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authorJohannes Ranke <jranke@uni-bremen.de>2021-10-05 17:33:52 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2021-10-05 17:33:52 +0200
commitff83d8b2ba623513d92ac90fac4a1b0ec98c2cb5 (patch)
tree7811a1e083951d84bd54bfce9bb62af640da329e /docs/dev/reference/saem.html
parent121e38654eea03c91aa117da58fc342feff01756 (diff)
Update docs
Diffstat (limited to 'docs/dev/reference/saem.html')
-rw-r--r--docs/dev/reference/saem.html388
1 files changed, 16 insertions, 372 deletions
diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html
index 8d986126..83a62359 100644
--- a/docs/dev/reference/saem.html
+++ b/docs/dev/reference/saem.html
@@ -287,28 +287,12 @@ using <a href='mmkin.html'>mmkin</a>.</p>
<span class='va'>f_mmkin_parent_p0_fixed</span> <span class='op'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='va'>ds</span>,
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] "Thu Sep 16 14:34:42 2021"
-#&gt; ....
-#&gt; Minimisation finished
-#&gt; [1] "Thu Sep 16 14:34:43 2021"</div><div class='input'>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: argument is not a function</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='error'>Error in rxModelVars_(obj): Not compatible with STRSXP: [type=NULL].</span></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] "Thu Sep 16 14:34:45 2021"
-#&gt; ....
-#&gt; Minimisation finished
-#&gt; [1] "Thu Sep 16 14:34:47 2021"</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] "Thu Sep 16 14:34:47 2021"
-#&gt; ....
-#&gt; Minimisation finished
-#&gt; [1] "Thu Sep 16 14:34:49 2021"</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] "Thu Sep 16 14:34:49 2021"
-#&gt; ....
-#&gt; Minimisation finished
-#&gt; [1] "Thu Sep 16 14:34:52 2021"</div><div class='input'>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: argument is not a function</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='error'>Error in rxModelVars_(obj): Not compatible with STRSXP: [type=NULL].</span></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; <span class='warning'>Warning: argument is not a function</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='error'>Error in rxModelVars_(obj): Not compatible with STRSXP: [type=NULL].</span></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; <span class='warning'>Warning: argument is not a function</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='error'>Error in rxModelVars_(obj): Not compatible with STRSXP: [type=NULL].</span></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>
@@ -317,53 +301,15 @@ using <a href='mmkin.html'>mmkin</a>.</p>
#&gt; <span class='message'>Attaching package: ‘saemix’</span></div><div class='output co'>#&gt; <span class='message'>The following object is masked from ‘package:RxODE’:</span>
#&gt; <span class='message'></span>
#&gt; <span class='message'> phi</span></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='va'>f_saem_sfo</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_dfop</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='message'>Likelihoods calculated by importance sampling</span></div><div class='output co'>#&gt; AIC BIC
-#&gt; 1 624.2484 622.2956
-#&gt; 2 467.7096 464.9757
-#&gt; 3 495.4373 491.9222</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"convergence"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; Plotting convergence plots</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_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"individual.fit"</span><span class='op'>)</span>
-</div><div class='img'><img src='saem-1.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; Plotting individual fits</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"npde"</span><span class='op'>)</span>
-</div><div class='img'><img src='saem-2.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; Simulating data using nsim = 1000 simulated datasets
-#&gt; Computing WRES and npde .
-#&gt; Plotting npde</div><div class='img'><img src='saem-3.png' alt='' width='700' height='433' /></div><div class='output co'>#&gt; ---------------------------------------------
-#&gt; Distribution of npde:
-#&gt; mean= -0.01528 (SE= 0.098 )
-#&gt; variance= 0.862 (SE= 0.13 )
-#&gt; skewness= 0.5016
-#&gt; kurtosis= 1.18
-#&gt; ---------------------------------------------
-#&gt;
-#&gt; Statistical tests
-#&gt; Wilcoxon signed rank test : 0.679
-#&gt; Fisher variance test : 0.36
-#&gt; SW test of normality : 0.0855 .
-#&gt; Global adjusted p-value : 0.257
-#&gt; ---
-#&gt; Signif. codes: '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1
-#&gt; ---------------------------------------------</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_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"vpc"</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; Performing simulations under the model.
-#&gt; Plotting VPC
-#&gt; Method used for VPC: binning by quantiles on X , dividing into the following intervals
-#&gt; Interval Centered.On
-#&gt; 1 (-1,3] 1.3
-#&gt; 2 (3,8] 7.4
-#&gt; 3 (8,14] 13.2
-#&gt; 4 (14,21] 20.5
-#&gt; 5 (21,37.7] 29.5
-#&gt; 6 (37.7,60] 50.4
-#&gt; 7 (60,90] 76.6
-#&gt; 8 (90,120] 109.0
-#&gt; 9 (120,180] 156.0 </div><div class='img'><img src='saem-4.png' alt='' width='700' height='433' /></div><div class='input'>
+</div><div class='output co'>#&gt; <span class='error'>Error in compare.saemix(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so): object 'f_saem_sfo' not found</span></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_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"convergence"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='error'>Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'plot': object 'f_saem_fomc' not found</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"individual.fit"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='error'>Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'plot': object 'f_saem_fomc' not found</span></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_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"npde"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='error'>Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'plot': object 'f_saem_fomc' not found</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/plot-SaemixObject-method.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, plot.type <span class='op'>=</span> <span class='st'>"vpc"</span><span class='op'>)</span>
+</div><div class='output co'>#&gt; <span class='error'>Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'plot': object 'f_saem_fomc' not found</span></div><div class='input'>
<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] "Thu Sep 16 14:34:55 2021"
-#&gt; ....
-#&gt; Minimisation finished
-#&gt; [1] "Thu Sep 16 14:35:00 2021"</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='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>
-</div><div class='output co'>#&gt; <span class='message'>Likelihoods calculated by importance sampling</span></div><div class='output co'>#&gt; AIC BIC
-#&gt; 1 467.7096 464.9757
-#&gt; 2 469.6831 466.5586</div><div class='input'>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: argument is not a function</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='error'>Error in rxModelVars_(obj): Not compatible with STRSXP: [type=NULL].</span></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='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>
+</div><div class='output co'>#&gt; <span class='error'>Error in compare.saemix(f_saem_fomc$so, f_saem_fomc_tc$so): object 'f_saem_fomc' not found</span></div><div class='input'>
<span class='va'>sfo_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='mkinmod.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='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><div class='input'><span class='va'>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='mkinmod.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='st'>"A1"</span><span class='op'>)</span>,
@@ -380,314 +326,12 @@ using <a href='mmkin.html'>mmkin</a>.</p>
<span class='co'># When using the analytical solutions written for mkin this took around</span>
<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] "Thu Sep 16 14:35:03 2021"
-#&gt; ....
-#&gt; Minimisation finished
-#&gt; [1] "Thu Sep 16 14:35:08 2021"</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] "Thu Sep 16 14:35:08 2021"
-#&gt; ....
-#&gt; Minimisation finished
-#&gt; [1] "Thu Sep 16 14:35:17 2021"</div><div class='input'><span class='co'># We can use print, plot and summary methods to check the results</span>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: argument is not a function</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='error'>Error in rxModelVars_(obj): Not compatible with STRSXP: [type=NULL].</span></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; <span class='warning'>Warning: argument is not a function</span></div><div class='output co'>#&gt; <span class='message'> </span></div><div class='output co'>#&gt; <span class='error'>Error in rxModelVars_(obj): Not compatible with STRSXP: [type=NULL].</span></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:
-#&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
-#&gt; time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))
-#&gt; * parent
-#&gt; d_A1/dt = + f_parent_to_A1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)
-#&gt; * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *
-#&gt; exp(-k2 * time))) * parent - k_A1 * A1
-#&gt;
-#&gt; Data:
-#&gt; 170 observations of 2 variable(s) grouped in 5 datasets
-#&gt;
-#&gt; Likelihood computed by importance sampling
-#&gt; AIC BIC logLik
-#&gt; 839.6 834.6 -406.8
-#&gt;
-#&gt; Fitted parameters:
-#&gt; estimate lower upper
-#&gt; parent_0 93.80521 91.22487 96.3856
-#&gt; log_k_A1 -6.06244 -8.26517 -3.8597
-#&gt; f_parent_qlogis -0.97319 -1.37024 -0.5761
-#&gt; log_k1 -2.55394 -4.00815 -1.0997
-#&gt; log_k2 -3.47160 -5.18763 -1.7556
-#&gt; g_qlogis -0.09324 -1.42737 1.2409
-#&gt; Var.parent_0 7.42157 -3.25683 18.1000
-#&gt; Var.log_k_A1 4.22850 -2.46339 10.9204
-#&gt; Var.f_parent_qlogis 0.19803 -0.05541 0.4515
-#&gt; Var.log_k1 2.28644 -0.86079 5.4337
-#&gt; Var.log_k2 3.35626 -1.14639 7.8589
-#&gt; Var.g_qlogis 0.20084 -1.32516 1.7268
-#&gt; a.1 1.88399 1.66794 2.1000
-#&gt; SD.parent_0 2.72425 0.76438 4.6841
-#&gt; SD.log_k_A1 2.05633 0.42919 3.6835
-#&gt; SD.f_parent_qlogis 0.44501 0.16025 0.7298
-#&gt; SD.log_k1 1.51210 0.47142 2.5528
-#&gt; SD.log_k2 1.83201 0.60313 3.0609
-#&gt; SD.g_qlogis 0.44816 -1.25437 2.1507</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
-#&gt; mkin version used for pre-fitting: 1.1.0
-#&gt; R version used for fitting: 4.1.1
-#&gt; Date of fit: Thu Sep 16 14:35:18 2021
-#&gt; Date of summary: Thu Sep 16 14:35:18 2021
-#&gt;
-#&gt; Equations:
-#&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
-#&gt; time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))
-#&gt; * parent
-#&gt; d_A1/dt = + f_parent_to_A1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g)
-#&gt; * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) *
-#&gt; exp(-k2 * time))) * parent - k_A1 * A1
-#&gt;
-#&gt; Data:
-#&gt; 170 observations of 2 variable(s) grouped in 5 datasets
-#&gt;
-#&gt; Model predictions using solution type analytical
-#&gt;
-#&gt; Fitted in 9.349 s using 300, 100 iterations
-#&gt;
-#&gt; Variance model: Constant variance
-#&gt;
-#&gt; Mean of starting values for individual parameters:
-#&gt; parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2
-#&gt; 93.8102 -5.3734 -0.9711 -1.8799 -4.2708
-#&gt; g_qlogis
-#&gt; 0.1356
-#&gt;
-#&gt; Fixed degradation parameter values:
-#&gt; None
-#&gt;
-#&gt; Results:
-#&gt;
-#&gt; Likelihood computed by importance sampling
-#&gt; AIC BIC logLik
-#&gt; 839.6 834.6 -406.8
-#&gt;
-#&gt; Optimised parameters:
-#&gt; est. lower upper
-#&gt; parent_0 93.80521 91.225 96.3856
-#&gt; log_k_A1 -6.06244 -8.265 -3.8597
-#&gt; f_parent_qlogis -0.97319 -1.370 -0.5761
-#&gt; log_k1 -2.55394 -4.008 -1.0997
-#&gt; log_k2 -3.47160 -5.188 -1.7556
-#&gt; g_qlogis -0.09324 -1.427 1.2409
-#&gt;
-#&gt; Correlation:
-#&gt; prnt_0 lg__A1 f_prn_ log_k1 log_k2
-#&gt; log_k_A1 -0.014
-#&gt; f_parent_qlogis -0.025 0.054
-#&gt; log_k1 0.027 -0.003 -0.005
-#&gt; log_k2 0.011 0.005 -0.002 -0.070
-#&gt; g_qlogis -0.067 -0.009 0.011 -0.189 -0.171
-#&gt;
-#&gt; Random effects:
-#&gt; est. lower upper
-#&gt; SD.parent_0 2.7243 0.7644 4.6841
-#&gt; SD.log_k_A1 2.0563 0.4292 3.6835
-#&gt; SD.f_parent_qlogis 0.4450 0.1602 0.7298
-#&gt; SD.log_k1 1.5121 0.4714 2.5528
-#&gt; SD.log_k2 1.8320 0.6031 3.0609
-#&gt; SD.g_qlogis 0.4482 -1.2544 2.1507
-#&gt;
-#&gt; Variance model:
-#&gt; est. lower upper
-#&gt; a.1 1.884 1.668 2.1
-#&gt;
-#&gt; Backtransformed parameters:
-#&gt; est. lower upper
-#&gt; parent_0 93.805214 9.122e+01 96.38556
-#&gt; k_A1 0.002329 2.573e-04 0.02107
-#&gt; f_parent_to_A1 0.274245 2.026e-01 0.35982
-#&gt; k1 0.077775 1.817e-02 0.33296
-#&gt; k2 0.031067 5.585e-03 0.17281
-#&gt; g 0.476707 1.935e-01 0.77572
-#&gt;
-#&gt; Resulting formation fractions:
-#&gt; ff
-#&gt; parent_A1 0.2742
-#&gt; parent_sink 0.7258
-#&gt;
-#&gt; Estimated disappearance times:
-#&gt; DT50 DT90 DT50back DT50_k1 DT50_k2
-#&gt; parent 13.96 55.4 16.68 8.912 22.31
-#&gt; A1 297.65 988.8 NA NA NA
-#&gt;
-#&gt; Data:
-#&gt; ds name time observed predicted residual std standardized
-#&gt; Dataset 6 parent 0 97.2 95.75408 1.445920 1.884 0.767479
-#&gt; Dataset 6 parent 0 96.4 95.75408 0.645920 1.884 0.342847
-#&gt; Dataset 6 parent 3 71.1 71.22466 -0.124662 1.884 -0.066169
-#&gt; Dataset 6 parent 3 69.2 71.22466 -2.024662 1.884 -1.074669
-#&gt; Dataset 6 parent 6 58.1 56.42290 1.677100 1.884 0.890187
-#&gt; Dataset 6 parent 6 56.6 56.42290 0.177100 1.884 0.094003
-#&gt; Dataset 6 parent 10 44.4 44.55255 -0.152554 1.884 -0.080974
-#&gt; Dataset 6 parent 10 43.4 44.55255 -1.152554 1.884 -0.611763
-#&gt; Dataset 6 parent 20 33.3 29.88846 3.411537 1.884 1.810807
-#&gt; Dataset 6 parent 20 29.2 29.88846 -0.688463 1.884 -0.365429
-#&gt; Dataset 6 parent 34 17.6 19.40826 -1.808260 1.884 -0.959805
-#&gt; Dataset 6 parent 34 18.0 19.40826 -1.408260 1.884 -0.747489
-#&gt; Dataset 6 parent 55 10.5 10.45560 0.044398 1.884 0.023566
-#&gt; Dataset 6 parent 55 9.3 10.45560 -1.155602 1.884 -0.613381
-#&gt; Dataset 6 parent 90 4.5 3.74026 0.759744 1.884 0.403264
-#&gt; Dataset 6 parent 90 4.7 3.74026 0.959744 1.884 0.509421
-#&gt; Dataset 6 parent 112 3.0 1.96015 1.039853 1.884 0.551943
-#&gt; Dataset 6 parent 112 3.4 1.96015 1.439853 1.884 0.764258
-#&gt; Dataset 6 parent 132 2.3 1.08940 1.210603 1.884 0.642575
-#&gt; Dataset 6 parent 132 2.7 1.08940 1.610603 1.884 0.854890
-#&gt; Dataset 6 A1 3 4.3 4.75601 -0.456009 1.884 -0.242045
-#&gt; Dataset 6 A1 3 4.6 4.75601 -0.156009 1.884 -0.082808
-#&gt; Dataset 6 A1 6 7.0 7.53839 -0.538391 1.884 -0.285772
-#&gt; Dataset 6 A1 6 7.2 7.53839 -0.338391 1.884 -0.179614
-#&gt; Dataset 6 A1 10 8.2 9.64728 -1.447276 1.884 -0.768198
-#&gt; Dataset 6 A1 10 8.0 9.64728 -1.647276 1.884 -0.874356
-#&gt; Dataset 6 A1 20 11.0 11.83954 -0.839545 1.884 -0.445621
-#&gt; Dataset 6 A1 20 13.7 11.83954 1.860455 1.884 0.987509
-#&gt; Dataset 6 A1 34 11.5 12.81233 -1.312327 1.884 -0.696569
-#&gt; Dataset 6 A1 34 12.7 12.81233 -0.112327 1.884 -0.059622
-#&gt; Dataset 6 A1 55 14.9 12.87919 2.020809 1.884 1.072624
-#&gt; Dataset 6 A1 55 14.5 12.87919 1.620809 1.884 0.860308
-#&gt; Dataset 6 A1 90 12.1 11.52464 0.575364 1.884 0.305397
-#&gt; Dataset 6 A1 90 12.3 11.52464 0.775364 1.884 0.411555
-#&gt; Dataset 6 A1 112 9.9 10.37694 -0.476938 1.884 -0.253153
-#&gt; Dataset 6 A1 112 10.2 10.37694 -0.176938 1.884 -0.093917
-#&gt; Dataset 6 A1 132 8.8 9.32474 -0.524742 1.884 -0.278528
-#&gt; Dataset 6 A1 132 7.8 9.32474 -1.524742 1.884 -0.809317
-#&gt; Dataset 7 parent 0 93.6 90.16918 3.430816 1.884 1.821040
-#&gt; Dataset 7 parent 0 92.3 90.16918 2.130816 1.884 1.131014
-#&gt; Dataset 7 parent 3 87.0 84.05442 2.945583 1.884 1.563483
-#&gt; Dataset 7 parent 3 82.2 84.05442 -1.854417 1.884 -0.984304
-#&gt; Dataset 7 parent 7 74.0 77.00960 -3.009596 1.884 -1.597461
-#&gt; Dataset 7 parent 7 73.9 77.00960 -3.109596 1.884 -1.650540
-#&gt; Dataset 7 parent 14 64.2 67.15684 -2.956840 1.884 -1.569459
-#&gt; Dataset 7 parent 14 69.5 67.15684 2.343160 1.884 1.243724
-#&gt; Dataset 7 parent 30 54.0 52.66290 1.337101 1.884 0.709719
-#&gt; Dataset 7 parent 30 54.6 52.66290 1.937101 1.884 1.028192
-#&gt; Dataset 7 parent 60 41.1 40.04995 1.050050 1.884 0.557355
-#&gt; Dataset 7 parent 60 38.4 40.04995 -1.649950 1.884 -0.875775
-#&gt; Dataset 7 parent 90 32.5 34.09675 -1.596746 1.884 -0.847535
-#&gt; Dataset 7 parent 90 35.5 34.09675 1.403254 1.884 0.744832
-#&gt; Dataset 7 parent 120 28.1 30.12281 -2.022814 1.884 -1.073688
-#&gt; Dataset 7 parent 120 29.0 30.12281 -1.122814 1.884 -0.595977
-#&gt; Dataset 7 parent 180 26.5 24.10888 2.391123 1.884 1.269182
-#&gt; Dataset 7 parent 180 27.6 24.10888 3.491123 1.884 1.853050
-#&gt; Dataset 7 A1 3 3.9 2.77684 1.123161 1.884 0.596161
-#&gt; Dataset 7 A1 3 3.1 2.77684 0.323161 1.884 0.171530
-#&gt; Dataset 7 A1 7 6.9 5.96705 0.932950 1.884 0.495200
-#&gt; Dataset 7 A1 7 6.6 5.96705 0.632950 1.884 0.335963
-#&gt; Dataset 7 A1 14 10.4 10.40535 -0.005348 1.884 -0.002839
-#&gt; Dataset 7 A1 14 8.3 10.40535 -2.105348 1.884 -1.117496
-#&gt; Dataset 7 A1 30 14.4 16.83722 -2.437216 1.884 -1.293648
-#&gt; Dataset 7 A1 30 13.7 16.83722 -3.137216 1.884 -1.665200
-#&gt; Dataset 7 A1 60 22.1 22.15018 -0.050179 1.884 -0.026635
-#&gt; Dataset 7 A1 60 22.3 22.15018 0.149821 1.884 0.079523
-#&gt; Dataset 7 A1 90 27.5 24.36286 3.137143 1.884 1.665161
-#&gt; Dataset 7 A1 90 25.4 24.36286 1.037143 1.884 0.550504
-#&gt; Dataset 7 A1 120 28.0 25.64064 2.359361 1.884 1.252323
-#&gt; Dataset 7 A1 120 26.6 25.64064 0.959361 1.884 0.509218
-#&gt; Dataset 7 A1 180 25.8 27.25486 -1.454858 1.884 -0.772223
-#&gt; Dataset 7 A1 180 25.3 27.25486 -1.954858 1.884 -1.037617
-#&gt; Dataset 8 parent 0 91.9 91.72652 0.173479 1.884 0.092081
-#&gt; Dataset 8 parent 0 90.8 91.72652 -0.926521 1.884 -0.491787
-#&gt; Dataset 8 parent 1 64.9 67.22810 -2.328104 1.884 -1.235732
-#&gt; Dataset 8 parent 1 66.2 67.22810 -1.028104 1.884 -0.545706
-#&gt; Dataset 8 parent 3 43.5 41.46375 2.036251 1.884 1.080820
-#&gt; Dataset 8 parent 3 44.1 41.46375 2.636251 1.884 1.399293
-#&gt; Dataset 8 parent 8 18.3 19.83597 -1.535968 1.884 -0.815275
-#&gt; Dataset 8 parent 8 18.1 19.83597 -1.735968 1.884 -0.921433
-#&gt; Dataset 8 parent 14 10.2 10.34793 -0.147927 1.884 -0.078518
-#&gt; Dataset 8 parent 14 10.8 10.34793 0.452073 1.884 0.239956
-#&gt; Dataset 8 parent 27 4.9 2.67641 2.223595 1.884 1.180260
-#&gt; Dataset 8 parent 27 3.3 2.67641 0.623595 1.884 0.330997
-#&gt; Dataset 8 parent 48 1.6 0.30218 1.297822 1.884 0.688870
-#&gt; Dataset 8 parent 48 1.5 0.30218 1.197822 1.884 0.635791
-#&gt; Dataset 8 parent 70 1.1 0.03075 1.069248 1.884 0.567545
-#&gt; Dataset 8 parent 70 0.9 0.03075 0.869248 1.884 0.461388
-#&gt; Dataset 8 A1 1 9.6 7.74066 1.859342 1.884 0.986918
-#&gt; Dataset 8 A1 1 7.7 7.74066 -0.040658 1.884 -0.021581
-#&gt; Dataset 8 A1 3 15.0 15.37549 -0.375495 1.884 -0.199309
-#&gt; Dataset 8 A1 3 15.1 15.37549 -0.275495 1.884 -0.146230
-#&gt; Dataset 8 A1 8 21.2 19.95900 1.241003 1.884 0.658711
-#&gt; Dataset 8 A1 8 21.1 19.95900 1.141003 1.884 0.605632
-#&gt; Dataset 8 A1 14 19.7 19.92898 -0.228978 1.884 -0.121539
-#&gt; Dataset 8 A1 14 18.9 19.92898 -1.028978 1.884 -0.546170
-#&gt; Dataset 8 A1 27 17.5 16.34046 1.159536 1.884 0.615469
-#&gt; Dataset 8 A1 27 15.9 16.34046 -0.440464 1.884 -0.233793
-#&gt; Dataset 8 A1 48 9.5 10.12131 -0.621313 1.884 -0.329786
-#&gt; Dataset 8 A1 48 9.8 10.12131 -0.321313 1.884 -0.170550
-#&gt; Dataset 8 A1 70 6.2 5.84753 0.352469 1.884 0.187087
-#&gt; Dataset 8 A1 70 6.1 5.84753 0.252469 1.884 0.134008
-#&gt; Dataset 9 parent 0 99.8 98.23600 1.564002 1.884 0.830155
-#&gt; Dataset 9 parent 0 98.3 98.23600 0.064002 1.884 0.033972
-#&gt; Dataset 9 parent 1 77.1 79.68007 -2.580074 1.884 -1.369475
-#&gt; Dataset 9 parent 1 77.2 79.68007 -2.480074 1.884 -1.316396
-#&gt; Dataset 9 parent 3 59.0 55.81142 3.188584 1.884 1.692465
-#&gt; Dataset 9 parent 3 58.1 55.81142 2.288584 1.884 1.214755
-#&gt; Dataset 9 parent 8 27.4 31.81995 -4.419948 1.884 -2.346060
-#&gt; Dataset 9 parent 8 29.2 31.81995 -2.619948 1.884 -1.390640
-#&gt; Dataset 9 parent 14 19.1 22.78328 -3.683282 1.884 -1.955046
-#&gt; Dataset 9 parent 14 29.6 22.78328 6.816718 1.884 3.618240
-#&gt; Dataset 9 parent 27 10.1 14.15172 -4.051720 1.884 -2.150609
-#&gt; Dataset 9 parent 27 18.2 14.15172 4.048280 1.884 2.148783
-#&gt; Dataset 9 parent 48 4.5 6.86094 -2.360941 1.884 -1.253162
-#&gt; Dataset 9 parent 48 9.1 6.86094 2.239059 1.884 1.188468
-#&gt; Dataset 9 parent 70 2.3 3.21580 -0.915798 1.884 -0.486096
-#&gt; Dataset 9 parent 70 2.9 3.21580 -0.315798 1.884 -0.167622
-#&gt; Dataset 9 parent 91 2.0 1.56010 0.439897 1.884 0.233492
-#&gt; Dataset 9 parent 91 1.8 1.56010 0.239897 1.884 0.127335
-#&gt; Dataset 9 parent 120 2.0 0.57458 1.425424 1.884 0.756600
-#&gt; Dataset 9 parent 120 2.2 0.57458 1.625424 1.884 0.862757
-#&gt; Dataset 9 A1 1 4.2 4.01796 0.182037 1.884 0.096623
-#&gt; Dataset 9 A1 1 3.9 4.01796 -0.117963 1.884 -0.062613
-#&gt; Dataset 9 A1 3 7.4 9.08527 -1.685270 1.884 -0.894523
-#&gt; Dataset 9 A1 3 7.9 9.08527 -1.185270 1.884 -0.629129
-#&gt; Dataset 9 A1 8 14.5 13.75054 0.749457 1.884 0.397804
-#&gt; Dataset 9 A1 8 13.7 13.75054 -0.050543 1.884 -0.026827
-#&gt; Dataset 9 A1 14 14.2 14.91180 -0.711804 1.884 -0.377818
-#&gt; Dataset 9 A1 14 12.2 14.91180 -2.711804 1.884 -1.439396
-#&gt; Dataset 9 A1 27 13.7 14.97813 -1.278129 1.884 -0.678417
-#&gt; Dataset 9 A1 27 13.2 14.97813 -1.778129 1.884 -0.943812
-#&gt; Dataset 9 A1 48 13.6 13.75574 -0.155745 1.884 -0.082668
-#&gt; Dataset 9 A1 48 15.4 13.75574 1.644255 1.884 0.872753
-#&gt; Dataset 9 A1 70 10.4 11.92861 -1.528608 1.884 -0.811369
-#&gt; Dataset 9 A1 70 11.6 11.92861 -0.328608 1.884 -0.174422
-#&gt; Dataset 9 A1 91 10.0 10.14395 -0.143947 1.884 -0.076405
-#&gt; Dataset 9 A1 91 9.5 10.14395 -0.643947 1.884 -0.341800
-#&gt; Dataset 9 A1 120 9.1 7.93869 1.161307 1.884 0.616409
-#&gt; Dataset 9 A1 120 9.0 7.93869 1.061307 1.884 0.563330
-#&gt; Dataset 10 parent 0 96.1 93.65914 2.440862 1.884 1.295583
-#&gt; Dataset 10 parent 0 94.3 93.65914 0.640862 1.884 0.340163
-#&gt; Dataset 10 parent 8 73.9 77.83065 -3.930647 1.884 -2.086344
-#&gt; Dataset 10 parent 8 73.9 77.83065 -3.930647 1.884 -2.086344
-#&gt; Dataset 10 parent 14 69.4 70.15862 -0.758619 1.884 -0.402667
-#&gt; Dataset 10 parent 14 73.1 70.15862 2.941381 1.884 1.561253
-#&gt; Dataset 10 parent 21 65.6 64.00840 1.591600 1.884 0.844804
-#&gt; Dataset 10 parent 21 65.3 64.00840 1.291600 1.884 0.685567
-#&gt; Dataset 10 parent 41 55.9 54.71192 1.188076 1.884 0.630618
-#&gt; Dataset 10 parent 41 54.4 54.71192 -0.311924 1.884 -0.165566
-#&gt; Dataset 10 parent 63 47.0 49.66775 -2.667747 1.884 -1.416011
-#&gt; Dataset 10 parent 63 49.3 49.66775 -0.367747 1.884 -0.195196
-#&gt; Dataset 10 parent 91 44.7 45.17119 -0.471186 1.884 -0.250101
-#&gt; Dataset 10 parent 91 46.7 45.17119 1.528814 1.884 0.811478
-#&gt; Dataset 10 parent 120 42.1 41.20430 0.895699 1.884 0.475427
-#&gt; Dataset 10 parent 120 41.3 41.20430 0.095699 1.884 0.050796
-#&gt; Dataset 10 A1 8 3.3 4.00920 -0.709204 1.884 -0.376438
-#&gt; Dataset 10 A1 8 3.4 4.00920 -0.609204 1.884 -0.323359
-#&gt; Dataset 10 A1 14 3.9 5.94267 -2.042668 1.884 -1.084226
-#&gt; Dataset 10 A1 14 2.9 5.94267 -3.042668 1.884 -1.615015
-#&gt; Dataset 10 A1 21 6.4 7.48222 -1.082219 1.884 -0.574430
-#&gt; Dataset 10 A1 21 7.2 7.48222 -0.282219 1.884 -0.149799
-#&gt; Dataset 10 A1 41 9.1 9.76246 -0.662460 1.884 -0.351626
-#&gt; Dataset 10 A1 41 8.5 9.76246 -1.262460 1.884 -0.670100
-#&gt; Dataset 10 A1 63 11.7 10.93972 0.760278 1.884 0.403547
-#&gt; Dataset 10 A1 63 12.0 10.93972 1.060278 1.884 0.562784
-#&gt; Dataset 10 A1 91 13.3 11.93666 1.363337 1.884 0.723645
-#&gt; Dataset 10 A1 91 13.2 11.93666 1.263337 1.884 0.670566
-#&gt; Dataset 10 A1 120 14.3 12.78218 1.517817 1.884 0.805641
-#&gt; Dataset 10 A1 120 12.1 12.78218 -0.682183 1.884 -0.362095</div><div class='input'>
+</div><div class='output co'>#&gt; <span class='error'>Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'print': object 'f_saem_dfop_sfo' not found</span></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='output co'>#&gt; <span class='error'>Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'plot': object 'f_saem_dfop_sfo' not found</span></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; <span class='error'>Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'summary': object 'f_saem_dfop_sfo' not found</span></div><div class='input'>
<span class='co'># The following takes about 6 minutes</span>
<span class='co'>#f_saem_dfop_sfo_deSolve &lt;- saem(f_mmkin["DFOP-SFO", ], solution_type = "deSolve",</span>
<span class='co'># control = list(nbiter.saemix = c(200, 80), nbdisplay = 10))</span>

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