From 60270e2849ebd48eaf57b83eb1aa9fbe53281f8b Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Sat, 24 Oct 2020 02:18:59 +0200
Subject: Fix a bug for nlme with parent only, improve examples
---
docs/dev/pkgdown.yml | 2 +-
docs/dev/reference/Rplot001.png | Bin 27839 -> 48355 bytes
docs/dev/reference/Rplot002.png | Bin 64132 -> 62018 bytes
docs/dev/reference/Rplot003.png | Bin 26194 -> 62243 bytes
docs/dev/reference/Rplot004.png | Bin 26783 -> 63952 bytes
docs/dev/reference/nlme.mmkin-1.png | Bin 79142 -> 135400 bytes
docs/dev/reference/nlme.mmkin-2.png | Bin 79539 -> 171122 bytes
docs/dev/reference/nlme.mmkin-3.png | Bin 79703 -> 171684 bytes
docs/dev/reference/nlme.mmkin-4.png | Bin 82209 -> 175495 bytes
docs/dev/reference/nlme.mmkin.html | 101 +++++-------------------------------
10 files changed, 14 insertions(+), 89 deletions(-)
(limited to 'docs/dev')
diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index 61fa6e5d..d6c3d6c9 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: 2020-10-23T23:38Z
+last_built: 2020-10-24T00:14Z
urls:
reference: https://pkgdown.jrwb.de/mkin/reference
article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png
index cfc5bc2b..bf7c274a 100644
Binary files a/docs/dev/reference/Rplot001.png and b/docs/dev/reference/Rplot001.png differ
diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png
index cffa10c1..965d4620 100644
Binary files a/docs/dev/reference/Rplot002.png and b/docs/dev/reference/Rplot002.png differ
diff --git a/docs/dev/reference/Rplot003.png b/docs/dev/reference/Rplot003.png
index 89ba6c49..057b525f 100644
Binary files a/docs/dev/reference/Rplot003.png and b/docs/dev/reference/Rplot003.png differ
diff --git a/docs/dev/reference/Rplot004.png b/docs/dev/reference/Rplot004.png
index 7d30a181..2b5ba960 100644
Binary files a/docs/dev/reference/Rplot004.png and b/docs/dev/reference/Rplot004.png differ
diff --git a/docs/dev/reference/nlme.mmkin-1.png b/docs/dev/reference/nlme.mmkin-1.png
index 564f7e2b..d0a1d7d4 100644
Binary files a/docs/dev/reference/nlme.mmkin-1.png and b/docs/dev/reference/nlme.mmkin-1.png differ
diff --git a/docs/dev/reference/nlme.mmkin-2.png b/docs/dev/reference/nlme.mmkin-2.png
index a9ce4636..b68dc3e0 100644
Binary files a/docs/dev/reference/nlme.mmkin-2.png and b/docs/dev/reference/nlme.mmkin-2.png differ
diff --git a/docs/dev/reference/nlme.mmkin-3.png b/docs/dev/reference/nlme.mmkin-3.png
index 0b7ce0f6..77804b2c 100644
Binary files a/docs/dev/reference/nlme.mmkin-3.png and b/docs/dev/reference/nlme.mmkin-3.png differ
diff --git a/docs/dev/reference/nlme.mmkin-4.png b/docs/dev/reference/nlme.mmkin-4.png
index d7c68dd5..96717087 100644
Binary files a/docs/dev/reference/nlme.mmkin-4.png and b/docs/dev/reference/nlme.mmkin-4.png differ
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>
#> StdDev: 2.488249 0.8447273 1.32965 0.3289311 2.321364
#>
#> Number of Observations: 90
-#> 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>
+#> 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'>#> $distimes
#> DT50 DT90 DT50back DT50_k1 DT50_k2
#> 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'><-</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'><-</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'><-</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'><-</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'><-</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'><-</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'><-</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'>#>
-#> **Iteration 1
-#> LME step: Loglik: -394.1603, nlminb iterations: 3
-#> reStruct parameters:
-#> ds1 ds2 ds3 ds4 ds5
-#> -0.2079793 0.8563830 1.7454105 1.0917354 1.2756825
-#> Beginning PNLS step: .. completed fit_nlme() step.
-#> PNLS step: RSS = 643.8803
-#> fixed effects: 94.17379 -5.473193 -0.6970236 -0.2025091 2.103883
-#> iterations: 100
-#> Convergence crit. (must all become <= tolerance = 0.0001):
-#> fixed reStruct
-#> 0.7960134 0.1447728
-#>
-#> **Iteration 2
-#> LME step: Loglik: -396.3824, nlminb iterations: 7
-#> reStruct parameters:
-#> ds1 ds2 ds3 ds4 ds5
-#> -1.712404e-01 -2.432655e-05 1.842120e+00 1.073975e+00 1.322925e+00
-#> Beginning PNLS step: .. completed fit_nlme() step.
-#> PNLS step: RSS = 643.8035
-#> fixed effects: 94.17385 -5.473487 -0.6970404 -0.2025137 2.103871
-#> iterations: 100
-#> Convergence crit. (must all become <= tolerance = 0.0001):
-#> fixed reStruct
-#> 5.382757e-05 1.236667e-03
-#>
-#> **Iteration 3
-#> LME step: Loglik: -396.3825, nlminb iterations: 7
-#> reStruct parameters:
-#> ds1 ds2 ds3 ds4 ds5
-#> -0.1712499044 -0.0001499831 1.8420971364 1.0739799123 1.3229167796
-#> Beginning PNLS step: .. completed fit_nlme() step.
-#> PNLS step: RSS = 643.7948
-#> fixed effects: 94.17386 -5.473521 -0.6970422 -0.2025144 2.10387
-#> iterations: 100
-#> Convergence crit. (must all become <= tolerance = 0.0001):
-#> fixed reStruct
-#> 6.072817e-06 1.400857e-04
-#>
-#> **Iteration 4
-#> LME step: Loglik: -396.3825, nlminb iterations: 7
-#> reStruct parameters:
-#> ds1 ds2 ds3 ds4 ds5
-#> -0.1712529502 -0.0001641277 1.8420957542 1.0739797181 1.3229173076
-#> Beginning PNLS step: .. completed fit_nlme() step.
-#> PNLS step: RSS = 643.7936
-#> fixed effects: 94.17386 -5.473526 -0.6970426 -0.2025146 2.103869
-#> iterations: 100
-#> Convergence crit. (must all become <= tolerance = 0.0001):
-#> fixed reStruct
-#> 1.027451e-06 2.275704e-05 </div><div class='input'> <span class='va'>f_nlme_dfop_sfo</span> <span class='op'><-</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'><-</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'>#>
#> **Iteration 1
@@ -415,17 +358,10 @@ with additional elements</p>
#> iterations: 120
#> Convergence crit. (must all become <= tolerance = 0.0005):
#> fixed reStruct
-#> 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'>#> Model df AIC BIC logLik Test L.Ratio p-value
-#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9273
-#> f_nlme_fomc_sfo 2 11 818.5149 853.0087 -398.2575 1 vs 2 21.33975 <.0001
-#> f_nlme_sfo_sfo 3 9 1085.1821 1113.4043 -533.5910 2 vs 3 270.66716 <.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>
+#> 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'>#> Model df AIC BIC logLik Test L.Ratio p-value
#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9273
#> f_nlme_sfo_sfo 2 9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3274 <.0001</div><div class='input'>
@@ -449,19 +385,8 @@ with additional elements</p>
#> A1 162.30536 539.1667 NA NA NA
#> </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'>></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 <- 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 <- nlme(f_2_tc["SFO-SFO", ], control = list(maxIter = 100))</span>
- <span class='co'>#f_nlme_dfop_sfo_tc <- nlme(f_2_tc["DFOP-SFO", ])</span>
- <span class='co'>#f_nlme_dfop_sfo_tc <- 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'><-</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'><-</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>
--
cgit v1.2.1