diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-10-08 09:31:35 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-10-08 09:31:35 +0200 |
| commit | bc3825ae2d12c18ea3d3caf17eb23c93fef180b8 (patch) | |
| tree | 112e70a29db2fb35dd624af20f4d400c579b0283 /docs/dev/reference/mkinfit.html | |
| parent | c7635af214729d2dc15dd8fbee2ebe6bc64493a4 (diff) | |
Fix issues for release
Diffstat (limited to 'docs/dev/reference/mkinfit.html')
| -rw-r--r-- | docs/dev/reference/mkinfit.html | 622 |
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'><-</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'>#> mkin version used for fitting: 0.9.50.3 -#> R version used for fitting: 4.0.0 -#> Date of fit: Wed May 27 07:43:45 2020 -#> Date of summary: Wed May 27 07:43:45 2020 +#> R version used for fitting: 4.0.2 +#> Date of fit: Thu Oct 8 09:12:15 2020 +#> Date of summary: Thu Oct 8 09:12:15 2020 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 222 model solutions performed in 0.044 s +#> Fitted using 222 model solutions performed in 0.045 s #> #> Error model: Constant variance #> @@ -467,10 +467,10 @@ Degradation Data. <em>Environments</em> 6(12) 124 #> #> Parameter correlation: #> parent_0 log_alpha log_beta sigma -#> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.770e-08 -#> log_alpha -1.565e-01 1.000e+00 9.564e-01 9.974e-08 -#> log_beta -3.142e-01 9.564e-01 1.000e+00 8.468e-08 -#> sigma 4.770e-08 9.974e-08 8.468e-08 1.000e+00 +#> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.758e-08 +#> log_alpha -1.565e-01 1.000e+00 9.564e-01 1.007e-07 +#> log_beta -3.142e-01 9.564e-01 1.000e+00 8.568e-08 +#> sigma 4.758e-08 1.007e-07 8.568e-08 1.000e+00 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. @@ -503,426 +503,118 @@ Degradation Data. <em>Environments</em> 6(12) 124 #> 91 parent 3.9 1.441 2.4590 #> 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'><-</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'><-</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'>#> <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'><-</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'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> user system elapsed -#> 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'>#> parent_0 k_parent k_m1 f_parent_to_m1 sigma -#> 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'>#> $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'>#> <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'><-</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'>#> <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'><-</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'>#> Likelihood ratio test +#> +#> Model 1: SFO_SFO with error model tc and fixed parameter(s) m1_0 +#> Model 2: SFO_SFO with error model const and fixed parameter(s) m1_0 +#> #Df LogLik Df Chisq Pr(>Chisq) +#> 1 6 -64.983 +#> 2 5 -97.224 -1 64.483 9.737e-16 *** +#> --- +#> 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'><-</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'>#> Likelihood ratio test +#> +#> Model 1: SFO_SFO with error model tc and fixed parameter(s) m1_0 +#> Model 2: SFO_SFO with error model obs and fixed parameter(s) m1_0 +#> #Df LogLik Df Chisq Pr(>Chisq) +#> 1 6 -64.983 +#> 2 6 -96.936 0 63.907 < 2.2e-16 *** +#> --- +#> 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'>#> parent_0 k_parent k_m1 f_parent_to_m1 sigma_low +#> 1.007343e+02 1.005562e-01 5.166712e-03 5.083933e-01 3.049891e-03 +#> rsd_high +#> 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'>#> $ff #> parent_m1 parent_sink -#> 0.514476 0.485524 +#> 0.5083933 0.4916067 #> #> $distimes -#> DT50 DT90 -#> parent 7.022929 23.32966 -#> m1 131.760724 437.69965 -#> </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'><-</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'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='message'>Ordinary least squares optimisation</span></div><div class='output co'>#> Sum of squared residuals at call 1: 15156.12 -#> Sum of squared residuals at call 2: 15156.12 -#> Sum of squared residuals at call 6: 8243.645 -#> Sum of squared residuals at call 12: 6290.712 -#> Sum of squared residuals at call 13: 6290.683 -#> Sum of squared residuals at call 15: 6290.452 -#> Sum of squared residuals at call 18: 1700.749 -#> Sum of squared residuals at call 20: 1700.611 -#> Sum of squared residuals at call 24: 1190.923 -#> Sum of squared residuals at call 26: 1190.922 -#> Sum of squared residuals at call 29: 1017.417 -#> Sum of squared residuals at call 31: 1017.417 -#> Sum of squared residuals at call 33: 1017.416 -#> Sum of squared residuals at call 34: 644.0472 -#> Sum of squared residuals at call 36: 644.047 -#> Sum of squared residuals at call 38: 644.047 -#> Sum of squared residuals at call 39: 590.5025 -#> Sum of squared residuals at call 41: 590.5022 -#> Sum of squared residuals at call 43: 590.5016 -#> Sum of squared residuals at call 44: 543.2196 -#> Sum of squared residuals at call 45: 543.2193 -#> Sum of squared residuals at call 46: 543.2192 -#> Sum of squared residuals at call 50: 391.348 -#> Sum of squared residuals at call 51: 391.3479 -#> Sum of squared residuals at call 56: 386.479 -#> Sum of squared residuals at call 58: 386.479 -#> Sum of squared residuals at call 60: 386.4779 -#> Sum of squared residuals at call 61: 384.0686 -#> Sum of squared residuals at call 63: 384.0686 -#> Sum of squared residuals at call 66: 382.7813 -#> Sum of squared residuals at call 68: 382.7813 -#> Sum of squared residuals at call 70: 382.7813 -#> Sum of squared residuals at call 71: 378.9273 -#> Sum of squared residuals at call 73: 378.9273 -#> Sum of squared residuals at call 75: 378.9272 -#> Sum of squared residuals at call 76: 377.4847 -#> Sum of squared residuals at call 78: 377.4846 -#> Sum of squared residuals at call 81: 375.9738 -#> Sum of squared residuals at call 83: 375.9738 -#> Sum of squared residuals at call 86: 375.3387 -#> Sum of squared residuals at call 88: 375.3387 -#> Sum of squared residuals at call 91: 374.5774 -#> Sum of squared residuals at call 93: 374.5774 -#> Sum of squared residuals at call 95: 374.5774 -#> Sum of squared residuals at call 96: 373.5438 -#> Sum of squared residuals at call 100: 373.5438 -#> Sum of squared residuals at call 102: 373.265 -#> Sum of squared residuals at call 104: 373.265 -#> Sum of squared residuals at call 107: 372.6825 -#> Sum of squared residuals at call 111: 372.6825 -#> Sum of squared residuals at call 114: 372.6356 -#> Sum of squared residuals at call 116: 372.6356 -#> Sum of squared residuals at call 119: 372.6199 -#> Sum of squared residuals at call 121: 372.6199 -#> Sum of squared residuals at call 123: 372.6199 -#> Sum of squared residuals at call 124: 372.5881 -#> Sum of squared residuals at call 126: 372.5881 -#> Sum of squared residuals at call 129: 372.5418 -#> Sum of squared residuals at call 130: 372.4866 -#> Sum of squared residuals at call 131: 372.2242 -#> Sum of squared residuals at call 132: 371.5237 -#> Sum of squared residuals at call 134: 371.5237 -#> Sum of squared residuals at call 137: 371.292 -#> Sum of squared residuals at call 139: 371.292 -#> Sum of squared residuals at call 143: 371.2256 -#> Sum of squared residuals at call 144: 371.2256 -#> Sum of squared residuals at call 146: 371.2256 -#> Sum of squared residuals at call 149: 371.2194 -#> Sum of squared residuals at call 150: 371.2147 -#> Sum of squared residuals at call 153: 371.2147 -#> Sum of squared residuals at call 155: 371.2137 -#> Sum of squared residuals at call 156: 371.2137 -#> Sum of squared residuals at call 157: 371.2137 -#> Sum of squared residuals at call 160: 371.2134 -#> Sum of squared residuals at call 164: 371.2134 -#> Sum of squared residuals at call 165: 371.2134 -#> Sum of squared residuals at call 167: 371.2134 -#> Negative log-likelihood at call 177: 97.22429</div><div class='output co'>#> <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#> user system elapsed -#> 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'>#> parent_0 k_parent k_m1 f_parent_to_m1 sigma -#> 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'>#> $ff -#> parent_m1 parent_sink -#> 0.514476 0.485524 -#> -#> $distimes -#> DT50 DT90 -#> parent 7.022929 23.32966 -#> m1 131.760721 437.69964 -#> </div><div class='input'><span class='co'># }</span> - -<span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, FOMC</span> +#> DT50 DT90 +#> parent 6.89313 22.89848 +#> m1 134.15635 445.65776 +#> </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'>#> test relative elapsed +#> 3 analytical 1.000 0.750 +#> 1 deSolve_compiled 2.288 1.716 +#> 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'><-</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'>#> <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'><-</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'>#> <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'><-</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'>#> <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'><-</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'>#> <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'><-</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'>#> <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'><-</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'>#> <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'><-</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'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <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'><-</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'>#> <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'><-</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'>#> <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'>#> mkin version used for fitting: 0.9.50.3 -#> R version used for fitting: 4.0.0 -#> Date of fit: Wed May 27 07:43:50 2020 -#> Date of summary: Wed May 27 07:43:50 2020 -#> -#> Equations: -#> d_parent/dt = - k_parent * parent -#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 -#> -#> Model predictions using solution type analytical -#> -#> Fitted using 421 model solutions performed in 0.125 s -#> -#> Error model: Constant variance -#> -#> Error model algorithm: OLS -#> -#> Starting values for parameters to be optimised: -#> value type -#> parent_0 100.7500 state -#> k_parent 0.1000 deparm -#> k_m1 0.1001 deparm -#> f_parent_to_m1 0.5000 deparm -#> -#> Starting values for the transformed parameters actually optimised: -#> value lower upper -#> parent_0 100.750000 -Inf Inf -#> log_k_parent -2.302585 -Inf Inf -#> log_k_m1 -2.301586 -Inf Inf -#> f_parent_ilr_1 0.000000 -Inf Inf -#> -#> Fixed parameter values: -#> value type -#> m1_0 0 state -#> -#> Results: -#> -#> AIC BIC logLik -#> 204.4486 212.6365 -97.22429 -#> -#> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> parent_0 99.60000 1.57000 96.40000 102.8000 -#> log_k_parent -2.31600 0.04087 -2.39900 -2.2330 -#> log_k_m1 -5.24800 0.13320 -5.51800 -4.9770 -#> f_parent_ilr_1 0.04096 0.06312 -0.08746 0.1694 -#> sigma 3.12600 0.35850 2.39600 3.8550 -#> -#> Parameter correlation: -#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma -#> parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -3.190e-07 -#> log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 3.168e-07 -#> log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 -1.406e-07 -#> f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 -1.587e-10 -#> sigma -3.190e-07 3.168e-07 -1.406e-07 -1.587e-10 1.000e+00 -#> -#> Backtransformed parameters: -#> Confidence intervals for internally transformed parameters are asymmetric. -#> t-test (unrealistically) based on the assumption of normal distribution -#> for estimators of untransformed parameters. -#> Estimate t value Pr(>t) Lower Upper -#> parent_0 99.600000 63.430 2.298e-36 96.400000 1.028e+02 -#> k_parent 0.098700 24.470 4.955e-23 0.090820 1.073e-01 -#> k_m1 0.005261 7.510 6.165e-09 0.004012 6.898e-03 -#> f_parent_to_m1 0.514500 23.070 3.104e-22 0.469100 5.596e-01 -#> sigma 3.126000 8.718 2.235e-10 2.396000 3.855e+00 -#> -#> FOCUS Chi2 error levels in percent: -#> err.min n.optim df -#> All data 6.398 4 15 -#> parent 6.459 2 7 -#> m1 4.690 2 8 -#> -#> Resulting formation fractions: -#> ff -#> parent_m1 0.5145 -#> parent_sink 0.4855 -#> -#> Estimated disappearance times: -#> DT50 DT90 -#> parent 7.023 23.33 -#> m1 131.761 437.70 -#> -#> Data: -#> time variable observed predicted residual -#> 0 parent 99.46 99.59848 -1.385e-01 -#> 0 parent 102.04 99.59848 2.442e+00 -#> 1 parent 93.50 90.23787 3.262e+00 -#> 1 parent 92.50 90.23787 2.262e+00 -#> 3 parent 63.23 74.07319 -1.084e+01 -#> 3 parent 68.99 74.07319 -5.083e+00 -#> 7 parent 52.32 49.91206 2.408e+00 -#> 7 parent 55.13 49.91206 5.218e+00 -#> 14 parent 27.27 25.01257 2.257e+00 -#> 14 parent 26.64 25.01257 1.627e+00 -#> 21 parent 11.50 12.53462 -1.035e+00 -#> 21 parent 11.64 12.53462 -8.946e-01 -#> 35 parent 2.85 3.14787 -2.979e-01 -#> 35 parent 2.91 3.14787 -2.379e-01 -#> 50 parent 0.69 0.71624 -2.624e-02 -#> 50 parent 0.63 0.71624 -8.624e-02 -#> 75 parent 0.05 0.06074 -1.074e-02 -#> 75 parent 0.06 0.06074 -7.381e-04 -#> 1 m1 4.84 4.80296 3.704e-02 -#> 1 m1 5.64 4.80296 8.370e-01 -#> 3 m1 12.91 13.02400 -1.140e-01 -#> 3 m1 12.96 13.02400 -6.400e-02 -#> 7 m1 22.97 25.04476 -2.075e+00 -#> 7 m1 24.47 25.04476 -5.748e-01 -#> 14 m1 41.69 36.69002 5.000e+00 -#> 14 m1 33.21 36.69002 -3.480e+00 -#> 21 m1 44.37 41.65310 2.717e+00 -#> 21 m1 46.44 41.65310 4.787e+00 -#> 35 m1 41.22 43.31312 -2.093e+00 -#> 35 m1 37.95 43.31312 -5.363e+00 -#> 50 m1 41.19 41.21831 -2.831e-02 -#> 50 m1 40.01 41.21831 -1.208e+00 -#> 75 m1 40.09 36.44703 3.643e+00 -#> 75 m1 33.85 36.44703 -2.597e+00 -#> 100 m1 31.04 31.98163 -9.416e-01 -#> 100 m1 33.13 31.98163 1.148e+00 -#> 120 m1 25.15 28.78984 -3.640e+00 -#> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.obs</span> <span class='kw'><-</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'>#> <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'>#> mkin version used for fitting: 0.9.50.3 -#> R version used for fitting: 4.0.0 -#> Date of fit: Wed May 27 07:43:51 2020 -#> 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'>#> <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'><-</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'>#> <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'><-</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'>#> Likelihood ratio test +#> +#> Model 1: FOMC_SFO with error model tc and fixed parameter(s) m1_0 +#> Model 2: SFO_SFO with error model tc and fixed parameter(s) m1_0 +#> #Df LogLik Df Chisq Pr(>Chisq) +#> 1 7 -64.829 +#> 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'>#> <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs produced</span></div><div class='output co'>#> <span class='warning'>Warning: diag(.) had 0 or NA entries; non-finite result is doubtful</span></div><div class='output co'>#> mkin version used for fitting: 0.9.50.3 +#> R version used for fitting: 4.0.2 +#> Date of fit: Thu Oct 8 09:12:29 2020 +#> Date of summary: Thu Oct 8 09:12:29 2020 #> #> Equations: -#> d_parent/dt = - k_parent * parent -#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 -#> -#> Model predictions using solution type analytical -#> -#> Fitted using 978 model solutions performed in 0.413 s -#> -#> Error model: Variance unique to each observed variable -#> -#> Error model algorithm: d_3 -#> Direct fitting and three-step fitting yield approximately the same likelihood -#> -#> Starting values for parameters to be optimised: -#> value type -#> parent_0 100.7500 state -#> k_parent 0.1000 deparm -#> k_m1 0.1001 deparm -#> f_parent_to_m1 0.5000 deparm -#> sigma_parent 3.0000 error -#> sigma_m1 3.0000 error -#> -#> Starting values for the transformed parameters actually optimised: -#> value lower upper -#> parent_0 100.750000 -Inf Inf -#> log_k_parent -2.302585 -Inf Inf -#> log_k_m1 -2.301586 -Inf Inf -#> f_parent_ilr_1 0.000000 -Inf Inf -#> sigma_parent 3.000000 0 Inf -#> sigma_m1 3.000000 0 Inf -#> -#> Fixed parameter values: -#> value type -#> m1_0 0 state -#> -#> Results: -#> -#> AIC BIC logLik -#> 205.8727 215.6982 -96.93634 -#> -#> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> parent_0 99.65000 1.70200 96.19000 103.1000 -#> log_k_parent -2.31300 0.04376 -2.40200 -2.2240 -#> log_k_m1 -5.25000 0.12430 -5.50400 -4.9970 -#> f_parent_ilr_1 0.03861 0.06171 -0.08708 0.1643 -#> sigma_parent 3.40100 0.56820 2.24400 4.5590 -#> sigma_m1 2.85500 0.45240 1.93400 3.7770 -#> -#> Parameter correlation: -#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma_parent -#> parent_0 1.00000 0.51078 -0.19133 -0.59997 0.035670 -#> log_k_parent 0.51078 1.00000 -0.37458 -0.59239 0.069833 -#> log_k_m1 -0.19133 -0.37458 1.00000 0.74398 -0.026158 -#> f_parent_ilr_1 -0.59997 -0.59239 0.74398 1.00000 -0.041369 -#> sigma_parent 0.03567 0.06983 -0.02616 -0.04137 1.000000 -#> sigma_m1 -0.03385 -0.06627 0.02482 0.03926 -0.004628 -#> sigma_m1 -#> parent_0 -0.033847 -#> log_k_parent -0.066265 -#> log_k_m1 0.024823 -#> f_parent_ilr_1 0.039256 -#> sigma_parent -0.004628 -#> sigma_m1 1.000000 -#> -#> Backtransformed parameters: -#> Confidence intervals for internally transformed parameters are asymmetric. -#> t-test (unrealistically) based on the assumption of normal distribution -#> for estimators of untransformed parameters. -#> Estimate t value Pr(>t) Lower Upper -#> parent_0 99.650000 58.560 2.004e-34 96.190000 1.031e+02 -#> k_parent 0.098970 22.850 1.099e-21 0.090530 1.082e-01 -#> k_m1 0.005245 8.046 1.732e-09 0.004072 6.756e-03 -#> f_parent_to_m1 0.513600 23.560 4.352e-22 0.469300 5.578e-01 -#> sigma_parent 3.401000 5.985 5.662e-07 2.244000 4.559e+00 -#> sigma_m1 2.855000 6.311 2.215e-07 1.934000 3.777e+00 -#> -#> FOCUS Chi2 error levels in percent: -#> err.min n.optim df -#> All data 6.398 4 15 -#> parent 6.464 2 7 -#> m1 4.682 2 8 -#> -#> Resulting formation fractions: -#> ff -#> parent_m1 0.5136 -#> parent_sink 0.4864 -#> -#> Estimated disappearance times: -#> DT50 DT90 -#> parent 7.003 23.26 -#> m1 132.154 439.01 -#> -#> Data: -#> time variable observed predicted residual -#> 0 parent 99.46 99.65417 -1.942e-01 -#> 0 parent 102.04 99.65417 2.386e+00 -#> 1 parent 93.50 90.26332 3.237e+00 -#> 1 parent 92.50 90.26332 2.237e+00 -#> 3 parent 63.23 74.05306 -1.082e+01 -#> 3 parent 68.99 74.05306 -5.063e+00 -#> 7 parent 52.32 49.84325 2.477e+00 -#> 7 parent 55.13 49.84325 5.287e+00 -#> 14 parent 27.27 24.92971 2.340e+00 -#> 14 parent 26.64 24.92971 1.710e+00 -#> 21 parent 11.50 12.46890 -9.689e-01 -#> 21 parent 11.64 12.46890 -8.289e-01 -#> 35 parent 2.85 3.11925 -2.692e-01 -#> 35 parent 2.91 3.11925 -2.092e-01 -#> 50 parent 0.69 0.70679 -1.679e-02 -#> 50 parent 0.63 0.70679 -7.679e-02 -#> 75 parent 0.05 0.05952 -9.523e-03 -#> 75 parent 0.06 0.05952 4.772e-04 -#> 1 m1 4.84 4.81075 2.925e-02 -#> 1 m1 5.64 4.81075 8.292e-01 -#> 3 m1 12.91 13.04196 -1.320e-01 -#> 3 m1 12.96 13.04196 -8.196e-02 -#> 7 m1 22.97 25.06847 -2.098e+00 -#> 7 m1 24.47 25.06847 -5.985e-01 -#> 14 m1 41.69 36.70308 4.987e+00 -#> 14 m1 33.21 36.70308 -3.493e+00 -#> 21 m1 44.37 41.65115 2.719e+00 -#> 21 m1 46.44 41.65115 4.789e+00 -#> 35 m1 41.22 43.29465 -2.075e+00 -#> 35 m1 37.95 43.29465 -5.345e+00 -#> 50 m1 41.19 41.19948 -9.479e-03 -#> 50 m1 40.01 41.19948 -1.189e+00 -#> 75 m1 40.09 36.44035 3.650e+00 -#> 75 m1 33.85 36.44035 -2.590e+00 -#> 100 m1 31.04 31.98773 -9.477e-01 -#> 100 m1 33.13 31.98773 1.142e+00 -#> 120 m1 25.15 28.80429 -3.654e+00 -#> 120 m1 33.31 28.80429 4.506e+00</div><div class='input'><span class='no'>f.tc</span> <span class='kw'><-</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'>#> <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'>#> mkin version used for fitting: 0.9.50.3 -#> R version used for fitting: 4.0.0 -#> Date of fit: Wed May 27 07:43:52 2020 -#> Date of summary: Wed May 27 07:43:52 2020 -#> -#> Equations: -#> d_parent/dt = - k_parent * parent -#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 +#> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent +#> d_m1/dt = + f_parent_to_m1 * (alpha/beta) * 1/((time/beta) + 1) * +#> parent - k_m1 * m1 #> -#> Model predictions using solution type analytical +#> Model predictions using solution type deSolve #> -#> Fitted using 2088 model solutions performed in 0.714 s +#> Fitted using 3611 model solutions performed in 2.61 s #> #> Error model: Two-component variance function #> #> Error model algorithm: d_3 -#> Direct fitting and three-step fitting yield approximately the same likelihood +#> Three-step fitting yielded a higher likelihood than direct fitting #> #> Starting values for parameters to be optimised: -#> value type -#> parent_0 100.7500 state -#> k_parent 0.1000 deparm -#> k_m1 0.1001 deparm -#> f_parent_to_m1 0.5000 deparm -#> sigma_low 0.1000 error -#> rsd_high 0.1000 error +#> value type +#> parent_0 100.75 state +#> alpha 1.00 deparm +#> beta 10.00 deparm +#> k_m1 0.10 deparm +#> f_parent_to_m1 0.50 deparm +#> sigma_low 0.10 error +#> rsd_high 0.10 error #> #> Starting values for the transformed parameters actually optimised: #> value lower upper #> parent_0 100.750000 -Inf Inf -#> log_k_parent -2.302585 -Inf Inf -#> log_k_m1 -2.301586 -Inf Inf +#> log_k_m1 -2.302585 -Inf Inf #> f_parent_ilr_1 0.000000 -Inf Inf +#> log_alpha 0.000000 -Inf Inf +#> log_beta 2.302585 -Inf Inf #> sigma_low 0.100000 0 Inf #> rsd_high 0.100000 0 Inf #> @@ -932,98 +624,70 @@ Degradation Data. <em>Environments</em> 6(12) 124 #> #> Results: #> -#> AIC BIC logLik -#> 141.9656 151.7911 -64.98278 +#> AIC BIC logLik +#> 143.658 155.1211 -64.82902 #> #> Optimised, transformed parameters with symmetric confidence intervals: -#> Estimate Std. Error Lower Upper -#> parent_0 100.70000 2.621000 95.400000 106.10000 -#> log_k_parent -2.29700 0.008862 -2.315000 -2.27900 -#> log_k_m1 -5.26600 0.091310 -5.452000 -5.08000 -#> f_parent_ilr_1 0.02374 0.055300 -0.088900 0.13640 -#> sigma_low 0.00305 0.004829 -0.006786 0.01289 -#> rsd_high 0.07928 0.009418 0.060100 0.09847 +#> Estimate Std. Error Lower Upper +#> parent_0 101.600000 2.6390000 96.240000 107.000000 +#> log_k_m1 -5.284000 0.0928900 -5.473000 -5.095000 +#> f_parent_ilr_1 0.001008 0.0541900 -0.109500 0.111500 +#> log_alpha 5.522000 0.0077300 5.506000 5.538000 +#> log_beta 7.806000 NaN NaN NaN +#> sigma_low 0.002488 0.0002431 0.001992 0.002984 +#> rsd_high 0.079210 0.0093280 0.060180 0.098230 #> #> Parameter correlation: -#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 sigma_low rsd_high -#> parent_0 1.00000 0.67644 -0.10215 -0.76822 0.14294 -0.08783 -#> log_k_parent 0.67644 1.00000 -0.15102 -0.59491 0.34611 -0.08125 -#> log_k_m1 -0.10215 -0.15102 1.00000 0.51808 -0.05236 0.01240 -#> f_parent_ilr_1 -0.76822 -0.59491 0.51808 1.00000 -0.13900 0.03248 -#> sigma_low 0.14294 0.34611 -0.05236 -0.13900 1.00000 -0.16546 -#> rsd_high -0.08783 -0.08125 0.01240 0.03248 -0.16546 1.00000 +#> parent_0 log_k_m1 f_parent_ilr_1 log_alpha log_beta sigma_low +#> parent_0 1.000000 -0.094697 -0.76654 0.70525 NaN 0.016099 +#> log_k_m1 -0.094697 1.000000 0.51404 -0.14347 NaN 0.001576 +#> f_parent_ilr_1 -0.766543 0.514038 1.00000 -0.61368 NaN 0.015465 +#> log_alpha 0.705247 -0.143468 -0.61368 1.00000 NaN 5.871780 +#> log_beta NaN NaN NaN NaN 1 NaN +#> sigma_low 0.016099 0.001576 0.01546 5.87178 NaN 1.000000 +#> rsd_high 0.006566 -0.011662 -0.05353 0.04845 NaN -0.652554 +#> rsd_high +#> parent_0 0.006566 +#> log_k_m1 -0.011662 +#> f_parent_ilr_1 -0.053525 +#> log_alpha 0.048451 +#> log_beta NaN +#> sigma_low -0.652554 +#> rsd_high 1.000000 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. #> t-test (unrealistically) based on the assumption of normal distribution #> for estimators of untransformed parameters. -#> Estimate t value Pr(>t) Lower Upper -#> parent_0 1.007e+02 38.4300 1.180e-28 95.400000 1.061e+02 -#> k_parent 1.006e-01 112.8000 1.718e-43 0.098760 1.024e-01 -#> k_m1 5.167e-03 10.9500 1.171e-12 0.004290 6.223e-03 -#> f_parent_to_m1 5.084e-01 26.0100 2.146e-23 0.468600 5.481e-01 -#> sigma_low 3.050e-03 0.6314 2.661e-01 -0.006786 1.289e-02 -#> rsd_high 7.928e-02 8.4170 6.418e-10 0.060100 9.847e-02 +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 1.016e+02 32.7800 6.312e-26 9.624e+01 1.070e+02 +#> k_m1 5.072e-03 10.1200 1.216e-11 4.197e-03 6.130e-03 +#> f_parent_to_m1 5.004e-01 20.8300 4.318e-20 4.614e-01 5.394e-01 +#> alpha 2.502e+02 0.5624 2.889e-01 2.463e+02 2.542e+02 +#> beta 2.455e+03 0.5549 2.915e-01 NA NA +#> sigma_low 2.488e-03 0.4843 3.158e-01 1.992e-03 2.984e-03 +#> rsd_high 7.921e-02 8.4300 8.001e-10 6.018e-02 9.823e-02 #> #> FOCUS Chi2 error levels in percent: #> err.min n.optim df -#> All data 6.475 4 15 -#> parent 6.573 2 7 -#> m1 4.671 2 8 +#> All data 6.781 5 14 +#> parent 7.141 3 6 +#> m1 4.640 2 8 #> #> Resulting formation fractions: #> ff -#> parent_m1 0.5084 -#> parent_sink 0.4916 +#> parent_m1 0.5004 +#> parent_sink 0.4996 #> #> Estimated disappearance times: -#> DT50 DT90 -#> parent 6.893 22.9 -#> m1 134.156 445.7 -#> -#> Data: -#> time variable observed predicted residual -#> 0 parent 99.46 100.73434 -1.274340 -#> 0 parent 102.04 100.73434 1.305660 -#> 1 parent 93.50 91.09751 2.402486 -#> 1 parent 92.50 91.09751 1.402486 -#> 3 parent 63.23 74.50141 -11.271410 -#> 3 parent 68.99 74.50141 -5.511410 -#> 7 parent 52.32 49.82880 2.491200 -#> 7 parent 55.13 49.82880 5.301200 -#> 14 parent 27.27 24.64809 2.621908 -#> 14 parent 26.64 24.64809 1.991908 -#> 21 parent 11.50 12.19232 -0.692315 -#> 21 parent 11.64 12.19232 -0.552315 -#> 35 parent 2.85 2.98327 -0.133266 -#> 35 parent 2.91 2.98327 -0.073266 -#> 50 parent 0.69 0.66013 0.029874 -#> 50 parent 0.63 0.66013 -0.030126 -#> 75 parent 0.05 0.05344 -0.003438 -#> 75 parent 0.06 0.05344 0.006562 -#> 1 m1 4.84 4.88645 -0.046451 -#> 1 m1 5.64 4.88645 0.753549 -#> 3 m1 12.91 13.22867 -0.318669 -#> 3 m1 12.96 13.22867 -0.268669 -#> 7 m1 22.97 25.36417 -2.394166 -#> 7 m1 24.47 25.36417 -0.894166 -#> 14 m1 41.69 37.00974 4.680263 -#> 14 m1 33.21 37.00974 -3.799737 -#> 21 m1 44.37 41.90133 2.468669 -#> 21 m1 46.44 41.90133 4.538669 -#> 35 m1 41.22 43.45691 -2.236913 -#> 35 m1 37.95 43.45691 -5.506913 -#> 50 m1 41.19 41.34199 -0.151985 -#> 50 m1 40.01 41.34199 -1.331985 -#> 75 m1 40.09 36.61471 3.475295 -#> 75 m1 33.85 36.61471 -2.764705 -#> 100 m1 31.04 32.20082 -1.160823 -#> 100 m1 33.13 32.20082 0.929177 -#> 120 m1 25.15 29.04130 -3.891304 -#> 120 m1 33.31 29.04130 4.268696</div><div class='input'># } - - -</div></pre> +#> DT50 DT90 DT50back +#> parent 6.812 22.7 6.834 +#> 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'><-</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"> |