Add printout of d24 model and update docs

12 files changed, 49 insertions, 30 deletions

diff --git a/R/D24_2014.R b/R/D24_2014.R
index bca56dc2..654e1106 100644
--- a/R/D24_2014.R
+++ b/R/D24_2014.R
@@ -27,4 +27,5 @@
 #' m_D24 = mkinmod(D24 = mkinsub("SFO", to = "DCP"),
 #'   DCP = mkinsub("SFO", to = "DCA"),
 #'   DCA = mkinsub("SFO"))
+#' print(D24_2014)
 "D24_2014"
diff --git a/docs/dev/404.html b/docs/dev/404.html
index 8ca69469..bea38406 100644
--- a/docs/dev/404.html
+++ b/docs/dev/404.html
@@ -120,7 +120,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/jranke/mkin/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html
index 81d49aa3..6daa6960 100644
--- a/docs/dev/articles/index.html
+++ b/docs/dev/articles/index.html
@@ -120,7 +120,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/jranke/mkin/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/authors.html b/docs/dev/authors.html
index 681b964d..d592b39f 100644
--- a/docs/dev/authors.html
+++ b/docs/dev/authors.html
@@ -120,7 +120,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/jranke/mkin/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/index.html b/docs/dev/index.html
index b1b64e6d..a4399963 100644
--- a/docs/dev/index.html
+++ b/docs/dev/index.html
@@ -87,7 +87,7 @@
 <ul class="nav navbar-nav navbar-right">
 <li>
   <a href="https://github.com/jranke/mkin/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html
index 7059189d..e21de4c2 100644
--- a/docs/dev/news/index.html
+++ b/docs/dev/news/index.html
@@ -120,7 +120,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/jranke/mkin/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index db10e692..a106449f 100644
--- a/docs/dev/pkgdown.yml
+++ b/docs/dev/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
   web_only/NAFTA_examples: NAFTA_examples.html
   web_only/benchmarks: benchmarks.html
   web_only/compiled_models: compiled_models.html
-last_built: 2020-12-11T14:39Z
+last_built: 2020-12-16T17:28Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/D24_2014.html b/docs/dev/reference/D24_2014.html
index e4a3216d..5ebf664e 100644
--- a/docs/dev/reference/D24_2014.html
+++ b/docs/dev/reference/D24_2014.html
@@ -220,7 +220,25 @@ specific pieces of information in the comments.</p>
 #&gt; 13  365  6.3</div><div class='input'><span class='va'>m_D24</span> <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>D24 <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"DCP"</span><span class='op'>)</span>,
   DCP <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, to <span class='op'>=</span> <span class='st'>"DCA"</span><span class='op'>)</span>,
   DCA <span class='op'>=</span> <span class='fu'><a href='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div></pre>
+</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>D24_2014</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; &lt;mkindsg&gt; holding 5 mkinds objects
+#&gt; Title $title:  Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 
+#&gt; Occurrene of observed compounds $observed_n:
+#&gt; D24 DCP DCA 
+#&gt;   5   4   4 
+#&gt; Meta information $meta:
+#&gt;                       study usda_soil_type study_moisture_ref_type rel_moisture
+#&gt; 1                Cohen 1991      Silt loam                    &lt;NA&gt;           NA
+#&gt; 2 Liu and Adelfinskaya 2011      Silt loam                     pF1          0.5
+#&gt; 3 Liu and Adelfinskaya 2011           Loam                     pF1          0.5
+#&gt; 4 Liu and Adelfinskaya 2011           Loam                     pF1          0.5
+#&gt; 5 Liu and Adelfinskaya 2011     Loamy sand                     pF1          0.5
+#&gt;   temperature
+#&gt; 1          25
+#&gt; 2          20
+#&gt; 3          20
+#&gt; 4          20
+#&gt; 5          20</div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <nav id="toc" data-toggle="toc" class="sticky-top">
diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html
index 5c964cf9..d2040184 100644
--- a/docs/dev/reference/index.html
+++ b/docs/dev/reference/index.html
@@ -120,7 +120,7 @@
       <ul class="nav navbar-nav navbar-right">
         <li>
   <a href="https://github.com/jranke/mkin/">
-    <span class="fab fa fab fa-github fa-lg"></span>
+    <span class="fab fa-github fa-lg"></span>
      
   </a>
 </li>
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html
index 73699e19..67468f89 100644
--- a/docs/dev/reference/saem.html
+++ b/docs/dev/reference/saem.html
@@ -160,7 +160,6 @@ Expectation Maximisation algorithm (SAEM).</p>
   solution_type <span class='op'>=</span> <span class='st'>"auto"</span>,
   control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>displayProgress <span class='op'>=</span> <span class='cn'>FALSE</span>, print <span class='op'>=</span> <span class='cn'>FALSE</span>, save <span class='op'>=</span> <span class='cn'>FALSE</span>, save.graphs <span class='op'>=</span>
     <span class='cn'>FALSE</span><span class='op'>)</span>,
-  cores <span class='op'>=</span> <span class='fl'>1</span>,
   verbose <span class='op'>=</span> <span class='cn'>FALSE</span>,
   suppressPlot <span class='op'>=</span> <span class='cn'>TRUE</span>,
   quiet <span class='op'>=</span> <span class='cn'>FALSE</span>,
@@ -174,7 +173,6 @@ Expectation Maximisation algorithm (SAEM).</p>
   <span class='va'>object</span>,
   solution_type <span class='op'>=</span> <span class='st'>"auto"</span>,
   transformations <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"mkin"</span>, <span class='st'>"saemix"</span><span class='op'>)</span>,
-  cores <span class='op'>=</span> <span class='fl'>1</span>,
   verbose <span class='op'>=</span> <span class='cn'>FALSE</span>,
   <span class='va'>...</span>
 <span class='op'>)</span>
@@ -262,27 +260,27 @@ using <a href='mmkin.html'>mmkin</a>.</p>
   state.ini <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, fixed_initials <span class='op'>=</span> <span class='st'>"parent"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 <span class='va'>f_saem_p0_fixed</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_p0_fixed</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Fri Dec 11 15:37:47 2020"
+#&gt; [1] "Wed Dec 16 18:27:30 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Fri Dec 11 15:37:49 2020"</div><div class='input'>
+#&gt; [1] "Wed Dec 16 18:27:31 2020"</div><div class='input'>
 <span class='va'>f_mmkin_parent</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'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</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><span class='op'>)</span>
 <span class='va'>f_saem_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Fri Dec 11 15:37:51 2020"
+#&gt; [1] "Wed Dec 16 18:27:33 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Fri Dec 11 15:37:52 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Wed Dec 16 18:27:35 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Fri Dec 11 15:37:52 2020"
+#&gt; [1] "Wed Dec 16 18:27:35 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Fri Dec 11 15:37:55 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Wed Dec 16 18:27:37 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Fri Dec 11 15:37:55 2020"
+#&gt; [1] "Wed Dec 16 18:27:37 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Fri Dec 11 15:37:58 2020"</div><div class='input'>
+#&gt; [1] "Wed Dec 16 18:27:40 2020"</div><div class='input'>
 <span class='co'># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span>
 <span class='co'># functions from saemix</span>
 <span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'>saemix</span><span class='op'>)</span>
@@ -328,10 +326,10 @@ using <a href='mmkin.html'>mmkin</a>.</p>
 <span class='va'>f_mmkin_parent_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_mmkin_parent</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
 <span class='va'>f_saem_fomc_tc</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_tc</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Fri Dec 11 15:38:01 2020"
+#&gt; [1] "Wed Dec 16 18:27:43 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Fri Dec 11 15:38:06 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
+#&gt; [1] "Wed Dec 16 18:27:48 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Likelihoods computed by importance sampling </div><div class='output co'>#&gt;        AIC      BIC
 #&gt; 1 467.7096 464.9757
 #&gt; 2 469.5208 466.3963</div><div class='input'>
@@ -352,15 +350,15 @@ using <a href='mmkin.html'>mmkin</a>.</p>
 <span class='co'># four minutes</span>
 <span class='va'>f_saem_sfo_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Fri Dec 11 15:38:09 2020"
+#&gt; [1] "Wed Dec 16 18:27:50 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Fri Dec 11 15:38:14 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
+#&gt; [1] "Wed Dec 16 18:27:55 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Running main SAEM algorithm
-#&gt; [1] "Fri Dec 11 15:38:15 2020"
+#&gt; [1] "Wed Dec 16 18:27:56 2020"
 #&gt; ....
 #&gt;     Minimisation finished
-#&gt; [1] "Fri Dec 11 15:38:24 2020"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span>
+#&gt; [1] "Wed Dec 16 18:28:05 2020"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span>
 <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; Kinetic nonlinear mixed-effects model fit by SAEM
 #&gt; Structural model:
@@ -375,6 +373,8 @@ using <a href='mmkin.html'>mmkin</a>.</p>
 #&gt; 170 observations of 2 variable(s) grouped in 5 datasets
 #&gt; 
 #&gt; Likelihood computed by importance sampling
+#&gt;                           
+#&gt; LL by is "-407.78 (df=13)"
 #&gt;     AIC   BIC logLik
 #&gt;   841.6 836.5 -407.8
 #&gt; 
@@ -400,11 +400,12 @@ using <a href='mmkin.html'>mmkin</a>.</p>
 #&gt; SD.log_k2            1.90634  0.70934  3.1033
 #&gt; SD.g_qlogis          0.44771 -0.86417  1.7596</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span><span class='op'>)</span>
 </div><div class='img'><img src='saem-5.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; saemix version used for fitting:      3.1.9000 
+</div><div class='output co'>#&gt;                           
+#&gt; LL by is "-407.78 (df=13)"</div><div class='output co'>#&gt; saemix version used for fitting:      3.1.9000 
 #&gt; mkin version used for pre-fitting:  0.9.50.4 
 #&gt; R version used for fitting:         4.0.3 
-#&gt; Date of fit:     Fri Dec 11 15:38:25 2020 
-#&gt; Date of summary: Fri Dec 11 15:38:25 2020 
+#&gt; Date of fit:     Wed Dec 16 18:28:06 2020 
+#&gt; Date of summary: Wed Dec 16 18:28:06 2020 
 #&gt; 
 #&gt; Equations:
 #&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -419,7 +420,7 @@ using <a href='mmkin.html'>mmkin</a>.</p>
 #&gt; 
 #&gt; Model predictions using solution type analytical 
 #&gt; 
-#&gt; Fitted in 10.096 s using 300, 100 iterations
+#&gt; Fitted in 9.889 s using 300, 100 iterations
 #&gt; 
 #&gt; Variance model: Constant variance 
 #&gt; 
diff --git a/man/D24_2014.Rd b/man/D24_2014.Rd
index d0ab516a..90fde27b 100644
--- a/man/D24_2014.Rd
+++ b/man/D24_2014.Rd
@@ -40,5 +40,6 @@ print(D24_2014$ds[[1]], data = TRUE)
 m_D24 = mkinmod(D24 = mkinsub("SFO", to = "DCP"),
   DCP = mkinsub("SFO", to = "DCA"),
   DCA = mkinsub("SFO"))
+print(D24_2014)
 }
 \keyword{datasets}
diff --git a/man/saem.Rd b/man/saem.Rd
index 1fdfb2c4..dba948bb 100644
--- a/man/saem.Rd
+++ b/man/saem.Rd
@@ -16,7 +16,6 @@ saem(object, ...)
   solution_type = "auto",
   control = list(displayProgress = FALSE, print = FALSE, save = FALSE, save.graphs =
     FALSE),
-  cores = 1,
   verbose = FALSE,
   suppressPlot = TRUE,
   quiet = FALSE,
@@ -29,7 +28,6 @@ saemix_model(
   object,
   solution_type = "auto",
   transformations = c("mkin", "saemix"),
-  cores = 1,
   verbose = FALSE,
   ...
 )