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-rw-r--r--docs/dev/reference/mkinfit.html154
1 files changed, 79 insertions, 75 deletions
diff --git a/docs/dev/reference/mkinfit.html b/docs/dev/reference/mkinfit.html
index 39bd12cb..b46c2cce 100644
--- a/docs/dev/reference/mkinfit.html
+++ b/docs/dev/reference/mkinfit.html
@@ -307,12 +307,11 @@ a lower bound for the rates in the optimisation.</p></td>
<tr>
<th>transform_fractions</th>
<td><p>Boolean specifying if formation fractions
-constants should be transformed in the model specification used in the
-fitting for better compliance with the assumption of normal distribution
-of the estimator. The default (TRUE) is to do transformations. If TRUE,
-the g parameter of the DFOP and HS models are also transformed, as they
-can also be seen as compositional data. The transformation used for these
-transformations is the <code><a href='ilr.html'>ilr()</a></code> transformation.</p></td>
+should be transformed in the model specification used in the fitting for
+better compliance with the assumption of normal distribution of the
+estimator. The default (TRUE) is to do transformations. If TRUE,
+the g parameter of the DFOP model is also transformed. Transformations
+are described in <a href='transform_odeparms.html'>transform_odeparms</a>.</p></td>
</tr>
<tr>
<th>quiet</th>
@@ -433,15 +432,15 @@ Degradation Data. <em>Environments</em> 6(12) 124
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.50.4
#&gt; R version used for fitting: 4.0.3
-#&gt; Date of fit: Thu Nov 5 08:25:42 2020
-#&gt; Date of summary: Thu Nov 5 08:25:42 2020
+#&gt; Date of fit: Thu Nov 5 23:14:40 2020
+#&gt; Date of summary: Thu Nov 5 23:14:40 2020
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted using 222 model solutions performed in 0.049 s
+#&gt; Fitted using 222 model solutions performed in 0.05 s
#&gt;
#&gt; Error model: Constant variance
#&gt;
@@ -521,8 +520,8 @@ Degradation Data. <em>Environments</em> 6(12) 124
</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
<span class='co'># Fit the model quietly to the FOCUS example dataset D using defaults</span>
<span class='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
-<span class='co'># Since mkin 0.9.50.3, we get a warning about non-normality of residuals,</span>
-<span class='co'># so we try an alternative error model</span>
+<span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span><span class='op'>(</span><span class='va'>fit</span><span class='op'>)</span>
+</div><div class='img'><img src='mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># As lower parent values appear to have lower variance, we try an alternative error model</span>
<span class='va'>fit.tc</span> <span class='op'>&lt;-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</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='co'># This avoids the warning, and the likelihood ratio test confirms it is preferable</span>
<span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>fit.tc</span>, <span class='va'>fit</span><span class='op'>)</span>
@@ -536,8 +535,7 @@ Degradation Data. <em>Environments</em> 6(12) 124
#&gt; ---
#&gt; Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='co'># We can also allow for different variances of parent and metabolite as error model</span>
<span class='va'>fit.obs</span> <span class='op'>&lt;-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>SFO_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span><span class='op'>)</span>
-<span class='co'># This also avoids the warning about non-normality, but the two-component error model</span>
-<span class='co'># has significantly higher likelihood</span>
+<span class='co'># The two-component error model has significantly higher likelihood</span>
<span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>fit.obs</span>, <span class='va'>fit.tc</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Likelihood ratio test
#&gt;
@@ -549,9 +547,9 @@ Degradation Data. <em>Environments</em> 6(12) 124
#&gt; ---
#&gt; Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1</div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span><span class='op'>(</span><span class='va'>fit.tc</span><span class='op'>)</span>
</div><div class='output co'>#&gt; parent_0 k_parent k_m1 f_parent_to_m1 sigma_low
-#&gt; 1.007343e+02 1.005562e-01 5.166712e-03 5.083933e-01 3.049891e-03
+#&gt; 1.007343e+02 1.005562e-01 5.166712e-03 5.083933e-01 3.049884e-03
#&gt; rsd_high
-#&gt; 7.928117e-02 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.tc</span><span class='op'>)</span>
+#&gt; 7.928118e-02 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>fit.tc</span><span class='op'>)</span>
</div><div class='output co'>#&gt; $ff
#&gt; parent_m1 parent_sink
#&gt; 0.5083933 0.4916067
@@ -559,7 +557,7 @@ Degradation Data. <em>Environments</em> 6(12) 124
#&gt; $distimes
#&gt; DT50 DT90
#&gt; parent 6.89313 22.89848
-#&gt; m1 134.15635 445.65776
+#&gt; m1 134.15634 445.65772
#&gt; </div><div class='input'>
<span class='co'># We can show a quick (only one replication) benchmark for this case, as we</span>
<span class='co'># have several alternative solution methods for the model. We skip</span>
@@ -576,9 +574,9 @@ Degradation Data. <em>Environments</em> 6(12) 124
solution_type <span class='op'>=</span> <span class='st'>"analytical"</span><span class='op'>)</span><span class='op'>)</span>
<span class='op'>}</span>
</div><div class='output co'>#&gt; <span class='message'>Loading required package: rbenchmark</span></div><div class='output co'>#&gt; test relative elapsed
-#&gt; 3 analytical 1.000 0.746
-#&gt; 1 deSolve_compiled 2.288 1.707
-#&gt; 2 eigen 2.708 2.020</div><div class='input'><span class='co'># }</span>
+#&gt; 3 analytical 1.000 0.532
+#&gt; 1 deSolve_compiled 1.765 0.939
+#&gt; 2 eigen 2.229 1.186</div><div class='input'><span class='co'># }</span>
<span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO</span>
<span class='co'># \dontrun{</span>
@@ -588,21 +586,22 @@ Degradation Data. <em>Environments</em> 6(12) 124
</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='va'>fit.FOMC_SFO</span> <span class='op'>&lt;-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>FOMC_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='co'># Again, we get a warning and try a more sophisticated error model</span>
<span class='va'>fit.FOMC_SFO.tc</span> <span class='op'>&lt;-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>FOMC_SFO</span>, <span class='va'>FOCUS_D</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='co'># This model has a higher likelihood, but not significantly so</span>
+</div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation did not converge:</span>
+#&gt; <span class='warning'>iteration limit reached without convergence (10)</span></div><div class='input'><span class='co'># This model has a higher likelihood, but not significantly so</span>
<span class='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span><span class='op'>(</span><span class='va'>fit.tc</span>, <span class='va'>fit.FOMC_SFO.tc</span><span class='op'>)</span>
</div><div class='output co'>#&gt; Likelihood ratio test
#&gt;
#&gt; Model 1: FOMC_SFO with error model tc and fixed parameter(s) m1_0
#&gt; Model 2: SFO_SFO with error model tc and fixed parameter(s) m1_0
#&gt; #Df LogLik Df Chisq Pr(&gt;Chisq)
-#&gt; 1 7 -64.829
-#&gt; 2 6 -64.983 -1 0.3075 0.5792</div><div class='input'><span class='co'># Also, the missing standard error for log_beta and the t-tests for alpha</span>
+#&gt; 1 7 -64.870
+#&gt; 2 6 -64.983 -1 0.2259 0.6346</div><div class='input'><span class='co'># Also, the missing standard error for log_beta and the t-tests for alpha</span>
<span class='co'># and beta indicate overparameterisation</span>
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>fit.FOMC_SFO.tc</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
-</div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#&gt; <span class='warning'>Warning: diag(.) had 0 or NA entries; non-finite result is doubtful</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.50.4
+</div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#&gt; <span class='warning'>Warning: diag(.) had 0 or NA entries; non-finite result is doubtful</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.50.4
#&gt; R version used for fitting: 4.0.3
-#&gt; Date of fit: Thu Nov 5 08:25:56 2020
-#&gt; Date of summary: Thu Nov 5 08:25:56 2020
+#&gt; Date of fit: Thu Nov 5 23:14:51 2020
+#&gt; Date of summary: Thu Nov 5 23:14:51 2020
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -611,7 +610,7 @@ Degradation Data. <em>Environments</em> 6(12) 124
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 3611 model solutions performed in 2.673 s
+#&gt; Fitted using 4273 model solutions performed in 3.081 s
#&gt;
#&gt; Error model: Two-component variance function
#&gt;
@@ -629,80 +628,85 @@ Degradation Data. <em>Environments</em> 6(12) 124
#&gt; rsd_high 0.10 error
#&gt;
#&gt; Starting values for the transformed parameters actually optimised:
-#&gt; value lower upper
-#&gt; parent_0 100.750000 -Inf Inf
-#&gt; log_k_m1 -2.302585 -Inf Inf
-#&gt; f_parent_ilr_1 0.000000 -Inf Inf
-#&gt; log_alpha 0.000000 -Inf Inf
-#&gt; log_beta 2.302585 -Inf Inf
-#&gt; sigma_low 0.100000 0 Inf
-#&gt; rsd_high 0.100000 0 Inf
+#&gt; value lower upper
+#&gt; parent_0 100.750000 -Inf Inf
+#&gt; log_k_m1 -2.302585 -Inf Inf
+#&gt; f_parent_qlogis 0.000000 -Inf Inf
+#&gt; log_alpha 0.000000 -Inf Inf
+#&gt; log_beta 2.302585 -Inf Inf
+#&gt; sigma_low 0.100000 0 Inf
+#&gt; rsd_high 0.100000 0 Inf
#&gt;
#&gt; Fixed parameter values:
#&gt; value type
#&gt; m1_0 0 state
#&gt;
+#&gt;
+#&gt; Warning(s):
+#&gt; Optimisation did not converge:
+#&gt; iteration limit reached without convergence (10)
+#&gt;
#&gt; Results:
#&gt;
-#&gt; AIC BIC logLik
-#&gt; 143.658 155.1211 -64.82902
+#&gt; AIC BIC logLik
+#&gt; 143.7396 155.2027 -64.86982
#&gt;
#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; Estimate Std. Error Lower Upper
-#&gt; parent_0 101.600000 2.6390000 96.240000 107.000000
-#&gt; log_k_m1 -5.284000 0.0928900 -5.473000 -5.095000
-#&gt; f_parent_ilr_1 0.001008 0.0541900 -0.109500 0.111500
-#&gt; log_alpha 5.522000 0.0077300 5.506000 5.538000
-#&gt; log_beta 7.806000 NaN NaN NaN
-#&gt; sigma_low 0.002488 0.0002431 0.001992 0.002984
-#&gt; rsd_high 0.079210 0.0093280 0.060180 0.098230
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 1.016e+02 1.90600 97.7400 105.5000
+#&gt; log_k_m1 -5.285e+00 0.09286 -5.4740 -5.0950
+#&gt; f_parent_qlogis 6.482e-04 0.06164 -0.1251 0.1264
+#&gt; log_alpha 5.467e+00 NaN NaN NaN
+#&gt; log_beta 7.750e+00 NaN NaN NaN
+#&gt; sigma_low 0.000e+00 NaN NaN NaN
+#&gt; rsd_high 7.989e-02 NaN NaN NaN
#&gt;
#&gt; Parameter correlation:
-#&gt; parent_0 log_k_m1 f_parent_ilr_1 log_alpha log_beta sigma_low
-#&gt; parent_0 1.000000 -0.094697 -0.76654 0.70525 NaN 0.016099
-#&gt; log_k_m1 -0.094697 1.000000 0.51404 -0.14347 NaN 0.001576
-#&gt; f_parent_ilr_1 -0.766543 0.514038 1.00000 -0.61368 NaN 0.015465
-#&gt; log_alpha 0.705247 -0.143468 -0.61368 1.00000 NaN 5.871780
-#&gt; log_beta NaN NaN NaN NaN 1 NaN
-#&gt; sigma_low 0.016099 0.001576 0.01546 5.87178 NaN 1.000000
-#&gt; rsd_high 0.006566 -0.011662 -0.05353 0.04845 NaN -0.652554
-#&gt; rsd_high
-#&gt; parent_0 0.006566
-#&gt; log_k_m1 -0.011662
-#&gt; f_parent_ilr_1 -0.053525
-#&gt; log_alpha 0.048451
-#&gt; log_beta NaN
-#&gt; sigma_low -0.652554
-#&gt; rsd_high 1.000000
+#&gt; parent_0 log_k_m1 f_parent_qlogis log_alpha log_beta
+#&gt; parent_0 1.0000000 -0.0002167 -0.6060 NaN NaN
+#&gt; log_k_m1 -0.0002167 1.0000000 0.5474 NaN NaN
+#&gt; f_parent_qlogis -0.6060320 0.5474423 1.0000 NaN NaN
+#&gt; log_alpha NaN NaN NaN 1 NaN
+#&gt; log_beta NaN NaN NaN NaN 1
+#&gt; sigma_low NaN NaN NaN NaN NaN
+#&gt; rsd_high NaN NaN NaN NaN NaN
+#&gt; sigma_low rsd_high
+#&gt; parent_0 NaN NaN
+#&gt; log_k_m1 NaN NaN
+#&gt; f_parent_qlogis NaN NaN
+#&gt; log_alpha NaN NaN
+#&gt; log_beta NaN NaN
+#&gt; sigma_low 1 NaN
+#&gt; rsd_high NaN 1
#&gt;
#&gt; Backtransformed parameters:
#&gt; Confidence intervals for internally transformed parameters are asymmetric.
#&gt; t-test (unrealistically) based on the assumption of normal distribution
#&gt; for estimators of untransformed parameters.
#&gt; Estimate t value Pr(&gt;t) Lower Upper
-#&gt; parent_0 1.016e+02 32.7800 6.312e-26 9.624e+01 1.070e+02
-#&gt; k_m1 5.072e-03 10.1200 1.216e-11 4.197e-03 6.130e-03
-#&gt; f_parent_to_m1 5.004e-01 20.8300 4.318e-20 4.614e-01 5.394e-01
-#&gt; alpha 2.502e+02 0.5624 2.889e-01 2.463e+02 2.542e+02
-#&gt; beta 2.455e+03 0.5549 2.915e-01 NA NA
-#&gt; sigma_low 2.488e-03 0.4843 3.158e-01 1.992e-03 2.984e-03
-#&gt; rsd_high 7.921e-02 8.4300 8.001e-10 6.018e-02 9.823e-02
+#&gt; parent_0 1.016e+02 32.5400 7.812e-26 97.740000 1.055e+02
+#&gt; k_m1 5.069e-03 10.0400 1.448e-11 0.004194 6.126e-03
+#&gt; f_parent_to_m1 5.002e-01 20.7300 5.001e-20 0.468800 5.315e-01
+#&gt; alpha 2.367e+02 0.6205 2.697e-01 NA NA
+#&gt; beta 2.322e+03 0.6114 2.727e-01 NA NA
+#&gt; sigma_low 0.000e+00 NaN NaN NaN NaN
+#&gt; rsd_high 7.989e-02 8.6630 4.393e-10 NaN NaN
#&gt;
#&gt; FOCUS Chi2 error levels in percent:
#&gt; err.min n.optim df
-#&gt; All data 6.781 5 14
-#&gt; parent 7.141 3 6
-#&gt; m1 4.640 2 8
+#&gt; All data 6.782 5 14
+#&gt; parent 7.142 3 6
+#&gt; m1 4.639 2 8
#&gt;
#&gt; Resulting formation fractions:
#&gt; ff
-#&gt; parent_m1 0.5004
-#&gt; parent_sink 0.4996
+#&gt; parent_m1 0.5002
+#&gt; parent_sink 0.4998
#&gt;
#&gt; Estimated disappearance times:
-#&gt; DT50 DT90 DT50back
-#&gt; parent 6.812 22.7 6.834
-#&gt; m1 136.661 454.0 NA</div><div class='input'>
+#&gt; DT50 DT90 DT50back
+#&gt; parent 6.81 22.7 6.833
+#&gt; m1 136.74 454.2 NA</div><div class='input'>
<span class='co'># We can easily use starting parameters from the parent only fit (only for illustration)</span>
<span class='va'>fit.FOMC</span> <span class='op'>=</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='va'>FOCUS_2006_D</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'>fit.FOMC_SFO</span> <span class='op'>&lt;-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='va'>FOMC_SFO</span>, <span class='va'>FOCUS_D</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>,

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