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-rw-r--r--docs/reference/Extract.mmkin.html711
1 files changed, 23 insertions, 688 deletions
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 09d7513c..6a75a530 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -120,7 +120,20 @@
#> SFO List,42
#> FOMC List,42
#> attr(,"class")
-#&gt; [1] &quot;mmkin&quot;</div><div class='input'> <span class='no'>fits</span>[, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]$<span class='no'>FOMC</span></div><div class='output co'>#&gt; $par
+#&gt; [1] &quot;mmkin&quot;</div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#&gt; dataset
+#&gt; model B
+#&gt; SFO List,42
+#&gt; attr(,&quot;class&quot;)
+#&gt; [1] &quot;mmkin&quot;</div><div class='input'>
+ <span class='fu'>head</span>(
+ <span class='co'># This extracts an mkinfit object with lots of components</span>
+ <span class='no'>fits</span><span class='kw'>[[</span><span class='st'>"FOMC"</span>, <span class='st'>"B"</span>]]
+ )</div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>Attaching package: ‘utils’</span></div><div class='output co'>#&gt; <span class='message'>The following objects are masked from ‘devtools_shims’:</span>
+#&gt; <span class='message'></span>
+#&gt; <span class='message'> ?, help</span></div><div class='output co'>#&gt; <span class='message'>The following object is masked from ‘package:inline’:</span>
+#&gt; <span class='message'></span>
+#&gt; <span class='message'> package.skeleton</span></div><div class='output co'>#&gt; $par
#&gt; parent_0 log_alpha log_beta
#&gt; 99.666193 2.549849 5.050586
#&gt;
@@ -139,689 +152,11 @@
#&gt;
#&gt; $counts
#&gt; [1] &quot;both X-convergence and relative convergence (5)&quot;
-#&gt;
-#&gt; $hessian
-#&gt; parent_0 log_alpha log_beta
-#&gt; parent_0 4.123033 -95.69983 93.17699
-#&gt; log_alpha -95.699832 6618.85833 -6352.46648
-#&gt; log_beta 93.176993 -6352.46648 6101.23483
-#&gt;
-#&gt; $residuals
-#&gt; parent parent parent parent parent parent
-#&gt; 1.046192647 -3.322396479 3.655156669 -1.705316770 0.406306255 -0.123734689
-#&gt; parent parent
-#&gt; -0.036886982 -0.006240458
-#&gt;
-#&gt; $ms
-#&gt; [1] 3.572863
-#&gt;
-#&gt; $var_ms
-#&gt; parent
-#&gt; 3.572863
-#&gt;
-#&gt; $var_ms_unscaled
-#&gt; parent
-#&gt; 3.572863
-#&gt;
-#&gt; $var_ms_unweighted
-#&gt; parent
-#&gt; 3.572863
-#&gt;
-#&gt; $rank
-#&gt; [1] 3
-#&gt;
-#&gt; $df.residual
-#&gt; [1] 5
-#&gt;
-#&gt; $solution_type
-#&gt; [1] &quot;analytical&quot;
-#&gt;
-#&gt; $transform_rates
-#&gt; [1] TRUE
-#&gt;
-#&gt; $transform_fractions
-#&gt; [1] TRUE
-#&gt;
-#&gt; $method.modFit
-#&gt; [1] &quot;Port&quot;
-#&gt;
-#&gt; $maxit.modFit
-#&gt; [1] &quot;auto&quot;
-#&gt;
-#&gt; $calls
-#&gt; [1] 111
-#&gt;
-#&gt; $time
-#&gt; user system elapsed
-#&gt; 0.256 0.000 0.255
-#&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: FOMC; $sink: TRUE
-#&gt;
-#&gt; $observed
-#&gt; name time value
-#&gt; 1 parent 0 98.62
-#&gt; 2 parent 3 81.43
-#&gt; 3 parent 7 53.18
-#&gt; 4 parent 14 34.89
-#&gt; 5 parent 30 10.09
-#&gt; 6 parent 62 1.50
-#&gt; 7 parent 90 0.33
-#&gt; 8 parent 118 0.08
-#&gt;
-#&gt; $obs_vars
-#&gt; [1] &quot;parent&quot;
-#&gt;
-#&gt; $predicted
-#&gt; name time value
-#&gt; 1 parent 0.000000 99.66619265
-#&gt; 2 parent 1.191919 90.41690342
-#&gt; 3 parent 2.383838 82.08630014
-#&gt; 4 parent 3.000000 78.10760352
-#&gt; 5 parent 3.575758 74.57722848
-#&gt; 6 parent 4.767677 67.80342415
-#&gt; 7 parent 5.959596 61.68822425
-#&gt; 8 parent 7.000000 56.83515667
-#&gt; 9 parent 7.151515 56.16343898
-#&gt; 10 parent 8.343434 51.16836285
-#&gt; 11 parent 9.535354 46.64890734
-#&gt; 12 parent 10.727273 42.55683931
-#&gt; 13 parent 11.919192 38.84911158
-#&gt; 14 parent 13.111111 35.48727414
-#&gt; 15 parent 14.000000 33.18468323
-#&gt; 16 parent 14.303030 32.43695565
-#&gt; 17 parent 15.494949 29.66740651
-#&gt; 18 parent 16.686869 27.15109578
-#&gt; 19 parent 17.878788 24.86335532
-#&gt; 20 parent 19.070707 22.78206538
-#&gt; 21 parent 20.262626 20.88737647
-#&gt; 22 parent 21.454545 19.16146324
-#&gt; 23 parent 22.646465 17.58830644
-#&gt; 24 parent 23.838384 16.15349953
-#&gt; 25 parent 25.030303 14.84407724
-#&gt; 26 parent 26.222222 13.64836315
-#&gt; 27 parent 27.414141 12.55583436
-#&gt; 28 parent 28.606061 11.55700107
-#&gt; 29 parent 29.797980 10.64329940
-#&gt; 30 parent 30.000000 10.49630626
-#&gt; 31 parent 30.989899 9.80699593
-#&gt; 32 parent 32.181818 9.04110261
-#&gt; 33 parent 33.373737 8.33930082
-#&gt; 34 parent 34.565657 7.69587362
-#&gt; 35 parent 35.757576 7.10564515
-#&gt; 36 parent 36.949495 6.56392657
-#&gt; 37 parent 38.141414 6.06646759
-#&gt; 38 parent 39.333333 5.60941311
-#&gt; 39 parent 40.525253 5.18926438
-#&gt; 40 parent 41.717172 4.80284421
-#&gt; 41 parent 42.909091 4.44726569
-#&gt; 42 parent 44.101010 4.11990420
-#&gt; 43 parent 45.292929 3.81837216
-#&gt; 44 parent 46.484848 3.54049644
-#&gt; 45 parent 47.676768 3.28429799
-#&gt; 46 parent 48.868687 3.04797350
-#&gt; 47 parent 50.060606 2.82987892
-#&gt; 48 parent 51.252525 2.62851456
-#&gt; 49 parent 52.444444 2.44251172
-#&gt; 50 parent 53.636364 2.27062056
-#&gt; 51 parent 54.828283 2.11169922
-#&gt; 52 parent 56.020202 1.96470393
-#&gt; 53 parent 57.212121 1.82868009
-#&gt; 54 parent 58.404040 1.70275424
-#&gt; 55 parent 59.595960 1.58612677
-#&gt; 56 parent 60.787879 1.47806529
-#&gt; 57 parent 61.979798 1.37789865
-#&gt; 58 parent 62.000000 1.37626531
-#&gt; 59 parent 63.171717 1.28501157
-#&gt; 60 parent 64.363636 1.19883967
-#&gt; 61 parent 65.555556 1.11886504
-#&gt; 62 parent 66.747475 1.04461220
-#&gt; 63 parent 67.939394 0.97564441
-#&gt; 64 parent 69.131313 0.91156031
-#&gt; 65 parent 70.323232 0.85199096
-#&gt; 66 parent 71.515152 0.79659697
-#&gt; 67 parent 72.707071 0.74506609
-#&gt; 68 parent 73.898990 0.69711084
-#&gt; 69 parent 75.090909 0.65246649
-#&gt; 70 parent 76.282828 0.61088912
-#&gt; 71 parent 77.474747 0.57215389
-#&gt; 72 parent 78.666667 0.53605348
-#&gt; 73 parent 79.858586 0.50239663
-#&gt; 74 parent 81.050505 0.47100683
-#&gt; 75 parent 82.242424 0.44172111
-#&gt; 76 parent 83.434343 0.41438896
-#&gt; 77 parent 84.626263 0.38887128
-#&gt; 78 parent 85.818182 0.36503953
-#&gt; 79 parent 87.010101 0.34277481
-#&gt; 80 parent 88.202020 0.32196716
-#&gt; 81 parent 89.393939 0.30251479
-#&gt; 82 parent 90.000000 0.29311302
-#&gt; 83 parent 90.585859 0.28432347
-#&gt; 84 parent 91.777778 0.26730596
-#&gt; 85 parent 92.969697 0.25138141
-#&gt; 86 parent 94.161616 0.23647487
-#&gt; 87 parent 95.353535 0.22251689
-#&gt; 88 parent 96.545455 0.20944302
-#&gt; 89 parent 97.737374 0.19719349
-#&gt; 90 parent 98.929293 0.18571281
-#&gt; 91 parent 100.121212 0.17494947
-#&gt; 92 parent 101.313131 0.16485560
-#&gt; 93 parent 102.505051 0.15538676
-#&gt; 94 parent 103.696970 0.14650163
-#&gt; 95 parent 104.888889 0.13816179
-#&gt; 96 parent 106.080808 0.13033150
-#&gt; 97 parent 107.272727 0.12297753
-#&gt; 98 parent 108.464646 0.11606895
-#&gt; 99 parent 109.656566 0.10957695
-#&gt; 100 parent 110.848485 0.10347470
-#&gt; 101 parent 112.040404 0.09773723
-#&gt; 102 parent 113.232323 0.09234125
-#&gt; 103 parent 114.424242 0.08726506
-#&gt; 104 parent 115.616162 0.08248842
-#&gt; 105 parent 116.808081 0.07799245
-#&gt; 106 parent 118.000000 0.07375954
-#&gt;
-#&gt; $cost
-#&gt; function (P)
-#&gt; {
-#&gt; assign(&quot;calls&quot;, calls + 1, inherits = TRUE)
-#&gt; if (trace_parms)
-#&gt; cat(P, &quot;\n&quot;)
-#&gt; if (length(state.ini.optim) &gt; 0) {
-#&gt; odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
-#&gt; names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
-#&gt; }
-#&gt; else {
-#&gt; odeini &lt;- state.ini.fixed
-#&gt; names(odeini) &lt;- state.ini.fixed.boxnames
-#&gt; }
-#&gt; odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)],
-#&gt; transparms.fixed)
-#&gt; parms &lt;- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates,
-#&gt; transform_fractions = transform_fractions)
-#&gt; out &lt;- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type,
-#&gt; use_compiled = use_compiled, method.ode = method.ode,
-#&gt; atol = atol, rtol = rtol, ...)
-#&gt; assign(&quot;out_predicted&quot;, out, inherits = TRUE)
-#&gt; mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight,
-#&gt; scaleVar = scaleVar)
-#&gt; if (mC$model &lt; cost.old) {
-#&gt; if (!quiet)
-#&gt; cat(&quot;Model cost at call &quot;, calls, &quot;: &quot;, mC$model,
-#&gt; &quot;\n&quot;)
-#&gt; if (plot) {
-#&gt; outtimes_plot = seq(min(observed$time), max(observed$time),
-#&gt; length.out = 100)
-#&gt; out_plot &lt;- mkinpredict(mkinmod, parms, odeini, outtimes_plot,
-#&gt; solution_type = solution_type, use_compiled = use_compiled,
-#&gt; method.ode = method.ode, atol = atol, rtol = rtol,
-#&gt; ...)
-#&gt; plot(0, type = &quot;n&quot;, xlim = range(observed$time),
-#&gt; ylim = c(0, max(observed$value, na.rm = TRUE)),
-#&gt; xlab = &quot;Time&quot;, ylab = &quot;Observed&quot;)
-#&gt; col_obs &lt;- pch_obs &lt;- 1:length(obs_vars)
-#&gt; lty_obs &lt;- rep(1, length(obs_vars))
-#&gt; names(col_obs) &lt;- names(pch_obs) &lt;- names(lty_obs) &lt;- obs_vars
-#&gt; for (obs_var in obs_vars) {
-#&gt; points(subset(observed, name == obs_var, c(time,
-#&gt; value)), pch = pch_obs[obs_var], col = col_obs[obs_var])
-#&gt; }
-#&gt; matlines(out_plot$time, out_plot[-1], col = col_obs,
-#&gt; lty = lty_obs)
-#&gt; legend(&quot;topright&quot;, inset = c(0.05, 0.05), legend = obs_vars,
-#&gt; col = col_obs, pch = pch_obs, lty = 1:length(pch_obs))
-#&gt; }
-#&gt; assign(&quot;cost.old&quot;, mC$model, inherits = TRUE)
-#&gt; }
-#&gt; return(mC)
-#&gt; }
-#&gt; &lt;environment: 0x3fc5fa0&gt;
-#&gt;
-#&gt; $cost_notrans
-#&gt; function (P)
-#&gt; {
-#&gt; if (length(state.ini.optim) &gt; 0) {
-#&gt; odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
-#&gt; names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
-#&gt; }
-#&gt; else {
-#&gt; odeini &lt;- state.ini.fixed
-#&gt; names(odeini) &lt;- state.ini.fixed.boxnames
-#&gt; }
-#&gt; odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)],
-#&gt; parms.fixed)
-#&gt; out &lt;- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type,
-#&gt; use_compiled = use_compiled, method.ode = method.ode,
-#&gt; atol = atol, rtol = rtol, ...)
-#&gt; mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight,
-#&gt; scaleVar = scaleVar)
-#&gt; return(mC)
-#&gt; }
-#&gt; &lt;environment: 0x3fc5fa0&gt;
-#&gt;
-#&gt; $hessian_notrans
-#&gt; parent_0 alpha beta
-#&gt; parent_0 4.1230329 -7.473531 0.5968527
-#&gt; alpha -7.4735307 40.365690 -3.1777189
-#&gt; beta 0.5968527 -3.177719 0.2503425
-#&gt;
-#&gt; $start
-#&gt; value type
-#&gt; parent_0 98.62 state
-#&gt; alpha 1.00 deparm
-#&gt; beta 10.00 deparm
-#&gt;
-#&gt; $start_transformed
-#&gt; value lower upper
-#&gt; parent_0 98.620000 -Inf Inf
-#&gt; log_alpha 0.000000 -Inf Inf
-#&gt; log_beta 2.302585 -Inf Inf
-#&gt;
-#&gt; $fixed
-#&gt; [1] value type
-#&gt; &lt;0 rows&gt; (or 0-length row.names)
-#&gt;
-#&gt; $data
-#&gt; time variable observed predicted residual
-#&gt; 1 0 parent 98.62 99.66619265 -1.046192647
-#&gt; 2 3 parent 81.43 78.10760352 3.322396479
-#&gt; 3 7 parent 53.18 56.83515667 -3.655156669
-#&gt; 4 14 parent 34.89 33.18468323 1.705316770
-#&gt; 5 30 parent 10.09 10.49630626 -0.406306255
-#&gt; 6 62 parent 1.50 1.37626531 0.123734689
-#&gt; 7 90 parent 0.33 0.29311302 0.036886982
-#&gt; 8 118 parent 0.08 0.07375954 0.006240458
-#&gt;
-#&gt; $atol
-#&gt; [1] 1e-08
-#&gt;
-#&gt; $rtol
-#&gt; [1] 1e-10
-#&gt;
-#&gt; $weight.ini
-#&gt; [1] &quot;none&quot;
-#&gt;
-#&gt; $reweight.tol
-#&gt; [1] 1e-08
-#&gt;
-#&gt; $reweight.max.iter
-#&gt; [1] 10
-#&gt;
-#&gt; $bparms.optim
-#&gt; parent_0 alpha beta
-#&gt; 99.66619 12.80517 156.11390
-#&gt;
-#&gt; $bparms.fixed
-#&gt; numeric(0)
-#&gt;
-#&gt; $bparms.ode
-#&gt; alpha beta
-#&gt; 12.80517 156.11390
-#&gt;
-#&gt; $bparms.state
-#&gt; parent
-#&gt; 99.66619
-#&gt;
-#&gt; $date
-#&gt; [1] &quot;Fri Nov 18 15:19:25 2016&quot;
-#&gt;
-#&gt; attr(,&quot;class&quot;)
-#&gt; [1] &quot;mkinfit&quot; &quot;modFit&quot; </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#&gt; dataset
-#&gt; model B
-#&gt; SFO List,42
-#&gt; attr(,&quot;class&quot;)
-#&gt; [1] &quot;mmkin&quot;</div><div class='input'> <span class='no'>fits</span><span class='kw'>[[</span><span class='st'>"SFO"</span>, <span class='st'>"B"</span>]] <span class='co'># This is equivalent to</span></div><div class='output co'>#&gt; $par
-#&gt; parent_0 log_k_parent_sink
-#&gt; 99.174072 -2.549028
-#&gt;
-#&gt; $ssr
-#&gt; [1] 30.65564
-#&gt;
-#&gt; $convergence
-#&gt; [1] 0
-#&gt;
-#&gt; $iterations
-#&gt; [1] 5
-#&gt;
-#&gt; $evaluations
-#&gt; function gradient
-#&gt; 8 15
-#&gt;
-#&gt; $counts
-#&gt; [1] &quot;relative convergence (4)&quot;
-#&gt;
-#&gt; $hessian
-#&gt; parent_0 log_k_parent_sink
-#&gt; parent_0 4.163631 -94.09343
-#&gt; log_k_parent_sink -94.093431 6311.34610
-#&gt;
-#&gt; $residuals
-#&gt; parent parent parent parent parent parent
-#&gt; 0.55407218 -2.98452128 4.20445742 -1.68599939 -0.58185357 -0.72033730
-#&gt; parent parent
-#&gt; -0.24260405 -0.07020339
-#&gt;
-#&gt; $ms
-#&gt; [1] 3.831956
-#&gt;
-#&gt; $var_ms
-#&gt; parent
-#&gt; 3.831956
-#&gt;
-#&gt; $var_ms_unscaled
-#&gt; parent
-#&gt; 3.831956
-#&gt;
-#&gt; $var_ms_unweighted
-#&gt; parent
-#&gt; 3.831956
-#&gt;
-#&gt; $rank
-#&gt; [1] 2
-#&gt;
-#&gt; $df.residual
-#&gt; [1] 6
-#&gt;
-#&gt; $solution_type
-#&gt; [1] &quot;analytical&quot;
-#&gt;
-#&gt; $transform_rates
-#&gt; [1] TRUE
-#&gt;
-#&gt; $transform_fractions
-#&gt; [1] TRUE
-#&gt;
-#&gt; $method.modFit
-#&gt; [1] &quot;Port&quot;
-#&gt;
-#&gt; $maxit.modFit
-#&gt; [1] &quot;auto&quot;
-#&gt;
-#&gt; $calls
-#&gt; [1] 29
-#&gt;
-#&gt; $time
-#&gt; user system elapsed
-#&gt; 0.064 0.000 0.066
-#&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: SFO; $sink: TRUE
-#&gt; Coefficient matrix $coefmat available
-#&gt;
-#&gt; $observed
-#&gt; name time value
-#&gt; 1 parent 0 98.62
-#&gt; 2 parent 3 81.43
-#&gt; 3 parent 7 53.18
-#&gt; 4 parent 14 34.89
-#&gt; 5 parent 30 10.09
-#&gt; 6 parent 62 1.50
-#&gt; 7 parent 90 0.33
-#&gt; 8 parent 118 0.08
-#&gt;
-#&gt; $obs_vars
-#&gt; [1] &quot;parent&quot;
-#&gt;
-#&gt; $predicted
-#&gt; name time value
-#&gt; 1 parent 0.000000 99.17407218
-#&gt; 2 parent 1.191919 90.35253561
-#&gt; 3 parent 2.383838 82.31567498
-#&gt; 4 parent 3.000000 78.44547872
-#&gt; 5 parent 3.575758 74.99369333
-#&gt; 6 parent 4.767677 68.32300215
-#&gt; 7 parent 5.959596 62.24566915
-#&gt; 8 parent 7.000000 57.38445742
-#&gt; 9 parent 7.151515 56.70891509
-#&gt; 10 parent 8.343434 51.66465547
-#&gt; 11 parent 9.535354 47.06908288
-#&gt; 12 parent 10.727273 42.88228661
-#&gt; 13 parent 11.919192 39.06790599
-#&gt; 14 parent 13.111111 35.59281463
-#&gt; 15 parent 14.000000 33.20400061
-#&gt; 16 parent 14.303030 32.42683275
-#&gt; 17 parent 15.494949 29.54246504
-#&gt; 18 parent 16.686869 26.91466193
-#&gt; 19 parent 17.878788 24.52060198
-#&gt; 20 parent 19.070707 22.33949373
-#&gt; 21 parent 20.262626 20.35239512
-#&gt; 22 parent 21.454545 18.54204899
-#&gt; 23 parent 22.646465 16.89273320
-#&gt; 24 parent 23.838384 15.39012410
-#&gt; 25 parent 25.030303 14.02117212
-#&gt; 26 parent 26.222222 12.77398846
-#&gt; 27 parent 27.414141 11.63774182
-#&gt; 28 parent 28.606061 10.60256435
-#&gt; 29 parent 29.797980 9.65946594
-#&gt; 30 parent 30.000000 9.50814643
-#&gt; 31 parent 30.989899 8.80025617
-#&gt; 32 parent 32.181818 8.01747313
-#&gt; 33 parent 33.373737 7.30431867
-#&gt; 34 parent 34.565657 6.65459931
-#&gt; 35 parent 35.757576 6.06267251
-#&gt; 36 parent 36.949495 5.52339762
-#&gt; 37 parent 38.141414 5.03209124
-#&gt; 38 parent 39.333333 4.58448658
-#&gt; 39 parent 40.525253 4.17669637
-#&gt; 40 parent 41.717172 3.80517911
-#&gt; 41 parent 42.909091 3.46670832
-#&gt; 42 parent 44.101010 3.15834451
-#&gt; 43 parent 45.292929 2.87740968
-#&gt; 44 parent 46.484848 2.62146400
-#&gt; 45 parent 47.676768 2.38828471
-#&gt; 46 parent 48.868687 2.17584671
-#&gt; 47 parent 50.060606 1.98230508
-#&gt; 48 parent 51.252525 1.80597899
-#&gt; 49 parent 52.444444 1.64533711
-#&gt; 50 parent 53.636364 1.49898432
-#&gt; 51 parent 54.828283 1.36564963
-#&gt; 52 parent 56.020202 1.24417505
-#&gt; 53 parent 57.212121 1.13350565
-#&gt; 54 parent 58.404040 1.03268029
-#&gt; 55 parent 59.595960 0.94082335
-#&gt; 56 parent 60.787879 0.85713708
-#&gt; 57 parent 61.979798 0.78089471
-#&gt; 58 parent 62.000000 0.77966270
-#&gt; 59 parent 63.171717 0.71143411
-#&gt; 60 parent 64.363636 0.64815202
-#&gt; 61 parent 65.555556 0.59049888
-#&gt; 62 parent 66.747475 0.53797399
-#&gt; 63 parent 67.939394 0.49012119
-#&gt; 64 parent 69.131313 0.44652489
-#&gt; 65 parent 70.323232 0.40680649
-#&gt; 66 parent 71.515152 0.37062104
-#&gt; 67 parent 72.707071 0.33765429
-#&gt; 68 parent 73.898990 0.30761993
-#&gt; 69 parent 75.090909 0.28025713
-#&gt; 70 parent 76.282828 0.25532825
-#&gt; 71 parent 77.474747 0.23261679
-#&gt; 72 parent 78.666667 0.21192552
-#&gt; 73 parent 79.858586 0.19307474
-#&gt; 74 parent 81.050505 0.17590074
-#&gt; 75 parent 82.242424 0.16025436
-#&gt; 76 parent 83.434343 0.14599973
-#&gt; 77 parent 84.626263 0.13301305
-#&gt; 78 parent 85.818182 0.12118154
-#&gt; 79 parent 87.010101 0.11040244
-#&gt; 80 parent 88.202020 0.10058214
-#&gt; 81 parent 89.393939 0.09163535
-#&gt; 82 parent 90.000000 0.08739595
-#&gt; 83 parent 90.585859 0.08348439
-#&gt; 84 parent 91.777778 0.07605845
-#&gt; 85 parent 92.969697 0.06929305
-#&gt; 86 parent 94.161616 0.06312943
-#&gt; 87 parent 95.353535 0.05751406
-#&gt; 88 parent 96.545455 0.05239819
-#&gt; 89 parent 97.737374 0.04773737
-#&gt; 90 parent 98.929293 0.04349113
-#&gt; 91 parent 100.121212 0.03962259
-#&gt; 92 parent 101.313131 0.03609816
-#&gt; 93 parent 102.505051 0.03288723
-#&gt; 94 parent 103.696970 0.02996191
-#&gt; 95 parent 104.888889 0.02729679
-#&gt; 96 parent 106.080808 0.02486874
-#&gt; 97 parent 107.272727 0.02265667
-#&gt; 98 parent 108.464646 0.02064136
-#&gt; 99 parent 109.656566 0.01880531
-#&gt; 100 parent 110.848485 0.01713257
-#&gt; 101 parent 112.040404 0.01560863
-#&gt; 102 parent 113.232323 0.01422024
-#&gt; 103 parent 114.424242 0.01295535
-#&gt; 104 parent 115.616162 0.01180297
-#&gt; 105 parent 116.808081 0.01075310
-#&gt; 106 parent 118.000000 0.00979661
-#&gt;
-#&gt; $cost
-#&gt; function (P)
-#&gt; {
-#&gt; assign(&quot;calls&quot;, calls + 1, inherits = TRUE)
-#&gt; if (trace_parms)
-#&gt; cat(P, &quot;\n&quot;)
-#&gt; if (length(state.ini.optim) &gt; 0) {
-#&gt; odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
-#&gt; names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
-#&gt; }
-#&gt; else {
-#&gt; odeini &lt;- state.ini.fixed
-#&gt; names(odeini) &lt;- state.ini.fixed.boxnames
-#&gt; }
-#&gt; odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)],
-#&gt; transparms.fixed)
-#&gt; parms &lt;- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates,
-#&gt; transform_fractions = transform_fractions)
-#&gt; out &lt;- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type,
-#&gt; use_compiled = use_compiled, method.ode = method.ode,
-#&gt; atol = atol, rtol = rtol, ...)
-#&gt; assign(&quot;out_predicted&quot;, out, inherits = TRUE)
-#&gt; mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight,
-#&gt; scaleVar = scaleVar)
-#&gt; if (mC$model &lt; cost.old) {
-#&gt; if (!quiet)
-#&gt; cat(&quot;Model cost at call &quot;, calls, &quot;: &quot;, mC$model,
-#&gt; &quot;\n&quot;)
-#&gt; if (plot) {
-#&gt; outtimes_plot = seq(min(observed$time), max(observed$time),
-#&gt; length.out = 100)
-#&gt; out_plot &lt;- mkinpredict(mkinmod, parms, odeini, outtimes_plot,
-#&gt; solution_type = solution_type, use_compiled = use_compiled,
-#&gt; method.ode = method.ode, atol = atol, rtol = rtol,
-#&gt; ...)
-#&gt; plot(0, type = &quot;n&quot;, xlim = range(observed$time),
-#&gt; ylim = c(0, max(observed$value, na.rm = TRUE)),
-#&gt; xlab = &quot;Time&quot;, ylab = &quot;Observed&quot;)
-#&gt; col_obs &lt;- pch_obs &lt;- 1:length(obs_vars)
-#&gt; lty_obs &lt;- rep(1, length(obs_vars))
-#&gt; names(col_obs) &lt;- names(pch_obs) &lt;- names(lty_obs) &lt;- obs_vars
-#&gt; for (obs_var in obs_vars) {
-#&gt; points(subset(observed, name == obs_var, c(time,
-#&gt; value)), pch = pch_obs[obs_var], col = col_obs[obs_var])
-#&gt; }
-#&gt; matlines(out_plot$time, out_plot[-1], col = col_obs,
-#&gt; lty = lty_obs)
-#&gt; legend(&quot;topright&quot;, inset = c(0.05, 0.05), legend = obs_vars,
-#&gt; col = col_obs, pch = pch_obs, lty = 1:length(pch_obs))
-#&gt; }
-#&gt; assign(&quot;cost.old&quot;, mC$model, inherits = TRUE)
-#&gt; }
-#&gt; return(mC)
-#&gt; }
-#&gt; &lt;environment: 0x3b66828&gt;
-#&gt;
-#&gt; $cost_notrans
-#&gt; function (P)
-#&gt; {
-#&gt; if (length(state.ini.optim) &gt; 0) {
-#&gt; odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
-#&gt; names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
-#&gt; }
-#&gt; else {
-#&gt; odeini &lt;- state.ini.fixed
-#&gt; names(odeini) &lt;- state.ini.fixed.boxnames
-#&gt; }
-#&gt; odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)],
-#&gt; parms.fixed)
-#&gt; out &lt;- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type,
-#&gt; use_compiled = use_compiled, method.ode = method.ode,
-#&gt; atol = atol, rtol = rtol, ...)
-#&gt; mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight,
-#&gt; scaleVar = scaleVar)
-#&gt; return(mC)
-#&gt; }
-#&gt; &lt;environment: 0x3b66828&gt;
-#&gt;
-#&gt; $hessian_notrans
-#&gt; parent_0 k_parent_sink
-#&gt; parent_0 4.163631 -1203.894
-#&gt; k_parent_sink -1203.893702 1033188.753
-#&gt;
-#&gt; $start
-#&gt; value type
-#&gt; parent_0 98.62 state
-#&gt; k_parent_sink 0.10 deparm
-#&gt;
-#&gt; $start_transformed
-#&gt; value lower upper
-#&gt; parent_0 98.620000 -Inf Inf
-#&gt; log_k_parent_sink -2.302585 -Inf Inf
-#&gt;
-#&gt; $fixed
-#&gt; [1] value type
-#&gt; &lt;0 rows&gt; (or 0-length row.names)
-#&gt;
-#&gt; $data
-#&gt; time variable observed predicted residual
-#&gt; 1 0 parent 98.62 99.17407218 -0.55407218
-#&gt; 2 3 parent 81.43 78.44547872 2.98452128
-#&gt; 3 7 parent 53.18 57.38445742 -4.20445742
-#&gt; 4 14 parent 34.89 33.20400061 1.68599939
-#&gt; 5 30 parent 10.09 9.50814643 0.58185357
-#&gt; 6 62 parent 1.50 0.77966270 0.72033730
-#&gt; 7 90 parent 0.33 0.08739595 0.24260405
-#&gt; 8 118 parent 0.08 0.00979661 0.07020339
-#&gt;
-#&gt; $atol
-#&gt; [1] 1e-08
-#&gt;
-#&gt; $rtol
-#&gt; [1] 1e-10
-#&gt;
-#&gt; $weight.ini
-#&gt; [1] &quot;none&quot;
-#&gt;
-#&gt; $reweight.tol
-#&gt; [1] 1e-08
-#&gt;
-#&gt; $reweight.max.iter
-#&gt; [1] 10
-#&gt;
-#&gt; $bparms.optim
-#&gt; parent_0 k_parent_sink
-#&gt; 99.17407218 0.07815759
-#&gt;
-#&gt; $bparms.fixed
-#&gt; numeric(0)
-#&gt;
-#&gt; $bparms.ode
-#&gt; k_parent_sink
-#&gt; 0.07815759
-#&gt;
-#&gt; $bparms.state
-#&gt; parent
-#&gt; 99.17407
-#&gt;
-#&gt; $date
-#&gt; [1] &quot;Fri Nov 18 15:19:25 2016&quot;
-#&gt;
-#&gt; attr(,&quot;class&quot;)
-#&gt; [1] &quot;mkinfit&quot; &quot;modFit&quot; </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]</div><div class='output co'>#&gt; [[1]]
+#&gt; </div><div class='input'>
+ <span class='fu'>head</span>(
+ <span class='co'># The same can be achieved by</span>
+ <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]
+ )</div><div class='output co'>#&gt; [[1]]
#&gt; $par
#&gt; parent_0 log_k_parent_sink
#&gt; 99.174072 -2.549028
@@ -894,7 +229,7 @@
#&gt;
#&gt; $time
#&gt; user system elapsed
-#&gt; 0.064 0.000 0.066
+#&gt; 0.068 0.000 0.070
#&gt;
#&gt; $mkinmod
#&gt; &lt;mkinmod&gt; model generated with
@@ -1081,7 +416,7 @@
#&gt; }
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x3b66828&gt;
+#&gt; &lt;environment: 0x3a3e8a8&gt;
#&gt;
#&gt; $cost_notrans
#&gt; function (P)
@@ -1103,7 +438,7 @@
#&gt; scaleVar = scaleVar)
#&gt; return(mC)
#&gt; }
-#&gt; &lt;environment: 0x3b66828&gt;
+#&gt; &lt;environment: 0x3a3e8a8&gt;
#&gt;
#&gt; $hessian_notrans
#&gt; parent_0 k_parent_sink
@@ -1166,7 +501,7 @@
#&gt; 99.17407
#&gt;
#&gt; $date
-#&gt; [1] &quot;Fri Nov 18 15:19:25 2016&quot;
+#&gt; [1] &quot;Fri Nov 18 16:03:57 2016&quot;
#&gt;
#&gt; attr(,&quot;class&quot;)
#&gt; [1] &quot;mkinfit&quot; &quot;modFit&quot;

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