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-rw-r--r--docs/reference/Extract.mmkin.html711
-rw-r--r--docs/reference/endpoints.html16
-rw-r--r--docs/reference/index.html23
-rw-r--r--docs/reference/mccall81_245T.html164
-rw-r--r--docs/reference/mkinerrmin.html9
-rw-r--r--docs/reference/mkinfit.html1372
-rw-r--r--docs/reference/mkinparplot.html12
-rw-r--r--docs/reference/mmkin-10.pngbin0 -> 30013 bytes
-rw-r--r--docs/reference/mmkin-12.pngbin0 -> 30013 bytes
-rw-r--r--docs/reference/mmkin-14.pngbin30013 -> 27062 bytes
-rw-r--r--docs/reference/mmkin-16.pngbin27062 -> 25359 bytes
-rw-r--r--docs/reference/mmkin-18.pngbin25359 -> 18905 bytes
-rw-r--r--docs/reference/mmkin-20.pngbin18905 -> 17036 bytes
-rw-r--r--docs/reference/mmkin.html1107
-rw-r--r--docs/reference/plot.mmkin.html7
-rw-r--r--docs/reference/print.mkinmod.html23
-rw-r--r--docs/reference/schaefer07_complex_case-4.pngbin0 -> 18198 bytes
-rw-r--r--docs/reference/schaefer07_complex_case.html1086
-rw-r--r--docs/reference/summary.mkinfit.html8
-rw-r--r--docs/reference/synthetic_data_for_UBA.html938
-rw-r--r--docs/reference/synthetic_data_for_UBA_2014-10.pngbin0 -> 18905 bytes
-rw-r--r--docs/reference/transform_odeparms.html297
22 files changed, 352 insertions, 5421 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;
diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
index 990ceadf..7e3455c9 100644
--- a/docs/reference/endpoints.html
+++ b/docs/reference/endpoints.html
@@ -106,6 +106,18 @@ with the advantage that the SFORB model can also be used for metabolites.</p>
<p>A list with the components mentioned above.</p>
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><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'>"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'>endpoints</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
+#&gt; logical(0)
+#&gt;
+#&gt; $SFORB
+#&gt; logical(0)
+#&gt;
+#&gt; $distimes
+#&gt; DT50 DT90 DT50back
+#&gt; parent 1.785233 15.1479 4.559973
+#&gt; </div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
@@ -115,7 +127,9 @@ with the advantage that the SFORB model can also be used for metabolites.</p>
<li><a href="#note">Note</a></li>
<li><a href="#value">Value</a></li>
- </ul>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
<h2>Author</h2>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 2d052a80..eff83260 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -119,8 +119,7 @@
<li><code><a href="mkinresplot.html">mkinresplot</a></code></li>
</ul>
- <p><a href="mkinparplot.html">Function to plot the confidence intervals obtained using
- list(list(&quot;mkinfit&quot;))</a></p>
+ <p><a href="mkinparplot.html">Function to plot the confidence intervals obtained using mkinfit</a></p>
<ul>
<li><code><a href="mkinparplot.html">mkinparplot</a></code></li>
</ul>
@@ -247,9 +246,9 @@
<p class="section-desc"><p>Parent only model solutions</p></p>
- <p><a href="DFOP.solution.html">Double First-Order in Parallel kinetics</a></p>
+ <p><a href="SFO.solution.html">Single First-Order kinetics</a></p>
<ul>
- <li><code><a href="DFOP.solution.html">DFOP.solution</a></code></li>
+ <li><code><a href="SFO.solution.html">SFO.solution</a></code></li>
</ul>
<p><a href="FOMC.solution.html">First-Order Multi-Compartment kinetics</a></p>
@@ -257,24 +256,24 @@
<li><code><a href="FOMC.solution.html">FOMC.solution</a></code></li>
</ul>
- <p><a href="HS.solution.html">Hockey-Stick kinetics</a></p>
+ <p><a href="DFOP.solution.html">Double First-Order in Parallel kinetics</a></p>
<ul>
- <li><code><a href="HS.solution.html">HS.solution</a></code></li>
+ <li><code><a href="DFOP.solution.html">DFOP.solution</a></code></li>
</ul>
- <p><a href="IORE.solution.html">Indeterminate order rate equation kinetics</a></p>
+ <p><a href="SFORB.solution.html">Single First-Order Reversible Binding kinetics</a></p>
<ul>
- <li><code><a href="IORE.solution.html">IORE.solution</a></code></li>
+ <li><code><a href="SFORB.solution.html">SFORB.solution</a></code></li>
</ul>
- <p><a href="SFO.solution.html">Single First-Order kinetics</a></p>
+ <p><a href="HS.solution.html">Hockey-Stick kinetics</a></p>
<ul>
- <li><code><a href="SFO.solution.html">SFO.solution</a></code></li>
+ <li><code><a href="HS.solution.html">HS.solution</a></code></li>
</ul>
- <p><a href="SFORB.solution.html">Single First-Order Reversible Binding kinetics</a></p>
+ <p><a href="IORE.solution.html">Indeterminate order rate equation kinetics</a></p>
<ul>
- <li><code><a href="SFORB.solution.html">SFORB.solution</a></code></li>
+ <li><code><a href="IORE.solution.html">IORE.solution</a></code></li>
</ul>
<h2 id="section-generate-synthetic-datasets" class="hasAnchor"><a href="#section-generate-synthetic-datasets" class="anchor"></a>Generate synthetic datasets</h2>
<p class="section-desc"></p>
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 7b294129..baf452d0 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -112,158 +112,11 @@
<pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"phenol"</span>),
<span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"anisole"</span>),
<span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
- <span class='no'>fit.1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>))</div><div class='output co'>#&gt; Model cost at call 1 : 13655.2
-#&gt; Model cost at call 2 : 13655.2
-#&gt; Model cost at call 8 : 9191.59
-#&gt; Model cost at call 16 : 5663.584
-#&gt; Model cost at call 17 : 5663.582
-#&gt; Model cost at call 18 : 5663.566
-#&gt; Model cost at call 19 : 5663.55
-#&gt; Model cost at call 23 : 3035.567
-#&gt; Model cost at call 24 : 3035.566
-#&gt; Model cost at call 26 : 3035.561
-#&gt; Model cost at call 27 : 3035.559
-#&gt; Model cost at call 28 : 3035.558
-#&gt; Model cost at call 30 : 2252.97
-#&gt; Model cost at call 31 : 2252.965
-#&gt; Model cost at call 32 : 2252.965
-#&gt; Model cost at call 36 : 2252.958
-#&gt; Model cost at call 37 : 1220.201
-#&gt; Model cost at call 38 : 1220.2
-#&gt; Model cost at call 39 : 1220.199
-#&gt; Model cost at call 41 : 1220.183
-#&gt; Model cost at call 45 : 507.1358
-#&gt; Model cost at call 48 : 507.1353
-#&gt; Model cost at call 52 : 198.5695
-#&gt; Model cost at call 55 : 198.5694
-#&gt; Model cost at call 60 : 175.8239
-#&gt; Model cost at call 63 : 175.8239
-#&gt; Model cost at call 67 : 170.6316
-#&gt; Model cost at call 69 : 170.6316
-#&gt; Model cost at call 74 : 165.881
-#&gt; Model cost at call 77 : 165.881
-#&gt; Model cost at call 81 : 161.6423
-#&gt; Model cost at call 84 : 161.6423
-#&gt; Model cost at call 88 : 158.2953
-#&gt; Model cost at call 91 : 158.2953
-#&gt; Model cost at call 95 : 156.7311
-#&gt; Model cost at call 97 : 156.731
-#&gt; Model cost at call 103 : 155.998
-#&gt; Model cost at call 106 : 155.998
-#&gt; Model cost at call 110 : 155.6263
-#&gt; Model cost at call 113 : 155.6262
-#&gt; Model cost at call 116 : 155.6262
-#&gt; Model cost at call 117 : 155.1202
-#&gt; Model cost at call 120 : 155.1202
-#&gt; Model cost at call 124 : 154.4133
-#&gt; Model cost at call 125 : 153.8489
-#&gt; Model cost at call 126 : 152.7413
-#&gt; Model cost at call 129 : 152.7413
-#&gt; Model cost at call 132 : 152.7413
-#&gt; Model cost at call 133 : 150.3995
-#&gt; Model cost at call 134 : 148.7256
-#&gt; Model cost at call 135 : 147.2618
-#&gt; Model cost at call 137 : 147.2618
-#&gt; Model cost at call 139 : 147.2618
-#&gt; Model cost at call 142 : 145.115
-#&gt; Model cost at call 144 : 145.115
-#&gt; Model cost at call 145 : 145.115
-#&gt; Model cost at call 146 : 145.115
-#&gt; Model cost at call 147 : 145.115
-#&gt; Model cost at call 150 : 143.7878
-#&gt; Model cost at call 157 : 142.8531
-#&gt; Model cost at call 160 : 142.8531
-#&gt; Model cost at call 164 : 142.7325
-#&gt; Model cost at call 167 : 142.7325
-#&gt; Model cost at call 169 : 142.7325
-#&gt; Model cost at call 172 : 141.8393
-#&gt; Model cost at call 173 : 141.8393
-#&gt; Model cost at call 174 : 141.8393
-#&gt; Model cost at call 179 : 141.3446
-#&gt; Model cost at call 180 : 141.3446
-#&gt; Model cost at call 181 : 141.3446
-#&gt; Model cost at call 186 : 141.1111
-#&gt; Model cost at call 193 : 140.7786
-#&gt; Model cost at call 200 : 140.451
-#&gt; Model cost at call 207 : 140.1395
-#&gt; Model cost at call 214 : 139.7903
-#&gt; Model cost at call 221 : 139.5476
-#&gt; Model cost at call 228 : 139.4441
-#&gt; Model cost at call 235 : 139.3204
-#&gt; Model cost at call 242 : 139.2508
-#&gt; Model cost at call 249 : 139.1891
-#&gt; Model cost at call 256 : 139.1561
-#&gt; Model cost at call 263 : 139.137
-#&gt; Model cost at call 270 : 139.1278
-#&gt; Model cost at call 271 : 139.1278
-#&gt; Model cost at call 279 : 139.1211
-#&gt; Model cost at call 280 : 139.1211
-#&gt; Model cost at call 281 : 139.1211
-#&gt; Model cost at call 282 : 139.1211
-#&gt; Model cost at call 286 : 139.1179
-#&gt; Model cost at call 287 : 139.1179
-#&gt; Model cost at call 291 : 139.1179
-#&gt; Model cost at call 294 : 139.1179
-#&gt; Model cost at call 298 : 139.1158
-#&gt; Model cost at call 299 : 139.1158
-#&gt; Model cost at call 302 : 139.1158
-#&gt; Model cost at call 310 : 139.1148
-#&gt; Model cost at call 311 : 139.1148
-#&gt; Model cost at call 315 : 139.1148
-#&gt; Model cost at call 322 : 139.1143
-#&gt; Model cost at call 323 : 139.1143
-#&gt; Model cost at call 326 : 139.1143
-#&gt; Model cost at call 334 : 139.114
-#&gt; Model cost at call 335 : 139.114
-#&gt; Model cost at call 338 : 139.114
-#&gt; Model cost at call 339 : 139.114
-#&gt; Model cost at call 346 : 139.1139
-#&gt; Model cost at call 347 : 139.1139
-#&gt; Model cost at call 350 : 139.1139
-#&gt; Model cost at call 351 : 139.1139
-#&gt; Model cost at call 358 : 139.1139
-#&gt; Model cost at call 359 : 139.1139
-#&gt; Model cost at call 362 : 139.1139
-#&gt; Model cost at call 363 : 139.1139
-#&gt; Model cost at call 370 : 139.1138
-#&gt; Model cost at call 382 : 139.1138
-#&gt; Model cost at call 390 : 139.1138
-#&gt; Model cost at call 395 : 139.1138
-#&gt; Model cost at call 403 : 139.1138
-#&gt; Model cost at call 408 : 139.1138
-#&gt; Model cost at call 416 : 139.1138
-#&gt; Model cost at call 421 : 139.1138
-#&gt; Model cost at call 429 : 139.1138
-#&gt; Model cost at call 434 : 139.1138
-#&gt; Model cost at call 442 : 139.1138
-#&gt; Model cost at call 447 : 139.1138
-#&gt; Model cost at call 455 : 139.1138
-#&gt; Model cost at call 460 : 139.1138
-#&gt; Model cost at call 468 : 139.1138
-#&gt; Model cost at call 473 : 139.1138
-#&gt; Model cost at call 481 : 139.1138
-#&gt; Model cost at call 486 : 139.1138
-#&gt; Model cost at call 494 : 139.1138
-#&gt; Model cost at call 499 : 139.1138
-#&gt; Model cost at call 507 : 139.1138
-#&gt; Model cost at call 512 : 139.1138
-#&gt; Model cost at call 519 : 139.1138
-#&gt; Model cost at call 520 : 139.1138
-#&gt; Model cost at call 525 : 139.1138
-#&gt; Model cost at call 538 : 139.1138
-#&gt; Model cost at call 545 : 139.1138
-#&gt; Model cost at call 546 : 139.1138
-#&gt; Model cost at call 551 : 139.1138
-#&gt; Model cost at call 558 : 139.1138
-#&gt; Model cost at call 559 : 139.1138
-#&gt; Model cost at call 564 : 139.1138
-#&gt; Model cost at call 571 : 139.1138
-#&gt; Model cost at call 580 : 139.1138
-#&gt; Model cost at call 588 : 139.1138 </div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation by method Port did not converge.</span>
+ <span class='no'>fit.1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Optimisation by method Port did not converge.</span>
#&gt; <span class='warning'>Convergence code is 1</span></div><div class='input'> <span class='fu'>summary</span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 18 15:19:33 2016
-#&gt; Date of summary: Fri Nov 18 15:19:33 2016
+#&gt; Date of fit: Fri Nov 18 16:08:19 2016
+#&gt; Date of summary: Fri Nov 18 16:08:19 2016
#&gt;
#&gt;
#&gt; Warning: Optimisation by method Port did not converge.
@@ -278,7 +131,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 590 model solutions performed in 3.45 s
+#&gt; Fitted with method Port using 590 model solutions performed in 3.568 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -350,14 +203,15 @@
#&gt; T245 15.982 53.091
#&gt; phenol 1.711 5.685
#&gt; anisole 103.784 344.763</div><div class='input'>
- <span class='co'># No covariance matrix and k_phenol_sink is really small, therefore fix it to zero</span>
+ <span class='co'># No convergence, no covariance matrix ...</span>
+ <span class='co'># k_phenol_sink is really small, therefore fix it to zero</span>
<span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>),
<span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>),
<span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 18 15:19:35 2016
-#&gt; Date of summary: Fri Nov 18 15:19:35 2016
+#&gt; Date of fit: Fri Nov 18 16:08:21 2016
+#&gt; Date of summary: Fri Nov 18 16:08:21 2016
#&gt;
#&gt; Equations:
#&gt; d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -367,7 +221,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.477 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.408 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html
index d212e3b2..a8557261 100644
--- a/docs/reference/mkinerrmin.html
+++ b/docs/reference/mkinerrmin.html
@@ -81,9 +81,8 @@
</div>
- <p>This function uses <code>optimize</code> in order to iteratively find the
-smallest relative error still resulting in passing the chi-squared test
-as defined in the FOCUS kinetics report from 2006.</p>
+ <p>This function finds the smallest relative error still resulting in passing the
+chi-squared test as defined in the FOCUS kinetics report from 2006.</p>
<pre><span class='fu'>mkinerrmin</span>(<span class='no'>fit</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.05</span>)</pre>
@@ -120,8 +119,8 @@ as defined in the FOCUS kinetics report from 2006.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'><span class='no'>SFO_SFO</span> <span class='kw'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>),
- <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
+ <pre class="examples"><div class='input'><span class='no'>SFO_SFO</span> <span class='kw'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</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'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
<span class='no'>fit_FOCUS_D</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_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='fu'>round</span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_D</span>), <span class='fl'>4</span>)</div><div class='output co'>#&gt; err.min n.optim df
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index f6ffd21d..99b10f43 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -359,15 +359,15 @@
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 18 15:19:37 2016
-#&gt; Date of summary: Fri Nov 18 15:19:37 2016
+#&gt; Date of fit: Fri Nov 18 15:36:12 2016
+#&gt; Date of summary: Fri Nov 18 15:36:12 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted with method Port using 64 model solutions performed in 0.152 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.157 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -436,7 +436,7 @@
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span>
<span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'>&lt;-</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'>#&gt; user system elapsed
-#&gt; 1.220 1.184 0.904 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 1.264 1.216 0.945 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
@@ -513,7 +513,7 @@
#&gt; Model cost at call 152 : 371.2134
#&gt; Optimisation by method Port successfully terminated.
#&gt; user system elapsed
-#&gt; 0.712 0.040 0.707 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 0.712 0.036 0.702 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
@@ -532,735 +532,32 @@
<span class='no'>FOMC_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"FOMC"</span>, <span class='st'>"m1"</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <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'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 18857.28
-#&gt; Model cost at call 4 : 18857.28
-#&gt; Model cost at call 5 : 18857.28
-#&gt; Model cost at call 8 : 15273.94
-#&gt; Model cost at call 9 : 15273.93
-#&gt; Model cost at call 12 : 15273.67
-#&gt; Model cost at call 13 : 15273.64
-#&gt; Model cost at call 14 : 12764.42
-#&gt; Model cost at call 15 : 8382.7
-#&gt; Model cost at call 20 : 8382.696
-#&gt; Model cost at call 23 : 2729.177
-#&gt; Model cost at call 24 : 2729.175
-#&gt; Model cost at call 26 : 2729.164
-#&gt; Model cost at call 30 : 2299.383
-#&gt; Model cost at call 34 : 2299.379
-#&gt; Model cost at call 35 : 2299.373
-#&gt; Model cost at call 36 : 1944.782
-#&gt; Model cost at call 40 : 1944.782
-#&gt; Model cost at call 42 : 1328.087
-#&gt; Model cost at call 43 : 908.661
-#&gt; Model cost at call 44 : 908.6604
-#&gt; Model cost at call 50 : 877.3556
-#&gt; Model cost at call 51 : 877.3554
-#&gt; Model cost at call 54 : 877.3546
-#&gt; Model cost at call 56 : 769.5186
-#&gt; Model cost at call 59 : 769.5157
-#&gt; Model cost at call 62 : 690.3426
-#&gt; Model cost at call 66 : 690.3425
-#&gt; Model cost at call 68 : 608.4032
-#&gt; Model cost at call 72 : 608.4031
-#&gt; Model cost at call 73 : 608.4031
-#&gt; Model cost at call 74 : 601.5178
-#&gt; Model cost at call 78 : 601.5174
-#&gt; Model cost at call 79 : 601.5174
-#&gt; Model cost at call 80 : 459.9885
-#&gt; Model cost at call 81 : 459.9883
-#&gt; Model cost at call 83 : 459.9878
-#&gt; Model cost at call 87 : 447.0145
-#&gt; Model cost at call 91 : 447.0145
-#&gt; Model cost at call 94 : 445.7322
-#&gt; Model cost at call 97 : 445.7322
-#&gt; Model cost at call 99 : 445.7322
-#&gt; Model cost at call 100 : 444.6965
-#&gt; Model cost at call 103 : 444.6965
-#&gt; Model cost at call 106 : 442.9742
-#&gt; Model cost at call 109 : 442.9742
-#&gt; Model cost at call 112 : 439.9665
-#&gt; Model cost at call 115 : 439.9665
-#&gt; Model cost at call 116 : 439.9664
-#&gt; Model cost at call 118 : 435.0752
-#&gt; Model cost at call 121 : 435.0751
-#&gt; Model cost at call 124 : 430.4718
-#&gt; Model cost at call 127 : 430.4717
-#&gt; Model cost at call 132 : 424.7004
-#&gt; Model cost at call 134 : 424.7003
-#&gt; Model cost at call 138 : 423.6102
-#&gt; Model cost at call 141 : 423.6102
-#&gt; Model cost at call 142 : 423.6102
-#&gt; Model cost at call 144 : 421.1786
-#&gt; Model cost at call 147 : 421.1786
-#&gt; Model cost at call 148 : 421.1786
-#&gt; Model cost at call 150 : 418.1431
-#&gt; Model cost at call 151 : 412.8665
-#&gt; Model cost at call 152 : 396.6067
-#&gt; Model cost at call 154 : 396.6067
-#&gt; Model cost at call 158 : 391.0492
-#&gt; Model cost at call 160 : 391.0492
-#&gt; Model cost at call 164 : 385.8205
-#&gt; Model cost at call 165 : 385.8205
-#&gt; Model cost at call 170 : 379.7674
-#&gt; Model cost at call 171 : 379.7674
-#&gt; Model cost at call 172 : 379.7674
-#&gt; Model cost at call 176 : 374.9389
-#&gt; Model cost at call 177 : 374.9389
-#&gt; Model cost at call 182 : 372.727
-#&gt; Model cost at call 185 : 372.727
-#&gt; Model cost at call 188 : 371.5297
-#&gt; Model cost at call 194 : 370.3738
-#&gt; Model cost at call 195 : 370.3738
-#&gt; Model cost at call 200 : 370.0182
-#&gt; Model cost at call 206 : 369.8634
-#&gt; Model cost at call 212 : 369.8188
-#&gt; Model cost at call 213 : 369.8188
-#&gt; Model cost at call 219 : 369.8114
-#&gt; Model cost at call 221 : 369.8114
-#&gt; Model cost at call 224 : 369.8114
-#&gt; Model cost at call 226 : 369.8114
-#&gt; Model cost at call 230 : 369.8105
-#&gt; Model cost at call 231 : 369.8105
-#&gt; Model cost at call 235 : 369.8105
-#&gt; Model cost at call 236 : 369.8105
-#&gt; Model cost at call 237 : 369.8105
-#&gt; Model cost at call 238 : 369.8105
-#&gt; Model cost at call 249 : 369.8105
-#&gt; Model cost at call 260 : 369.8105
-#&gt; Model cost at call 275 : 369.8105
-#&gt; Model cost at call 276 : 369.8105
-#&gt; Optimisation by method Port successfully terminated.</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>)</div><div class='output co'>#&gt; Model cost at call 1 : 3237.008
-#&gt; Model cost at call 3 : 3237.007
-#&gt; Model cost at call 6 : 671.2571
-#&gt; Model cost at call 7 : 671.2559
-#&gt; Model cost at call 8 : 671.2301
-#&gt; Model cost at call 9 : 671.2249
-#&gt; Model cost at call 10 : 468.4899
-#&gt; Model cost at call 12 : 468.4899
-#&gt; Model cost at call 14 : 371.3486
-#&gt; Model cost at call 16 : 371.3485
-#&gt; Model cost at call 18 : 346.2972
-#&gt; Model cost at call 19 : 346.2971
-#&gt; Model cost at call 20 : 346.297
-#&gt; Model cost at call 21 : 346.2969
-#&gt; Model cost at call 22 : 269.7053
-#&gt; Model cost at call 23 : 269.7053
-#&gt; Model cost at call 26 : 243.9936
-#&gt; Model cost at call 27 : 235.1625
-#&gt; Model cost at call 28 : 235.1624
-#&gt; Model cost at call 30 : 235.1624
-#&gt; Model cost at call 31 : 224.2195
-#&gt; Model cost at call 35 : 218.1922
-#&gt; Model cost at call 36 : 218.1922
-#&gt; Model cost at call 38 : 218.1922
-#&gt; Model cost at call 39 : 211.5012
-#&gt; Model cost at call 41 : 211.5012
-#&gt; Model cost at call 43 : 207.9511
-#&gt; Model cost at call 44 : 207.9511
-#&gt; Model cost at call 47 : 206.5377
-#&gt; Model cost at call 51 : 205.8736
-#&gt; Model cost at call 55 : 205.5625
-#&gt; Model cost at call 59 : 205.4704
-#&gt; Model cost at call 63 : 205.4499
-#&gt; Model cost at call 67 : 205.448
-#&gt; Model cost at call 69 : 205.448
-#&gt; Model cost at call 70 : 205.448
-#&gt; Model cost at call 73 : 205.448
-#&gt; Model cost at call 74 : 205.4478
-#&gt; Model cost at call 75 : 205.4478
-#&gt; Model cost at call 77 : 205.4478
-#&gt; Model cost at call 79 : 205.4478
-#&gt; Model cost at call 84 : 205.4478
-#&gt; Model cost at call 95 : 205.4478
-#&gt; Model cost at call 98 : 205.4478
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='no'>fit.FOMC_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_2006_D</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'>#&gt; Model cost at call 1 : 15169.96
-#&gt; Model cost at call 2 : 15169.96
-#&gt; Model cost at call 7 : 8247.462
-#&gt; Model cost at call 14 : 6734.371
-#&gt; Model cost at call 15 : 6734.339
-#&gt; Model cost at call 16 : 6734.136
-#&gt; Model cost at call 20 : 4855.056
-#&gt; Model cost at call 24 : 4855.038
-#&gt; Model cost at call 27 : 1239.986
-#&gt; Model cost at call 29 : 1239.985
-#&gt; Model cost at call 34 : 1030.523
-#&gt; Model cost at call 38 : 1030.523
-#&gt; Model cost at call 40 : 894.2766
-#&gt; Model cost at call 43 : 894.275
-#&gt; Model cost at call 46 : 750.3629
-#&gt; Model cost at call 49 : 750.3623
-#&gt; Model cost at call 52 : 627.6819
-#&gt; Model cost at call 55 : 627.6818
-#&gt; Model cost at call 58 : 546.2947
-#&gt; Model cost at call 61 : 546.2944
-#&gt; Model cost at call 65 : 502.5529
-#&gt; Model cost at call 69 : 502.5525
-#&gt; Model cost at call 70 : 502.5525
-#&gt; Model cost at call 71 : 475.2423
-#&gt; Model cost at call 72 : 465.5298
-#&gt; Model cost at call 75 : 465.5298
-#&gt; Model cost at call 76 : 465.5297
-#&gt; Model cost at call 78 : 464.9476
-#&gt; Model cost at call 81 : 464.9476
-#&gt; Model cost at call 82 : 464.9473
-#&gt; Model cost at call 84 : 426.9626
-#&gt; Model cost at call 88 : 426.9626
-#&gt; Model cost at call 90 : 414.5235
-#&gt; Model cost at call 93 : 414.5234
-#&gt; Model cost at call 96 : 412.1478
-#&gt; Model cost at call 99 : 412.1477
-#&gt; Model cost at call 100 : 412.1477
-#&gt; Model cost at call 101 : 412.1477
-#&gt; Model cost at call 102 : 394.146
-#&gt; Model cost at call 105 : 394.146
-#&gt; Model cost at call 106 : 394.146
-#&gt; Model cost at call 107 : 394.146
-#&gt; Model cost at call 108 : 384.2002
-#&gt; Model cost at call 112 : 384.2001
-#&gt; Model cost at call 113 : 384.2001
-#&gt; Model cost at call 115 : 380.5495
-#&gt; Model cost at call 119 : 380.5494
-#&gt; Model cost at call 120 : 380.5494
-#&gt; Model cost at call 121 : 378.4803
-#&gt; Model cost at call 123 : 378.4802
-#&gt; Model cost at call 124 : 378.4792
-#&gt; Model cost at call 127 : 374.8432
-#&gt; Model cost at call 129 : 374.8431
-#&gt; Model cost at call 133 : 372.8364
-#&gt; Model cost at call 136 : 372.8364
-#&gt; Model cost at call 137 : 372.8363
-#&gt; Model cost at call 138 : 372.8363
-#&gt; Model cost at call 141 : 372.668
-#&gt; Model cost at call 145 : 372.6679
-#&gt; Model cost at call 147 : 372.5882
-#&gt; Model cost at call 150 : 372.5882
-#&gt; Model cost at call 153 : 372.4828
-#&gt; Model cost at call 156 : 372.4828
-#&gt; Model cost at call 159 : 372.3639
-#&gt; Model cost at call 162 : 372.3639
-#&gt; Model cost at call 163 : 372.3639
-#&gt; Model cost at call 164 : 372.3639
-#&gt; Model cost at call 165 : 372.1959
-#&gt; Model cost at call 168 : 372.1959
-#&gt; Model cost at call 171 : 371.9627
-#&gt; Model cost at call 172 : 371.7467
-#&gt; Model cost at call 173 : 371.1161
-#&gt; Model cost at call 174 : 370.3326
-#&gt; Model cost at call 177 : 370.3326
-#&gt; Model cost at call 178 : 370.3326
-#&gt; Model cost at call 180 : 370.3267
-#&gt; Model cost at call 186 : 370.0471
-#&gt; Model cost at call 187 : 370.0471
-#&gt; Model cost at call 193 : 369.9649
-#&gt; Model cost at call 194 : 369.9649
-#&gt; Model cost at call 196 : 369.9649
-#&gt; Model cost at call 199 : 369.8684
-#&gt; Model cost at call 200 : 369.8684
-#&gt; Model cost at call 204 : 369.8684
-#&gt; Model cost at call 206 : 369.8349
-#&gt; Model cost at call 207 : 369.8349
-#&gt; Model cost at call 209 : 369.8349
-#&gt; Model cost at call 210 : 369.8349
-#&gt; Model cost at call 211 : 369.8349
-#&gt; Model cost at call 212 : 369.8105
-#&gt; Model cost at call 214 : 369.8105
-#&gt; Model cost at call 218 : 369.8105
-#&gt; Model cost at call 220 : 369.8105
-#&gt; Model cost at call 225 : 369.8105
-#&gt; Model cost at call 229 : 369.8105
-#&gt; Model cost at call 231 : 369.8105
-#&gt; Model cost at call 232 : 369.8105
-#&gt; Model cost at call 236 : 369.8105
-#&gt; Model cost at call 239 : 369.8105
-#&gt; Model cost at call 240 : 369.8105
-#&gt; Model cost at call 255 : 369.8105
-#&gt; Model cost at call 258 : 369.8105
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'>
+<span class='no'>fit.FOMC_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='co'># Use starting parameters from parent only FOMC fit</span>
+<span class='no'>fit.FOMC</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='no'>fit.FOMC_SFO</span> <span class='kw'>&lt;-</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>)
+
<span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, SFORB</span>
<span class='no'>SFORB_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFORB"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <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'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 19233.21
-#&gt; Model cost at call 2 : 19233.21
-#&gt; Model cost at call 5 : 19233.21
-#&gt; Model cost at call 8 : 14482.65
-#&gt; Model cost at call 11 : 14482.51
-#&gt; Model cost at call 13 : 14482.17
-#&gt; Model cost at call 15 : 6973.814
-#&gt; Model cost at call 16 : 5161.041
-#&gt; Model cost at call 17 : 5161.029
-#&gt; Model cost at call 22 : 5161.026
-#&gt; Model cost at call 24 : 3249.595
-#&gt; Model cost at call 26 : 3249.595
-#&gt; Model cost at call 27 : 3249.519
-#&gt; Model cost at call 31 : 2615.891
-#&gt; Model cost at call 32 : 2615.888
-#&gt; Model cost at call 39 : 989.1788
-#&gt; Model cost at call 44 : 989.1772
-#&gt; Model cost at call 45 : 989.1771
-#&gt; Model cost at call 47 : 647.4307
-#&gt; Model cost at call 50 : 647.4302
-#&gt; Model cost at call 51 : 647.4261
-#&gt; Model cost at call 54 : 626.7937
-#&gt; Model cost at call 55 : 626.7935
-#&gt; Model cost at call 56 : 626.7931
-#&gt; Model cost at call 61 : 527.9042
-#&gt; Model cost at call 62 : 527.9041
-#&gt; Model cost at call 68 : 505.8828
-#&gt; Model cost at call 70 : 505.8828
-#&gt; Model cost at call 73 : 505.8827
-#&gt; Model cost at call 75 : 452.8932
-#&gt; Model cost at call 77 : 452.893
-#&gt; Model cost at call 82 : 414.4918
-#&gt; Model cost at call 83 : 414.4918
-#&gt; Model cost at call 84 : 414.4918
-#&gt; Model cost at call 88 : 414.4917
-#&gt; Model cost at call 89 : 408.2617
-#&gt; Model cost at call 90 : 408.2616
-#&gt; Model cost at call 91 : 408.2616
-#&gt; Model cost at call 95 : 408.2615
-#&gt; Model cost at call 96 : 384.4461
-#&gt; Model cost at call 102 : 384.4461
-#&gt; Model cost at call 104 : 383.4905
-#&gt; Model cost at call 105 : 383.4905
-#&gt; Model cost at call 106 : 383.4905
-#&gt; Model cost at call 109 : 383.4904
-#&gt; Model cost at call 111 : 381.8828
-#&gt; Model cost at call 112 : 381.8827
-#&gt; Model cost at call 118 : 380.8499
-#&gt; Model cost at call 120 : 380.8499
-#&gt; Model cost at call 123 : 380.8499
-#&gt; Model cost at call 125 : 379.1403
-#&gt; Model cost at call 127 : 379.1402
-#&gt; Model cost at call 132 : 376.4962
-#&gt; Model cost at call 133 : 373.0958
-#&gt; Model cost at call 134 : 365.247
-#&gt; Model cost at call 137 : 365.2469
-#&gt; Model cost at call 142 : 360.8231
-#&gt; Model cost at call 143 : 360.8231
-#&gt; Model cost at call 146 : 360.8231
-#&gt; Model cost at call 148 : 360.8231
-#&gt; Model cost at call 149 : 358.3976
-#&gt; Model cost at call 152 : 358.3976
-#&gt; Model cost at call 154 : 358.3976
-#&gt; Model cost at call 156 : 355.9066
-#&gt; Model cost at call 157 : 355.9066
-#&gt; Model cost at call 163 : 354.3386
-#&gt; Model cost at call 164 : 353.6335
-#&gt; Model cost at call 172 : 353.2094
-#&gt; Model cost at call 173 : 353.2094
-#&gt; Model cost at call 174 : 353.2093
-#&gt; Model cost at call 177 : 353.2093
-#&gt; Model cost at call 178 : 353.2093
-#&gt; Model cost at call 179 : 352.6641
-#&gt; Model cost at call 182 : 352.6641
-#&gt; Model cost at call 183 : 352.6641
-#&gt; Model cost at call 186 : 352.4908
-#&gt; Model cost at call 187 : 352.4429
-#&gt; Model cost at call 195 : 352.3246
-#&gt; Model cost at call 203 : 352.2858
-#&gt; Model cost at call 204 : 352.2858
-#&gt; Model cost at call 205 : 352.2858
-#&gt; Model cost at call 206 : 352.2858
-#&gt; Model cost at call 207 : 352.2858
-#&gt; Model cost at call 210 : 352.2332
-#&gt; Model cost at call 211 : 352.2081
-#&gt; Model cost at call 214 : 352.2081
-#&gt; Model cost at call 216 : 352.2081
-#&gt; Model cost at call 218 : 352.2049
-#&gt; Model cost at call 219 : 352.2049
-#&gt; Model cost at call 220 : 352.2049
-#&gt; Model cost at call 226 : 352.2048
-#&gt; Model cost at call 228 : 352.2048
-#&gt; Model cost at call 231 : 352.2048
-#&gt; Model cost at call 232 : 352.2048
-#&gt; Model cost at call 238 : 352.2048
-#&gt; Model cost at call 239 : 352.2048
-#&gt; Model cost at call 251 : 352.2048
-#&gt; Model cost at call 264 : 352.2048
-#&gt; Model cost at call 283 : 352.2048
-#&gt; Model cost at call 284 : 352.2048
-#&gt; Model cost at call 285 : 352.2048
-#&gt; Model cost at call 286 : 352.2048
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='no'>fit.SFORB_SFO.deSolve</span> <span class='kw'>&lt;-</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>)</div><div class='output co'>#&gt; Model cost at call 1 : 19233.21
-#&gt; Model cost at call 2 : 19233.21
-#&gt; Model cost at call 5 : 19233.21
-#&gt; Model cost at call 8 : 14482.65
-#&gt; Model cost at call 11 : 14482.51
-#&gt; Model cost at call 13 : 14482.17
-#&gt; Model cost at call 15 : 6973.814
-#&gt; Model cost at call 16 : 5161.041
-#&gt; Model cost at call 17 : 5161.029
-#&gt; Model cost at call 22 : 5161.026
-#&gt; Model cost at call 24 : 3249.595
-#&gt; Model cost at call 26 : 3249.595
-#&gt; Model cost at call 27 : 3249.519
-#&gt; Model cost at call 31 : 2615.891
-#&gt; Model cost at call 32 : 2615.888
-#&gt; Model cost at call 39 : 989.1788
-#&gt; Model cost at call 44 : 989.1772
-#&gt; Model cost at call 45 : 989.1771
-#&gt; Model cost at call 47 : 647.4307
-#&gt; Model cost at call 50 : 647.4302
-#&gt; Model cost at call 51 : 647.4261
-#&gt; Model cost at call 54 : 626.7937
-#&gt; Model cost at call 55 : 626.7935
-#&gt; Model cost at call 56 : 626.7931
-#&gt; Model cost at call 61 : 527.9042
-#&gt; Model cost at call 62 : 527.9041
-#&gt; Model cost at call 68 : 505.8828
-#&gt; Model cost at call 70 : 505.8828
-#&gt; Model cost at call 73 : 505.8827
-#&gt; Model cost at call 75 : 452.8932
-#&gt; Model cost at call 77 : 452.893
-#&gt; Model cost at call 82 : 414.4918
-#&gt; Model cost at call 83 : 414.4918
-#&gt; Model cost at call 84 : 414.4918
-#&gt; Model cost at call 88 : 414.4917
-#&gt; Model cost at call 89 : 408.2617
-#&gt; Model cost at call 90 : 408.2616
-#&gt; Model cost at call 91 : 408.2616
-#&gt; Model cost at call 95 : 408.2615
-#&gt; Model cost at call 96 : 384.4461
-#&gt; Model cost at call 102 : 384.4461
-#&gt; Model cost at call 104 : 383.4905
-#&gt; Model cost at call 105 : 383.4905
-#&gt; Model cost at call 106 : 383.4905
-#&gt; Model cost at call 109 : 383.4904
-#&gt; Model cost at call 111 : 381.8828
-#&gt; Model cost at call 112 : 381.8827
-#&gt; Model cost at call 118 : 380.8499
-#&gt; Model cost at call 120 : 380.8499
-#&gt; Model cost at call 123 : 380.8499
-#&gt; Model cost at call 125 : 379.1403
-#&gt; Model cost at call 127 : 379.1402
-#&gt; Model cost at call 132 : 376.4962
-#&gt; Model cost at call 133 : 373.0958
-#&gt; Model cost at call 134 : 365.247
-#&gt; Model cost at call 137 : 365.2469
-#&gt; Model cost at call 142 : 360.8231
-#&gt; Model cost at call 143 : 360.8231
-#&gt; Model cost at call 146 : 360.8231
-#&gt; Model cost at call 148 : 360.8231
-#&gt; Model cost at call 149 : 358.3976
-#&gt; Model cost at call 152 : 358.3976
-#&gt; Model cost at call 154 : 358.3976
-#&gt; Model cost at call 156 : 355.9066
-#&gt; Model cost at call 157 : 355.9066
-#&gt; Model cost at call 163 : 354.3386
-#&gt; Model cost at call 164 : 353.6335
-#&gt; Model cost at call 172 : 353.2094
-#&gt; Model cost at call 173 : 353.2094
-#&gt; Model cost at call 174 : 353.2093
-#&gt; Model cost at call 177 : 353.2093
-#&gt; Model cost at call 178 : 353.2093
-#&gt; Model cost at call 179 : 352.6641
-#&gt; Model cost at call 182 : 352.6641
-#&gt; Model cost at call 183 : 352.6641
-#&gt; Model cost at call 186 : 352.4908
-#&gt; Model cost at call 187 : 352.4429
-#&gt; Model cost at call 195 : 352.3246
-#&gt; Model cost at call 203 : 352.2858
-#&gt; Model cost at call 204 : 352.2858
-#&gt; Model cost at call 205 : 352.2858
-#&gt; Model cost at call 206 : 352.2858
-#&gt; Model cost at call 207 : 352.2858
-#&gt; Model cost at call 210 : 352.2332
-#&gt; Model cost at call 211 : 352.2081
-#&gt; Model cost at call 214 : 352.2081
-#&gt; Model cost at call 216 : 352.2081
-#&gt; Model cost at call 218 : 352.2049
-#&gt; Model cost at call 219 : 352.2049
-#&gt; Model cost at call 220 : 352.2049
-#&gt; Model cost at call 226 : 352.2048
-#&gt; Model cost at call 228 : 352.2048
-#&gt; Model cost at call 231 : 352.2048
-#&gt; Model cost at call 232 : 352.2048
-#&gt; Model cost at call 238 : 352.2048
-#&gt; Model cost at call 239 : 352.2048
-#&gt; Model cost at call 251 : 352.2048
-#&gt; Model cost at call 264 : 352.2048
-#&gt; Model cost at call 283 : 352.2048
-#&gt; Model cost at call 284 : 352.2048
-#&gt; Model cost at call 285 : 352.2048
-#&gt; Model cost at call 286 : 352.2048
-#&gt; Optimisation by method Port successfully terminated.</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>)</div><div class='output co'>#&gt; Model cost at call 1 : 10426.65
-#&gt; Model cost at call 3 : 10426.65
-#&gt; Model cost at call 6 : 1995.326
-#&gt; Model cost at call 7 : 1995.322
-#&gt; Model cost at call 8 : 1995.14
-#&gt; Model cost at call 11 : 718.5568
-#&gt; Model cost at call 12 : 718.5566
-#&gt; Model cost at call 13 : 718.5563
-#&gt; Model cost at call 16 : 408.9208
-#&gt; Model cost at call 17 : 408.9204
-#&gt; Model cost at call 18 : 408.9204
-#&gt; Model cost at call 20 : 408.9203
-#&gt; Model cost at call 21 : 402.7935
-#&gt; Model cost at call 22 : 402.793
-#&gt; Model cost at call 26 : 202.0443
-#&gt; Model cost at call 28 : 202.0443
-#&gt; Model cost at call 30 : 202.0443
-#&gt; Model cost at call 31 : 196.438
-#&gt; Model cost at call 36 : 196.1947
-#&gt; Model cost at call 37 : 196.1947
-#&gt; Model cost at call 41 : 192.9338
-#&gt; Model cost at call 43 : 192.9338
-#&gt; Model cost at call 45 : 192.9338
-#&gt; Model cost at call 46 : 191.6452
-#&gt; Model cost at call 47 : 191.6452
-#&gt; Model cost at call 51 : 188.9328
-#&gt; Model cost at call 54 : 188.9328
-#&gt; Model cost at call 55 : 188.9328
-#&gt; Model cost at call 56 : 183.6499
-#&gt; Model cost at call 59 : 183.6499
-#&gt; Model cost at call 62 : 181.9039
-#&gt; Model cost at call 67 : 179.0543
-#&gt; Model cost at call 68 : 179.0543
-#&gt; Model cost at call 69 : 179.0543
-#&gt; Model cost at call 70 : 179.0543
-#&gt; Model cost at call 72 : 176.749
-#&gt; Model cost at call 73 : 176.2321
-#&gt; Model cost at call 74 : 176.232
-#&gt; Model cost at call 75 : 176.232
-#&gt; Model cost at call 76 : 176.232
-#&gt; Model cost at call 78 : 175.3914
-#&gt; Model cost at call 79 : 175.3914
-#&gt; Model cost at call 81 : 175.3913
-#&gt; Model cost at call 83 : 174.6257
-#&gt; Model cost at call 84 : 174.6257
-#&gt; Model cost at call 89 : 174.1476
-#&gt; Model cost at call 92 : 174.1476
-#&gt; Model cost at call 93 : 174.1476
-#&gt; Model cost at call 94 : 173.8512
-#&gt; Model cost at call 99 : 173.6987
-#&gt; Model cost at call 104 : 173.6813
-#&gt; Model cost at call 105 : 173.6813
-#&gt; Model cost at call 106 : 173.6813
-#&gt; Model cost at call 107 : 173.6813
-#&gt; Model cost at call 108 : 173.6813
-#&gt; Model cost at call 109 : 173.6802
-#&gt; Model cost at call 110 : 173.6802
-#&gt; Model cost at call 111 : 173.6802
-#&gt; Model cost at call 112 : 173.6802
-#&gt; Model cost at call 113 : 173.6802
-#&gt; Model cost at call 114 : 173.6799
-#&gt; Model cost at call 116 : 173.6799
-#&gt; Model cost at call 118 : 173.6799
-#&gt; Model cost at call 119 : 173.6799
-#&gt; Model cost at call 120 : 173.6799
-#&gt; Model cost at call 129 : 173.6799
-#&gt; Model cost at call 141 : 173.6799
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='no'>fit.SFORB_SFO</span> <span class='kw'>&lt;-</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>)</div><div class='output co'>#&gt; Model cost at call 1 : 18365.33
-#&gt; Model cost at call 2 : 18365.33
-#&gt; Model cost at call 8 : 11666.4
-#&gt; Model cost at call 9 : 10992.15
-#&gt; Model cost at call 10 : 10992.13
-#&gt; Model cost at call 11 : 10991.95
-#&gt; Model cost at call 12 : 10991.17
-#&gt; Model cost at call 14 : 10990.65
-#&gt; Model cost at call 17 : 3940.801
-#&gt; Model cost at call 20 : 3940.8
-#&gt; Model cost at call 22 : 3940.798
-#&gt; Model cost at call 24 : 3241.199
-#&gt; Model cost at call 27 : 3241.198
-#&gt; Model cost at call 30 : 3241.192
-#&gt; Model cost at call 31 : 1518.749
-#&gt; Model cost at call 37 : 1518.747
-#&gt; Model cost at call 39 : 1091.836
-#&gt; Model cost at call 42 : 1091.835
-#&gt; Model cost at call 43 : 1091.835
-#&gt; Model cost at call 44 : 1091.804
-#&gt; Model cost at call 46 : 927.8538
-#&gt; Model cost at call 49 : 927.8529
-#&gt; Model cost at call 53 : 638.102
-#&gt; Model cost at call 56 : 638.1019
-#&gt; Model cost at call 58 : 638.1018
-#&gt; Model cost at call 61 : 560.4352
-#&gt; Model cost at call 62 : 560.435
-#&gt; Model cost at call 63 : 560.4327
-#&gt; Model cost at call 68 : 423.9629
-#&gt; Model cost at call 69 : 423.9629
-#&gt; Model cost at call 70 : 423.9629
-#&gt; Model cost at call 71 : 423.9628
-#&gt; Model cost at call 73 : 423.9628
-#&gt; Model cost at call 75 : 395.8015
-#&gt; Model cost at call 78 : 395.8013
-#&gt; Model cost at call 79 : 395.8013
-#&gt; Model cost at call 83 : 365.6975
-#&gt; Model cost at call 84 : 365.6975
-#&gt; Model cost at call 88 : 365.6975
-#&gt; Model cost at call 91 : 362.9843
-#&gt; Model cost at call 93 : 362.9843
-#&gt; Model cost at call 98 : 361.5506
-#&gt; Model cost at call 99 : 361.5506
-#&gt; Model cost at call 100 : 361.5505
-#&gt; Model cost at call 105 : 359.0492
-#&gt; Model cost at call 106 : 359.0492
-#&gt; Model cost at call 112 : 357.6574
-#&gt; Model cost at call 113 : 357.6574
-#&gt; Model cost at call 114 : 357.6574
-#&gt; Model cost at call 115 : 357.6574
-#&gt; Model cost at call 119 : 355.4518
-#&gt; Model cost at call 120 : 355.4518
-#&gt; Model cost at call 127 : 354.9045
-#&gt; Model cost at call 129 : 354.9045
-#&gt; Model cost at call 131 : 354.9045
-#&gt; Model cost at call 134 : 354.4168
-#&gt; Model cost at call 135 : 354.4168
-#&gt; Model cost at call 137 : 354.4167
-#&gt; Model cost at call 141 : 353.7901
-#&gt; Model cost at call 142 : 353.7901
-#&gt; Model cost at call 143 : 353.7899
-#&gt; Model cost at call 149 : 353.3233
-#&gt; Model cost at call 151 : 353.3233
-#&gt; Model cost at call 154 : 353.3233
-#&gt; Model cost at call 156 : 353.2939
-#&gt; Model cost at call 158 : 353.2938
-#&gt; Model cost at call 159 : 353.2938
-#&gt; Model cost at call 160 : 353.2938
-#&gt; Model cost at call 163 : 353.0571
-#&gt; Model cost at call 165 : 353.0571
-#&gt; Model cost at call 170 : 352.9457
-#&gt; Model cost at call 171 : 352.7458
-#&gt; Model cost at call 173 : 352.7457
-#&gt; Model cost at call 178 : 352.6377
-#&gt; Model cost at call 180 : 352.6377
-#&gt; Model cost at call 183 : 352.6377
-#&gt; Model cost at call 185 : 352.5377
-#&gt; Model cost at call 187 : 352.5377
-#&gt; Model cost at call 188 : 352.5377
-#&gt; Model cost at call 191 : 352.5377
-#&gt; Model cost at call 193 : 352.4479
-#&gt; Model cost at call 195 : 352.4479
-#&gt; Model cost at call 198 : 352.4479
-#&gt; Model cost at call 200 : 352.4021
-#&gt; Model cost at call 202 : 352.4021
-#&gt; Model cost at call 205 : 352.4021
-#&gt; Model cost at call 207 : 352.3465
-#&gt; Model cost at call 210 : 352.3465
-#&gt; Model cost at call 214 : 352.3031
-#&gt; Model cost at call 216 : 352.3031
-#&gt; Model cost at call 221 : 352.2632
-#&gt; Model cost at call 223 : 352.2632
-#&gt; Model cost at call 228 : 352.2367
-#&gt; Model cost at call 230 : 352.2367
-#&gt; Model cost at call 231 : 352.2367
-#&gt; Model cost at call 233 : 352.2367
-#&gt; Model cost at call 235 : 352.215
-#&gt; Model cost at call 238 : 352.215
-#&gt; Model cost at call 239 : 352.215
-#&gt; Model cost at call 242 : 352.207
-#&gt; Model cost at call 245 : 352.207
-#&gt; Model cost at call 250 : 352.2053
-#&gt; Model cost at call 251 : 352.2053
-#&gt; Model cost at call 253 : 352.2053
-#&gt; Model cost at call 256 : 352.2053
-#&gt; Model cost at call 258 : 352.2053
-#&gt; Model cost at call 259 : 352.2052
-#&gt; Model cost at call 260 : 352.2052
-#&gt; Model cost at call 263 : 352.2052
-#&gt; Model cost at call 271 : 352.2048
-#&gt; Model cost at call 273 : 352.2048
-#&gt; Model cost at call 274 : 352.2048
-#&gt; Model cost at call 281 : 352.2048
-#&gt; Model cost at call 282 : 352.2048
-#&gt; Model cost at call 286 : 352.2048
-#&gt; Model cost at call 289 : 352.2048
-#&gt; Model cost at call 294 : 352.2048
-#&gt; Model cost at call 296 : 352.2048
-#&gt; Model cost at call 300 : 352.2048
-#&gt; Model cost at call 307 : 352.2048
-#&gt; Model cost at call 325 : 352.2048
-#&gt; Model cost at call 331 : 352.2048
-#&gt; Model cost at call 333 : 352.2048
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'>
+<span class='no'>fit.SFORB_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='no'>fit.SFORB_SFO.deSolve</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>,
+ <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='co'># Use starting parameters from parent only SFORB fit (not really needed in this case)</span>
+<span class='no'>fit.SFORB</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"SFORB"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='no'>fit.SFORB_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.SFORB</span>$<span class='no'>bparms.ode</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+
<span class='co'># Weighted fits, including IRLS</span>
<span class='no'>SFO_SFO.ff</span> <span class='kw'>&lt;-</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'>#&gt; <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'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 15156.12
-#&gt; Model cost at call 2 : 15156.12
-#&gt; Model cost at call 6 : 8243.644
-#&gt; Model cost at call 12 : 6290.714
-#&gt; Model cost at call 13 : 6290.684
-#&gt; Model cost at call 15 : 6290.453
-#&gt; Model cost at call 18 : 1700.75
-#&gt; Model cost at call 20 : 1700.612
-#&gt; Model cost at call 24 : 1190.923
-#&gt; Model cost at call 26 : 1190.922
-#&gt; Model cost at call 29 : 1017.417
-#&gt; Model cost at call 31 : 1017.417
-#&gt; Model cost at call 33 : 1017.416
-#&gt; Model cost at call 34 : 644.0471
-#&gt; Model cost at call 36 : 644.0469
-#&gt; Model cost at call 38 : 644.0468
-#&gt; Model cost at call 39 : 590.5024
-#&gt; Model cost at call 41 : 590.5021
-#&gt; Model cost at call 43 : 590.5015
-#&gt; Model cost at call 44 : 543.2187
-#&gt; Model cost at call 45 : 543.2183
-#&gt; Model cost at call 46 : 543.2182
-#&gt; Model cost at call 50 : 391.348
-#&gt; Model cost at call 51 : 391.3479
-#&gt; Model cost at call 56 : 386.4789
-#&gt; Model cost at call 58 : 386.4789
-#&gt; Model cost at call 60 : 386.4779
-#&gt; Model cost at call 61 : 384.0686
-#&gt; Model cost at call 63 : 384.0686
-#&gt; Model cost at call 66 : 382.7812
-#&gt; Model cost at call 68 : 382.7812
-#&gt; Model cost at call 70 : 382.7812
-#&gt; Model cost at call 71 : 378.9272
-#&gt; Model cost at call 73 : 378.9272
-#&gt; Model cost at call 75 : 378.9272
-#&gt; Model cost at call 76 : 377.4846
-#&gt; Model cost at call 78 : 377.4846
-#&gt; Model cost at call 81 : 375.9738
-#&gt; Model cost at call 83 : 375.9738
-#&gt; Model cost at call 86 : 375.3387
-#&gt; Model cost at call 88 : 375.3387
-#&gt; Model cost at call 91 : 374.5774
-#&gt; Model cost at call 93 : 374.5774
-#&gt; Model cost at call 95 : 374.5774
-#&gt; Model cost at call 96 : 373.5447
-#&gt; Model cost at call 100 : 373.5446
-#&gt; Model cost at call 102 : 373.2643
-#&gt; Model cost at call 104 : 373.2643
-#&gt; Model cost at call 107 : 372.6799
-#&gt; Model cost at call 111 : 372.6798
-#&gt; Model cost at call 114 : 372.6325
-#&gt; Model cost at call 116 : 372.6325
-#&gt; Model cost at call 119 : 372.6159
-#&gt; Model cost at call 121 : 372.6159
-#&gt; Model cost at call 123 : 372.6159
-#&gt; Model cost at call 124 : 372.5845
-#&gt; Model cost at call 126 : 372.5845
-#&gt; Model cost at call 129 : 372.5375
-#&gt; Model cost at call 130 : 372.4771
-#&gt; Model cost at call 131 : 372.2008
-#&gt; Model cost at call 132 : 371.4923
-#&gt; Model cost at call 134 : 371.4923
-#&gt; Model cost at call 137 : 371.3022
-#&gt; Model cost at call 139 : 371.3022
-#&gt; Model cost at call 143 : 371.2271
-#&gt; Model cost at call 144 : 371.2271
-#&gt; Model cost at call 148 : 371.2202
-#&gt; Model cost at call 149 : 371.215
-#&gt; Model cost at call 152 : 371.215
-#&gt; Model cost at call 154 : 371.2136
-#&gt; Model cost at call 155 : 371.2136
-#&gt; Model cost at call 156 : 371.2136
-#&gt; Model cost at call 160 : 371.2134
-#&gt; Model cost at call 164 : 371.2134
-#&gt; Model cost at call 167 : 371.2134
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+ <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'>#&gt; <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'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 18 15:19:47 2016
-#&gt; Date of summary: Fri Nov 18 15:19:47 2016
+#&gt; Date of fit: Fri Nov 18 15:36:22 2016
+#&gt; Date of summary: Fri Nov 18 15:36:22 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1268,7 +565,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 185 model solutions performed in 0.748 s
+#&gt; Fitted with method Port using 185 model solutions performed in 0.752 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -1377,146 +674,11 @@
#&gt; 100 m1 31.04 3.198e+01 -9.416e-01
#&gt; 100 m1 33.13 3.198e+01 1.148e+00
#&gt; 120 m1 25.15 2.879e+01 -3.640e+00
-#&gt; 120 m1 33.31 2.879e+01 4.520e+00</div><div class='input'><span class='no'>f.irls</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 15156.12
-#&gt; Model cost at call 2 : 15156.12
-#&gt; Model cost at call 6 : 8243.644
-#&gt; Model cost at call 12 : 6290.714
-#&gt; Model cost at call 13 : 6290.684
-#&gt; Model cost at call 15 : 6290.453
-#&gt; Model cost at call 18 : 1700.75
-#&gt; Model cost at call 20 : 1700.612
-#&gt; Model cost at call 24 : 1190.923
-#&gt; Model cost at call 26 : 1190.922
-#&gt; Model cost at call 29 : 1017.417
-#&gt; Model cost at call 31 : 1017.417
-#&gt; Model cost at call 33 : 1017.416
-#&gt; Model cost at call 34 : 644.0471
-#&gt; Model cost at call 36 : 644.0469
-#&gt; Model cost at call 38 : 644.0468
-#&gt; Model cost at call 39 : 590.5024
-#&gt; Model cost at call 41 : 590.5021
-#&gt; Model cost at call 43 : 590.5015
-#&gt; Model cost at call 44 : 543.2187
-#&gt; Model cost at call 45 : 543.2183
-#&gt; Model cost at call 46 : 543.2182
-#&gt; Model cost at call 50 : 391.348
-#&gt; Model cost at call 51 : 391.3479
-#&gt; Model cost at call 56 : 386.4789
-#&gt; Model cost at call 58 : 386.4789
-#&gt; Model cost at call 60 : 386.4779
-#&gt; Model cost at call 61 : 384.0686
-#&gt; Model cost at call 63 : 384.0686
-#&gt; Model cost at call 66 : 382.7812
-#&gt; Model cost at call 68 : 382.7812
-#&gt; Model cost at call 70 : 382.7812
-#&gt; Model cost at call 71 : 378.9272
-#&gt; Model cost at call 73 : 378.9272
-#&gt; Model cost at call 75 : 378.9272
-#&gt; Model cost at call 76 : 377.4846
-#&gt; Model cost at call 78 : 377.4846
-#&gt; Model cost at call 81 : 375.9738
-#&gt; Model cost at call 83 : 375.9738
-#&gt; Model cost at call 86 : 375.3387
-#&gt; Model cost at call 88 : 375.3387
-#&gt; Model cost at call 91 : 374.5774
-#&gt; Model cost at call 93 : 374.5774
-#&gt; Model cost at call 95 : 374.5774
-#&gt; Model cost at call 96 : 373.5447
-#&gt; Model cost at call 100 : 373.5446
-#&gt; Model cost at call 102 : 373.2643
-#&gt; Model cost at call 104 : 373.2643
-#&gt; Model cost at call 107 : 372.6799
-#&gt; Model cost at call 111 : 372.6798
-#&gt; Model cost at call 114 : 372.6325
-#&gt; Model cost at call 116 : 372.6325
-#&gt; Model cost at call 119 : 372.6159
-#&gt; Model cost at call 121 : 372.6159
-#&gt; Model cost at call 123 : 372.6159
-#&gt; Model cost at call 124 : 372.5845
-#&gt; Model cost at call 126 : 372.5845
-#&gt; Model cost at call 129 : 372.5375
-#&gt; Model cost at call 130 : 372.4771
-#&gt; Model cost at call 131 : 372.2008
-#&gt; Model cost at call 132 : 371.4923
-#&gt; Model cost at call 134 : 371.4923
-#&gt; Model cost at call 137 : 371.3022
-#&gt; Model cost at call 139 : 371.3022
-#&gt; Model cost at call 143 : 371.2271
-#&gt; Model cost at call 144 : 371.2271
-#&gt; Model cost at call 148 : 371.2202
-#&gt; Model cost at call 149 : 371.215
-#&gt; Model cost at call 152 : 371.215
-#&gt; Model cost at call 154 : 371.2136
-#&gt; Model cost at call 155 : 371.2136
-#&gt; Model cost at call 156 : 371.2136
-#&gt; Model cost at call 160 : 371.2134
-#&gt; Model cost at call 164 : 371.2134
-#&gt; Model cost at call 167 : 371.2134
-#&gt; IRLS based on variance estimates for each observed variable
-#&gt; Initial variance estimates are:
-#&gt; parent m1
-#&gt; 11.552581 7.421226
-#&gt; Model cost at call 186 : 40
-#&gt; Model cost at call 188 : 40
-#&gt; Model cost at call 194 : 39.99562
-#&gt; Model cost at call 195 : 39.99562
-#&gt; Model cost at call 201 : 39.9956
-#&gt; Model cost at call 203 : 39.99528
-#&gt; Model cost at call 205 : 39.99528
-#&gt; Model cost at call 207 : 39.99528
-#&gt; Model cost at call 209 : 39.99515
-#&gt; Model cost at call 211 : 39.99515
-#&gt; Model cost at call 214 : 39.99515
-#&gt; Model cost at call 215 : 39.99505
-#&gt; Model cost at call 217 : 39.99505
-#&gt; Model cost at call 219 : 39.99505
-#&gt; Model cost at call 220 : 39.99489
-#&gt; Model cost at call 222 : 39.99489
-#&gt; Model cost at call 224 : 39.99489
-#&gt; Model cost at call 225 : 39.99479
-#&gt; Model cost at call 227 : 39.99479
-#&gt; Model cost at call 231 : 39.99467
-#&gt; Model cost at call 234 : 39.99467
-#&gt; Model cost at call 235 : 39.99467
-#&gt; Model cost at call 236 : 39.99458
-#&gt; Model cost at call 238 : 39.99458
-#&gt; Model cost at call 239 : 39.99458
-#&gt; Model cost at call 241 : 39.99452
-#&gt; Model cost at call 242 : 39.99444
-#&gt; Model cost at call 243 : 39.99433
-#&gt; Model cost at call 245 : 39.99433
-#&gt; Model cost at call 248 : 39.99383
-#&gt; Model cost at call 250 : 39.99383
-#&gt; Model cost at call 251 : 39.99383
-#&gt; Model cost at call 252 : 39.99383
-#&gt; Model cost at call 253 : 39.9935
-#&gt; Model cost at call 254 : 39.99309
-#&gt; Model cost at call 256 : 39.99309
-#&gt; Model cost at call 261 : 39.99295
-#&gt; Model cost at call 264 : 39.99295
-#&gt; Model cost at call 267 : 39.99281
-#&gt; Model cost at call 272 : 39.99281
-#&gt; Model cost at call 273 : 39.99278
-#&gt; Model cost at call 276 : 39.99278
-#&gt; Model cost at call 278 : 39.99278
-#&gt; Model cost at call 279 : 39.99278
-#&gt; Model cost at call 281 : 39.99278
-#&gt; Model cost at call 283 : 39.99278
-#&gt; Model cost at call 286 : 39.99278
-#&gt; Model cost at call 289 : 39.99278
-#&gt; Model cost at call 290 : 39.99278
-#&gt; Iteration 1 yields variance estimates:
-#&gt; parent m1
-#&gt; 11.573172 7.407968
-#&gt; Sum of squared differences to last variance estimates: 1.5e-05
-#&gt; Iteration 2 yields variance estimates:
-#&gt; parent m1
-#&gt; 11.573405 7.407846
-#&gt; Sum of squared differences to last variance estimates: 1.7e-09
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+#&gt; 120 m1 33.31 2.879e+01 4.520e+00</div><div class='input'><span class='no'>f.irls</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 18 15:19:50 2016
-#&gt; Date of summary: Fri Nov 18 15:19:50 2016
+#&gt; Date of fit: Fri Nov 18 15:36:24 2016
+#&gt; Date of summary: Fri Nov 18 15:36:24 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1524,7 +686,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 486 model solutions performed in 2.052 s
+#&gt; Fitted with method Port using 486 model solutions performed in 2.047 s
#&gt;
#&gt; Weighting: none then iterative reweighting method obs
#&gt;
@@ -1633,62 +795,11 @@
#&gt; 100 m1 31.04 3.199e+01 -9.497e-01 2.722
#&gt; 100 m1 33.13 3.199e+01 1.140e+00 2.722
#&gt; 120 m1 25.15 2.881e+01 -3.659e+00 2.722
-#&gt; 120 m1 33.31 2.881e+01 4.501e+00 2.722</div><div class='input'><span class='no'>f.w.mean</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 19.80132
-#&gt; Model cost at call 2 : 19.80132
-#&gt; Model cost at call 6 : 10.68776
-#&gt; Model cost at call 12 : 7.14353
-#&gt; Model cost at call 13 : 7.143529
-#&gt; Model cost at call 15 : 7.143511
-#&gt; Model cost at call 18 : 2.189024
-#&gt; Model cost at call 20 : 2.189019
-#&gt; Model cost at call 23 : 1.587262
-#&gt; Model cost at call 25 : 1.587261
-#&gt; Model cost at call 26 : 1.58726
-#&gt; Model cost at call 28 : 1.036794
-#&gt; Model cost at call 29 : 1.036794
-#&gt; Model cost at call 30 : 1.036793
-#&gt; Model cost at call 34 : 0.4939937
-#&gt; Model cost at call 35 : 0.4939937
-#&gt; Model cost at call 38 : 0.4939936
-#&gt; Model cost at call 39 : 0.4018506
-#&gt; Model cost at call 43 : 0.4018505
-#&gt; Model cost at call 45 : 0.3797853
-#&gt; Model cost at call 51 : 0.3669779
-#&gt; Model cost at call 55 : 0.3669778
-#&gt; Model cost at call 56 : 0.3585654
-#&gt; Model cost at call 57 : 0.3533252
-#&gt; Model cost at call 62 : 0.3502505
-#&gt; Model cost at call 64 : 0.3502505
-#&gt; Model cost at call 66 : 0.3502505
-#&gt; Model cost at call 67 : 0.3501535
-#&gt; Model cost at call 72 : 0.3501187
-#&gt; Model cost at call 74 : 0.3501187
-#&gt; Model cost at call 75 : 0.3501187
-#&gt; Model cost at call 77 : 0.3500378
-#&gt; Model cost at call 79 : 0.3500378
-#&gt; Model cost at call 83 : 0.349831
-#&gt; Model cost at call 88 : 0.3494286
-#&gt; Model cost at call 93 : 0.3488101
-#&gt; Model cost at call 98 : 0.3481444
-#&gt; Model cost at call 103 : 0.3478528
-#&gt; Model cost at call 108 : 0.3478092
-#&gt; Model cost at call 109 : 0.3478092
-#&gt; Model cost at call 113 : 0.347807
-#&gt; Model cost at call 116 : 0.347807
-#&gt; Model cost at call 117 : 0.347807
-#&gt; Model cost at call 119 : 0.347807
-#&gt; Model cost at call 120 : 0.347807
-#&gt; Model cost at call 125 : 0.347807
-#&gt; Model cost at call 126 : 0.347807
-#&gt; Model cost at call 128 : 0.347807
-#&gt; Model cost at call 137 : 0.347807
-#&gt; Model cost at call 148 : 0.347807
-#&gt; Model cost at call 152 : 0.347807
-#&gt; Model cost at call 154 : 0.347807
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+#&gt; 120 m1 33.31 2.881e+01 4.501e+00 2.722</div><div class='input'><span class='no'>f.w.mean</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 18 15:19:50 2016
-#&gt; Date of summary: Fri Nov 18 15:19:50 2016
+#&gt; Date of fit: Fri Nov 18 15:36:25 2016
+#&gt; Date of summary: Fri Nov 18 15:36:25 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1696,7 +807,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 155 model solutions performed in 0.636 s
+#&gt; Fitted with method Port using 155 model solutions performed in 0.653 s
#&gt;
#&gt; Weighting: mean
#&gt;
@@ -1805,68 +916,12 @@
#&gt; 100 m1 31.04 31.996124 -0.956124
#&gt; 100 m1 33.13 31.996124 1.133876
#&gt; 120 m1 25.15 28.824128 -3.674128
-#&gt; 120 m1 33.31 28.824128 4.485872</div><div class='input'><span class='no'>f.w.value</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='fu'>subset</span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"value"</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 11.21571
-#&gt; Model cost at call 2 : 11.21571
-#&gt; Model cost at call 3 : 11.21571
-#&gt; Model cost at call 8 : 11.12803
-#&gt; Model cost at call 10 : 11.128
-#&gt; Model cost at call 13 : 10.88016
-#&gt; Model cost at call 15 : 10.88016
-#&gt; Model cost at call 18 : 10.58819
-#&gt; Model cost at call 20 : 10.58819
-#&gt; Model cost at call 23 : 9.71699
-#&gt; Model cost at call 24 : 7.794026
-#&gt; Model cost at call 26 : 7.794026
-#&gt; Model cost at call 31 : 6.89734
-#&gt; Model cost at call 33 : 6.897337
-#&gt; Model cost at call 36 : 5.2239
-#&gt; Model cost at call 37 : 3.357735
-#&gt; Model cost at call 41 : 3.357733
-#&gt; Model cost at call 44 : 2.982323
-#&gt; Model cost at call 46 : 2.982322
-#&gt; Model cost at call 49 : 2.703946
-#&gt; Model cost at call 50 : 2.080395
-#&gt; Model cost at call 55 : 0.5307591
-#&gt; Model cost at call 56 : 0.5307591
-#&gt; Model cost at call 57 : 0.5307591
-#&gt; Model cost at call 59 : 0.5307584
-#&gt; Model cost at call 60 : 0.3240066
-#&gt; Model cost at call 61 : 0.3240066
-#&gt; Model cost at call 64 : 0.3240066
-#&gt; Model cost at call 65 : 0.2601108
-#&gt; Model cost at call 70 : 0.2414055
-#&gt; Model cost at call 74 : 0.2414055
-#&gt; Model cost at call 75 : 0.2404251
-#&gt; Model cost at call 80 : 0.2404087
-#&gt; Model cost at call 82 : 0.2404087
-#&gt; Model cost at call 85 : 0.2404054
-#&gt; Model cost at call 88 : 0.2404054
-#&gt; Model cost at call 92 : 0.2403931
-#&gt; Model cost at call 93 : 0.2403784
-#&gt; Model cost at call 98 : 0.2403784
-#&gt; Model cost at call 99 : 0.2403322
-#&gt; Model cost at call 104 : 0.2402188
-#&gt; Model cost at call 109 : 0.2400275
-#&gt; Model cost at call 114 : 0.239844
-#&gt; Model cost at call 119 : 0.2397153
-#&gt; Model cost at call 120 : 0.2397153
-#&gt; Model cost at call 124 : 0.2396978
-#&gt; Model cost at call 126 : 0.2396978
-#&gt; Model cost at call 130 : 0.239697
-#&gt; Model cost at call 131 : 0.2396963
-#&gt; Model cost at call 133 : 0.2396963
-#&gt; Model cost at call 138 : 0.2396962
-#&gt; Model cost at call 139 : 0.2396962
-#&gt; Model cost at call 141 : 0.2396962
-#&gt; Model cost at call 144 : 0.2396962
-#&gt; Model cost at call 147 : 0.2396962
-#&gt; Model cost at call 156 : 0.2396962
-#&gt; Model cost at call 167 : 0.2396962
-#&gt; Model cost at call 169 : 0.2396962
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+#&gt; 120 m1 33.31 28.824128 4.485872</div><div class='input'><span class='no'>f.w.value</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='fu'>subset</span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"value"</span>,
+ <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 18 15:19:51 2016
-#&gt; Date of summary: Fri Nov 18 15:19:51 2016
+#&gt; Date of fit: Fri Nov 18 15:36:26 2016
+#&gt; Date of summary: Fri Nov 18 15:36:26 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1874,7 +929,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 174 model solutions performed in 0.789 s
+#&gt; Fitted with method Port using 174 model solutions performed in 0.708 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1984,139 +1039,11 @@
<span class='no'>dw</span> <span class='kw'>&lt;-</span> <span class='no'>FOCUS_2006_D</span>
<span class='no'>errors</span> <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>1</span>)
<span class='no'>dw</span>$<span class='no'>err.man</span> <span class='kw'>&lt;-</span> <span class='no'>errors</span>[<span class='no'>FOCUS_2006_D</span>$<span class='no'>name</span>]
-<span class='no'>f.w.man</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 3949.676
-#&gt; Model cost at call 2 : 3949.676
-#&gt; Model cost at call 5 : 3949.676
-#&gt; Model cost at call 6 : 2252.859
-#&gt; Model cost at call 8 : 2252.858
-#&gt; Model cost at call 9 : 2252.826
-#&gt; Model cost at call 13 : 1567.343
-#&gt; Model cost at call 14 : 1567.342
-#&gt; Model cost at call 15 : 1567.333
-#&gt; Model cost at call 18 : 1041.524
-#&gt; Model cost at call 19 : 1041.522
-#&gt; Model cost at call 24 : 840.4649
-#&gt; Model cost at call 26 : 840.4646
-#&gt; Model cost at call 29 : 782.303
-#&gt; Model cost at call 31 : 782.3028
-#&gt; Model cost at call 34 : 664.539
-#&gt; Model cost at call 36 : 664.5389
-#&gt; Model cost at call 40 : 615.7908
-#&gt; Model cost at call 42 : 615.7907
-#&gt; Model cost at call 45 : 569.5971
-#&gt; Model cost at call 47 : 569.597
-#&gt; Model cost at call 50 : 517.3175
-#&gt; Model cost at call 52 : 517.3173
-#&gt; Model cost at call 56 : 464.8158
-#&gt; Model cost at call 58 : 464.8157
-#&gt; Model cost at call 62 : 433.0031
-#&gt; Model cost at call 64 : 433.003
-#&gt; Model cost at call 67 : 423.7407
-#&gt; Model cost at call 69 : 423.7406
-#&gt; Model cost at call 70 : 423.7392
-#&gt; Model cost at call 72 : 346.2781
-#&gt; Model cost at call 74 : 346.278
-#&gt; Model cost at call 75 : 346.2779
-#&gt; Model cost at call 78 : 334.5399
-#&gt; Model cost at call 80 : 334.5398
-#&gt; Model cost at call 83 : 324.139
-#&gt; Model cost at call 85 : 324.1389
-#&gt; Model cost at call 88 : 319.7514
-#&gt; Model cost at call 90 : 319.7514
-#&gt; Model cost at call 94 : 300.9426
-#&gt; Model cost at call 96 : 300.9425
-#&gt; Model cost at call 100 : 295.8803
-#&gt; Model cost at call 102 : 295.8803
-#&gt; Model cost at call 105 : 290.3288
-#&gt; Model cost at call 107 : 290.3287
-#&gt; Model cost at call 111 : 284.3257
-#&gt; Model cost at call 113 : 284.3257
-#&gt; Model cost at call 116 : 282.3972
-#&gt; Model cost at call 118 : 282.3972
-#&gt; Model cost at call 122 : 273.7385
-#&gt; Model cost at call 124 : 273.7385
-#&gt; Model cost at call 128 : 271.8379
-#&gt; Model cost at call 130 : 271.8379
-#&gt; Model cost at call 133 : 270.064
-#&gt; Model cost at call 135 : 270.064
-#&gt; Model cost at call 138 : 268.0107
-#&gt; Model cost at call 140 : 268.0107
-#&gt; Model cost at call 144 : 265.6194
-#&gt; Model cost at call 146 : 265.6194
-#&gt; Model cost at call 148 : 265.6194
-#&gt; Model cost at call 149 : 263.4825
-#&gt; Model cost at call 151 : 263.4825
-#&gt; Model cost at call 153 : 263.4824
-#&gt; Model cost at call 154 : 262.0988
-#&gt; Model cost at call 156 : 262.0988
-#&gt; Model cost at call 160 : 260.7078
-#&gt; Model cost at call 162 : 260.7078
-#&gt; Model cost at call 165 : 259.9453
-#&gt; Model cost at call 167 : 259.9453
-#&gt; Model cost at call 170 : 258.9623
-#&gt; Model cost at call 172 : 258.9623
-#&gt; Model cost at call 174 : 258.962
-#&gt; Model cost at call 176 : 258.0119
-#&gt; Model cost at call 178 : 258.0119
-#&gt; Model cost at call 180 : 258.0119
-#&gt; Model cost at call 181 : 257.8698
-#&gt; Model cost at call 183 : 257.8698
-#&gt; Model cost at call 186 : 256.8608
-#&gt; Model cost at call 188 : 256.8608
-#&gt; Model cost at call 190 : 256.8608
-#&gt; Model cost at call 191 : 256.2306
-#&gt; Model cost at call 193 : 256.2306
-#&gt; Model cost at call 195 : 256.2305
-#&gt; Model cost at call 196 : 255.7119
-#&gt; Model cost at call 198 : 255.7118
-#&gt; Model cost at call 201 : 255.3323
-#&gt; Model cost at call 203 : 255.3323
-#&gt; Model cost at call 205 : 255.3323
-#&gt; Model cost at call 206 : 254.6653
-#&gt; Model cost at call 208 : 254.6653
-#&gt; Model cost at call 211 : 254.3984
-#&gt; Model cost at call 213 : 254.3984
-#&gt; Model cost at call 216 : 253.3199
-#&gt; Model cost at call 218 : 253.3199
-#&gt; Model cost at call 220 : 253.3198
-#&gt; Model cost at call 221 : 252.4845
-#&gt; Model cost at call 223 : 252.4845
-#&gt; Model cost at call 225 : 252.4845
-#&gt; Model cost at call 226 : 251.6917
-#&gt; Model cost at call 229 : 251.6917
-#&gt; Model cost at call 230 : 251.6917
-#&gt; Model cost at call 233 : 251.0189
-#&gt; Model cost at call 235 : 251.0189
-#&gt; Model cost at call 238 : 250.6912
-#&gt; Model cost at call 240 : 250.6912
-#&gt; Model cost at call 243 : 250.5546
-#&gt; Model cost at call 245 : 250.5546
-#&gt; Model cost at call 248 : 250.466
-#&gt; Model cost at call 249 : 250.3744
-#&gt; Model cost at call 250 : 249.9681
-#&gt; Model cost at call 251 : 249.2215
-#&gt; Model cost at call 260 : 248.919
-#&gt; Model cost at call 264 : 248.919
-#&gt; Model cost at call 265 : 248.8876
-#&gt; Model cost at call 267 : 248.8876
-#&gt; Model cost at call 270 : 248.8521
-#&gt; Model cost at call 271 : 248.8178
-#&gt; Model cost at call 272 : 248.6837
-#&gt; Model cost at call 273 : 248.5989
-#&gt; Model cost at call 276 : 248.5989
-#&gt; Model cost at call 278 : 248.5935
-#&gt; Model cost at call 280 : 248.5935
-#&gt; Model cost at call 282 : 248.5935
-#&gt; Model cost at call 283 : 248.5902
-#&gt; Model cost at call 284 : 248.5902
-#&gt; Model cost at call 289 : 248.5902
-#&gt; Model cost at call 298 : 248.5902
-#&gt; Model cost at call 309 : 248.5902
-#&gt; Model cost at call 311 : 248.5902
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+<span class='no'>f.w.man</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 18 15:19:53 2016
-#&gt; Date of summary: Fri Nov 18 15:19:53 2016
+#&gt; Date of fit: Fri Nov 18 15:36:27 2016
+#&gt; Date of summary: Fri Nov 18 15:36:27 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -2124,7 +1051,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 316 model solutions performed in 1.337 s
+#&gt; Fitted with method Port using 316 model solutions performed in 1.288 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -2233,211 +1160,12 @@
#&gt; 100 m1 31.04 31.969288 -0.929288 2
#&gt; 100 m1 33.13 31.969288 1.160712 2
#&gt; 120 m1 25.15 28.760615 -3.610615 2
-#&gt; 120 m1 33.31 28.760615 4.549385 2</div><div class='input'><span class='no'>f.w.man.irls</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>,
- <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 3949.676
-#&gt; Model cost at call 2 : 3949.676
-#&gt; Model cost at call 5 : 3949.676
-#&gt; Model cost at call 6 : 2252.859
-#&gt; Model cost at call 8 : 2252.858
-#&gt; Model cost at call 9 : 2252.826
-#&gt; Model cost at call 13 : 1567.343
-#&gt; Model cost at call 14 : 1567.342
-#&gt; Model cost at call 15 : 1567.333
-#&gt; Model cost at call 18 : 1041.524
-#&gt; Model cost at call 19 : 1041.522
-#&gt; Model cost at call 24 : 840.4649
-#&gt; Model cost at call 26 : 840.4646
-#&gt; Model cost at call 29 : 782.303
-#&gt; Model cost at call 31 : 782.3028
-#&gt; Model cost at call 34 : 664.539
-#&gt; Model cost at call 36 : 664.5389
-#&gt; Model cost at call 40 : 615.7908
-#&gt; Model cost at call 42 : 615.7907
-#&gt; Model cost at call 45 : 569.5971
-#&gt; Model cost at call 47 : 569.597
-#&gt; Model cost at call 50 : 517.3175
-#&gt; Model cost at call 52 : 517.3173
-#&gt; Model cost at call 56 : 464.8158
-#&gt; Model cost at call 58 : 464.8157
-#&gt; Model cost at call 62 : 433.0031
-#&gt; Model cost at call 64 : 433.003
-#&gt; Model cost at call 67 : 423.7407
-#&gt; Model cost at call 69 : 423.7406
-#&gt; Model cost at call 70 : 423.7392
-#&gt; Model cost at call 72 : 346.2781
-#&gt; Model cost at call 74 : 346.278
-#&gt; Model cost at call 75 : 346.2779
-#&gt; Model cost at call 78 : 334.5399
-#&gt; Model cost at call 80 : 334.5398
-#&gt; Model cost at call 83 : 324.139
-#&gt; Model cost at call 85 : 324.1389
-#&gt; Model cost at call 88 : 319.7514
-#&gt; Model cost at call 90 : 319.7514
-#&gt; Model cost at call 94 : 300.9426
-#&gt; Model cost at call 96 : 300.9425
-#&gt; Model cost at call 100 : 295.8803
-#&gt; Model cost at call 102 : 295.8803
-#&gt; Model cost at call 105 : 290.3288
-#&gt; Model cost at call 107 : 290.3287
-#&gt; Model cost at call 111 : 284.3257
-#&gt; Model cost at call 113 : 284.3257
-#&gt; Model cost at call 116 : 282.3972
-#&gt; Model cost at call 118 : 282.3972
-#&gt; Model cost at call 122 : 273.7385
-#&gt; Model cost at call 124 : 273.7385
-#&gt; Model cost at call 128 : 271.8379
-#&gt; Model cost at call 130 : 271.8379
-#&gt; Model cost at call 133 : 270.064
-#&gt; Model cost at call 135 : 270.064
-#&gt; Model cost at call 138 : 268.0107
-#&gt; Model cost at call 140 : 268.0107
-#&gt; Model cost at call 144 : 265.6194
-#&gt; Model cost at call 146 : 265.6194
-#&gt; Model cost at call 148 : 265.6194
-#&gt; Model cost at call 149 : 263.4825
-#&gt; Model cost at call 151 : 263.4825
-#&gt; Model cost at call 153 : 263.4824
-#&gt; Model cost at call 154 : 262.0988
-#&gt; Model cost at call 156 : 262.0988
-#&gt; Model cost at call 160 : 260.7078
-#&gt; Model cost at call 162 : 260.7078
-#&gt; Model cost at call 165 : 259.9453
-#&gt; Model cost at call 167 : 259.9453
-#&gt; Model cost at call 170 : 258.9623
-#&gt; Model cost at call 172 : 258.9623
-#&gt; Model cost at call 174 : 258.962
-#&gt; Model cost at call 176 : 258.0119
-#&gt; Model cost at call 178 : 258.0119
-#&gt; Model cost at call 180 : 258.0119
-#&gt; Model cost at call 181 : 257.8698
-#&gt; Model cost at call 183 : 257.8698
-#&gt; Model cost at call 186 : 256.8608
-#&gt; Model cost at call 188 : 256.8608
-#&gt; Model cost at call 190 : 256.8608
-#&gt; Model cost at call 191 : 256.2306
-#&gt; Model cost at call 193 : 256.2306
-#&gt; Model cost at call 195 : 256.2305
-#&gt; Model cost at call 196 : 255.7119
-#&gt; Model cost at call 198 : 255.7118
-#&gt; Model cost at call 201 : 255.3323
-#&gt; Model cost at call 203 : 255.3323
-#&gt; Model cost at call 205 : 255.3323
-#&gt; Model cost at call 206 : 254.6653
-#&gt; Model cost at call 208 : 254.6653
-#&gt; Model cost at call 211 : 254.3984
-#&gt; Model cost at call 213 : 254.3984
-#&gt; Model cost at call 216 : 253.3199
-#&gt; Model cost at call 218 : 253.3199
-#&gt; Model cost at call 220 : 253.3198
-#&gt; Model cost at call 221 : 252.4845
-#&gt; Model cost at call 223 : 252.4845
-#&gt; Model cost at call 225 : 252.4845
-#&gt; Model cost at call 226 : 251.6917
-#&gt; Model cost at call 229 : 251.6917
-#&gt; Model cost at call 230 : 251.6917
-#&gt; Model cost at call 233 : 251.0189
-#&gt; Model cost at call 235 : 251.0189
-#&gt; Model cost at call 238 : 250.6912
-#&gt; Model cost at call 240 : 250.6912
-#&gt; Model cost at call 243 : 250.5546
-#&gt; Model cost at call 245 : 250.5546
-#&gt; Model cost at call 248 : 250.466
-#&gt; Model cost at call 249 : 250.3744
-#&gt; Model cost at call 250 : 249.9681
-#&gt; Model cost at call 251 : 249.2215
-#&gt; Model cost at call 260 : 248.919
-#&gt; Model cost at call 264 : 248.919
-#&gt; Model cost at call 265 : 248.8876
-#&gt; Model cost at call 267 : 248.8876
-#&gt; Model cost at call 270 : 248.8521
-#&gt; Model cost at call 271 : 248.8178
-#&gt; Model cost at call 272 : 248.6837
-#&gt; Model cost at call 273 : 248.5989
-#&gt; Model cost at call 276 : 248.5989
-#&gt; Model cost at call 278 : 248.5935
-#&gt; Model cost at call 280 : 248.5935
-#&gt; Model cost at call 282 : 248.5935
-#&gt; Model cost at call 283 : 248.5902
-#&gt; Model cost at call 284 : 248.5902
-#&gt; Model cost at call 289 : 248.5902
-#&gt; Model cost at call 298 : 248.5902
-#&gt; Model cost at call 309 : 248.5902
-#&gt; Model cost at call 311 : 248.5902
-#&gt; IRLS based on variance estimates for each observed variable
-#&gt; Initial variance estimates are:
-#&gt; parent m1
-#&gt; 11.536305 7.443046
-#&gt; Model cost at call 317 : 40
-#&gt; Model cost at call 319 : 40
-#&gt; Model cost at call 324 : 39.98891
-#&gt; Model cost at call 325 : 39.9889
-#&gt; Model cost at call 327 : 39.98886
-#&gt; Model cost at call 331 : 39.98871
-#&gt; Model cost at call 333 : 39.97254
-#&gt; Model cost at call 336 : 39.97253
-#&gt; Model cost at call 338 : 39.96929
-#&gt; Model cost at call 340 : 39.96929
-#&gt; Model cost at call 344 : 39.96849
-#&gt; Model cost at call 346 : 39.96849
-#&gt; Model cost at call 348 : 39.96849
-#&gt; Model cost at call 349 : 39.96774
-#&gt; Model cost at call 351 : 39.96774
-#&gt; Model cost at call 353 : 39.96774
-#&gt; Model cost at call 354 : 39.96714
-#&gt; Model cost at call 356 : 39.96714
-#&gt; Model cost at call 359 : 39.96617
-#&gt; Model cost at call 361 : 39.96617
-#&gt; Model cost at call 364 : 39.96606
-#&gt; Model cost at call 366 : 39.96606
-#&gt; Model cost at call 369 : 39.96551
-#&gt; Model cost at call 371 : 39.96551
-#&gt; Model cost at call 372 : 39.96551
-#&gt; Model cost at call 375 : 39.96527
-#&gt; Model cost at call 378 : 39.96527
-#&gt; Model cost at call 379 : 39.96527
-#&gt; Model cost at call 380 : 39.96525
-#&gt; Model cost at call 382 : 39.96525
-#&gt; Model cost at call 385 : 39.9651
-#&gt; Model cost at call 387 : 39.9651
-#&gt; Model cost at call 388 : 39.9651
-#&gt; Model cost at call 390 : 39.96502
-#&gt; Model cost at call 393 : 39.96502
-#&gt; Model cost at call 396 : 39.96502
-#&gt; Model cost at call 397 : 39.96467
-#&gt; Model cost at call 398 : 39.96422
-#&gt; Model cost at call 399 : 39.9624
-#&gt; Model cost at call 400 : 39.95909
-#&gt; Model cost at call 402 : 39.95909
-#&gt; Model cost at call 405 : 39.9571
-#&gt; Model cost at call 407 : 39.95709
-#&gt; Model cost at call 413 : 39.95479
-#&gt; Model cost at call 414 : 39.95479
-#&gt; Model cost at call 415 : 39.95479
-#&gt; Model cost at call 417 : 39.95479
-#&gt; Model cost at call 419 : 39.95398
-#&gt; Model cost at call 422 : 39.95398
-#&gt; Model cost at call 424 : 39.95387
-#&gt; Model cost at call 429 : 39.95384
-#&gt; Model cost at call 432 : 39.95384
-#&gt; Model cost at call 435 : 39.95384
-#&gt; Model cost at call 437 : 39.95384
-#&gt; Model cost at call 438 : 39.95384
-#&gt; Model cost at call 446 : 39.95384
-#&gt; Model cost at call 455 : 39.95384
-#&gt; Model cost at call 469 : 39.95384
-#&gt; Model cost at call 473 : 39.95384
-#&gt; Iteration 1 yields variance estimates:
-#&gt; parent m1
-#&gt; 11.572891 7.408116
-#&gt; Sum of squared differences to last variance estimates: 7e-05
-#&gt; Iteration 2 yields variance estimates:
-#&gt; parent m1
-#&gt; 11.573402 7.407847
-#&gt; Sum of squared differences to last variance estimates: 8.1e-09
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+#&gt; 120 m1 33.31 28.760615 4.549385 2</div><div class='input'><span class='no'>f.w.man.irls</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>)
+<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 18 15:19:55 2016
-#&gt; Date of summary: Fri Nov 18 15:19:55 2016
+#&gt; Date of fit: Fri Nov 18 15:36:30 2016
+#&gt; Date of summary: Fri Nov 18 15:36:30 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -2445,7 +1173,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 648 model solutions performed in 2.716 s
+#&gt; Fitted with method Port using 648 model solutions performed in 2.694 s
#&gt;
#&gt; Weighting: manual then iterative reweighting method obs
#&gt;
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index 764f1ab4..acc21bd4 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -6,8 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<title>Function to plot the confidence intervals obtained using
- list(list("mkinfit")) — mkinparplot • mkin</title>
+<title>Function to plot the confidence intervals obtained using mkinfit — mkinparplot • mkin</title>
<!-- jquery -->
<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -78,8 +77,7 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
- <h1>Function to plot the confidence intervals obtained using
- list(list("mkinfit"))</h1>
+ <h1>Function to plot the confidence intervals obtained using mkinfit</h1>
</div>
@@ -104,9 +102,9 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'><span class='no'>model</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
- <span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"phenol"</span>), <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
- <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"anisole"</span>)),
- <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></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='no'>model</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+ <span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"phenol"</span>), <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
+ <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"anisole"</span>)),
+ <span class='kw'>anisole</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'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></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='no'>model</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>mkinparplot</span>(<span class='no'>fit</span>)</div><img src='mkinparplot-4.png' alt='' width='540' height='400' /></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
diff --git a/docs/reference/mmkin-10.png b/docs/reference/mmkin-10.png
new file mode 100644
index 00000000..9e40d451
--- /dev/null
+++ b/docs/reference/mmkin-10.png
Binary files differ
diff --git a/docs/reference/mmkin-12.png b/docs/reference/mmkin-12.png
new file mode 100644
index 00000000..9e40d451
--- /dev/null
+++ b/docs/reference/mmkin-12.png
Binary files differ
diff --git a/docs/reference/mmkin-14.png b/docs/reference/mmkin-14.png
index 9e40d451..72cfc5e7 100644
--- a/docs/reference/mmkin-14.png
+++ b/docs/reference/mmkin-14.png
Binary files differ
diff --git a/docs/reference/mmkin-16.png b/docs/reference/mmkin-16.png
index 72cfc5e7..0b315b1a 100644
--- a/docs/reference/mmkin-16.png
+++ b/docs/reference/mmkin-16.png
Binary files differ
diff --git a/docs/reference/mmkin-18.png b/docs/reference/mmkin-18.png
index 0b315b1a..b98940ff 100644
--- a/docs/reference/mmkin-18.png
+++ b/docs/reference/mmkin-18.png
Binary files differ
diff --git a/docs/reference/mmkin-20.png b/docs/reference/mmkin-20.png
index b98940ff..c2e9e5ae 100644
--- a/docs/reference/mmkin-20.png
+++ b/docs/reference/mmkin-20.png
Binary files differ
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 0e39dac0..45a246f9 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -139,1091 +139,32 @@
<span class='no'>datasets</span> <span class='kw'>&lt;-</span> <span class='fu'>lapply</span>(<span class='no'>synthetic_data_for_UBA_2014</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='kw'>function</span>(<span class='no'>x</span>) <span class='no'>x</span>$<span class='no'>data</span>)
<span class='fu'>names</span>(<span class='no'>datasets</span>) <span class='kw'>&lt;-</span> <span class='fu'>paste</span>(<span class='st'>"Dataset"</span>, <span class='fl'>1</span>:<span class='fl'>3</span>)
-<span class='no'>time_default</span> <span class='kw'>&lt;-</span> <span class='fu'>system.time</span>(<span class='no'>fits.0</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>))
-<span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'>system.time</span>(<span class='no'>fits.1</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>))</div><div class='output co'>#&gt; Model cost at call 1 : 31054.59
-#&gt; Model cost at call 3 : 31054.59
-#&gt; Model cost at call 8 : 15089.57
-#&gt; Model cost at call 9 : 11464.3
-#&gt; Model cost at call 11 : 11464.1
-#&gt; Model cost at call 16 : 5723.32
-#&gt; Model cost at call 17 : 5723.318
-#&gt; Model cost at call 19 : 5723.304
-#&gt; Model cost at call 21 : 5723.304
-#&gt; Model cost at call 24 : 3968.126
-#&gt; Model cost at call 25 : 3968.124
-#&gt; Model cost at call 28 : 3968.119
-#&gt; Model cost at call 31 : 3416.421
-#&gt; Model cost at call 32 : 3416.42
-#&gt; Model cost at call 36 : 3416.418
-#&gt; Model cost at call 38 : 866.5564
-#&gt; Model cost at call 42 : 866.5557
-#&gt; Model cost at call 45 : 670.4833
-#&gt; Model cost at call 47 : 670.476
-#&gt; Model cost at call 53 : 312.9905
-#&gt; Model cost at call 57 : 312.9904
-#&gt; Model cost at call 58 : 312.9904
-#&gt; Model cost at call 61 : 287.8916
-#&gt; Model cost at call 63 : 287.8916
-#&gt; Model cost at call 66 : 287.8916
-#&gt; Model cost at call 69 : 284.5441
-#&gt; Model cost at call 71 : 284.5441
-#&gt; Model cost at call 73 : 284.5441
-#&gt; Model cost at call 76 : 283.4533
-#&gt; Model cost at call 78 : 283.4533
-#&gt; Model cost at call 83 : 282.1356
-#&gt; Model cost at call 85 : 282.1356
-#&gt; Model cost at call 88 : 282.1356
-#&gt; Model cost at call 90 : 280.7846
-#&gt; Model cost at call 92 : 280.7846
-#&gt; Model cost at call 95 : 280.7846
-#&gt; Model cost at call 97 : 278.4856
-#&gt; Model cost at call 98 : 274.5025
-#&gt; Model cost at call 99 : 269.2866
-#&gt; Model cost at call 101 : 269.2866
-#&gt; Model cost at call 102 : 269.2866
-#&gt; Model cost at call 103 : 269.2866
-#&gt; Model cost at call 106 : 254.1284
-#&gt; Model cost at call 108 : 254.1283
-#&gt; Model cost at call 109 : 254.1283
-#&gt; Model cost at call 112 : 254.128
-#&gt; Model cost at call 114 : 233.1376
-#&gt; Model cost at call 116 : 233.1376
-#&gt; Model cost at call 118 : 233.1375
-#&gt; Model cost at call 121 : 227.5879
-#&gt; Model cost at call 124 : 227.5879
-#&gt; Model cost at call 125 : 227.5878
-#&gt; Model cost at call 129 : 217.0041
-#&gt; Model cost at call 133 : 217.0041
-#&gt; Model cost at call 135 : 217.0041
-#&gt; Model cost at call 136 : 215.1367
-#&gt; Model cost at call 138 : 215.1367
-#&gt; Model cost at call 143 : 213.3794
-#&gt; Model cost at call 145 : 213.3794
-#&gt; Model cost at call 150 : 211.0201
-#&gt; Model cost at call 152 : 211.0201
-#&gt; Model cost at call 154 : 211.0201
-#&gt; Model cost at call 155 : 211.0201
-#&gt; Model cost at call 157 : 210.6426
-#&gt; Model cost at call 159 : 210.6426
-#&gt; Model cost at call 160 : 210.6425
-#&gt; Model cost at call 164 : 207.6331
-#&gt; Model cost at call 167 : 207.6331
-#&gt; Model cost at call 171 : 206.2366
-#&gt; Model cost at call 173 : 206.2366
-#&gt; Model cost at call 174 : 206.2366
-#&gt; Model cost at call 178 : 204.8117
-#&gt; Model cost at call 180 : 204.8117
-#&gt; Model cost at call 185 : 204.7988
-#&gt; Model cost at call 187 : 204.7988
-#&gt; Model cost at call 190 : 204.7988
-#&gt; Model cost at call 192 : 203.5122
-#&gt; Model cost at call 194 : 203.5122
-#&gt; Model cost at call 197 : 203.5122
-#&gt; Model cost at call 198 : 203.5122
-#&gt; Model cost at call 199 : 203.354
-#&gt; Model cost at call 201 : 203.354
-#&gt; Model cost at call 204 : 203.354
-#&gt; Model cost at call 206 : 202.6825
-#&gt; Model cost at call 208 : 202.6825
-#&gt; Model cost at call 209 : 202.6825
-#&gt; Model cost at call 212 : 202.6825
-#&gt; Model cost at call 213 : 202.4582
-#&gt; Model cost at call 215 : 202.4582
-#&gt; Model cost at call 220 : 202.3261
-#&gt; Model cost at call 222 : 202.3261
-#&gt; Model cost at call 227 : 202.2306
-#&gt; Model cost at call 229 : 202.2306
-#&gt; Model cost at call 231 : 202.2306
-#&gt; Model cost at call 234 : 202.115
-#&gt; Model cost at call 236 : 202.115
-#&gt; Model cost at call 238 : 202.115
-#&gt; Model cost at call 241 : 202.0397
-#&gt; Model cost at call 243 : 202.0397
-#&gt; Model cost at call 248 : 201.8989
-#&gt; Model cost at call 249 : 201.8551
-#&gt; Model cost at call 252 : 201.8551
-#&gt; Model cost at call 257 : 201.676
-#&gt; Model cost at call 259 : 201.676
-#&gt; Model cost at call 264 : 201.6285
-#&gt; Model cost at call 266 : 201.6285
-#&gt; Model cost at call 270 : 201.6284
-#&gt; Model cost at call 271 : 201.5876
-#&gt; Model cost at call 272 : 201.5876
-#&gt; Model cost at call 278 : 201.5317
-#&gt; Model cost at call 279 : 201.5317
-#&gt; Model cost at call 286 : 201.5207
-#&gt; Model cost at call 287 : 201.5207
-#&gt; Model cost at call 289 : 201.5207
-#&gt; Model cost at call 293 : 201.5207
-#&gt; Model cost at call 294 : 201.5207
-#&gt; Model cost at call 296 : 201.5174
-#&gt; Model cost at call 301 : 201.5174
-#&gt; Model cost at call 304 : 201.5169
-#&gt; Model cost at call 305 : 201.5169
-#&gt; Model cost at call 306 : 201.5169
-#&gt; Model cost at call 309 : 201.5169
-#&gt; Model cost at call 312 : 201.5169
-#&gt; Model cost at call 314 : 201.5169
-#&gt; Model cost at call 322 : 201.5169
-#&gt; Model cost at call 325 : 201.5169
-#&gt; Model cost at call 340 : 201.5169
-#&gt; Optimisation by method Port successfully terminated.
-#&gt; Model cost at call 1 : 35974.4
-#&gt; Model cost at call 3 : 35974.4
-#&gt; Model cost at call 5 : 35974.4
-#&gt; Model cost at call 7 : 35974.4
-#&gt; Model cost at call 9 : 13270.14
-#&gt; Model cost at call 10 : 12432.22
-#&gt; Model cost at call 14 : 12432.12
-#&gt; Model cost at call 16 : 12431.88
-#&gt; Model cost at call 18 : 5356.271
-#&gt; Model cost at call 19 : 5356.268
-#&gt; Model cost at call 20 : 5356.251
-#&gt; Model cost at call 22 : 5356.245
-#&gt; Model cost at call 27 : 1507.839
-#&gt; Model cost at call 33 : 1507.839
-#&gt; Model cost at call 35 : 582.0818
-#&gt; Model cost at call 36 : 582.0813
-#&gt; Model cost at call 38 : 582.0802
-#&gt; Model cost at call 40 : 582.0799
-#&gt; Model cost at call 44 : 328.9337
-#&gt; Model cost at call 45 : 328.9335
-#&gt; Model cost at call 51 : 328.9328
-#&gt; Model cost at call 53 : 313.4901
-#&gt; Model cost at call 59 : 313.49
-#&gt; Model cost at call 60 : 313.4899
-#&gt; Model cost at call 61 : 308.6268
-#&gt; Model cost at call 63 : 308.6267
-#&gt; Model cost at call 69 : 302.4454
-#&gt; Model cost at call 73 : 302.4453
-#&gt; Model cost at call 77 : 298.0751
-#&gt; Model cost at call 79 : 298.075
-#&gt; Model cost at call 85 : 293.1404
-#&gt; Model cost at call 86 : 289.6645
-#&gt; Model cost at call 88 : 289.6645
-#&gt; Model cost at call 95 : 288.1617
-#&gt; Model cost at call 101 : 288.1616
-#&gt; Model cost at call 102 : 288.1615
-#&gt; Model cost at call 103 : 286.7649
-#&gt; Model cost at call 109 : 286.7649
-#&gt; Model cost at call 111 : 284.5224
-#&gt; Model cost at call 117 : 284.5224
-#&gt; Model cost at call 118 : 284.5224
-#&gt; Model cost at call 119 : 281.3466
-#&gt; Model cost at call 125 : 281.3466
-#&gt; Model cost at call 127 : 274.0924
-#&gt; Model cost at call 128 : 264.929
-#&gt; Model cost at call 133 : 264.929
-#&gt; Model cost at call 136 : 251.3329
-#&gt; Model cost at call 137 : 251.3329
-#&gt; Model cost at call 140 : 251.3329
-#&gt; Model cost at call 141 : 251.3329
-#&gt; Model cost at call 146 : 247.7019
-#&gt; Model cost at call 147 : 247.7019
-#&gt; Model cost at call 149 : 247.7018
-#&gt; Model cost at call 154 : 247.3465
-#&gt; Model cost at call 158 : 247.3465
-#&gt; Model cost at call 160 : 247.3464
-#&gt; Model cost at call 162 : 244.622
-#&gt; Model cost at call 166 : 244.622
-#&gt; Model cost at call 170 : 242.5961
-#&gt; Model cost at call 171 : 241.6973
-#&gt; Model cost at call 173 : 241.6973
-#&gt; Model cost at call 174 : 241.6973
-#&gt; Model cost at call 175 : 241.6973
-#&gt; Model cost at call 179 : 238.8924
-#&gt; Model cost at call 181 : 238.8923
-#&gt; Model cost at call 187 : 236.0921
-#&gt; Model cost at call 190 : 236.0921
-#&gt; Model cost at call 192 : 236.092
-#&gt; Model cost at call 195 : 233.9082
-#&gt; Model cost at call 197 : 233.9082
-#&gt; Model cost at call 201 : 233.9082
-#&gt; Model cost at call 202 : 233.9082
-#&gt; Model cost at call 203 : 228.1486
-#&gt; Model cost at call 205 : 228.1486
-#&gt; Model cost at call 206 : 228.1485
-#&gt; Model cost at call 207 : 228.1485
-#&gt; Model cost at call 211 : 225.0879
-#&gt; Model cost at call 214 : 225.0879
-#&gt; Model cost at call 216 : 225.0879
-#&gt; Model cost at call 218 : 225.0879
-#&gt; Model cost at call 219 : 220.9928
-#&gt; Model cost at call 221 : 220.9928
-#&gt; Model cost at call 227 : 219.1889
-#&gt; Model cost at call 229 : 219.1888
-#&gt; Model cost at call 233 : 219.1888
-#&gt; Model cost at call 235 : 218.6966
-#&gt; Model cost at call 238 : 218.6966
-#&gt; Model cost at call 239 : 218.6966
-#&gt; Model cost at call 240 : 218.6966
-#&gt; Model cost at call 241 : 218.6966
-#&gt; Model cost at call 242 : 218.6966
-#&gt; Model cost at call 243 : 214.4307
-#&gt; Model cost at call 247 : 214.4307
-#&gt; Model cost at call 251 : 213.6076
-#&gt; Model cost at call 253 : 213.6076
-#&gt; Model cost at call 254 : 213.6076
-#&gt; Model cost at call 256 : 213.6076
-#&gt; Model cost at call 259 : 211.0287
-#&gt; Model cost at call 262 : 211.0287
-#&gt; Model cost at call 263 : 211.0287
-#&gt; Model cost at call 267 : 209.6141
-#&gt; Model cost at call 270 : 209.6141
-#&gt; Model cost at call 271 : 209.6141
-#&gt; Model cost at call 276 : 207.896
-#&gt; Model cost at call 278 : 207.896
-#&gt; Model cost at call 284 : 206.4468
-#&gt; Model cost at call 286 : 206.4468
-#&gt; Model cost at call 289 : 206.4468
-#&gt; Model cost at call 292 : 205.8789
-#&gt; Model cost at call 296 : 205.8789
-#&gt; Model cost at call 298 : 205.8789
-#&gt; Model cost at call 299 : 205.8789
-#&gt; Model cost at call 300 : 204.2634
-#&gt; Model cost at call 301 : 204.2634
-#&gt; Model cost at call 303 : 204.2634
-#&gt; Model cost at call 305 : 204.2634
-#&gt; Model cost at call 308 : 203.5453
-#&gt; Model cost at call 309 : 203.338
-#&gt; Model cost at call 310 : 203.338
-#&gt; Model cost at call 313 : 203.338
-#&gt; Model cost at call 314 : 203.338
-#&gt; Model cost at call 316 : 203.338
-#&gt; Model cost at call 318 : 202.797
-#&gt; Model cost at call 321 : 202.797
-#&gt; Model cost at call 326 : 202.4377
-#&gt; Model cost at call 327 : 202.4377
-#&gt; Model cost at call 334 : 202.0027
-#&gt; Model cost at call 335 : 202.0027
-#&gt; Model cost at call 342 : 201.8249
-#&gt; Model cost at call 344 : 201.8249
-#&gt; Model cost at call 349 : 201.8249
-#&gt; Model cost at call 351 : 201.7123
-#&gt; Model cost at call 352 : 201.7123
-#&gt; Model cost at call 359 : 201.6476
-#&gt; Model cost at call 361 : 201.6476
-#&gt; Model cost at call 365 : 201.6476
-#&gt; Model cost at call 368 : 201.5827
-#&gt; Model cost at call 371 : 201.5827
-#&gt; Model cost at call 378 : 201.5531
-#&gt; Model cost at call 379 : 201.5531
-#&gt; Model cost at call 386 : 201.5531
-#&gt; Model cost at call 390 : 201.537
-#&gt; Model cost at call 391 : 201.537
-#&gt; Model cost at call 401 : 201.5281
-#&gt; Model cost at call 402 : 201.5281
-#&gt; Model cost at call 404 : 201.5281
-#&gt; Model cost at call 407 : 201.5281
-#&gt; Model cost at call 413 : 201.5231
-#&gt; Model cost at call 417 : 201.5231
-#&gt; Model cost at call 418 : 201.5231
-#&gt; Model cost at call 420 : 201.5231
-#&gt; Model cost at call 426 : 201.5199
-#&gt; Model cost at call 428 : 201.5199
-#&gt; Model cost at call 439 : 201.5184
-#&gt; Model cost at call 443 : 201.5184
-#&gt; Model cost at call 444 : 201.5184
-#&gt; Model cost at call 446 : 201.5184
-#&gt; Model cost at call 454 : 201.5177
-#&gt; Model cost at call 457 : 201.5177
-#&gt; Model cost at call 469 : 201.5174
-#&gt; Model cost at call 473 : 201.5174
-#&gt; Model cost at call 476 : 201.5174
-#&gt; Model cost at call 480 : 201.5174
-#&gt; Model cost at call 483 : 201.5174
-#&gt; Model cost at call 484 : 201.5171
-#&gt; Model cost at call 487 : 201.5171
-#&gt; Model cost at call 499 : 201.517
-#&gt; Model cost at call 506 : 201.517
-#&gt; Model cost at call 510 : 201.517
-#&gt; Model cost at call 514 : 201.517
-#&gt; Model cost at call 522 : 201.517
-#&gt; Model cost at call 526 : 201.517
-#&gt; Model cost at call 527 : 201.517
-#&gt; Model cost at call 529 : 201.5169
-#&gt; Model cost at call 536 : 201.5169
-#&gt; Model cost at call 540 : 201.5169
-#&gt; Model cost at call 544 : 201.5169
-#&gt; Model cost at call 556 : 201.5169
-#&gt; Model cost at call 557 : 201.5169
-#&gt; Model cost at call 559 : 201.5169
-#&gt; Model cost at call 574 : 201.5169
-#&gt; Model cost at call 575 : 201.5169
-#&gt; Model cost at call 578 : 201.5169
-#&gt; Model cost at call 582 : 201.5169
-#&gt; Model cost at call 586 : 201.5169
-#&gt; Model cost at call 589 : 201.5169
-#&gt; Model cost at call 590 : 201.5169
-#&gt; Model cost at call 601 : 201.5169
-#&gt; Model cost at call 604 : 201.5169
-#&gt; Model cost at call 617 : 201.5169
-#&gt; Model cost at call 632 : 201.5169
-#&gt; Model cost at call 647 : 201.5169
-#&gt; Model cost at call 662 : 201.5169
-#&gt; Model cost at call 680 : 201.5169
-#&gt; Optimisation by method Port successfully terminated.
-#&gt; Model cost at call 1 : 30689.89
-#&gt; Model cost at call 3 : 30689.89
-#&gt; Model cost at call 8 : 16294.04
-#&gt; Model cost at call 9 : 12699.33
-#&gt; Model cost at call 11 : 12699.26
-#&gt; Model cost at call 14 : 12699.05
-#&gt; Model cost at call 17 : 9202.163
-#&gt; Model cost at call 18 : 9202.16
-#&gt; Model cost at call 20 : 9202.147
-#&gt; Model cost at call 22 : 9202.147
-#&gt; Model cost at call 25 : 6601.043
-#&gt; Model cost at call 26 : 6601.041
-#&gt; Model cost at call 30 : 6601.04
-#&gt; Model cost at call 32 : 4223.705
-#&gt; Model cost at call 34 : 4223.703
-#&gt; Model cost at call 39 : 4223.703
-#&gt; Model cost at call 40 : 1443.507
-#&gt; Model cost at call 45 : 1443.507
-#&gt; Model cost at call 49 : 1191.267
-#&gt; Model cost at call 51 : 1191.267
-#&gt; Model cost at call 56 : 1186.498
-#&gt; Model cost at call 57 : 1186.498
-#&gt; Model cost at call 58 : 1186.497
-#&gt; Model cost at call 59 : 1186.497
-#&gt; Model cost at call 61 : 1186.496
-#&gt; Model cost at call 62 : 1186.494
-#&gt; Model cost at call 63 : 1130.799
-#&gt; Model cost at call 64 : 1130.799
-#&gt; Model cost at call 71 : 1126.363
-#&gt; Model cost at call 73 : 1126.363
-#&gt; Model cost at call 78 : 1122.848
-#&gt; Model cost at call 80 : 1122.848
-#&gt; Model cost at call 82 : 1122.848
-#&gt; Model cost at call 85 : 1120.954
-#&gt; Model cost at call 87 : 1120.954
-#&gt; Model cost at call 88 : 1120.954
-#&gt; Model cost at call 89 : 1120.954
-#&gt; Model cost at call 92 : 1117.156
-#&gt; Model cost at call 95 : 1117.156
-#&gt; Model cost at call 96 : 1117.156
-#&gt; Model cost at call 99 : 1116.894
-#&gt; Model cost at call 101 : 1116.894
-#&gt; Model cost at call 104 : 1116.894
-#&gt; Model cost at call 106 : 1113.955
-#&gt; Model cost at call 108 : 1113.955
-#&gt; Model cost at call 112 : 1113.955
-#&gt; Model cost at call 113 : 1113.03
-#&gt; Model cost at call 115 : 1113.03
-#&gt; Model cost at call 120 : 1111.643
-#&gt; Model cost at call 122 : 1111.643
-#&gt; Model cost at call 127 : 1109.657
-#&gt; Model cost at call 129 : 1109.657
-#&gt; Model cost at call 131 : 1109.657
-#&gt; Model cost at call 134 : 1106.725
-#&gt; Model cost at call 136 : 1106.725
-#&gt; Model cost at call 137 : 1106.725
-#&gt; Model cost at call 142 : 1106.005
-#&gt; Model cost at call 144 : 1106.005
-#&gt; Model cost at call 145 : 1106.005
-#&gt; Model cost at call 147 : 1106.005
-#&gt; Model cost at call 149 : 1105.268
-#&gt; Model cost at call 151 : 1105.268
-#&gt; Model cost at call 153 : 1105.268
-#&gt; Model cost at call 156 : 1104.247
-#&gt; Model cost at call 158 : 1104.247
-#&gt; Model cost at call 159 : 1104.247
-#&gt; Model cost at call 161 : 1104.247
-#&gt; Model cost at call 163 : 1103.813
-#&gt; Model cost at call 165 : 1103.813
-#&gt; Model cost at call 167 : 1103.813
-#&gt; Model cost at call 170 : 1103.075
-#&gt; Model cost at call 172 : 1103.075
-#&gt; Model cost at call 173 : 1103.075
-#&gt; Model cost at call 177 : 1102.447
-#&gt; Model cost at call 179 : 1102.447
-#&gt; Model cost at call 180 : 1102.447
-#&gt; Model cost at call 183 : 1102.447
-#&gt; Model cost at call 184 : 1102.038
-#&gt; Model cost at call 185 : 1101.712
-#&gt; Model cost at call 186 : 1101.337
-#&gt; Model cost at call 188 : 1101.337
-#&gt; Model cost at call 193 : 1100.37
-#&gt; Model cost at call 195 : 1100.37
-#&gt; Model cost at call 197 : 1100.37
-#&gt; Model cost at call 200 : 1099.46
-#&gt; Model cost at call 202 : 1099.46
-#&gt; Model cost at call 207 : 1099.262
-#&gt; Model cost at call 209 : 1099.262
-#&gt; Model cost at call 211 : 1099.262
-#&gt; Model cost at call 212 : 1099.261
-#&gt; Model cost at call 214 : 1099.227
-#&gt; Model cost at call 216 : 1099.227
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-#&gt; Model cost at call 218 : 1099.227
-#&gt; Model cost at call 221 : 1098.331
-#&gt; Model cost at call 223 : 1098.331
-#&gt; Model cost at call 224 : 1098.331
-#&gt; Model cost at call 230 : 1098.24
-#&gt; Model cost at call 235 : 1098.24
-#&gt; Model cost at call 236 : 1098.24
-#&gt; Model cost at call 238 : 1098.231
-#&gt; Model cost at call 240 : 1098.231
-#&gt; Model cost at call 245 : 1098.228
-#&gt; Model cost at call 247 : 1098.228
-#&gt; Model cost at call 252 : 1098.221
-#&gt; Model cost at call 254 : 1098.221
-#&gt; Model cost at call 255 : 1098.221
-#&gt; Model cost at call 258 : 1098.221
-#&gt; Model cost at call 261 : 1098.214
-#&gt; Model cost at call 263 : 1098.214
-#&gt; Model cost at call 268 : 1098.204
-#&gt; Model cost at call 269 : 1098.196
-#&gt; Model cost at call 270 : 1098.187
-#&gt; Model cost at call 272 : 1098.187
-#&gt; Model cost at call 273 : 1098.187
-#&gt; Model cost at call 279 : 1098.181
-#&gt; Model cost at call 281 : 1098.181
-#&gt; Model cost at call 282 : 1098.181
-#&gt; Model cost at call 284 : 1098.181
-#&gt; Model cost at call 285 : 1098.181
-#&gt; Model cost at call 287 : 1098.172
-#&gt; Model cost at call 291 : 1098.172
-#&gt; Model cost at call 293 : 1098.172
-#&gt; Model cost at call 294 : 1098.169
-#&gt; Model cost at call 295 : 1098.169
-#&gt; Model cost at call 296 : 1098.169
-#&gt; Model cost at call 301 : 1098.169
-#&gt; Model cost at call 305 : 1098.169
-#&gt; Model cost at call 306 : 1098.169
-#&gt; Model cost at call 309 : 1098.169
-#&gt; Model cost at call 314 : 1098.169
-#&gt; Model cost at call 318 : 1098.169
-#&gt; Model cost at call 319 : 1098.169
-#&gt; Model cost at call 321 : 1098.169
-#&gt; Model cost at call 324 : 1098.169
-#&gt; Model cost at call 325 : 1098.169
-#&gt; Model cost at call 331 : 1098.169
-#&gt; Model cost at call 333 : 1098.169
-#&gt; Model cost at call 336 : 1098.169
-#&gt; Model cost at call 342 : 1098.169
-#&gt; Model cost at call 344 : 1098.169
-#&gt; Model cost at call 348 : 1098.169
-#&gt; Model cost at call 352 : 1098.169
-#&gt; Model cost at call 357 : 1098.169
-#&gt; Model cost at call 370 : 1098.169
-#&gt; Model cost at call 385 : 1098.169
-#&gt; Model cost at call 386 : 1098.169
-#&gt; Optimisation by method Port successfully terminated.
-#&gt; Model cost at call 1 : 34499.23
-#&gt; Model cost at call 3 : 34499.23
-#&gt; Model cost at call 5 : 34499.23
-#&gt; Model cost at call 7 : 34499.23
-#&gt; Model cost at call 9 : 14274.95
-#&gt; Model cost at call 10 : 14162.89
-#&gt; Model cost at call 14 : 14162.68
-#&gt; Model cost at call 18 : 13341.49
-#&gt; Model cost at call 19 : 13341.48
-#&gt; Model cost at call 20 : 13341.47
-#&gt; Model cost at call 22 : 13341.44
-#&gt; Model cost at call 27 : 10055.95
-#&gt; Model cost at call 28 : 10055.95
-#&gt; Model cost at call 30 : 10055.95
-#&gt; Model cost at call 35 : 7732.384
-#&gt; Model cost at call 36 : 7732.381
-#&gt; Model cost at call 39 : 7732.381
-#&gt; Model cost at call 44 : 6325.124
-#&gt; Model cost at call 45 : 6325.122
-#&gt; Model cost at call 47 : 6325.117
-#&gt; Model cost at call 52 : 3732.612
-#&gt; Model cost at call 54 : 3732.611
-#&gt; Model cost at call 61 : 1371.768
-#&gt; Model cost at call 64 : 1371.768
-#&gt; Model cost at call 67 : 1371.768
-#&gt; Model cost at call 70 : 1302.633
-#&gt; Model cost at call 74 : 1302.633
-#&gt; Model cost at call 75 : 1302.633
-#&gt; Model cost at call 78 : 1298.854
-#&gt; Model cost at call 82 : 1298.854
-#&gt; Model cost at call 84 : 1298.854
-#&gt; Model cost at call 86 : 1245.775
-#&gt; Model cost at call 91 : 1245.775
-#&gt; Model cost at call 94 : 1230.679
-#&gt; Model cost at call 96 : 1230.679
-#&gt; Model cost at call 100 : 1230.679
-#&gt; Model cost at call 103 : 1227.471
-#&gt; Model cost at call 105 : 1227.471
-#&gt; Model cost at call 109 : 1227.471
-#&gt; Model cost at call 111 : 1225.318
-#&gt; Model cost at call 113 : 1225.318
-#&gt; Model cost at call 117 : 1225.318
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-#&gt; Model cost at call 119 : 1221.478
-#&gt; Model cost at call 121 : 1221.478
-#&gt; Model cost at call 127 : 1214.191
-#&gt; Model cost at call 128 : 1203.986
-#&gt; Model cost at call 129 : 1164.433
-#&gt; Model cost at call 135 : 1164.433
-#&gt; Model cost at call 140 : 1158.843
-#&gt; Model cost at call 145 : 1158.843
-#&gt; Model cost at call 148 : 1156.585
-#&gt; Model cost at call 154 : 1156.585
-#&gt; Model cost at call 156 : 1155.177
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-#&gt; Model cost at call 161 : 1155.176
-#&gt; Model cost at call 164 : 1151.603
-#&gt; Model cost at call 166 : 1151.603
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-#&gt; Model cost at call 173 : 1150.467
-#&gt; Model cost at call 175 : 1150.467
-#&gt; Model cost at call 176 : 1150.467
-#&gt; Model cost at call 181 : 1150.117
-#&gt; Model cost at call 184 : 1150.117
-#&gt; Model cost at call 185 : 1150.117
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-#&gt; Model cost at call 189 : 1149.03
-#&gt; Model cost at call 193 : 1149.03
-#&gt; Model cost at call 195 : 1149.03
-#&gt; Model cost at call 197 : 1148.468
-#&gt; Model cost at call 199 : 1148.468
-#&gt; Model cost at call 205 : 1147.297
-#&gt; Model cost at call 207 : 1147.297
-#&gt; Model cost at call 211 : 1147.297
-#&gt; Model cost at call 213 : 1146.841
-#&gt; Model cost at call 216 : 1146.841
-#&gt; Model cost at call 217 : 1146.841
-#&gt; Model cost at call 219 : 1146.841
-#&gt; Model cost at call 221 : 1144.548
-#&gt; Model cost at call 223 : 1144.548
-#&gt; Model cost at call 229 : 1143.258
-#&gt; Model cost at call 231 : 1143.258
-#&gt; Model cost at call 237 : 1141.772
-#&gt; Model cost at call 239 : 1141.772
-#&gt; Model cost at call 240 : 1141.772
-#&gt; Model cost at call 241 : 1141.772
-#&gt; Model cost at call 243 : 1141.772
-#&gt; Model cost at call 245 : 1140.849
-#&gt; Model cost at call 251 : 1140.849
-#&gt; Model cost at call 252 : 1140.849
-#&gt; Model cost at call 253 : 1139.456
-#&gt; Model cost at call 259 : 1139.456
-#&gt; Model cost at call 261 : 1137.678
-#&gt; Model cost at call 263 : 1137.678
-#&gt; Model cost at call 269 : 1135.358
-#&gt; Model cost at call 270 : 1134.128
-#&gt; Model cost at call 272 : 1134.128
-#&gt; Model cost at call 280 : 1133.342
-#&gt; Model cost at call 283 : 1133.342
-#&gt; Model cost at call 286 : 1133.342
-#&gt; Model cost at call 288 : 1133.229
-#&gt; Model cost at call 292 : 1133.229
-#&gt; Model cost at call 294 : 1133.229
-#&gt; Model cost at call 295 : 1133.229
-#&gt; Model cost at call 296 : 1132.641
-#&gt; Model cost at call 300 : 1132.641
-#&gt; Model cost at call 304 : 1132.126
-#&gt; Model cost at call 310 : 1132.126
-#&gt; Model cost at call 312 : 1131.169
-#&gt; Model cost at call 318 : 1131.169
-#&gt; Model cost at call 320 : 1130.405
-#&gt; Model cost at call 324 : 1130.405
-#&gt; Model cost at call 328 : 1129.635
-#&gt; Model cost at call 330 : 1129.635
-#&gt; Model cost at call 332 : 1129.635
-#&gt; Model cost at call 334 : 1129.635
-#&gt; Model cost at call 336 : 1128.526
-#&gt; Model cost at call 338 : 1128.526
-#&gt; Model cost at call 343 : 1128.526
-#&gt; Model cost at call 344 : 1127.498
-#&gt; Model cost at call 346 : 1127.498
-#&gt; Model cost at call 350 : 1127.498
-#&gt; Model cost at call 352 : 1126.06
-#&gt; Model cost at call 353 : 1124.911
-#&gt; Model cost at call 356 : 1124.911
-#&gt; Model cost at call 362 : 1120.309
-#&gt; Model cost at call 366 : 1120.309
-#&gt; Model cost at call 368 : 1120.308
-#&gt; Model cost at call 369 : 1120.308
-#&gt; Model cost at call 370 : 1117.687
-#&gt; Model cost at call 374 : 1117.687
-#&gt; Model cost at call 375 : 1117.687
-#&gt; Model cost at call 378 : 1112.013
-#&gt; Model cost at call 379 : 1112.013
-#&gt; Model cost at call 381 : 1112.013
-#&gt; Model cost at call 386 : 1108.648
-#&gt; Model cost at call 387 : 1108.251
-#&gt; Model cost at call 388 : 1108.251
-#&gt; Model cost at call 391 : 1108.251
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-#&gt; Model cost at call 395 : 1104.73
-#&gt; Model cost at call 396 : 1104.73
-#&gt; Model cost at call 397 : 1104.73
-#&gt; Model cost at call 403 : 1103.277
-#&gt; Model cost at call 404 : 1103.277
-#&gt; Model cost at call 411 : 1101.351
-#&gt; Model cost at call 414 : 1101.351
-#&gt; Model cost at call 416 : 1101.351
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-#&gt; Model cost at call 419 : 1100.36
-#&gt; Model cost at call 420 : 1100.36
-#&gt; Model cost at call 421 : 1100.36
-#&gt; Model cost at call 427 : 1099.596
-#&gt; Model cost at call 431 : 1099.596
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-#&gt; Model cost at call 435 : 1099.029
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-#&gt; Model cost at call 444 : 1098.722
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-#&gt; Model cost at call 453 : 1098.441
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-#&gt; Model cost at call 463 : 1098.314
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-#&gt; Model cost at call 469 : 1098.314
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-#&gt; Model cost at call 475 : 1098.245
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-#&gt; Model cost at call 480 : 1098.245
-#&gt; Model cost at call 486 : 1098.209
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-#&gt; Model cost at call 489 : 1098.209
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-#&gt; Model cost at call 505 : 1098.209
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-#&gt; Model cost at call 510 : 1098.209
-#&gt; Model cost at call 518 : 1098.209
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-#&gt; Model cost at call 522 : 1098.209
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-#&gt; Model cost at call 528 : 1098.209
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-#&gt; Model cost at call 549 : 1098.207
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-#&gt; Model cost at call 564 : 1098.205
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-#&gt; Model cost at call 567 : 1098.205
-#&gt; Model cost at call 570 : 1098.205
-#&gt; Model cost at call 579 : 1098.2
-#&gt; Model cost at call 580 : 1098.191
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-#&gt; Model cost at call 586 : 1098.191
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-#&gt; Model cost at call 595 : 1098.186
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-#&gt; Model cost at call 606 : 1098.18
-#&gt; Model cost at call 609 : 1098.18
-#&gt; Model cost at call 610 : 1098.18
-#&gt; Model cost at call 616 : 1098.177
-#&gt; Model cost at call 619 : 1098.177
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-#&gt; Model cost at call 627 : 1098.173
-#&gt; Model cost at call 630 : 1098.173
-#&gt; Model cost at call 631 : 1098.173
-#&gt; Model cost at call 636 : 1098.173
-#&gt; Model cost at call 641 : 1098.172
-#&gt; Model cost at call 642 : 1098.172
-#&gt; Model cost at call 653 : 1098.172
-#&gt; Model cost at call 654 : 1098.172
-#&gt; Model cost at call 664 : 1098.172
-#&gt; Model cost at call 669 : 1098.172
-#&gt; Model cost at call 671 : 1098.172
-#&gt; Model cost at call 675 : 1098.172
-#&gt; Model cost at call 678 : 1098.172
-#&gt; Model cost at call 680 : 1098.172
-#&gt; Model cost at call 683 : 1098.172
-#&gt; Model cost at call 684 : 1098.172
-#&gt; Model cost at call 686 : 1098.172
-#&gt; Model cost at call 690 : 1098.172
-#&gt; Model cost at call 702 : 1098.172
-#&gt; Model cost at call 704 : 1098.172
-#&gt; Model cost at call 708 : 1098.172
-#&gt; Model cost at call 721 : 1098.172
-#&gt; Model cost at call 723 : 1098.172
-#&gt; Model cost at call 736 : 1098.172
-#&gt; Model cost at call 738 : 1098.172
-#&gt; Model cost at call 751 : 1098.172
-#&gt; Model cost at call 753 : 1098.172
-#&gt; Model cost at call 766 : 1098.172
-#&gt; Model cost at call 767 : 1098.172
-#&gt; Model cost at call 768 : 1098.172
-#&gt; Model cost at call 770 : 1098.172
-#&gt; Model cost at call 783 : 1098.172
-#&gt; Model cost at call 784 : 1098.172
-#&gt; Model cost at call 785 : 1098.172
-#&gt; Model cost at call 799 : 1098.172
-#&gt; Model cost at call 800 : 1098.172
-#&gt; Model cost at call 814 : 1098.172
-#&gt; Model cost at call 815 : 1098.172
-#&gt; Model cost at call 816 : 1098.172
-#&gt; Model cost at call 822 : 1098.172
-#&gt; Model cost at call 830 : 1098.172
-#&gt; Model cost at call 831 : 1098.172
-#&gt; Model cost at call 834 : 1098.172
-#&gt; Model cost at call 845 : 1098.172
-#&gt; Model cost at call 846 : 1098.172
-#&gt; Model cost at call 849 : 1098.172
-#&gt; Model cost at call 860 : 1098.171
-#&gt; Model cost at call 861 : 1098.171
-#&gt; Model cost at call 864 : 1098.171
-#&gt; Model cost at call 875 : 1098.171
-#&gt; Model cost at call 876 : 1098.171
-#&gt; Model cost at call 879 : 1098.171
-#&gt; Model cost at call 890 : 1098.17
-#&gt; Model cost at call 891 : 1098.17
-#&gt; Model cost at call 894 : 1098.17
-#&gt; Model cost at call 904 : 1098.169
-#&gt; Model cost at call 905 : 1098.169
-#&gt; Model cost at call 908 : 1098.169
-#&gt; Model cost at call 909 : 1098.169
-#&gt; Model cost at call 919 : 1098.169
-#&gt; Model cost at call 921 : 1098.169
-#&gt; Model cost at call 931 : 1098.169
-#&gt; Model cost at call 932 : 1098.169
-#&gt; Model cost at call 934 : 1098.169
-#&gt; Model cost at call 936 : 1098.169
-#&gt; Model cost at call 937 : 1098.169
-#&gt; Model cost at call 944 : 1098.169
-#&gt; Model cost at call 947 : 1098.169
-#&gt; Model cost at call 949 : 1098.169
-#&gt; Model cost at call 951 : 1098.169
-#&gt; Model cost at call 952 : 1098.169
-#&gt; Model cost at call 954 : 1098.169
-#&gt; Model cost at call 964 : 1098.169
-#&gt; Model cost at call 967 : 1098.169
-#&gt; Model cost at call 969 : 1098.169
-#&gt; Model cost at call 982 : 1098.169
-#&gt; Model cost at call 1017 : 1098.169
-#&gt; Model cost at call 1018 : 1098.169
-#&gt; Model cost at call 1022 : 1098.169
-#&gt; Model cost at call 1029 : 1098.169
-#&gt; Model cost at call 1033 : 1098.169
-#&gt; Model cost at call 1038 : 1098.169
-#&gt; Model cost at call 1048 : 1098.169
-#&gt; Model cost at call 1049 : 1098.169
-#&gt; Model cost at call 1055 : 1098.169
-#&gt; Model cost at call 1063 : 1098.169
-#&gt; Model cost at call 1074 : 1098.169
-#&gt; Model cost at call 1079 : 1098.169
-#&gt; Model cost at call 1089 : 1098.169
-#&gt; Model cost at call 1120 : 1098.169
-#&gt; Model cost at call 1124 : 1098.169
-#&gt; Model cost at call 1139 : 1098.169
-#&gt; Model cost at call 1154 : 1098.169
-#&gt; Model cost at call 1170 : 1098.169
-#&gt; Model cost at call 1185 : 1098.169
-#&gt; Model cost at call 1200 : 1098.169
-#&gt; Model cost at call 1215 : 1098.169
-#&gt; Model cost at call 1231 : 1098.169
-#&gt; Model cost at call 1246 : 1098.169
-#&gt; Model cost at call 1247 : 1098.169
-#&gt; Model cost at call 1248 : 1098.169
-#&gt; Model cost at call 1258 : 1098.169
-#&gt; Model cost at call 1263 : 1098.169
-#&gt; Model cost at call 1278 : 1098.169
-#&gt; Model cost at call 1295 : 1098.169
-#&gt; Model cost at call 1296 : 1098.169
-#&gt; Model cost at call 1297 : 1098.169
-#&gt; Model cost at call 1298 : 1098.169
-#&gt; Model cost at call 1306 : 1098.169
-#&gt; Model cost at call 1308 : 1098.169
-#&gt; Optimisation by method Port successfully terminated.
-#&gt; Model cost at call 1 : 31389.19
-#&gt; Model cost at call 3 : 31389.19
-#&gt; Model cost at call 8 : 15003.41
-#&gt; Model cost at call 9 : 11136.21
-#&gt; Model cost at call 11 : 11135.87
-#&gt; Model cost at call 16 : 4800.182
-#&gt; Model cost at call 17 : 4800.181
-#&gt; Model cost at call 19 : 4800.163
-#&gt; Model cost at call 24 : 3036.068
-#&gt; Model cost at call 25 : 3036.068
-#&gt; Model cost at call 26 : 3036.052
-#&gt; Model cost at call 31 : 1361.371
-#&gt; Model cost at call 33 : 1361.371
-#&gt; Model cost at call 40 : 494.6738
-#&gt; Model cost at call 41 : 494.6736
-#&gt; Model cost at call 45 : 494.6734
-#&gt; Model cost at call 48 : 260.2631
-#&gt; Model cost at call 49 : 260.2629
-#&gt; Model cost at call 55 : 248.3035
-#&gt; Model cost at call 56 : 248.3034
-#&gt; Model cost at call 57 : 248.3023
-#&gt; Model cost at call 62 : 171.6337
-#&gt; Model cost at call 63 : 171.6337
-#&gt; Model cost at call 70 : 167.3473
-#&gt; Model cost at call 72 : 167.3473
-#&gt; Model cost at call 73 : 167.3473
-#&gt; Model cost at call 78 : 165.9868
-#&gt; Model cost at call 80 : 165.9868
-#&gt; Model cost at call 83 : 165.9868
-#&gt; Model cost at call 85 : 165.2025
-#&gt; Model cost at call 87 : 165.2024
-#&gt; Model cost at call 92 : 163.5932
-#&gt; Model cost at call 94 : 163.5932
-#&gt; Model cost at call 96 : 163.5932
-#&gt; Model cost at call 99 : 159.4289
-#&gt; Model cost at call 100 : 147.5939
-#&gt; Model cost at call 105 : 147.5939
-#&gt; Model cost at call 108 : 139.3925
-#&gt; Model cost at call 113 : 139.3925
-#&gt; Model cost at call 115 : 139.392
-#&gt; Model cost at call 116 : 123.9799
-#&gt; Model cost at call 117 : 123.9798
-#&gt; Model cost at call 118 : 123.9795
-#&gt; Model cost at call 124 : 103.8653
-#&gt; Model cost at call 125 : 103.8653
-#&gt; Model cost at call 126 : 103.8652
-#&gt; Model cost at call 131 : 96.14276
-#&gt; Model cost at call 134 : 96.14275
-#&gt; Model cost at call 135 : 96.14274
-#&gt; Model cost at call 139 : 95.96056
-#&gt; Model cost at call 141 : 95.96056
-#&gt; Model cost at call 142 : 95.96056
-#&gt; Model cost at call 145 : 95.96056
-#&gt; Model cost at call 146 : 95.90851
-#&gt; Model cost at call 148 : 95.9085
-#&gt; Model cost at call 153 : 95.84671
-#&gt; Model cost at call 155 : 95.8467
-#&gt; Model cost at call 161 : 95.82479
-#&gt; Model cost at call 163 : 95.82479
-#&gt; Model cost at call 166 : 95.82479
-#&gt; Model cost at call 168 : 95.81938
-#&gt; Model cost at call 170 : 95.81938
-#&gt; Model cost at call 174 : 95.81938
-#&gt; Model cost at call 175 : 95.81558
-#&gt; Model cost at call 177 : 95.81558
-#&gt; Model cost at call 178 : 95.81558
-#&gt; Model cost at call 180 : 95.81558
-#&gt; Model cost at call 181 : 95.81558
-#&gt; Model cost at call 183 : 95.81558
-#&gt; Model cost at call 184 : 95.8118
-#&gt; Model cost at call 186 : 95.8118
-#&gt; Model cost at call 188 : 95.8118
-#&gt; Model cost at call 191 : 95.80885
-#&gt; Model cost at call 192 : 95.80353
-#&gt; Model cost at call 193 : 95.78121
-#&gt; Model cost at call 194 : 95.72164
-#&gt; Model cost at call 197 : 95.72164
-#&gt; Model cost at call 201 : 95.72163
-#&gt; Model cost at call 206 : 95.71206
-#&gt; Model cost at call 208 : 95.71205
-#&gt; Model cost at call 213 : 95.70874
-#&gt; Model cost at call 215 : 95.70874
-#&gt; Model cost at call 219 : 95.70874
-#&gt; Model cost at call 221 : 95.70751
-#&gt; Model cost at call 222 : 95.70404
-#&gt; Model cost at call 223 : 95.69259
-#&gt; Model cost at call 224 : 95.68092
-#&gt; Model cost at call 226 : 95.68092
-#&gt; Model cost at call 227 : 95.68092
-#&gt; Model cost at call 233 : 95.67595
-#&gt; Model cost at call 235 : 95.67595
-#&gt; Model cost at call 236 : 95.67595
-#&gt; Model cost at call 242 : 95.67219
-#&gt; Model cost at call 244 : 95.67219
-#&gt; Model cost at call 245 : 95.67219
-#&gt; Model cost at call 249 : 95.66939
-#&gt; Model cost at call 251 : 95.66939
-#&gt; Model cost at call 253 : 95.66939
-#&gt; Model cost at call 254 : 95.66939
-#&gt; Model cost at call 256 : 95.66904
-#&gt; Model cost at call 257 : 95.66904
-#&gt; Model cost at call 260 : 95.66904
-#&gt; Model cost at call 265 : 95.66857
-#&gt; Model cost at call 267 : 95.66856
-#&gt; Model cost at call 273 : 95.66822
-#&gt; Model cost at call 275 : 95.66822
-#&gt; Model cost at call 276 : 95.66822
-#&gt; Model cost at call 282 : 95.66809
-#&gt; Model cost at call 283 : 95.66809
-#&gt; Model cost at call 291 : 95.66805
-#&gt; Model cost at call 293 : 95.66805
-#&gt; Model cost at call 295 : 95.66805
-#&gt; Model cost at call 297 : 95.66805
-#&gt; Model cost at call 298 : 95.66805
-#&gt; Model cost at call 302 : 95.66805
-#&gt; Model cost at call 304 : 95.66805
-#&gt; Model cost at call 306 : 95.66805
-#&gt; Model cost at call 309 : 95.66805
-#&gt; Model cost at call 314 : 95.66805
-#&gt; Model cost at call 315 : 95.66805
-#&gt; Model cost at call 328 : 95.66805
-#&gt; Optimisation by method Port successfully terminated.
-#&gt; Model cost at call 1 : 36597.78
-#&gt; Model cost at call 3 : 36597.78
-#&gt; Model cost at call 5 : 36597.78
-#&gt; Model cost at call 7 : 36597.78
-#&gt; Model cost at call 9 : 13188.26
-#&gt; Model cost at call 10 : 12648.25
-#&gt; Model cost at call 14 : 12648.13
-#&gt; Model cost at call 16 : 12647.92
-#&gt; Model cost at call 18 : 6148.715
-#&gt; Model cost at call 19 : 6148.712
-#&gt; Model cost at call 20 : 6148.695
-#&gt; Model cost at call 22 : 6148.683
-#&gt; Model cost at call 27 : 1490.597
-#&gt; Model cost at call 33 : 1490.597
-#&gt; Model cost at call 35 : 594.2031
-#&gt; Model cost at call 36 : 594.2023
-#&gt; Model cost at call 38 : 594.201
-#&gt; Model cost at call 40 : 594.2009
-#&gt; Model cost at call 44 : 230.6504
-#&gt; Model cost at call 45 : 230.6503
-#&gt; Model cost at call 48 : 230.6503
-#&gt; Model cost at call 50 : 230.6495
-#&gt; Model cost at call 51 : 230.6494
-#&gt; Model cost at call 53 : 186.2336
-#&gt; Model cost at call 57 : 186.2336
-#&gt; Model cost at call 59 : 186.2336
-#&gt; Model cost at call 60 : 186.2336
-#&gt; Model cost at call 62 : 181.3507
-#&gt; Model cost at call 66 : 181.3507
-#&gt; Model cost at call 70 : 180.733
-#&gt; Model cost at call 74 : 180.733
-#&gt; Model cost at call 76 : 180.7329
-#&gt; Model cost at call 77 : 180.7329
-#&gt; Model cost at call 78 : 175.5254
-#&gt; Model cost at call 80 : 175.5253
-#&gt; Model cost at call 86 : 173.1139
-#&gt; Model cost at call 88 : 173.1139
-#&gt; Model cost at call 94 : 168.0503
-#&gt; Model cost at call 96 : 168.0502
-#&gt; Model cost at call 102 : 164.9084
-#&gt; Model cost at call 104 : 164.9084
-#&gt; Model cost at call 105 : 164.9084
-#&gt; Model cost at call 110 : 159.7912
-#&gt; Model cost at call 112 : 159.7912
-#&gt; Model cost at call 113 : 159.7912
-#&gt; Model cost at call 116 : 159.7911
-#&gt; Model cost at call 117 : 159.7911
-#&gt; Model cost at call 118 : 158.6003
-#&gt; Model cost at call 122 : 158.6002
-#&gt; Model cost at call 124 : 158.6002
-#&gt; Model cost at call 126 : 150.4132
-#&gt; Model cost at call 132 : 150.4132
-#&gt; Model cost at call 133 : 150.4132
-#&gt; Model cost at call 134 : 146.5123
-#&gt; Model cost at call 140 : 146.5122
-#&gt; Model cost at call 142 : 136.6018
-#&gt; Model cost at call 145 : 136.6018
-#&gt; Model cost at call 149 : 136.6018
-#&gt; Model cost at call 150 : 133.91
-#&gt; Model cost at call 153 : 133.91
-#&gt; Model cost at call 155 : 133.91
-#&gt; Model cost at call 156 : 133.91
-#&gt; Model cost at call 158 : 124.7878
-#&gt; Model cost at call 162 : 124.7878
-#&gt; Model cost at call 163 : 124.7878
-#&gt; Model cost at call 167 : 124.2615
-#&gt; Model cost at call 169 : 124.2614
-#&gt; Model cost at call 170 : 124.2614
-#&gt; Model cost at call 175 : 123.2425
-#&gt; Model cost at call 179 : 123.2425
-#&gt; Model cost at call 180 : 123.2425
-#&gt; Model cost at call 181 : 123.2425
-#&gt; Model cost at call 182 : 123.2425
-#&gt; Model cost at call 183 : 120.7214
-#&gt; Model cost at call 185 : 120.7214
-#&gt; Model cost at call 191 : 119.2706
-#&gt; Model cost at call 192 : 117.872
-#&gt; Model cost at call 193 : 114.6257
-#&gt; Model cost at call 198 : 114.6257
-#&gt; Model cost at call 201 : 111.8985
-#&gt; Model cost at call 203 : 111.8985
-#&gt; Model cost at call 206 : 111.8984
-#&gt; Model cost at call 209 : 111.6987
-#&gt; Model cost at call 212 : 111.6987
-#&gt; Model cost at call 213 : 111.6986
-#&gt; Model cost at call 217 : 107.9995
-#&gt; Model cost at call 219 : 107.9995
-#&gt; Model cost at call 225 : 106.1322
-#&gt; Model cost at call 226 : 104.6907
-#&gt; Model cost at call 227 : 104.6316
-#&gt; Model cost at call 229 : 104.6316
-#&gt; Model cost at call 232 : 104.6315
-#&gt; Model cost at call 239 : 103.3421
-#&gt; Model cost at call 245 : 103.3421
-#&gt; Model cost at call 246 : 103.3421
-#&gt; Model cost at call 247 : 103.1772
-#&gt; Model cost at call 248 : 103.1772
-#&gt; Model cost at call 249 : 103.1772
-#&gt; Model cost at call 250 : 103.1772
-#&gt; Model cost at call 253 : 103.1772
-#&gt; Model cost at call 255 : 102.8623
-#&gt; Model cost at call 256 : 102.8623
-#&gt; Model cost at call 262 : 102.8623
-#&gt; Model cost at call 263 : 102.6013
-#&gt; Model cost at call 266 : 102.6013
-#&gt; Model cost at call 271 : 102.0341
-#&gt; Model cost at call 272 : 101.25
-#&gt; Model cost at call 273 : 99.17557
-#&gt; Model cost at call 274 : 99.17556
-#&gt; Model cost at call 282 : 99.06481
-#&gt; Model cost at call 284 : 99.06479
-#&gt; Model cost at call 290 : 98.57515
-#&gt; Model cost at call 294 : 98.57514
-#&gt; Model cost at call 296 : 98.57514
-#&gt; Model cost at call 298 : 98.05781
-#&gt; Model cost at call 304 : 98.05781
-#&gt; Model cost at call 305 : 98.05781
-#&gt; Model cost at call 306 : 97.81766
-#&gt; Model cost at call 307 : 97.63972
-#&gt; Model cost at call 308 : 97.63971
-#&gt; Model cost at call 315 : 97.15447
-#&gt; Model cost at call 317 : 97.15447
-#&gt; Model cost at call 321 : 97.15446
-#&gt; Model cost at call 323 : 96.25231
-#&gt; Model cost at call 324 : 96.25231
-#&gt; Model cost at call 328 : 96.25231
-#&gt; Model cost at call 331 : 95.48051
-#&gt; Model cost at call 334 : 95.4805
-#&gt; Model cost at call 339 : 95.08754
-#&gt; Model cost at call 341 : 95.08754
-#&gt; Model cost at call 347 : 94.9916
-#&gt; Model cost at call 348 : 94.9916
-#&gt; Model cost at call 350 : 94.9916
-#&gt; Model cost at call 355 : 94.93856
-#&gt; Model cost at call 356 : 94.93856
-#&gt; Model cost at call 357 : 94.93856
-#&gt; Model cost at call 363 : 94.92067
-#&gt; Model cost at call 366 : 94.92067
-#&gt; Model cost at call 367 : 94.92067
-#&gt; Model cost at call 369 : 94.92067
-#&gt; Model cost at call 370 : 94.92067
-#&gt; Model cost at call 371 : 94.91762
-#&gt; Model cost at call 372 : 94.91762
-#&gt; Model cost at call 373 : 94.91762
-#&gt; Model cost at call 379 : 94.91744
-#&gt; Model cost at call 380 : 94.91744
-#&gt; Model cost at call 385 : 94.91744
-#&gt; Model cost at call 387 : 94.91744
-#&gt; Model cost at call 393 : 94.91743
-#&gt; Model cost at call 394 : 94.91743
-#&gt; Model cost at call 404 : 94.91743
-#&gt; Model cost at call 407 : 94.91743
-#&gt; Model cost at call 408 : 94.91743
-#&gt; Model cost at call 423 : 94.91743
-#&gt; Model cost at call 442 : 94.91743
-#&gt; Model cost at call 446 : 94.91743
-#&gt; Model cost at call 447 : 94.91743
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'>
+<span class='no'>time_default</span> <span class='kw'>&lt;-</span> <span class='fu'>system.time</span>(<span class='no'>fits.0</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))
+<span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'>system.time</span>(<span class='no'>fits.4</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))
+
<span class='no'>time_default</span></div><div class='output co'>#&gt; user system elapsed
-#&gt; 16.180 0.132 9.130 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; user system elapsed
-#&gt; 22.856 0.000 22.858 </div><div class='input'>
-<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#&gt; <span class='error'>Error in endpoints(fits[[&quot;SFO_lin&quot;, 2]]): Objekt &#39;fits&#39; nicht gefunden</span></div><div class='input'>
-<span class='co'># Plot.mkinfit handles rows or columns of mmkin result objects</span>
-<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ])</div><img src='mmkin-14.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ], <span class='kw'>obs_var</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>))</div><img src='mmkin-16.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fits.0</span>[, <span class='fl'>1</span>])</div><img src='mmkin-18.png' alt='' width='540' height='400' /><div class='input'><span class='co'># Use double brackets to extract a single mkinfit object, which will be plotted</span>
-<span class='co'># by plot.mkinfit</span>
-<span class='fu'>plot</span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span>]], <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='mmkin-20.png' alt='' width='540' height='400' /><div class='input'><span class='co'># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span>
+#&gt; 17.340 0.088 9.561 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt; user system elapsed
+#&gt; 22.868 0.000 22.866 </div><div class='input'>
+<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#&gt; $ff
+#&gt; parent_M1 parent_sink M1_M2 M1_sink
+#&gt; 0.7340479 0.2659521 0.7505687 0.2494313
+#&gt;
+#&gt; $SFORB
+#&gt; logical(0)
+#&gt;
+#&gt; $distimes
+#&gt; DT50 DT90
+#&gt; parent 0.8777688 2.915885
+#&gt; M1 2.3257456 7.725960
+#&gt; M2 33.7200881 112.015708
+#&gt; </div><div class='input'>
+<span class='co'># plot.mkinfit handles rows or columns of mmkin result objects</span>
+<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ])</div><img src='mmkin-12.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ], <span class='kw'>obs_var</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>))</div><img src='mmkin-14.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fits.0</span>[, <span class='fl'>1</span>])</div><img src='mmkin-16.png' alt='' width='540' height='400' /><div class='input'><span class='co'># Use double brackets to extract a single mkinfit object, which will be plotted</span>
+<span class='co'># by plot.mkinfit and can be plotted using plot_sep</span>
+<span class='fu'>plot</span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span>]], <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='mmkin-18.png' alt='' width='540' height='400' /><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span>]])
+<span class='co'># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span>
<span class='co'># allow to plot the observed variables separately</span>
-<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, <span class='fl'>1</span>])</div><img src='mmkin-22.png' alt='' width='540' height='400' /><div class='input'>
+<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, <span class='fl'>1</span>])</div><img src='mmkin-20.png' alt='' width='540' height='400' /><div class='input'>
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index f171ab5b..0fc7a05a 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -133,12 +133,13 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<pre class="examples"><div class='input'> <span class='co'># Only use one core not to offend CRAN checks, use Levenberg-Marquardt for speed</span>
- <span class='no'>fits</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'>c</span>(<span class='st'>"FOMC"</span>, <span class='st'>"HS"</span>), <span class='fu'>list</span>(<span class='st'>"FOCUS B"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='st'>"FOCUS C"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>),
+ <span class='no'>fits</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'>c</span>(<span class='st'>"FOMC"</span>, <span class='st'>"HS"</span>),
+ <span class='fu'>list</span>(<span class='st'>"FOCUS B"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='st'>"FOCUS C"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>), <span class='co'># named list for titles</span>
<span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>)
<span class='fu'>plot</span>(<span class='no'>fits</span>[, <span class='st'>"FOCUS C"</span>])</div><img src='plot.mmkin-2.png' alt='' width='540' height='400' /><div class='input'> <span class='fu'>plot</span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ])</div><img src='plot.mmkin-4.png' alt='' width='540' height='400' /><div class='input'>
- <span class='co'># We can also plot a single fit, if we like the way mmkin works, but then the plot</span>
+ <span class='co'># We can also plot a single fit, if we like the way plot.mmkin works, but then the plot</span>
<span class='co'># height should be smaller than the plot width (this is not possible for the html pages</span>
- <span class='co'># generated by staticdocs, as far as I know).</span>
+ <span class='co'># generated by pkgdown, as far as I know).</span>
<span class='fu'>plot</span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, <span class='st'>"FOCUS C"</span>]) <span class='co'># same as plot(fits[1, 2])</span></div><img src='plot.mmkin-6.png' alt='' width='540' height='400' /></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html
index 2034ea10..ab10b0b2 100644
--- a/docs/reference/print.mkinmod.html
+++ b/docs/reference/print.mkinmod.html
@@ -100,12 +100,33 @@
</dl>
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'> <span class='no'>m_synth_SFO_lin</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M1"</span>),
+ <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M2"</span>),
+ <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
+ <span class='fu'>print</span>(<span class='no'>m_synth_SFO_lin</span>)</div><div class='output co'>#&gt; &lt;mkinmod&gt; model generated with
+#&gt; Use of formation fractions $use_of_ff: max
+#&gt; Specification $spec:
+#&gt; $parent
+#&gt; $type: SFO; $to: M1; $sink: TRUE
+#&gt; $M1
+#&gt; $type: SFO; $to: M2; $sink: TRUE
+#&gt; $M2
+#&gt; $type: SFO; $sink: TRUE
+#&gt; Coefficient matrix $coefmat available
+#&gt; Compiled model $cf available
+#&gt; Differential equations:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt; d_M1/dt = + f_parent_to_M1 * k_parent * parent - k_M1 * M1
+#&gt; d_M2/dt = + f_M1_to_M2 * k_M1 * M1 - k_M2 * M2</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
- </ul>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
</div>
</div>
diff --git a/docs/reference/schaefer07_complex_case-4.png b/docs/reference/schaefer07_complex_case-4.png
new file mode 100644
index 00000000..b87ccb82
--- /dev/null
+++ b/docs/reference/schaefer07_complex_case-4.png
Binary files differ
diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index 9bb6d4ee..1bcc1826 100644
--- a/docs/reference/schaefer07_complex_case.html
+++ b/docs/reference/schaefer07_complex_case.html
@@ -116,1059 +116,39 @@
<span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A2"</span>),
<span class='kw'>B1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
<span class='kw'>C1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
- <span class='kw'>A2</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>data</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 2511.655
-#&gt; Model cost at call 2 : 2511.655
-#&gt; Model cost at call 11 : 1436.639
-#&gt; Model cost at call 12 : 1436.638
-#&gt; Model cost at call 13 : 1436.566
-#&gt; Model cost at call 21 : 643.6583
-#&gt; Model cost at call 22 : 643.6583
-#&gt; Model cost at call 23 : 643.6582
-#&gt; Model cost at call 29 : 643.6576
-#&gt; Model cost at call 31 : 454.0244
-#&gt; Model cost at call 32 : 454.0241
-#&gt; Model cost at call 34 : 454.0229
-#&gt; Model cost at call 43 : 378.1144
-#&gt; Model cost at call 45 : 378.1143
-#&gt; Model cost at call 53 : 357.245
-#&gt; Model cost at call 55 : 357.2449
-#&gt; Model cost at call 56 : 357.2447
-#&gt; Model cost at call 63 : 354.3415
-#&gt; Model cost at call 64 : 354.3415
-#&gt; Model cost at call 65 : 354.3413
-#&gt; Model cost at call 73 : 332.49
-#&gt; Model cost at call 74 : 332.49
-#&gt; Model cost at call 81 : 332.4899
-#&gt; Model cost at call 83 : 315.2962
-#&gt; Model cost at call 84 : 306.3085
-#&gt; Model cost at call 86 : 306.3084
-#&gt; Model cost at call 87 : 306.3084
-#&gt; Model cost at call 92 : 306.3083
-#&gt; Model cost at call 94 : 290.6377
-#&gt; Model cost at call 96 : 290.6375
-#&gt; Model cost at call 98 : 290.6375
-#&gt; Model cost at call 101 : 290.6371
-#&gt; Model cost at call 105 : 269.09
-#&gt; Model cost at call 107 : 269.0899
-#&gt; Model cost at call 115 : 259.7551
-#&gt; Model cost at call 120 : 259.7549
-#&gt; Model cost at call 123 : 259.7547
-#&gt; Model cost at call 126 : 253.7973
-#&gt; Model cost at call 128 : 253.7972
-#&gt; Model cost at call 137 : 251.7358
-#&gt; Model cost at call 139 : 251.7358
-#&gt; Model cost at call 147 : 250.7394
-#&gt; Model cost at call 149 : 250.7393
-#&gt; Model cost at call 157 : 249.1148
-#&gt; Model cost at call 159 : 249.1148
-#&gt; Model cost at call 167 : 246.8768
-#&gt; Model cost at call 169 : 246.8768
-#&gt; Model cost at call 177 : 244.9758
-#&gt; Model cost at call 179 : 244.9758
-#&gt; Model cost at call 187 : 243.2914
-#&gt; Model cost at call 189 : 243.2914
-#&gt; Model cost at call 190 : 243.2914
-#&gt; Model cost at call 194 : 243.2914
-#&gt; Model cost at call 199 : 242.9202
-#&gt; Model cost at call 201 : 242.9202
-#&gt; Model cost at call 202 : 242.9202
-#&gt; Model cost at call 209 : 242.7695
-#&gt; Model cost at call 211 : 242.7695
-#&gt; Model cost at call 216 : 242.7695
-#&gt; Model cost at call 219 : 242.5771
-#&gt; Model cost at call 221 : 242.5771
-#&gt; Model cost at call 229 : 242.4402
-#&gt; Model cost at call 231 : 242.4402
-#&gt; Model cost at call 239 : 242.1878
-#&gt; Model cost at call 241 : 242.1878
-#&gt; Model cost at call 249 : 242.0553
-#&gt; Model cost at call 251 : 242.0553
-#&gt; Model cost at call 256 : 242.0553
-#&gt; Model cost at call 259 : 241.8761
-#&gt; Model cost at call 260 : 241.7412
-#&gt; Model cost at call 261 : 241.6954
-#&gt; Model cost at call 264 : 241.6954
-#&gt; Model cost at call 275 : 241.5982
-#&gt; Model cost at call 277 : 241.5982
-#&gt; Model cost at call 285 : 241.5459
-#&gt; Model cost at call 287 : 241.5459
-#&gt; Model cost at call 295 : 241.4837
-#&gt; Model cost at call 297 : 241.4837
-#&gt; Model cost at call 305 : 241.3882
-#&gt; Model cost at call 306 : 241.3161
-#&gt; Model cost at call 307 : 241.2315
-#&gt; Model cost at call 309 : 241.2315
-#&gt; Model cost at call 314 : 241.2315
-#&gt; Model cost at call 317 : 240.9738
-#&gt; Model cost at call 322 : 240.9738
-#&gt; Model cost at call 327 : 240.8244
-#&gt; Model cost at call 329 : 240.8244
-#&gt; Model cost at call 337 : 240.7005
-#&gt; Model cost at call 339 : 240.7005
-#&gt; Model cost at call 342 : 240.7005
-#&gt; Model cost at call 347 : 240.629
-#&gt; Model cost at call 350 : 240.629
-#&gt; Model cost at call 357 : 240.6193
-#&gt; Model cost at call 358 : 240.6193
-#&gt; Model cost at call 364 : 240.6193
-#&gt; Model cost at call 367 : 240.6193
-#&gt; Model cost at call 369 : 240.5873
-#&gt; Model cost at call 374 : 240.5873
-#&gt; Model cost at call 380 : 240.578
-#&gt; Model cost at call 382 : 240.578
-#&gt; Model cost at call 390 : 240.5723
-#&gt; Model cost at call 393 : 240.5723
-#&gt; Model cost at call 403 : 240.569
-#&gt; Model cost at call 404 : 240.569
-#&gt; Model cost at call 413 : 240.569
-#&gt; Model cost at call 415 : 240.5688
-#&gt; Model cost at call 416 : 240.5688
-#&gt; Model cost at call 417 : 240.5688
-#&gt; Model cost at call 431 : 240.5686
-#&gt; Model cost at call 432 : 240.5686
-#&gt; Model cost at call 434 : 240.5686
-#&gt; Model cost at call 443 : 240.5686
-#&gt; Model cost at call 444 : 240.5686
-#&gt; Model cost at call 447 : 240.5686
-#&gt; Model cost at call 449 : 240.5686
-#&gt; Model cost at call 450 : 240.5686
-#&gt; Model cost at call 466 : 240.5686
-#&gt; Model cost at call 470 : 240.5686
-#&gt; Model cost at call 485 : 240.5686
-#&gt; Model cost at call 509 : 240.5686
-#&gt; Optimisation by method Port successfully terminated.</div><div class='output co'>#&gt; $par
-#&gt; parent_0 log_k_parent log_k_A1 log_k_B1 log_k_C1
-#&gt; 91.9181598 -3.0020485 -4.2735924 -3.9846764 -2.7852180
-#&gt; log_k_A2 f_parent_ilr_1 f_parent_ilr_2 f_A1_ilr_1
-#&gt; -3.7166415 0.4718588 -0.3589948 -0.1477244
-#&gt;
-#&gt; $ssr
-#&gt; [1] 240.5686
-#&gt;
-#&gt; $convergence
-#&gt; [1] 0
-#&gt;
-#&gt; $iterations
-#&gt; [1] 43
-#&gt;
-#&gt; $evaluations
-#&gt; function gradient
-#&gt; 62 441
-#&gt;
-#&gt; $counts
-#&gt; [1] &quot;relative convergence (4)&quot;
-#&gt;
-#&gt; $hessian
-#&gt; parent_0 log_k_parent log_k_A1 log_k_B1
-#&gt; parent_0 7.3650812 -92.141920 -1.001134e+01 -2.432415e+00
-#&gt; log_k_parent -92.1419204 6632.673492 -4.316240e+01 -1.320833e+01
-#&gt; log_k_A1 -10.0113364 -43.162398 6.071628e+02 0.000000e+00
-#&gt; log_k_B1 -2.4324147 -13.208329 0.000000e+00 1.572303e+02
-#&gt; log_k_C1 -4.7153201 -118.288037 -5.878291e-05 -3.073041e-06
-#&gt; log_k_A2 -0.4360727 -5.304259 -1.977980e+01 0.000000e+00
-#&gt; f_parent_ilr_1 10.5460899 271.145438 -5.299954e+02 1.874235e+02
-#&gt; f_parent_ilr_2 11.6409409 222.570696 -4.773816e+02 -1.159875e+02
-#&gt; f_A1_ilr_1 0.5572072 10.374810 2.850173e+01 0.000000e+00
-#&gt; log_k_C1 log_k_A2 f_parent_ilr_1 f_parent_ilr_2
-#&gt; parent_0 -4.715320e+00 -4.360727e-01 10.54609 11.64094
-#&gt; log_k_parent -1.182880e+02 -5.304259e+00 271.14544 222.57070
-#&gt; log_k_A1 -5.878291e-05 -1.977980e+01 -529.99537 -477.38164
-#&gt; log_k_B1 -3.073041e-06 0.000000e+00 187.42348 -115.98754
-#&gt; log_k_C1 3.372749e+02 -2.395674e-06 56.85184 305.98862
-#&gt; log_k_A2 -2.395674e-06 2.749192e+01 -23.08549 -20.79373
-#&gt; f_parent_ilr_1 5.685184e+01 -2.308549e+01 1256.24941 632.09769
-#&gt; f_parent_ilr_2 3.059886e+02 -2.079373e+01 632.09769 1250.65147
-#&gt; f_A1_ilr_1 3.158891e-06 -3.129286e+01 29.49830 26.56991
-#&gt; f_A1_ilr_1
-#&gt; parent_0 5.572072e-01
-#&gt; log_k_parent 1.037481e+01
-#&gt; log_k_A1 2.850173e+01
-#&gt; log_k_B1 0.000000e+00
-#&gt; log_k_C1 3.158891e-06
-#&gt; log_k_A2 -3.129286e+01
-#&gt; f_parent_ilr_1 2.949830e+01
-#&gt; f_parent_ilr_2 2.656991e+01
-#&gt; f_A1_ilr_1 3.998554e+01
-#&gt;
-#&gt; $residuals
-#&gt; parent parent parent parent parent parent parent
-#&gt; -1.2818402 -1.9372115 -0.5105519 3.8165318 -2.3531716 4.8043342 -2.2775432
-#&gt; parent A1 A1 A1 A1 A1 A1
-#&gt; -5.3608524 4.1967522 2.9032987 -1.3124875 -0.6021093 2.5092324 -1.8861396
-#&gt; B1 B1 B1 B1 B1 C1 C1
-#&gt; 4.3801768 5.5002481 -5.7917184 1.3852658 0.5313301 1.2796458 1.7105311
-#&gt; C1 C1 C1 C1 C1 A2 A2
-#&gt; 3.7116712 -0.1182953 0.5228429 -0.8570298 -3.5476556 -0.5447276 -1.3652404
-#&gt; A2 A2 A2 A2 A2
-#&gt; -0.3330261 -0.5802059 0.1285850 0.2119280 -0.1381990
-#&gt;
-#&gt; $ms
-#&gt; [1] 7.289956
-#&gt;
-#&gt; $var_ms
-#&gt; parent A1 B1 C1 A2
-#&gt; 10.3459333 6.3301336 17.0367907 4.5639474 0.3841002
-#&gt;
-#&gt; $var_ms_unscaled
-#&gt; parent A1 B1 C1 A2
-#&gt; 10.3459333 6.3301336 17.0367907 4.5639474 0.3841002
-#&gt;
-#&gt; $var_ms_unweighted
-#&gt; parent A1 B1 C1 A2
-#&gt; 10.3459333 6.3301336 17.0367907 4.5639474 0.3841002
-#&gt;
-#&gt; $rank
-#&gt; [1] 9
-#&gt;
-#&gt; $df.residual
-#&gt; [1] 24
-#&gt;
-#&gt; $solution_type
-#&gt; [1] &quot;deSolve&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] 523
-#&gt;
-#&gt; $time
-#&gt; user system elapsed
-#&gt; 5.004 0.000 5.004
-#&gt;
-#&gt; $mkinmod
-#&gt; &lt;mkinmod&gt; model generated with
-#&gt; Use of formation fractions $use_of_ff: max
-#&gt; Specification $spec:
-#&gt; $parent
-#&gt; $type: SFO; $to: A1, B1, C1; $sink: FALSE
-#&gt; $A1
-#&gt; $type: SFO; $to: A2; $sink: TRUE
-#&gt; $B1
-#&gt; $type: SFO; $sink: TRUE
-#&gt; $C1
-#&gt; $type: SFO; $sink: TRUE
-#&gt; $A2
-#&gt; $type: SFO; $sink: TRUE
-#&gt; Coefficient matrix $coefmat available
-#&gt; Compiled model $cf available
-#&gt;
-#&gt; $observed
-#&gt; name time value
-#&gt; 1 parent 0 93.20
-#&gt; 2 parent 1 89.40
-#&gt; 3 parent 3 79.70
-#&gt; 4 parent 7 61.10
-#&gt; 5 parent 14 48.20
-#&gt; 6 parent 30 15.90
-#&gt; 7 parent 62 6.50
-#&gt; 8 parent 100 6.00
-#&gt; 9 A1 0 NA
-#&gt; 10 A1 1 NA
-#&gt; 11 A1 3 0.55
-#&gt; 12 A1 7 6.87
-#&gt; 13 A1 14 17.08
-#&gt; 14 A1 30 21.68
-#&gt; 15 A1 62 15.77
-#&gt; 16 A1 100 13.63
-#&gt; 17 B1 0 NA
-#&gt; 18 B1 1 NA
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-#&gt; 387 C1 62.626263 3.789499444
-#&gt; 388 C1 63.636364 3.642728760
-#&gt; 389 C1 64.646465 3.500802233
-#&gt; 390 C1 65.656566 3.363624171
-#&gt; 391 C1 66.666667 3.231095021
-#&gt; 392 C1 67.676768 3.103112069
-#&gt; 393 C1 68.686869 2.979570086
-#&gt; 394 C1 69.696970 2.860361903
-#&gt; 395 C1 70.707071 2.745378939
-#&gt; 396 C1 71.717172 2.634511667
-#&gt; 397 C1 72.727273 2.527650041
-#&gt; 398 C1 73.737374 2.424683880
-#&gt; 399 C1 74.747475 2.325503203
-#&gt; 400 C1 75.757576 2.229998536
-#&gt; 401 C1 76.767677 2.138061182
-#&gt; 402 C1 77.777778 2.049583458
-#&gt; 403 C1 78.787879 1.964458908
-#&gt; 404 C1 79.797980 1.882582485
-#&gt; 405 C1 80.808081 1.803850715
-#&gt; 406 C1 81.818182 1.728161832
-#&gt; 407 C1 82.828283 1.655415900
-#&gt; 408 C1 83.838384 1.585514911
-#&gt; 409 C1 84.848485 1.518362874
-#&gt; 410 C1 85.858586 1.453865880
-#&gt; 411 C1 86.868687 1.391932162
-#&gt; 412 C1 87.878788 1.332472134
-#&gt; 413 C1 88.888889 1.275398429
-#&gt; 414 C1 89.898990 1.220625918
-#&gt; 415 C1 90.909091 1.168071723
-#&gt; 416 C1 91.919192 1.117655227
-#&gt; 417 C1 92.929293 1.069298066
-#&gt; 418 C1 93.939394 1.022924125
-#&gt; 419 C1 94.949495 0.978459525
-#&gt; 420 C1 95.959596 0.935832597
-#&gt; 421 C1 96.969697 0.894973866
-#&gt; 422 C1 97.979798 0.855816021
-#&gt; 423 C1 98.989899 0.818293881
-#&gt; 424 C1 100.000000 0.782344364
-#&gt; 425 A2 0.000000 0.000000000
-#&gt; 426 A2 1.000000 0.005272357
-#&gt; 427 A2 1.010101 0.005377817
-#&gt; 428 A2 2.020202 0.020885524
-#&gt; 429 A2 3.000000 0.044759575
-#&gt; 430 A2 3.030303 0.045628064
-#&gt; 431 A2 4.040404 0.078765936
-#&gt; 432 A2 5.050505 0.119512155
-#&gt; 433 A2 6.060606 0.167129381
-#&gt; 434 A2 7.000000 0.216973934
-#&gt; 435 A2 7.070707 0.220927189
-#&gt; 436 A2 8.080808 0.280259484
-#&gt; 437 A2 9.090909 0.344522046
-#&gt; 438 A2 10.101010 0.413150206
-#&gt; 439 A2 11.111111 0.485616641
-#&gt; 440 A2 12.121212 0.561429288
-#&gt; 441 A2 13.131313 0.640129357
-#&gt; 442 A2 14.000000 0.709794102
-#&gt; 443 A2 14.141414 0.721289460
-#&gt; 444 A2 15.151515 0.804511827
-#&gt; 445 A2 16.161616 0.889426625
-#&gt; 446 A2 17.171717 0.975690359
-#&gt; 447 A2 18.181818 1.062984358
-#&gt; 448 A2 19.191919 1.151013342
-#&gt; 449 A2 20.202020 1.239504068
-#&gt; 450 A2 21.212121 1.328204041
-#&gt; 451 A2 22.222222 1.416880297
-#&gt; 452 A2 23.232323 1.505318253
-#&gt; 453 A2 24.242424 1.593320615
-#&gt; 454 A2 25.252525 1.680706344
-#&gt; 455 A2 26.262626 1.767309680
-#&gt; 456 A2 27.272727 1.852979219
-#&gt; 457 A2 28.282828 1.937577034
-#&gt; 458 A2 29.292929 2.020977853
-#&gt; 459 A2 30.000000 2.078585030
-#&gt; 460 A2 30.303030 2.103068270
-#&gt; 461 A2 31.313131 2.183746011
-#&gt; 462 A2 32.323232 2.262919231
-#&gt; 463 A2 33.333333 2.340505852
-#&gt; 464 A2 34.343434 2.416432940
-#&gt; 465 A2 35.353535 2.490636111
-#&gt; 466 A2 36.363636 2.563058979
-#&gt; 467 A2 37.373737 2.633652622
-#&gt; 468 A2 38.383838 2.702375089
-#&gt; 469 A2 39.393939 2.769190926
-#&gt; 470 A2 40.404040 2.834070737
-#&gt; 471 A2 41.414141 2.896990764
-#&gt; 472 A2 42.424242 2.957932489
-#&gt; 473 A2 43.434343 3.016882265
-#&gt; 474 A2 44.444444 3.073830964
-#&gt; 475 A2 45.454545 3.128773647
-#&gt; 476 A2 46.464646 3.181709250
-#&gt; 477 A2 47.474747 3.232640290
-#&gt; 478 A2 48.484848 3.281572591
-#&gt; 479 A2 49.494949 3.328515022
-#&gt; 480 A2 50.505051 3.373479253
-#&gt; 481 A2 51.515152 3.416479521
-#&gt; 482 A2 52.525253 3.457532417
-#&gt; 483 A2 53.535354 3.496656681
-#&gt; 484 A2 54.545455 3.533873012
-#&gt; 485 A2 55.555556 3.569203883
-#&gt; 486 A2 56.565657 3.602673379
-#&gt; 487 A2 57.575758 3.634307034
-#&gt; 488 A2 58.585859 3.664131686
-#&gt; 489 A2 59.595960 3.692175334
-#&gt; 490 A2 60.606061 3.718467012
-#&gt; 491 A2 61.616162 3.743036663
-#&gt; 492 A2 62.000000 3.751927986
-#&gt; 493 A2 62.626263 3.765915028
-#&gt; 494 A2 63.636364 3.787133539
-#&gt; 495 A2 64.646465 3.806724217
-#&gt; 496 A2 65.656566 3.824719582
-#&gt; 497 A2 66.666667 3.841152565
-#&gt; 498 A2 67.676768 3.856056426
-#&gt; 499 A2 68.686869 3.869464684
-#&gt; 500 A2 69.696970 3.881411040
-#&gt; 501 A2 70.707071 3.891929316
-#&gt; 502 A2 71.717172 3.901053396
-#&gt; 503 A2 72.727273 3.908817168
-#&gt; 504 A2 73.737374 3.915254472
-#&gt; 505 A2 74.747475 3.920399054
-#&gt; 506 A2 75.757576 3.924284521
-#&gt; 507 A2 76.767677 3.926944303
-#&gt; 508 A2 77.777778 3.928411610
-#&gt; 509 A2 78.787879 3.928719404
-#&gt; 510 A2 79.797980 3.927900364
-#&gt; 511 A2 80.808081 3.925986861
-#&gt; 512 A2 81.818182 3.923010926
-#&gt; 513 A2 82.828283 3.919004234
-#&gt; 514 A2 83.838384 3.913998077
-#&gt; 515 A2 84.848485 3.908023347
-#&gt; 516 A2 85.858586 3.901110518
-#&gt; 517 A2 86.868687 3.893289633
-#&gt; 518 A2 87.878788 3.884590288
-#&gt; 519 A2 88.888889 3.875041619
-#&gt; 520 A2 89.898990 3.864672297
-#&gt; 521 A2 90.909091 3.853510511
-#&gt; 522 A2 91.919192 3.841583970
-#&gt; 523 A2 92.929293 3.828919886
-#&gt; 524 A2 93.939394 3.815544978
-#&gt; 525 A2 94.949495 3.801485462
-#&gt; 526 A2 95.959596 3.786767051
-#&gt; 527 A2 96.969697 3.771414951
-#&gt; 528 A2 97.979798 3.755453860
-#&gt; 529 A2 98.989899 3.738907968
-#&gt; 530 A2 100.000000 3.721800959
-#&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: 0x36a83b0&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: 0x36a83b0&gt;
-#&gt;
-#&gt; $hessian_notrans
-#&gt; parent_0 k_parent k_A1 k_B1
-#&gt; parent_0 7.365081 -1854.5113 -7.186039e+02 -1.307858e+02
-#&gt; k_parent -1854.511330 2686790.7676 -6.235542e+04 -1.429363e+04
-#&gt; k_A1 -718.603865 -62355.4211 3.128242e+06 0.000000e+00
-#&gt; k_B1 -130.785796 -14293.6348 0.000000e+00 4.545506e+05
-#&gt; k_C1 -76.404274 -38575.9391 1.190516e-02 -9.422820e-04
-#&gt; k_A2 -17.933942 -4390.5079 -5.838973e+04 0.000000e+00
-#&gt; f_parent_to_A1 75.150866 43257.2599 -1.733841e+05 0.000000e+00
-#&gt; f_parent_to_B1 29.265575 17940.1132 0.000000e+00 -6.150198e+04
-#&gt; f_parent_to_C1 20.661354 19692.5582 -6.146186e-05 -1.990817e-03
-#&gt; f_A1_to_A2 1.593279 597.0744 5.849840e+03 0.000000e+00
-#&gt; k_C1 k_A2 f_parent_to_A1 f_parent_to_B1
-#&gt; parent_0 -7.640427e+01 -1.793394e+01 7.515087e+01 2.926558e+01
-#&gt; k_parent -3.857594e+04 -4.390508e+03 4.325726e+04 1.794011e+04
-#&gt; k_A1 1.190516e-02 -5.838973e+04 -1.733841e+05 0.000000e+00
-#&gt; k_B1 -9.422820e-04 0.000000e+00 0.000000e+00 -6.150198e+04
-#&gt; k_C1 8.855106e+04 4.105787e-04 -1.354551e-03 5.852620e-04
-#&gt; k_A2 4.105787e-04 4.649850e+04 -4.327086e+03 0.000000e+00
-#&gt; f_parent_to_A1 -1.354551e-03 -4.327086e+03 1.813234e+04 0.000000e+00
-#&gt; f_parent_to_B1 5.852620e-04 0.000000e+00 0.000000e+00 1.376213e+04
-#&gt; f_parent_to_C1 -1.658031e+04 2.903794e-04 1.946385e-03 1.325258e-03
-#&gt; f_A1_to_A2 -4.367402e-05 -3.679910e+03 3.844249e+02 0.000000e+00
-#&gt; f_parent_to_C1 f_A1_to_A2
-#&gt; parent_0 2.066135e+01 1.593279e+00
-#&gt; k_parent 1.969256e+04 5.970744e+02
-#&gt; k_A1 -6.146186e-05 5.849840e+03
-#&gt; k_B1 -1.990817e-03 0.000000e+00
-#&gt; k_C1 -1.658031e+04 -4.367402e-05
-#&gt; k_A2 2.903794e-04 -3.679910e+03
-#&gt; f_parent_to_A1 1.946385e-03 3.844249e+02
-#&gt; f_parent_to_B1 1.325258e-03 0.000000e+00
-#&gt; f_parent_to_C1 4.483759e+03 -3.796730e-05
-#&gt; f_A1_to_A2 -3.796730e-05 3.269288e+02
-#&gt;
-#&gt; $start
-#&gt; value type
-#&gt; parent_0 93.2000000 state
-#&gt; k_parent 0.1000000 deparm
-#&gt; k_A1 0.1001000 deparm
-#&gt; k_B1 0.1002000 deparm
-#&gt; k_C1 0.1003000 deparm
-#&gt; k_A2 0.1004000 deparm
-#&gt; f_parent_to_A1 0.3333333 deparm
-#&gt; f_parent_to_B1 0.3333333 deparm
-#&gt; f_parent_to_C1 0.3333333 deparm
-#&gt; f_A1_to_A2 0.5000000 deparm
-#&gt;
-#&gt; $start_transformed
-#&gt; value lower upper
-#&gt; parent_0 93.200000 -Inf Inf
-#&gt; log_k_parent -2.302585 -Inf Inf
-#&gt; log_k_A1 -2.301586 -Inf Inf
-#&gt; log_k_B1 -2.300587 -Inf Inf
-#&gt; log_k_C1 -2.299590 -Inf Inf
-#&gt; log_k_A2 -2.298593 -Inf Inf
-#&gt; f_parent_ilr_1 0.000000 -Inf Inf
-#&gt; f_parent_ilr_2 0.000000 -Inf Inf
-#&gt; f_A1_ilr_1 0.000000 -Inf Inf
-#&gt;
-#&gt; $fixed
-#&gt; value type
-#&gt; A1_0 0 state
-#&gt; B1_0 0 state
-#&gt; C1_0 0 state
-#&gt; A2_0 0 state
-#&gt;
-#&gt; $data
-#&gt; time variable observed predicted residual
-#&gt; 1 0 parent 93.20 91.918159794 1.2818402
-#&gt; 2 1 parent 89.40 87.462788491 1.9372115
-#&gt; 3 3 parent 79.70 79.189448055 0.5105519
-#&gt; 4 7 parent 61.10 64.916531757 -3.8165318
-#&gt; 5 14 parent 48.20 45.846828365 2.3531716
-#&gt; 6 30 parent 15.90 20.704334210 -4.8043342
-#&gt; 7 62 parent 6.50 4.222456793 2.2775432
-#&gt; 8 100 parent 6.00 0.639147580 5.3608524
-#&gt; 9 0 A1 NA 0.000000000 NA
-#&gt; 10 1 A1 NA 1.685461006 NA
-#&gt; 11 3 A1 0.55 4.746752202 -4.1967522
-#&gt; 12 7 A1 6.87 9.773298725 -2.9032987
-#&gt; 13 14 A1 17.08 15.767512526 1.3124875
-#&gt; 14 30 A1 21.68 21.077890710 0.6021093
-#&gt; 15 62 A1 15.77 18.279232408 -2.5092324
-#&gt; 16 100 A1 13.63 11.743860400 1.8861396
-#&gt; 17 0 B1 NA 0.000000000 NA
-#&gt; 18 1 B1 NA 0.862762059 NA
-#&gt; 19 3 B1 NA 2.418226457 NA
-#&gt; 20 7 B1 0.55 4.930176837 -4.3801768
-#&gt; 21 14 B1 2.31 7.810248132 -5.5002481
-#&gt; 22 30 B1 15.76 9.968281596 5.7917184
-#&gt; 23 62 B1 6.36 7.745265792 -1.3852658
-#&gt; 24 100 B1 3.74 4.271330056 -0.5313301
-#&gt; 25 0 C1 NA 0.000000000 NA
-#&gt; 26 1 C1 0.55 1.829645786 -1.2796458
-#&gt; 27 3 C1 3.20 4.910531064 -1.7105311
-#&gt; 28 7 C1 5.46 9.171671206 -3.7116712
-#&gt; 29 14 C1 12.55 12.431704739 0.1182953
-#&gt; 30 30 C1 10.45 10.972842888 -0.5228429
-#&gt; 31 62 C1 4.74 3.882970158 0.8570298
-#&gt; 32 100 C1 4.33 0.782344364 3.5476556
-#&gt; 33 0 A2 NA 0.000000000 NA
-#&gt; 34 1 A2 0.55 0.005272357 0.5447276
-#&gt; 35 3 A2 1.41 0.044759575 1.3652404
-#&gt; 36 7 A2 0.55 0.216973934 0.3330261
-#&gt; 37 14 A2 1.29 0.709794102 0.5802059
-#&gt; 38 30 A2 1.95 2.078585030 -0.1285850
-#&gt; 39 62 A2 3.54 3.751927986 -0.2119280
-#&gt; 40 100 A2 3.86 3.721800959 0.1381990
-#&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 k_A1 k_B1 k_C1
-#&gt; 91.91815979 0.04968519 0.01393165 0.01859846 0.06171564
-#&gt; k_A2 f_parent_to_A1 f_parent_to_B1 f_parent_to_C1 f_A1_to_A2
-#&gt; 0.02431549 0.38096192 0.19546676 0.42357132 0.44796066
-#&gt;
-#&gt; $bparms.fixed
-#&gt; A1_0 B1_0 C1_0 A2_0
-#&gt; 0 0 0 0
-#&gt;
-#&gt; $bparms.ode
-#&gt; k_parent f_parent_to_A1 f_parent_to_B1 f_parent_to_C1 k_A1
-#&gt; 0.04968519 0.38096192 0.19546676 0.42357132 0.01393165
-#&gt; f_A1_to_A2 k_B1 k_C1 k_A2
-#&gt; 0.44796066 0.01859846 0.06171564 0.02431549
-#&gt;
-#&gt; $bparms.state
-#&gt; parent A1 B1 C1 A2
-#&gt; 91.91816 0.00000 0.00000 0.00000 0.00000
-#&gt;
-#&gt; $date
-#&gt; [1] &quot;Fri Nov 18 15:20:45 2016&quot;
-#&gt;
-#&gt; attr(,&quot;class&quot;)
-#&gt; [1] &quot;mkinfit&quot; &quot;modFit&quot; </div></pre>
+ <span class='kw'>A2</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></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='no'>model</span>, <span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+ <span class='fu'>plot</span>(<span class='no'>fit</span>)</div><img src='schaefer07_complex_case-4.png' alt='' width='540' height='400' /><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
+#&gt; parent_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink
+#&gt; 0.3809619 0.1954668 0.4235713 0.0000000 0.4479607 0.5520393
+#&gt;
+#&gt; $SFORB
+#&gt; logical(0)
+#&gt;
+#&gt; $distimes
+#&gt; DT50 DT90
+#&gt; parent 13.95078 46.34349
+#&gt; A1 49.75343 165.27732
+#&gt; B1 37.26906 123.80513
+#&gt; C1 11.23131 37.30959
+#&gt; A2 28.50640 94.69621
+#&gt; </div><div class='input'>
+ <span class='co'># Compare with the results obtained in the original publication</span>
+ <span class='fu'>print</span>(<span class='no'>schaefer07_complex_results</span>)</div><div class='output co'>#&gt; compound parameter KinGUI ModelMaker deviation
+#&gt; 1 parent degradation rate 0.0496 0.0506 2.0
+#&gt; 2 parent DT50 13.9900 13.6900 2.2
+#&gt; 3 metabolite A1 formation fraction 0.3803 0.3696 2.9
+#&gt; 4 metabolite A1 degradation rate 0.0139 0.0136 2.2
+#&gt; 5 metabolite A1 DT50 49.9600 50.8900 1.8
+#&gt; 6 metabolite B1 formation fraction 0.1866 0.1818 2.6
+#&gt; 7 metabolite B1 degradation rate 0.0175 0.0172 1.7
+#&gt; 8 metabolite B1 DT50 39.6100 40.2400 1.6
+#&gt; 9 metabolite C1 formation fraction 0.4331 0.4486 3.5
+#&gt; 10 metabolite C1 degradation rate 0.0638 0.0700 8.9
+#&gt; 11 metabolite C1 DT50 10.8700 9.9000 9.8
+#&gt; 12 metabolite A2 formation fraction 0.4529 0.4559 0.7
+#&gt; 13 metabolite A2 degradation rate 0.0245 0.0244 0.4
+#&gt; 14 metabolite A2 DT50 28.2400 28.4500 0.7</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
<h2>Contents</h2>
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index b334b3aa..8adb5aff 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -140,17 +140,17 @@
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
- <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+ <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></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='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 18 15:20:45 2016
-#&gt; Date of summary: Fri Nov 18 15:20:45 2016
+#&gt; Date of fit: Fri Nov 18 15:44:43 2016
+#&gt; Date of summary: Fri Nov 18 15:44:43 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted with method Port using 35 model solutions performed in 0.081 s
+#&gt; Fitted with method Port using 35 model solutions performed in 0.085 s
#&gt;
#&gt; Weighting: none
#&gt;
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index 97407402..c2794427 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -137,722 +137,24 @@
<span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>),
<span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
<span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_SFO_lin</span>, <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 31054.59
-#&gt; Model cost at call 3 : 31054.59
-#&gt; Model cost at call 8 : 15089.57
-#&gt; Model cost at call 9 : 11464.3
-#&gt; Model cost at call 11 : 11464.1
-#&gt; Model cost at call 16 : 5723.32
-#&gt; Model cost at call 17 : 5723.318
-#&gt; Model cost at call 19 : 5723.304
-#&gt; Model cost at call 21 : 5723.304
-#&gt; Model cost at call 24 : 3968.126
-#&gt; Model cost at call 25 : 3968.124
-#&gt; Model cost at call 28 : 3968.119
-#&gt; Model cost at call 31 : 3416.421
-#&gt; Model cost at call 32 : 3416.42
-#&gt; Model cost at call 36 : 3416.418
-#&gt; Model cost at call 38 : 866.5564
-#&gt; Model cost at call 42 : 866.5557
-#&gt; Model cost at call 45 : 670.4833
-#&gt; Model cost at call 47 : 670.476
-#&gt; Model cost at call 53 : 312.9905
-#&gt; Model cost at call 57 : 312.9904
-#&gt; Model cost at call 58 : 312.9904
-#&gt; Model cost at call 61 : 287.8916
-#&gt; Model cost at call 63 : 287.8916
-#&gt; Model cost at call 66 : 287.8916
-#&gt; Model cost at call 69 : 284.5441
-#&gt; Model cost at call 71 : 284.5441
-#&gt; Model cost at call 73 : 284.5441
-#&gt; Model cost at call 76 : 283.4533
-#&gt; Model cost at call 78 : 283.4533
-#&gt; Model cost at call 83 : 282.1356
-#&gt; Model cost at call 85 : 282.1356
-#&gt; Model cost at call 88 : 282.1356
-#&gt; Model cost at call 90 : 280.7846
-#&gt; Model cost at call 92 : 280.7846
-#&gt; Model cost at call 95 : 280.7846
-#&gt; Model cost at call 97 : 278.4856
-#&gt; Model cost at call 98 : 274.5025
-#&gt; Model cost at call 99 : 269.2866
-#&gt; Model cost at call 101 : 269.2866
-#&gt; Model cost at call 102 : 269.2866
-#&gt; Model cost at call 103 : 269.2866
-#&gt; Model cost at call 106 : 254.1284
-#&gt; Model cost at call 108 : 254.1283
-#&gt; Model cost at call 109 : 254.1283
-#&gt; Model cost at call 112 : 254.128
-#&gt; Model cost at call 114 : 233.1376
-#&gt; Model cost at call 116 : 233.1376
-#&gt; Model cost at call 118 : 233.1375
-#&gt; Model cost at call 121 : 227.5879
-#&gt; Model cost at call 124 : 227.5879
-#&gt; Model cost at call 125 : 227.5878
-#&gt; Model cost at call 129 : 217.0041
-#&gt; Model cost at call 133 : 217.0041
-#&gt; Model cost at call 135 : 217.0041
-#&gt; Model cost at call 136 : 215.1367
-#&gt; Model cost at call 138 : 215.1367
-#&gt; Model cost at call 143 : 213.3794
-#&gt; Model cost at call 145 : 213.3794
-#&gt; Model cost at call 150 : 211.0201
-#&gt; Model cost at call 152 : 211.0201
-#&gt; Model cost at call 154 : 211.0201
-#&gt; Model cost at call 155 : 211.0201
-#&gt; Model cost at call 157 : 210.6426
-#&gt; Model cost at call 159 : 210.6426
-#&gt; Model cost at call 160 : 210.6425
-#&gt; Model cost at call 164 : 207.6331
-#&gt; Model cost at call 167 : 207.6331
-#&gt; Model cost at call 171 : 206.2366
-#&gt; Model cost at call 173 : 206.2366
-#&gt; Model cost at call 174 : 206.2366
-#&gt; Model cost at call 178 : 204.8117
-#&gt; Model cost at call 180 : 204.8117
-#&gt; Model cost at call 185 : 204.7988
-#&gt; Model cost at call 187 : 204.7988
-#&gt; Model cost at call 190 : 204.7988
-#&gt; Model cost at call 192 : 203.5122
-#&gt; Model cost at call 194 : 203.5122
-#&gt; Model cost at call 197 : 203.5122
-#&gt; Model cost at call 198 : 203.5122
-#&gt; Model cost at call 199 : 203.354
-#&gt; Model cost at call 201 : 203.354
-#&gt; Model cost at call 204 : 203.354
-#&gt; Model cost at call 206 : 202.6825
-#&gt; Model cost at call 208 : 202.6825
-#&gt; Model cost at call 209 : 202.6825
-#&gt; Model cost at call 212 : 202.6825
-#&gt; Model cost at call 213 : 202.4582
-#&gt; Model cost at call 215 : 202.4582
-#&gt; Model cost at call 220 : 202.3261
-#&gt; Model cost at call 222 : 202.3261
-#&gt; Model cost at call 227 : 202.2306
-#&gt; Model cost at call 229 : 202.2306
-#&gt; Model cost at call 231 : 202.2306
-#&gt; Model cost at call 234 : 202.115
-#&gt; Model cost at call 236 : 202.115
-#&gt; Model cost at call 238 : 202.115
-#&gt; Model cost at call 241 : 202.0397
-#&gt; Model cost at call 243 : 202.0397
-#&gt; Model cost at call 248 : 201.8989
-#&gt; Model cost at call 249 : 201.8551
-#&gt; Model cost at call 252 : 201.8551
-#&gt; Model cost at call 257 : 201.676
-#&gt; Model cost at call 259 : 201.676
-#&gt; Model cost at call 264 : 201.6285
-#&gt; Model cost at call 266 : 201.6285
-#&gt; Model cost at call 270 : 201.6284
-#&gt; Model cost at call 271 : 201.5876
-#&gt; Model cost at call 272 : 201.5876
-#&gt; Model cost at call 278 : 201.5317
-#&gt; Model cost at call 279 : 201.5317
-#&gt; Model cost at call 286 : 201.5207
-#&gt; Model cost at call 287 : 201.5207
-#&gt; Model cost at call 289 : 201.5207
-#&gt; Model cost at call 293 : 201.5207
-#&gt; Model cost at call 294 : 201.5207
-#&gt; Model cost at call 296 : 201.5174
-#&gt; Model cost at call 301 : 201.5174
-#&gt; Model cost at call 304 : 201.5169
-#&gt; Model cost at call 305 : 201.5169
-#&gt; Model cost at call 306 : 201.5169
-#&gt; Model cost at call 309 : 201.5169
-#&gt; Model cost at call 312 : 201.5169
-#&gt; Model cost at call 314 : 201.5169
-#&gt; Model cost at call 322 : 201.5169
-#&gt; Model cost at call 325 : 201.5169
-#&gt; Model cost at call 340 : 201.5169
-#&gt; Optimisation by method Port successfully terminated.</div><div class='output co'>#&gt; $par
-#&gt; parent_0 log_k_parent log_k_M1 log_k_M2 f_parent_ilr_1
-#&gt; 102.0624835 -0.3020316 -1.2067882 -3.9007519 0.8491684
-#&gt; f_M1_ilr_1
-#&gt; 0.6780411
+<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_SFO_lin</span>, <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fit</span>)</div><img src='synthetic_data_for_UBA_2014-10.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+#&gt; R version: 3.3.2
+#&gt; Date of fit: Fri Nov 18 16:16:12 2016
+#&gt; Date of summary: Fri Nov 18 16:16:12 2016
#&gt;
-#&gt; $ssr
-#&gt; [1] 201.5169
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt; d_M1/dt = + f_parent_to_M1 * k_parent * parent - k_M1 * M1
+#&gt; d_M2/dt = + f_M1_to_M2 * k_M1 * M1 - k_M2 * M2
#&gt;
-#&gt; $convergence
-#&gt; [1] 0
+#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; $iterations
-#&gt; [1] 43
+#&gt; Fitted with method Port using 351 model solutions performed in 2.193 s
#&gt;
-#&gt; $evaluations
-#&gt; function gradient
-#&gt; 56 281
+#&gt; Weighting: none
#&gt;
-#&gt; $counts
-#&gt; [1] &quot;relative convergence (4)&quot;
-#&gt;
-#&gt; $hessian
-#&gt; parent_0 log_k_parent log_k_M1 log_k_M2 f_parent_ilr_1
-#&gt; parent_0 8.433594 -29.66715 -18.40708 -68.90161 115.9976
-#&gt; log_k_parent -29.667146 10561.33531 675.33998 55.94284 1666.8940
-#&gt; log_k_M1 -18.407082 675.33998 6274.11801 44.01714 -614.5674
-#&gt; log_k_M2 -68.901614 55.94284 44.01714 5021.66991 -2300.4467
-#&gt; f_parent_ilr_1 115.997604 1666.89403 -614.56735 -2300.44667 3872.8569
-#&gt; f_M1_ilr_1 92.819176 604.06870 1483.45826 -2755.79082 3098.9947
-#&gt; f_M1_ilr_1
-#&gt; parent_0 92.81918
-#&gt; log_k_parent 604.06870
-#&gt; log_k_M1 1483.45826
-#&gt; log_k_M2 -2755.79082
-#&gt; f_parent_ilr_1 3098.99466
-#&gt; f_M1_ilr_1 3712.39824
-#&gt;
-#&gt; $residuals
-#&gt; parent parent parent parent parent parent
-#&gt; 0.56248353 0.86248353 -5.17118695 1.22881305 0.70772795 3.50772795
-#&gt; parent parent parent parent parent parent
-#&gt; -0.52282962 0.27717038 -3.49673606 -3.19999990 -0.60000000 -3.50000000
-#&gt; M1 M1 M1 M1 M1 M1
-#&gt; -1.61088639 -2.61088639 5.07026619 -0.42973381 0.38714436 -2.31285564
-#&gt; M1 M1 M1 M1 M1 M1
-#&gt; -3.80468869 0.79531131 -0.49999789 -3.20000000 -1.50000000 -0.60000000
-#&gt; M2 M2 M2 M2 M2 M2
-#&gt; -0.34517017 0.62526794 2.22526794 -0.07941701 -1.17941701 -3.83353798
-#&gt; M2 M2 M2 M2 M2 M2
-#&gt; 1.26646202 0.87274743 2.47274743 -0.21837410 0.98162590 -0.47130583
-#&gt; M2 M2 M2
-#&gt; -0.67130583 -4.27893112 2.22106888
-#&gt;
-#&gt; $ms
-#&gt; [1] 5.1671
-#&gt;
-#&gt; $var_ms
-#&gt; parent M1 M2
-#&gt; 6.461983 5.750942 3.664121
-#&gt;
-#&gt; $var_ms_unscaled
-#&gt; parent M1 M2
-#&gt; 6.461983 5.750942 3.664121
-#&gt;
-#&gt; $var_ms_unweighted
-#&gt; parent M1 M2
-#&gt; 6.461983 5.750942 3.664121
-#&gt;
-#&gt; $rank
-#&gt; [1] 6
-#&gt;
-#&gt; $df.residual
-#&gt; [1] 33
-#&gt;
-#&gt; $solution_type
-#&gt; [1] &quot;deSolve&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] 351
-#&gt;
-#&gt; $time
-#&gt; user system elapsed
-#&gt; 2.116 0.000 2.113
-#&gt;
-#&gt; $mkinmod
-#&gt; &lt;mkinmod&gt; model generated with
-#&gt; Use of formation fractions $use_of_ff: max
-#&gt; Specification $spec:
-#&gt; $parent
-#&gt; $type: SFO; $to: M1; $sink: TRUE
-#&gt; $M1
-#&gt; $type: SFO; $to: M2; $sink: TRUE
-#&gt; $M2
-#&gt; $type: SFO; $sink: TRUE
-#&gt; Coefficient matrix $coefmat available
-#&gt; Compiled model $cf available
-#&gt;
-#&gt; $observed
-#&gt; name time value override err
-#&gt; 1 parent 0 101.5 NA 1
-#&gt; 2 parent 0 101.2 NA 1
-#&gt; 3 parent 1 53.9 NA 1
-#&gt; 4 parent 1 47.5 NA 1
-#&gt; 5 parent 3 10.4 NA 1
-#&gt; 6 parent 3 7.6 NA 1
-#&gt; 7 parent 7 1.1 NA 1
-#&gt; 8 parent 7 0.3 NA 1
-#&gt; 9 parent 14 NA NA 1
-#&gt; 10 parent 14 3.5 NA 1
-#&gt; 11 parent 28 NA NA 1
-#&gt; 12 parent 28 3.2 NA 1
-#&gt; 13 parent 60 NA NA 1
-#&gt; 14 parent 60 NA NA 1
-#&gt; 15 parent 90 0.6 NA 1
-#&gt; 16 parent 90 NA NA 1
-#&gt; 17 parent 120 NA NA 1
-#&gt; 18 parent 120 3.5 NA 1
-#&gt; 19 M1 0 NA NA 1
-#&gt; 20 M1 0 NA NA 1
-#&gt; 21 M1 1 36.4 NA 1
-#&gt; 22 M1 1 37.4 NA 1
-#&gt; 23 M1 3 34.3 NA 1
-#&gt; 24 M1 3 39.8 NA 1
-#&gt; 25 M1 7 15.1 NA 1
-#&gt; 26 M1 7 17.8 NA 1
-#&gt; 27 M1 14 5.8 NA 1
-#&gt; 28 M1 14 1.2 NA 1
-#&gt; 29 M1 28 NA NA 1
-#&gt; 30 M1 28 NA NA 1
-#&gt; 31 M1 60 0.5 NA 1
-#&gt; 32 M1 60 NA NA 1
-#&gt; 33 M1 90 NA NA 1
-#&gt; 34 M1 90 3.2 NA 1
-#&gt; 35 M1 120 1.5 NA 1
-#&gt; 36 M1 120 0.6 NA 1
-#&gt; 37 M2 0 NA NA 1
-#&gt; 38 M2 0 NA NA 1
-#&gt; 39 M2 1 NA NA 1
-#&gt; 40 M2 1 4.8 NA 1
-#&gt; 41 M2 3 20.9 NA 1
-#&gt; 42 M2 3 19.3 NA 1
-#&gt; 43 M2 7 42.0 NA 1
-#&gt; 44 M2 7 43.1 NA 1
-#&gt; 45 M2 14 49.4 NA 1
-#&gt; 46 M2 14 44.3 NA 1
-#&gt; 47 M2 28 34.6 NA 1
-#&gt; 48 M2 28 33.0 NA 1
-#&gt; 49 M2 60 18.8 NA 1
-#&gt; 50 M2 60 17.6 NA 1
-#&gt; 51 M2 90 10.6 NA 1
-#&gt; 52 M2 90 10.8 NA 1
-#&gt; 53 M2 120 9.8 NA 1
-#&gt; 54 M2 120 3.3 NA 1
-#&gt;
-#&gt; $obs_vars
-#&gt; [1] &quot;parent&quot; &quot;M1&quot; &quot;M2&quot;
-#&gt;
-#&gt; $predicted
-#&gt; name time value
-#&gt; 1 parent 0.000000 1.020625e+02
-#&gt; 2 parent 1.000000 4.872881e+01
-#&gt; 3 parent 1.212121 4.165603e+01
-#&gt; 4 parent 2.424242 1.700159e+01
-#&gt; 5 parent 3.000000 1.110773e+01
-#&gt; 6 parent 3.636364 6.939072e+00
-#&gt; 7 parent 4.848485 2.832130e+00
-#&gt; 8 parent 6.060606 1.155912e+00
-#&gt; 9 parent 7.000000 5.771704e-01
-#&gt; 10 parent 7.272727 4.717769e-01
-#&gt; 11 parent 8.484848 1.925522e-01
-#&gt; 12 parent 9.696970 7.858872e-02
-#&gt; 13 parent 10.909091 3.207539e-02
-#&gt; 14 parent 12.121212 1.309133e-02
-#&gt; 15 parent 13.333333 5.343128e-03
-#&gt; 16 parent 14.000000 3.263939e-03
-#&gt; 17 parent 14.545455 2.180757e-03
-#&gt; 18 parent 15.757576 8.900590e-04
-#&gt; 19 parent 16.969697 3.632705e-04
-#&gt; 20 parent 18.181818 1.482660e-04
-#&gt; 21 parent 19.393939 6.051327e-05
-#&gt; 22 parent 20.606061 2.469808e-05
-#&gt; 23 parent 21.818182 1.008035e-05
-#&gt; 24 parent 23.030303 4.114467e-06
-#&gt; 25 parent 24.242424 1.679140e-06
-#&gt; 26 parent 25.454545 6.853728e-07
-#&gt; 27 parent 26.666667 2.797450e-07
-#&gt; 28 parent 27.878788 1.142138e-07
-#&gt; 29 parent 28.000000 1.044512e-07
-#&gt; 30 parent 29.090909 4.657425e-08
-#&gt; 31 parent 30.303030 1.900245e-08
-#&gt; 32 parent 31.515152 7.760238e-09
-#&gt; 33 parent 32.727273 3.164577e-09
-#&gt; 34 parent 33.939394 1.291779e-09
-#&gt; 35 parent 35.151515 5.261577e-10
-#&gt; 36 parent 36.363636 2.132915e-10
-#&gt; 37 parent 37.575758 8.767818e-11
-#&gt; 38 parent 38.787879 3.442792e-11
-#&gt; 39 parent 40.000000 1.827291e-11
-#&gt; 40 parent 41.212121 3.771071e-12
-#&gt; 41 parent 42.424242 6.084856e-12
-#&gt; 42 parent 43.636364 -3.377858e-12
-#&gt; 43 parent 44.848485 5.870338e-12
-#&gt; 44 parent 46.060606 -6.263257e-12
-#&gt; 45 parent 47.272727 8.743492e-12
-#&gt; 46 parent 48.484848 -9.381771e-12
-#&gt; 47 parent 49.696970 1.403389e-11
-#&gt; 48 parent 50.909091 -3.592528e-11
-#&gt; 49 parent 52.121212 -8.487459e-11
-#&gt; 50 parent 53.333333 -3.309153e-12
-#&gt; 51 parent 54.545455 -2.966799e-11
-#&gt; 52 parent 55.757576 -4.723329e-11
-#&gt; 53 parent 56.969697 7.635833e-11
-#&gt; 54 parent 58.181818 -1.887064e-11
-#&gt; 55 parent 59.393939 -1.548352e-10
-#&gt; 56 parent 60.000000 -1.053819e-10
-#&gt; 57 parent 60.606061 5.780435e-12
-#&gt; 58 parent 61.818182 9.056244e-11
-#&gt; 59 parent 63.030303 -8.889581e-11
-#&gt; 60 parent 64.242424 -6.653389e-11
-#&gt; 61 parent 65.454545 1.181114e-10
-#&gt; 62 parent 66.666667 -9.226329e-12
-#&gt; 63 parent 67.878788 -8.897326e-11
-#&gt; 64 parent 69.090909 1.984998e-10
-#&gt; 65 parent 70.303030 3.255550e-11
-#&gt; 66 parent 71.515152 -2.991002e-10
-#&gt; 67 parent 72.727273 2.254268e-10
-#&gt; 68 parent 73.939394 2.696039e-10
-#&gt; 69 parent 75.151515 1.226806e-10
-#&gt; 70 parent 76.363636 3.447399e-11
-#&gt; 71 parent 77.575758 2.048902e-11
-#&gt; 72 parent 78.787879 6.830755e-12
-#&gt; 73 parent 80.000000 8.242171e-13
-#&gt; 74 parent 81.212121 -5.357740e-12
-#&gt; 75 parent 82.424242 2.198907e-11
-#&gt; 76 parent 83.636364 3.739511e-11
-#&gt; 77 parent 84.848485 -6.616091e-12
-#&gt; 78 parent 86.060606 -2.562689e-12
-#&gt; 79 parent 87.272727 4.089395e-11
-#&gt; 80 parent 88.484848 -2.042159e-11
-#&gt; 81 parent 89.696970 -4.088127e-11
-#&gt; 82 parent 90.000000 -1.874889e-11
-#&gt; 83 parent 90.909091 4.225747e-11
-#&gt; 84 parent 92.121212 8.054402e-12
-#&gt; 85 parent 93.333333 3.917595e-12
-#&gt; 86 parent 94.545455 6.591454e-12
-#&gt; 87 parent 95.757576 2.790958e-11
-#&gt; 88 parent 96.969697 2.720721e-12
-#&gt; 89 parent 98.181818 -1.304470e-12
-#&gt; 90 parent 99.393939 1.345055e-11
-#&gt; 91 parent 100.606061 -9.662077e-12
-#&gt; 92 parent 101.818182 -2.086798e-11
-#&gt; 93 parent 103.030303 9.332507e-12
-#&gt; 94 parent 104.242424 -6.752606e-12
-#&gt; 95 parent 105.454545 -3.326620e-11
-#&gt; 96 parent 106.666667 2.500680e-11
-#&gt; 97 parent 107.878788 2.184148e-11
-#&gt; 98 parent 109.090909 -5.985657e-11
-#&gt; 99 parent 110.303030 -8.750836e-14
-#&gt; 100 parent 111.515152 1.820588e-12
-#&gt; 101 parent 112.727273 -1.261472e-11
-#&gt; 102 parent 113.939394 1.455439e-11
-#&gt; 103 parent 115.151515 1.945812e-12
-#&gt; 104 parent 116.363636 9.598249e-13
-#&gt; 105 parent 117.575758 1.724679e-12
-#&gt; 106 parent 118.787879 -1.334504e-12
-#&gt; 107 parent 120.000000 -2.804801e-11
-#&gt; 108 M1 0.000000 0.000000e+00
-#&gt; 109 M1 1.000000 3.478911e+01
-#&gt; 110 M1 1.212121 3.791354e+01
-#&gt; 111 M1 2.424242 4.185645e+01
-#&gt; 112 M1 3.000000 3.937027e+01
-#&gt; 113 M1 3.636364 3.544167e+01
-#&gt; 114 M1 4.848485 2.723995e+01
-#&gt; 115 M1 6.060606 2.000711e+01
-#&gt; 116 M1 7.000000 1.548714e+01
-#&gt; 117 M1 7.272727 1.435144e+01
-#&gt; 118 M1 8.484848 1.016177e+01
-#&gt; 119 M1 9.696970 7.142649e+00
-#&gt; 120 M1 10.909091 4.999441e+00
-#&gt; 121 M1 12.121212 3.490801e+00
-#&gt; 122 M1 13.333333 2.433954e+00
-#&gt; 123 M1 14.000000 1.995311e+00
-#&gt; 124 M1 14.545455 1.695664e+00
-#&gt; 125 M1 15.757576 1.180746e+00
-#&gt; 126 M1 16.969697 8.219589e-01
-#&gt; 127 M1 18.181818 5.720991e-01
-#&gt; 128 M1 19.393939 3.981531e-01
-#&gt; 129 M1 20.606061 2.770793e-01
-#&gt; 130 M1 21.818182 1.928162e-01
-#&gt; 131 M1 23.030303 1.341758e-01
-#&gt; 132 M1 24.242424 9.336844e-02
-#&gt; 133 M1 25.454545 6.497152e-02
-#&gt; 134 M1 26.666667 4.521101e-02
-#&gt; 135 M1 27.878788 3.146041e-02
-#&gt; 136 M1 28.000000 3.034005e-02
-#&gt; 137 M1 29.090909 2.189192e-02
-#&gt; 138 M1 30.303030 1.523362e-02
-#&gt; 139 M1 31.515152 1.060040e-02
-#&gt; 140 M1 32.727273 7.376345e-03
-#&gt; 141 M1 33.939394 5.132870e-03
-#&gt; 142 M1 35.151515 3.571730e-03
-#&gt; 143 M1 36.363636 2.485406e-03
-#&gt; 144 M1 37.575758 1.729482e-03
-#&gt; 145 M1 38.787879 1.203467e-03
-#&gt; 146 M1 40.000000 8.374380e-04
-#&gt; 147 M1 41.212121 5.827347e-04
-#&gt; 148 M1 42.424242 4.054989e-04
-#&gt; 149 M1 43.636364 2.821681e-04
-#&gt; 150 M1 44.848485 1.963481e-04
-#&gt; 151 M1 46.060606 1.366297e-04
-#&gt; 152 M1 47.272727 9.507439e-05
-#&gt; 153 M1 48.484848 6.615797e-05
-#&gt; 154 M1 49.696970 4.603629e-05
-#&gt; 155 M1 50.909091 3.203434e-05
-#&gt; 156 M1 52.121212 2.229196e-05
-#&gt; 157 M1 53.333333 1.551223e-05
-#&gt; 158 M1 54.545455 1.079420e-05
-#&gt; 159 M1 55.757576 7.511255e-06
-#&gt; 160 M1 56.969697 5.226640e-06
-#&gt; 161 M1 58.181818 3.636450e-06
-#&gt; 162 M1 59.393939 2.530191e-06
-#&gt; 163 M1 60.000000 2.110651e-06
-#&gt; 164 M1 60.606061 1.760625e-06
-#&gt; 165 M1 61.818182 1.225095e-06
-#&gt; 166 M1 63.030303 8.527010e-07
-#&gt; 167 M1 64.242424 5.934161e-07
-#&gt; 168 M1 65.454545 4.127474e-07
-#&gt; 169 M1 66.666667 2.874114e-07
-#&gt; 170 M1 67.878788 2.001921e-07
-#&gt; 171 M1 69.090909 1.389331e-07
-#&gt; 172 M1 70.303030 9.678549e-08
-#&gt; 173 M1 71.515152 6.777214e-08
-#&gt; 174 M1 72.727273 4.658761e-08
-#&gt; 175 M1 73.939394 3.226837e-08
-#&gt; 176 M1 75.151515 2.253752e-08
-#&gt; 177 M1 76.363636 1.574843e-08
-#&gt; 178 M1 77.575758 1.096303e-08
-#&gt; 179 M1 78.787879 7.638209e-09
-#&gt; 180 M1 80.000000 5.319996e-09
-#&gt; 181 M1 81.212121 3.709993e-09
-#&gt; 182 M1 82.424242 2.548810e-09
-#&gt; 183 M1 83.636364 1.744629e-09
-#&gt; 184 M1 84.848485 1.256081e-09
-#&gt; 185 M1 86.060606 8.714672e-10
-#&gt; 186 M1 87.272727 5.511830e-10
-#&gt; 187 M1 88.484848 4.466725e-10
-#&gt; 188 M1 89.696970 3.452654e-10
-#&gt; 189 M1 90.000000 2.913252e-10
-#&gt; 190 M1 90.909091 1.489262e-10
-#&gt; 191 M1 92.121212 1.311985e-10
-#&gt; 192 M1 93.333333 9.347248e-11
-#&gt; 193 M1 94.545455 6.004640e-11
-#&gt; 194 M1 95.757576 1.166926e-11
-#&gt; 195 M1 96.969697 2.968203e-11
-#&gt; 196 M1 98.181818 2.478228e-11
-#&gt; 197 M1 99.393939 -1.291838e-12
-#&gt; 198 M1 100.606061 2.366481e-11
-#&gt; 199 M1 101.818182 3.472871e-11
-#&gt; 200 M1 103.030303 -6.633877e-12
-#&gt; 201 M1 104.242424 1.248743e-11
-#&gt; 202 M1 105.454545 4.557313e-11
-#&gt; 203 M1 106.666667 -3.046261e-11
-#&gt; 204 M1 107.878788 -2.693037e-11
-#&gt; 205 M1 109.090909 7.816593e-11
-#&gt; 206 M1 110.303030 7.276098e-13
-#&gt; 207 M1 111.515152 -1.922924e-12
-#&gt; 208 M1 112.727273 1.658481e-11
-#&gt; 209 M1 113.939394 -1.858452e-11
-#&gt; 210 M1 115.151515 -2.368198e-12
-#&gt; 211 M1 116.363636 -1.138989e-12
-#&gt; 212 M1 117.575758 -2.157011e-12
-#&gt; 213 M1 118.787879 1.771568e-12
-#&gt; 214 M1 120.000000 3.624738e-11
-#&gt; 215 M2 0.000000 0.000000e+00
-#&gt; 216 M2 1.000000 4.454830e+00
-#&gt; 217 M2 1.212121 6.103803e+00
-#&gt; 218 M2 2.424242 1.667567e+01
-#&gt; 219 M2 3.000000 2.152527e+01
-#&gt; 220 M2 3.636364 2.637280e+01
-#&gt; 221 M2 4.848485 3.384106e+01
-#&gt; 222 M2 6.060606 3.910279e+01
-#&gt; 223 M2 7.000000 4.192058e+01
-#&gt; 224 M2 7.272727 4.256708e+01
-#&gt; 225 M2 8.484848 4.467909e+01
-#&gt; 226 M2 9.696970 4.581396e+01
-#&gt; 227 M2 10.909091 4.625927e+01
-#&gt; 228 M2 12.121212 4.622588e+01
-#&gt; 229 M2 13.333333 4.586473e+01
-#&gt; 230 M2 14.000000 4.556646e+01
-#&gt; 231 M2 14.545455 4.528249e+01
-#&gt; 232 M2 15.757576 4.455394e+01
-#&gt; 233 M2 16.969697 4.373119e+01
-#&gt; 234 M2 18.181818 4.285048e+01
-#&gt; 235 M2 19.393939 4.193685e+01
-#&gt; 236 M2 20.606061 4.100759e+01
-#&gt; 237 M2 21.818182 4.007456e+01
-#&gt; 238 M2 23.030303 3.914584e+01
-#&gt; 239 M2 24.242424 3.822688e+01
-#&gt; 240 M2 25.454545 3.732133e+01
-#&gt; 241 M2 26.666667 3.643154e+01
-#&gt; 242 M2 27.878788 3.555901e+01
-#&gt; 243 M2 28.000000 3.547275e+01
-#&gt; 244 M2 29.090909 3.470463e+01
-#&gt; 245 M2 30.303030 3.386887e+01
-#&gt; 246 M2 31.515152 3.305190e+01
-#&gt; 247 M2 32.727273 3.225371e+01
-#&gt; 248 M2 33.939394 3.147416e+01
-#&gt; 249 M2 35.151515 3.071300e+01
-#&gt; 250 M2 36.363636 2.996993e+01
-#&gt; 251 M2 37.575758 2.924463e+01
-#&gt; 252 M2 38.787879 2.853672e+01
-#&gt; 253 M2 40.000000 2.784585e+01
-#&gt; 254 M2 41.212121 2.717163e+01
-#&gt; 255 M2 42.424242 2.651368e+01
-#&gt; 256 M2 43.636364 2.587163e+01
-#&gt; 257 M2 44.848485 2.524511e+01
-#&gt; 258 M2 46.060606 2.463374e+01
-#&gt; 259 M2 47.272727 2.403716e+01
-#&gt; 260 M2 48.484848 2.345502e+01
-#&gt; 261 M2 49.696970 2.288698e+01
-#&gt; 262 M2 50.909091 2.233268e+01
-#&gt; 263 M2 52.121212 2.179181e+01
-#&gt; 264 M2 53.333333 2.126404e+01
-#&gt; 265 M2 54.545455 2.074905e+01
-#&gt; 266 M2 55.757576 2.024653e+01
-#&gt; 267 M2 56.969697 1.975618e+01
-#&gt; 268 M2 58.181818 1.927770e+01
-#&gt; 269 M2 59.393939 1.881081e+01
-#&gt; 270 M2 60.000000 1.858163e+01
-#&gt; 271 M2 60.606061 1.835523e+01
-#&gt; 272 M2 61.818182 1.791068e+01
-#&gt; 273 M2 63.030303 1.747690e+01
-#&gt; 274 M2 64.242424 1.705363e+01
-#&gt; 275 M2 65.454545 1.664061e+01
-#&gt; 276 M2 66.666667 1.623759e+01
-#&gt; 277 M2 67.878788 1.584433e+01
-#&gt; 278 M2 69.090909 1.546059e+01
-#&gt; 279 M2 70.303030 1.508615e+01
-#&gt; 280 M2 71.515152 1.472078e+01
-#&gt; 281 M2 72.727273 1.436425e+01
-#&gt; 282 M2 73.939394 1.401636e+01
-#&gt; 283 M2 75.151515 1.367690e+01
-#&gt; 284 M2 76.363636 1.334566e+01
-#&gt; 285 M2 77.575758 1.302244e+01
-#&gt; 286 M2 78.787879 1.270705e+01
-#&gt; 287 M2 80.000000 1.239929e+01
-#&gt; 288 M2 81.212121 1.209899e+01
-#&gt; 289 M2 82.424242 1.180597e+01
-#&gt; 290 M2 83.636364 1.152004e+01
-#&gt; 291 M2 84.848485 1.124103e+01
-#&gt; 292 M2 86.060606 1.096878e+01
-#&gt; 293 M2 87.272727 1.070313e+01
-#&gt; 294 M2 88.484848 1.044391e+01
-#&gt; 295 M2 89.696970 1.019097e+01
-#&gt; 296 M2 90.000000 1.012869e+01
-#&gt; 297 M2 90.909091 9.944151e+00
-#&gt; 298 M2 92.121212 9.703312e+00
-#&gt; 299 M2 93.333333 9.468307e+00
-#&gt; 300 M2 94.545455 9.238993e+00
-#&gt; 301 M2 95.757576 9.015233e+00
-#&gt; 302 M2 96.969697 8.796892e+00
-#&gt; 303 M2 98.181818 8.583839e+00
-#&gt; 304 M2 99.393939 8.375946e+00
-#&gt; 305 M2 100.606061 8.173088e+00
-#&gt; 306 M2 101.818182 7.975143e+00
-#&gt; 307 M2 103.030303 7.781992e+00
-#&gt; 308 M2 104.242424 7.593520e+00
-#&gt; 309 M2 105.454545 7.409611e+00
-#&gt; 310 M2 106.666667 7.230157e+00
-#&gt; 311 M2 107.878788 7.055049e+00
-#&gt; 312 M2 109.090909 6.884182e+00
-#&gt; 313 M2 110.303030 6.717454e+00
-#&gt; 314 M2 111.515152 6.554763e+00
-#&gt; 315 M2 112.727273 6.396012e+00
-#&gt; 316 M2 113.939394 6.241107e+00
-#&gt; 317 M2 115.151515 6.089953e+00
-#&gt; 318 M2 116.363636 5.942460e+00
-#&gt; 319 M2 117.575758 5.798538e+00
-#&gt; 320 M2 118.787879 5.658103e+00
-#&gt; 321 M2 120.000000 5.521069e+00
-#&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: 0x3ff8420&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: 0x3ff8420&gt;
-#&gt;
-#&gt; $hessian_notrans
-#&gt; parent_0 k_parent k_M1 k_M2 f_parent_to_M1
-#&gt; parent_0 8.433594 -40.12785 -61.53042 -3406.469 461.2995
-#&gt; k_parent -40.127847 19322.43697 3053.54654 3740.691 8966.4055
-#&gt; k_M1 -61.530424 3053.54654 70106.05907 7274.316 -8169.6841
-#&gt; k_M2 -3406.468786 3740.69112 7274.31610 12274341.595 -452294.7998
-#&gt; f_parent_to_M1 461.299501 8966.40549 -8169.68407 -452294.800 61249.1755
-#&gt; f_M1_to_M2 327.648696 2884.22668 17504.38651 -480941.198 43503.6440
-#&gt; f_M1_to_M2
-#&gt; parent_0 327.6487
-#&gt; k_parent 2884.2267
-#&gt; k_M1 17504.3865
-#&gt; k_M2 -480941.1983
-#&gt; f_parent_to_M1 43503.6440
-#&gt; f_M1_to_M2 46258.9775
-#&gt;
-#&gt; $start
+#&gt; Starting values for parameters to be optimised:
#&gt; value type
#&gt; parent_0 101.3500 state
#&gt; k_parent 0.1000 deparm
@@ -861,7 +163,7 @@
#&gt; f_parent_to_M1 0.5000 deparm
#&gt; f_M1_to_M2 0.5000 deparm
#&gt;
-#&gt; $start_transformed
+#&gt; Starting values for the transformed parameters actually optimised:
#&gt; value lower upper
#&gt; parent_0 101.350000 -Inf Inf
#&gt; log_k_parent -2.302585 -Inf Inf
@@ -870,106 +172,126 @@
#&gt; f_parent_ilr_1 0.000000 -Inf Inf
#&gt; f_M1_ilr_1 0.000000 -Inf Inf
#&gt;
-#&gt; $fixed
+#&gt; Fixed parameter values:
#&gt; value type
#&gt; M1_0 0 state
#&gt; M2_0 0 state
#&gt;
-#&gt; $data
-#&gt; time variable observed predicted residual
-#&gt; 1 0 parent 101.5 1.020625e+02 -0.56248353
-#&gt; 2 0 parent 101.2 1.020625e+02 -0.86248353
-#&gt; 3 1 parent 53.9 4.872881e+01 5.17118695
-#&gt; 4 1 parent 47.5 4.872881e+01 -1.22881305
-#&gt; 5 3 parent 10.4 1.110773e+01 -0.70772795
-#&gt; 6 3 parent 7.6 1.110773e+01 -3.50772795
-#&gt; 7 7 parent 1.1 5.771704e-01 0.52282962
-#&gt; 8 7 parent 0.3 5.771704e-01 -0.27717038
-#&gt; 9 14 parent NA 3.263939e-03 NA
-#&gt; 10 14 parent 3.5 3.263939e-03 3.49673606
-#&gt; 11 28 parent NA 1.044512e-07 NA
-#&gt; 12 28 parent 3.2 1.044512e-07 3.19999990
-#&gt; 13 60 parent NA -1.053819e-10 NA
-#&gt; 14 60 parent NA -1.053819e-10 NA
-#&gt; 15 90 parent 0.6 -1.874889e-11 0.60000000
-#&gt; 16 90 parent NA -1.874889e-11 NA
-#&gt; 17 120 parent NA -2.804801e-11 NA
-#&gt; 18 120 parent 3.5 -2.804801e-11 3.50000000
-#&gt; 19 0 M1 NA 0.000000e+00 NA
-#&gt; 20 0 M1 NA 0.000000e+00 NA
-#&gt; 21 1 M1 36.4 3.478911e+01 1.61088639
-#&gt; 22 1 M1 37.4 3.478911e+01 2.61088639
-#&gt; 23 3 M1 34.3 3.937027e+01 -5.07026619
-#&gt; 24 3 M1 39.8 3.937027e+01 0.42973381
-#&gt; 25 7 M1 15.1 1.548714e+01 -0.38714436
-#&gt; 26 7 M1 17.8 1.548714e+01 2.31285564
-#&gt; 27 14 M1 5.8 1.995311e+00 3.80468869
-#&gt; 28 14 M1 1.2 1.995311e+00 -0.79531131
-#&gt; 29 28 M1 NA 3.034005e-02 NA
-#&gt; 30 28 M1 NA 3.034005e-02 NA
-#&gt; 31 60 M1 0.5 2.110651e-06 0.49999789
-#&gt; 32 60 M1 NA 2.110651e-06 NA
-#&gt; 33 90 M1 NA 2.913252e-10 NA
-#&gt; 34 90 M1 3.2 2.913252e-10 3.20000000
-#&gt; 35 120 M1 1.5 3.624738e-11 1.50000000
-#&gt; 36 120 M1 0.6 3.624738e-11 0.60000000
-#&gt; 37 0 M2 NA 0.000000e+00 NA
-#&gt; 38 0 M2 NA 0.000000e+00 NA
-#&gt; 39 1 M2 NA 4.454830e+00 NA
-#&gt; 40 1 M2 4.8 4.454830e+00 0.34517017
-#&gt; 41 3 M2 20.9 2.152527e+01 -0.62526794
-#&gt; 42 3 M2 19.3 2.152527e+01 -2.22526794
-#&gt; 43 7 M2 42.0 4.192058e+01 0.07941701
-#&gt; 44 7 M2 43.1 4.192058e+01 1.17941701
-#&gt; 45 14 M2 49.4 4.556646e+01 3.83353798
-#&gt; 46 14 M2 44.3 4.556646e+01 -1.26646202
-#&gt; 47 28 M2 34.6 3.547275e+01 -0.87274743
-#&gt; 48 28 M2 33.0 3.547275e+01 -2.47274743
-#&gt; 49 60 M2 18.8 1.858163e+01 0.21837410
-#&gt; 50 60 M2 17.6 1.858163e+01 -0.98162590
-#&gt; 51 90 M2 10.6 1.012869e+01 0.47130583
-#&gt; 52 90 M2 10.8 1.012869e+01 0.67130583
-#&gt; 53 120 M2 9.8 5.521069e+00 4.27893112
-#&gt; 54 120 M2 3.3 5.521069e+00 -2.22106888
-#&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 k_M1 k_M2 f_parent_to_M1
-#&gt; 102.0624835 0.7393147 0.2991566 0.0202267 0.7686858
-#&gt; f_M1_to_M2
-#&gt; 0.7229005
-#&gt;
-#&gt; $bparms.fixed
-#&gt; M1_0 M2_0
-#&gt; 0 0
-#&gt;
-#&gt; $bparms.ode
-#&gt; k_parent f_parent_to_M1 k_M1 f_M1_to_M2 k_M2
-#&gt; 0.7393147 0.7686858 0.2991566 0.7229005 0.0202267
-#&gt;
-#&gt; $bparms.state
-#&gt; parent M1 M2
-#&gt; 102.0625 0.0000 0.0000
-#&gt;
-#&gt; $date
-#&gt; [1] &quot;Fri Nov 18 15:20:48 2016&quot;
-#&gt;
-#&gt; attr(,&quot;class&quot;)
-#&gt; [1] &quot;mkinfit&quot; &quot;modFit&quot; </div><div class='input'>
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 102.1000 1.71400 98.5800 105.5000
+#&gt; log_k_parent -0.3020 0.04294 -0.3894 -0.2147
+#&gt; log_k_M1 -1.2070 0.07599 -1.3610 -1.0520
+#&gt; log_k_M2 -3.9010 0.06952 -4.0420 -3.7590
+#&gt; f_parent_ilr_1 0.8492 0.18090 0.4812 1.2170
+#&gt; f_M1_ilr_1 0.6780 0.18860 0.2943 1.0620
+#&gt;
+#&gt; Parameter correlation:
+#&gt; parent_0 log_k_parent log_k_M1 log_k_M2 f_parent_ilr_1
+#&gt; parent_0 1.00000 0.40213 -0.1693 0.02912 -0.4726
+#&gt; log_k_parent 0.40213 1.00000 -0.4210 0.07241 -0.5837
+#&gt; log_k_M1 -0.16931 -0.42102 1.0000 -0.37657 0.7438
+#&gt; log_k_M2 0.02912 0.07241 -0.3766 1.00000 -0.2518
+#&gt; f_parent_ilr_1 -0.47263 -0.58367 0.7438 -0.25177 1.0000
+#&gt; f_M1_ilr_1 0.17148 0.42642 -0.8054 0.52648 -0.8602
+#&gt; f_M1_ilr_1
+#&gt; parent_0 0.1715
+#&gt; log_k_parent 0.4264
+#&gt; log_k_M1 -0.8054
+#&gt; log_k_M2 0.5265
+#&gt; f_parent_ilr_1 -0.8602
+#&gt; f_M1_ilr_1 1.0000
+#&gt;
+#&gt; Residual standard error: 2.471 on 33 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 102.10000 59.55 1.815e-35 98.58000 105.5000
+#&gt; k_parent 0.73930 23.29 2.337e-22 0.67750 0.8068
+#&gt; k_M1 0.29920 13.16 5.552e-15 0.25630 0.3492
+#&gt; k_M2 0.02023 14.38 4.497e-16 0.01756 0.0233
+#&gt; f_parent_to_M1 0.76870 16.90 4.093e-18 0.66380 0.8483
+#&gt; f_M1_to_M2 0.72290 13.53 2.557e-15 0.60260 0.8178
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 8.454 6 17
+#&gt; parent 8.660 2 6
+#&gt; M1 10.583 2 5
+#&gt; M2 3.586 2 6
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; parent_M1 0.7687
+#&gt; parent_sink 0.2313
+#&gt; M1_M2 0.7229
+#&gt; M1_sink 0.2771
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; parent 0.9376 3.114
+#&gt; M1 2.3170 7.697
+#&gt; M2 34.2689 113.839
+#&gt;
+#&gt; Data:
+#&gt; time variable observed predicted residual
+#&gt; 0 parent 101.5 1.021e+02 -0.56248
+#&gt; 0 parent 101.2 1.021e+02 -0.86248
+#&gt; 1 parent 53.9 4.873e+01 5.17119
+#&gt; 1 parent 47.5 4.873e+01 -1.22881
+#&gt; 3 parent 10.4 1.111e+01 -0.70773
+#&gt; 3 parent 7.6 1.111e+01 -3.50773
+#&gt; 7 parent 1.1 5.772e-01 0.52283
+#&gt; 7 parent 0.3 5.772e-01 -0.27717
+#&gt; 14 parent NA 3.264e-03 NA
+#&gt; 14 parent 3.5 3.264e-03 3.49674
+#&gt; 28 parent NA 1.045e-07 NA
+#&gt; 28 parent 3.2 1.045e-07 3.20000
+#&gt; 60 parent NA -1.054e-10 NA
+#&gt; 60 parent NA -1.054e-10 NA
+#&gt; 90 parent 0.6 -1.875e-11 0.60000
+#&gt; 90 parent NA -1.875e-11 NA
+#&gt; 120 parent NA -2.805e-11 NA
+#&gt; 120 parent 3.5 -2.805e-11 3.50000
+#&gt; 0 M1 NA 0.000e+00 NA
+#&gt; 0 M1 NA 0.000e+00 NA
+#&gt; 1 M1 36.4 3.479e+01 1.61089
+#&gt; 1 M1 37.4 3.479e+01 2.61089
+#&gt; 3 M1 34.3 3.937e+01 -5.07027
+#&gt; 3 M1 39.8 3.937e+01 0.42973
+#&gt; 7 M1 15.1 1.549e+01 -0.38714
+#&gt; 7 M1 17.8 1.549e+01 2.31286
+#&gt; 14 M1 5.8 1.995e+00 3.80469
+#&gt; 14 M1 1.2 1.995e+00 -0.79531
+#&gt; 28 M1 NA 3.034e-02 NA
+#&gt; 28 M1 NA 3.034e-02 NA
+#&gt; 60 M1 0.5 2.111e-06 0.50000
+#&gt; 60 M1 NA 2.111e-06 NA
+#&gt; 90 M1 NA 2.913e-10 NA
+#&gt; 90 M1 3.2 2.913e-10 3.20000
+#&gt; 120 M1 1.5 3.625e-11 1.50000
+#&gt; 120 M1 0.6 3.625e-11 0.60000
+#&gt; 0 M2 NA 0.000e+00 NA
+#&gt; 0 M2 NA 0.000e+00 NA
+#&gt; 1 M2 NA 4.455e+00 NA
+#&gt; 1 M2 4.8 4.455e+00 0.34517
+#&gt; 3 M2 20.9 2.153e+01 -0.62527
+#&gt; 3 M2 19.3 2.153e+01 -2.22527
+#&gt; 7 M2 42.0 4.192e+01 0.07942
+#&gt; 7 M2 43.1 4.192e+01 1.17942
+#&gt; 14 M2 49.4 4.557e+01 3.83354
+#&gt; 14 M2 44.3 4.557e+01 -1.26646
+#&gt; 28 M2 34.6 3.547e+01 -0.87275
+#&gt; 28 M2 33.0 3.547e+01 -2.47275
+#&gt; 60 M2 18.8 1.858e+01 0.21837
+#&gt; 60 M2 17.6 1.858e+01 -0.98163
+#&gt; 90 M2 10.6 1.013e+01 0.47131
+#&gt; 90 M2 10.8 1.013e+01 0.67131
+#&gt; 120 M2 9.8 5.521e+00 4.27893
+#&gt; 120 M2 3.3 5.521e+00 -2.22107</div><div class='input'>
</div></pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
diff --git a/docs/reference/synthetic_data_for_UBA_2014-10.png b/docs/reference/synthetic_data_for_UBA_2014-10.png
new file mode 100644
index 00000000..b98940ff
--- /dev/null
+++ b/docs/reference/synthetic_data_for_UBA_2014-10.png
Binary files differ
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 08fbf368..2aff0468 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -149,8 +149,8 @@
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_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='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 18 15:20:49 2016
-#&gt; Date of summary: Fri Nov 18 15:20:49 2016
+#&gt; Date of fit: Fri Nov 18 16:24:02 2016
+#&gt; Date of summary: Fri Nov 18 16:24:02 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -158,7 +158,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 153 model solutions performed in 0.681 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.708 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -223,148 +223,11 @@
#&gt; parent 7.023 23.33
#&gt; m1 131.761 437.70</div><div class='input'>
-<span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 18915.53
-#&gt; Model cost at call 2 : 18915.53
-#&gt; Model cost at call 7 : 10205.88
-#&gt; Model cost at call 10 : 10205.05
-#&gt; Model cost at call 13 : 8136.609
-#&gt; Model cost at call 18 : 2504.352
-#&gt; Model cost at call 20 : 2504.35
-#&gt; Model cost at call 22 : 2504.285
-#&gt; Model cost at call 25 : 1747.542
-#&gt; Model cost at call 27 : 1745.941
-#&gt; Model cost at call 29 : 1745.431
-#&gt; Model cost at call 30 : 1341.034
-#&gt; Model cost at call 34 : 1341.034
-#&gt; Model cost at call 35 : 1032.65
-#&gt; Model cost at call 39 : 1032.649
-#&gt; Model cost at call 40 : 919.9522
-#&gt; Model cost at call 42 : 919.952
-#&gt; Model cost at call 44 : 919.9518
-#&gt; Model cost at call 45 : 903.8272
-#&gt; Model cost at call 47 : 903.827
-#&gt; Model cost at call 49 : 903.8268
-#&gt; Model cost at call 50 : 780.8699
-#&gt; Model cost at call 52 : 780.8698
-#&gt; Model cost at call 54 : 780.8697
-#&gt; Model cost at call 55 : 734.3043
-#&gt; Model cost at call 57 : 734.3036
-#&gt; Model cost at call 60 : 717.8438
-#&gt; Model cost at call 67 : 676.3908
-#&gt; Model cost at call 68 : 676.3907
-#&gt; Model cost at call 69 : 676.3906
-#&gt; Model cost at call 71 : 676.3885
-#&gt; Model cost at call 72 : 642.2738
-#&gt; Model cost at call 73 : 642.2738
-#&gt; Model cost at call 76 : 642.2738
-#&gt; Model cost at call 77 : 604.7128
-#&gt; Model cost at call 78 : 604.7126
-#&gt; Model cost at call 82 : 560.1285
-#&gt; Model cost at call 83 : 560.1285
-#&gt; Model cost at call 86 : 560.1285
-#&gt; Model cost at call 87 : 521.6932
-#&gt; Model cost at call 88 : 521.6932
-#&gt; Model cost at call 91 : 521.6931
-#&gt; Model cost at call 92 : 453.6483
-#&gt; Model cost at call 93 : 453.6483
-#&gt; Model cost at call 96 : 453.6483
-#&gt; Model cost at call 98 : 422.5498
-#&gt; Model cost at call 102 : 422.5497
-#&gt; Model cost at call 106 : 413.6426
-#&gt; Model cost at call 108 : 413.6416
-#&gt; Model cost at call 111 : 407.4639
-#&gt; Model cost at call 113 : 407.4639
-#&gt; Model cost at call 115 : 407.4639
-#&gt; Model cost at call 116 : 403.6974
-#&gt; Model cost at call 118 : 403.6973
-#&gt; Model cost at call 120 : 403.6973
-#&gt; Model cost at call 121 : 396.004
-#&gt; Model cost at call 123 : 396.004
-#&gt; Model cost at call 126 : 391.2533
-#&gt; Model cost at call 128 : 391.2533
-#&gt; Model cost at call 130 : 391.2533
-#&gt; Model cost at call 131 : 388.4056
-#&gt; Model cost at call 133 : 388.4056
-#&gt; Model cost at call 135 : 388.4055
-#&gt; Model cost at call 137 : 384.0739
-#&gt; Model cost at call 139 : 384.0734
-#&gt; Model cost at call 143 : 383.6352
-#&gt; Model cost at call 145 : 383.635
-#&gt; Model cost at call 148 : 381.1342
-#&gt; Model cost at call 152 : 381.1342
-#&gt; Model cost at call 153 : 380.1443
-#&gt; Model cost at call 157 : 380.1443
-#&gt; Model cost at call 158 : 378.5615
-#&gt; Model cost at call 162 : 378.5614
-#&gt; Model cost at call 164 : 378.4583
-#&gt; Model cost at call 168 : 378.4583
-#&gt; Model cost at call 169 : 377.7047
-#&gt; Model cost at call 173 : 377.7047
-#&gt; Model cost at call 175 : 377.7042
-#&gt; Model cost at call 178 : 377.7042
-#&gt; Model cost at call 179 : 377.7042
-#&gt; Model cost at call 180 : 377.1553
-#&gt; Model cost at call 182 : 377.1553
-#&gt; Model cost at call 183 : 377.1553
-#&gt; Model cost at call 185 : 377.0866
-#&gt; Model cost at call 187 : 377.0866
-#&gt; Model cost at call 190 : 377.0288
-#&gt; Model cost at call 194 : 377.0288
-#&gt; Model cost at call 196 : 376.9814
-#&gt; Model cost at call 200 : 376.9814
-#&gt; Model cost at call 201 : 376.9488
-#&gt; Model cost at call 203 : 376.9488
-#&gt; Model cost at call 205 : 376.9488
-#&gt; Model cost at call 206 : 376.9184
-#&gt; Model cost at call 208 : 376.9184
-#&gt; Model cost at call 211 : 376.9095
-#&gt; Model cost at call 213 : 376.9095
-#&gt; Model cost at call 215 : 376.9095
-#&gt; Model cost at call 216 : 376.901
-#&gt; Model cost at call 218 : 376.901
-#&gt; Model cost at call 221 : 376.8936
-#&gt; Model cost at call 225 : 376.8936
-#&gt; Model cost at call 226 : 376.8848
-#&gt; Model cost at call 227 : 376.8608
-#&gt; Model cost at call 228 : 376.7665
-#&gt; Model cost at call 229 : 376.4162
-#&gt; Model cost at call 230 : 375.4439
-#&gt; Model cost at call 235 : 375.4439
-#&gt; Model cost at call 237 : 375.2281
-#&gt; Model cost at call 241 : 375.2281
-#&gt; Model cost at call 242 : 374.3381
-#&gt; Model cost at call 244 : 374.3381
-#&gt; Model cost at call 251 : 374.2632
-#&gt; Model cost at call 253 : 374.2632
-#&gt; Model cost at call 256 : 374.2391
-#&gt; Model cost at call 257 : 374.2247
-#&gt; Model cost at call 259 : 374.2247
-#&gt; Model cost at call 261 : 374.2247
-#&gt; Model cost at call 263 : 374.2024
-#&gt; Model cost at call 266 : 374.2024
-#&gt; Model cost at call 270 : 374.1952
-#&gt; Model cost at call 274 : 374.1952
-#&gt; Model cost at call 275 : 374.186
-#&gt; Model cost at call 279 : 374.186
-#&gt; Model cost at call 280 : 374.1724
-#&gt; Model cost at call 281 : 374.156
-#&gt; Model cost at call 282 : 374.0763
-#&gt; Model cost at call 283 : 373.7692
-#&gt; Model cost at call 284 : 372.729
-#&gt; Model cost at call 285 : 371.4251
-#&gt; Model cost at call 287 : 371.4251
-#&gt; Model cost at call 290 : 371.2142
-#&gt; Model cost at call 291 : 371.2142
-#&gt; Model cost at call 292 : 371.2142
-#&gt; Model cost at call 295 : 371.2134
-#&gt; Model cost at call 298 : 371.2134
-#&gt; Model cost at call 300 : 371.2134
-#&gt; Model cost at call 309 : 371.2134
-#&gt; Model cost at call 320 : 371.2134
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+<span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 18 15:20:51 2016
-#&gt; Date of summary: Fri Nov 18 15:20:51 2016
+#&gt; Date of fit: Fri Nov 18 16:24:03 2016
+#&gt; Date of summary: Fri Nov 18 16:24:03 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -372,7 +235,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 327 model solutions performed in 1.34 s
+#&gt; Fitted with method Port using 327 model solutions performed in 1.341 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -450,85 +313,11 @@
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
<span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-<span class='no'>fit.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 15156.12
-#&gt; Model cost at call 2 : 15156.12
-#&gt; Model cost at call 6 : 8243.644
-#&gt; Model cost at call 12 : 6290.714
-#&gt; Model cost at call 13 : 6290.684
-#&gt; Model cost at call 15 : 6290.453
-#&gt; Model cost at call 18 : 1700.75
-#&gt; Model cost at call 20 : 1700.612
-#&gt; Model cost at call 24 : 1190.923
-#&gt; Model cost at call 26 : 1190.922
-#&gt; Model cost at call 29 : 1017.417
-#&gt; Model cost at call 31 : 1017.417
-#&gt; Model cost at call 33 : 1017.416
-#&gt; Model cost at call 34 : 644.0471
-#&gt; Model cost at call 36 : 644.0469
-#&gt; Model cost at call 38 : 644.0468
-#&gt; Model cost at call 39 : 590.5024
-#&gt; Model cost at call 41 : 590.5021
-#&gt; Model cost at call 43 : 590.5015
-#&gt; Model cost at call 44 : 543.2187
-#&gt; Model cost at call 45 : 543.2183
-#&gt; Model cost at call 46 : 543.2182
-#&gt; Model cost at call 50 : 391.348
-#&gt; Model cost at call 51 : 391.3479
-#&gt; Model cost at call 56 : 386.4789
-#&gt; Model cost at call 58 : 386.4789
-#&gt; Model cost at call 60 : 386.4779
-#&gt; Model cost at call 61 : 384.0686
-#&gt; Model cost at call 63 : 384.0686
-#&gt; Model cost at call 66 : 382.7812
-#&gt; Model cost at call 68 : 382.7812
-#&gt; Model cost at call 70 : 382.7812
-#&gt; Model cost at call 71 : 378.9272
-#&gt; Model cost at call 73 : 378.9272
-#&gt; Model cost at call 75 : 378.9272
-#&gt; Model cost at call 76 : 377.4846
-#&gt; Model cost at call 78 : 377.4846
-#&gt; Model cost at call 81 : 375.9738
-#&gt; Model cost at call 83 : 375.9738
-#&gt; Model cost at call 86 : 375.3387
-#&gt; Model cost at call 88 : 375.3387
-#&gt; Model cost at call 91 : 374.5774
-#&gt; Model cost at call 93 : 374.5774
-#&gt; Model cost at call 95 : 374.5774
-#&gt; Model cost at call 96 : 373.5447
-#&gt; Model cost at call 100 : 373.5446
-#&gt; Model cost at call 102 : 373.2643
-#&gt; Model cost at call 104 : 373.2643
-#&gt; Model cost at call 107 : 372.6799
-#&gt; Model cost at call 111 : 372.6798
-#&gt; Model cost at call 114 : 372.6325
-#&gt; Model cost at call 116 : 372.6325
-#&gt; Model cost at call 119 : 372.6159
-#&gt; Model cost at call 121 : 372.6159
-#&gt; Model cost at call 123 : 372.6159
-#&gt; Model cost at call 124 : 372.5845
-#&gt; Model cost at call 126 : 372.5845
-#&gt; Model cost at call 129 : 372.5375
-#&gt; Model cost at call 130 : 372.4771
-#&gt; Model cost at call 131 : 372.2008
-#&gt; Model cost at call 132 : 371.4923
-#&gt; Model cost at call 134 : 371.4923
-#&gt; Model cost at call 137 : 371.3022
-#&gt; Model cost at call 139 : 371.3022
-#&gt; Model cost at call 143 : 371.2271
-#&gt; Model cost at call 144 : 371.2271
-#&gt; Model cost at call 148 : 371.2202
-#&gt; Model cost at call 149 : 371.215
-#&gt; Model cost at call 152 : 371.215
-#&gt; Model cost at call 154 : 371.2136
-#&gt; Model cost at call 155 : 371.2136
-#&gt; Model cost at call 156 : 371.2136
-#&gt; Model cost at call 160 : 371.2134
-#&gt; Model cost at call 164 : 371.2134
-#&gt; Model cost at call 167 : 371.2134
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+<span class='no'>fit.ff</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'>summary</span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 18 15:20:52 2016
-#&gt; Date of summary: Fri Nov 18 15:20:52 2016
+#&gt; Date of fit: Fri Nov 18 16:24:04 2016
+#&gt; Date of summary: Fri Nov 18 16:24:04 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -536,7 +325,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 185 model solutions performed in 0.764 s
+#&gt; Fitted with method Port using 185 model solutions performed in 0.756 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -608,61 +397,11 @@
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>),
<span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
-<span class='no'>fit.ff.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.2</span>, <span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 12435.14
-#&gt; Model cost at call 2 : 12435.14
-#&gt; Model cost at call 5 : 8276.306
-#&gt; Model cost at call 6 : 8276.294
-#&gt; Model cost at call 7 : 8275.676
-#&gt; Model cost at call 9 : 5256.953
-#&gt; Model cost at call 11 : 5256.951
-#&gt; Model cost at call 12 : 5256.943
-#&gt; Model cost at call 14 : 4469.745
-#&gt; Model cost at call 18 : 4462.927
-#&gt; Model cost at call 21 : 4462.925
-#&gt; Model cost at call 22 : 4376.059
-#&gt; Model cost at call 24 : 4376.058
-#&gt; Model cost at call 27 : 4366.956
-#&gt; Model cost at call 29 : 4366.956
-#&gt; Model cost at call 31 : 4365.275
-#&gt; Model cost at call 33 : 4365.275
-#&gt; Model cost at call 35 : 4351.877
-#&gt; Model cost at call 37 : 4351.877
-#&gt; Model cost at call 39 : 4338.109
-#&gt; Model cost at call 41 : 4338.109
-#&gt; Model cost at call 43 : 4297.053
-#&gt; Model cost at call 44 : 4218.591
-#&gt; Model cost at call 45 : 3940.397
-#&gt; Model cost at call 46 : 3690.395
-#&gt; Model cost at call 48 : 3690.395
-#&gt; Model cost at call 49 : 3690.385
-#&gt; Model cost at call 50 : 3038.366
-#&gt; Model cost at call 53 : 3038.365
-#&gt; Model cost at call 54 : 2637.866
-#&gt; Model cost at call 57 : 2637.865
-#&gt; Model cost at call 59 : 2588.01
-#&gt; Model cost at call 60 : 2588.009
-#&gt; Model cost at call 63 : 2576.742
-#&gt; Model cost at call 66 : 2576.742
-#&gt; Model cost at call 67 : 2574
-#&gt; Model cost at call 68 : 2574
-#&gt; Model cost at call 69 : 2574
-#&gt; Model cost at call 71 : 2569.76
-#&gt; Model cost at call 73 : 2569.76
-#&gt; Model cost at call 74 : 2569.76
-#&gt; Model cost at call 75 : 2569.403
-#&gt; Model cost at call 76 : 2569.403
-#&gt; Model cost at call 79 : 2569.4
-#&gt; Model cost at call 80 : 2569.4
-#&gt; Model cost at call 81 : 2569.4
-#&gt; Model cost at call 83 : 2569.4
-#&gt; Model cost at call 86 : 2569.4
-#&gt; Model cost at call 90 : 2569.4
-#&gt; Model cost at call 99 : 2569.4
-#&gt; Model cost at call 100 : 2569.4
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>fit.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+<span class='no'>fit.ff.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'>summary</span>(<span class='no'>fit.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 18 15:20:52 2016
-#&gt; Date of summary: Fri Nov 18 15:20:52 2016
+#&gt; Date of fit: Fri Nov 18 16:24:05 2016
+#&gt; Date of summary: Fri Nov 18 16:24:05 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -670,7 +409,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 104 model solutions performed in 0.44 s
+#&gt; Fitted with method Port using 104 model solutions performed in 0.416 s
#&gt;
#&gt; Weighting: none
#&gt;

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