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-rw-r--r--docs/reference/update.mkinfit.html350
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'>&lt;-</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'>#&gt; $par
-#&gt; parent_0 log_k1 log_k2 g_ilr sigma_low rsd_high
-#&gt; 100.85489822 8.84468217 -2.29693632 -14.95263998 0.00375222 0.06763435
-#&gt;
-#&gt; $objective
-#&gt; [1] 19.40656
-#&gt;
-#&gt; $convergence
-#&gt; [1] 0
-#&gt;
-#&gt; $iterations
-#&gt; [1] 120
-#&gt;
-#&gt; $evaluations
-#&gt; function gradient
-#&gt; 144 847
-#&gt;
-#&gt; $message
-#&gt; [1] "relative convergence (4)"
-#&gt;
-#&gt; $logLik
-#&gt; [1] -19.40656
-#&gt;
-#&gt; $d_3_message
-#&gt; threestep
-#&gt; "Three-step fitting yielded a higher likelihood than direct fitting"
-#&gt;
-#&gt; $hessian
-#&gt; parent_0 log_k1 log_k2 g_ilr sigma_low
-#&gt; parent_0 3.662473e-01 -2.914408e-16 -7.241561e+01 -3.021629e-08 1.923504e+01
-#&gt; log_k1 -2.914408e-16 0.000000e+00 -2.215935e-13 -7.291307e-25 3.416474e-15
-#&gt; log_k2 -7.241561e+01 -2.215935e-13 3.127457e+04 6.766544e-06 -1.495826e+04
-#&gt; g_ilr -3.021629e-08 -7.291307e-25 6.766544e-06 3.122099e-09 -1.797429e-06
-#&gt; sigma_low 1.923504e+01 3.416474e-15 -1.495826e+04 -1.797429e-06 7.759299e+04
-#&gt; rsd_high 3.902119e+00 -1.801019e-16 -1.685343e+02 -3.750713e-07 3.984179e+03
-#&gt; rsd_high
-#&gt; parent_0 3.902119e+00
-#&gt; log_k1 -1.801019e-16
-#&gt; log_k2 -1.685343e+02
-#&gt; g_ilr -3.750713e-07
-#&gt; sigma_low 3.984179e+03
-#&gt; rsd_high 7.188991e+03
-#&gt;
-#&gt; $hessian_notrans
-#&gt; parent_0 k1 k2 g sigma_low
-#&gt; parent_0 3.662473e-01 -3.714445e-19 -7.201669e+02 -3.261485e+01 1.923504e+01
-#&gt; k1 -3.714445e-19 0.000000e+00 -4.258512e-15 7.218123e-21 4.355854e-18
-#&gt; k2 -7.201669e+02 -4.258512e-15 3.092510e+06 7.263235e+04 -1.456870e+05
-#&gt; g -3.261485e+01 7.218123e-21 7.263235e+04 3.291750e+03 -1.939948e+03
-#&gt; sigma_low 1.923504e+01 4.355854e-18 -1.456870e+05 -1.939948e+03 7.759299e+04
-#&gt; rsd_high 3.902119e+00 -2.259812e-19 -1.779680e+03 -4.048658e+02 3.984179e+03
-#&gt; rsd_high
-#&gt; parent_0 3.902119e+00
-#&gt; k1 -2.259812e-19
-#&gt; k2 -1.779680e+03
-#&gt; g -4.048658e+02
-#&gt; sigma_low 3.984179e+03
-#&gt; rsd_high 7.188991e+03
-#&gt;
-#&gt; $call
-#&gt; mkinfit(mkinmod = "DFOP", observed = subset(FOCUS_2006_D, value !=
-#&gt; 0), parms.ini = c(k1 = 0.699298911979803, k2 = 0.0899931270871125,
-#&gt; g = 0.0923391681138686), state.ini = c(parent = 101.948852047129),
-#&gt; quiet = TRUE, error_model = "tc")
-#&gt;
-#&gt; $error_model_algorithm
-#&gt; [1] "d_3"
-#&gt;
-#&gt; $solution_type
-#&gt; [1] "analytical"
-#&gt;
-#&gt; $transform_rates
-#&gt; [1] TRUE
-#&gt;
-#&gt; $transform_fractions
-#&gt; [1] TRUE
-#&gt;
-#&gt; $reweight.tol
-#&gt; [1] 1e-08
-#&gt;
-#&gt; $reweight.max.iter
-#&gt; [1] 10
-#&gt;
-#&gt; $control
-#&gt; $control$eval.max
-#&gt; [1] 300
-#&gt;
-#&gt; $control$iter.max
-#&gt; [1] 200
-#&gt;
-#&gt;
-#&gt; $calls
-#&gt; [1] 3105
-#&gt;
-#&gt; $time
-#&gt; User System verstrichen
-#&gt; 10.251 0.000 10.257
-#&gt;
-#&gt; $mkinmod
-#&gt; &lt;mkinmod&gt; model generated with
-#&gt; Use of formation fractions $use_of_ff: min
-#&gt; Specification $spec:
-#&gt; $parent
-#&gt; $type: DFOP; $sink: TRUE
-#&gt; Differential equations:
-#&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
-#&gt; time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))
-#&gt; * parent
-#&gt;
-#&gt; $observed
-#&gt; name time value
-#&gt; 1 parent 0 99.46
-#&gt; 2 parent 0 102.04
-#&gt; 3 parent 1 93.50
-#&gt; 4 parent 1 92.50
-#&gt; 5 parent 3 63.23
-#&gt; 6 parent 3 68.99
-#&gt; 7 parent 7 52.32
-#&gt; 8 parent 7 55.13
-#&gt; 9 parent 14 27.27
-#&gt; 10 parent 14 26.64
-#&gt; 11 parent 21 11.50
-#&gt; 12 parent 21 11.64
-#&gt; 13 parent 35 2.85
-#&gt; 14 parent 35 2.91
-#&gt; 15 parent 50 0.69
-#&gt; 16 parent 50 0.63
-#&gt; 17 parent 75 0.05
-#&gt; 18 parent 75 0.06
-#&gt;
-#&gt; $obs_vars
-#&gt; [1] "parent"
-#&gt;
-#&gt; $predicted
-#&gt; name time value
-#&gt; 1 parent 0.0000000 100.85489822
-#&gt; 2 parent 0.7575758 93.45650191
-#&gt; 3 parent 1.0000000 91.20560523
-#&gt; 4 parent 1.5151515 86.60082860
-#&gt; 5 parent 2.2727273 80.24806580
-#&gt; 6 parent 3.0000000 74.58828105
-#&gt; 7 parent 3.0303030 74.36132158
-#&gt; 8 parent 3.7878788 68.90641029
-#&gt; 9 parent 4.5454545 63.85165403
-#&gt; 10 parent 5.3030303 59.16769870
-#&gt; 11 parent 6.0606061 54.82734352
-#&gt; 12 parent 6.8181818 50.80538306
-#&gt; 13 parent 7.0000000 49.88485755
-#&gt; 14 parent 7.5757576 47.07846089
-#&gt; 15 parent 8.3333333 43.62493394
-#&gt; 16 parent 9.0909091 40.42474681
-#&gt; 17 parent 9.8484848 37.45931528
-#&gt; 18 parent 10.6060606 34.71141842
-#&gt; 19 parent 11.3636364 32.16509858
-#&gt; 20 parent 12.1212121 29.80556871
-#&gt; 21 parent 12.8787879 27.61912649
-#&gt; 22 parent 13.6363636 25.59307475
-#&gt; 23 parent 14.0000000 24.67405211
-#&gt; 24 parent 14.3939394 23.71564776
-#&gt; 25 parent 15.1515152 21.97594287
-#&gt; 26 parent 15.9090909 20.36385722
-#&gt; 27 parent 16.6666667 18.87002909
-#&gt; 28 parent 17.4242424 17.48578345
-#&gt; 29 parent 18.1818182 16.20308170
-#&gt; 30 parent 18.9393939 15.01447489
-#&gt; 31 parent 19.6969697 13.91306051
-#&gt; 32 parent 20.4545455 12.89244241
-#&gt; 33 parent 21.0000000 12.20428157
-#&gt; 34 parent 21.2121212 11.94669362
-#&gt; 35 parent 21.9696970 11.07032198
-#&gt; 36 parent 22.7272727 10.25823818
-#&gt; 37 parent 23.4848485 9.50572628
-#&gt; 38 parent 24.2424242 8.80841627
-#&gt; 39 parent 25.0000000 8.16225872
-#&gt; 40 parent 25.7575758 7.56350125
-#&gt; 41 parent 26.5151515 7.00866672
-#&gt; 42 parent 27.2727273 6.49453311
-#&gt; 43 parent 28.0303030 6.01811471
-#&gt; 44 parent 28.7878788 5.57664485
-#&gt; 45 parent 29.5454545 5.16755983
-#&gt; 46 parent 30.3030303 4.78848399
-#&gt; 47 parent 31.0606061 4.43721595
-#&gt; 48 parent 31.8181818 4.11171583
-#&gt; 49 parent 32.5757576 3.81009336
-#&gt; 50 parent 33.3333333 3.53059697
-#&gt; 51 parent 34.0909091 3.27160354
-#&gt; 52 parent 34.8484848 3.03160906
-#&gt; 53 parent 35.0000000 2.98576554
-#&gt; 54 parent 35.6060606 2.80921981
-#&gt; 55 parent 36.3636364 2.60314433
-#&gt; 56 parent 37.1212121 2.41218590
-#&gt; 57 parent 37.8787879 2.23523557
-#&gt; 58 parent 38.6363636 2.07126576
-#&gt; 59 parent 39.3939394 1.91932426
-#&gt; 60 parent 40.1515152 1.77852870
-#&gt; 61 parent 40.9090909 1.64806147
-#&gt; 62 parent 41.6666667 1.52716489
-#&gt; 63 parent 42.4242424 1.41513691
-#&gt; 64 parent 43.1818182 1.31132694
-#&gt; 65 parent 43.9393939 1.21513214
-#&gt; 66 parent 44.6969697 1.12599389
-#&gt; 67 parent 45.4545455 1.04339454
-#&gt; 68 parent 46.2121212 0.96685442
-#&gt; 69 parent 46.9696970 0.89592904
-#&gt; 70 parent 47.7272727 0.83020652
-#&gt; 71 parent 48.4848485 0.76930520
-#&gt; 72 parent 49.2424242 0.71287140
-#&gt; 73 parent 50.0000000 0.66057741
-#&gt; 74 parent 50.7575758 0.61211954
-#&gt; 75 parent 51.5151515 0.56721639
-#&gt; 76 parent 52.2727273 0.52560719
-#&gt; 77 parent 53.0303030 0.48705031
-#&gt; 78 parent 53.7878788 0.45132184
-#&gt; 79 parent 54.5454545 0.41821430
-#&gt; 80 parent 55.3030303 0.38753542
-#&gt; 81 parent 56.0606061 0.35910705
-#&gt; 82 parent 56.8181818 0.33276409
-#&gt; 83 parent 57.5757576 0.30835357
-#&gt; 84 parent 58.3333333 0.28573373
-#&gt; 85 parent 59.0909091 0.26477320
-#&gt; 86 parent 59.8484848 0.24535028
-#&gt; 87 parent 60.6060606 0.22735216
-#&gt; 88 parent 61.3636364 0.21067432
-#&gt; 89 parent 62.1212121 0.19521992
-#&gt; 90 parent 62.8787879 0.18089921
-#&gt; 91 parent 63.6363636 0.16762901
-#&gt; 92 parent 64.3939394 0.15533228
-#&gt; 93 parent 65.1515152 0.14393759
-#&gt; 94 parent 65.9090909 0.13337879
-#&gt; 95 parent 66.6666667 0.12359454
-#&gt; 96 parent 67.4242424 0.11452804
-#&gt; 97 parent 68.1818182 0.10612662
-#&gt; 98 parent 68.9393939 0.09834151
-#&gt; 99 parent 69.6969697 0.09112749
-#&gt; 100 parent 70.4545455 0.08444266
-#&gt; 101 parent 71.2121212 0.07824822
-#&gt; 102 parent 71.9696970 0.07250818
-#&gt; 103 parent 72.7272727 0.06718920
-#&gt; 104 parent 73.4848485 0.06226042
-#&gt; 105 parent 74.2424242 0.05769319
-#&gt; 106 parent 75.0000000 0.05346100
-#&gt;
-#&gt; $rss
-#&gt; function (P)
-#&gt; cost_function(P, OLS = TRUE, update_data = FALSE)
-#&gt; &lt;bytecode: 0x555558e48258&gt;
-#&gt; &lt;environment: 0x55555caa08e0&gt;
-#&gt;
-#&gt; $ll
-#&gt; function (P, fixed_degparms = FALSE, fixed_errparms = FALSE)
-#&gt; {
-#&gt; -cost_function(P, trans = FALSE, fixed_degparms = fixed_degparms,
-#&gt; fixed_errparms = fixed_errparms, OLS = FALSE, update_data = FALSE)
-#&gt; }
-#&gt; &lt;bytecode: 0x555558e47e30&gt;
-#&gt; &lt;environment: 0x55555caa08e0&gt;
-#&gt;
-#&gt; $start
-#&gt; value type
-#&gt; parent_0 101.94885205 state
-#&gt; k1 0.69929891 deparm
-#&gt; k2 0.08999313 deparm
-#&gt; g 0.09233917 deparm
-#&gt; sigma_low 0.10000000 error
-#&gt; rsd_high 0.10000000 error
-#&gt;
-#&gt; $start_transformed
-#&gt; value lower upper
-#&gt; parent_0 101.948852 -Inf Inf
-#&gt; log_k1 -0.357677 -Inf Inf
-#&gt; log_k2 -2.408022 -Inf Inf
-#&gt; g_ilr -1.616024 -Inf Inf
-#&gt; sigma_low 0.100000 0 Inf
-#&gt; rsd_high 0.100000 0 Inf
-#&gt;
-#&gt; $fixed
-#&gt; [1] value type
-#&gt; &lt;0 Zeilen&gt; (oder row.names mit Länge 0)
-#&gt;
-#&gt; $data
-#&gt; time variable observed predicted residual
-#&gt; 1 0 parent 99.46 100.8548982 -1.39489822
-#&gt; 2 0 parent 102.04 100.8548982 1.18510178
-#&gt; 3 1 parent 93.50 91.2056052 2.29439477
-#&gt; 4 1 parent 92.50 91.2056052 1.29439477
-#&gt; 5 3 parent 63.23 74.5882810 -11.35828105
-#&gt; 6 3 parent 68.99 74.5882810 -5.59828105
-#&gt; 7 7 parent 52.32 49.8848576 2.43514245
-#&gt; 8 7 parent 55.13 49.8848576 5.24514245
-#&gt; 9 14 parent 27.27 24.6740521 2.59594789
-#&gt; 10 14 parent 26.64 24.6740521 1.96594789
-#&gt; 11 21 parent 11.50 12.2042816 -0.70428157
-#&gt; 12 21 parent 11.64 12.2042816 -0.56428157
-#&gt; 13 35 parent 2.85 2.9857655 -0.13576554
-#&gt; 14 35 parent 2.91 2.9857655 -0.07576554
-#&gt; 15 50 parent 0.69 0.6605774 0.02942259
-#&gt; 16 50 parent 0.63 0.6605774 -0.03057741
-#&gt; 17 75 parent 0.05 0.0534610 -0.00346100
-#&gt; 18 75 parent 0.06 0.0534610 0.00653900
-#&gt;
-#&gt; $atol
-#&gt; [1] 1e-08
-#&gt;
-#&gt; $rtol
-#&gt; [1] 1e-10
-#&gt;
-#&gt; $err_mod
-#&gt; [1] "tc"
-#&gt;
-#&gt; $bparms.optim
-#&gt; parent_0 k1 k2 g
-#&gt; 1.008549e+02 6.937399e+03 1.005665e-01 6.551046e-10
-#&gt;
-#&gt; $bparms.fixed
-#&gt; numeric(0)
-#&gt;
-#&gt; $bparms.ode
-#&gt; k1 k2 g
-#&gt; 6.937399e+03 1.005665e-01 6.551046e-10
-#&gt;
-#&gt; $bparms.state
-#&gt; parent
-#&gt; 100.8549
-#&gt;
-#&gt; $errparms
-#&gt; sigma_low rsd_high
-#&gt; 0.00375222 0.06763435
-#&gt;
-#&gt; $df.residual
-#&gt; [1] 12
-#&gt;
-#&gt; $date
-#&gt; [1] "Fri Nov 1 10:10:42 2019"
-#&gt;
-#&gt; $version
-#&gt; [1] "0.9.49.6"
-#&gt;
-#&gt; $Rversion
-#&gt; [1] "3.6.1"
-#&gt;
-#&gt; attr(,"class")
-#&gt; [1] "mkinfit" "modFit" </div><div class='input'># }
+<span class='no'>fit</span> <span class='kw'>&lt;-</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'>#&gt; parent_0 k_parent_sink sigma
+#&gt; 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'>&lt;-</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'>#&gt; parent_0 k_parent_sink sigma_low rsd_high
+#&gt; 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>
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