aboutsummaryrefslogtreecommitdiff
path: root/docs/reference/mkinfit.html
diff options
context:
space:
mode:
Diffstat (limited to 'docs/reference/mkinfit.html')
-rw-r--r--docs/reference/mkinfit.html339
1 files changed, 149 insertions, 190 deletions
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 8c14fc9d..b75b7c95 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -360,17 +360,17 @@ Per default, parameters in the kinetic models are internally transformed in
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><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://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.4
+<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.4
#&gt; R version used for fitting: 3.6.0
-#&gt; Date of fit: Fri May 3 19:07:19 2019
-#&gt; Date of summary: Fri May 3 19:07:19 2019
+#&gt; Date of fit: Tue May 7 08:08:23 2019
+#&gt; Date of summary: Tue May 7 08:08:23 2019
#&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 0.463 s
+#&gt; Fitted using 66 model solutions performed in 0.139 s
#&gt;
#&gt; Error model:
#&gt; Constant variance
@@ -393,28 +393,23 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; None
#&gt;
#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; Estimate Std. Error Lower Upper
-#&gt; parent_0 85.87000 1.8070 81.23000 90.5200
-#&gt; log_alpha 0.05192 0.1353 -0.29580 0.3996
-#&gt; log_beta 0.65100 0.2287 0.06315 1.2390
-#&gt; sigma 1.85700 0.4378 0.73200 2.9830
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 85.87000 NA NA NA
+#&gt; log_alpha 0.05192 NA NA NA
+#&gt; log_beta 0.65100 NA NA NA
+#&gt; sigma 1.85700 NA NA NA
#&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;
+#&gt; No covariance matrix
#&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 85.870 47.530 3.893e-08 81.2300 90.520
-#&gt; alpha 1.053 7.393 3.562e-04 0.7439 1.491
-#&gt; beta 1.917 4.373 3.601e-03 1.0650 3.451
-#&gt; sigma 1.857 4.243 4.074e-03 0.7320 2.983
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 85.870 NA NA NA NA
+#&gt; alpha 1.053 NA NA NA NA
+#&gt; beta 1.917 NA NA NA NA
+#&gt; sigma 1.857 NA NA NA NA
#&gt;
#&gt; FOCUS Chi2 error levels in percent:
#&gt; err.min n.optim df
@@ -443,7 +438,7 @@ Per default, parameters in the kinetic models are internally transformed in
<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://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>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 verstrichen
-#&gt; 1.493 0.000 1.494 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; NULL</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
+#&gt; 0.637 0.000 0.640 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; NULL</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
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
#&gt;
@@ -514,10 +509,8 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; Sum of squared residuals at call 125: 371.2134
#&gt; Sum of squared residuals at call 126: 371.2134
#&gt; Sum of squared residuals at call 135: 371.2134
-#&gt; Negative log-likelihood at call 145: 97.22429
-#&gt; Optimisation successfully terminated.
-#&gt; User System verstrichen
-#&gt; 1.082 0.000 1.083 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; NULL</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; Negative log-likelihood at call 145: 97.22429</div><div class='output co'>#&gt; <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#&gt; User System verstrichen
+#&gt; 0.544 0.000 0.550 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; NULL</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; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
#&gt;
@@ -547,10 +540,10 @@ Per default, parameters in the kinetic models are internally transformed in
<span class='no'>fit.SFORB_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.SFORB</span>$<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='input'>
</div><div class='input'><span class='co'># Weighted fits, including IRLS</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://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.4
+ <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://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.4
#&gt; R version used for fitting: 3.6.0
-#&gt; Date of fit: Fri May 3 19:07:35 2019
-#&gt; Date of summary: Fri May 3 19:07:35 2019
+#&gt; Date of fit: Tue May 7 08:08:30 2019
+#&gt; Date of summary: Tue May 7 08:08:30 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -558,7 +551,7 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 421 model solutions performed in 1.099 s
+#&gt; Fitted using 185 model solutions performed in 0.499 s
#&gt;
#&gt; Error model:
#&gt; Constant variance
@@ -584,31 +577,25 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; m1_0 0 state
#&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; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.60000 NA NA NA
+#&gt; log_k_parent -2.31600 NA NA NA
+#&gt; log_k_m1 -5.24800 NA NA NA
+#&gt; f_parent_ilr_1 0.04096 NA NA NA
+#&gt; sigma 3.12600 NA NA NA
#&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 -2.265e-07
-#&gt; log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 3.785e-07
-#&gt; log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 -1.386e-07
-#&gt; f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 -3.641e-08
-#&gt; sigma -2.265e-07 3.785e-07 -1.386e-07 -3.641e-08 1.000e+00
-#&gt;
+#&gt; No covariance matrix
#&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; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.600000 NA NA NA NA
+#&gt; k_parent 0.098700 NA NA NA NA
+#&gt; k_m1 0.005261 NA NA NA NA
+#&gt; f_parent_to_m1 0.514500 NA NA NA NA
+#&gt; sigma 3.126000 NA NA NA NA
#&gt;
#&gt; FOCUS Chi2 error levels in percent:
#&gt; err.min n.optim df
@@ -665,10 +652,10 @@ Per default, parameters in the kinetic models are internally transformed in
#&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://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.4
+#&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://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.obs</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.4
#&gt; R version used for fitting: 3.6.0
-#&gt; Date of fit: Fri May 3 19:07:37 2019
-#&gt; Date of summary: Fri May 3 19:07:37 2019
+#&gt; Date of fit: Tue May 7 08:08:32 2019
+#&gt; Date of summary: Tue May 7 08:08:32 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -676,7 +663,7 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 756 model solutions performed in 1.973 s
+#&gt; Fitted using 426 model solutions performed in 1.139 s
#&gt;
#&gt; Error model:
#&gt; Variance unique to each observed variable
@@ -704,41 +691,27 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; m1_0 0 state
#&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; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.65000 NA NA NA
+#&gt; log_k_parent -2.31300 NA NA NA
+#&gt; log_k_m1 -5.25000 NA NA NA
+#&gt; f_parent_ilr_1 0.03861 NA NA NA
+#&gt; sigma_parent 3.40100 NA NA NA
+#&gt; sigma_m1 2.85500 NA NA NA
#&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 0.035685
-#&gt; log_k_parent 0.51078 1.00000 -0.37458 -0.59239 0.069840
-#&gt; log_k_m1 -0.19133 -0.37458 1.00000 0.74398 -0.026160
-#&gt; f_parent_ilr_1 -0.59997 -0.59239 0.74398 1.00000 -0.041377
-#&gt; sigma_parent 0.03569 0.06984 -0.02616 -0.04138 1.000000
-#&gt; sigma_m1 -0.03385 -0.06626 0.02482 0.03925 -0.004628
-#&gt; sigma_m1
-#&gt; parent_0 -0.033847
-#&gt; log_k_parent -0.066264
-#&gt; log_k_m1 0.024822
-#&gt; f_parent_ilr_1 0.039254
-#&gt; sigma_parent -0.004628
-#&gt; sigma_m1 1.000000
-#&gt;
+#&gt; No covariance matrix
#&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; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.650000 NA NA NA NA
+#&gt; k_parent 0.098970 NA NA NA NA
+#&gt; k_m1 0.005245 NA NA NA NA
+#&gt; f_parent_to_m1 0.513600 NA NA NA NA
+#&gt; sigma_parent 3.401000 NA NA NA NA
+#&gt; sigma_m1 2.855000 NA NA NA NA
#&gt;
#&gt; FOCUS Chi2 error levels in percent:
#&gt; err.min n.optim df
@@ -758,47 +731,47 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Data:
#&gt; time variable observed predicted residual
-#&gt; 0 parent 99.46 99.65425 -1.942e-01
-#&gt; 0 parent 102.04 99.65425 2.386e+00
-#&gt; 1 parent 93.50 90.26338 3.237e+00
-#&gt; 1 parent 92.50 90.26338 2.237e+00
-#&gt; 3 parent 63.23 74.05309 -1.082e+01
-#&gt; 3 parent 68.99 74.05309 -5.063e+00
-#&gt; 7 parent 52.32 49.84326 2.477e+00
-#&gt; 7 parent 55.13 49.84326 5.287e+00
-#&gt; 14 parent 27.27 24.92970 2.340e+00
-#&gt; 14 parent 26.64 24.92970 1.710e+00
-#&gt; 21 parent 11.50 12.46888 -9.689e-01
-#&gt; 21 parent 11.64 12.46888 -8.289e-01
-#&gt; 35 parent 2.85 3.11924 -2.692e-01
-#&gt; 35 parent 2.91 3.11924 -2.092e-01
-#&gt; 50 parent 0.69 0.70678 -1.678e-02
-#&gt; 50 parent 0.63 0.70678 -7.678e-02
-#&gt; 75 parent 0.05 0.05952 -9.522e-03
-#&gt; 75 parent 0.06 0.05952 4.776e-04
+#&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 13.04197 -1.320e-01
-#&gt; 3 m1 12.96 13.04197 -8.197e-02
-#&gt; 7 m1 22.97 25.06848 -2.098e+00
-#&gt; 7 m1 24.47 25.06848 -5.985e-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 43.29464 -2.075e+00
-#&gt; 35 m1 37.95 43.29464 -5.345e+00
-#&gt; 50 m1 41.19 41.19947 -9.473e-03
-#&gt; 50 m1 40.01 41.19947 -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; 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 -9.481e-03
+#&gt; 50 m1 40.01 41.19948 -1.189e+00
+#&gt; 75 m1 40.09 36.44036 3.650e+00
+#&gt; 75 m1 33.85 36.44036 -2.590e+00
+#&gt; 100 m1 31.04 31.98774 -9.477e-01
+#&gt; 100 m1 33.13 31.98774 1.142e+00
#&gt; 120 m1 25.15 28.80430 -3.654e+00
-#&gt; 120 m1 33.31 28.80430 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://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#&gt; <span class='warning'>Warning: NaNs wurden erzeugt</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: 0.9.49.4
+#&gt; 120 m1 33.31 28.80430 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://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.tc</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Could not calculate correlation; no covariance matrix</span></div><div class='output co'>#&gt; mkin version used for fitting: 0.9.49.4
#&gt; R version used for fitting: 3.6.0
-#&gt; Date of fit: Fri May 3 19:07:40 2019
-#&gt; Date of summary: Fri May 3 19:07:40 2019
+#&gt; Date of fit: Tue May 7 08:08:34 2019
+#&gt; Date of summary: Tue May 7 08:08:34 2019
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -806,7 +779,7 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted using 888 model solutions performed in 3.579 s
+#&gt; Fitted using 489 model solutions performed in 2.013 s
#&gt;
#&gt; Error model:
#&gt; Two-component variance function
@@ -834,98 +807,84 @@ Per default, parameters in the kinetic models are internally transformed in
#&gt; m1_0 0 state
#&gt;
#&gt; Optimised, transformed parameters with symmetric confidence intervals:
-#&gt; Estimate Std. Error Lower Upper
-#&gt; parent_0 100.30000 3.06400 94.08000 106.60000
-#&gt; log_k_parent -2.31100 0.02913 -2.37100 -2.25200
-#&gt; log_k_m1 -5.27800 0.10890 -5.49900 -5.05600
-#&gt; f_parent_ilr_1 0.02128 0.07223 -0.12590 0.16840
-#&gt; sigma_low 0.99650 NaN NaN NaN
-#&gt; rsd_high 0.07560 0.01059 0.05402 0.09717
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 100.70000 NA NA NA
+#&gt; log_k_parent -2.29700 NA NA NA
+#&gt; log_k_m1 -5.26600 NA NA NA
+#&gt; f_parent_ilr_1 0.02374 NA NA NA
+#&gt; sigma_low 0.00305 NA NA NA
+#&gt; rsd_high 0.07928 NA NA NA
#&gt;
#&gt; Parameter correlation:
-#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma_low
-#&gt; parent_0 1.00000 0.64703 -0.220160 -0.79035 NaN
-#&gt; log_k_parent 0.64703 1.00000 -0.339633 -0.67982 NaN
-#&gt; log_k_m1 -0.22016 -0.33963 1.000000 0.62815 NaN
-#&gt; f_parent_ilr_1 -0.79035 -0.67982 0.628148 1.00000 NaN
-#&gt; sigma_low NaN NaN NaN NaN 1
-#&gt; rsd_high -0.05745 -0.01123 0.003502 0.00568 NaN
-#&gt; rsd_high
-#&gt; parent_0 -0.057450
-#&gt; log_k_parent -0.011230
-#&gt; log_k_m1 0.003502
-#&gt; f_parent_ilr_1 0.005680
-#&gt; sigma_low NaN
-#&gt; rsd_high 1.000000
-#&gt;
+#&gt; No covariance matrix
#&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 1.003e+02 32.740 1.759e-26 94.080000 1.066e+02
-#&gt; k_parent 9.914e-02 34.330 4.045e-27 0.093430 1.052e-01
-#&gt; k_m1 5.105e-03 9.186 8.682e-11 0.004089 6.372e-03
-#&gt; f_parent_to_m1 5.075e-01 19.880 7.143e-20 0.455600 5.593e-01
-#&gt; sigma_low 9.965e-01 NaN NaN NaN NaN
-#&gt; rsd_high 7.560e-02 7.137 2.114e-08 0.054020 9.717e-02
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 1.007e+02 NA NA NA NA
+#&gt; k_parent 1.006e-01 NA NA NA NA
+#&gt; k_m1 5.167e-03 NA NA NA NA
+#&gt; f_parent_to_m1 5.084e-01 NA NA NA NA
+#&gt; sigma_low 3.050e-03 NA NA NA NA
+#&gt; rsd_high 7.928e-02 NA NA NA NA
#&gt;
#&gt; FOCUS Chi2 error levels in percent:
#&gt; err.min n.optim df
-#&gt; All data 6.433 4 15
-#&gt; parent 6.506 2 7
-#&gt; m1 4.692 2 8
+#&gt; All data 6.475 4 15
+#&gt; parent 6.573 2 7
+#&gt; m1 4.671 2 8
#&gt;
#&gt; Resulting formation fractions:
#&gt; ff
-#&gt; parent_m1 0.5075
-#&gt; parent_sink 0.4925
+#&gt; parent_m1 0.5084
+#&gt; parent_sink 0.4916
#&gt;
#&gt; Estimated disappearance times:
-#&gt; DT50 DT90
-#&gt; parent 6.992 23.23
-#&gt; m1 135.787 451.08
+#&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 99.46 100.32122 -0.861220
-#&gt; 0 parent 102.04 100.32122 1.718780
-#&gt; 1 parent 93.50 90.85266 2.647340
-#&gt; 1 parent 92.50 90.85266 1.647340
-#&gt; 3 parent 63.23 74.51219 -11.282190
-#&gt; 3 parent 68.99 74.51219 -5.522190
-#&gt; 7 parent 52.32 50.11950 2.200504
-#&gt; 7 parent 55.13 50.11950 5.010504
-#&gt; 14 parent 27.27 25.03921 2.230792
-#&gt; 14 parent 26.64 25.03921 1.600792
-#&gt; 21 parent 11.50 12.50934 -1.009342
-#&gt; 21 parent 11.64 12.50934 -0.869342
-#&gt; 35 parent 2.85 3.12221 -0.272211
-#&gt; 35 parent 2.91 3.12221 -0.212211
-#&gt; 50 parent 0.69 0.70572 -0.015724
-#&gt; 50 parent 0.63 0.70572 -0.075724
-#&gt; 75 parent 0.05 0.05919 -0.009191
-#&gt; 75 parent 0.06 0.05919 0.000809
-#&gt; 1 m1 4.84 4.79307 0.046928
-#&gt; 1 m1 5.64 4.79307 0.846928
-#&gt; 3 m1 12.91 12.99398 -0.083980
-#&gt; 3 m1 12.96 12.99398 -0.033980
-#&gt; 7 m1 22.97 24.97744 -2.007441
-#&gt; 7 m1 24.47 24.97744 -0.507441
-#&gt; 14 m1 41.69 36.57917 5.110827
-#&gt; 14 m1 33.21 36.57917 -3.369173
-#&gt; 21 m1 44.37 41.52931 2.840692
-#&gt; 21 m1 46.44 41.52931 4.910692
-#&gt; 35 m1 41.22 43.22614 -2.006138
-#&gt; 35 m1 37.95 43.22614 -5.276138
-#&gt; 50 m1 41.19 41.20972 -0.019717
-#&gt; 50 m1 40.01 41.20972 -1.199717
-#&gt; 75 m1 40.09 36.57312 3.516882
-#&gt; 75 m1 33.85 36.57312 -2.723118
-#&gt; 100 m1 31.04 32.21655 -1.176546
-#&gt; 100 m1 33.13 32.21655 0.913454
-#&gt; 120 m1 25.15 29.09181 -3.941814
-#&gt; 120 m1 33.31 29.09181 4.218186</div><div class='input'>
+#&gt; 0 parent 99.46 100.73433 -1.274329
+#&gt; 0 parent 102.04 100.73433 1.305671
+#&gt; 1 parent 93.50 91.09750 2.402495
+#&gt; 1 parent 92.50 91.09750 1.402495
+#&gt; 3 parent 63.23 74.50140 -11.271403
+#&gt; 3 parent 68.99 74.50140 -5.511403
+#&gt; 7 parent 52.32 49.82880 2.491205
+#&gt; 7 parent 55.13 49.82880 5.301205
+#&gt; 14 parent 27.27 24.64809 2.621909
+#&gt; 14 parent 26.64 24.64809 1.991909
+#&gt; 21 parent 11.50 12.19231 -0.692315
+#&gt; 21 parent 11.64 12.19231 -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 -0.318668
+#&gt; 3 m1 12.96 13.22867 -0.268668
+#&gt; 7 m1 22.97 25.36416 -2.394164
+#&gt; 7 m1 24.47 25.36416 -0.894164
+#&gt; 14 m1 41.69 37.00974 4.680265
+#&gt; 14 m1 33.21 37.00974 -3.799735
+#&gt; 21 m1 44.37 41.90133 2.468670
+#&gt; 21 m1 46.44 41.90133 4.538670
+#&gt; 35 m1 41.22 43.45691 -2.236914
+#&gt; 35 m1 37.95 43.45691 -5.506914
+#&gt; 50 m1 41.19 41.34199 -0.151988
+#&gt; 50 m1 40.01 41.34199 -1.331988
+#&gt; 75 m1 40.09 36.61471 3.475290
+#&gt; 75 m1 33.85 36.61471 -2.764710
+#&gt; 100 m1 31.04 32.20083 -1.160830
+#&gt; 100 m1 33.13 32.20083 0.929170
+#&gt; 120 m1 25.15 29.04131 -3.891312
+#&gt; 120 m1 33.31 29.04131 4.268688</div><div class='input'>
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">

Contact - Imprint