aboutsummaryrefslogtreecommitdiff
path: root/docs/dev/reference/mkinfit.html
diff options
context:
space:
mode:
authorJohannes Ranke <jranke@uni-bremen.de>2020-10-08 09:31:35 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-10-08 09:31:35 +0200
commitbc3825ae2d12c18ea3d3caf17eb23c93fef180b8 (patch)
tree112e70a29db2fb35dd624af20f4d400c579b0283 /docs/dev/reference/mkinfit.html
parentc7635af214729d2dc15dd8fbee2ebe6bc64493a4 (diff)
Fix issues for release
Diffstat (limited to 'docs/dev/reference/mkinfit.html')
-rw-r--r--docs/dev/reference/mkinfit.html622
1 files changed, 143 insertions, 479 deletions
diff --git a/docs/dev/reference/mkinfit.html b/docs/dev/reference/mkinfit.html
index e1e75767..90fb26be 100644
--- a/docs/dev/reference/mkinfit.html
+++ b/docs/dev/reference/mkinfit.html
@@ -423,16 +423,16 @@ Degradation Data. <em>Environments</em> 6(12) 124
<span class='co'># Use shorthand notation for parent only degradation</span>
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.50.3
-#&gt; R version used for fitting: 4.0.0
-#&gt; Date of fit: Wed May 27 07:43:45 2020
-#&gt; Date of summary: Wed May 27 07:43:45 2020
+#&gt; R version used for fitting: 4.0.2
+#&gt; Date of fit: Thu Oct 8 09:12:15 2020
+#&gt; Date of summary: Thu Oct 8 09:12:15 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 0.044 s
+#&gt; Fitted using 222 model solutions performed in 0.045 s
#&gt;
#&gt; Error model: Constant variance
#&gt;
@@ -467,10 +467,10 @@ Degradation Data. <em>Environments</em> 6(12) 124
#&gt;
#&gt; Parameter correlation:
#&gt; parent_0 log_alpha log_beta sigma
-#&gt; parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.770e-08
-#&gt; log_alpha -1.565e-01 1.000e+00 9.564e-01 9.974e-08
-#&gt; log_beta -3.142e-01 9.564e-01 1.000e+00 8.468e-08
-#&gt; sigma 4.770e-08 9.974e-08 8.468e-08 1.000e+00
+#&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;
#&gt; Backtransformed parameters:
#&gt; Confidence intervals for internally transformed parameters are asymmetric.
@@ -503,426 +503,118 @@ Degradation Data. <em>Environments</em> 6(12) 124
#&gt; 91 parent 3.9 1.441 2.4590
#&gt; 119 parent 0.6 1.092 -0.4919</div><div class='input'>
<span class='co'># One parent compound, one metabolite, both single first order.</span>
+<span class='co'># We remove zero values from FOCUS dataset D in order to avoid warnings</span>
+<span class='no'>FOCUS_D</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>)
<span class='co'># Use mkinsub for convenience in model formulation. Pathway to sink included per default.</span>
<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
- <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</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 to the FOCUS example dataset D using defaults</span>
-<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
- <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; user system elapsed
-#&gt; 0.405 0.001 0.407 </div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 k_parent k_m1 f_parent_to_m1 sigma
-#&gt; 99.598481046 0.098697740 0.005260651 0.514475962 3.125503875 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
+ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</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='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0165</span></div><div class='input'><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='no'>fit.tc</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</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='no'>fit.tc</span>, <span class='no'>fit</span>)</div><div class='output co'>#&gt; Likelihood ratio test
+#&gt;
+#&gt; Model 1: SFO_SFO with error model tc and fixed parameter(s) m1_0
+#&gt; Model 2: SFO_SFO with error model const and fixed parameter(s) m1_0
+#&gt; #Df LogLik Df Chisq Pr(&gt;Chisq)
+#&gt; 1 6 -64.983
+#&gt; 2 5 -97.224 -1 64.483 9.737e-16 ***
+#&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='no'>fit.obs</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</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='fu'><a href='https://rdrr.io/pkg/lmtest/man/lrtest.html'>lrtest</a></span>(<span class='no'>fit.obs</span>, <span class='no'>fit.tc</span>)</div><div class='output co'>#&gt; Likelihood ratio test
+#&gt;
+#&gt; Model 1: SFO_SFO with error model tc and fixed parameter(s) m1_0
+#&gt; Model 2: SFO_SFO with error model obs and fixed parameter(s) m1_0
+#&gt; #Df LogLik Df Chisq Pr(&gt;Chisq)
+#&gt; 1 6 -64.983
+#&gt; 2 6 -96.936 0 63.907 &lt; 2.2e-16 ***
+#&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='no'>fit.tc</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; rsd_high
+#&gt; 7.928117e-02 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.tc</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_m1 parent_sink
-#&gt; 0.514476 0.485524
+#&gt; 0.5083933 0.4916067
#&gt;
#&gt; $distimes
-#&gt; DT50 DT90
-#&gt; parent 7.022929 23.32966
-#&gt; m1 131.760724 437.69965
-#&gt; </div><div class='input'><span class='co'># \dontrun{</span>
-<span class='co'># deSolve is slower when no C compiler (gcc) was available during model generation</span>
-<span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fit.deSolve</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
- <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)))</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; <span class='message'>Ordinary least squares optimisation</span></div><div class='output co'>#&gt; Sum of squared residuals at call 1: 15156.12
-#&gt; Sum of squared residuals at call 2: 15156.12
-#&gt; Sum of squared residuals at call 6: 8243.645
-#&gt; Sum of squared residuals at call 12: 6290.712
-#&gt; Sum of squared residuals at call 13: 6290.683
-#&gt; Sum of squared residuals at call 15: 6290.452
-#&gt; Sum of squared residuals at call 18: 1700.749
-#&gt; Sum of squared residuals at call 20: 1700.611
-#&gt; Sum of squared residuals at call 24: 1190.923
-#&gt; Sum of squared residuals at call 26: 1190.922
-#&gt; Sum of squared residuals at call 29: 1017.417
-#&gt; Sum of squared residuals at call 31: 1017.417
-#&gt; Sum of squared residuals at call 33: 1017.416
-#&gt; Sum of squared residuals at call 34: 644.0472
-#&gt; Sum of squared residuals at call 36: 644.047
-#&gt; Sum of squared residuals at call 38: 644.047
-#&gt; Sum of squared residuals at call 39: 590.5025
-#&gt; Sum of squared residuals at call 41: 590.5022
-#&gt; Sum of squared residuals at call 43: 590.5016
-#&gt; Sum of squared residuals at call 44: 543.2196
-#&gt; Sum of squared residuals at call 45: 543.2193
-#&gt; Sum of squared residuals at call 46: 543.2192
-#&gt; Sum of squared residuals at call 50: 391.348
-#&gt; Sum of squared residuals at call 51: 391.3479
-#&gt; Sum of squared residuals at call 56: 386.479
-#&gt; Sum of squared residuals at call 58: 386.479
-#&gt; Sum of squared residuals at call 60: 386.4779
-#&gt; Sum of squared residuals at call 61: 384.0686
-#&gt; Sum of squared residuals at call 63: 384.0686
-#&gt; Sum of squared residuals at call 66: 382.7813
-#&gt; Sum of squared residuals at call 68: 382.7813
-#&gt; Sum of squared residuals at call 70: 382.7813
-#&gt; Sum of squared residuals at call 71: 378.9273
-#&gt; Sum of squared residuals at call 73: 378.9273
-#&gt; Sum of squared residuals at call 75: 378.9272
-#&gt; Sum of squared residuals at call 76: 377.4847
-#&gt; Sum of squared residuals at call 78: 377.4846
-#&gt; Sum of squared residuals at call 81: 375.9738
-#&gt; Sum of squared residuals at call 83: 375.9738
-#&gt; Sum of squared residuals at call 86: 375.3387
-#&gt; Sum of squared residuals at call 88: 375.3387
-#&gt; Sum of squared residuals at call 91: 374.5774
-#&gt; Sum of squared residuals at call 93: 374.5774
-#&gt; Sum of squared residuals at call 95: 374.5774
-#&gt; Sum of squared residuals at call 96: 373.5438
-#&gt; Sum of squared residuals at call 100: 373.5438
-#&gt; Sum of squared residuals at call 102: 373.265
-#&gt; Sum of squared residuals at call 104: 373.265
-#&gt; Sum of squared residuals at call 107: 372.6825
-#&gt; Sum of squared residuals at call 111: 372.6825
-#&gt; Sum of squared residuals at call 114: 372.6356
-#&gt; Sum of squared residuals at call 116: 372.6356
-#&gt; Sum of squared residuals at call 119: 372.6199
-#&gt; Sum of squared residuals at call 121: 372.6199
-#&gt; Sum of squared residuals at call 123: 372.6199
-#&gt; Sum of squared residuals at call 124: 372.5881
-#&gt; Sum of squared residuals at call 126: 372.5881
-#&gt; Sum of squared residuals at call 129: 372.5418
-#&gt; Sum of squared residuals at call 130: 372.4866
-#&gt; Sum of squared residuals at call 131: 372.2242
-#&gt; Sum of squared residuals at call 132: 371.5237
-#&gt; Sum of squared residuals at call 134: 371.5237
-#&gt; Sum of squared residuals at call 137: 371.292
-#&gt; Sum of squared residuals at call 139: 371.292
-#&gt; Sum of squared residuals at call 143: 371.2256
-#&gt; Sum of squared residuals at call 144: 371.2256
-#&gt; Sum of squared residuals at call 146: 371.2256
-#&gt; Sum of squared residuals at call 149: 371.2194
-#&gt; Sum of squared residuals at call 150: 371.2147
-#&gt; Sum of squared residuals at call 153: 371.2147
-#&gt; Sum of squared residuals at call 155: 371.2137
-#&gt; Sum of squared residuals at call 156: 371.2137
-#&gt; Sum of squared residuals at call 157: 371.2137
-#&gt; Sum of squared residuals at call 160: 371.2134
-#&gt; Sum of squared residuals at call 164: 371.2134
-#&gt; Sum of squared residuals at call 165: 371.2134
-#&gt; Sum of squared residuals at call 167: 371.2134
-#&gt; Negative log-likelihood at call 177: 97.22429</div><div class='output co'>#&gt; <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#&gt; user system elapsed
-#&gt; 0.361 0.000 0.361 </div><div class='input'><span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; parent_0 k_parent k_m1 f_parent_to_m1 sigma
-#&gt; 99.598480300 0.098697739 0.005260651 0.514475968 3.125503874 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; $ff
-#&gt; parent_m1 parent_sink
-#&gt; 0.514476 0.485524
-#&gt;
-#&gt; $distimes
-#&gt; DT50 DT90
-#&gt; parent 7.022929 23.32966
-#&gt; m1 131.760721 437.69964
-#&gt; </div><div class='input'><span class='co'># }</span>
-
-<span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, FOMC</span>
+#&gt; DT50 DT90
+#&gt; parent 6.89313 22.89848
+#&gt; m1 134.15635 445.65776
+#&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>
+<span class='co'># uncompiled deSolve, as it is so slow. More benchmarks are found in the</span>
+<span class='co'># benchmark vignette</span>
+<span class='co'># \dontrun{</span>
+<span class='kw'>if</span>(<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>rbenchmark</span>)) {
+ <span class='fu'><a href='https://rdrr.io/pkg/rbenchmark/man/benchmark.html'>benchmark</a></span>(<span class='kw'>replications</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>order</span> <span class='kw'>=</span> <span class='st'>"relative"</span>, <span class='kw'>columns</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"test"</span>, <span class='st'>"relative"</span>, <span class='st'>"elapsed"</span>),
+ <span class='kw'>deSolve_compiled</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>,
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
+ <span class='kw'>eigen</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>,
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>),
+ <span class='kw'>analytical</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>,
+ <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>))
+}</div><div class='output co'>#&gt; test relative elapsed
+#&gt; 3 analytical 1.000 0.750
+#&gt; 1 deSolve_compiled 2.288 1.716
+#&gt; 2 eigen 2.821 2.116</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>
<span class='no'>FOMC_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"FOMC"</span>, <span class='st'>"m1"</span>),
- <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</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 to the FOCUS example dataset D using defaults</span>
-<span class='no'>fit.FOMC_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='co'># Use starting parameters from parent only FOMC fit</span>
-<span class='no'>fit.FOMC</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='no'>fit.FOMC_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
- <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.FOMC</span>$<span class='no'>bparms.ode</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'>
-<span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, SFORB</span>
-<span class='no'>SFORB_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
- <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFORB"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
- <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</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 to the FOCUS example dataset D using defaults</span>
-<span class='no'>fit.SFORB_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='no'>fit.SFORB_SFO.deSolve</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>,
- <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='co'># Use starting parameters from parent only SFORB fit (not really needed in this case)</span>
-<span class='no'>fit.SFORB</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"SFORB"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='no'>fit.SFORB_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.SFORB</span>$<span class='no'>bparms.ode</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#&gt; <span class='warning'>Warning: Initial parameter(s) k_parent_free_sink not used in the model</span></div><div class='input'><span class='co'># }</span>
-
-<span class='co'># \dontrun{</span>
-<span class='co'># Weighted fits, including IRLS (error_model = "obs")</span>
-<span class='no'>SFO_SFO.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
- <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</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='no'>f.noweight</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.50.3
-#&gt; R version used for fitting: 4.0.0
-#&gt; Date of fit: Wed May 27 07:43:50 2020
-#&gt; Date of summary: Wed May 27 07:43:50 2020
-#&gt;
-#&gt; Equations:
-#&gt; d_parent/dt = - k_parent * parent
-#&gt; d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
-#&gt;
-#&gt; Model predictions using solution type analytical
-#&gt;
-#&gt; Fitted using 421 model solutions performed in 0.125 s
-#&gt;
-#&gt; Error model: Constant variance
-#&gt;
-#&gt; Error model algorithm: OLS
-#&gt;
-#&gt; Starting values for parameters to be optimised:
-#&gt; value type
-#&gt; parent_0 100.7500 state
-#&gt; k_parent 0.1000 deparm
-#&gt; k_m1 0.1001 deparm
-#&gt; f_parent_to_m1 0.5000 deparm
-#&gt;
-#&gt; Starting values for the transformed parameters actually optimised:
-#&gt; value lower upper
-#&gt; parent_0 100.750000 -Inf Inf
-#&gt; log_k_parent -2.302585 -Inf Inf
-#&gt; log_k_m1 -2.301586 -Inf Inf
-#&gt; f_parent_ilr_1 0.000000 -Inf Inf
-#&gt;
-#&gt; Fixed parameter values:
-#&gt; value type
-#&gt; m1_0 0 state
-#&gt;
-#&gt; Results:
-#&gt;
-#&gt; AIC BIC logLik
-#&gt; 204.4486 212.6365 -97.22429
-#&gt;
-#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; Estimate Std. Error Lower Upper
-#&gt; parent_0 99.60000 1.57000 96.40000 102.8000
-#&gt; log_k_parent -2.31600 0.04087 -2.39900 -2.2330
-#&gt; log_k_m1 -5.24800 0.13320 -5.51800 -4.9770
-#&gt; f_parent_ilr_1 0.04096 0.06312 -0.08746 0.1694
-#&gt; sigma 3.12600 0.35850 2.39600 3.8550
-#&gt;
-#&gt; Parameter correlation:
-#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma
-#&gt; parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -3.190e-07
-#&gt; log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 3.168e-07
-#&gt; log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 -1.406e-07
-#&gt; f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 -1.587e-10
-#&gt; sigma -3.190e-07 3.168e-07 -1.406e-07 -1.587e-10 1.000e+00
-#&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 99.600000 63.430 2.298e-36 96.400000 1.028e+02
-#&gt; k_parent 0.098700 24.470 4.955e-23 0.090820 1.073e-01
-#&gt; k_m1 0.005261 7.510 6.165e-09 0.004012 6.898e-03
-#&gt; f_parent_to_m1 0.514500 23.070 3.104e-22 0.469100 5.596e-01
-#&gt; sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00
-#&gt;
-#&gt; FOCUS Chi2 error levels in percent:
-#&gt; err.min n.optim df
-#&gt; All data 6.398 4 15
-#&gt; parent 6.459 2 7
-#&gt; m1 4.690 2 8
-#&gt;
-#&gt; Resulting formation fractions:
-#&gt; ff
-#&gt; parent_m1 0.5145
-#&gt; parent_sink 0.4855
-#&gt;
-#&gt; Estimated disappearance times:
-#&gt; DT50 DT90
-#&gt; parent 7.023 23.33
-#&gt; m1 131.761 437.70
-#&gt;
-#&gt; Data:
-#&gt; time variable observed predicted residual
-#&gt; 0 parent 99.46 99.59848 -1.385e-01
-#&gt; 0 parent 102.04 99.59848 2.442e+00
-#&gt; 1 parent 93.50 90.23787 3.262e+00
-#&gt; 1 parent 92.50 90.23787 2.262e+00
-#&gt; 3 parent 63.23 74.07319 -1.084e+01
-#&gt; 3 parent 68.99 74.07319 -5.083e+00
-#&gt; 7 parent 52.32 49.91206 2.408e+00
-#&gt; 7 parent 55.13 49.91206 5.218e+00
-#&gt; 14 parent 27.27 25.01257 2.257e+00
-#&gt; 14 parent 26.64 25.01257 1.627e+00
-#&gt; 21 parent 11.50 12.53462 -1.035e+00
-#&gt; 21 parent 11.64 12.53462 -8.946e-01
-#&gt; 35 parent 2.85 3.14787 -2.979e-01
-#&gt; 35 parent 2.91 3.14787 -2.379e-01
-#&gt; 50 parent 0.69 0.71624 -2.624e-02
-#&gt; 50 parent 0.63 0.71624 -8.624e-02
-#&gt; 75 parent 0.05 0.06074 -1.074e-02
-#&gt; 75 parent 0.06 0.06074 -7.381e-04
-#&gt; 1 m1 4.84 4.80296 3.704e-02
-#&gt; 1 m1 5.64 4.80296 8.370e-01
-#&gt; 3 m1 12.91 13.02400 -1.140e-01
-#&gt; 3 m1 12.96 13.02400 -6.400e-02
-#&gt; 7 m1 22.97 25.04476 -2.075e+00
-#&gt; 7 m1 24.47 25.04476 -5.748e-01
-#&gt; 14 m1 41.69 36.69002 5.000e+00
-#&gt; 14 m1 33.21 36.69002 -3.480e+00
-#&gt; 21 m1 44.37 41.65310 2.717e+00
-#&gt; 21 m1 46.44 41.65310 4.787e+00
-#&gt; 35 m1 41.22 43.31312 -2.093e+00
-#&gt; 35 m1 37.95 43.31312 -5.363e+00
-#&gt; 50 m1 41.19 41.21831 -2.831e-02
-#&gt; 50 m1 40.01 41.21831 -1.208e+00
-#&gt; 75 m1 40.09 36.44703 3.643e+00
-#&gt; 75 m1 33.85 36.44703 -2.597e+00
-#&gt; 100 m1 31.04 31.98163 -9.416e-01
-#&gt; 100 m1 33.13 31.98163 1.148e+00
-#&gt; 120 m1 25.15 28.78984 -3.640e+00
-#&gt; 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.50.3
-#&gt; R version used for fitting: 4.0.0
-#&gt; Date of fit: Wed May 27 07:43:51 2020
-#&gt; Date of summary: Wed May 27 07:43:51 2020
+ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</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='no'>fit.FOMC_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Shapiro-Wilk test for standardized residuals: p = 0.0499</span></div><div class='input'><span class='co'># Again, we get a warning and try a more sophisticated error model</span>
+<span class='no'>fit.FOMC_SFO.tc</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</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='no'>fit.tc</span>, <span class='no'>fit.FOMC_SFO.tc</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>
+<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='no'>fit.FOMC_SFO.tc</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</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: 0.9.50.3
+#&gt; R version used for fitting: 4.0.2
+#&gt; Date of fit: Thu Oct 8 09:12:29 2020
+#&gt; Date of summary: Thu Oct 8 09:12:29 2020
#&gt;
#&gt; Equations:
-#&gt; d_parent/dt = - k_parent * parent
-#&gt; d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
-#&gt;
-#&gt; Model predictions using solution type analytical
-#&gt;
-#&gt; Fitted using 978 model solutions performed in 0.413 s
-#&gt;
-#&gt; Error model: Variance unique to each observed variable
-#&gt;
-#&gt; Error model algorithm: d_3
-#&gt; Direct fitting and three-step fitting yield approximately the same likelihood
-#&gt;
-#&gt; Starting values for parameters to be optimised:
-#&gt; value type
-#&gt; parent_0 100.7500 state
-#&gt; k_parent 0.1000 deparm
-#&gt; k_m1 0.1001 deparm
-#&gt; f_parent_to_m1 0.5000 deparm
-#&gt; sigma_parent 3.0000 error
-#&gt; sigma_m1 3.0000 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_parent -2.302585 -Inf Inf
-#&gt; log_k_m1 -2.301586 -Inf Inf
-#&gt; f_parent_ilr_1 0.000000 -Inf Inf
-#&gt; sigma_parent 3.000000 0 Inf
-#&gt; sigma_m1 3.000000 0 Inf
-#&gt;
-#&gt; Fixed parameter values:
-#&gt; value type
-#&gt; m1_0 0 state
-#&gt;
-#&gt; Results:
-#&gt;
-#&gt; AIC BIC logLik
-#&gt; 205.8727 215.6982 -96.93634
-#&gt;
-#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; Estimate Std. Error Lower Upper
-#&gt; parent_0 99.65000 1.70200 96.19000 103.1000
-#&gt; log_k_parent -2.31300 0.04376 -2.40200 -2.2240
-#&gt; log_k_m1 -5.25000 0.12430 -5.50400 -4.9970
-#&gt; f_parent_ilr_1 0.03861 0.06171 -0.08708 0.1643
-#&gt; sigma_parent 3.40100 0.56820 2.24400 4.5590
-#&gt; sigma_m1 2.85500 0.45240 1.93400 3.7770
-#&gt;
-#&gt; Parameter correlation:
-#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma_parent
-#&gt; parent_0 1.00000 0.51078 -0.19133 -0.59997 0.035670
-#&gt; log_k_parent 0.51078 1.00000 -0.37458 -0.59239 0.069833
-#&gt; log_k_m1 -0.19133 -0.37458 1.00000 0.74398 -0.026158
-#&gt; f_parent_ilr_1 -0.59997 -0.59239 0.74398 1.00000 -0.041369
-#&gt; sigma_parent 0.03567 0.06983 -0.02616 -0.04137 1.000000
-#&gt; sigma_m1 -0.03385 -0.06627 0.02482 0.03926 -0.004628
-#&gt; sigma_m1
-#&gt; parent_0 -0.033847
-#&gt; log_k_parent -0.066265
-#&gt; log_k_m1 0.024823
-#&gt; f_parent_ilr_1 0.039256
-#&gt; sigma_parent -0.004628
-#&gt; sigma_m1 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 99.650000 58.560 2.004e-34 96.190000 1.031e+02
-#&gt; k_parent 0.098970 22.850 1.099e-21 0.090530 1.082e-01
-#&gt; k_m1 0.005245 8.046 1.732e-09 0.004072 6.756e-03
-#&gt; f_parent_to_m1 0.513600 23.560 4.352e-22 0.469300 5.578e-01
-#&gt; sigma_parent 3.401000 5.985 5.662e-07 2.244000 4.559e+00
-#&gt; sigma_m1 2.855000 6.311 2.215e-07 1.934000 3.777e+00
-#&gt;
-#&gt; FOCUS Chi2 error levels in percent:
-#&gt; err.min n.optim df
-#&gt; All data 6.398 4 15
-#&gt; parent 6.464 2 7
-#&gt; m1 4.682 2 8
-#&gt;
-#&gt; Resulting formation fractions:
-#&gt; ff
-#&gt; parent_m1 0.5136
-#&gt; parent_sink 0.4864
-#&gt;
-#&gt; Estimated disappearance times:
-#&gt; DT50 DT90
-#&gt; parent 7.003 23.26
-#&gt; m1 132.154 439.01
-#&gt;
-#&gt; Data:
-#&gt; time variable observed predicted residual
-#&gt; 0 parent 99.46 99.65417 -1.942e-01
-#&gt; 0 parent 102.04 99.65417 2.386e+00
-#&gt; 1 parent 93.50 90.26332 3.237e+00
-#&gt; 1 parent 92.50 90.26332 2.237e+00
-#&gt; 3 parent 63.23 74.05306 -1.082e+01
-#&gt; 3 parent 68.99 74.05306 -5.063e+00
-#&gt; 7 parent 52.32 49.84325 2.477e+00
-#&gt; 7 parent 55.13 49.84325 5.287e+00
-#&gt; 14 parent 27.27 24.92971 2.340e+00
-#&gt; 14 parent 26.64 24.92971 1.710e+00
-#&gt; 21 parent 11.50 12.46890 -9.689e-01
-#&gt; 21 parent 11.64 12.46890 -8.289e-01
-#&gt; 35 parent 2.85 3.11925 -2.692e-01
-#&gt; 35 parent 2.91 3.11925 -2.092e-01
-#&gt; 50 parent 0.69 0.70679 -1.679e-02
-#&gt; 50 parent 0.63 0.70679 -7.679e-02
-#&gt; 75 parent 0.05 0.05952 -9.523e-03
-#&gt; 75 parent 0.06 0.05952 4.772e-04
-#&gt; 1 m1 4.84 4.81075 2.925e-02
-#&gt; 1 m1 5.64 4.81075 8.292e-01
-#&gt; 3 m1 12.91 13.04196 -1.320e-01
-#&gt; 3 m1 12.96 13.04196 -8.196e-02
-#&gt; 7 m1 22.97 25.06847 -2.098e+00
-#&gt; 7 m1 24.47 25.06847 -5.985e-01
-#&gt; 14 m1 41.69 36.70308 4.987e+00
-#&gt; 14 m1 33.21 36.70308 -3.493e+00
-#&gt; 21 m1 44.37 41.65115 2.719e+00
-#&gt; 21 m1 46.44 41.65115 4.789e+00
-#&gt; 35 m1 41.22 43.29465 -2.075e+00
-#&gt; 35 m1 37.95 43.29465 -5.345e+00
-#&gt; 50 m1 41.19 41.19948 -9.479e-03
-#&gt; 50 m1 40.01 41.19948 -1.189e+00
-#&gt; 75 m1 40.09 36.44035 3.650e+00
-#&gt; 75 m1 33.85 36.44035 -2.590e+00
-#&gt; 100 m1 31.04 31.98773 -9.477e-01
-#&gt; 100 m1 33.13 31.98773 1.142e+00
-#&gt; 120 m1 25.15 28.80429 -3.654e+00
-#&gt; 120 m1 33.31 28.80429 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.50.3
-#&gt; R version used for fitting: 4.0.0
-#&gt; Date of fit: Wed May 27 07:43:52 2020
-#&gt; Date of summary: Wed May 27 07:43:52 2020
-#&gt;
-#&gt; Equations:
-#&gt; d_parent/dt = - k_parent * parent
-#&gt; d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
+#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
+#&gt; d_m1/dt = + f_parent_to_m1 * (alpha/beta) * 1/((time/beta) + 1) *
+#&gt; parent - k_m1 * m1
#&gt;
-#&gt; Model predictions using solution type analytical
+#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 2088 model solutions performed in 0.714 s
+#&gt; Fitted using 3611 model solutions performed in 2.61 s
#&gt;
#&gt; Error model: Two-component variance function
#&gt;
#&gt; Error model algorithm: d_3
-#&gt; Direct fitting and three-step fitting yield approximately the same likelihood
+#&gt; Three-step fitting yielded a higher likelihood than direct fitting
#&gt;
#&gt; Starting values for parameters to be optimised:
-#&gt; value type
-#&gt; parent_0 100.7500 state
-#&gt; k_parent 0.1000 deparm
-#&gt; k_m1 0.1001 deparm
-#&gt; f_parent_to_m1 0.5000 deparm
-#&gt; sigma_low 0.1000 error
-#&gt; rsd_high 0.1000 error
+#&gt; value type
+#&gt; parent_0 100.75 state
+#&gt; alpha 1.00 deparm
+#&gt; beta 10.00 deparm
+#&gt; k_m1 0.10 deparm
+#&gt; f_parent_to_m1 0.50 deparm
+#&gt; sigma_low 0.10 error
+#&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_parent -2.302585 -Inf Inf
-#&gt; log_k_m1 -2.301586 -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;
@@ -932,98 +624,70 @@ Degradation Data. <em>Environments</em> 6(12) 124
#&gt;
#&gt; Results:
#&gt;
-#&gt; AIC BIC logLik
-#&gt; 141.9656 151.7911 -64.98278
+#&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_0 100.70000 2.621000 95.400000 106.10000
-#&gt; log_k_parent -2.29700 0.008862 -2.315000 -2.27900
-#&gt; log_k_m1 -5.26600 0.091310 -5.452000 -5.08000
-#&gt; f_parent_ilr_1 0.02374 0.055300 -0.088900 0.13640
-#&gt; sigma_low 0.00305 0.004829 -0.006786 0.01289
-#&gt; rsd_high 0.07928 0.009418 0.060100 0.09847
+#&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;
#&gt; Parameter correlation:
-#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma_low rsd_high
-#&gt; parent_0 1.00000 0.67644 -0.10215 -0.76822 0.14294 -0.08783
-#&gt; log_k_parent 0.67644 1.00000 -0.15102 -0.59491 0.34611 -0.08125
-#&gt; log_k_m1 -0.10215 -0.15102 1.00000 0.51808 -0.05236 0.01240
-#&gt; f_parent_ilr_1 -0.76822 -0.59491 0.51808 1.00000 -0.13900 0.03248
-#&gt; sigma_low 0.14294 0.34611 -0.05236 -0.13900 1.00000 -0.16546
-#&gt; rsd_high -0.08783 -0.08125 0.01240 0.03248 -0.16546 1.00000
+#&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;
#&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 1.007e+02 38.4300 1.180e-28 95.400000 1.061e+02
-#&gt; k_parent 1.006e-01 112.8000 1.718e-43 0.098760 1.024e-01
-#&gt; k_m1 5.167e-03 10.9500 1.171e-12 0.004290 6.223e-03
-#&gt; f_parent_to_m1 5.084e-01 26.0100 2.146e-23 0.468600 5.481e-01
-#&gt; sigma_low 3.050e-03 0.6314 2.661e-01 -0.006786 1.289e-02
-#&gt; rsd_high 7.928e-02 8.4170 6.418e-10 0.060100 9.847e-02
+#&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;
#&gt; FOCUS Chi2 error levels in percent:
#&gt; err.min n.optim df
-#&gt; All data 6.475 4 15
-#&gt; parent 6.573 2 7
-#&gt; m1 4.671 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 0.5084
-#&gt; parent_sink 0.4916
+#&gt; parent_m1 0.5004
+#&gt; parent_sink 0.4996
#&gt;
#&gt; Estimated disappearance times:
-#&gt; DT50 DT90
-#&gt; parent 6.893 22.9
-#&gt; m1 134.156 445.7
-#&gt;
-#&gt; Data:
-#&gt; time variable observed predicted residual
-#&gt; 0 parent 99.46 100.73434 -1.274340
-#&gt; 0 parent 102.04 100.73434 1.305660
-#&gt; 1 parent 93.50 91.09751 2.402486
-#&gt; 1 parent 92.50 91.09751 1.402486
-#&gt; 3 parent 63.23 74.50141 -11.271410
-#&gt; 3 parent 68.99 74.50141 -5.511410
-#&gt; 7 parent 52.32 49.82880 2.491200
-#&gt; 7 parent 55.13 49.82880 5.301200
-#&gt; 14 parent 27.27 24.64809 2.621908
-#&gt; 14 parent 26.64 24.64809 1.991908
-#&gt; 21 parent 11.50 12.19232 -0.692315
-#&gt; 21 parent 11.64 12.19232 -0.552315
-#&gt; 35 parent 2.85 2.98327 -0.133266
-#&gt; 35 parent 2.91 2.98327 -0.073266
-#&gt; 50 parent 0.69 0.66013 0.029874
-#&gt; 50 parent 0.63 0.66013 -0.030126
-#&gt; 75 parent 0.05 0.05344 -0.003438
-#&gt; 75 parent 0.06 0.05344 0.006562
-#&gt; 1 m1 4.84 4.88645 -0.046451
-#&gt; 1 m1 5.64 4.88645 0.753549
-#&gt; 3 m1 12.91 13.22867 -0.318669
-#&gt; 3 m1 12.96 13.22867 -0.268669
-#&gt; 7 m1 22.97 25.36417 -2.394166
-#&gt; 7 m1 24.47 25.36417 -0.894166
-#&gt; 14 m1 41.69 37.00974 4.680263
-#&gt; 14 m1 33.21 37.00974 -3.799737
-#&gt; 21 m1 44.37 41.90133 2.468669
-#&gt; 21 m1 46.44 41.90133 4.538669
-#&gt; 35 m1 41.22 43.45691 -2.236913
-#&gt; 35 m1 37.95 43.45691 -5.506913
-#&gt; 50 m1 41.19 41.34199 -0.151985
-#&gt; 50 m1 40.01 41.34199 -1.331985
-#&gt; 75 m1 40.09 36.61471 3.475295
-#&gt; 75 m1 33.85 36.61471 -2.764705
-#&gt; 100 m1 31.04 32.20082 -1.160823
-#&gt; 100 m1 33.13 32.20082 0.929177
-#&gt; 120 m1 25.15 29.04130 -3.891304
-#&gt; 120 m1 33.31 29.04130 4.268696</div><div class='input'># }
-
-
-</div></pre>
+#&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='no'>fit.FOMC</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>)
+<span class='no'>fit.FOMC_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.FOMC</span>$<span class='no'>bparms.ode</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>)
+<span class='co'># }</span></div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">

Contact - Imprint