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authorJohannes Ranke <jranke@uni-bremen.de>2016-09-10 05:21:52 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2016-09-10 05:55:25 +0200
commita350a16bb2c11986faf5883a2804d46b03bd7c8f (patch)
tree00ca40222b1f4c9bcffca081982e006763e697d8 /docs/Extract.mmkin.html
parent3b399df5231576880fd9e0ae7253064d82edfe86 (diff)
Static documentation rebuilt with current staticdocs
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@@ -0,0 +1,1199 @@
+<!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>
+
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+ <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>
+ </footer>
+ </div>
+ </body>
+</html> \ No newline at end of file

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