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diff --git a/docs/Extract.mmkin.html b/docs/Extract.mmkin.html new file mode 100644 index 00000000..b4686a6c --- /dev/null +++ b/docs/Extract.mmkin.html @@ -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 +"> + +<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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