Fix a bug for nlme with parent only, improve examples

9 files changed, 13 insertions, 88 deletions

diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png
index cfc5bc2b..bf7c274a 100644
--- a/docs/dev/reference/Rplot001.png
+++ b/docs/dev/reference/Rplot001.png
diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png
index cffa10c1..965d4620 100644
--- a/docs/dev/reference/Rplot002.png
+++ b/docs/dev/reference/Rplot002.png
diff --git a/docs/dev/reference/Rplot003.png b/docs/dev/reference/Rplot003.png
index 89ba6c49..057b525f 100644
--- a/docs/dev/reference/Rplot003.png
+++ b/docs/dev/reference/Rplot003.png
diff --git a/docs/dev/reference/Rplot004.png b/docs/dev/reference/Rplot004.png
index 7d30a181..2b5ba960 100644
--- a/docs/dev/reference/Rplot004.png
+++ b/docs/dev/reference/Rplot004.png
diff --git a/docs/dev/reference/nlme.mmkin-1.png b/docs/dev/reference/nlme.mmkin-1.png
index 564f7e2b..d0a1d7d4 100644
--- a/docs/dev/reference/nlme.mmkin-1.png
+++ b/docs/dev/reference/nlme.mmkin-1.png
diff --git a/docs/dev/reference/nlme.mmkin-2.png b/docs/dev/reference/nlme.mmkin-2.png
index a9ce4636..b68dc3e0 100644
--- a/docs/dev/reference/nlme.mmkin-2.png
+++ b/docs/dev/reference/nlme.mmkin-2.png
diff --git a/docs/dev/reference/nlme.mmkin-3.png b/docs/dev/reference/nlme.mmkin-3.png
index 0b7ce0f6..77804b2c 100644
--- a/docs/dev/reference/nlme.mmkin-3.png
+++ b/docs/dev/reference/nlme.mmkin-3.png
diff --git a/docs/dev/reference/nlme.mmkin-4.png b/docs/dev/reference/nlme.mmkin-4.png
index d7c68dd5..96717087 100644
--- a/docs/dev/reference/nlme.mmkin-4.png
+++ b/docs/dev/reference/nlme.mmkin-4.png
diff --git a/docs/dev/reference/nlme.mmkin.html b/docs/dev/reference/nlme.mmkin.html
index 6e83b700..3c84abe2 100644
--- a/docs/dev/reference/nlme.mmkin.html
+++ b/docs/dev/reference/nlme.mmkin.html
@@ -286,7 +286,8 @@ with additional elements</p>
 #&gt; StdDev: 2.488249 0.8447273 1.32965 0.3289311 2.321364
 #&gt; 
 #&gt; Number of Observations: 90
-#&gt; Number of Groups: 5 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span>
+#&gt; Number of Groups: 5 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span>
+</div><div class='img'><img src='nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; $distimes
 #&gt;            DT50     DT90 DT50back  DT50_k1  DT50_k2
 #&gt; parent 10.79857 100.7937 30.34193 4.193938 43.85443
@@ -313,82 +314,24 @@ with additional elements</p>
     A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"min"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
   <span class='va'>m_sfo_sfo_ff</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
     A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, use_of_ff <span class='op'>=</span> <span class='st'>"max"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-  <span class='va'>m_fomc_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
-    A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
   <span class='va'>m_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
     A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 
   <span class='va'>f_2</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/list.html'>list</a></span><span class='op'>(</span><span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>m_sfo_sfo</span>,
    <span class='st'>"SFO-SFO-ff"</span> <span class='op'>=</span> <span class='va'>m_sfo_sfo_ff</span>,
-   <span class='st'>"FOMC-SFO"</span> <span class='op'>=</span> <span class='va'>m_fomc_sfo</span>,
    <span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>m_dfop_sfo</span><span class='op'>)</span>,
     <span class='va'>ds_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>]</span><span class='op'>)</span> <span class='co'># Separate fits for datasets 3 and 4</span>
-</div><div class='img'><img src='nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'>
+
   <span class='va'>f_nlme_sfo_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span>
-  <span class='co'># plot(f_nlme_sfo_sfo) # not feasible with pkgdown figures</span>
-  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>)</span> <span class='co'># Global mixed model: Fits for datasets 3 and 4</span>
+  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span>
 </div><div class='img'><img src='nlme.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'>
   <span class='co'># With formation fractions</span>
   <span class='va'>f_nlme_sfo_sfo_ff</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"SFO-SFO-ff"</span>, <span class='op'>]</span><span class='op'>)</span>
-  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo_ff</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>)</span> <span class='co'># chi2 different due to different df attribution</span>
+  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo_ff</span><span class='op'>)</span>
 </div><div class='img'><img src='nlme.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'>
-  <span class='co'># For more parameters, we need to increase pnlsMaxIter and the tolerance</span>
+  <span class='co'># For the following fit we need to increase pnlsMaxIter and the tolerance</span>
   <span class='co'># to get convergence</span>
-  <span class='va'>f_nlme_fomc_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"FOMC-SFO"</span>, <span class='op'>]</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>pnlsMaxIter <span class='op'>=</span> <span class='fl'>100</span>, tolerance <span class='op'>=</span> <span class='fl'>1e-4</span><span class='op'>)</span>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; 
-#&gt; **Iteration 1
-#&gt; LME step: Loglik: -394.1603, nlminb iterations: 3
-#&gt; reStruct  parameters:
-#&gt;        ds1        ds2        ds3        ds4        ds5 
-#&gt; -0.2079793  0.8563830  1.7454105  1.0917354  1.2756825 
-#&gt;  Beginning PNLS step: ..  completed fit_nlme() step.
-#&gt; PNLS step: RSS =  643.8803 
-#&gt;  fixed effects: 94.17379  -5.473193  -0.6970236  -0.2025091  2.103883  
-#&gt;  iterations: 100 
-#&gt; Convergence crit. (must all become &lt;= tolerance = 0.0001):
-#&gt;     fixed  reStruct 
-#&gt; 0.7960134 0.1447728 
-#&gt; 
-#&gt; **Iteration 2
-#&gt; LME step: Loglik: -396.3824, nlminb iterations: 7
-#&gt; reStruct  parameters:
-#&gt;           ds1           ds2           ds3           ds4           ds5 
-#&gt; -1.712404e-01 -2.432655e-05  1.842120e+00  1.073975e+00  1.322925e+00 
-#&gt;  Beginning PNLS step: ..  completed fit_nlme() step.
-#&gt; PNLS step: RSS =  643.8035 
-#&gt;  fixed effects: 94.17385  -5.473487  -0.6970404  -0.2025137  2.103871  
-#&gt;  iterations: 100 
-#&gt; Convergence crit. (must all become &lt;= tolerance = 0.0001):
-#&gt;        fixed     reStruct 
-#&gt; 5.382757e-05 1.236667e-03 
-#&gt; 
-#&gt; **Iteration 3
-#&gt; LME step: Loglik: -396.3825, nlminb iterations: 7
-#&gt; reStruct  parameters:
-#&gt;           ds1           ds2           ds3           ds4           ds5 
-#&gt; -0.1712499044 -0.0001499831  1.8420971364  1.0739799123  1.3229167796 
-#&gt;  Beginning PNLS step: ..  completed fit_nlme() step.
-#&gt; PNLS step: RSS =  643.7948 
-#&gt;  fixed effects: 94.17386  -5.473521  -0.6970422  -0.2025144  2.10387  
-#&gt;  iterations: 100 
-#&gt; Convergence crit. (must all become &lt;= tolerance = 0.0001):
-#&gt;        fixed     reStruct 
-#&gt; 6.072817e-06 1.400857e-04 
-#&gt; 
-#&gt; **Iteration 4
-#&gt; LME step: Loglik: -396.3825, nlminb iterations: 7
-#&gt; reStruct  parameters:
-#&gt;           ds1           ds2           ds3           ds4           ds5 
-#&gt; -0.1712529502 -0.0001641277  1.8420957542  1.0739797181  1.3229173076 
-#&gt;  Beginning PNLS step: ..  completed fit_nlme() step.
-#&gt; PNLS step: RSS =  643.7936 
-#&gt;  fixed effects: 94.17386  -5.473526  -0.6970426  -0.2025146  2.103869  
-#&gt;  iterations: 100 
-#&gt; Convergence crit. (must all become &lt;= tolerance = 0.0001):
-#&gt;        fixed     reStruct 
-#&gt; 1.027451e-06 2.275704e-05 </div><div class='input'>  <span class='va'>f_nlme_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span>,
+  <span class='va'>f_nlme_dfop_sfo</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</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>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>5e-4</span><span class='op'>)</span>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
 </div><div class='output co'>#&gt; 
 #&gt; **Iteration 1
@@ -415,17 +358,10 @@ with additional elements</p>
 #&gt;  iterations: 120 
 #&gt; Convergence crit. (must all become &lt;= tolerance = 0.0005):
 #&gt;        fixed     reStruct 
-#&gt; 4.789774e-07 2.200661e-05 </div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"FOMC-SFO"</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>]</span><span class='op'>)</span>
-</div><div class='img'><img src='nlme.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_fomc_sfo</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>)</span>
-</div><div class='img'><img src='nlme.mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'>
-  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_2</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>]</span><span class='op'>)</span>
-</div><div class='img'><img src='nlme.mmkin-6.png' alt='' width='700' height='433' /></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>)</span>
-</div><div class='img'><img src='nlme.mmkin-7.png' alt='' width='700' height='433' /></div><div class='input'>
-  <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='va'>f_nlme_fomc_sfo</span>, <span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span>
-</div><div class='output co'>#&gt;                 Model df       AIC       BIC    logLik   Test   L.Ratio p-value
-#&gt; f_nlme_dfop_sfo     1 13  843.8547  884.6201 -408.9273                         
-#&gt; f_nlme_fomc_sfo     2 11  818.5149  853.0087 -398.2575 1 vs 2  21.33975  &lt;.0001
-#&gt; f_nlme_sfo_sfo      3  9 1085.1821 1113.4043 -533.5910 2 vs 3 270.66716  &lt;.0001</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span> <span class='co'># if we ignore FOMC</span>
+#&gt; 4.789774e-07 2.200661e-05 </div><div class='input'>
+  <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span><span class='op'>)</span>
+</div><div class='img'><img src='nlme.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'>
+  <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span>
 </div><div class='output co'>#&gt;                 Model df       AIC       BIC    logLik   Test  L.Ratio p-value
 #&gt; f_nlme_dfop_sfo     1 13  843.8547  884.6201 -408.9273                        
 #&gt; f_nlme_sfo_sfo      2  9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3274  &lt;.0001</div><div class='input'>
@@ -449,19 +385,8 @@ with additional elements</p>
 #&gt; A1     162.30536 539.1667       NA       NA       NA
 #&gt; </div><div class='input'>
   <span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='fu'>findFunction</span><span class='op'>(</span><span class='st'>"varConstProp"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>&gt;</span> <span class='fl'>0</span><span class='op'>)</span> <span class='op'>{</span> <span class='co'># tc error model for nlme available</span>
-    <span class='co'># Attempts to fit metabolite kinetics with the tc error model</span>
-    <span class='co'>#f_2_tc &lt;- mmkin(list("SFO-SFO" = m_sfo_sfo,</span>
-    <span class='co'>#  "SFO-SFO-ff" = m_sfo_sfo_ff,</span>
-    <span class='co'>#  "FOMC-SFO" = m_fomc_sfo,</span>
-    <span class='co'>#  "DFOP-SFO" = m_dfop_sfo),</span>
-    <span class='co'>#   ds_2, quiet = TRUE,</span>
-    <span class='co'>#   error_model = "tc")</span>
-    <span class='co'>#f_nlme_sfo_sfo_tc &lt;- nlme(f_2_tc["SFO-SFO", ], control = list(maxIter = 100))</span>
-    <span class='co'>#f_nlme_dfop_sfo_tc &lt;- nlme(f_2_tc["DFOP-SFO", ])</span>
-    <span class='co'>#f_nlme_dfop_sfo_tc &lt;- update(f_nlme_dfop_sfo, weights = varConstProp(),</span>
-    <span class='co'>#  control = list(sigma = 1, msMaxIter = 100, pnlsMaxIter = 15))</span>
-    <span class='co'># Fitting metabolite kinetics with nlme.mmkin and the two-component</span>
-    <span class='co'># error model currently does not work, at least not with these data.</span>
+    <span class='co'># Attempts to fit metabolite kinetics with the tc error model are possible,</span>
+    <span class='co'># but need tweeking of control values and sometimes do not converge</span>
 
     <span class='va'>f_tc</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'>"DFOP"</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span>
     <span class='va'>f_nlme_sfo_tc</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f_tc</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span>