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authorJohannes Ranke <jranke@uni-bremen.de>2016-10-06 09:40:35 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2016-10-06 09:40:35 +0200
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tree57da1e788f84fe95352ff66d22a9da56dc86f9c3 /docs/Extract.mmkin.html
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-<!DOCTYPE html>
-<html lang="en">
- <head>
- <meta charset="utf-8">
-<title>[.mmkin. mkin 0.9.44.9000</title>
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-<meta name="author" content="
- Johannes Ranke
-">
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- <body>
- <div class="navbar">
- <div class="navbar-inner">
- <div class="container">
- <a class="brand" href="index.html">mkin 0.9.44.9000</a>
- <div class="nav">
- <ul class="nav">
- <li><a href="index.html">Home</a></li>
- <li><a href="reference.html">Reference</a></li>
- </ul>
- </div>
- </div>
- </div>
-</div>
-
-
- <div class="container">
- <header>
-
- </header>
-
- <h1>Subsetting method for mmkin objects</h1>
-
-<div class="row">
- <div class="span8">
- <h2>Usage</h2>
- <pre><div># S3 method for mmkin
-[(x, i, j, ..., drop&nbsp;=&nbsp;FALSE)</div></pre>
-
- <h2>Arguments</h2>
- <dl>
- <dt>x</dt>
- <dd>An <code><a href='mmkin.html'>mmkin</a> object</code></dd>
- <dt>i</dt>
- <dd>Row index selecting the fits for specific models</dd>
- <dt>j</dt>
- <dd>Column index selecting the fits to specific datasets</dd>
- <dt>...</dt>
- <dd>Not used, only there to satisfy the generic method definition</dd>
- <dt>drop</dt>
- <dd>If FALSE, the method always returns an mmkin object, otherwise either
- a list of mkinfit objects or a single mkinfit object.</dd>
- </dl>
-
- <div class="Description">
- <h2>Description</h2>
-
- <p>Subsetting method for mmkin objects.</p>
-
- </div>
-
- <div class="Value">
- <h2>Value</h2>
-
- <p><dl>
- An object of class <code><a href='mmkin.html'>mmkin</a></code>.
-</dl></p>
-
- </div>
-
- <h2 id="examples">Examples</h2>
- <pre class="examples"><div class='input'> <span class="comment"># Only use one core, to pass R CMD check --as-cran</span>
- <span class="symbol">fits</span> <span class="assignement">&lt;-</span> <span class="functioncall"><a href='mmkin.html'>mmkin</a></span><span class="keyword">(</span><span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/c'>c</a></span><span class="keyword">(</span><span class="string">"SFO"</span><span class="keyword">,</span> <span class="string">"FOMC"</span><span class="keyword">)</span><span class="keyword">,</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/list'>list</a></span><span class="keyword">(</span><span class="argument">B</span> <span class="argument">=</span> <span class="symbol">FOCUS_2006_B</span><span class="keyword">,</span> <span class="argument">C</span> <span class="argument">=</span> <span class="symbol">FOCUS_2006_C</span><span class="keyword">)</span><span class="keyword">,</span>
- <span class="argument">cores</span> <span class="argument">=</span> <span class="number">1</span><span class="keyword">,</span> <span class="argument">quiet</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">)</span>
- <span class="symbol">fits</span><span class="keyword">[</span><span class="string">"FOMC"</span><span class="keyword">,</span> <span class="keyword">]</span></div>
-<div class='output'> dataset
-model B C
- FOMC List,42 List,42
-attr(,&quot;class&quot;)
-[1] &quot;mmkin&quot;
-</div>
-<div class='input'> <span class="symbol">fits</span><span class="keyword">[</span><span class="keyword">,</span> <span class="string">"B"</span><span class="keyword">]</span></div>
-<div class='output'> dataset
-model B
- SFO List,42
- FOMC List,42
-attr(,&quot;class&quot;)
-[1] &quot;mmkin&quot;
-</div>
-<div class='input'> <span class="symbol">fits</span><span class="keyword">[</span><span class="keyword">,</span> <span class="string">"B"</span><span class="keyword">,</span> <span class="argument">drop</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">]</span><span class="keyword">$</span><span class="symbol">FOMC</span></div>
-<div class='output'>$par
- parent_0 log_alpha log_beta
-99.666193 2.549849 5.050586
-
-$ssr
-[1] 28.58291
-
-$convergence
-[1] 0
-
-$iterations
-[1] 21
-
-$evaluations
-function gradient
- 25 78
-
-$counts
-[1] &quot;both X-convergence and relative convergence (5)&quot;
-
-$hessian
- parent_0 log_alpha log_beta
-parent_0 4.123033 -95.69983 93.17699
-log_alpha -95.699832 6618.85833 -6352.46648
-log_beta 93.176993 -6352.46648 6101.23483
-
-$residuals
- parent parent parent parent parent parent
- 1.046192647 -3.322396479 3.655156669 -1.705316770 0.406306255 -0.123734689
- parent parent
--0.036886982 -0.006240458
-
-$ms
-[1] 3.572863
-
-$var_ms
- parent
-3.572863
-
-$var_ms_unscaled
- parent
-3.572863
-
-$var_ms_unweighted
- parent
-3.572863
-
-$rank
-[1] 3
-
-$df.residual
-[1] 5
-
-$solution_type
-[1] &quot;analytical&quot;
-
-$transform_rates
-[1] TRUE
-
-$transform_fractions
-[1] TRUE
-
-$method.modFit
-[1] &quot;Port&quot;
-
-$maxit.modFit
-[1] &quot;auto&quot;
-
-$calls
-[1] 111
-
-$time
- user system elapsed
- 0.276 0.000 0.277
-
-$mkinmod
-&lt;mkinmod&gt; model generated with
-Use of formation fractions $use_of_ff: min
-Specification $spec:
-$parent
-$type: FOMC; $sink: TRUE
-
-$observed
- name time value
-1 parent 0 98.62
-2 parent 3 81.43
-3 parent 7 53.18
-4 parent 14 34.89
-5 parent 30 10.09
-6 parent 62 1.50
-7 parent 90 0.33
-8 parent 118 0.08
-
-$obs_vars
-[1] &quot;parent&quot;
-
-$predicted
- name time value
-1 parent 0.000000 99.66619265
-2 parent 1.191919 90.41690342
-3 parent 2.383838 82.08630014
-4 parent 3.000000 78.10760352
-5 parent 3.575758 74.57722848
-6 parent 4.767677 67.80342415
-7 parent 5.959596 61.68822425
-8 parent 7.000000 56.83515667
-9 parent 7.151515 56.16343898
-10 parent 8.343434 51.16836285
-11 parent 9.535354 46.64890734
-12 parent 10.727273 42.55683931
-13 parent 11.919192 38.84911158
-14 parent 13.111111 35.48727414
-15 parent 14.000000 33.18468323
-16 parent 14.303030 32.43695565
-17 parent 15.494949 29.66740651
-18 parent 16.686869 27.15109578
-19 parent 17.878788 24.86335532
-20 parent 19.070707 22.78206538
-21 parent 20.262626 20.88737647
-22 parent 21.454545 19.16146324
-23 parent 22.646465 17.58830644
-24 parent 23.838384 16.15349953
-25 parent 25.030303 14.84407724
-26 parent 26.222222 13.64836315
-27 parent 27.414141 12.55583436
-28 parent 28.606061 11.55700107
-29 parent 29.797980 10.64329940
-30 parent 30.000000 10.49630626
-31 parent 30.989899 9.80699593
-32 parent 32.181818 9.04110261
-33 parent 33.373737 8.33930082
-34 parent 34.565657 7.69587362
-35 parent 35.757576 7.10564515
-36 parent 36.949495 6.56392657
-37 parent 38.141414 6.06646759
-38 parent 39.333333 5.60941311
-39 parent 40.525253 5.18926438
-40 parent 41.717172 4.80284421
-41 parent 42.909091 4.44726569
-42 parent 44.101010 4.11990420
-43 parent 45.292929 3.81837216
-44 parent 46.484848 3.54049644
-45 parent 47.676768 3.28429799
-46 parent 48.868687 3.04797350
-47 parent 50.060606 2.82987892
-48 parent 51.252525 2.62851456
-49 parent 52.444444 2.44251172
-50 parent 53.636364 2.27062056
-51 parent 54.828283 2.11169922
-52 parent 56.020202 1.96470393
-53 parent 57.212121 1.82868009
-54 parent 58.404040 1.70275424
-55 parent 59.595960 1.58612677
-56 parent 60.787879 1.47806529
-57 parent 61.979798 1.37789865
-58 parent 62.000000 1.37626531
-59 parent 63.171717 1.28501157
-60 parent 64.363636 1.19883967
-61 parent 65.555556 1.11886504
-62 parent 66.747475 1.04461220
-63 parent 67.939394 0.97564441
-64 parent 69.131313 0.91156031
-65 parent 70.323232 0.85199096
-66 parent 71.515152 0.79659697
-67 parent 72.707071 0.74506609
-68 parent 73.898990 0.69711084
-69 parent 75.090909 0.65246649
-70 parent 76.282828 0.61088912
-71 parent 77.474747 0.57215389
-72 parent 78.666667 0.53605348
-73 parent 79.858586 0.50239663
-74 parent 81.050505 0.47100683
-75 parent 82.242424 0.44172111
-76 parent 83.434343 0.41438896
-77 parent 84.626263 0.38887128
-78 parent 85.818182 0.36503953
-79 parent 87.010101 0.34277481
-80 parent 88.202020 0.32196716
-81 parent 89.393939 0.30251479
-82 parent 90.000000 0.29311302
-83 parent 90.585859 0.28432347
-84 parent 91.777778 0.26730596
-85 parent 92.969697 0.25138141
-86 parent 94.161616 0.23647487
-87 parent 95.353535 0.22251689
-88 parent 96.545455 0.20944302
-89 parent 97.737374 0.19719349
-90 parent 98.929293 0.18571281
-91 parent 100.121212 0.17494947
-92 parent 101.313131 0.16485560
-93 parent 102.505051 0.15538676
-94 parent 103.696970 0.14650163
-95 parent 104.888889 0.13816179
-96 parent 106.080808 0.13033150
-97 parent 107.272727 0.12297753
-98 parent 108.464646 0.11606895
-99 parent 109.656566 0.10957695
-100 parent 110.848485 0.10347470
-101 parent 112.040404 0.09773723
-102 parent 113.232323 0.09234125
-103 parent 114.424242 0.08726506
-104 parent 115.616162 0.08248842
-105 parent 116.808081 0.07799245
-106 parent 118.000000 0.07375954
-
-$cost
-function (P)
-{
- assign(&quot;calls&quot;, calls + 1, inherits = TRUE)
- if (trace_parms)
- cat(P, &quot;\n&quot;)
- if (length(state.ini.optim) &gt; 0) {
- odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
- names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
- }
- else {
- odeini &lt;- state.ini.fixed
- names(odeini) &lt;- state.ini.fixed.boxnames
- }
- odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)],
- transparms.fixed)
- parms &lt;- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates,
- transform_fractions = transform_fractions)
- out &lt;- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type,
- use_compiled = use_compiled, method.ode = method.ode,
- atol = atol, rtol = rtol, ...)
- assign(&quot;out_predicted&quot;, out, inherits = TRUE)
- mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight,
- scaleVar = scaleVar)
- if (mC$model &lt; cost.old) {
- if (!quiet)
- cat(&quot;Model cost at call &quot;, calls, &quot;: &quot;, mC$model,
- &quot;\n&quot;)
- if (plot) {
- outtimes_plot = seq(min(observed$time), max(observed$time),
- length.out = 100)
- out_plot &lt;- mkinpredict(mkinmod, parms, odeini, outtimes_plot,
- solution_type = solution_type, use_compiled = use_compiled,
- method.ode = method.ode, atol = atol, rtol = rtol,
- ...)
- plot(0, type = &quot;n&quot;, xlim = range(observed$time),
- ylim = c(0, max(observed$value, na.rm = TRUE)),
- xlab = &quot;Time&quot;, ylab = &quot;Observed&quot;)
- col_obs &lt;- pch_obs &lt;- 1:length(obs_vars)
- lty_obs &lt;- rep(1, length(obs_vars))
- names(col_obs) &lt;- names(pch_obs) &lt;- names(lty_obs) &lt;- obs_vars
- for (obs_var in obs_vars) {
- points(subset(observed, name == obs_var, c(time,
- value)), pch = pch_obs[obs_var], col = col_obs[obs_var])
- }
- matlines(out_plot$time, out_plot[-1], col = col_obs,
- lty = lty_obs)
- legend(&quot;topright&quot;, inset = c(0.05, 0.05), legend = obs_vars,
- col = col_obs, pch = pch_obs, lty = 1:length(pch_obs))
- }
- assign(&quot;cost.old&quot;, mC$model, inherits = TRUE)
- }
- return(mC)
-}
-&lt;environment: 0x44a0b88&gt;
-
-$cost_notrans
-function (P)
-{
- if (length(state.ini.optim) &gt; 0) {
- odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
- names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
- }
- else {
- odeini &lt;- state.ini.fixed
- names(odeini) &lt;- state.ini.fixed.boxnames
- }
- odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)],
- parms.fixed)
- out &lt;- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type,
- use_compiled = use_compiled, method.ode = method.ode,
- atol = atol, rtol = rtol, ...)
- mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight,
- scaleVar = scaleVar)
- return(mC)
-}
-&lt;environment: 0x44a0b88&gt;
-
-$hessian_notrans
- parent_0 alpha beta
-parent_0 4.1230329 -7.473531 0.5968527
-alpha -7.4735307 40.365690 -3.1777189
-beta 0.5968527 -3.177719 0.2503425
-
-$start
- value type
-parent_0 98.62 state
-alpha 1.00 deparm
-beta 10.00 deparm
-
-$start_transformed
- value lower upper
-parent_0 98.620000 -Inf Inf
-log_alpha 0.000000 -Inf Inf
-log_beta 2.302585 -Inf Inf
-
-$fixed
-[1] value type
-&lt;0 rows&gt; (or 0-length row.names)
-
-$data
- time variable observed predicted residual
-1 0 parent 98.62 99.66619265 -1.046192647
-2 3 parent 81.43 78.10760352 3.322396479
-3 7 parent 53.18 56.83515667 -3.655156669
-4 14 parent 34.89 33.18468323 1.705316770
-5 30 parent 10.09 10.49630626 -0.406306255
-6 62 parent 1.50 1.37626531 0.123734689
-7 90 parent 0.33 0.29311302 0.036886982
-8 118 parent 0.08 0.07375954 0.006240458
-
-$atol
-[1] 1e-08
-
-$rtol
-[1] 1e-10
-
-$weight.ini
-[1] &quot;none&quot;
-
-$reweight.tol
-[1] 1e-08
-
-$reweight.max.iter
-[1] 10
-
-$bparms.optim
- parent_0 alpha beta
- 99.66619 12.80517 156.11390
-
-$bparms.fixed
-numeric(0)
-
-$bparms.ode
- alpha beta
- 12.80517 156.11390
-
-$bparms.state
- parent
-99.66619
-
-$date
-[1] &quot;Sat Sep 10 05:52:53 2016&quot;
-
-attr(,&quot;class&quot;)
-[1] &quot;mkinfit&quot; &quot;modFit&quot;
-</div>
-<div class='input'> <span class="symbol">fits</span><span class="keyword">[</span><span class="string">"SFO"</span><span class="keyword">,</span> <span class="string">"B"</span><span class="keyword">]</span></div>
-<div class='output'> dataset
-model B
- SFO List,42
-attr(,&quot;class&quot;)
-[1] &quot;mmkin&quot;
-</div>
-<div class='input'> <span class="symbol">fits</span><span class="keyword">[[</span><span class="string">"SFO"</span><span class="keyword">,</span> <span class="string">"B"</span><span class="keyword">]</span><span class="keyword">]</span> <span class="comment"># This is equivalent to</span></div>
-<div class='output'>$par
- parent_0 log_k_parent_sink
- 99.174072 -2.549028
-
-$ssr
-[1] 30.65564
-
-$convergence
-[1] 0
-
-$iterations
-[1] 5
-
-$evaluations
-function gradient
- 8 15
-
-$counts
-[1] &quot;relative convergence (4)&quot;
-
-$hessian
- parent_0 log_k_parent_sink
-parent_0 4.163631 -94.09343
-log_k_parent_sink -94.093431 6311.34610
-
-$residuals
- parent parent parent parent parent parent
- 0.55407218 -2.98452128 4.20445742 -1.68599939 -0.58185357 -0.72033730
- parent parent
--0.24260405 -0.07020339
-
-$ms
-[1] 3.831956
-
-$var_ms
- parent
-3.831956
-
-$var_ms_unscaled
- parent
-3.831956
-
-$var_ms_unweighted
- parent
-3.831956
-
-$rank
-[1] 2
-
-$df.residual
-[1] 6
-
-$solution_type
-[1] &quot;analytical&quot;
-
-$transform_rates
-[1] TRUE
-
-$transform_fractions
-[1] TRUE
-
-$method.modFit
-[1] &quot;Port&quot;
-
-$maxit.modFit
-[1] &quot;auto&quot;
-
-$calls
-[1] 29
-
-$time
- user system elapsed
- 0.108 0.000 0.106
-
-$mkinmod
-&lt;mkinmod&gt; model generated with
-Use of formation fractions $use_of_ff: min
-Specification $spec:
-$parent
-$type: SFO; $sink: TRUE
-Coefficient matrix $coefmat available
-
-$observed
- name time value
-1 parent 0 98.62
-2 parent 3 81.43
-3 parent 7 53.18
-4 parent 14 34.89
-5 parent 30 10.09
-6 parent 62 1.50
-7 parent 90 0.33
-8 parent 118 0.08
-
-$obs_vars
-[1] &quot;parent&quot;
-
-$predicted
- name time value
-1 parent 0.000000 99.17407218
-2 parent 1.191919 90.35253561
-3 parent 2.383838 82.31567498
-4 parent 3.000000 78.44547872
-5 parent 3.575758 74.99369333
-6 parent 4.767677 68.32300215
-7 parent 5.959596 62.24566915
-8 parent 7.000000 57.38445742
-9 parent 7.151515 56.70891509
-10 parent 8.343434 51.66465547
-11 parent 9.535354 47.06908288
-12 parent 10.727273 42.88228661
-13 parent 11.919192 39.06790599
-14 parent 13.111111 35.59281463
-15 parent 14.000000 33.20400061
-16 parent 14.303030 32.42683275
-17 parent 15.494949 29.54246504
-18 parent 16.686869 26.91466193
-19 parent 17.878788 24.52060198
-20 parent 19.070707 22.33949373
-21 parent 20.262626 20.35239512
-22 parent 21.454545 18.54204899
-23 parent 22.646465 16.89273320
-24 parent 23.838384 15.39012410
-25 parent 25.030303 14.02117212
-26 parent 26.222222 12.77398846
-27 parent 27.414141 11.63774182
-28 parent 28.606061 10.60256435
-29 parent 29.797980 9.65946594
-30 parent 30.000000 9.50814643
-31 parent 30.989899 8.80025617
-32 parent 32.181818 8.01747313
-33 parent 33.373737 7.30431867
-34 parent 34.565657 6.65459931
-35 parent 35.757576 6.06267251
-36 parent 36.949495 5.52339762
-37 parent 38.141414 5.03209124
-38 parent 39.333333 4.58448658
-39 parent 40.525253 4.17669637
-40 parent 41.717172 3.80517911
-41 parent 42.909091 3.46670832
-42 parent 44.101010 3.15834451
-43 parent 45.292929 2.87740968
-44 parent 46.484848 2.62146400
-45 parent 47.676768 2.38828471
-46 parent 48.868687 2.17584671
-47 parent 50.060606 1.98230508
-48 parent 51.252525 1.80597899
-49 parent 52.444444 1.64533711
-50 parent 53.636364 1.49898432
-51 parent 54.828283 1.36564963
-52 parent 56.020202 1.24417505
-53 parent 57.212121 1.13350565
-54 parent 58.404040 1.03268029
-55 parent 59.595960 0.94082335
-56 parent 60.787879 0.85713708
-57 parent 61.979798 0.78089471
-58 parent 62.000000 0.77966270
-59 parent 63.171717 0.71143411
-60 parent 64.363636 0.64815202
-61 parent 65.555556 0.59049888
-62 parent 66.747475 0.53797399
-63 parent 67.939394 0.49012119
-64 parent 69.131313 0.44652489
-65 parent 70.323232 0.40680649
-66 parent 71.515152 0.37062104
-67 parent 72.707071 0.33765429
-68 parent 73.898990 0.30761993
-69 parent 75.090909 0.28025713
-70 parent 76.282828 0.25532825
-71 parent 77.474747 0.23261679
-72 parent 78.666667 0.21192552
-73 parent 79.858586 0.19307474
-74 parent 81.050505 0.17590074
-75 parent 82.242424 0.16025436
-76 parent 83.434343 0.14599973
-77 parent 84.626263 0.13301305
-78 parent 85.818182 0.12118154
-79 parent 87.010101 0.11040244
-80 parent 88.202020 0.10058214
-81 parent 89.393939 0.09163535
-82 parent 90.000000 0.08739595
-83 parent 90.585859 0.08348439
-84 parent 91.777778 0.07605845
-85 parent 92.969697 0.06929305
-86 parent 94.161616 0.06312943
-87 parent 95.353535 0.05751406
-88 parent 96.545455 0.05239819
-89 parent 97.737374 0.04773737
-90 parent 98.929293 0.04349113
-91 parent 100.121212 0.03962259
-92 parent 101.313131 0.03609816
-93 parent 102.505051 0.03288723
-94 parent 103.696970 0.02996191
-95 parent 104.888889 0.02729679
-96 parent 106.080808 0.02486874
-97 parent 107.272727 0.02265667
-98 parent 108.464646 0.02064136
-99 parent 109.656566 0.01880531
-100 parent 110.848485 0.01713257
-101 parent 112.040404 0.01560863
-102 parent 113.232323 0.01422024
-103 parent 114.424242 0.01295535
-104 parent 115.616162 0.01180297
-105 parent 116.808081 0.01075310
-106 parent 118.000000 0.00979661
-
-$cost
-function (P)
-{
- assign(&quot;calls&quot;, calls + 1, inherits = TRUE)
- if (trace_parms)
- cat(P, &quot;\n&quot;)
- if (length(state.ini.optim) &gt; 0) {
- odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
- names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
- }
- else {
- odeini &lt;- state.ini.fixed
- names(odeini) &lt;- state.ini.fixed.boxnames
- }
- odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)],
- transparms.fixed)
- parms &lt;- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates,
- transform_fractions = transform_fractions)
- out &lt;- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type,
- use_compiled = use_compiled, method.ode = method.ode,
- atol = atol, rtol = rtol, ...)
- assign(&quot;out_predicted&quot;, out, inherits = TRUE)
- mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight,
- scaleVar = scaleVar)
- if (mC$model &lt; cost.old) {
- if (!quiet)
- cat(&quot;Model cost at call &quot;, calls, &quot;: &quot;, mC$model,
- &quot;\n&quot;)
- if (plot) {
- outtimes_plot = seq(min(observed$time), max(observed$time),
- length.out = 100)
- out_plot &lt;- mkinpredict(mkinmod, parms, odeini, outtimes_plot,
- solution_type = solution_type, use_compiled = use_compiled,
- method.ode = method.ode, atol = atol, rtol = rtol,
- ...)
- plot(0, type = &quot;n&quot;, xlim = range(observed$time),
- ylim = c(0, max(observed$value, na.rm = TRUE)),
- xlab = &quot;Time&quot;, ylab = &quot;Observed&quot;)
- col_obs &lt;- pch_obs &lt;- 1:length(obs_vars)
- lty_obs &lt;- rep(1, length(obs_vars))
- names(col_obs) &lt;- names(pch_obs) &lt;- names(lty_obs) &lt;- obs_vars
- for (obs_var in obs_vars) {
- points(subset(observed, name == obs_var, c(time,
- value)), pch = pch_obs[obs_var], col = col_obs[obs_var])
- }
- matlines(out_plot$time, out_plot[-1], col = col_obs,
- lty = lty_obs)
- legend(&quot;topright&quot;, inset = c(0.05, 0.05), legend = obs_vars,
- col = col_obs, pch = pch_obs, lty = 1:length(pch_obs))
- }
- assign(&quot;cost.old&quot;, mC$model, inherits = TRUE)
- }
- return(mC)
-}
-&lt;environment: 0x43a7a48&gt;
-
-$cost_notrans
-function (P)
-{
- if (length(state.ini.optim) &gt; 0) {
- odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
- names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
- }
- else {
- odeini &lt;- state.ini.fixed
- names(odeini) &lt;- state.ini.fixed.boxnames
- }
- odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)],
- parms.fixed)
- out &lt;- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type,
- use_compiled = use_compiled, method.ode = method.ode,
- atol = atol, rtol = rtol, ...)
- mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight,
- scaleVar = scaleVar)
- return(mC)
-}
-&lt;environment: 0x43a7a48&gt;
-
-$hessian_notrans
- parent_0 k_parent_sink
-parent_0 4.163631 -1203.894
-k_parent_sink -1203.893702 1033188.753
-
-$start
- value type
-parent_0 98.62 state
-k_parent_sink 0.10 deparm
-
-$start_transformed
- value lower upper
-parent_0 98.620000 -Inf Inf
-log_k_parent_sink -2.302585 -Inf Inf
-
-$fixed
-[1] value type
-&lt;0 rows&gt; (or 0-length row.names)
-
-$data
- time variable observed predicted residual
-1 0 parent 98.62 99.17407218 -0.55407218
-2 3 parent 81.43 78.44547872 2.98452128
-3 7 parent 53.18 57.38445742 -4.20445742
-4 14 parent 34.89 33.20400061 1.68599939
-5 30 parent 10.09 9.50814643 0.58185357
-6 62 parent 1.50 0.77966270 0.72033730
-7 90 parent 0.33 0.08739595 0.24260405
-8 118 parent 0.08 0.00979661 0.07020339
-
-$atol
-[1] 1e-08
-
-$rtol
-[1] 1e-10
-
-$weight.ini
-[1] &quot;none&quot;
-
-$reweight.tol
-[1] 1e-08
-
-$reweight.max.iter
-[1] 10
-
-$bparms.optim
- parent_0 k_parent_sink
- 99.17407218 0.07815759
-
-$bparms.fixed
-numeric(0)
-
-$bparms.ode
-k_parent_sink
- 0.07815759
-
-$bparms.state
- parent
-99.17407
-
-$date
-[1] &quot;Sat Sep 10 05:52:53 2016&quot;
-
-attr(,&quot;class&quot;)
-[1] &quot;mkinfit&quot; &quot;modFit&quot;
-</div>
-<div class='input'> <span class="symbol">fits</span><span class="keyword">[</span><span class="string">"SFO"</span><span class="keyword">,</span> <span class="string">"B"</span><span class="keyword">,</span> <span class="argument">drop</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">]</span></div>
-<div class='output'>[[1]]
-$par
- parent_0 log_k_parent_sink
- 99.174072 -2.549028
-
-$ssr
-[1] 30.65564
-
-$convergence
-[1] 0
-
-$iterations
-[1] 5
-
-$evaluations
-function gradient
- 8 15
-
-$counts
-[1] &quot;relative convergence (4)&quot;
-
-$hessian
- parent_0 log_k_parent_sink
-parent_0 4.163631 -94.09343
-log_k_parent_sink -94.093431 6311.34610
-
-$residuals
- parent parent parent parent parent parent
- 0.55407218 -2.98452128 4.20445742 -1.68599939 -0.58185357 -0.72033730
- parent parent
--0.24260405 -0.07020339
-
-$ms
-[1] 3.831956
-
-$var_ms
- parent
-3.831956
-
-$var_ms_unscaled
- parent
-3.831956
-
-$var_ms_unweighted
- parent
-3.831956
-
-$rank
-[1] 2
-
-$df.residual
-[1] 6
-
-$solution_type
-[1] &quot;analytical&quot;
-
-$transform_rates
-[1] TRUE
-
-$transform_fractions
-[1] TRUE
-
-$method.modFit
-[1] &quot;Port&quot;
-
-$maxit.modFit
-[1] &quot;auto&quot;
-
-$calls
-[1] 29
-
-$time
- user system elapsed
- 0.108 0.000 0.106
-
-$mkinmod
-&lt;mkinmod&gt; model generated with
-Use of formation fractions $use_of_ff: min
-Specification $spec:
-$parent
-$type: SFO; $sink: TRUE
-Coefficient matrix $coefmat available
-
-$observed
- name time value
-1 parent 0 98.62
-2 parent 3 81.43
-3 parent 7 53.18
-4 parent 14 34.89
-5 parent 30 10.09
-6 parent 62 1.50
-7 parent 90 0.33
-8 parent 118 0.08
-
-$obs_vars
-[1] &quot;parent&quot;
-
-$predicted
- name time value
-1 parent 0.000000 99.17407218
-2 parent 1.191919 90.35253561
-3 parent 2.383838 82.31567498
-4 parent 3.000000 78.44547872
-5 parent 3.575758 74.99369333
-6 parent 4.767677 68.32300215
-7 parent 5.959596 62.24566915
-8 parent 7.000000 57.38445742
-9 parent 7.151515 56.70891509
-10 parent 8.343434 51.66465547
-11 parent 9.535354 47.06908288
-12 parent 10.727273 42.88228661
-13 parent 11.919192 39.06790599
-14 parent 13.111111 35.59281463
-15 parent 14.000000 33.20400061
-16 parent 14.303030 32.42683275
-17 parent 15.494949 29.54246504
-18 parent 16.686869 26.91466193
-19 parent 17.878788 24.52060198
-20 parent 19.070707 22.33949373
-21 parent 20.262626 20.35239512
-22 parent 21.454545 18.54204899
-23 parent 22.646465 16.89273320
-24 parent 23.838384 15.39012410
-25 parent 25.030303 14.02117212
-26 parent 26.222222 12.77398846
-27 parent 27.414141 11.63774182
-28 parent 28.606061 10.60256435
-29 parent 29.797980 9.65946594
-30 parent 30.000000 9.50814643
-31 parent 30.989899 8.80025617
-32 parent 32.181818 8.01747313
-33 parent 33.373737 7.30431867
-34 parent 34.565657 6.65459931
-35 parent 35.757576 6.06267251
-36 parent 36.949495 5.52339762
-37 parent 38.141414 5.03209124
-38 parent 39.333333 4.58448658
-39 parent 40.525253 4.17669637
-40 parent 41.717172 3.80517911
-41 parent 42.909091 3.46670832
-42 parent 44.101010 3.15834451
-43 parent 45.292929 2.87740968
-44 parent 46.484848 2.62146400
-45 parent 47.676768 2.38828471
-46 parent 48.868687 2.17584671
-47 parent 50.060606 1.98230508
-48 parent 51.252525 1.80597899
-49 parent 52.444444 1.64533711
-50 parent 53.636364 1.49898432
-51 parent 54.828283 1.36564963
-52 parent 56.020202 1.24417505
-53 parent 57.212121 1.13350565
-54 parent 58.404040 1.03268029
-55 parent 59.595960 0.94082335
-56 parent 60.787879 0.85713708
-57 parent 61.979798 0.78089471
-58 parent 62.000000 0.77966270
-59 parent 63.171717 0.71143411
-60 parent 64.363636 0.64815202
-61 parent 65.555556 0.59049888
-62 parent 66.747475 0.53797399
-63 parent 67.939394 0.49012119
-64 parent 69.131313 0.44652489
-65 parent 70.323232 0.40680649
-66 parent 71.515152 0.37062104
-67 parent 72.707071 0.33765429
-68 parent 73.898990 0.30761993
-69 parent 75.090909 0.28025713
-70 parent 76.282828 0.25532825
-71 parent 77.474747 0.23261679
-72 parent 78.666667 0.21192552
-73 parent 79.858586 0.19307474
-74 parent 81.050505 0.17590074
-75 parent 82.242424 0.16025436
-76 parent 83.434343 0.14599973
-77 parent 84.626263 0.13301305
-78 parent 85.818182 0.12118154
-79 parent 87.010101 0.11040244
-80 parent 88.202020 0.10058214
-81 parent 89.393939 0.09163535
-82 parent 90.000000 0.08739595
-83 parent 90.585859 0.08348439
-84 parent 91.777778 0.07605845
-85 parent 92.969697 0.06929305
-86 parent 94.161616 0.06312943
-87 parent 95.353535 0.05751406
-88 parent 96.545455 0.05239819
-89 parent 97.737374 0.04773737
-90 parent 98.929293 0.04349113
-91 parent 100.121212 0.03962259
-92 parent 101.313131 0.03609816
-93 parent 102.505051 0.03288723
-94 parent 103.696970 0.02996191
-95 parent 104.888889 0.02729679
-96 parent 106.080808 0.02486874
-97 parent 107.272727 0.02265667
-98 parent 108.464646 0.02064136
-99 parent 109.656566 0.01880531
-100 parent 110.848485 0.01713257
-101 parent 112.040404 0.01560863
-102 parent 113.232323 0.01422024
-103 parent 114.424242 0.01295535
-104 parent 115.616162 0.01180297
-105 parent 116.808081 0.01075310
-106 parent 118.000000 0.00979661
-
-$cost
-function (P)
-{
- assign(&quot;calls&quot;, calls + 1, inherits = TRUE)
- if (trace_parms)
- cat(P, &quot;\n&quot;)
- if (length(state.ini.optim) &gt; 0) {
- odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
- names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
- }
- else {
- odeini &lt;- state.ini.fixed
- names(odeini) &lt;- state.ini.fixed.boxnames
- }
- odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)],
- transparms.fixed)
- parms &lt;- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates,
- transform_fractions = transform_fractions)
- out &lt;- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type,
- use_compiled = use_compiled, method.ode = method.ode,
- atol = atol, rtol = rtol, ...)
- assign(&quot;out_predicted&quot;, out, inherits = TRUE)
- mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight,
- scaleVar = scaleVar)
- if (mC$model &lt; cost.old) {
- if (!quiet)
- cat(&quot;Model cost at call &quot;, calls, &quot;: &quot;, mC$model,
- &quot;\n&quot;)
- if (plot) {
- outtimes_plot = seq(min(observed$time), max(observed$time),
- length.out = 100)
- out_plot &lt;- mkinpredict(mkinmod, parms, odeini, outtimes_plot,
- solution_type = solution_type, use_compiled = use_compiled,
- method.ode = method.ode, atol = atol, rtol = rtol,
- ...)
- plot(0, type = &quot;n&quot;, xlim = range(observed$time),
- ylim = c(0, max(observed$value, na.rm = TRUE)),
- xlab = &quot;Time&quot;, ylab = &quot;Observed&quot;)
- col_obs &lt;- pch_obs &lt;- 1:length(obs_vars)
- lty_obs &lt;- rep(1, length(obs_vars))
- names(col_obs) &lt;- names(pch_obs) &lt;- names(lty_obs) &lt;- obs_vars
- for (obs_var in obs_vars) {
- points(subset(observed, name == obs_var, c(time,
- value)), pch = pch_obs[obs_var], col = col_obs[obs_var])
- }
- matlines(out_plot$time, out_plot[-1], col = col_obs,
- lty = lty_obs)
- legend(&quot;topright&quot;, inset = c(0.05, 0.05), legend = obs_vars,
- col = col_obs, pch = pch_obs, lty = 1:length(pch_obs))
- }
- assign(&quot;cost.old&quot;, mC$model, inherits = TRUE)
- }
- return(mC)
-}
-&lt;environment: 0x43a7a48&gt;
-
-$cost_notrans
-function (P)
-{
- if (length(state.ini.optim) &gt; 0) {
- odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
- names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
- }
- else {
- odeini &lt;- state.ini.fixed
- names(odeini) &lt;- state.ini.fixed.boxnames
- }
- odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)],
- parms.fixed)
- out &lt;- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type,
- use_compiled = use_compiled, method.ode = method.ode,
- atol = atol, rtol = rtol, ...)
- mC &lt;- modCost(out, observed, y = &quot;value&quot;, err = err, weight = weight,
- scaleVar = scaleVar)
- return(mC)
-}
-&lt;environment: 0x43a7a48&gt;
-
-$hessian_notrans
- parent_0 k_parent_sink
-parent_0 4.163631 -1203.894
-k_parent_sink -1203.893702 1033188.753
-
-$start
- value type
-parent_0 98.62 state
-k_parent_sink 0.10 deparm
-
-$start_transformed
- value lower upper
-parent_0 98.620000 -Inf Inf
-log_k_parent_sink -2.302585 -Inf Inf
-
-$fixed
-[1] value type
-&lt;0 rows&gt; (or 0-length row.names)
-
-$data
- time variable observed predicted residual
-1 0 parent 98.62 99.17407218 -0.55407218
-2 3 parent 81.43 78.44547872 2.98452128
-3 7 parent 53.18 57.38445742 -4.20445742
-4 14 parent 34.89 33.20400061 1.68599939
-5 30 parent 10.09 9.50814643 0.58185357
-6 62 parent 1.50 0.77966270 0.72033730
-7 90 parent 0.33 0.08739595 0.24260405
-8 118 parent 0.08 0.00979661 0.07020339
-
-$atol
-[1] 1e-08
-
-$rtol
-[1] 1e-10
-
-$weight.ini
-[1] &quot;none&quot;
-
-$reweight.tol
-[1] 1e-08
-
-$reweight.max.iter
-[1] 10
-
-$bparms.optim
- parent_0 k_parent_sink
- 99.17407218 0.07815759
-
-$bparms.fixed
-numeric(0)
-
-$bparms.ode
-k_parent_sink
- 0.07815759
-
-$bparms.state
- parent
-99.17407
-
-$date
-[1] &quot;Sat Sep 10 05:52:53 2016&quot;
-
-attr(,&quot;class&quot;)
-[1] &quot;mkinfit&quot; &quot;modFit&quot;
-
-</div></pre>
- </div>
- <div class="span4 sidebar">
- <!-- <ul>
- <li>[.mmkin</li>
- </ul>
- <ul>
-
- </ul> -->
-
-
-
- <h2>Author</h2>
-
- Johannes Ranke
-
-
- </div>
-</div>
-
- <footer>
- <p class="pull-right"><a href="#">Back to top</a></p>
-<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="https://getbootstrap.com/2.0.4/">bootstrap</a>.</p>
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