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Diffstat (limited to 'docs/reference/mkinfit.html')
| -rw-r--r-- | docs/reference/mkinfit.html | 836 |
1 files changed, 798 insertions, 38 deletions
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index b1c42168..13029e91 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -71,7 +71,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.3</span> + <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.9.47.4</span> </span> </div> @@ -432,17 +432,17 @@ <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'><-</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'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.3 +<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 06:39:09 2018 -#> Date of summary: Fri Sep 14 06:39:09 2018 +#> Date of fit: Fri Sep 14 11:34:54 2018 +#> Date of summary: Fri Sep 14 11:34:54 2018 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.157 s +#> Fitted with method Port using 64 model solutions performed in 0.141 s #> #> Weighting: none #> @@ -511,7 +511,7 @@ <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'>print</span>(<span class='fu'>system.time</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'>#> User System verstrichen -#> 0.892 0.000 0.892 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.906 0.000 0.907 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750 </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 #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -523,19 +523,86 @@ #> DT50 DT90 #> parent 7.022929 23.32967 #> m1 131.760712 437.69961 -#> </div><span class='co'># NOT RUN {</span> -<span class='co'># deSolve is slower when no C compiler (gcc) was available during model generation</span> +#> </div><div class='input'><span class='co'># deSolve is slower when no C compiler (gcc) was available during model generation</span> <span class='fu'>print</span>(<span class='fu'>system.time</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>))) -<span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>) -<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>) -<span class='co'># }</span><div class='input'> + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)))</div><div class='output co'>#> Model cost at call 1 : 18915.53 +#> Model cost at call 2 : 18915.53 +#> Model cost at call 6 : 11424.02 +#> Model cost at call 10 : 11424 +#> Model cost at call 12 : 4094.396 +#> Model cost at call 16 : 4094.396 +#> Model cost at call 19 : 1340.595 +#> Model cost at call 20 : 1340.593 +#> Model cost at call 25 : 1072.239 +#> Model cost at call 28 : 1072.236 +#> Model cost at call 30 : 874.2615 +#> Model cost at call 33 : 874.2611 +#> Model cost at call 35 : 616.2377 +#> Model cost at call 37 : 616.2372 +#> Model cost at call 40 : 467.4386 +#> Model cost at call 42 : 467.4381 +#> Model cost at call 46 : 398.2914 +#> Model cost at call 48 : 398.2914 +#> Model cost at call 49 : 398.2913 +#> Model cost at call 51 : 395.0712 +#> Model cost at call 54 : 395.0711 +#> Model cost at call 56 : 378.3298 +#> Model cost at call 59 : 378.3298 +#> Model cost at call 62 : 376.9812 +#> Model cost at call 64 : 376.9811 +#> Model cost at call 67 : 375.2085 +#> Model cost at call 69 : 375.2085 +#> Model cost at call 70 : 375.2085 +#> Model cost at call 71 : 375.2085 +#> Model cost at call 72 : 374.5723 +#> Model cost at call 74 : 374.5723 +#> Model cost at call 77 : 374.0075 +#> Model cost at call 79 : 374.0075 +#> Model cost at call 80 : 374.0075 +#> Model cost at call 82 : 373.1711 +#> Model cost at call 84 : 373.1711 +#> Model cost at call 87 : 372.6445 +#> Model cost at call 88 : 372.1614 +#> Model cost at call 90 : 372.1614 +#> Model cost at call 91 : 372.1614 +#> Model cost at call 94 : 371.6464 +#> Model cost at call 99 : 371.4299 +#> Model cost at call 101 : 371.4299 +#> Model cost at call 104 : 371.4071 +#> Model cost at call 106 : 371.4071 +#> Model cost at call 107 : 371.4071 +#> Model cost at call 109 : 371.2524 +#> Model cost at call 113 : 371.2524 +#> Model cost at call 114 : 371.2136 +#> Model cost at call 115 : 371.2136 +#> Model cost at call 116 : 371.2136 +#> Model cost at call 119 : 371.2134 +#> Model cost at call 120 : 371.2134 +#> Model cost at call 122 : 371.2134 +#> Model cost at call 123 : 371.2134 +#> Model cost at call 125 : 371.2134 +#> Model cost at call 126 : 371.2134 +#> Model cost at call 135 : 371.2134 +#> Model cost at call 146 : 371.2134 +#> Optimisation by method Port successfully terminated. +#> User System verstrichen +#> 0.714 0.000 0.715 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 99.59848 -3.03822 -2.98030 -5.24750 </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_sink parent_m1 m1_sink +#> 0.485524 0.514476 1.000000 +#> +#> $SFORB +#> logical(0) +#> +#> $distimes +#> DT50 DT90 +#> parent 7.022929 23.32967 +#> m1 131.760711 437.69961 +#> </div><div class='input'> # Use stepwise fitting, using optimised parameters from parent only fit, FOMC -</div><span class='co'># NOT RUN {</span> -<span class='no'>FOMC_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( +</div><div class='input'><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>)) -<span class='co'># Fit the model to the FOCUS example dataset D using defaults</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>) <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>) @@ -545,40 +612,733 @@ <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'>list</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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)) -<span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</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>) <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>) <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>) -<span class='co'># }</span><div class='input'> -</div><span class='co'># NOT RUN {</span> -<span class='co'># Weighted fits, including IRLS</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='input'> +</div><div class='input'><span class='co'># Weighted fits, including IRLS</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>) -<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>) -<span class='fu'>summary</span>(<span class='no'>f.noweight</span>) -<span class='no'>f.irls</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'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>f.irls</span>) -<span class='no'>f.w.mean</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'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>f.w.mean</span>) -<span class='no'>f.w.value</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='fu'>subset</span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"value"</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>) +<span class='fu'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 +#> R version used for fitting: 3.5.1 +#> Date of fit: Fri Sep 14 11:35:05 2018 +#> Date of summary: Fri Sep 14 11:35:05 2018 +#> +#> 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 deSolve +#> +#> Fitted with method Port using 186 model solutions performed in 0.763 s +#> +#> Weighting: none +#> +#> 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 +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 99.60000 1.61400 96.3300 102.9000 +#> log_k_parent -2.31600 0.04187 -2.4010 -2.2310 +#> log_k_m1 -5.24800 0.13610 -5.5230 -4.9720 +#> f_parent_ilr_1 0.04096 0.06477 -0.0904 0.1723 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.0000 0.5178 -0.1701 -0.5489 +#> log_k_parent 0.5178 1.0000 -0.3285 -0.5451 +#> log_k_m1 -0.1701 -0.3285 1.0000 0.7466 +#> f_parent_ilr_1 -0.5489 -0.5451 0.7466 1.0000 +#> +#> Residual standard error: 3.211 on 36 degrees of freedom +#> +#> 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 61.720 2.024e-38 96.330000 1.029e+02 +#> k_parent 0.098700 23.880 5.700e-24 0.090660 1.074e-01 +#> k_m1 0.005261 7.349 5.758e-09 0.003992 6.933e-03 +#> f_parent_to_m1 0.514500 22.490 4.375e-23 0.468100 5.606e-01 +#> +#> 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 +#> 0 m1 0.00 0.00000 0.000e+00 +#> 0 m1 0.00 0.00000 0.000e+00 +#> 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.irls</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'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 +#> R version used for fitting: 3.5.1 +#> Date of fit: Fri Sep 14 11:35:07 2018 +#> Date of summary: Fri Sep 14 11:35:07 2018 +#> +#> 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 deSolve +#> +#> Fitted with method Port using 551 model solutions performed in 2.297 s +#> +#> Weighting: none +#> +#> Iterative reweighting with method obs +#> Final mean squared residuals of observed variables: +#> parent m1 +#> 11.573407 7.407845 +#> +#> 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 +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 99.67000 1.79200 96.04000 103.300 +#> log_k_parent -2.31200 0.04560 -2.40400 -2.219 +#> log_k_m1 -5.25100 0.12510 -5.50500 -4.998 +#> f_parent_ilr_1 0.03785 0.06318 -0.09027 0.166 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.0000 0.5083 -0.1979 -0.6148 +#> log_k_parent 0.5083 1.0000 -0.3894 -0.6062 +#> log_k_m1 -0.1979 -0.3894 1.0000 0.7417 +#> f_parent_ilr_1 -0.6148 -0.6062 0.7417 1.0000 +#> +#> Residual standard error: 1.054 on 36 degrees of freedom +#> +#> 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 99.67000 55.630 8.185e-37 96.040000 1.033e+02 +#> k_parent 0.09906 21.930 1.016e-22 0.090310 1.087e-01 +#> k_m1 0.00524 7.996 8.486e-10 0.004066 6.753e-03 +#> f_parent_to_m1 0.51340 23.000 2.038e-23 0.468100 5.584e-01 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.399 4 15 +#> parent 6.466 2 7 +#> m1 4.679 2 8 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.5134 +#> parent_sink 0.4866 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 6.997 23.24 +#> m1 132.282 439.43 +#> +#> Data: +#> time variable observed predicted residual err +#> 0 parent 99.46 99.67218 -2.122e-01 3.402 +#> 0 parent 102.04 99.67218 2.368e+00 3.402 +#> 1 parent 93.50 90.27153 3.228e+00 3.402 +#> 1 parent 92.50 90.27153 2.228e+00 3.402 +#> 3 parent 63.23 74.04648 -1.082e+01 3.402 +#> 3 parent 68.99 74.04648 -5.056e+00 3.402 +#> 7 parent 52.32 49.82092 2.499e+00 3.402 +#> 7 parent 55.13 49.82092 5.309e+00 3.402 +#> 14 parent 27.27 24.90288 2.367e+00 3.402 +#> 14 parent 26.64 24.90288 1.737e+00 3.402 +#> 21 parent 11.50 12.44765 -9.476e-01 3.402 +#> 21 parent 11.64 12.44765 -8.076e-01 3.402 +#> 35 parent 2.85 3.11002 -2.600e-01 3.402 +#> 35 parent 2.91 3.11002 -2.000e-01 3.402 +#> 50 parent 0.69 0.70374 -1.374e-02 3.402 +#> 50 parent 0.63 0.70374 -7.374e-02 3.402 +#> 75 parent 0.05 0.05913 -9.134e-03 3.402 +#> 75 parent 0.06 0.05913 8.662e-04 3.402 +#> 0 m1 0.00 0.00000 0.000e+00 2.722 +#> 0 m1 0.00 0.00000 0.000e+00 2.722 +#> 1 m1 4.84 4.81328 2.672e-02 2.722 +#> 1 m1 5.64 4.81328 8.267e-01 2.722 +#> 3 m1 12.91 13.04779 -1.378e-01 2.722 +#> 3 m1 12.96 13.04779 -8.779e-02 2.722 +#> 7 m1 22.97 25.07615 -2.106e+00 2.722 +#> 7 m1 24.47 25.07615 -6.062e-01 2.722 +#> 14 m1 41.69 36.70729 4.983e+00 2.722 +#> 14 m1 33.21 36.70729 -3.497e+00 2.722 +#> 21 m1 44.37 41.65050 2.720e+00 2.722 +#> 21 m1 46.44 41.65050 4.790e+00 2.722 +#> 35 m1 41.22 43.28866 -2.069e+00 2.722 +#> 35 m1 37.95 43.28866 -5.339e+00 2.722 +#> 50 m1 41.19 41.19339 -3.386e-03 2.722 +#> 50 m1 40.01 41.19339 -1.183e+00 2.722 +#> 75 m1 40.09 36.43820 3.652e+00 2.722 +#> 75 m1 33.85 36.43820 -2.588e+00 2.722 +#> 100 m1 31.04 31.98971 -9.497e-01 2.722 +#> 100 m1 33.13 31.98971 1.140e+00 2.722 +#> 120 m1 25.15 28.80898 -3.659e+00 2.722 +#> 120 m1 33.31 28.80898 4.501e+00 2.722</div><div class='input'><span class='no'>f.w.mean</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'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 +#> R version used for fitting: 3.5.1 +#> Date of fit: Fri Sep 14 11:35:08 2018 +#> Date of summary: Fri Sep 14 11:35:08 2018 +#> +#> 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 deSolve +#> +#> Fitted with method Port using 155 model solutions performed in 0.618 s +#> +#> Weighting: mean +#> +#> 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 +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 99.7300 1.93200 95.81000 103.6000 +#> log_k_parent -2.3090 0.04837 -2.40700 -2.2110 +#> log_k_m1 -5.2550 0.12070 -5.49900 -5.0100 +#> f_parent_ilr_1 0.0354 0.06344 -0.09327 0.1641 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.0000 0.5004 -0.2143 -0.6514 +#> log_k_parent 0.5004 1.0000 -0.4282 -0.6383 +#> log_k_m1 -0.2143 -0.4282 1.0000 0.7390 +#> f_parent_ilr_1 -0.6514 -0.6383 0.7390 1.0000 +#> +#> Residual standard error: 0.09829 on 36 degrees of freedom +#> +#> 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 99.730000 51.630 1.166e-35 95.81000 1.036e+02 +#> k_parent 0.099360 20.670 7.304e-22 0.09007 1.096e-01 +#> k_m1 0.005224 8.287 3.649e-10 0.00409 6.672e-03 +#> f_parent_to_m1 0.512500 22.860 2.497e-23 0.46710 5.578e-01 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.401 4 15 +#> parent 6.473 2 7 +#> m1 4.671 2 8 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.5125 +#> parent_sink 0.4875 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 6.976 23.18 +#> m1 132.696 440.81 +#> +#> Data: +#> time variable observed predicted residual +#> 0 parent 99.46 99.73057 -0.270570 +#> 0 parent 102.04 99.73057 2.309430 +#> 1 parent 93.50 90.29805 3.201945 +#> 1 parent 92.50 90.29805 2.201945 +#> 3 parent 63.23 74.02503 -10.795028 +#> 3 parent 68.99 74.02503 -5.035028 +#> 7 parent 52.32 49.74838 2.571618 +#> 7 parent 55.13 49.74838 5.381618 +#> 14 parent 27.27 24.81588 2.454124 +#> 14 parent 26.64 24.81588 1.824124 +#> 21 parent 11.50 12.37885 -0.878849 +#> 21 parent 11.64 12.37885 -0.738849 +#> 35 parent 2.85 3.08022 -0.230219 +#> 35 parent 2.91 3.08022 -0.170219 +#> 50 parent 0.69 0.69396 -0.003958 +#> 50 parent 0.63 0.69396 -0.063958 +#> 75 parent 0.05 0.05789 -0.007888 +#> 75 parent 0.06 0.05789 0.002112 +#> 0 m1 0.00 0.00000 0.000000 +#> 0 m1 0.00 0.00000 0.000000 +#> 1 m1 4.84 4.82149 0.018512 +#> 1 m1 5.64 4.82149 0.818512 +#> 3 m1 12.91 13.06669 -0.156692 +#> 3 m1 12.96 13.06669 -0.106692 +#> 7 m1 22.97 25.10106 -2.131058 +#> 7 m1 24.47 25.10106 -0.631058 +#> 14 m1 41.69 36.72092 4.969077 +#> 14 m1 33.21 36.72092 -3.510923 +#> 21 m1 44.37 41.64835 2.721647 +#> 21 m1 46.44 41.64835 4.791647 +#> 35 m1 41.22 43.26923 -2.049225 +#> 35 m1 37.95 43.26923 -5.319225 +#> 50 m1 41.19 41.17364 0.016361 +#> 50 m1 40.01 41.17364 -1.163639 +#> 75 m1 40.09 36.43122 3.658776 +#> 75 m1 33.85 36.43122 -2.581224 +#> 100 m1 31.04 31.99612 -0.956124 +#> 100 m1 33.13 31.99612 1.133876 +#> 120 m1 25.15 28.82413 -3.674128 +#> 120 m1 33.31 28.82413 4.485872</div><div class='input'><span class='no'>f.w.value</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='fu'>subset</span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"value"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>f.w.value</span>) -<span class='co'># }</span><div class='input'> -</div><span class='co'># NOT RUN {</span> -<span class='co'># Manual weighting</span> +<span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 +#> R version used for fitting: 3.5.1 +#> Date of fit: Fri Sep 14 11:35:09 2018 +#> Date of summary: Fri Sep 14 11:35:09 2018 +#> +#> 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 deSolve +#> +#> Fitted with method Port using 174 model solutions performed in 0.704 s +#> +#> Weighting: manual +#> +#> 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 +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 99.6600 2.712000 94.14000 105.2000 +#> log_k_parent -2.2980 0.008118 -2.31500 -2.2820 +#> log_k_m1 -5.2410 0.096690 -5.43800 -5.0450 +#> f_parent_ilr_1 0.0231 0.057990 -0.09474 0.1409 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.00000 0.6843 -0.08687 -0.7564 +#> log_k_parent 0.68435 1.0000 -0.12695 -0.5812 +#> log_k_m1 -0.08687 -0.1269 1.00000 0.5195 +#> f_parent_ilr_1 -0.75644 -0.5812 0.51952 1.0000 +#> +#> Residual standard error: 0.08396 on 34 degrees of freedom +#> +#> 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 99.660000 36.75 2.957e-29 94.14000 1.052e+02 +#> k_parent 0.100400 123.20 5.927e-47 0.09878 1.021e-01 +#> k_m1 0.005295 10.34 2.447e-12 0.00435 6.444e-03 +#> f_parent_to_m1 0.508200 24.79 1.184e-23 0.46660 5.497e-01 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.461 4 15 +#> parent 6.520 2 7 +#> m1 4.744 2 8 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.5082 +#> parent_sink 0.4918 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 6.902 22.93 +#> m1 130.916 434.89 +#> +#> Data: +#> time variable observed predicted residual err +#> 0 parent 99.46 99.65571 -0.195715 99.46 +#> 0 parent 102.04 99.65571 2.384285 102.04 +#> 1 parent 93.50 90.13383 3.366170 93.50 +#> 1 parent 92.50 90.13383 2.366170 92.50 +#> 3 parent 63.23 73.73252 -10.502518 63.23 +#> 3 parent 68.99 73.73252 -4.742518 68.99 +#> 7 parent 52.32 49.34027 2.979728 52.32 +#> 7 parent 55.13 49.34027 5.789728 55.13 +#> 14 parent 27.27 24.42873 2.841271 27.27 +#> 14 parent 26.64 24.42873 2.211271 26.64 +#> 21 parent 11.50 12.09484 -0.594842 11.50 +#> 21 parent 11.64 12.09484 -0.454842 11.64 +#> 35 parent 2.85 2.96482 -0.114824 2.85 +#> 35 parent 2.91 2.96482 -0.054824 2.91 +#> 50 parent 0.69 0.65733 0.032670 0.69 +#> 50 parent 0.63 0.65733 -0.027330 0.63 +#> 75 parent 0.05 0.05339 -0.003386 0.05 +#> 75 parent 0.06 0.05339 0.006614 0.06 +#> 1 m1 4.84 4.82570 0.014301 4.84 +#> 1 m1 5.64 4.82570 0.814301 5.64 +#> 3 m1 12.91 13.06402 -0.154020 12.91 +#> 3 m1 12.96 13.06402 -0.104020 12.96 +#> 7 m1 22.97 25.04656 -2.076564 22.97 +#> 7 m1 24.47 25.04656 -0.576564 24.47 +#> 14 m1 41.69 36.53601 5.153988 41.69 +#> 14 m1 33.21 36.53601 -3.326012 33.21 +#> 21 m1 44.37 41.34639 3.023609 44.37 +#> 21 m1 46.44 41.34639 5.093609 46.44 +#> 35 m1 41.22 42.82669 -1.606690 41.22 +#> 35 m1 37.95 42.82669 -4.876690 37.95 +#> 50 m1 41.19 40.67342 0.516578 41.19 +#> 50 m1 40.01 40.67342 -0.663422 40.01 +#> 75 m1 40.09 35.91105 4.178947 40.09 +#> 75 m1 33.85 35.91105 -2.061053 33.85 +#> 100 m1 31.04 31.48161 -0.441612 31.04 +#> 100 m1 33.13 31.48161 1.648388 33.13 +#> 120 m1 25.15 28.32018 -3.170181 25.15 +#> 120 m1 33.31 28.32018 4.989819 33.31</div><div class='input'> +</div><div class='input'><span class='co'># Manual weighting</span> <span class='no'>dw</span> <span class='kw'><-</span> <span class='no'>FOCUS_2006_D</span> <span class='no'>errors</span> <span class='kw'><-</span> <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>1</span>) <span class='no'>dw</span>$<span class='no'>err.man</span> <span class='kw'><-</span> <span class='no'>errors</span>[<span class='no'>FOCUS_2006_D</span>$<span class='no'>name</span>] <span class='no'>f.w.man</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'>summary</span>(<span class='no'>f.w.man</span>) -<span class='no'>f.w.man.irls</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, +<span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 +#> R version used for fitting: 3.5.1 +#> Date of fit: Fri Sep 14 11:35:10 2018 +#> Date of summary: Fri Sep 14 11:35:10 2018 +#> +#> 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 deSolve +#> +#> Fitted with method Port using 270 model solutions performed in 1.109 s +#> +#> Weighting: manual +#> +#> 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 +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 99.49000 1.33200 96.7800 102.2000 +#> log_k_parent -2.32100 0.03550 -2.3930 -2.2490 +#> log_k_m1 -5.24100 0.21280 -5.6730 -4.8100 +#> f_parent_ilr_1 0.04571 0.08966 -0.1361 0.2275 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.00000 0.5312 -0.09456 -0.3351 +#> log_k_parent 0.53123 1.0000 -0.17800 -0.3360 +#> log_k_m1 -0.09456 -0.1780 1.00000 0.7616 +#> f_parent_ilr_1 -0.33514 -0.3360 0.76156 1.0000 +#> +#> Residual standard error: 2.628 on 36 degrees of freedom +#> +#> 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 99.490000 74.69 2.221e-41 96.780000 1.022e+02 +#> k_parent 0.098140 28.17 2.012e-26 0.091320 1.055e-01 +#> k_m1 0.005292 4.70 1.873e-05 0.003437 8.148e-03 +#> f_parent_to_m1 0.516200 16.30 1.686e-18 0.452000 5.798e-01 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.400 4 15 +#> parent 6.454 2 7 +#> m1 4.708 2 8 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.5162 +#> parent_sink 0.4838 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 7.063 23.46 +#> m1 130.971 435.08 +#> +#> Data: +#> time variable observed predicted residual err +#> 0 parent 99.46 99.48598 -0.025979 1 +#> 0 parent 102.04 99.48598 2.554021 1 +#> 1 parent 93.50 90.18612 3.313880 1 +#> 1 parent 92.50 90.18612 2.313880 1 +#> 3 parent 63.23 74.11316 -10.883163 1 +#> 3 parent 68.99 74.11316 -5.123163 1 +#> 7 parent 52.32 50.05030 2.269705 1 +#> 7 parent 55.13 50.05030 5.079705 1 +#> 14 parent 27.27 25.17975 2.090250 1 +#> 14 parent 26.64 25.17975 1.460250 1 +#> 21 parent 11.50 12.66765 -1.167654 1 +#> 21 parent 11.64 12.66765 -1.027654 1 +#> 35 parent 2.85 3.20616 -0.356164 1 +#> 35 parent 2.91 3.20616 -0.296164 1 +#> 50 parent 0.69 0.73562 -0.045619 1 +#> 50 parent 0.63 0.73562 -0.105619 1 +#> 75 parent 0.05 0.06326 -0.013256 1 +#> 75 parent 0.06 0.06326 -0.003256 1 +#> 0 m1 0.00 0.00000 0.000000 2 +#> 0 m1 0.00 0.00000 0.000000 2 +#> 1 m1 4.84 4.78729 0.052713 2 +#> 1 m1 5.64 4.78729 0.852713 2 +#> 3 m1 12.91 12.98785 -0.077848 2 +#> 3 m1 12.96 12.98785 -0.027848 2 +#> 7 m1 22.97 24.99695 -2.026946 2 +#> 7 m1 24.47 24.99695 -0.526946 2 +#> 14 m1 41.69 36.66353 5.026472 2 +#> 14 m1 33.21 36.66353 -3.453528 2 +#> 21 m1 44.37 41.65681 2.713186 2 +#> 21 m1 46.44 41.65681 4.783186 2 +#> 35 m1 41.22 43.35031 -2.130314 2 +#> 35 m1 37.95 43.35031 -5.400314 2 +#> 50 m1 41.19 41.25637 -0.066368 2 +#> 50 m1 40.01 41.25637 -1.246368 2 +#> 75 m1 40.09 36.46057 3.629429 2 +#> 75 m1 33.85 36.46057 -2.610571 2 +#> 100 m1 31.04 31.96929 -0.929293 2 +#> 100 m1 33.13 31.96929 1.160707 2 +#> 120 m1 25.15 28.76062 -3.610621 2 +#> 120 m1 33.31 28.76062 4.549379 2</div><div class='input'><span class='no'>f.w.man.irls</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>) -<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>) -<span class='co'># }</span></pre> +<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.4 +#> R version used for fitting: 3.5.1 +#> Date of fit: Fri Sep 14 11:35:13 2018 +#> Date of summary: Fri Sep 14 11:35:13 2018 +#> +#> 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 deSolve +#> +#> Fitted with method Port using 692 model solutions performed in 2.903 s +#> +#> Weighting: manual +#> +#> Iterative reweighting with method obs +#> Final mean squared residuals of observed variables: +#> parent m1 +#> 11.573406 7.407846 +#> +#> 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 +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 99.67000 1.79200 96.04000 103.300 +#> log_k_parent -2.31200 0.04560 -2.40400 -2.220 +#> log_k_m1 -5.25100 0.12510 -5.50500 -4.998 +#> f_parent_ilr_1 0.03785 0.06318 -0.09027 0.166 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.0000 0.5083 -0.1979 -0.6148 +#> log_k_parent 0.5083 1.0000 -0.3894 -0.6062 +#> log_k_m1 -0.1979 -0.3894 1.0000 0.7417 +#> f_parent_ilr_1 -0.6148 -0.6062 0.7417 1.0000 +#> +#> Residual standard error: 1.054 on 36 degrees of freedom +#> +#> 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 99.67000 55.630 8.185e-37 96.040000 1.033e+02 +#> k_parent 0.09906 21.930 1.016e-22 0.090310 1.087e-01 +#> k_m1 0.00524 7.996 8.486e-10 0.004066 6.753e-03 +#> f_parent_to_m1 0.51340 23.000 2.039e-23 0.468100 5.584e-01 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.399 4 15 +#> parent 6.466 2 7 +#> m1 4.679 2 8 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.5134 +#> parent_sink 0.4866 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 6.997 23.24 +#> m1 132.282 439.43 +#> +#> Data: +#> time variable observed predicted residual err.ini err +#> 0 parent 99.46 99.67217 -2.122e-01 1 3.402 +#> 0 parent 102.04 99.67217 2.368e+00 1 3.402 +#> 1 parent 93.50 90.27152 3.228e+00 1 3.402 +#> 1 parent 92.50 90.27152 2.228e+00 1 3.402 +#> 3 parent 63.23 74.04648 -1.082e+01 1 3.402 +#> 3 parent 68.99 74.04648 -5.056e+00 1 3.402 +#> 7 parent 52.32 49.82092 2.499e+00 1 3.402 +#> 7 parent 55.13 49.82092 5.309e+00 1 3.402 +#> 14 parent 27.27 24.90288 2.367e+00 1 3.402 +#> 14 parent 26.64 24.90288 1.737e+00 1 3.402 +#> 21 parent 11.50 12.44765 -9.477e-01 1 3.402 +#> 21 parent 11.64 12.44765 -8.077e-01 1 3.402 +#> 35 parent 2.85 3.11002 -2.600e-01 1 3.402 +#> 35 parent 2.91 3.11002 -2.000e-01 1 3.402 +#> 50 parent 0.69 0.70375 -1.375e-02 1 3.402 +#> 50 parent 0.63 0.70375 -7.375e-02 1 3.402 +#> 75 parent 0.05 0.05913 -9.134e-03 1 3.402 +#> 75 parent 0.06 0.05913 8.661e-04 1 3.402 +#> 0 m1 0.00 0.00000 0.000e+00 2 2.722 +#> 0 m1 0.00 0.00000 0.000e+00 2 2.722 +#> 1 m1 4.84 4.81328 2.672e-02 2 2.722 +#> 1 m1 5.64 4.81328 8.267e-01 2 2.722 +#> 3 m1 12.91 13.04779 -1.378e-01 2 2.722 +#> 3 m1 12.96 13.04779 -8.779e-02 2 2.722 +#> 7 m1 22.97 25.07615 -2.106e+00 2 2.722 +#> 7 m1 24.47 25.07615 -6.062e-01 2 2.722 +#> 14 m1 41.69 36.70729 4.983e+00 2 2.722 +#> 14 m1 33.21 36.70729 -3.497e+00 2 2.722 +#> 21 m1 44.37 41.65050 2.719e+00 2 2.722 +#> 21 m1 46.44 41.65050 4.789e+00 2 2.722 +#> 35 m1 41.22 43.28866 -2.069e+00 2 2.722 +#> 35 m1 37.95 43.28866 -5.339e+00 2 2.722 +#> 50 m1 41.19 41.19339 -3.387e-03 2 2.722 +#> 50 m1 40.01 41.19339 -1.183e+00 2 2.722 +#> 75 m1 40.09 36.43820 3.652e+00 2 2.722 +#> 75 m1 33.85 36.43820 -2.588e+00 2 2.722 +#> 100 m1 31.04 31.98971 -9.497e-01 2 2.722 +#> 100 m1 33.13 31.98971 1.140e+00 2 2.722 +#> 120 m1 25.15 28.80897 -3.659e+00 2 2.722 +#> 120 m1 33.31 28.80897 4.501e+00 2 2.722</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> |