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diff --git a/docs/Extract.mmkin.html b/docs/Extract.mmkin.html deleted file mode 100644 index b4686a6c..00000000 --- a/docs/Extract.mmkin.html +++ /dev/null @@ -1,1199 +0,0 @@ -<!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 -"> - -<link href="css/bootstrap.css" rel="stylesheet"> -<link href="css/bootstrap-responsive.css" rel="stylesheet"> -<link href="css/highlight.css" rel="stylesheet"> -<link href="css/staticdocs.css" rel="stylesheet"> - -<!--[if lt IE 9]> - <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script> -<![endif]--> - -<script type="text/x-mathjax-config"> - MathJax.Hub.Config({ - tex2jax: { - inlineMath: [ ['$','$'], ["\\(","\\)"] ], - processEscapes: true - } - }); -</script> -<script type="text/javascript" - src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"> -</script> - </head> - - <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 = 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"><-</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(,"class") -[1] "mmkin" -</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(,"class") -[1] "mmkin" -</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 - -$counts -[1] "both X-convergence and relative convergence (5)" - -$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] "analytical" - -$transform_rates -[1] TRUE - -$transform_fractions -[1] TRUE - -$method.modFit -[1] "Port" - -$maxit.modFit -[1] "auto" - -$calls -[1] 111 - -$time - user system elapsed - 0.276 0.000 0.277 - -$mkinmod -<mkinmod> 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 - -$obs_vars -[1] "parent" - -$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 - -$cost -function (P) -{ - assign("calls", calls + 1, inherits = TRUE) - if (trace_parms) - cat(P, "\n") - if (length(state.ini.optim) > 0) { - odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed) - names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames) - } - else { - odeini <- state.ini.fixed - names(odeini) <- state.ini.fixed.boxnames - } - odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], - transparms.fixed) - parms <- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates, - transform_fractions = transform_fractions) - out <- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type, - use_compiled = use_compiled, method.ode = method.ode, - atol = atol, rtol = rtol, ...) - assign("out_predicted", out, inherits = TRUE) - mC <- modCost(out, observed, y = "value", err = err, weight = weight, - scaleVar = scaleVar) - if (mC$model < cost.old) { - if (!quiet) - cat("Model cost at call ", calls, ": ", mC$model, - "\n") - if (plot) { - outtimes_plot = seq(min(observed$time), max(observed$time), - length.out = 100) - out_plot <- mkinpredict(mkinmod, parms, odeini, outtimes_plot, - solution_type = solution_type, use_compiled = use_compiled, - method.ode = method.ode, atol = atol, rtol = rtol, - ...) - plot(0, type = "n", xlim = range(observed$time), - ylim = c(0, max(observed$value, na.rm = TRUE)), - xlab = "Time", ylab = "Observed") - col_obs <- pch_obs <- 1:length(obs_vars) - lty_obs <- rep(1, length(obs_vars)) - names(col_obs) <- names(pch_obs) <- names(lty_obs) <- obs_vars - for (obs_var in obs_vars) { - points(subset(observed, name == obs_var, c(time, - value)), pch = pch_obs[obs_var], col = col_obs[obs_var]) - } - matlines(out_plot$time, out_plot[-1], col = col_obs, - lty = lty_obs) - legend("topright", inset = c(0.05, 0.05), legend = obs_vars, - col = col_obs, pch = pch_obs, lty = 1:length(pch_obs)) - } - assign("cost.old", mC$model, inherits = TRUE) - } - return(mC) -} -<environment: 0x44a0b88> - -$cost_notrans -function (P) -{ - if (length(state.ini.optim) > 0) { - odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed) - names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames) - } - else { - odeini <- state.ini.fixed - names(odeini) <- state.ini.fixed.boxnames - } - odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], - parms.fixed) - out <- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type, - use_compiled = use_compiled, method.ode = method.ode, - atol = atol, rtol = rtol, ...) - mC <- modCost(out, observed, y = "value", err = err, weight = weight, - scaleVar = scaleVar) - return(mC) -} -<environment: 0x44a0b88> - -$hessian_notrans - parent_0 alpha beta -parent_0 4.1230329 -7.473531 0.5968527 -alpha -7.4735307 40.365690 -3.1777189 -beta 0.5968527 -3.177719 0.2503425 - -$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 -<0 rows> (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] "none" - -$reweight.tol -[1] 1e-08 - -$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 - -$date -[1] "Sat Sep 10 05:52:53 2016" - -attr(,"class") -[1] "mkinfit" "modFit" -</div> -<div class='input'> <span class="symbol">fits</span><span class="keyword">[</span><span class="string">"SFO"</span><span class="keyword">,</span> <span class="string">"B"</span><span class="keyword">]</span></div> -<div class='output'> dataset -model B - SFO List,42 -attr(,"class") -[1] "mmkin" -</div> -<div class='input'> <span class="symbol">fits</span><span class="keyword">[[</span><span class="string">"SFO"</span><span class="keyword">,</span> <span class="string">"B"</span><span class="keyword">]</span><span class="keyword">]</span> <span class="comment"># This is equivalent to</span></div> -<div class='output'>$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 - -$counts -[1] "relative convergence (4)" - -$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] "analytical" - -$transform_rates -[1] TRUE - -$transform_fractions -[1] TRUE - -$method.modFit -[1] "Port" - -$maxit.modFit -[1] "auto" - -$calls -[1] 29 - -$time - user system elapsed - 0.108 0.000 0.106 - -$mkinmod -<mkinmod> 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 - -$obs_vars -[1] "parent" - -$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 - -$cost -function (P) -{ - assign("calls", calls + 1, inherits = TRUE) - if (trace_parms) - cat(P, "\n") - if (length(state.ini.optim) > 0) { - odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed) - names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames) - } - else { - odeini <- state.ini.fixed - names(odeini) <- state.ini.fixed.boxnames - } - odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], - transparms.fixed) - parms <- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates, - transform_fractions = transform_fractions) - out <- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type, - use_compiled = use_compiled, method.ode = method.ode, - atol = atol, rtol = rtol, ...) - assign("out_predicted", out, inherits = TRUE) - mC <- modCost(out, observed, y = "value", err = err, weight = weight, - scaleVar = scaleVar) - if (mC$model < cost.old) { - if (!quiet) - cat("Model cost at call ", calls, ": ", mC$model, - "\n") - if (plot) { - outtimes_plot = seq(min(observed$time), max(observed$time), - length.out = 100) - out_plot <- mkinpredict(mkinmod, parms, odeini, outtimes_plot, - solution_type = solution_type, use_compiled = use_compiled, - method.ode = method.ode, atol = atol, rtol = rtol, - ...) - plot(0, type = "n", xlim = range(observed$time), - ylim = c(0, max(observed$value, na.rm = TRUE)), - xlab = "Time", ylab = "Observed") - col_obs <- pch_obs <- 1:length(obs_vars) - lty_obs <- rep(1, length(obs_vars)) - names(col_obs) <- names(pch_obs) <- names(lty_obs) <- obs_vars - for (obs_var in obs_vars) { - points(subset(observed, name == obs_var, c(time, - value)), pch = pch_obs[obs_var], col = col_obs[obs_var]) - } - matlines(out_plot$time, out_plot[-1], col = col_obs, - lty = lty_obs) - legend("topright", inset = c(0.05, 0.05), legend = obs_vars, - col = col_obs, pch = pch_obs, lty = 1:length(pch_obs)) - } - assign("cost.old", mC$model, inherits = TRUE) - } - return(mC) -} -<environment: 0x43a7a48> - -$cost_notrans -function (P) -{ - if (length(state.ini.optim) > 0) { - odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed) - names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames) - } - else { - odeini <- state.ini.fixed - names(odeini) <- state.ini.fixed.boxnames - } - odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], - parms.fixed) - out <- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type, - use_compiled = use_compiled, method.ode = method.ode, - atol = atol, rtol = rtol, ...) - mC <- modCost(out, observed, y = "value", err = err, weight = weight, - scaleVar = scaleVar) - return(mC) -} -<environment: 0x43a7a48> - -$hessian_notrans - parent_0 k_parent_sink -parent_0 4.163631 -1203.894 -k_parent_sink -1203.893702 1033188.753 - -$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 -<0 rows> (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] "none" - -$reweight.tol -[1] 1e-08 - -$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 - -$date -[1] "Sat Sep 10 05:52:53 2016" - -attr(,"class") -[1] "mkinfit" "modFit" -</div> -<div class='input'> <span class="symbol">fits</span><span class="keyword">[</span><span class="string">"SFO"</span><span class="keyword">,</span> <span class="string">"B"</span><span class="keyword">,</span> <span class="argument">drop</span> <span class="argument">=</span> <span class="number">TRUE</span><span class="keyword">]</span></div> -<div class='output'>[[1]] -$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 - -$counts -[1] "relative convergence (4)" - -$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] "analytical" - -$transform_rates -[1] TRUE - -$transform_fractions -[1] TRUE - -$method.modFit -[1] "Port" - -$maxit.modFit -[1] "auto" - -$calls -[1] 29 - -$time - user system elapsed - 0.108 0.000 0.106 - -$mkinmod -<mkinmod> 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 - -$obs_vars -[1] "parent" - -$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 - -$cost -function (P) -{ - assign("calls", calls + 1, inherits = TRUE) - if (trace_parms) - cat(P, "\n") - if (length(state.ini.optim) > 0) { - odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed) - names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames) - } - else { - odeini <- state.ini.fixed - names(odeini) <- state.ini.fixed.boxnames - } - odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], - transparms.fixed) - parms <- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates, - transform_fractions = transform_fractions) - out <- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type, - use_compiled = use_compiled, method.ode = method.ode, - atol = atol, rtol = rtol, ...) - assign("out_predicted", out, inherits = TRUE) - mC <- modCost(out, observed, y = "value", err = err, weight = weight, - scaleVar = scaleVar) - if (mC$model < cost.old) { - if (!quiet) - cat("Model cost at call ", calls, ": ", mC$model, - "\n") - if (plot) { - outtimes_plot = seq(min(observed$time), max(observed$time), - length.out = 100) - out_plot <- mkinpredict(mkinmod, parms, odeini, outtimes_plot, - solution_type = solution_type, use_compiled = use_compiled, - method.ode = method.ode, atol = atol, rtol = rtol, - ...) - plot(0, type = "n", xlim = range(observed$time), - ylim = c(0, max(observed$value, na.rm = TRUE)), - xlab = "Time", ylab = "Observed") - col_obs <- pch_obs <- 1:length(obs_vars) - lty_obs <- rep(1, length(obs_vars)) - names(col_obs) <- names(pch_obs) <- names(lty_obs) <- obs_vars - for (obs_var in obs_vars) { - points(subset(observed, name == obs_var, c(time, - value)), pch = pch_obs[obs_var], col = col_obs[obs_var]) - } - matlines(out_plot$time, out_plot[-1], col = col_obs, - lty = lty_obs) - legend("topright", inset = c(0.05, 0.05), legend = obs_vars, - col = col_obs, pch = pch_obs, lty = 1:length(pch_obs)) - } - assign("cost.old", mC$model, inherits = TRUE) - } - return(mC) -} -<environment: 0x43a7a48> - -$cost_notrans -function (P) -{ - if (length(state.ini.optim) > 0) { - odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed) - names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames) - } - else { - odeini <- state.ini.fixed - names(odeini) <- state.ini.fixed.boxnames - } - odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], - parms.fixed) - out <- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type, - use_compiled = use_compiled, method.ode = method.ode, - atol = atol, rtol = rtol, ...) - mC <- modCost(out, observed, y = "value", err = err, weight = weight, - scaleVar = scaleVar) - return(mC) -} -<environment: 0x43a7a48> - -$hessian_notrans - parent_0 k_parent_sink -parent_0 4.163631 -1203.894 -k_parent_sink -1203.893702 1033188.753 - -$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 -<0 rows> (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] "none" - -$reweight.tol -[1] 1e-08 - -$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] "Sat Sep 10 05:52:53 2016" - -attr(,"class") -[1] "mkinfit" "modFit" - -</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>
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