--- a/R/nlme.mmkin.R
+++ b/R/nlme.mmkin.R
@@ -59,12 +59,11 @@ get_deg_func <- function() {
 #' @examples
 #' ds <- lapply(experimental_data_for_UBA_2019[6:10],
 #'  function(x) subset(x$data[c("name", "time", "value")], name == "parent"))
-#' f <- mmkin(c("SFO", "DFOP"), ds, quiet = TRUE, cores = 1)
-#' library(nlme)
-#' f_nlme_sfo <- nlme(f["SFO", ])
 #'
 #' \dontrun{
-#'
+#'   f <- mmkin(c("SFO", "DFOP"), ds, quiet = TRUE, cores = 1)
+#'   library(nlme)
+#'   f_nlme_sfo <- nlme(f["SFO", ])
 #'   f_nlme_dfop <- nlme(f["DFOP", ])
 #'   anova(f_nlme_sfo, f_nlme_dfop)
 #'   print(f_nlme_dfop)
diff --git a/R/summary.nlme.mmkin.R b/R/summary.nlme.mmkin.R
index be7f0441..1dd73301 100644
--- a/R/summary.nlme.mmkin.R
+++ b/R/summary.nlme.mmkin.R
@@ -62,11 +62,13 @@
 #'     n = 1)[[1]]
 #' })
 #'
+#' \dontrun{
 #' # Evaluate using mmkin and nlme
 #' library(nlme)
 #' f_mmkin <- mmkin("SFO", ds_sfo_syn, quiet = TRUE, error_model = "tc", cores = 1)
 #' f_nlme <- nlme(f_mmkin)
 #' summary(f_nlme, data = TRUE)
+#' }
 #'
 #' @export
 summary.nlme.mmkin <- function(object, data = FALSE, verbose = FALSE, distimes = TRUE, alpha = 0.05, ...) {
diff --git a/check.log b/check.log
index 89847aab..807e2f33 100644
--- a/check.log
+++ b/check.log
@@ -1,5 +1,5 @@
 * using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’
-* using R version 4.1.2 (2021-11-01)
+* using R version 4.1.3 (2022-03-10)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * using session charset: UTF-8
 * using options ‘--no-tests --as-cran’
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index d789805b..59854491 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -11,7 +11,7 @@ articles:
   benchmarks: web_only/benchmarks.html
   compiled_models: web_only/compiled_models.html
   dimethenamid_2018: web_only/dimethenamid_2018.html
-last_built: 2022-03-09T08:50Z
+last_built: 2022-03-14T07:56Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png
index ca982688..17a35806 100644
--- a/docs/reference/Rplot001.png
+++ b/docs/reference/Rplot001.png
diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png
index de2d61aa..ddd3a0d7 100644
--- a/docs/reference/Rplot002.png
+++ b/docs/reference/Rplot002.png
diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png
index f8bf10bb..fa29fc43 100644
--- a/docs/reference/Rplot003.png
+++ b/docs/reference/Rplot003.png
diff --git a/docs/reference/create_deg_func.html b/docs/reference/create_deg_func.html
index 57516fba..2516edff 100644
--- a/docs/reference/create_deg_func.html
+++ b/docs/reference/create_deg_func.html
@@ -111,8 +111,8 @@
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
 <span class="r-in"><span class="va">FOCUS_D</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span> <span class="co"># to avoid warnings</span></span>
 <span class="r-in"><span class="va">fit_1</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"analytical"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span class="r-in"><span class="va">fit_2</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
 <span class="r-in"><span class="co"># \dontrun{</span></span>
+<span class="r-in"><span class="va">fit_2</span> <span class="op">&lt;-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
 <span class="r-in"><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="va"><a href="http://rbenchmark.googlecode.com" class="external-link">rbenchmark</a></span><span class="op">)</span><span class="op">)</span></span>
 <span class="r-in">  <span class="fu"><a href="https://rdrr.io/pkg/rbenchmark/man/benchmark.html" class="external-link">benchmark</a></span><span class="op">(</span></span>
 <span class="r-in">    analytical <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">SFO_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"analytical"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span>
@@ -120,8 +120,8 @@
 <span class="r-in">    replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Loading required package: rbenchmark</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>         test replications elapsed relative user.self sys.self user.child</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1 analytical            2   0.406    1.000     0.407    0.000          0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2    deSolve            2   0.698    1.719     0.695    0.003          0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 analytical            2   0.394    1.000     0.393        0          0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2    deSolve            2   0.678    1.721     0.677        0          0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   sys.child</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1         0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 2         0</span>
@@ -134,8 +134,8 @@
 <span class="r-in">    deSolve <span class="op">=</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="va">DFOP_SFO</span>, <span class="va">FOCUS_D</span>, solution_type <span class="op">=</span> <span class="st">"deSolve"</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span>
 <span class="r-in">    replications <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>         test replications elapsed relative user.self sys.self user.child</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1 analytical            2   0.855    1.000     0.856        0          0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2    deSolve            2   1.588    1.857     1.587        0          0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1 analytical            2   0.829    1.000     0.829        0          0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2    deSolve            2   1.559    1.881     1.559        0          0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   sys.child</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1         0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 2         0</span>
diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html
index 4b59afed..1f071ffa 100644
--- a/docs/reference/nlme.mmkin.html
+++ b/docs/reference/nlme.mmkin.html
@@ -97,7 +97,7 @@ have been obtained by fitting the same model to a list of datasets.</p>
   data <span class="op">=</span> <span class="st">"auto"</span>,
   fixed <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">as.list</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">model</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>, <span class="kw">function</span><span class="op">(</span><span class="va">el</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/eval.html" class="external-link">eval</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/parse.html" class="external-link">parse</a></span><span class="op">(</span>text <span class="op">=</span>
     <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="va">el</span>, <span class="fl">1</span>, sep <span class="op">=</span> <span class="st">"~"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>,
-  random <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/pdDiag.html" class="external-link">pdDiag</a></span><span class="op">(</span><span class="va">fixed</span><span class="op">)</span>,
+  random <span class="op">=</span> <span class="fu">pdDiag</span><span class="op">(</span><span class="va">fixed</span><span class="op">)</span>,
   <span class="va">groups</span>,
   start <span class="op">=</span> <span class="fu"><a href="mean_degparms.html">mean_degparms</a></span><span class="op">(</span><span class="va">model</span>, random <span class="op">=</span> <span class="cn">TRUE</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,
   correlation <span class="op">=</span> <span class="cn">NULL</span>,
@@ -187,12 +187,11 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
     <h2>Examples</h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="va">ds</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span>
 <span class="r-in"> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"name"</span>, <span class="st">"time"</span>, <span class="st">"value"</span><span class="op">)</span><span class="op">]</span>, <span class="va">name</span> <span class="op">==</span> <span class="st">"parent"</span><span class="op">)</span><span class="op">)</span></span>
-<span class="r-in"><span class="va">f</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span>
-<span class="r-in"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span>
-<span class="r-in"><span class="va">f_nlme_sfo</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span></span>
 <span class="r-in"></span>
 <span class="r-in"><span class="co"># \dontrun{</span></span>
-<span class="r-in"></span>
+<span class="r-in">  <span class="va">f</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, <span class="va">ds</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span>
+<span class="r-in">  <span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span>
+<span class="r-in">  <span class="va">f_nlme_sfo</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span></span>
 <span class="r-in">  <span class="va">f_nlme_dfop</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span></span>
 <span class="r-in">  <span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span><span class="va">f_nlme_sfo</span>, <span class="va">f_nlme_dfop</span><span class="op">)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>             Model df      AIC      BIC    logLik   Test  L.Ratio p-value</span>
diff --git a/docs/reference/summary.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html
index d2ed2a86..3f98bec7 100644
--- a/docs/reference/summary.nlme.mmkin.html
+++ b/docs/reference/summary.nlme.mmkin.html
@@ -96,7 +96,7 @@ endpoints such as formation fractions and DT50 values. Optionally
 
     <div id="ref-usage">
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for nlme.mmkin</span>
-<span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span>
+<span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span>
   <span class="va">object</span>,
   data <span class="op">=</span> <span class="cn">FALSE</span>,
   verbose <span class="op">=</span> <span class="cn">FALSE</span>,
@@ -193,16 +193,20 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p>
 <span class="r-in">    n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span></span>
 <span class="r-in"><span class="op">}</span><span class="op">)</span></span>
 <span class="r-in"></span>
+<span class="r-in"><span class="co"># \dontrun{</span></span>
 <span class="r-in"><span class="co"># Evaluate using mmkin and nlme</span></span>
 <span class="r-in"><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://svn.r-project.org/R-packages/trunk/nlme/" class="external-link">nlme</a></span><span class="op">)</span></span>
 <span class="r-in"><span class="va">f_mmkin</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">ds_sfo_syn</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Optimisation did not converge:</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> iteration limit reached without convergence (10)</span>
 <span class="r-in"><span class="va">f_nlme</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span><span class="va">f_mmkin</span><span class="op">)</span></span>
-<span class="r-in"><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_nlme</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)</span>
+<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">f_nlme</span>, data <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> nlme version used for fitting:      3.1.155 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting:  1.1.0 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:         4.1.2 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Mon Mar  7 13:15:33 2022 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Mon Mar  7 13:15:33 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting:         4.1.3 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit:     Mon Mar 14 08:58:29 2022 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Mon Mar 14 08:58:29 2022 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> d_parent/dt = - k_parent * parent</span>
@@ -212,7 +216,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type analytical </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 0.528 s using 4 iterations</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 0.527 s using 4 iterations</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Variance model: Two-component variance function </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
@@ -352,6 +356,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent   90     20.8    22.692  -1.89165 1.7926    -1.055273</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent  120     13.4    13.768  -0.36790 1.0876    -0.338259</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  ds 5 parent  120     13.8    13.768   0.03210 1.0876     0.029517</span>
+<span class="r-in"><span class="co"># }</span></span>
 <span class="r-in"></span>
 </code></pre></div>
     </div>
diff --git a/man/create_deg_func.Rd b/man/create_deg_func.Rd
index 69058038..7b419342 100644
--- a/man/create_deg_func.Rd
+++ b/man/create_deg_func.Rd
@@ -24,8 +24,8 @@ SFO_SFO <- mkinmod(
   m1 = mkinsub("SFO"))
 FOCUS_D <- subset(FOCUS_2006_D, value != 0) # to avoid warnings
 fit_1 <- mkinfit(SFO_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE)
-fit_2 <- mkinfit(SFO_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE)
 \dontrun{
+fit_2 <- mkinfit(SFO_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE)
 if (require(rbenchmark))
   benchmark(
     analytical = mkinfit(SFO_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE),
diff --git a/man/nlme.mmkin.Rd b/man/nlme.mmkin.Rd
index ed58d603..ed19c0d3 100644
--- a/man/nlme.mmkin.Rd
+++ b/man/nlme.mmkin.Rd
@@ -92,12 +92,11 @@ methods that will automatically work on 'nlme.mmkin' objects, such as
 \examples{
 ds <- lapply(experimental_data_for_UBA_2019[6:10],
  function(x) subset(x$data[c("name", "time", "value")], name == "parent"))
-f <- mmkin(c("SFO", "DFOP"), ds, quiet = TRUE, cores = 1)
-library(nlme)
-f_nlme_sfo <- nlme(f["SFO", ])
 
 \dontrun{
-
+  f <- mmkin(c("SFO", "DFOP"), ds, quiet = TRUE, cores = 1)
+  library(nlme)
+  f_nlme_sfo <- nlme(f["SFO", ])
   f_nlme_dfop <- nlme(f["DFOP", ])
   anova(f_nlme_sfo, f_nlme_dfop)
   print(f_nlme_dfop)
diff --git a/man/summary.nlme.mmkin.Rd b/man/summary.nlme.mmkin.Rd
index d7e61074..425df096 100644
--- a/man/summary.nlme.mmkin.Rd
+++ b/man/summary.nlme.mmkin.Rd
@@ -87,11 +87,13 @@ ds_sfo_syn <- lapply(ds_sfo_mean, function(ds) {
     n = 1)[[1]]
 })
 
+\dontrun{
 # Evaluate using mmkin and nlme
 library(nlme)
 f_mmkin <- mmkin("SFO", ds_sfo_syn, quiet = TRUE, error_model = "tc", cores = 1)
 f_nlme <- nlme(f_mmkin)
 summary(f_nlme, data = TRUE)
+}
 
 }
 \author{
diff --git a/test.log b/test.log
index a02ab432..cd168e7f 100644
--- a/test.log
+++ b/test.log
@@ -7,14 +7,14 @@ Loading required package: parallel
 ✔ |         5 | Calculation of Akaike weights
 ✔ |         2 | Export dataset for reading into CAKE
 ✔ |        12 | Confidence intervals and p-values [1.0s]
-✔ |     1  12 | Dimethenamid data from 2018 [31.0s]
+✔ |     1  12 | Dimethenamid data from 2018 [31.2s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_dmta.R:98:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data
 Reason: Fitting this ODE model with saemix takes about 15 minutes on my system
 ────────────────────────────────────────────────────────────────────────────────
 ✔ |        14 | Error model fitting [4.7s]
 ✔ |         5 | Time step normalisation
-✔ |         4 | Calculation of FOCUS chi2 error levels [0.5s]
+✔ |         4 | Calculation of FOCUS chi2 error levels [0.6s]
 ✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s]
 ✔ |         4 | Test fitting the decline of metabolites from their maximum [0.3s]
 ✔ |         1 | Fitting the logistic model [0.2s]
@@ -25,27 +25,43 @@ Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ────────────────────────────────────────────────────────────────────────────────
 ✔ |         3 | Test dataset classes mkinds and mkindsg
 ✔ |        10 | Special cases of mkinfit calls [0.4s]
-✔ |         3 | mkinfit features [0.6s]
-✔ |         8 | mkinmod model generation and printing [0.2s]
-✔ |         3 | Model predictions with mkinpredict [0.3s]
-✔ |        16 | Evaluations according to 2015 NAFTA guidance [1.4s]
-✔ |         9 | Nonlinear mixed-effects models with nlme [8.0s]
-✔ |        16 | Plotting [1.3s]
+✔ |         3 | mkinfit features [0.7s]
+✔ |         8 | mkinmod model generation and printing [0.3s]
+✔ |         3 | Model predictions with mkinpredict [0.4s]
+✔ |        16 | Evaluations according to 2015 NAFTA guidance [1.5s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [8.2s]
+✔ |   5    16 | Plotting [10.5s]
+────────────────────────────────────────────────────────────────────────────────
+Warning (test_plot.R:48:3): Plotting mkinfit, mmkin and mixed model objects is reproducible
+Adding new file snapshot: 'tests/testhat/_snaps/mixed-model-fit-for-mmkin-object.svg'
+
+Warning (test_plot.R:51:3): Plotting mkinfit, mmkin and mixed model objects is reproducible
+Adding new file snapshot: 'tests/testhat/_snaps/mixed-model-fit-for-saem-object-with-saemix-transformations.svg'
+
+Warning (test_plot.R:56:3): Plotting mkinfit, mmkin and mixed model objects is reproducible
+Adding new file snapshot: 'tests/testhat/_snaps/mixed-model-fit-for-nlme-object.svg'
+
+Warning (test_plot.R:64:3): Plotting mkinfit, mmkin and mixed model objects is reproducible
+Adding new file snapshot: 'tests/testhat/_snaps/mixed-model-fit-for-saem-object-with-mkin-transformations.svg'
+
+Warning (test_plot.R:68:3): Plotting mkinfit, mmkin and mixed model objects is reproducible
+Adding new file snapshot: 'tests/testhat/_snaps/plot-errmod-with-focus-d-obs-eigen.svg'
+────────────────────────────────────────────────────────────────────────────────
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |        23 | saemix parent models [26.7s]
-✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s]
-✔ |         7 | Fitting the SFORB model [3.7s]
+✔ |        23 | saemix parent models [28.9s]
+✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.5s]
+✔ |         7 | Fitting the SFORB model [3.8s]
 ✔ |         1 | Summaries of old mkinfit objects
 ✔ |         4 | Summary [0.1s]
-✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.1s]
-✔ |         9 | Hypothesis tests [8.1s]
-✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.3s]
+✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s]
+✔ |         9 | Hypothesis tests [8.2s]
+✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 99.1 s
+Duration: 111.6 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 15 minutes on my system (1)
 • Fitting with saemix takes around 10 minutes when using deSolve (1)
 
-[ FAIL 0 | WARN 0 | SKIP 2 | PASS 221 ]
+[ FAIL 0 | WARN 5 | SKIP 2 | PASS 221 ]
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R
index 10696082..8ffe0b9d 100644
--- a/tests/testthat/setup_script.R
+++ b/tests/testthat/setup_script.R
@@ -202,17 +202,3 @@ dfop_saemix_2 <- saem(mmkin_dfop_1, quiet = TRUE, transformations = "saemix")
 saem_biphasic_m <- saem(mmkin_biphasic, transformations = "mkin", quiet = TRUE)
 saem_biphasic_s <- saem(mmkin_biphasic, transformations = "saemix", quiet = TRUE)
 
-# UBA datasets
-ds_uba <- lapply(experimental_data_for_UBA_2019[6:10],
-  function(x) subset(x$data[c("name", "time", "value")]))
-names(ds_uba) <- paste("Dataset", 6:10)
-sfo_sfo_uba <- mkinmod(parent = mkinsub("SFO", "A1"),
-  A1 = mkinsub("SFO"), quiet = TRUE)
-dfop_sfo_uba <- mkinmod(parent = mkinsub("DFOP", "A1"),
-  A1 = mkinsub("SFO"), quiet = TRUE)
-f_uba_mmkin <- mmkin(list("SFO-SFO" = sfo_sfo_uba, "DFOP-SFO" = dfop_sfo_uba),
-  ds_uba, quiet = TRUE, cores = n_cores)
-f_uba_dfop_sfo_mixed <- mixed(f_uba_mmkin[2, ])
-
-f_uba_sfo_sfo_saem <- saem(f_uba_mmkin["SFO-SFO", ], quiet = TRUE, transformations = "saemix")
-f_uba_dfop_sfo_saem <- saem(f_uba_mmkin["DFOP-SFO", ], quiet = TRUE, transformations = "saemix")
diff --git a/tests/testthat/test_analytical.R b/tests/testthat/test_analytical.R
index 66fb1ace..e6cb7ed3 100644
--- a/tests/testthat/test_analytical.R
+++ b/tests/testthat/test_analytical.R
@@ -1,9 +1,7 @@
 context("Analytical solutions for coupled models")
 
-# We do not want the warnings due to non-normality of residuals here
-warn_option <- options(warn=-1)
-
 test_that("The analytical solutions for SFO-SFO are correct", {
+  skip_on_cran()
   # No sink, no formation fractions
   SFO_SFO_nosink <- mkinmod(
     parent = mkinsub("SFO", to = "m1", sink = FALSE),
@@ -50,6 +48,7 @@ test_that("The analytical solutions for SFO-SFO are correct", {
 })
 
 test_that("The analytical solution for DFOP-SFO are correct", {
+  skip_on_cran()
   # With formation fraction
   f_dfop_sfo_analytical <- mkinfit(DFOP_SFO, FOCUS_D,
     solution_type = "analytical", quiet = TRUE)
@@ -61,5 +60,3 @@ test_that("The analytical solution for DFOP-SFO are correct", {
     tolerance = 5e-6
   )
 })
-
-options(warn = warn_option$warn)
diff --git a/tests/testthat/test_plot.R b/tests/testthat/test_plot.R
index 4f484cf3..58a00662 100644
--- a/tests/testthat/test_plot.R
+++ b/tests/testthat/test_plot.R
@@ -30,6 +30,20 @@ test_that("Plotting mkinfit, mmkin and mixed model objects is reproducible", {
   plot_err_sfo_sfo <- function() plot_err(f_sfo_sfo_desolve)
   vdiffr::expect_doppelganger("plot_err for FOCUS D", plot_err_sfo_sfo)
 
+  # UBA datasets
+  ds_uba <- lapply(experimental_data_for_UBA_2019[6:10],
+    function(x) subset(x$data[c("name", "time", "value")]))
+  names(ds_uba) <- paste("Dataset", 6:10)
+  sfo_sfo_uba <- mkinmod(parent = mkinsub("SFO", "A1"),
+    A1 = mkinsub("SFO"), quiet = TRUE)
+  dfop_sfo_uba <- mkinmod(parent = mkinsub("DFOP", "A1"),
+    A1 = mkinsub("SFO"), quiet = TRUE)
+  f_uba_mmkin <- mmkin(list("DFOP-SFO" = dfop_sfo_uba),
+    ds_uba, quiet = TRUE, cores = n_cores)
+  f_uba_dfop_sfo_mixed <- mixed(f_uba_mmkin["DFOP-SFO", ])
+
+  f_uba_dfop_sfo_saem <- saem(f_uba_mmkin["DFOP-SFO", ], quiet = TRUE, transformations = "saemix")
+
   plot_biphasic_mmkin <- function() plot(f_uba_dfop_sfo_mixed)
   vdiffr::expect_doppelganger("mixed model fit for mmkin object", plot_biphasic_mmkin)
 
diff --git a/tests/testthat/test_saemix_parent.R b/tests/testthat/test_saemix_parent.R
index 8beceba9..340db6f1 100644
--- a/tests/testthat/test_saemix_parent.R
+++ b/tests/testthat/test_saemix_parent.R
@@ -2,6 +2,7 @@ context("saemix parent models")
 
 test_that("Parent fits using saemix are correctly implemented", {
 
+  skip_on_cran()
   expect_error(saem(fits), "Only row objects")
   # Some fits were done in the setup script
   mmkin_sfo_2 <- update(mmkin_sfo_1, fixed_initials = c(parent = 100))
author	Johannes Ranke <jranke@uni-bremen.de>	2022-03-14 15:41:56 +0100
committer	Johannes Ranke <jranke@uni-bremen.de>	2022-03-14 15:41:56 +0100
commit	3cddc58e6fcdd5341b354dc5b5f784ec8190f62b (patch)
tree	8303617316a207e3e4ed7c1b554abf0ed77e3d39
parent	72ef221369df14a527c2751c002b5cf3db29520d (diff)