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-rw-r--r--docs/dev/reference/mkinfit.html132
1 files changed, 63 insertions, 69 deletions
diff --git a/docs/dev/reference/mkinfit.html b/docs/dev/reference/mkinfit.html
index 6ae7b343..5910038f 100644
--- a/docs/dev/reference/mkinfit.html
+++ b/docs/dev/reference/mkinfit.html
@@ -80,7 +80,7 @@ likelihood function." />
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span>
+ <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">1.0.3.9000</span>
</span>
</div>
@@ -431,17 +431,17 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6
<span class='co'># Use shorthand notation for parent only degradation</span>
<span class='va'>fit</span> <span class='op'>&lt;-</span> <span class='fu'>mkinfit</span><span class='op'>(</span><span class='st'>"FOMC"</span>, <span class='va'>FOCUS_2006_C</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<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
+</div><div class='output co'>#&gt; mkin version used for fitting: 1.0.3.9000
#&gt; R version used for fitting: 4.0.3
-#&gt; Date of fit: Mon Jan 11 12:41:45 2021
-#&gt; Date of summary: Mon Jan 11 12:41:45 2021
+#&gt; Date of fit: Mon Feb 15 17:09:39 2021
+#&gt; Date of summary: Mon Feb 15 17:09:39 2021
#&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 0.046 s
+#&gt; Fitted using 222 model solutions performed in 0.045 s
#&gt;
#&gt; Error model: Constant variance
#&gt;
@@ -476,10 +476,10 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6
#&gt;
#&gt; Parameter correlation:
#&gt; parent_0 log_alpha log_beta sigma
-#&gt; parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.758e-08
-#&gt; log_alpha -1.565e-01 1.000e+00 9.564e-01 1.007e-07
-#&gt; log_beta -3.142e-01 9.564e-01 1.000e+00 8.568e-08
-#&gt; sigma 4.758e-08 1.007e-07 8.568e-08 1.000e+00
+#&gt; parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.772e-08
+#&gt; log_alpha -1.565e-01 1.000e+00 9.564e-01 1.005e-07
+#&gt; log_beta -3.142e-01 9.564e-01 1.000e+00 8.541e-08
+#&gt; sigma 4.772e-08 1.005e-07 8.541e-08 1.000e+00
#&gt;
#&gt; Backtransformed parameters:
#&gt; Confidence intervals for internally transformed parameters are asymmetric.
@@ -548,7 +548,7 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6
#&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 3.049884e-03
+#&gt; 1.007343e+02 1.005562e-01 5.166712e-03 5.083933e-01 3.049883e-03
#&gt; rsd_high
#&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
@@ -574,10 +574,10 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6
analytical <span class='op'>=</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>,
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 0.526
-#&gt; 1 deSolve_compiled 1.903 1.001
-#&gt; 2 eigen 2.308 1.214</div><div class='input'><span class='co'># }</span>
+</div><div class='output co'>#&gt; test relative elapsed
+#&gt; 3 analytical 1.000 0.563
+#&gt; 1 deSolve_compiled 1.702 0.958
+#&gt; 2 eigen 2.597 1.462</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>
@@ -587,22 +587,21 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6
</div><div class='output co'>#&gt; <span class='message'>Temporary DLL for differentials generated and loaded</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>
-</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='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 -64.870
-#&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>
+#&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>
<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: 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: diag(.) had 0 or NA entries; non-finite result is doubtful</span></div><div class='output co'>#&gt; mkin version used for fitting: 1.0.3.9000
#&gt; R version used for fitting: 4.0.3
-#&gt; Date of fit: Mon Jan 11 12:41:56 2021
-#&gt; Date of summary: Mon Jan 11 12:41:56 2021
+#&gt; Date of fit: Mon Feb 15 17:09:50 2021
+#&gt; Date of summary: Mon Feb 15 17:09:50 2021
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -611,12 +610,12 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 4273 model solutions performed in 3.456 s
+#&gt; Fitted using 3729 model solutions performed in 2.815 s
#&gt;
#&gt; Error model: Two-component variance function
#&gt;
#&gt; Error model algorithm: d_3
-#&gt; Three-step fitting yielded a higher likelihood than direct fitting
+#&gt; Direct fitting and three-step fitting yield approximately the same likelihood
#&gt;
#&gt; Starting values for parameters to be optimised:
#&gt; value type
@@ -642,72 +641,67 @@ doi: <a href='https://doi.org/10.3390/environments6120124'>10.3390/environments6
#&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; 143.7396 155.2027 -64.86982
+#&gt; AIC BIC logLik
+#&gt; 143.658 155.1211 -64.82902
#&gt;
#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&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; Estimate Std. Error Lower Upper
+#&gt; parent_0 101.600000 2.6400000 96.240000 107.000000
+#&gt; log_k_m1 -5.284000 0.0929100 -5.474000 -5.095000
+#&gt; f_parent_qlogis 0.001426 0.0767000 -0.155000 0.157800
+#&gt; log_alpha 5.522000 0.0077320 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;
#&gt; Parameter correlation:
-#&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; parent_0 log_k_m1 f_parent_qlogis log_alpha log_beta
+#&gt; parent_0 1.000000 -0.095226 -0.76678 0.70544 NaN
+#&gt; log_k_m1 -0.095226 1.000000 0.51432 -0.14387 NaN
+#&gt; f_parent_qlogis -0.766780 0.514321 1.00000 -0.61396 NaN
+#&gt; log_alpha 0.705444 -0.143872 -0.61396 1.00000 NaN
+#&gt; log_beta NaN NaN NaN NaN 1
+#&gt; sigma_low 0.016073 0.001586 0.01548 5.87007 NaN
+#&gt; rsd_high 0.006626 -0.011700 -0.05357 0.04849 NaN
+#&gt; sigma_low rsd_high
+#&gt; parent_0 0.016073 0.006626
+#&gt; log_k_m1 0.001586 -0.011700
+#&gt; f_parent_qlogis 0.015476 -0.053566
+#&gt; log_alpha 5.870075 0.048487
+#&gt; log_beta NaN NaN
+#&gt; sigma_low 1.000000 -0.652558
+#&gt; rsd_high -0.652558 1.000000
#&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 32.5400 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; parent_0 1.016e+02 32.7800 6.311e-26 9.624e+01 1.070e+02
+#&gt; k_m1 5.072e-03 10.1200 1.216e-11 4.196e-03 6.130e-03
+#&gt; f_parent_to_m1 5.004e-01 20.8300 4.317e-20 4.613e-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;
#&gt; FOCUS Chi2 error levels in percent:
#&gt; err.min n.optim df
-#&gt; All data 6.782 5 14
-#&gt; parent 7.142 3 6
-#&gt; m1 4.639 2 8
+#&gt; All data 6.781 5 14
+#&gt; parent 7.141 3 6
+#&gt; m1 4.640 2 8
#&gt;
#&gt; Resulting formation fractions:
#&gt; ff
-#&gt; parent_m1 0.5002
-#&gt; parent_sink 0.4998
+#&gt; parent_m1 0.5004
+#&gt; parent_sink 0.4996
#&gt;
#&gt; Estimated disappearance times:
-#&gt; DT50 DT90 DT50back
-#&gt; parent 6.81 22.7 6.833
-#&gt; m1 136.74 454.2 NA</div><div class='input'>
+#&gt; DT50 DT90 DT50back
+#&gt; parent 6.812 22.7 6.834
+#&gt; m1 136.661 454.0 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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