diff options
Diffstat (limited to 'docs/reference/update.mkinfit.html')
| -rw-r--r-- | docs/reference/update.mkinfit.html | 350 |
1 files changed, 6 insertions, 344 deletions
diff --git a/docs/reference/update.mkinfit.html b/docs/reference/update.mkinfit.html index b9f6f9a9..bb93a61e 100644 --- a/docs/reference/update.mkinfit.html +++ b/docs/reference/update.mkinfit.html @@ -72,7 +72,7 @@ override these starting values." /> </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">0.9.49.6</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.8</span> </span> </div> @@ -167,349 +167,11 @@ remove arguments given in the original call</p></td> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> -<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"DFOP"</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='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) -<span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>fit</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>)</div><div class='output co'>#> $par -#> parent_0 log_k1 log_k2 g_ilr sigma_low rsd_high -#> 100.85489822 8.84468217 -2.29693632 -14.95263998 0.00375222 0.06763435 -#> -#> $objective -#> [1] 19.40656 -#> -#> $convergence -#> [1] 0 -#> -#> $iterations -#> [1] 120 -#> -#> $evaluations -#> function gradient -#> 144 847 -#> -#> $message -#> [1] "relative convergence (4)" -#> -#> $logLik -#> [1] -19.40656 -#> -#> $d_3_message -#> threestep -#> "Three-step fitting yielded a higher likelihood than direct fitting" -#> -#> $hessian -#> parent_0 log_k1 log_k2 g_ilr sigma_low -#> parent_0 3.662473e-01 -2.914408e-16 -7.241561e+01 -3.021629e-08 1.923504e+01 -#> log_k1 -2.914408e-16 0.000000e+00 -2.215935e-13 -7.291307e-25 3.416474e-15 -#> log_k2 -7.241561e+01 -2.215935e-13 3.127457e+04 6.766544e-06 -1.495826e+04 -#> g_ilr -3.021629e-08 -7.291307e-25 6.766544e-06 3.122099e-09 -1.797429e-06 -#> sigma_low 1.923504e+01 3.416474e-15 -1.495826e+04 -1.797429e-06 7.759299e+04 -#> rsd_high 3.902119e+00 -1.801019e-16 -1.685343e+02 -3.750713e-07 3.984179e+03 -#> rsd_high -#> parent_0 3.902119e+00 -#> log_k1 -1.801019e-16 -#> log_k2 -1.685343e+02 -#> g_ilr -3.750713e-07 -#> sigma_low 3.984179e+03 -#> rsd_high 7.188991e+03 -#> -#> $hessian_notrans -#> parent_0 k1 k2 g sigma_low -#> parent_0 3.662473e-01 -3.714445e-19 -7.201669e+02 -3.261485e+01 1.923504e+01 -#> k1 -3.714445e-19 0.000000e+00 -4.258512e-15 7.218123e-21 4.355854e-18 -#> k2 -7.201669e+02 -4.258512e-15 3.092510e+06 7.263235e+04 -1.456870e+05 -#> g -3.261485e+01 7.218123e-21 7.263235e+04 3.291750e+03 -1.939948e+03 -#> sigma_low 1.923504e+01 4.355854e-18 -1.456870e+05 -1.939948e+03 7.759299e+04 -#> rsd_high 3.902119e+00 -2.259812e-19 -1.779680e+03 -4.048658e+02 3.984179e+03 -#> rsd_high -#> parent_0 3.902119e+00 -#> k1 -2.259812e-19 -#> k2 -1.779680e+03 -#> g -4.048658e+02 -#> sigma_low 3.984179e+03 -#> rsd_high 7.188991e+03 -#> -#> $call -#> mkinfit(mkinmod = "DFOP", observed = subset(FOCUS_2006_D, value != -#> 0), parms.ini = c(k1 = 0.699298911979803, k2 = 0.0899931270871125, -#> g = 0.0923391681138686), state.ini = c(parent = 101.948852047129), -#> quiet = TRUE, error_model = "tc") -#> -#> $error_model_algorithm -#> [1] "d_3" -#> -#> $solution_type -#> [1] "analytical" -#> -#> $transform_rates -#> [1] TRUE -#> -#> $transform_fractions -#> [1] TRUE -#> -#> $reweight.tol -#> [1] 1e-08 -#> -#> $reweight.max.iter -#> [1] 10 -#> -#> $control -#> $control$eval.max -#> [1] 300 -#> -#> $control$iter.max -#> [1] 200 -#> -#> -#> $calls -#> [1] 3105 -#> -#> $time -#> User System verstrichen -#> 10.251 0.000 10.257 -#> -#> $mkinmod -#> <mkinmod> model generated with -#> Use of formation fractions $use_of_ff: min -#> Specification $spec: -#> $parent -#> $type: DFOP; $sink: TRUE -#> Differential equations: -#> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * -#> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) -#> * parent -#> -#> $observed -#> name time value -#> 1 parent 0 99.46 -#> 2 parent 0 102.04 -#> 3 parent 1 93.50 -#> 4 parent 1 92.50 -#> 5 parent 3 63.23 -#> 6 parent 3 68.99 -#> 7 parent 7 52.32 -#> 8 parent 7 55.13 -#> 9 parent 14 27.27 -#> 10 parent 14 26.64 -#> 11 parent 21 11.50 -#> 12 parent 21 11.64 -#> 13 parent 35 2.85 -#> 14 parent 35 2.91 -#> 15 parent 50 0.69 -#> 16 parent 50 0.63 -#> 17 parent 75 0.05 -#> 18 parent 75 0.06 -#> -#> $obs_vars -#> [1] "parent" -#> -#> $predicted -#> name time value -#> 1 parent 0.0000000 100.85489822 -#> 2 parent 0.7575758 93.45650191 -#> 3 parent 1.0000000 91.20560523 -#> 4 parent 1.5151515 86.60082860 -#> 5 parent 2.2727273 80.24806580 -#> 6 parent 3.0000000 74.58828105 -#> 7 parent 3.0303030 74.36132158 -#> 8 parent 3.7878788 68.90641029 -#> 9 parent 4.5454545 63.85165403 -#> 10 parent 5.3030303 59.16769870 -#> 11 parent 6.0606061 54.82734352 -#> 12 parent 6.8181818 50.80538306 -#> 13 parent 7.0000000 49.88485755 -#> 14 parent 7.5757576 47.07846089 -#> 15 parent 8.3333333 43.62493394 -#> 16 parent 9.0909091 40.42474681 -#> 17 parent 9.8484848 37.45931528 -#> 18 parent 10.6060606 34.71141842 -#> 19 parent 11.3636364 32.16509858 -#> 20 parent 12.1212121 29.80556871 -#> 21 parent 12.8787879 27.61912649 -#> 22 parent 13.6363636 25.59307475 -#> 23 parent 14.0000000 24.67405211 -#> 24 parent 14.3939394 23.71564776 -#> 25 parent 15.1515152 21.97594287 -#> 26 parent 15.9090909 20.36385722 -#> 27 parent 16.6666667 18.87002909 -#> 28 parent 17.4242424 17.48578345 -#> 29 parent 18.1818182 16.20308170 -#> 30 parent 18.9393939 15.01447489 -#> 31 parent 19.6969697 13.91306051 -#> 32 parent 20.4545455 12.89244241 -#> 33 parent 21.0000000 12.20428157 -#> 34 parent 21.2121212 11.94669362 -#> 35 parent 21.9696970 11.07032198 -#> 36 parent 22.7272727 10.25823818 -#> 37 parent 23.4848485 9.50572628 -#> 38 parent 24.2424242 8.80841627 -#> 39 parent 25.0000000 8.16225872 -#> 40 parent 25.7575758 7.56350125 -#> 41 parent 26.5151515 7.00866672 -#> 42 parent 27.2727273 6.49453311 -#> 43 parent 28.0303030 6.01811471 -#> 44 parent 28.7878788 5.57664485 -#> 45 parent 29.5454545 5.16755983 -#> 46 parent 30.3030303 4.78848399 -#> 47 parent 31.0606061 4.43721595 -#> 48 parent 31.8181818 4.11171583 -#> 49 parent 32.5757576 3.81009336 -#> 50 parent 33.3333333 3.53059697 -#> 51 parent 34.0909091 3.27160354 -#> 52 parent 34.8484848 3.03160906 -#> 53 parent 35.0000000 2.98576554 -#> 54 parent 35.6060606 2.80921981 -#> 55 parent 36.3636364 2.60314433 -#> 56 parent 37.1212121 2.41218590 -#> 57 parent 37.8787879 2.23523557 -#> 58 parent 38.6363636 2.07126576 -#> 59 parent 39.3939394 1.91932426 -#> 60 parent 40.1515152 1.77852870 -#> 61 parent 40.9090909 1.64806147 -#> 62 parent 41.6666667 1.52716489 -#> 63 parent 42.4242424 1.41513691 -#> 64 parent 43.1818182 1.31132694 -#> 65 parent 43.9393939 1.21513214 -#> 66 parent 44.6969697 1.12599389 -#> 67 parent 45.4545455 1.04339454 -#> 68 parent 46.2121212 0.96685442 -#> 69 parent 46.9696970 0.89592904 -#> 70 parent 47.7272727 0.83020652 -#> 71 parent 48.4848485 0.76930520 -#> 72 parent 49.2424242 0.71287140 -#> 73 parent 50.0000000 0.66057741 -#> 74 parent 50.7575758 0.61211954 -#> 75 parent 51.5151515 0.56721639 -#> 76 parent 52.2727273 0.52560719 -#> 77 parent 53.0303030 0.48705031 -#> 78 parent 53.7878788 0.45132184 -#> 79 parent 54.5454545 0.41821430 -#> 80 parent 55.3030303 0.38753542 -#> 81 parent 56.0606061 0.35910705 -#> 82 parent 56.8181818 0.33276409 -#> 83 parent 57.5757576 0.30835357 -#> 84 parent 58.3333333 0.28573373 -#> 85 parent 59.0909091 0.26477320 -#> 86 parent 59.8484848 0.24535028 -#> 87 parent 60.6060606 0.22735216 -#> 88 parent 61.3636364 0.21067432 -#> 89 parent 62.1212121 0.19521992 -#> 90 parent 62.8787879 0.18089921 -#> 91 parent 63.6363636 0.16762901 -#> 92 parent 64.3939394 0.15533228 -#> 93 parent 65.1515152 0.14393759 -#> 94 parent 65.9090909 0.13337879 -#> 95 parent 66.6666667 0.12359454 -#> 96 parent 67.4242424 0.11452804 -#> 97 parent 68.1818182 0.10612662 -#> 98 parent 68.9393939 0.09834151 -#> 99 parent 69.6969697 0.09112749 -#> 100 parent 70.4545455 0.08444266 -#> 101 parent 71.2121212 0.07824822 -#> 102 parent 71.9696970 0.07250818 -#> 103 parent 72.7272727 0.06718920 -#> 104 parent 73.4848485 0.06226042 -#> 105 parent 74.2424242 0.05769319 -#> 106 parent 75.0000000 0.05346100 -#> -#> $rss -#> function (P) -#> cost_function(P, OLS = TRUE, update_data = FALSE) -#> <bytecode: 0x555558e48258> -#> <environment: 0x55555caa08e0> -#> -#> $ll -#> function (P, fixed_degparms = FALSE, fixed_errparms = FALSE) -#> { -#> -cost_function(P, trans = FALSE, fixed_degparms = fixed_degparms, -#> fixed_errparms = fixed_errparms, OLS = FALSE, update_data = FALSE) -#> } -#> <bytecode: 0x555558e47e30> -#> <environment: 0x55555caa08e0> -#> -#> $start -#> value type -#> parent_0 101.94885205 state -#> k1 0.69929891 deparm -#> k2 0.08999313 deparm -#> g 0.09233917 deparm -#> sigma_low 0.10000000 error -#> rsd_high 0.10000000 error -#> -#> $start_transformed -#> value lower upper -#> parent_0 101.948852 -Inf Inf -#> log_k1 -0.357677 -Inf Inf -#> log_k2 -2.408022 -Inf Inf -#> g_ilr -1.616024 -Inf Inf -#> sigma_low 0.100000 0 Inf -#> rsd_high 0.100000 0 Inf -#> -#> $fixed -#> [1] value type -#> <0 Zeilen> (oder row.names mit Länge 0) -#> -#> $data -#> time variable observed predicted residual -#> 1 0 parent 99.46 100.8548982 -1.39489822 -#> 2 0 parent 102.04 100.8548982 1.18510178 -#> 3 1 parent 93.50 91.2056052 2.29439477 -#> 4 1 parent 92.50 91.2056052 1.29439477 -#> 5 3 parent 63.23 74.5882810 -11.35828105 -#> 6 3 parent 68.99 74.5882810 -5.59828105 -#> 7 7 parent 52.32 49.8848576 2.43514245 -#> 8 7 parent 55.13 49.8848576 5.24514245 -#> 9 14 parent 27.27 24.6740521 2.59594789 -#> 10 14 parent 26.64 24.6740521 1.96594789 -#> 11 21 parent 11.50 12.2042816 -0.70428157 -#> 12 21 parent 11.64 12.2042816 -0.56428157 -#> 13 35 parent 2.85 2.9857655 -0.13576554 -#> 14 35 parent 2.91 2.9857655 -0.07576554 -#> 15 50 parent 0.69 0.6605774 0.02942259 -#> 16 50 parent 0.63 0.6605774 -0.03057741 -#> 17 75 parent 0.05 0.0534610 -0.00346100 -#> 18 75 parent 0.06 0.0534610 0.00653900 -#> -#> $atol -#> [1] 1e-08 -#> -#> $rtol -#> [1] 1e-10 -#> -#> $err_mod -#> [1] "tc" -#> -#> $bparms.optim -#> parent_0 k1 k2 g -#> 1.008549e+02 6.937399e+03 1.005665e-01 6.551046e-10 -#> -#> $bparms.fixed -#> numeric(0) -#> -#> $bparms.ode -#> k1 k2 g -#> 6.937399e+03 1.005665e-01 6.551046e-10 -#> -#> $bparms.state -#> parent -#> 100.8549 -#> -#> $errparms -#> sigma_low rsd_high -#> 0.00375222 0.06763435 -#> -#> $df.residual -#> [1] 12 -#> -#> $date -#> [1] "Fri Nov 1 10:10:42 2019" -#> -#> $version -#> [1] "0.9.49.6" -#> -#> $Rversion -#> [1] "3.6.1" -#> -#> attr(,"class") -#> [1] "mkinfit" "modFit" </div><div class='input'># } +<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFO"</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='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<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 sigma +#> 99.44423886 0.09793574 3.39632469 </div><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_err</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='update.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='no'>fit_2</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>fit</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>) +<span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit_2</span>)</div><div class='output co'>#> parent_0 k_parent_sink sigma_low rsd_high +#> 1.008549e+02 1.005665e-01 3.752222e-03 6.763434e-02 </div><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_err</a></span>(<span class='no'>fit_2</span>)</div><div class='img'><img src='update.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'># } </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> |