diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-11 05:15:19 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-05-11 05:18:32 +0200 |
| commit | 234c9059a95e104917e488a6ddd2313234a96cdc (patch) | |
| tree | f6e54098f79d94578434ef727b62f7cc5d5e79b7 /docs/reference/mkinfit.html | |
| parent | d113cd79b178fdc91aecb894707ed356129dfb75 (diff) | |
Avoid merge() and data.frame() in cost function
also for deSolve and eigenvalue based solutions. This noticeably increases
performance for these methods, see test.log and benchmark vignette.
Diffstat (limited to 'docs/reference/mkinfit.html')
| -rw-r--r-- | docs/reference/mkinfit.html | 328 |
1 files changed, 218 insertions, 110 deletions
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 62823c58..9974b66b 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -78,7 +78,7 @@ likelihood function." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span> </span> </div> @@ -174,7 +174,6 @@ likelihood function.</p> <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, - <span class='kw'>n.outtimes</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"const"</span>, <span class='st'>"obs"</span>, <span class='st'>"tc"</span>), <span class='kw'>error_model_algorithm</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"auto"</span>, <span class='st'>"d_3"</span>, <span class='st'>"direct"</span>, <span class='st'>"twostep"</span>, <span class='st'>"threestep"</span>, <span class='st'>"fourstep"</span>, <span class='st'>"IRLS"</span>, <span class='st'>"OLS"</span>), @@ -325,13 +324,6 @@ is 1e-8, lower than in <code>lsoda</code>.</p></td> is 1e-10, much lower than in <code>lsoda</code>.</p></td> </tr> <tr> - <th>n.outtimes</th> - <td><p>The length of the dataseries that is produced by the model -prediction function <code><a href='mkinpredict.html'>mkinpredict</a></code>. This impacts the accuracy -of the numerical solver if that is used (see <code>solution_type</code> -argument. The default value is 100.</p></td> - </tr> - <tr> <th>error_model</th> <td><p>If the error model is "const", a constant standard deviation is assumed.</p> @@ -422,7 +414,87 @@ estimators.</p> <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>)</div><div class='output co'>#> <span class='error'>Error in (function (t, parent_0, alpha, beta) { parent = parent_0/(t/beta + 1)^alpha})(t = c(0, 1, 1.2020202020202, 2.4040404040404, 3, 3.60606060606061, 4.80808080808081, 6.01010101010101, 7, 7.21212121212121, 8.41414141414141, 9.61616161616162, 10.8181818181818, 12.020202020202, 13.2222222222222, 14, 14.4242424242424, 15.6262626262626, 16.8282828282828, 18.030303030303, 19.2323232323232, 20.4343434343434, 21.6363636363636, 22.8383838383838, 24.040404040404, 25.2424242424242, 26.4444444444444, 27.6464646464646, 28, 28.8484848484848, 30.050505050505, 31.2525252525253, 32.4545454545455, 33.6565656565657, 34.8585858585859, 36.0606060606061, 37.2626262626263, 38.4646464646465, 39.6666666666667, 40.8686868686869, 42.0707070707071, 43.2727272727273, 44.4747474747475, 45.6767676767677, 46.8787878787879, 48.0808080808081, 49.2828282828283, 50.4848484848485, 51.6868686868687, 52.8888888888889, 54.0909090909091, 55.2929292929293, 56.4949494949495, 57.6969696969697, 58.8989898989899, 60.1010101010101, 61.3030303030303, 62.5050505050505, 63, 63.7070707070707, 64.9090909090909, 66.1111111111111, 67.3131313131313, 68.5151515151515, 69.7171717171717, 70.9191919191919, 72.1212121212121, 73.3232323232323, 74.5252525252525, 75.7272727272727, 76.9292929292929, 78.1313131313131, 79.3333333333333, 80.5353535353535, 81.7373737373737, 82.9393939393939, 84.1414141414141, 85.3434343434343, 86.5454545454545, 87.7474747474747, 88.9494949494949, 90.1515151515152, 91, 91.3535353535353, 92.5555555555556, 93.7575757575758, 94.959595959596, 96.1616161616162, 97.3636363636364, 98.5656565656566, 99.7676767676768, 100.969696969697, 102.171717171717, 103.373737373737, 104.575757575758, 105.777777777778, 106.979797979798, 108.181818181818, 109.383838383838, 110.585858585859, 111.787878787879, 112.989898989899, 114.191919191919, 115.393939393939, 116.59595959596, 117.79797979798, 119), parent.0 = c(parent = 85.1), alpha = 1, beta = 10): unbenutztes Argument (parent.0 = 85.1)</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0 0 0.001</span></div><div class='input'><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'>#> <span class='error'>Error in summary(fit): Objekt 'fit' nicht gefunden</span></div><div class='input'> +<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 +#> R version used for fitting: 4.0.0 +#> Date of fit: Mon May 11 05:14:26 2020 +#> Date of summary: Mon May 11 05:14:26 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 0.043 s +#> +#> Error model: Constant variance +#> +#> Error model algorithm: OLS +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 85.1 state +#> alpha 1.0 deparm +#> beta 10.0 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 85.100000 -Inf Inf +#> log_alpha 0.000000 -Inf Inf +#> log_beta 2.302585 -Inf Inf +#> +#> Fixed parameter values: +#> None +#> +#> Results: +#> +#> AIC BIC logLik +#> 44.68652 45.47542 -18.34326 +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 85.87000 1.8070 81.23000 90.5200 +#> log_alpha 0.05192 0.1353 -0.29580 0.3996 +#> log_beta 0.65100 0.2287 0.06315 1.2390 +#> sigma 1.85700 0.4378 0.73200 2.9830 +#> +#> Parameter correlation: +#> parent_0 log_alpha log_beta sigma +#> 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. +#> t-test (unrealistically) based on the assumption of normal distribution +#> for estimators of untransformed parameters. +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 85.870 47.530 3.893e-08 81.2300 90.520 +#> alpha 1.053 7.393 3.562e-04 0.7439 1.491 +#> beta 1.917 4.373 3.601e-03 1.0650 3.451 +#> sigma 1.857 4.243 4.074e-03 0.7320 2.983 +#> +#> FOCUS Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.657 3 6 +#> parent 6.657 3 6 +#> +#> Estimated disappearance times: +#> DT50 DT90 DT50back +#> parent 1.785 15.15 4.56 +#> +#> Data: +#> time variable observed predicted residual +#> 0 parent 85.1 85.875 -0.7749 +#> 1 parent 57.9 55.191 2.7091 +#> 3 parent 29.9 31.845 -1.9452 +#> 7 parent 14.6 17.012 -2.4124 +#> 14 parent 9.7 9.241 0.4590 +#> 28 parent 6.6 4.754 1.8460 +#> 63 parent 4.0 2.102 1.8977 +#> 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'># 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>( @@ -430,86 +502,105 @@ estimators.</p> <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 verstrichen -#> 1.526 0.000 1.526 </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_sink k_parent_m1 k_m1_sink sigma -#> 99.598483069 0.047920122 0.050777612 0.005260651 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 -#> parent_sink parent_m1 m1_sink -#> 0.485524 0.514476 1.000000 +#> 0.407 0.002 0.409 </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 +#> 99.598483222 0.098697734 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 +#> parent_m1 parent_sink +#> 0.514476 0.485524 #> #> $distimes #> DT50 DT90 #> parent 7.022929 23.32967 -#> m1 131.760712 437.69961 +#> m1 131.760715 437.69962 #> </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: 18915.53 -#> Sum of squared residuals at call 2: 18915.53 -#> Sum of squared residuals at call 6: 11424.02 -#> Sum of squared residuals at call 10: 11424 -#> Sum of squared residuals at call 12: 4094.396 -#> Sum of squared residuals at call 16: 4094.396 -#> Sum of squared residuals at call 19: 1340.595 -#> Sum of squared residuals at call 20: 1340.593 -#> Sum of squared residuals at call 25: 1072.239 -#> Sum of squared residuals at call 28: 1072.236 -#> Sum of squared residuals at call 30: 874.2615 -#> Sum of squared residuals at call 33: 874.2611 -#> Sum of squared residuals at call 35: 616.2375 -#> Sum of squared residuals at call 37: 616.237 -#> Sum of squared residuals at call 40: 467.4386 -#> Sum of squared residuals at call 42: 467.438 -#> Sum of squared residuals at call 46: 398.2913 -#> Sum of squared residuals at call 48: 398.2913 -#> Sum of squared residuals at call 49: 398.2912 -#> Sum of squared residuals at call 51: 395.0711 -#> Sum of squared residuals at call 54: 395.071 -#> Sum of squared residuals at call 56: 378.3298 -#> Sum of squared residuals at call 59: 378.3298 -#> Sum of squared residuals at call 62: 376.9812 -#> Sum of squared residuals at call 64: 376.9811 -#> Sum of squared residuals at call 67: 375.2085 -#> Sum of squared residuals at call 69: 375.2085 -#> Sum of squared residuals at call 70: 375.2085 -#> Sum of squared residuals at call 71: 375.2085 -#> Sum of squared residuals at call 72: 374.5723 -#> Sum of squared residuals at call 74: 374.5723 -#> Sum of squared residuals at call 77: 374.0075 -#> Sum of squared residuals at call 79: 374.0075 -#> Sum of squared residuals at call 80: 374.0075 -#> Sum of squared residuals at call 82: 373.1711 -#> Sum of squared residuals at call 84: 373.1711 -#> Sum of squared residuals at call 87: 372.6445 -#> Sum of squared residuals at call 88: 372.1614 -#> Sum of squared residuals at call 90: 372.1614 -#> Sum of squared residuals at call 91: 372.1614 -#> Sum of squared residuals at call 94: 371.6464 -#> Sum of squared residuals at call 99: 371.4299 -#> Sum of squared residuals at call 101: 371.4299 -#> Sum of squared residuals at call 104: 371.4071 -#> Sum of squared residuals at call 106: 371.4071 -#> Sum of squared residuals at call 107: 371.4071 -#> Sum of squared residuals at call 109: 371.2524 -#> Sum of squared residuals at call 113: 371.2524 -#> Sum of squared residuals at call 114: 371.2136 -#> Sum of squared residuals at call 115: 371.2136 -#> Sum of squared residuals at call 116: 371.2136 -#> Sum of squared residuals at call 119: 371.2134 -#> Sum of squared residuals at call 120: 371.2134 -#> Sum of squared residuals at call 122: 371.2134 -#> Sum of squared residuals at call 123: 371.2134 -#> Sum of squared residuals at call 125: 371.2134 -#> Sum of squared residuals at call 126: 371.2134 -#> Sum of squared residuals at call 135: 371.2134 -#> Negative log-likelihood at call 145: 97.22429</div><div class='output co'>#> <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#> User System verstrichen -#> 1.084 0.000 1.085 </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_sink k_parent_m1 k_m1_sink sigma -#> 99.598483072 0.047920122 0.050777612 0.005260651 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_sink parent_m1 m1_sink -#> 0.485524 0.514476 1.000000 + <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: 644.0471 +#> Sum of squared residuals at call 36: 644.0469 +#> Sum of squared residuals at call 38: 644.0469 +#> 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: 543.219 +#> Sum of squared residuals at call 45: 543.2187 +#> Sum of squared residuals at call 46: 543.2186 +#> 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: 386.4789 +#> Sum of squared residuals at call 58: 386.4789 +#> 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: 373.5433 +#> Sum of squared residuals at call 100: 373.5433 +#> Sum of squared residuals at call 102: 373.2654 +#> Sum of squared residuals at call 104: 373.2654 +#> Sum of squared residuals at call 107: 372.6841 +#> Sum of squared residuals at call 111: 372.684 +#> Sum of squared residuals at call 114: 372.6374 +#> Sum of squared residuals at call 116: 372.6374 +#> Sum of squared residuals at call 119: 372.6223 +#> Sum of squared residuals at call 121: 372.6223 +#> Sum of squared residuals at call 123: 372.6223 +#> Sum of squared residuals at call 124: 372.5903 +#> Sum of squared residuals at call 126: 372.5903 +#> Sum of squared residuals at call 129: 372.5445 +#> Sum of squared residuals at call 130: 372.4921 +#> Sum of squared residuals at call 131: 372.2377 +#> Sum of squared residuals at call 132: 371.5434 +#> Sum of squared residuals at call 134: 371.5434 +#> Sum of squared residuals at call 137: 371.2857 +#> Sum of squared residuals at call 139: 371.2857 +#> Sum of squared residuals at call 143: 371.2247 +#> Sum of squared residuals at call 144: 371.2247 +#> Sum of squared residuals at call 149: 371.2189 +#> Sum of squared residuals at call 150: 371.2145 +#> Sum of squared residuals at call 153: 371.2145 +#> Sum of squared residuals at call 155: 371.2138 +#> Sum of squared residuals at call 156: 371.2138 +#> Sum of squared residuals at call 157: 371.2138 +#> Sum of squared residuals at call 161: 371.2134 +#> Sum of squared residuals at call 162: 371.2134 +#> Sum of squared residuals at call 165: 371.2134 +#> Sum of squared residuals at call 166: 371.2134 +#> Sum of squared residuals at call 168: 371.2134 +#> Negative log-likelihood at call 178: 97.22429</div><div class='output co'>#> <span class='message'>Optimisation successfully terminated.</span></div><div class='output co'>#> User System verstrichen +#> 0.349 0.000 0.350 </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 +#> 99.598480759 0.098697739 0.005260651 0.514475958 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 23.32967 -#> m1 131.760712 437.69961 +#> parent 7.022929 23.32966 +#> m1 131.760731 437.69967 #> </div><div class='input'><span class='co'># }</span> <span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, FOMC</span> @@ -518,31 +609,33 @@ estimators.</p> <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>)</div><div class='output co'>#> <span class='error'>Error in (function (t, parent_0, alpha, beta) { parent = parent_0/(t/beta + 1)^alpha})(t = c(0, 0.757575757575758, 1, 1.51515151515152, 2.27272727272727, 3, 3.03030303030303, 3.78787878787879, 4.54545454545454, 5.3030303030303, 6.06060606060606, 6.81818181818182, 7, 7.57575757575758, 8.33333333333333, 9.09090909090909, 9.84848484848485, 10.6060606060606, 11.3636363636364, 12.1212121212121, 12.8787878787879, 13.6363636363636, 14, 14.3939393939394, 15.1515151515152, 15.9090909090909, 16.6666666666667, 17.4242424242424, 18.1818181818182, 18.9393939393939, 19.6969696969697, 20.4545454545455, 21, 21.2121212121212, 21.969696969697, 22.7272727272727, 23.4848484848485, 24.2424242424242, 25, 25.7575757575758, 26.5151515151515, 27.2727272727273, 28.030303030303, 28.7878787878788, 29.5454545454545, 30.3030303030303, 31.0606060606061, 31.8181818181818, 32.5757575757576, 33.3333333333333, 34.0909090909091, 34.8484848484849, 35, 35.6060606060606, 36.3636363636364, 37.1212121212121, 37.8787878787879, 38.6363636363636, 39.3939393939394, 40.1515151515151, 40.9090909090909, 41.6666666666667, 42.4242424242424, 43.1818181818182, 43.9393939393939, 44.6969696969697, 45.4545454545455, 46.2121212121212, 46.969696969697, 47.7272727272727, 48.4848484848485, 49.2424242424242, 50, 50.7575757575758, 51.5151515151515, 52.2727272727273, 53.030303030303, 53.7878787878788, 54.5454545454545, 55.3030303030303, 56.0606060606061, 56.8181818181818, 57.5757575757576, 58.3333333333333, 59.0909090909091, 59.8484848484849, 60.6060606060606, 61.3636363636364, 62.1212121212121, 62.8787878787879, 63.6363636363636, 64.3939393939394, 65.1515151515152, 65.9090909090909, 66.6666666666667, 67.4242424242424, 68.1818181818182, 68.9393939393939, 69.6969696969697, 70.4545454545455, 71.2121212121212, 71.969696969697, 72.7272727272727, 73.4848484848485, 74.2424242424242, 75), parent.0 = c(parent = 100.75), alpha = 1, beta = 10): unbenutztes Argument (parent.0 = 100.75)</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0 0 0.001</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_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='output co'>#> <span class='error'>Error in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE, parms.ini = fit.FOMC$bparms.ode): Objekt 'fit.FOMC' nicht gefunden</span></div><div class='input'> +<span class='no'>fit.FOMC</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='no'>fit.FOMC_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.FOMC</span>$<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>)</div><div class='output co'>#> <span class='error'>Error in (function (t, parent_0, k_12, k_21, k_1output) { sqrt_exp = sqrt(1/4 * (k_12 + k_21 + k_1output)^2 + k_12 * k_21 - (k_12 + k_1output) * k_21) b1 = 0.5 * (k_12 + k_21 + k_1output) + sqrt_exp b2 = 0.5 * (k_12 + k_21 + k_1output) - sqrt_exp parent = parent_0 * (((k_12 + k_21 - b1)/(b2 - b1)) * exp(-b1 * t) + ((k_12 + k_21 - b2)/(b1 - b2)) * exp(-b2 * t))})(t = c(0, 0.757575757575758, 1, 1.51515151515152, 2.27272727272727, 3, 3.03030303030303, 3.78787878787879, 4.54545454545454, 5.3030303030303, 6.06060606060606, 6.81818181818182, 7, 7.57575757575758, 8.33333333333333, 9.09090909090909, 9.84848484848485, 10.6060606060606, 11.3636363636364, 12.1212121212121, 12.8787878787879, 13.6363636363636, 14, 14.3939393939394, 15.1515151515152, 15.9090909090909, 16.6666666666667, 17.4242424242424, 18.1818181818182, 18.9393939393939, 19.6969696969697, 20.4545454545455, 21, 21.2121212121212, 21.969696969697, 22.7272727272727, 23.4848484848485, 24.2424242424242, 25, 25.7575757575758, 26.5151515151515, 27.2727272727273, 28.030303030303, 28.7878787878788, 29.5454545454545, 30.3030303030303, 31.0606060606061, 31.8181818181818, 32.5757575757576, 33.3333333333333, 34.0909090909091, 34.8484848484849, 35, 35.6060606060606, 36.3636363636364, 37.1212121212121, 37.8787878787879, 38.6363636363636, 39.3939393939394, 40.1515151515151, 40.9090909090909, 41.6666666666667, 42.4242424242424, 43.1818181818182, 43.9393939393939, 44.6969696969697, 45.4545454545455, 46.2121212121212, 46.969696969697, 47.7272727272727, 48.4848484848485, 49.2424242424242, 50, 50.7575757575758, 51.5151515151515, 52.2727272727273, 53.030303030303, 53.7878787878788, 54.5454545454545, 55.3030303030303, 56.0606060606061, 56.8181818181818, 57.5757575757576, 58.3333333333333, 59.0909090909091, 59.8484848484849, 60.6060606060606, 61.3636363636364, 62.1212121212121, 62.8787878787879, 63.6363636363636, 64.3939393939394, 65.1515151515152, 65.9090909090909, 66.6666666666667, 67.4242424242424, 68.1818181818182, 68.9393939393939, 69.6969696969697, 70.4545454545455, 71.2121212121212, 71.969696969697, 72.7272727272727, 73.4848484848485, 74.2424242424242, 75), parent.0 = c(parent_free = 100.75), k_1output = 0.1, k_12 = 0.1, k_21 = 0.02): unbenutztes Argument (parent.0 = 100.75)</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0.001 0 0.001</span></div><div class='input'><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>$<span class='no'>bparms.ode</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div><div class='output co'>#> <span class='error'>Error in mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode, quiet = TRUE): Objekt 'fit.SFORB' nicht gefunden</span></div><div class='input'><span class='co'># }</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</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: 0.9.49.11 + <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 #> R version used for fitting: 4.0.0 -#> Date of fit: Thu May 7 08:59:03 2020 -#> Date of summary: Thu May 7 08:59:03 2020 +#> Date of fit: Mon May 11 05:14:31 2020 +#> Date of summary: Mon May 11 05:14:31 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 deSolve +#> Model predictions using solution type analytical #> -#> Fitted using 422 model solutions performed in 1.106 s +#> Fitted using 421 model solutions performed in 0.124 s #> #> Error model: Constant variance #> @@ -566,6 +659,11 @@ estimators.</p> #> 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 @@ -576,11 +674,11 @@ estimators.</p> #> #> 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 -2.443e-07 -#> log_k_parent 5.174e-01 1.000e+00 -3.263e-01 -5.426e-01 3.181e-07 -#> log_k_m1 -1.688e-01 -3.263e-01 1.000e+00 7.478e-01 -1.369e-07 -#> f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 -2.287e-08 -#> sigma -2.443e-07 3.181e-07 -1.369e-07 -2.287e-08 1.000e+00 +#> parent_0 1.000e+00 5.174e-01 -1.688e-01 -5.471e-01 -3.214e-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 -1.410e-07 +#> f_parent_ilr_1 -5.471e-01 -5.426e-01 7.478e-01 1.000e+00 5.093e-10 +#> sigma -3.214e-07 3.168e-07 -1.410e-07 5.093e-10 1.000e+00 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. @@ -648,18 +746,18 @@ estimators.</p> #> 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: 0.9.49.11 +#> 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 #> R version used for fitting: 4.0.0 -#> Date of fit: Thu May 7 08:59:06 2020 -#> Date of summary: Thu May 7 08:59:06 2020 +#> Date of fit: Mon May 11 05:14:32 2020 +#> Date of summary: Mon May 11 05:14:32 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 deSolve +#> Model predictions using solution type analytical #> -#> Fitted using 979 model solutions performed in 2.604 s +#> Fitted using 978 model solutions performed in 0.336 s #> #> Error model: Variance unique to each observed variable #> @@ -688,6 +786,11 @@ estimators.</p> #> 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 @@ -780,23 +883,23 @@ estimators.</p> #> 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: 0.9.49.11 +#> 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 #> R version used for fitting: 4.0.0 -#> Date of fit: Thu May 7 08:59:16 2020 -#> Date of summary: Thu May 7 08:59:16 2020 +#> Date of fit: Mon May 11 05:14:32 2020 +#> Date of summary: Mon May 11 05:14:32 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 deSolve +#> Model predictions using solution type analytical #> -#> Fitted using 2552 model solutions performed in 10.544 s +#> Fitted using 1875 model solutions performed in 0.642 s #> #> Error model: Two-component variance function #> #> Error model algorithm: d_3 -#> Three-step fitting yielded a higher likelihood than direct fitting +#> Direct fitting and three-step fitting yield approximately the same likelihood #> #> Starting values for parameters to be optimised: #> value type @@ -820,6 +923,11 @@ estimators.</p> #> value type #> m1_0 0 state #> +#> Results: +#> +#> AIC BIC logLik +#> 141.9656 151.7911 -64.98278 +#> #> Optimised, transformed parameters with symmetric confidence intervals: #> Estimate Std. Error Lower Upper #> parent_0 100.70000 2.621000 95.400000 106.10000 @@ -868,14 +976,14 @@ estimators.</p> #> #> Data: #> time variable observed predicted residual -#> 0 parent 99.46 100.73434 -1.274339 -#> 0 parent 102.04 100.73434 1.305661 +#> 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 2.491201 -#> 7 parent 55.13 49.82880 5.301201 +#> 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 @@ -902,8 +1010,8 @@ estimators.</p> #> 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 -1.160824 -#> 100 m1 33.13 32.20082 0.929176 +#> 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'># } |