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diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html new file mode 100644 index 00000000..3422c206 --- /dev/null +++ b/docs/reference/DFOP.solution.html @@ -0,0 +1,132 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>DFOP.solution. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>Function describing decline from a defined starting value using the sum + of two exponential decline functions.</p> + + + <pre><span class='fu'>DFOP.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>g</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>t</dt> + <dd> Time. </dd> + <dt>parent.0</dt> + <dd> Starting value for the response variable at time zero. </dd> + <dt>k1</dt> + <dd> First kinetic constant. </dd> + <dt>k2</dt> + <dd> Second kinetic constant. </dd> + <dt>g</dt> + <dd> Fraction of the starting value declining according to the + first kinetic constant. + </dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>The value of the response variable at time <code>t</code>.</p> + </div> + + <div class="References"> + <h2>References</h2> + + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + Degradation Kinetics from Environmental Fate Studies on Pesticides in EU + Registration” Report of the FOCUS Work Group on Degradation Kinetics, + EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, + <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>DFOP.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>5</span>, <span class='fl'>0.5</span>, <span class='fl'>0.3</span>), <span class='fl'>0</span>, <span class='fl'>4</span>, <span class='kw'>ylim</span><span class='kw'>=</span><span class='fu'>c</span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><img src='unknown-2.png' alt='' width='540' height='400' /></pre> + </div> + <div class="col-md-3"> + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html new file mode 100644 index 00000000..b811eb95 --- /dev/null +++ b/docs/reference/Extract.mmkin.html @@ -0,0 +1,1192 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>[.mmkin. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1>Subsetting method for mmkin objects</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>Subsetting method for mmkin objects.</p> + + + <pre># S3 method for mmkin +[(x, i, j, ..., drop = FALSE)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>x</dt> + <dd>An <code>mmkin 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="Value"> + <h2>Value</h2> + + <p>An object of class <code>mmkin</code>.</p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'> <span class='co'># Only use one core, to pass R CMD check --as-cran</span> + <span class='no'>fits</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='fu'>c</span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>), <span class='fu'>list</span>(<span class='kw'>B</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='kw'>C</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>), + <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ]</div><div class='output co'>#> dataset +#> model B C +#> FOMC List,42 List,42 +#> attr(,"class") +#> [1] "mmkin" +#> </div><div class='input'> <span class='no'>fits</span>[, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset +#> model B +#> SFO List,42 +#> FOMC List,42 +#> attr(,"class") +#> [1] "mmkin" +#> </div><div class='input'> <span class='no'>fits</span>[, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]$<span class='no'>FOMC</span></div><div class='output co'>#> $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 +#> 0.256 0.000 0.257 +#> +#> $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: 0x27fc328> +#> +#> $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: 0x27fc328> +#> +#> $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] "Thu Oct 6 09:17:52 2016" +#> +#> attr(,"class") +#> [1] "mkinfit" "modFit" +#> </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset +#> model B +#> SFO List,42 +#> attr(,"class") +#> [1] "mmkin" +#> </div><div class='input'> <span class='no'>fits</span><span class='kw'>[[</span><span class='st'>"SFO"</span>, <span class='st'>"B"</span>]] <span class='co'># This is equivalent to</span></div><div class='output co'>#> $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 +#> 0.068 0.000 0.068 +#> +#> $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: 0x2e966b0> +#> +#> $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: 0x2e966b0> +#> +#> $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] "Thu Oct 6 09:17:51 2016" +#> +#> attr(,"class") +#> [1] "mkinfit" "modFit" +#> </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]</div><div class='output co'>#> [[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 +#> 0.068 0.000 0.068 +#> +#> $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: 0x2e966b0> +#> +#> $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: 0x2e966b0> +#> +#> $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] "Thu Oct 6 09:17:51 2016" +#> +#> attr(,"class") +#> [1] "mkinfit" "modFit" +#> +#> </div></pre> + </div> + <div class="col-md-3"> + <h2>Author</h2> + + Johannes Ranke + + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html new file mode 100644 index 00000000..5c0faa43 --- /dev/null +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -0,0 +1,129 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>FOCUS_2006_DFOP_ref_A_to_B. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>A table with the fitted parameters and the resulting DT50 and DT90 values +generated with different software packages. Taken directly from FOCUS (2006). +The results from fitting the data with the Topfit software was removed, as +the initial concentration of the parent compound was fixed to a value of 100 +in this fit.</p> + + + <pre><span class='fu'>data</span>(<span class='no'>FOCUS_2006_DFOP_ref_A_to_B</span>)</pre> + + <div class="Format"> + <h2>Format</h2> + + <p>A data frame containing the following variables. + <dl class='dl-horizontal'> + <dt><code>package</code></dt><dd>a factor giving the name of the software package</dd> + <dt><code>M0</code></dt><dd>The fitted initial concentration of the parent compound</dd> + <dt><code>f</code></dt><dd>The fitted f parameter</dd> + <dt><code>k1</code></dt><dd>The fitted k1 parameter</dd> + <dt><code>k2</code></dt><dd>The fitted k2 parameter</dd> + <dt><code>DT50</code></dt><dd>The resulting half-life of the parent compound</dd> + <dt><code>DT90</code></dt><dd>The resulting DT90 of the parent compound</dd> + <dt><code>dataset</code></dt><dd>The FOCUS dataset that was used</dd> + </dl></p> + </div> + + <div class="Source"> + <h2>Source</h2> + + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + Degradation Kinetics from Environmental Fate Studies on Pesticides in EU + Registration” Report of the FOCUS Work Group on Degradation Kinetics, + EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, + <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>FOCUS_2006_DFOP_ref_A_to_B</span>)</div></pre> + </div> + <div class="col-md-3"> + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html new file mode 100644 index 00000000..89faecbf --- /dev/null +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -0,0 +1,128 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>FOCUS_2006_FOMC_ref_A_to_F. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>A table with the fitted parameters and the resulting DT50 and DT90 values +generated with different software packages. Taken directly from FOCUS (2006). +The results from fitting the data with the Topfit software was removed, as +the initial concentration of the parent compound was fixed to a value of 100 +in this fit.</p> + + + <pre><span class='fu'>data</span>(<span class='no'>FOCUS_2006_FOMC_ref_A_to_F</span>)</pre> + + <div class="Format"> + <h2>Format</h2> + + <p>A data frame containing the following variables. + <dl class='dl-horizontal'> + <dt><code>package</code></dt><dd>a factor giving the name of the software package</dd> + <dt><code>M0</code></dt><dd>The fitted initial concentration of the parent compound</dd> + <dt><code>alpha</code></dt><dd>The fitted alpha parameter</dd> + <dt><code>beta</code></dt><dd>The fitted beta parameter</dd> + <dt><code>DT50</code></dt><dd>The resulting half-life of the parent compound</dd> + <dt><code>DT90</code></dt><dd>The resulting DT90 of the parent compound</dd> + <dt><code>dataset</code></dt><dd>The FOCUS dataset that was used</dd> + </dl></p> + </div> + + <div class="Source"> + <h2>Source</h2> + + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + Degradation Kinetics from Environmental Fate Studies on Pesticides in EU + Registration” Report of the FOCUS Work Group on Degradation Kinetics, + EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, + <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>FOCUS_2006_FOMC_ref_A_to_F</span>)</div></pre> + </div> + <div class="col-md-3"> + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html new file mode 100644 index 00000000..2dfafec6 --- /dev/null +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -0,0 +1,129 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>FOCUS_2006_HS_ref_A_to_F. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>A table with the fitted parameters and the resulting DT50 and DT90 values +generated with different software packages. Taken directly from FOCUS (2006). +The results from fitting the data with the Topfit software was removed, as +the initial concentration of the parent compound was fixed to a value of 100 +in this fit.</p> + + + <pre><span class='fu'>data</span>(<span class='no'>FOCUS_2006_HS_ref_A_to_F</span>)</pre> + + <div class="Format"> + <h2>Format</h2> + + <p>A data frame containing the following variables. + <dl class='dl-horizontal'> + <dt><code>package</code></dt><dd>a factor giving the name of the software package</dd> + <dt><code>M0</code></dt><dd>The fitted initial concentration of the parent compound</dd> + <dt><code>tb</code></dt><dd>The fitted tb parameter</dd> + <dt><code>k1</code></dt><dd>The fitted k1 parameter</dd> + <dt><code>k2</code></dt><dd>The fitted k2 parameter</dd> + <dt><code>DT50</code></dt><dd>The resulting half-life of the parent compound</dd> + <dt><code>DT90</code></dt><dd>The resulting DT90 of the parent compound</dd> + <dt><code>dataset</code></dt><dd>The FOCUS dataset that was used</dd> + </dl></p> + </div> + + <div class="Source"> + <h2>Source</h2> + + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + Degradation Kinetics from Environmental Fate Studies on Pesticides in EU + Registration” Report of the FOCUS Work Group on Degradation Kinetics, + EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, + <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>FOCUS_2006_HS_ref_A_to_F</span>)</div></pre> + </div> + <div class="col-md-3"> + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html new file mode 100644 index 00000000..ed3a4aff --- /dev/null +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -0,0 +1,127 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>FOCUS_2006_SFO_ref_A_to_F. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>A table with the fitted parameters and the resulting DT50 and DT90 values +generated with different software packages. Taken directly from FOCUS (2006). +The results from fitting the data with the Topfit software was removed, as +the initial concentration of the parent compound was fixed to a value of 100 +in this fit.</p> + + + <pre><span class='fu'>data</span>(<span class='no'>FOCUS_2006_SFO_ref_A_to_F</span>)</pre> + + <div class="Format"> + <h2>Format</h2> + + <p>A data frame containing the following variables. + <dl class='dl-horizontal'> + <dt><code>package</code></dt><dd>a factor giving the name of the software package</dd> + <dt><code>M0</code></dt><dd>The fitted initial concentration of the parent compound</dd> + <dt><code>k</code></dt><dd>The fitted first-order degradation rate constant</dd> + <dt><code>DT50</code></dt><dd>The resulting half-life of the parent compound</dd> + <dt><code>DT90</code></dt><dd>The resulting DT90 of the parent compound</dd> + <dt><code>dataset</code></dt><dd>The FOCUS dataset that was used</dd> + </dl></p> + </div> + + <div class="Source"> + <h2>Source</h2> + + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + Degradation Kinetics from Environmental Fate Studies on Pesticides in EU + Registration” Report of the FOCUS Work Group on Degradation Kinetics, + EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, + <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>FOCUS_2006_SFO_ref_A_to_F</span>)</div></pre> + </div> + <div class="col-md-3"> + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html new file mode 100644 index 00000000..c1eacbd8 --- /dev/null +++ b/docs/reference/FOCUS_2006_datasets.html @@ -0,0 +1,130 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>FOCUS_2006_datasets. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>Data taken from FOCUS (2006), p. 258.</p> + + + <pre><span class='no'>FOCUS_2006_datasets</span></pre> + + <div class="Format"> + <h2>Format</h2> + + <p>6 datasets with observations on the following variables. + <dl class='dl-horizontal'> + <dt><code>name</code></dt><dd>a factor containing the name of the observed variable</dd> + <dt><code>time</code></dt><dd>a numeric vector containing time points</dd> + <dt><code>value</code></dt><dd>a numeric vector containing concentrations in percent of applied radioactivity</dd> + </dl></p> + </div> + + <div class="Source"> + <h2>Source</h2> + + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + Degradation Kinetics from Environmental Fate Studies on Pesticides in EU + Registration” Report of the FOCUS Work Group on Degradation Kinetics, + EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, + <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class='no'>FOCUS_2006_C</span></div><div class='output co'>#> name time value +#> 1 parent 0 85.1 +#> 2 parent 1 57.9 +#> 3 parent 3 29.9 +#> 4 parent 7 14.6 +#> 5 parent 14 9.7 +#> 6 parent 28 6.6 +#> 7 parent 63 4.0 +#> 8 parent 91 3.9 +#> 9 parent 119 0.6 +#> </div></pre> + </div> + <div class="col-md-3"> + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html new file mode 100644 index 00000000..912cf414 --- /dev/null +++ b/docs/reference/FOMC.solution.html @@ -0,0 +1,147 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>FOMC.solution. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> First-Order Multi-Compartment kinetics </h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>Function describing exponential decline from a defined starting value, with + a decreasing rate constant.</p> + + <p>The form given here differs slightly from the original reference by Gustafson + and Holden (1990). The parameter <code>beta</code> corresponds to 1/beta in the + original equation.</p> + + + <pre><span class='fu'>FOMC.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>alpha</span>, <span class='no'>beta</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>t</dt> + <dd> Time. </dd> + <dt>parent.0</dt> + <dd> Starting value for the response variable at time zero. </dd> + <dt>alpha</dt> + <dd> + Shape parameter determined by coefficient of variation of rate constant + values. </dd> + <dt>beta</dt> + <dd> + Location parameter. +</dd> + </dl> + + <div class="Note"> + <h2>Note</h2> + + <p>The solution of the FOMC kinetic model reduces to the + <code>SFO.solution</code> for large values of <code>alpha</code> and + <code>beta</code> with + \(k = \frac{\beta}{\alpha}\).</p> + </div> + + <div class="Value"> + <h2>Value</h2> + + <p>The value of the response variable at time <code>t</code>.</p> + </div> + + <div class="References"> + <h2>References</h2> + + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + Degradation Kinetics from Environmental Fate Studies on Pesticides in EU + Registration” Report of the FOCUS Work Group on Degradation Kinetics, + EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, + <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> + <p>Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: A + new model based on spatial variability. <em>Environmental Science and + Technology</em> <b>24</b>, 1032-1038</p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>FOMC.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>10</span>, <span class='fl'>2</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><img src='unknown-2.png' alt='' width='540' height='400' /></pre> + </div> + <div class="col-md-3"> + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html new file mode 100644 index 00000000..994f8373 --- /dev/null +++ b/docs/reference/HS.solution.html @@ -0,0 +1,131 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>HS.solution. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> Hockey-Stick kinetics </h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>Function describing two exponential decline functions with a break point + between them.</p> + + + <pre><span class='fu'>HS.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k1</span>, <span class='no'>k2</span>, <span class='no'>tb</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>t</dt> + <dd> Time. </dd> + <dt>parent.0</dt> + <dd> Starting value for the response variable at time zero. </dd> + <dt>k1</dt> + <dd> First kinetic constant. </dd> + <dt>k2</dt> + <dd> Second kinetic constant. </dd> + <dt>tb</dt> + <dd> Break point. Before this time, exponential decline according + to <code>k1</code> is calculated, after this time, exponential decline proceeds + according to <code>k2</code>. </dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>The value of the response variable at time <code>t</code>.</p> + </div> + + <div class="References"> + <h2>References</h2> + + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + Degradation Kinetics from Environmental Fate Studies on Pesticides in EU + Registration” Report of the FOCUS Work Group on Degradation Kinetics, + EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, + <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>HS.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>2</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, <span class='kw'>ylim</span><span class='kw'>=</span><span class='fu'>c</span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><img src='unknown-2.png' alt='' width='540' height='400' /></pre> + </div> + <div class="col-md-3"> + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html new file mode 100644 index 00000000..06f5c1ad --- /dev/null +++ b/docs/reference/IORE.solution.html @@ -0,0 +1,149 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>IORE.solution. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> Indeterminate order rate equation kinetics </h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>Function describing exponential decline from a defined starting value, with + a concentration dependent rate constant.</p> + + + <pre><span class='fu'>IORE.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k__iore</span>, <span class='no'>N</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>t</dt> + <dd> Time. </dd> + <dt>parent.0</dt> + <dd> Starting value for the response variable at time zero. </dd> + <dt>k__iore</dt> + <dd> Rate constant. Note that this depends on the concentration units used. </dd> + <dt>N</dt> + <dd> Exponent describing the nonlinearity of the rate equation </dd> + </dl> + + <div class="Note"> + <h2>Note</h2> + + <p>The solution of the IORE kinetic model reduces to the + <code>SFO.solution</code> if N = 1. + The parameters of the IORE model can be transformed to equivalent parameters + of the FOMC mode - see the NAFTA guidance for details.</p> + </div> + + <div class="Value"> + <h2>Value</h2> + + <p>The value of the response variable at time <code>t</code>.</p> + </div> + + <div class="References"> + <h2>References</h2> + + <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for + Evaluating and Calculating Degradation Kinetics in Environmental + Media</p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'> <span class='fu'>plot</span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>IORE.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.2</span>, <span class='fl'>1.3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>, + <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><img src='unknown-2.png' alt='' width='540' height='400' /><div class='input'> <span class='no'>fit.fomc</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='no'>fit.iore</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"IORE"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='no'>fit.iore.deS</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"IORE"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + + <span class='fu'>print</span>(<span class='fu'>data.frame</span>(<span class='fu'>coef</span>(<span class='no'>fit.fomc</span>), <span class='fu'>coef</span>(<span class='no'>fit.iore</span>), <span class='fu'>coef</span>(<span class='no'>fit.iore.deS</span>), + <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fu'>paste</span>(<span class='st'>"model par"</span>, <span class='fl'>1</span>:<span class='fl'>3</span>)))</div><div class='output co'>#> coef.fit.fomc. coef.fit.iore. coef.fit.iore.deS. +#> model par 1 85.87489063 85.874891 85.874890 +#> model par 2 0.05192238 -4.826631 -4.826631 +#> model par 3 0.65096665 1.949403 1.949403 +#> </div><div class='input'> <span class='fu'>print</span>(<span class='fu'>rbind</span>(<span class='kw'>fomc</span> <span class='kw'>=</span> <span class='fu'>endpoints</span>(<span class='no'>fit.fomc</span>)$<span class='no'>distimes</span>, <span class='kw'>iore</span> <span class='kw'>=</span> <span class='fu'>endpoints</span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>, + <span class='kw'>iore.deS</span> <span class='kw'>=</span> <span class='fu'>endpoints</span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>))</div><div class='output co'>#> DT50 DT90 DT50back +#> fomc 1.785233 15.1479 4.559973 +#> iore 1.785233 15.1479 4.559973 +#> iore.deS 1.785233 15.1479 4.559973 +#> </div></pre> + </div> + <div class="col-md-3"> + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html new file mode 100644 index 00000000..9cf069d7 --- /dev/null +++ b/docs/reference/SFO.solution.html @@ -0,0 +1,124 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>SFO.solution. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> Single First-Order kinetics </h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>Function describing exponential decline from a defined starting value.</p> + + + <pre><span class='fu'>SFO.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>t</dt> + <dd> Time. </dd> + <dt>parent.0</dt> + <dd> Starting value for the response variable at time zero. </dd> + <dt>k</dt> + <dd> Kinetic constant. </dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>The value of the response variable at time <code>t</code>.</p> + </div> + + <div class="References"> + <h2>References</h2> + + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + Degradation Kinetics from Environmental Fate Studies on Pesticides in EU + Registration” Report of the FOCUS Work Group on Degradation Kinetics, + EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, + <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'> <span class='co'>## Not run: plot(function(x) SFO.solution(x, 100, 3), 0, 2)</span></div></pre> + </div> + <div class="col-md-3"> + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html new file mode 100644 index 00000000..57959f26 --- /dev/null +++ b/docs/reference/SFORB.solution.html @@ -0,0 +1,133 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>SFORB.solution. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> Single First-Order Reversible Binding kinetics </h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>Function describing the solution of the differential equations describing + the kinetic model with first-order terms for a two-way transfer from a free + to a bound fraction, and a first-order degradation term for the free + fraction. The initial condition is a defined amount in the free fraction and + no substance in the bound fraction.</p> + + + <pre><span class='fu'>SFORB.solution</span>(<span class='no'>t</span>, <span class='no'>parent.0</span>, <span class='no'>k_12</span>, <span class='no'>k_21</span>, <span class='no'>k_1output</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>t</dt> + <dd> Time. </dd> + <dt>parent.0</dt> + <dd> Starting value for the response variable at time zero. </dd> + <dt>k_12</dt> + <dd> Kinetic constant describing transfer from free to bound. </dd> + <dt>k_21</dt> + <dd> Kinetic constant describing transfer from bound to free. </dd> + <dt>k_1output</dt> + <dd> Kinetic constant describing degradation of the free fraction. </dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>The value of the response variable, which is the sum of free and bound + fractions at time <code>t</code>.</p> + </div> + + <div class="References"> + <h2>References</h2> + + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + Degradation Kinetics from Environmental Fate Studies on Pesticides in EU + Registration” Report of the FOCUS Work Group on Degradation Kinetics, + EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, + <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'> <span class='co'>## Not run: plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)</span></div></pre> + </div> + <div class="col-md-3"> + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html new file mode 100644 index 00000000..cbc925ca --- /dev/null +++ b/docs/reference/add_err.html @@ -0,0 +1,196 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>add_err. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>Normally distributed errors are added to data predicted for a specific + degradation model using <code>mkinpredict</code>. The variance of the error + may depend on the predicted value and is specified as a standard deviation.</p> + + + <pre><span class='fu'>add_err</span>(<span class='no'>prediction</span>, <span class='no'>sdfunc</span>, + <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1000</span>, <span class='kw'>LOD</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>reps</span> <span class='kw'>=</span> <span class='fl'>2</span>, + <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>prediction</dt> + <dd> + A prediction from a kinetic model as produced by <code>mkinpredict</code>. + </dd> + <dt>sdfunc</dt> + <dd> + A function taking the predicted value as its only argument and returning + a standard deviation that should be used for generating the random error + terms for this value. + </dd> + <dt>n</dt> + <dd> + The number of datasets to be generated. + </dd> + <dt>LOD</dt> + <dd> + The limit of detection (LOD). Values that are below the LOD after adding + the random error will be set to NA. + </dd> + <dt>reps</dt> + <dd> + The number of replicates to be generated within the datasets. + </dd> + <dt>digits</dt> + <dd> + The number of digits to which the values will be rounded. + </dd> + <dt>seed</dt> + <dd> + The seed used for the generation of random numbers. If NA, the seed + is not set. + </dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>A list of datasets compatible with <code>mmkin</code>, i.e. + the components of the list are datasets compatible with + <code>mkinfit</code>.</p> + </div> + + <div class="References"> + <h2>References</h2> + + <p>Ranke J and Lehmann R (2015) To t-test or not to t-test, that is the question. XV Symposium on Pesticide Chemistry 2-4 September 2015, Piacenza, Italy + http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf</p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class='co'># The kinetic model</span> +<span class='no'>m_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"M1"</span>), + <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> +<span class='co'># Generate a prediction for a specific set of parameters</span> +<span class='no'>sampling_times</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span>) + +<span class='co'># This is the prediction used for the "Type 2 datasets" on the Piacenza poster</span> +<span class='co'># from 2015</span> +<span class='no'>d_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinpredict</span>(<span class='no'>m_SFO_SFO</span>, + <span class='fu'>c</span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>f_parent_to_M1</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, + <span class='kw'>k_M1</span> <span class='kw'>=</span> <span class='fu'>log</span>(<span class='fl'>2</span>)/<span class='fl'>1000</span>), + <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fl'>0</span>), + <span class='no'>sampling_times</span>) + +<span class='co'># Add an error term with a constant (independent of the value) standard deviation</span> +<span class='co'># of 10, and generate three datasets</span> +<span class='no'>d_SFO_SFO_err</span> <span class='kw'><-</span> <span class='fu'>add_err</span>(<span class='no'>d_SFO_SFO</span>, <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fl'>10</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456789</span> ) + +<span class='co'># Name the datasets for nicer plotting</span> +<span class='fu'>names</span>(<span class='no'>d_SFO_SFO_err</span>) <span class='kw'><-</span> <span class='fu'>paste</span>(<span class='st'>"Dataset"</span>, <span class='fl'>1</span>:<span class='fl'>3</span>) + +<span class='co'># Name the model in the list of models (with only one member in this case)</span> +<span class='co'># for nicer plotting later on.</span> +<span class='co'># Be quiet and use the faster Levenberg-Marquardt algorithm, as the datasets</span> +<span class='co'># are easy and examples are run often. Use only one core not to offend CRAN</span> +<span class='co'># checks</span> +<span class='no'>f_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='fu'>list</span>(<span class='st'>"SFO-SFO"</span> <span class='kw'>=</span> <span class='no'>m_SFO_SFO</span>), + <span class='no'>d_SFO_SFO_err</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, + <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>) + +<span class='fu'>plot</span>(<span class='no'>f_SFO_SFO</span>)</div><img src='unknown-4.png' alt='' width='540' height='400' /><div class='input'> +<span class='co'># We would like to inspect the fit for dataset 3 more closely</span> +<span class='co'># Using double brackets makes the returned object an mkinfit object</span> +<span class='co'># instead of a list of mkinfit objects, so plot.mkinfit is used</span> +<span class='fu'>plot</span>(<span class='no'>f_SFO_SFO</span><span class='kw'>[[</span><span class='fl'>3</span>]], <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='unknown-6.png' alt='' width='540' height='400' /><div class='input'> +<span class='co'># If we use single brackets, we should give two indices (model and dataset),</span> +<span class='co'># and plot.mmkin is used</span> +<span class='fu'>plot</span>(<span class='no'>f_SFO_SFO</span>[<span class='fl'>1</span>, <span class='fl'>3</span>])</div><img src='unknown-8.png' alt='' width='540' height='400' /><div class='input'> +</div></pre> + </div> + <div class="col-md-3"> + <h2>Author</h2> + + Johannes Ranke + + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html new file mode 100644 index 00000000..8ceb39d9 --- /dev/null +++ b/docs/reference/endpoints.html @@ -0,0 +1,123 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>endpoints. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>This function calculates DT50 and DT90 values as well as formation fractions from kinetic models +fitted with mkinfit. If the SFORB model was specified for one of the parents or metabolites, +the Eigenvalues are returned. These are equivalent to the rate constantes of the DFOP model, but +with the advantage that the SFORB model can also be used for metabolites.</p> + + + <pre><span class='fu'>endpoints</span>(<span class='no'>fit</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>fit</dt> + <dd> + An object of class <code>mkinfit</code>. + </dd> + </dl> + + <div class="Note"> + <h2>Note</h2> + + <p>The function is used internally by <code>summary.mkinfit</code>.</p> + </div> + + <div class="Value"> + <h2>Value</h2> + + <p>A list with the components mentioned above.</p> + </div> + </div> + <div class="col-md-3"> + <h2>Author</h2> + + Johannes Ranke + + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html new file mode 100644 index 00000000..1d9a9e66 --- /dev/null +++ b/docs/reference/geometric_mean.html @@ -0,0 +1,115 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>geometric_mean. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> Calculate the geometric mean </h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>Function calculating the geometric mean of numeric vectors</p> + + + <pre><span class='fu'>geometric_mean</span>(<span class='no'>x</span>, <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>x</dt> + <dd> A numeric vector </dd> + <dt>na.rm</dt> + <dd> Should NA values be ignored </dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>The geometric mean.</p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>3</span>, <span class='fl'>9</span>))</div><div class='output co'>#> [1] 3 +#> </div><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>3</span>, <span class='fl'>NA</span>))</div><div class='output co'>#> [1] NA +#> </div><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>3</span>, <span class='fl'>NA</span>), <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> [1] 1.732051 +#> </div></pre> + </div> + <div class="col-md-3"> + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html new file mode 100644 index 00000000..355cbb78 --- /dev/null +++ b/docs/reference/ilr.html @@ -0,0 +1,152 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>ilr. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>This implementation is a special case of the class of isometric log-ratio transformations.</p> + + + <pre><span class='fu'>ilr</span>(<span class='no'>x</span>) + <span class='fu'>invilr</span>(<span class='no'>x</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>x</dt> + <dd> + A numeric vector. Naturally, the forward transformation is only sensible for + vectors with all elements being greater than zero. + </dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>The result of the forward or backward transformation. The returned components always + sum to 1 for the case of the inverse log-ratio transformation.</p> + </div> + + <div class="References"> + <h2>References</h2> + + <p>Peter Filzmoser, Karel Hron (2008) Outlier Detection for Compositional Data Using Robust Methods. Math Geosci 40 233-248</p> + </div> + + <div class="See also"> + <h2>See also</h2> + + <p>Another implementation can be found in R package <code>robCompositions</code>.</p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class='co'># Order matters</span> +<span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>0.1</span>, <span class='fl'>1</span>, <span class='fl'>10</span>))</div><div class='output co'>#> [1] -1.628174 -2.820079 +#> </div><div class='input'><span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>10</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>))</div><div class='output co'>#> [1] 1.628174 2.820079 +#> </div><div class='input'><span class='co'># Equal entries give ilr transformations with zeros as elements</span> +<span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>3</span>, <span class='fl'>3</span>, <span class='fl'>3</span>))</div><div class='output co'>#> [1] 0 0 +#> </div><div class='input'><span class='co'># Almost equal entries give small numbers</span> +<span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>0.3</span>, <span class='fl'>0.4</span>, <span class='fl'>0.3</span>))</div><div class='output co'>#> [1] -0.2034219 0.1174457 +#> </div><div class='input'><span class='co'># Only the ratio between the numbers counts, not their sum</span> +<span class='fu'>invilr</span>(<span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='fl'>0.7</span>, <span class='fl'>0.29</span>, <span class='fl'>0.01</span>)))</div><div class='output co'>#> [1] 0.70 0.29 0.01 +#> </div><div class='input'><span class='fu'>invilr</span>(<span class='fu'>ilr</span>(<span class='fl'>2.1</span> * <span class='fu'>c</span>(<span class='fl'>0.7</span>, <span class='fl'>0.29</span>, <span class='fl'>0.01</span>)))</div><div class='output co'>#> [1] 0.70 0.29 0.01 +#> </div><div class='input'><span class='co'># Inverse transformation of larger numbers gives unequal elements</span> +<span class='fu'>invilr</span>(-<span class='fl'>10</span>)</div><div class='output co'>#> [1] 7.213536e-07 9.999993e-01 +#> </div><div class='input'><span class='fu'>invilr</span>(<span class='fu'>c</span>(-<span class='fl'>10</span>, <span class='fl'>0</span>))</div><div class='output co'>#> [1] 7.207415e-07 9.991507e-01 8.486044e-04 +#> </div><div class='input'><span class='co'># The sum of the elements of the inverse ilr is 1</span> +<span class='fu'>sum</span>(<span class='fu'>invilr</span>(<span class='fu'>c</span>(-<span class='fl'>10</span>, <span class='fl'>0</span>)))</div><div class='output co'>#> [1] 1 +#> </div><div class='input'><span class='co'># This is why we do not need all elements of the inverse transformation to go back:</span> +<span class='no'>a</span> <span class='kw'><-</span> <span class='fu'>c</span>(<span class='fl'>0.1</span>, <span class='fl'>0.3</span>, <span class='fl'>0.5</span>) +<span class='no'>b</span> <span class='kw'><-</span> <span class='fu'>invilr</span>(<span class='no'>a</span>) +<span class='fu'>length</span>(<span class='no'>b</span>) <span class='co'># Four elements</span></div><div class='output co'>#> [1] 4 +#> </div><div class='input'><span class='fu'>ilr</span>(<span class='fu'>c</span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='fl'>1</span> - <span class='fu'>sum</span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>]))) <span class='co'># Gives c(0.1, 0.3, 0.5)</span></div><div class='output co'>#> [1] 0.1 0.3 0.5 +#> </div></pre> + </div> + <div class="col-md-3"> + <h2>Author</h2> + + René Lehmann and Johannes Ranke + + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. 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Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html new file mode 100644 index 00000000..edfce55a --- /dev/null +++ b/docs/reference/mccall81_245T.html @@ -0,0 +1,229 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>mccall81_245T. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding + 2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether + extracts.</p> + + + <pre><span class='no'>mccall81_245T</span></pre> + + <div class="Format"> + <h2>Format</h2> + + <p>A dataframe containing the following variables. + <dl class='dl-horizontal'> + <dt><code>name</code></dt><dd>the name of the compound observed. Note that T245 is used as + an acronym for 2,4,5-T. T245 is a legitimate object name + in R, which is necessary for specifying models using + <code>mkinmod</code>.</dd> + <dt><code>time</code></dt><dd>a numeric vector containing sampling times in days after + treatment</dd> + <dt><code>value</code></dt><dd>a numeric vector containing concentrations in percent of applied radioactivity</dd> + <dt><code>soil</code></dt><dd>a factor containing the name of the soil</dd> + </dl></p> + </div> + + <div class="Source"> + <h2>Source</h2> + + <p>McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labeled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107 + <a href = 'http://dx.doi.org/10.1021/jf00103a026'>http://dx.doi.org/10.1021/jf00103a026</a></p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"phenol"</span>), + <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"anisole"</span>), + <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> <span class='co'>## Not run: ------------------------------------</span> +<span class='co'># fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"))</span> +<span class='co'># summary(fit.1, data = FALSE)</span> +<span class='co'># </span> +<span class='co'>## ---------------------------------------------</span> + <span class='co'># No covariance matrix and k_phenol_sink is really small, therefore fix it to zero</span> + <span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), + <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>), + <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 +#> R version: 3.3.1 +#> Date of fit: Thu Oct 6 09:17:57 2016 +#> Date of summary: Thu Oct 6 09:17:57 2016 +#> +#> Equations: +#> d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245 +#> d_phenol = + k_T245_phenol * T245 - k_phenol_sink * phenol - +#> k_phenol_anisole * phenol +#> d_anisole = + k_phenol_anisole * phenol - k_anisole_sink * anisole +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 246 model solutions performed in 1.508 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> T245_0 100.9000 state +#> k_T245_sink 0.1000 deparm +#> k_T245_phenol 0.1001 deparm +#> k_phenol_anisole 0.1002 deparm +#> k_anisole_sink 0.1003 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> T245_0 100.900000 -Inf Inf +#> log_k_T245_sink -2.302585 -Inf Inf +#> log_k_T245_phenol -2.301586 -Inf Inf +#> log_k_phenol_anisole -2.300587 -Inf Inf +#> log_k_anisole_sink -2.299590 -Inf Inf +#> +#> Fixed parameter values: +#> value type +#> phenol_0 0 state +#> anisole_0 0 state +#> k_phenol_sink 0 deparm +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> T245_0 103.9000 2.35200 98.930 108.8000 +#> log_k_T245_sink -4.1130 0.13250 -4.390 -3.8350 +#> log_k_T245_phenol -3.6120 0.05002 -3.716 -3.5070 +#> log_k_phenol_anisole -0.9037 0.30580 -1.544 -0.2637 +#> log_k_anisole_sink -5.0090 0.11180 -5.243 -4.7750 +#> +#> Parameter correlation: +#> T245_0 log_k_T245_sink log_k_T245_phenol +#> T245_0 1.00000 0.63761 -0.1742 +#> log_k_T245_sink 0.63761 1.00000 -0.3831 +#> log_k_T245_phenol -0.17416 -0.38313 1.0000 +#> log_k_phenol_anisole -0.05948 0.08745 -0.3047 +#> log_k_anisole_sink -0.16208 -0.60469 0.5227 +#> log_k_phenol_anisole log_k_anisole_sink +#> T245_0 -0.05948 -0.1621 +#> log_k_T245_sink 0.08745 -0.6047 +#> log_k_T245_phenol -0.30470 0.5227 +#> log_k_phenol_anisole 1.00000 -0.1774 +#> log_k_anisole_sink -0.17744 1.0000 +#> +#> Residual standard error: 2.706 on 19 degrees of freedom +#> +#> Backtransformed parameters: +#> Confidence intervals for internally transformed parameters are asymmetric. +#> t-test (unrealistically) based on the assumption of normal distribution +#> for estimators of untransformed parameters. +#> Estimate t value Pr(>t) Lower Upper +#> T245_0 1.039e+02 44.160 6.462e-21 98.930000 108.80000 +#> k_T245_sink 1.636e-02 7.545 1.978e-07 0.012400 0.02159 +#> k_T245_phenol 2.701e-02 19.990 1.607e-14 0.024320 0.02999 +#> k_phenol_anisole 4.051e-01 3.270 2.014e-03 0.213600 0.76820 +#> k_anisole_sink 6.679e-03 8.942 1.544e-08 0.005285 0.00844 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 9.831 5 17 +#> T245 7.908 3 5 +#> phenol 99.808 1 6 +#> anisole 5.379 1 6 +#> +#> Resulting formation fractions: +#> ff +#> T245_sink 0.3772 +#> T245_phenol 0.6228 +#> phenol_anisole 1.0000 +#> phenol_sink 0.0000 +#> anisole_sink 1.0000 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> T245 15.982 53.091 +#> phenol 1.711 5.685 +#> anisole 103.784 344.763 +#> </div></pre> + </div> + <div class="col-md-3"> + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html new file mode 100644 index 00000000..5b1a8353 --- /dev/null +++ b/docs/reference/mkin_long_to_wide.html @@ -0,0 +1,152 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>mkin_long_to_wide. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>This function takes a dataframe in the long form as required by <code>modCost</code> + and converts it into a dataframe with one independent variable and several + dependent variables as columns.</p> + + + <pre><span class='fu'>mkin_long_to_wide</span>(<span class='no'>long_data</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>, <span class='kw'>outtime</span> <span class='kw'>=</span> <span class='st'>"time"</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>long_data</dt> + <dd> + The dataframe must contain one variable called "time" with the time values specified by the + <code>time</code> argument, one column called "name" with the grouping of the observed values, and + finally one column of observed values called "value". +</dd> + <dt>time</dt> + <dd> + The name of the time variable in the long input data. +</dd> + <dt>outtime</dt> + <dd> + The name of the time variable in the wide output data. +</dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>Dataframe in wide format.</p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class='fu'>mkin_long_to_wide</span>(<span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#> time parent m1 +#> 1 0 99.46 0.00 +#> 2 0 102.04 0.00 +#> 3 1 93.50 4.84 +#> 4 1 92.50 5.64 +#> 5 3 63.23 12.91 +#> 6 3 68.99 12.96 +#> 7 7 52.32 22.97 +#> 8 7 55.13 24.47 +#> 9 14 27.27 41.69 +#> 10 14 26.64 33.21 +#> 11 21 11.50 44.37 +#> 12 21 11.64 46.44 +#> 13 35 2.85 41.22 +#> 14 35 2.91 37.95 +#> 15 50 0.69 41.19 +#> 16 50 0.63 40.01 +#> 17 75 0.05 40.09 +#> 18 75 0.06 33.85 +#> 19 100 NA 31.04 +#> 20 100 NA 33.13 +#> 21 120 NA 25.15 +#> 22 120 NA 33.31 +#> </div></pre> + </div> + <div class="col-md-3"> + <h2>Author</h2> + + Johannes Ranke + + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html new file mode 100644 index 00000000..2a70ebbe --- /dev/null +++ b/docs/reference/mkin_wide_to_long.html @@ -0,0 +1,131 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>mkin_wide_to_long. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>This function simply takes a dataframe with one independent variable and several + dependent variable and converts it into the long form as required by <code>modCost</code>.</p> + + + <pre><span class='fu'>mkin_wide_to_long</span>(<span class='no'>wide_data</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"t"</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>wide_data</dt> + <dd> + The dataframe must contain one variable with the time values specified by the + <code>time</code> argument and usually more than one column of observed values. +</dd> + <dt>time</dt> + <dd> + The name of the time variable. +</dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>Dataframe in long format as needed for <code>modCost</code>.</p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class='no'>wide</span> <span class='kw'><-</span> <span class='fu'>data.frame</span>(<span class='kw'>t</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>2</span>,<span class='fl'>3</span>), <span class='kw'>x</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>1</span>,<span class='fl'>4</span>,<span class='fl'>7</span>), <span class='kw'>y</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>3</span>,<span class='fl'>4</span>,<span class='fl'>5</span>)) +<span class='fu'>mkin_wide_to_long</span>(<span class='no'>wide</span>)</div><div class='output co'>#> name time value +#> 1 x 1 1 +#> 2 x 2 4 +#> 3 x 3 7 +#> 4 y 1 3 +#> 5 y 2 4 +#> 6 y 3 5 +#> </div></pre> + </div> + <div class="col-md-3"> + <h2>Author</h2> + + Johannes Ranke + + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html new file mode 100644 index 00000000..0b4341aa --- /dev/null +++ b/docs/reference/mkinds.html @@ -0,0 +1,120 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>mkinds. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1>A dataset class for mkin</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>A dataset class for mkin</p> + + + <pre><span class='no'>mkinds</span></pre> + + <div class="Format"> + <h2>Format</h2> + + <p>An <code>R6Class</code> generator object.</p> + </div> + + <div class="Fields"> + <h2>Fields</h2> + + <p></p> + <p><dl class='dl-horizontal'> +<dt><code>title</code></dt><dd>A full title for the dataset</dd></p> + <p><dt><code>sampling</code></dt><dd>times The sampling times</dd></p> + <p><dt><code>time_unit</code></dt><dd>The time unit</dd></p> + <p><dt><code>observed</code></dt><dd>Names of the observed compounds</dd></p> + <p><dt><code>unit</code></dt><dd>The unit of the observations</dd></p> + <p><dt><code>replicates</code></dt><dd>The number of replicates</dd></p> + <p><dt><code>data</code></dt><dd>A dataframe with at least the columns name, time and value +in order to be compatible with mkinfit</dd> +</dl></p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class='no'>mds</span> <span class='kw'><-</span> <span class='no'>mkinds</span>$<span class='fu'>new</span>(<span class='st'>"FOCUS A"</span>, <span class='no'>FOCUS_2006_A</span>)</div></pre> + </div> + <div class="col-md-3"> + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. 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<div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>This function uses <code>optimize</code> in order to iteratively find the +smallest relative error still resulting in passing the chi-squared test +as defined in the FOCUS kinetics report from 2006.</p> + + + <pre><span class='fu'>mkinerrmin</span>(<span class='no'>fit</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.05</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>fit</dt> + <dd> + an object of class <code>mkinfit</code>. + </dd> + <dt>alpha</dt> + <dd> + The confidence level chosen for the chi-squared test. +</dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>A dataframe with the following components:</p> + <p>The dataframe has one row for the total dataset and one further row for + each observed state variable in the model.</p> + </div> + + <div class="Details"> + <h2>Details</h2> + + <p>This function is used internally by <code>summary.mkinfit</code>.</p> + </div> + + <div class="References"> + <h2>References</h2> + + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + Degradation Kinetics from Environmental Fate Studies on Pesticides in EU + Registration” Report of the FOCUS Work Group on Degradation Kinetics, + EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, + <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class='no'>SFO_SFO</span> <span class='kw'>=</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>), + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), + <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> +<span class='no'>fit_FOCUS_D</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='fu'>round</span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_D</span>), <span class='fl'>4</span>)</div><div class='output co'>#> err.min n.optim df +#> All data 0.0640 4 15 +#> parent 0.0646 2 7 +#> m1 0.0469 2 8 +#> </div><div class='input'><span class='no'>fit_FOCUS_E</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_E</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='fu'>round</span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_E</span>), <span class='fl'>4</span>)</div><div class='output co'>#> err.min n.optim df +#> All data 0.1544 4 13 +#> parent 0.1659 2 7 +#> m1 0.1095 2 6 +#> </div></pre> + </div> + <div class="col-md-3"> + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html new file mode 100644 index 00000000..d1441f8b --- /dev/null +++ b/docs/reference/mkinfit.html @@ -0,0 +1,531 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>mkinfit. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>This function uses the Flexible Modelling Environment package + <code>FME</code> to create a function calculating the model cost, i.e. the + deviation between the kinetic model and the observed data. This model cost is + then minimised using the Port algorithm <code>nlminb</code>, + using the specified initial or fixed parameters and starting values. + Per default, parameters in the kinetic models are internally transformed in order + to better satisfy the assumption of a normal distribution of their estimators. + In each step of the optimsation, the kinetic model is solved using the + function <code>mkinpredict</code>. The variance of the residuals for each + observed variable can optionally be iteratively reweighted until convergence + using the argument <code>reweight.method = "obs"</code>.</p> + + + <pre><span class='fu'>mkinfit</span>(<span class='no'>mkinmod</span>, <span class='no'>observed</span>, + <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>state.ini</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>fixed_initials</span> <span class='kw'>=</span> <span class='fu'>names</span>(<span class='no'>mkinmod</span>$<span class='no'>diffs</span>)[-<span class='fl'>1</span>], + <span class='kw'>from_max_mean</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"auto"</span>, <span class='st'>"analytical"</span>, <span class='st'>"eigen"</span>, <span class='st'>"deSolve"</span>), + <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, + <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>method.modFit</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"Port"</span>, <span class='st'>"Marq"</span>, <span class='st'>"SANN"</span>, <span class='st'>"Nelder-Mead"</span>, <span class='st'>"BFGS"</span>, <span class='st'>"CG"</span>, <span class='st'>"L-BFGS-B"</span>), + <span class='kw'>maxit.modFit</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, + <span class='kw'>control.modFit</span> <span class='kw'>=</span> <span class='fu'>list</span>(), + <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>plot</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"none"</span>, + <span class='kw'>scaleVar</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, + <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-8</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, <span class='kw'>n.outtimes</span> <span class='kw'>=</span> <span class='fl'>100</span>, + <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, + <span class='kw'>reweight.tol</span> <span class='kw'>=</span> <span class='fl'>1e-8</span>, <span class='kw'>reweight.max.iter</span> <span class='kw'>=</span> <span class='fl'>10</span>, + <span class='kw'>trace_parms</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>mkinmod</dt> + <dd> + A list of class <code>mkinmod</code>, containing the kinetic model to be + fitted to the data, or one of the shorthand names ("SFO", "FOMC", "DFOP", + "HS", "SFORB"). If a shorthand name is given, a parent only degradation + model is generated for the variable with the highest value in + <code>observed</code>. + </dd> + <dt>observed</dt> + <dd> + The observed data. It has to be in the long format as described in + <code>modFit</code>, i.e. the first column called "name" must contain the + name of the observed variable for each data point. The second column must + contain the times of observation, named "time". The third column must be + named "value" and contain the observed values. Optionally, a further column + can contain weights for each data point. Its name must be passed as a + further argument named <code>err</code> which is then passed on to + <code>modFit</code>. + </dd> + <dt>parms.ini</dt> + <dd> + A named vector of initial values for the parameters, including parameters + to be optimised and potentially also fixed parameters as indicated by + <code>fixed_parms</code>. If set to "auto", initial values for rate constants + are set to default values. Using parameter names that are not in the model + gives an error. + + It is possible to only specify a subset of the parameters that the model + needs. You can use the parameter lists "bparms.ode" from a previously + fitted model, which contains the differential equation parameters from this + model. This works nicely if the models are nested. An example is given + below. + </dd> + <dt>state.ini</dt> + <dd> + A named vector of initial values for the state variables of the model. In + case the observed variables are represented by more than one model + variable, the names will differ from the names of the observed variables + (see <code>map</code> component of <code>mkinmod</code>). The default is to set + the initial value of the first model variable to the mean of the time zero + values for the variable with the maximum observed value, and all others to 0. + If this variable has no time zero observations, its initial value is set to 100. + </dd> + <dt>fixed_parms</dt> + <dd> + The names of parameters that should not be optimised but rather kept at the + values specified in <code>parms.ini</code>. + </dd> + <dt>fixed_initials</dt> + <dd> + The names of model variables for which the initial state at time 0 should + be excluded from the optimisation. Defaults to all state variables except + for the first one. + </dd> + <dt>from_max_mean</dt> + <dd> + If this is set to TRUE, and the model has only one observed variable, then + data before the time of the maximum observed value (after averaging for each + sampling time) are discarded, and this time is subtracted from all + remaining time values, so the time of the maximum observed mean value is + the new time zero. + </dd> + <dt>solution_type</dt> + <dd> + If set to "eigen", the solution of the system of differential equations is + based on the spectral decomposition of the coefficient matrix in cases that + this is possible. If set to "deSolve", a numerical ode solver from package + <code>deSolve</code> is used. If set to "analytical", an analytical + solution of the model is used. This is only implemented for simple + degradation experiments with only one state variable, i.e. with no + metabolites. The default is "auto", which uses "analytical" if possible, + otherwise "eigen" if the model can be expressed using eigenvalues and + eigenvectors, and finally "deSolve" for the remaining models (time + dependence of degradation rates and metabolites). This argument is passed + on to the helper function <code>mkinpredict</code>. + </dd> + <dt>method.ode</dt> + <dd> + The solution method passed via <code>mkinpredict</code> to + <code>ode</code> in case the solution type is "deSolve". The default + "lsoda" is performant, but sometimes fails to converge. + </dd> + <dt>use_compiled</dt> + <dd> + If set to <code>FALSE</code>, no compiled version of the <code>mkinmod</code> + model is used, in the calls to <code>mkinpredict</code> even if + a compiled verion is present. + </dd> + <dt>method.modFit</dt> + <dd> + The optimisation method passed to <code>modFit</code>. + + In order to optimally deal with problems where local minima occur, the + "Port" algorithm is now used per default as it is less prone to get trapped + in local minima and depends less on starting values for parameters than + the Levenberg Marquardt variant selected by "Marq". However, "Port" needs + more iterations. + + The former default "Marq" is the Levenberg Marquardt algorithm + <code>nls.lm</code> from the package <code>minpack.lm</code> and usually needs + the least number of iterations. + + The "Pseudo" algorithm is not included because it needs finite parameter bounds + which are currently not supported. + + The "Newton" algorithm is not included because its number of iterations + can not be controlled by <code>control.modFit</code> and it does not appear + to provide advantages over the other algorithms. + </dd> + <dt>maxit.modFit</dt> + <dd> + Maximum number of iterations in the optimisation. If not "auto", this will + be passed to the method called by <code>modFit</code>, overriding + what may be specified in the next argument <code>control.modFit</code>. + </dd> + <dt>control.modFit</dt> + <dd> + Additional arguments passed to the optimisation method used by + <code>modFit</code>. + </dd> + <dt>transform_rates</dt> + <dd> + Boolean specifying if kinetic rate constants should be transformed in the + model specification used in the fitting for better compliance with the + assumption of normal distribution of the estimator. If TRUE, also + alpha and beta parameters of the FOMC model are log-transformed, as well + as k1 and k2 rate constants for the DFOP and HS models and the break point + tb of the HS model. + If FALSE, zero is used as a lower bound for the rates in the optimisation. + </dd> + <dt>transform_fractions</dt> + <dd> + Boolean specifying if formation fractions constants should be transformed in the + model specification used in the fitting for better compliance with the + assumption of normal distribution of the estimator. The default (TRUE) is + to do transformations. If TRUE, the g parameter of the DFOP and HS + models are also transformed, as they can also be seen as compositional + data. The transformation used for these transformations is the + <code>ilr</code> transformation. + </dd> + <dt>plot</dt> + <dd> + Should the observed values and the numerical solutions be plotted at each + stage of the optimisation? + </dd> + <dt>quiet</dt> + <dd> + Suppress printing out the current model cost after each improvement? + </dd> + <dt>err </dt> + <dd>either <code>NULL</code>, or the name of the column with the + <em>error</em> estimates, used to weigh the residuals (see details of + <code>modCost</code>); if <code>NULL</code>, then the residuals are not weighed. + </dd> + <dt>weight</dt> + <dd> + only if <code>err</code>=<code>NULL</code>: how to weight the residuals, one of "none", + "std", "mean", see details of <code>modCost</code>. + </dd> + <dt>scaleVar</dt> + <dd> + Will be passed to <code>modCost</code>. Default is not to scale Variables + according to the number of observations. + </dd> + <dt>atol</dt> + <dd> + Absolute error tolerance, passed to <code>ode</code>. Default is 1e-8, + lower than in <code>lsoda</code>. + </dd> + <dt>rtol</dt> + <dd> + Absolute error tolerance, passed to <code>ode</code>. Default is 1e-10, + much lower than in <code>lsoda</code>. + </dd> + <dt>n.outtimes</dt> + <dd> + The length of the dataseries that is produced by the model prediction + function <code>mkinpredict</code>. This impacts the accuracy of + the numerical solver if that is used (see <code>solution_type</code> argument. + The default value is 100. + </dd> + <dt>reweight.method</dt> + <dd> + The method used for iteratively reweighting residuals, also known + as iteratively reweighted least squares (IRLS). Default is NULL, + the other method implemented is called "obs", meaning that each + observed variable is assumed to have its own variance, this is + estimated from the fit and used for weighting the residuals + in each iteration until convergence of this estimate up to + <code>reweight.tol</code> or up to the maximum number of iterations + specified by <code>reweight.max.iter</code>. + </dd> + <dt>reweight.tol</dt> + <dd> + Tolerance for convergence criterion for the variance components + in IRLS fits. + </dd> + <dt>reweight.max.iter</dt> + <dd> + Maximum iterations in IRLS fits. + </dd> + <dt>trace_parms</dt> + <dd> + Should a trace of the parameter values be listed? + </dd> + <dt>&#8230;</dt> + <dd> + Further arguments that will be passed to <code>modFit</code>. + </dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>A list with "mkinfit" and "modFit" in the class attribute. + A summary can be obtained by <code>summary.mkinfit</code>.</p> + </div> + + <div class="See also"> + <h2>See also</h2> + + <p>Plotting methods <code>plot.mkinfit</code> and + <code>mkinparplot</code>.</p> + <p>Fitting of several models to several datasets in a single call to + <code>mmkin</code>.</p> + </div> + + <div class="Note"> + <h2>Note</h2> + + <p>The implementation of iteratively reweighted least squares is inspired by the + work of the KinGUII team at Bayer Crop Science (Walter Schmitt and Zhenglei + Gao). A similar implemention can also be found in CAKE 2.0, which is the + other GUI derivative of mkin, sponsored by Syngenta.</p> + </div> + + <div class="Note"> + <h2>Note</h2> + + <p>When using the "IORE" submodel for metabolites, fitting with + "transform_rates = TRUE" (the default) often leads to failures of the + numerical ODE solver. In this situation it may help to switch off the + internal rate transformation.</p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class='co'># Use shorthand notation for parent only degradation</span> +<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 +#> R version: 3.3.1 +#> Date of fit: Thu Oct 6 09:17:59 2016 +#> Date of summary: Thu Oct 6 09:17:59 2016 +#> +#> Equations: +#> d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent +#> +#> Model predictions using solution type analytical +#> +#> Fitted with method Port using 64 model solutions performed in 0.153 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 85.1 state +#> alpha 1.0 deparm +#> beta 10.0 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 85.100000 -Inf Inf +#> log_alpha 0.000000 -Inf Inf +#> log_beta 2.302585 -Inf Inf +#> +#> Fixed parameter values: +#> None +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 85.87000 2.2460 80.38000 91.3700 +#> log_alpha 0.05192 0.1605 -0.34080 0.4446 +#> log_beta 0.65100 0.2801 -0.03452 1.3360 +#> +#> Parameter correlation: +#> parent_0 log_alpha log_beta +#> parent_0 1.0000 -0.2033 -0.3624 +#> log_alpha -0.2033 1.0000 0.9547 +#> log_beta -0.3624 0.9547 1.0000 +#> +#> Residual standard error: 2.275 on 6 degrees of freedom +#> +#> Backtransformed parameters: +#> Confidence intervals for internally transformed parameters are asymmetric. +#> t-test (unrealistically) based on the assumption of normal distribution +#> for estimators of untransformed parameters. +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 85.870 38.230 1.069e-08 80.3800 91.370 +#> alpha 1.053 6.231 3.953e-04 0.7112 1.560 +#> beta 1.917 3.570 5.895e-03 0.9661 3.806 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.657 3 6 +#> parent 6.657 3 6 +#> +#> Estimated disappearance times: +#> DT50 DT90 DT50back +#> parent 1.785 15.15 4.56 +#> +#> Data: +#> time variable observed predicted residual +#> 0 parent 85.1 85.875 -0.7749 +#> 1 parent 57.9 55.191 2.7091 +#> 3 parent 29.9 31.845 -1.9452 +#> 7 parent 14.6 17.012 -2.4124 +#> 14 parent 9.7 9.241 0.4590 +#> 28 parent 6.6 4.754 1.8460 +#> 63 parent 4.0 2.102 1.8977 +#> 91 parent 3.9 1.441 2.4590 +#> 119 parent 0.6 1.092 -0.4919 +#> </div><div class='input'> +<span class='co'># One parent compound, one metabolite, both single first order.</span> +<span class='co'># Use mkinsub for convenience in model formulation. Pathway to sink included per default.</span> +<span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( + <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> +<span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#> user system elapsed +#> 1.252 1.176 0.914 +#> </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 99.59848 -3.03822 -2.98030 -5.24750 +#> </div><div class='input'><span class='fu'>endpoints</span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff +#> parent_sink parent_m1 m1_sink +#> 0.485524 0.514476 1.000000 +#> +#> $SFORB +#> logical(0) +#> +#> $distimes +#> DT50 DT90 +#> parent 7.022929 23.32967 +#> m1 131.760712 437.69961 +#> +#> </div><div class='input'><span class='co'>## Not run: ------------------------------------</span> +<span class='co'># # deSolve is slower when no C compiler (gcc) was available during model generation</span> +<span class='co'># print(system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D, </span> +<span class='co'># solution_type = "deSolve")))</span> +<span class='co'># coef(fit.deSolve)</span> +<span class='co'># endpoints(fit.deSolve)</span> +<span class='co'>## ---------------------------------------------</span> + +<span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, FOMC</span> +<span class='co'>## Not run: ------------------------------------</span> +<span class='co'># FOMC_SFO <- mkinmod(</span> +<span class='co'># parent = mkinsub("FOMC", "m1"),</span> +<span class='co'># m1 = mkinsub("SFO"))</span> +<span class='co'># # Fit the model to the FOCUS example dataset D using defaults</span> +<span class='co'># fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D)</span> +<span class='co'># # Use starting parameters from parent only FOMC fit</span> +<span class='co'># fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, plot=TRUE)</span> +<span class='co'># fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, </span> +<span class='co'># parms.ini = fit.FOMC$bparms.ode, plot=TRUE)</span> +<span class='co'># </span> +<span class='co'># # Use stepwise fitting, using optimised parameters from parent only fit, SFORB</span> +<span class='co'># SFORB_SFO <- mkinmod(</span> +<span class='co'># parent = list(type = "SFORB", to = "m1", sink = TRUE),</span> +<span class='co'># m1 = list(type = "SFO"))</span> +<span class='co'># # Fit the model to the FOCUS example dataset D using defaults</span> +<span class='co'># fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D)</span> +<span class='co'># fit.SFORB_SFO.deSolve <- mkinfit(SFORB_SFO, FOCUS_2006_D, solution_type = "deSolve")</span> +<span class='co'># # Use starting parameters from parent only SFORB fit (not really needed in this case)</span> +<span class='co'># fit.SFORB = mkinfit("SFORB", FOCUS_2006_D)</span> +<span class='co'># fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode)</span> +<span class='co'>## ---------------------------------------------</span> + +<span class='co'>## Not run: ------------------------------------</span> +<span class='co'># # Weighted fits, including IRLS</span> +<span class='co'># SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"),</span> +<span class='co'># m1 = mkinsub("SFO"), use_of_ff = "max")</span> +<span class='co'># f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D)</span> +<span class='co'># summary(f.noweight)</span> +<span class='co'># f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs")</span> +<span class='co'># summary(f.irls)</span> +<span class='co'># f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean")</span> +<span class='co'># summary(f.w.mean)</span> +<span class='co'># f.w.value <- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), err = "value")</span> +<span class='co'># summary(f.w.value)</span> +<span class='co'>## ---------------------------------------------</span> + +<span class='co'>## Not run: ------------------------------------</span> +<span class='co'># # Manual weighting</span> +<span class='co'># dw <- FOCUS_2006_D</span> +<span class='co'># errors <- c(parent = 2, m1 = 1)</span> +<span class='co'># dw$err.man <- errors[FOCUS_2006_D$name]</span> +<span class='co'># f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man")</span> +<span class='co'># summary(f.w.man)</span> +<span class='co'># f.w.man.irls <- mkinfit(SFO_SFO.ff, dw, err = "err.man",</span> +<span class='co'># reweight.method = "obs")</span> +<span class='co'># summary(f.w.man.irls)</span> +<span class='co'>## ---------------------------------------------</span></div></pre> + </div> + <div class="col-md-3"> + <h2>Author</h2> + + Johannes Ranke + + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html new file mode 100644 index 00000000..9dd8fca0 --- /dev/null +++ b/docs/reference/mkinmod.html @@ -0,0 +1,206 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>mkinmod. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>The function usually takes several expressions, each assigning a compound name to + a list, specifying the kinetic model type and reaction or transfer to other + observed compartments. Instead of specifying several expressions, a list + of lists can be given in the speclist argument.</p> + + <p>For the definition of model types and their parameters, the equations given + in the FOCUS and NAFTA guidance documents are used.</p> + + + <pre><span class='fu'>mkinmod</span>(<span class='no'>...</span>, <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"min"</span>, <span class='kw'>speclist</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>...</dt> + <dd> + For each observed variable, a list has to be specified as an argument, containing + at least a component <code>type</code>, specifying the type of kinetics to use + for the variable. Currently, single first order kinetics "SFO", + indeterminate order rate equation kinetics "IORE", or + single first order with reversible binding "SFORB" are implemented for all + variables, while + "FOMC", "DFOP" and "HS" can additionally be chosen for the first + variable which is assumed to be the source compartment. + Additionally, each component of the list can include a character vector <code>to</code>, + specifying names of variables to which a transfer is to be assumed in the + model. + If the argument <code>use_of_ff</code> is set to "min" (default) and the model for + the compartment is "SFO" or "SFORB", an additional component of the list + can be "sink=FALSE" effectively fixing the flux to sink to zero. + </dd> + <dt>use_of_ff</dt> + <dd> + Specification of the use of formation fractions in the model equations and, if + applicable, the coefficient matrix. If "min", a minimum use of formation + fractions is made in order to avoid fitting the product of formation fractions + and rate constants. If "max", formation fractions are always used. + </dd> + <dt>speclist</dt> + <dd> + The specification of the observed variables and their submodel types and + pathways can be given as a single list using this argument. Default is NULL. + </dd> + <dt>quiet</dt> + <dd> + Should messages be suppressed? + </dd> + <dt>verbose</dt> + <dd> + If <code>TRUE</code>, passed to <code>cfunction</code> if applicable to give + detailed information about the C function being built. + </dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>A list of class <code>mkinmod</code> for use with <code>mkinfit</code>, containing</p> + </div> + + <div class="Note"> + <h2>Note</h2> + + <p>The IORE submodel is not well tested (yet). When using this model for metabolites, + you may want to read the second note in the help page to + <code>mkinfit</code>.</p> + </div> + + <div class="References"> + <h2>References</h2> + + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + Degradation Kinetics from Environmental Fate Studies on Pesticides in EU + Registration” Report of the FOCUS Work Group on Degradation Kinetics, + EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, + <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> + <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for + Evaluating and Calculating Degradation Kinetics in Environmental + Media</p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class='co'># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span> +<span class='no'>SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)) + +<span class='co'># One parent compound, one metabolite, both single first order</span> +<span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( + <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> +<span class='co'>## Not run: ------------------------------------</span> +<span class='co'># # The above model used to be specified like this, before the advent of mkinsub()</span> +<span class='co'># SFO_SFO <- mkinmod(</span> +<span class='co'># parent = list(type = "SFO", to = "m1"),</span> +<span class='co'># m1 = list(type = "SFO"))</span> +<span class='co'># </span> +<span class='co'># # Show details of creating the C function</span> +<span class='co'># SFO_SFO <- mkinmod(</span> +<span class='co'># parent = mkinsub("SFO", "m1"),</span> +<span class='co'># m1 = mkinsub("SFO"), verbose = TRUE)</span> +<span class='co'># </span> +<span class='co'># # If we have several parallel metabolites </span> +<span class='co'># # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span> +<span class='co'># m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),</span> +<span class='co'># M1 = mkinsub("SFO"),</span> +<span class='co'># M2 = mkinsub("SFO"),</span> +<span class='co'># use_of_ff = "max", quiet = TRUE)</span> +<span class='co'># </span> +<span class='co'># fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, </span> +<span class='co'># synthetic_data_for_UBA_2014[[12]]$data,</span> +<span class='co'># quiet = TRUE)</span> +<span class='co'>## ---------------------------------------------</span></div></pre> + </div> + <div class="col-md-3"> + <h2>Author</h2> + + Johannes Ranke + + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html new file mode 100644 index 00000000..f2fae22d --- /dev/null +++ b/docs/reference/mkinparplot.html @@ -0,0 +1,122 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>mkinparplot. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>This function plots the confidence intervals for the parameters + fitted using <code>mkinfit</code>.</p> + + + <pre><span class='fu'>mkinparplot</span>(<span class='no'>object</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>object</dt> + <dd> + A fit represented in an <code>mkinfit</code> object. + </dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class='no'>model</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( + <span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"phenol"</span>), <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>), + <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"anisole"</span>)), + <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>model</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='fu'>mkinparplot</span>(<span class='no'>fit</span>)</div><img src='unknown-4.png' alt='' width='540' height='400' /></pre> + </div> + <div class="col-md-3"> + <h2>Author</h2> + + Johannes Ranke + + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html new file mode 100644 index 00000000..51ca3992 --- /dev/null +++ b/docs/reference/mkinplot.html @@ -0,0 +1,118 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>mkinplot. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>Deprecated function. It now only calls the plot method <code>plot.mkinfit</code>.</p> + + + <pre><span class='fu'>mkinplot</span>(<span class='no'>fit</span>, <span class='no'>...</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>fit</dt> + <dd> + an object of class <code>mkinfit</code>. + </dd> + <dt>&#8230;</dt> + <dd> + further arguments passed to <code>plot.mkinfit</code>. +</dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>The function is called for its side effect.</p> + </div> + </div> + <div class="col-md-3"> + <h2>Author</h2> + + Johannes Ranke + + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html new file mode 100644 index 00000000..730792c1 --- /dev/null +++ b/docs/reference/mkinpredict.html @@ -0,0 +1,318 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>mkinpredict. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>This function produces a time series for all the observed variables in a + kinetic model as specified by <code>mkinmod</code>, using a specific set of + kinetic parameters and initial values for the state variables.</p> + + + <pre><span class='fu'>mkinpredict</span>(<span class='no'>mkinmod</span>, <span class='no'>odeparms</span>, <span class='no'>odeini</span>, <span class='no'>outtimes</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, + <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>method.ode</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>, <span class='kw'>atol</span> <span class='kw'>=</span> <span class='fl'>1e-08</span>, <span class='kw'>rtol</span> <span class='kw'>=</span> <span class='fl'>1e-10</span>, + <span class='kw'>map_output</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>mkinmod</dt> + <dd> + A kinetic model as produced by <code>mkinmod</code>. + </dd> + <dt>odeparms</dt> + <dd> + A numeric vector specifying the parameters used in the kinetic model, which + is generally defined as a set of ordinary differential equations. + </dd> + <dt>odeini</dt> + <dd> + A numeric vectory containing the initial values of the state variables of + the model. Note that the state variables can differ from the observed + variables, for example in the case of the SFORB model. + </dd> + <dt>outtimes</dt> + <dd> + A numeric vector specifying the time points for which model predictions + should be generated. + </dd> + <dt>solution_type</dt> + <dd> + The method that should be used for producing the predictions. This should + generally be "analytical" if there is only one observed variable, and + usually "deSolve" in the case of several observed variables. The third + possibility "eigen" is faster but not applicable to some models e.g. + using FOMC for the parent compound. + </dd> + <dt>method.ode</dt> + <dd> + The solution method passed via <code>mkinpredict</code> to + <code>ode</code> in case the solution type is "deSolve". The default + "lsoda" is performant, but sometimes fails to converge. + </dd> + <dt>use_compiled</dt> + <dd> + If set to <code>FALSE</code>, no compiled version of the <code>mkinmod</code> + model is used, even if is present. + </dd> + <dt>atol</dt> + <dd> + Absolute error tolerance, passed to <code>ode</code>. Default is 1e-8, + lower than in <code>lsoda</code>. + </dd> + <dt>rtol</dt> + <dd> + Absolute error tolerance, passed to <code>ode</code>. Default is 1e-10, + much lower than in <code>lsoda</code>. + </dd> + <dt>map_output</dt> + <dd> + Boolean to specify if the output should list values for the observed + variables (default) or for all state variables (if set to FALSE). + </dd> + <dt>&#8230;</dt> + <dd> + Further arguments passed to the ode solver in case such a solver is used. + </dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>A matrix in the same format as the output of <code>ode</code>.</p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'> <span class='no'>SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)) + <span class='co'># Compare solution types</span> + <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)</div><div class='output co'>#> time degradinol +#> 1 0 100.0000000 +#> 2 1 74.0818221 +#> 3 2 54.8811636 +#> 4 3 40.6569660 +#> 5 4 30.1194212 +#> 6 5 22.3130160 +#> 7 6 16.5298888 +#> 8 7 12.2456428 +#> 9 8 9.0717953 +#> 10 9 6.7205513 +#> 11 10 4.9787068 +#> 12 11 3.6883167 +#> 13 12 2.7323722 +#> 14 13 2.0241911 +#> 15 14 1.4995577 +#> 16 15 1.1108997 +#> 17 16 0.8229747 +#> 18 17 0.6096747 +#> 19 18 0.4516581 +#> 20 19 0.3345965 +#> 21 20 0.2478752 +#> </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)</div><div class='output co'>#> time degradinol +#> 1 0 100.0000000 +#> 2 1 74.0818221 +#> 3 2 54.8811636 +#> 4 3 40.6569660 +#> 5 4 30.1194212 +#> 6 5 22.3130160 +#> 7 6 16.5298888 +#> 8 7 12.2456428 +#> 9 8 9.0717953 +#> 10 9 6.7205513 +#> 11 10 4.9787068 +#> 12 11 3.6883167 +#> 13 12 2.7323722 +#> 14 13 2.0241911 +#> 15 14 1.4995577 +#> 16 15 1.1108996 +#> 17 16 0.8229747 +#> 18 17 0.6096747 +#> 19 18 0.4516581 +#> 20 19 0.3345965 +#> 21 20 0.2478752 +#> </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> time degradinol +#> 1 0 100.0000000 +#> 2 1 74.0818221 +#> 3 2 54.8811636 +#> 4 3 40.6569660 +#> 5 4 30.1194212 +#> 6 5 22.3130160 +#> 7 6 16.5298888 +#> 8 7 12.2456428 +#> 9 8 9.0717953 +#> 10 9 6.7205513 +#> 11 10 4.9787068 +#> 12 11 3.6883167 +#> 13 12 2.7323722 +#> 14 13 2.0241911 +#> 15 14 1.4995577 +#> 16 15 1.1108996 +#> 17 16 0.8229747 +#> 18 17 0.6096747 +#> 19 18 0.4516581 +#> 20 19 0.3345965 +#> 21 20 0.2478752 +#> </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)</div><div class='output co'>#> time degradinol +#> 1 0 100.0000000 +#> 2 1 74.0818221 +#> 3 2 54.8811636 +#> 4 3 40.6569660 +#> 5 4 30.1194212 +#> 6 5 22.3130160 +#> 7 6 16.5298888 +#> 8 7 12.2456428 +#> 9 8 9.0717953 +#> 10 9 6.7205513 +#> 11 10 4.9787068 +#> 12 11 3.6883167 +#> 13 12 2.7323722 +#> 14 13 2.0241911 +#> 15 14 1.4995577 +#> 16 15 1.1108997 +#> 17 16 0.8229747 +#> 18 17 0.6096747 +#> 19 18 0.4516581 +#> 20 19 0.3345965 +#> 21 20 0.2478752 +#> </div><div class='input'> + + <span class='co'># Compare integration methods to analytical solution</span> + <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#> time degradinol +#> 21 20 0.2478752 +#> </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, + <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#> time degradinol +#> 21 20 0.2478752 +#> </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, + <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"ode45"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#> time degradinol +#> 21 20 0.2478752 +#> </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>, + <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"rk4"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#> time degradinol +#> 21 20 0.2480043 +#> </div><div class='input'> <span class='co'># rk4 is not as precise here</span> + + <span class='co'># The number of output times used to make a lot of difference until the</span> + <span class='co'># default for atol was adjusted</span> + <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), + <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>))[<span class='fl'>201</span>,]</div><div class='output co'>#> time degradinol +#> 201 20 0.2478752 +#> </div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'>c</span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), + <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.01</span>))[<span class='fl'>2001</span>,]</div><div class='output co'>#> time degradinol +#> 2001 20 0.2478752 +#> </div><div class='input'> + <span class='co'># Check compiled model versions - they are faster than the eigenvalue based solutions!</span> + <span class='no'>SFO_SFO</span> <span class='kw'>=</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>), + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> <span class='fu'>system.time</span>( + <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), + <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 +#> 201 20 4.978707 27.46227 +#> </div><div class='output co'>#> user system elapsed +#> 0.000 0.028 0.004 +#> </div><div class='input'> <span class='fu'>system.time</span>( + <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), + <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 +#> 201 20 4.978707 27.46227 +#> </div><div class='output co'>#> user system elapsed +#> 0.016 0.004 0.002 +#> </div><div class='input'> <span class='fu'>system.time</span>( + <span class='fu'>print</span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'>c</span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>), + <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'>seq</span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)[<span class='fl'>201</span>,]))</div><div class='output co'>#> time parent m1 +#> 201 20 4.978707 27.46227 +#> </div><div class='output co'>#> user system elapsed +#> 0.036 0.000 0.035 +#> </div></pre> + </div> + <div class="col-md-3"> + <h2>Author</h2> + + Johannes Ranke + + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html new file mode 100644 index 00000000..fb9ab40d --- /dev/null +++ b/docs/reference/mkinresplot.html @@ -0,0 +1,166 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>mkinresplot. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>This function plots the residuals for the specified subset of the + observed variables from an mkinfit object. A combined plot of the fitted + model and the residuals can be obtained using <code>plot.mkinfit</code> + using the argument <code>show_residuals = TRUE</code>.</p> + + + <pre><span class='fu'>mkinresplot</span>(<span class='no'>object</span>, + <span class='kw'>obs_vars</span> <span class='kw'>=</span> <span class='fu'>names</span>(<span class='no'>object</span>$<span class='no'>mkinmod</span>$<span class='no'>map</span>), + <span class='kw'>xlim</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>1.1</span> * <span class='fu'>max</span>(<span class='no'>object</span>$<span class='no'>data</span>$<span class='no'>time</span>)), + <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Residual"</span>, + <span class='kw'>maxabs</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='st'>"topright"</span>, <span class='no'>...</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>object</dt> + <dd> + A fit represented in an <code>mkinfit</code> object. +</dd> + <dt>obs_vars</dt> + <dd> + A character vector of names of the observed variables for which residuals + should be plotted. Defaults to all observed variables in the model +</dd> + <dt>xlim</dt> + <dd> + plot range in x direction. + </dd> + <dt>xlab</dt> + <dd> + Label for the x axis. Defaults to "Time [days]". +</dd> + <dt>ylab</dt> + <dd> + Label for the y axis. Defaults to "Residual [% of applied radioactivity]". +</dd> + <dt>maxabs</dt> + <dd> + Maximum absolute value of the residuals. This is used for the scaling of + the y axis and defaults to "auto". +</dd> + <dt>legend</dt> + <dd> + Should a legend be plotted? Defaults to "TRUE". +</dd> + <dt>lpos</dt> + <dd> + Where should the legend be placed? Default is "topright". Will be passed on to + <code>legend</code>. </dd> + <dt>&#8230;</dt> + <dd> + further arguments passed to <code>plot</code>. +</dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p> + </div> + + <div class="See also"> + <h2>See also</h2> + + <p><code>mkinplot</code>, for a way to plot the data and the fitted lines of the + mkinfit object.</p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class='no'>model</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>model</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='fu'>mkinresplot</span>(<span class='no'>fit</span>, <span class='st'>"m1"</span>)</div><img src='unknown-4.png' alt='' width='540' height='400' /></pre> + </div> + <div class="col-md-3"> + <h2>Author</h2> + + Johannes Ranke + + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html new file mode 100644 index 00000000..6b079c40 --- /dev/null +++ b/docs/reference/mkinsub.html @@ -0,0 +1,147 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>mkinsub. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>This is a convenience function to set up the lists used as arguments for + <code>mkinmod</code>.</p> + + + <pre><span class='fu'>mkinsub</span>(<span class='no'>submodel</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='fl'>NA</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>submodel</dt> + <dd> + Character vector of length one to specify the submodel type. See + <code>mkinmod</code> for the list of allowed submodel names. + </dd> + <dt>to</dt> + <dd> + Vector of the names of the state variable to which a transformation + shall be included in the model. + </dd> + <dt>sink</dt> + <dd> + Should a pathway to sink be included in the model in addition to the + pathways to other state variables? + </dd> + <dt>full_name</dt> + <dd> + An optional name to be used e.g. for plotting fits performed with the model. + You can use non-ASCII characters here, but then your R code will not be + portable, <em>i.e.</em> may produce unintended plot results on other + operating systems or system configurations. + </dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>A list for use with <code>mkinmod</code>.</p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class='co'># One parent compound, one metabolite, both single first order.</span> +<span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( + <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>), + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> +<span class='co'># The same model using mkinsub</span> +<span class='no'>SFO_SFO.2</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( + <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> +<span class='co'># Now supplying full names</span> +<span class='no'>SFO_SFO.2</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( + <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Test compound"</span>), + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='kw'>full_name</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div></pre> + </div> + <div class="col-md-3"> + <h2>Author</h2> + + Johannes Ranke + + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html new file mode 100644 index 00000000..5b624893 --- /dev/null +++ b/docs/reference/mmkin.html @@ -0,0 +1,178 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>mmkin. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>This function calls <code>mkinfit</code> on all combinations of models and datasets + specified in its first two arguments.</p> + + + <pre><span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, + <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'>round</span>(<span class='fu'>detectCores</span>()/<span class='fl'>2</span>), <span class='kw'>cluster</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>models</dt> + <dd> + Either a character vector of shorthand names ("SFO", "FOMC", "DFOP", + "HS", "SFORB"), or an optionally named list of <code>mkinmod</code> + objects. + </dd> + <dt>datasets</dt> + <dd> + An optionally named list of datasets suitable as observed data for + <code>mkinfit</code>. + </dd> + <dt>cores</dt> + <dd> + The number of cores to be used for multicore processing. This is only + used when the <code>cluster</code> argument is <code>NULL</code>. + </dd> + <dt>cluster</dt> + <dd> + A cluster as returned by <code>makeCluster</code> to be used for parallel + execution. + </dd> + <dt>&#8230;</dt> + <dd> + Further arguments that will be passed to <code>mkinfit</code>. + </dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>A matrix of <code>mkinfit</code> objects that can be indexed using the model + and dataset names as row and column indices.</p> + </div> + + <div class="See also"> + <h2>See also</h2> + + <p><code>[.mmkin</code> for subsetting, <code>plot.mmkin</code> for plotting.</p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class='co'>## Not run: ------------------------------------</span> +<span class='co'># m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),</span> +<span class='co'># M1 = mkinsub("SFO", "M2"),</span> +<span class='co'># M2 = mkinsub("SFO"), use_of_ff = "max")</span> +<span class='co'># </span> +<span class='co'># m_synth_FOMC_lin <- mkinmod(parent = mkinsub("FOMC", "M1"),</span> +<span class='co'># M1 = mkinsub("SFO", "M2"),</span> +<span class='co'># M2 = mkinsub("SFO"), use_of_ff = "max")</span> +<span class='co'># </span> +<span class='co'># models <- list(SFO_lin = m_synth_SFO_lin, FOMC_lin = m_synth_FOMC_lin)</span> +<span class='co'># datasets <- lapply(synthetic_data_for_UBA_2014[1:3], function(x) x$data)</span> +<span class='co'># names(datasets) <- paste("Dataset", 1:3)</span> +<span class='co'># </span> +<span class='co'># time_default <- system.time(fits.0 <- mmkin(models, datasets))</span> +<span class='co'># time_1 <- system.time(fits.1 <- mmkin(models, datasets, cores = 1))</span> +<span class='co'># </span> +<span class='co'># time_default</span> +<span class='co'># time_1</span> +<span class='co'># </span> +<span class='co'># endpoints(fits[["SFO_lin", 2]])</span> +<span class='co'># </span> +<span class='co'># # Plot.mkinfit handles rows or columns of mmkin result objects</span> +<span class='co'># plot(fits.0[1, ])</span> +<span class='co'># plot(fits.0[1, ], obs_var = c("M1", "M2"))</span> +<span class='co'># plot(fits.0[, 1])</span> +<span class='co'># # Use double brackets to extract a single mkinfit object, which will be plotted</span> +<span class='co'># # by plot.mkinfit</span> +<span class='co'># plot(fits.0[[1, 1]], sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE)</span> +<span class='co'># # Plotting with mmkin (single brackets, extracting an mmkin object) does not</span> +<span class='co'># # allow to plot the observed variables separately</span> +<span class='co'># plot(fits.0[1, 1])</span> +<span class='co'>## ---------------------------------------------</span></div></pre> + </div> + <div class="col-md-3"> + <h2>Author</h2> + + Johannes Ranke + + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html new file mode 100644 index 00000000..94aebf63 --- /dev/null +++ b/docs/reference/plot.mkinfit.html @@ -0,0 +1,231 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>plot.mkinfit. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>Solves the differential equations with the optimised and fixed parameters + from a previous successful call to <code>mkinfit</code> and plots + the observed data together with the solution of the fitted model.</p> + + + <pre># S3 method for mkinfit +plot(x, fit = x, + obs_vars = names(fit$mkinmod$map), + xlab = "Time", ylab = "Observed", + xlim = range(fit$data$time), + ylim = "default", + col_obs = 1:length(obs_vars), pch_obs = col_obs, + lty_obs = rep(1, length(obs_vars)), + add = FALSE, legend = !add, + show_residuals = FALSE, maxabs = "auto", + sep_obs = FALSE, rel.height.middle = 0.9, + lpos = "topright", inset = c(0.05, 0.05), + show_errmin = FALSE, errmin_digits = 3, …) +plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, …)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>x</dt> + <dd> + Alias for fit introduced for compatibility with the generic S3 method. + </dd> + <dt>fit</dt> + <dd> + An object of class <code>mkinfit</code>. + </dd> + <dt>obs_vars</dt> + <dd> + A character vector of names of the observed variables for which the + data and the model should be plotted. Defauls to all observed variables + in the model. + </dd> + <dt>xlab</dt> + <dd> + Label for the x axis. + </dd> + <dt>ylab</dt> + <dd> + Label for the y axis. + </dd> + <dt>xlim</dt> + <dd> + Plot range in x direction. + </dd> + <dt>ylim</dt> + <dd> + Plot range in y direction. + </dd> + <dt>col_obs</dt> + <dd> + Colors used for plotting the observed data and the corresponding model prediction lines. + </dd> + <dt>pch_obs</dt> + <dd> + Symbols to be used for plotting the data. + </dd> + <dt>lty_obs</dt> + <dd> + Line types to be used for the model predictions. + </dd> + <dt>add</dt> + <dd> + Should the plot be added to an existing plot? + </dd> + <dt>legend</dt> + <dd> + Should a legend be added to the plot? + </dd> + <dt>show_residuals</dt> + <dd> + Should residuals be shown? If only one plot of the fits is shown, the + residual plot is in the lower third of the plot? Otherwise, i.e. if + "sep_obs" is given, the residual plots will be located to the right of + the plots of the fitted curves. + </dd> + <dt>maxabs</dt> + <dd> + Maximum absolute value of the residuals. This is used for the scaling of + the y axis and defaults to "auto". + </dd> + <dt>sep_obs</dt> + <dd> + Should the observed variables be shown in separate subplots? If yes, residual plots + requested by "show_residuals" will be shown next to, not below the plot of the fits. + </dd> + <dt>rel.height.middle</dt> + <dd> + The relative height of the middle plot, if more than two rows of plots are shown. + </dd> + <dt>lpos</dt> + <dd> + Position(s) of the legend(s). Passed to <code>legend</code> as the first argument. + If not length one, this should be of the same length as the obs_var argument. + </dd> + <dt>inset</dt> + <dd> + Passed to <code>legend</code> if applicable. + </dd> + <dt>show_errmin</dt> + <dd> + Should the FOCUS chi2 error value be shown in the upper margin of the plot? + </dd> + <dt>errmin_digits</dt> + <dd> + The number of significant digits for rounding the FOCUS chi2 error percentage. + </dd> + <dt>&#8230;</dt> + <dd> + Further arguments passed to <code>plot</code>. + </dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>The function is called for its side effect.</p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class='co'># One parent compound, one metabolite, both single first order, path from</span> +<span class='co'># parent to sink included, use Levenberg-Marquardt for speed</span> +<span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>, <span class='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Parent"</span>), + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='kw'>full</span> <span class='kw'>=</span> <span class='st'>"Metabolite M1"</span> ))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>) +<span class='fu'>plot</span>(<span class='no'>fit</span>)</div><img src='unknown-4.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='unknown-6.png' alt='' width='540' height='400' /><div class='input'> +<span class='co'># Show the observed variables separately</span> +<span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><img src='unknown-8.png' alt='' width='540' height='400' /><div class='input'> +<span class='co'># Show the observed variables separately, with residuals</span> +<span class='fu'>plot</span>(<span class='no'>fit</span>, <span class='kw'>sep_obs</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>), + <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><img src='unknown-10.png' alt='' width='540' height='400' /><div class='input'> +<span class='co'># The same can be obtained with less typing, using the convenience function plot_sep</span> +<span class='fu'>plot_sep</span>(<span class='no'>fit</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div></pre> + </div> + <div class="col-md-3"> + <h2>Author</h2> + + Johannes Ranke + + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html new file mode 100644 index 00000000..358da679 --- /dev/null +++ b/docs/reference/plot.mmkin.html @@ -0,0 +1,156 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>plot.mmkin. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>When x is a row selected from an mmkin object (<code>[.mmkin</code>), the same model + fitted for at least one dataset is shown. When it is a column, the fit of at least one model + to the same dataset is shown.</p> + + + <pre><span class='co'># S3 method for mmkin</span> +<span class='fu'>plot</span>(<span class='no'>x</span>, <span class='kw'>main</span> <span class='kw'>=</span> <span class='st'>"auto"</span>, <span class='kw'>legends</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>errmin_var</span> <span class='kw'>=</span> <span class='st'>"All data"</span>, <span class='kw'>errmin_digits</span> <span class='kw'>=</span> <span class='fl'>3</span>, + <span class='kw'>cex</span> <span class='kw'>=</span> <span class='fl'>0.7</span>, <span class='kw'>rel.height.middle</span> <span class='kw'>=</span> <span class='fl'>0.9</span>, <span class='no'>...</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>x</dt> + <dd> + An object of class <code>mmkin</code>, with either one row or one column. +</dd> + <dt>main</dt> + <dd> + The main title placed on the outer margin of the plot. +</dd> + <dt>legends</dt> + <dd> + An index for the fits for which legends should be shown. +</dd> + <dt>errmin_var</dt> + <dd> + The variable for which the FOCUS chi2 error value should be shown. +</dd> + <dt>errmin_digits</dt> + <dd> + The number of significant digits for rounding the FOCUS chi2 error percentage. +</dd> + <dt>cex</dt> + <dd> + Passed to the plot functions and <code>mtext</code>. +</dd> + <dt>rel.height.middle</dt> + <dd> + The relative height of the middle plot, if more than two rows of plots are shown. +</dd> + <dt>&#8230;</dt> + <dd> + Further arguments passed to <code>plot.mkinfit</code> and <code>mkinresplot</code>. +</dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>The function is called for its side effect.</p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'> <span class='co'># Only use one core not to offend CRAN checks, use Levenberg-Marquardt for speed</span> + <span class='no'>fits</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='fu'>c</span>(<span class='st'>"FOMC"</span>, <span class='st'>"HS"</span>), <span class='fu'>list</span>(<span class='st'>"FOCUS B"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='st'>"FOCUS C"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>), + <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>method.modFit</span> <span class='kw'>=</span> <span class='st'>"Marq"</span>) + <span class='fu'>plot</span>(<span class='no'>fits</span>[, <span class='st'>"FOCUS C"</span>])</div><img src='unknown-2.png' alt='' width='540' height='400' /><div class='input'> <span class='fu'>plot</span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ])</div><img src='unknown-4.png' alt='' width='540' height='400' /><div class='input'> + <span class='co'># We can also plot a single fit, if we like the way mmkin works, but then the plot </span> + <span class='co'># height should be smaller than the plot width (this is not possible for the html pages</span> + <span class='co'># generated by staticdocs, as far as I know).</span> + <span class='fu'>plot</span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, <span class='st'>"FOCUS C"</span>]) <span class='co'># same as plot(fits[1, 2])</span></div><img src='unknown-6.png' alt='' width='540' height='400' /></pre> + </div> + <div class="col-md-3"> + <h2>Author</h2> + + Johannes Ranke + + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html new file mode 100644 index 00000000..dea5f75c --- /dev/null +++ b/docs/reference/print.mkinds.html @@ -0,0 +1,109 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>print.mkinds. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>Print mkinds objects.</p> + + + <pre><span class='co'># S3 method for mkinds</span> +<span class='fu'>print</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>x</dt> + <dd> + An <code>mkinds</code> object. + </dd> + <dt>&#8230;</dt> + <dd> + Not used. + </dd> + </dl> + </div> + <div class="col-md-3"> + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html new file mode 100644 index 00000000..38663f8f --- /dev/null +++ b/docs/reference/print.mkinmod.html @@ -0,0 +1,109 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>print.mkinmod. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>Print mkinmod objects in a way that the user finds his way to get to its components.</p> + + + <pre><span class='co'># S3 method for mkinmod</span> +<span class='fu'>print</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>x</dt> + <dd> + An <code>mkinmod</code> object. + </dd> + <dt>&#8230;</dt> + <dd> + Not used. + </dd> + </dl> + </div> + <div class="col-md-3"> + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html new file mode 100644 index 00000000..12776c74 --- /dev/null +++ b/docs/reference/schaefer07_complex_case.html @@ -0,0 +1,131 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>schaefer07_complex_case. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>This dataset was used for a comparison of KinGUI and ModelMaker to check the + software quality of KinGUI in the original publication (Schäfer et al., 2007). + The results from the fitting are also included.</p> + + + <pre><span class='fu'>data</span>(<span class='no'>schaefer07_complex_case</span>)</pre> + + <div class="Format"> + <h2>Format</h2> + + <p>The data set is a data frame with 8 observations on the following 6 variables. + <dl class='dl-horizontal'> + <dt><code>time</code></dt><dd>a numeric vector</dd> + <dt><code>parent</code></dt><dd>a numeric vector</dd> + <dt><code>A1</code></dt><dd>a numeric vector</dd> + <dt><code>B1</code></dt><dd>a numeric vector</dd> + <dt><code>C1</code></dt><dd>a numeric vector</dd> + <dt><code>A2</code></dt><dd>a numeric vector</dd> + </dl></p> + <p>The results are a data frame with 14 results for different parameter values</p> + </div> + + <div class="References"> + <h2>References</h2> + + <p>Schäfer D, Mikolasch B, Rainbird P and Harvey B (2007). KinGUI: a new kinetic + software tool for evaluations according to FOCUS degradation kinetics. In: Del + Re AAM, Capri E, Fragoulis G and Trevisan M (Eds.). Proceedings of the XIII + Symposium Pesticide Chemistry, Piacenza, 2007, p. 916-923.</p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class='no'>data</span> <span class='kw'><-</span> <span class='fu'>mkin_wide_to_long</span>(<span class='no'>schaefer07_complex_case</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>) +<span class='no'>model</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( + <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"A1"</span>, <span class='st'>"B1"</span>, <span class='st'>"C1"</span>), <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>), + <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A2"</span>), + <span class='kw'>B1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), + <span class='kw'>C1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), + <span class='kw'>A2</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='co'>## Not run: mkinfit(model, data, plot=TRUE)</span></div></pre> + </div> + <div class="col-md-3"> + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html new file mode 100644 index 00000000..e0cdfe23 --- /dev/null +++ b/docs/reference/summary.mkinfit.html @@ -0,0 +1,229 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>summary.mkinfit. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>Lists model equations, the summary as returned by <code>summary.modFit</code>, + the chi2 error levels calculated according to FOCUS guidance (2006) as far + as defined therein, and optionally the data, consisting of observed, predicted + and residual values.</p> + + + <pre><span class='co'># S3 method for mkinfit</span> +<span class='fu'>summary</span>(<span class='no'>object</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>distimes</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='no'>...</span>) +<span class='co'># S3 method for summary.mkinfit</span> +<span class='fu'>print</span>(<span class='no'>x</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fu'>max</span>(<span class='fl'>3</span>, <span class='fu'>getOption</span>(<span class='st'>"digits"</span>) - <span class='fl'>3</span>), <span class='no'>...</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>object</dt> + <dd> + an object of class <code>mkinfit</code>. +</dd> + <dt>x</dt> + <dd> + an object of class <code>summary.mkinfit</code>. +</dd> + <dt>data</dt> + <dd> + logical, indicating whether the data should be included in the summary. +</dd> + <dt>distimes</dt> + <dd> + logical, indicating whether DT50 and DT90 values should be included. +</dd> + <dt>alpha</dt> + <dd> + error level for confidence interval estimation from t distribution +</dd> + <dt>digits</dt> + <dd> + Number of digits to use for printing +</dd> + <dt>&#8230;</dt> + <dd> + optional arguments passed to methods like <code>print</code>. +</dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>The summary function returns a list derived from + <code>summary.modFit</code>, with components, among others</p> + <p>The print method is called for its side effect, i.e. printing the summary.</p> + </div> + + <div class="References"> + <h2>References</h2> + + <p>FOCUS (2006) “Guidance Document on Estimating Persistence and + Degradation Kinetics from Environmental Fate Studies on Pesticides in EU + Registration” Report of the FOCUS Work Group on Degradation Kinetics, + EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, + <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'> <span class='fu'>summary</span>(<span class='fu'>mkinfit</span>(<span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version: 0.9.44.9000 +#> R version: 3.3.1 +#> Date of fit: Thu Oct 6 09:18:07 2016 +#> Date of summary: Thu Oct 6 09:18:07 2016 +#> +#> Equations: +#> d_parent = - k_parent_sink * parent +#> +#> Model predictions using solution type analytical +#> +#> Fitted with method Port using 35 model solutions performed in 0.079 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 101.24 state +#> k_parent_sink 0.10 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 101.240000 -Inf Inf +#> log_k_parent_sink -2.302585 -Inf Inf +#> +#> Fixed parameter values: +#> None +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 109.200 4.3910 98.410 119.900 +#> log_k_parent_sink -3.291 0.1152 -3.573 -3.009 +#> +#> Parameter correlation: +#> parent_0 log_k_parent_sink +#> parent_0 1.000 0.575 +#> log_k_parent_sink 0.575 1.000 +#> +#> Residual standard error: 6.08 on 6 degrees of freedom +#> +#> Backtransformed parameters: +#> Confidence intervals for internally transformed parameters are asymmetric. +#> t-test (unrealistically) based on the assumption of normal distribution +#> for estimators of untransformed parameters. +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 109.20000 24.860 1.394e-07 98.41000 119.90000 +#> k_parent_sink 0.03722 8.679 6.457e-05 0.02807 0.04934 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 8.385 2 6 +#> parent 8.385 2 6 +#> +#> Resulting formation fractions: +#> ff +#> parent_sink 1 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 18.62 61.87 +#> +#> Data: +#> time variable observed predicted residual +#> 0 parent 101.24 109.153 -7.9132 +#> 3 parent 99.27 97.622 1.6484 +#> 7 parent 90.11 84.119 5.9913 +#> 14 parent 72.19 64.826 7.3641 +#> 30 parent 29.71 35.738 -6.0283 +#> 62 parent 5.98 10.862 -4.8818 +#> 90 parent 1.54 3.831 -2.2911 +#> 118 parent 0.39 1.351 -0.9613 +#> </div></pre> + </div> + <div class="col-md-3"> + <h2>Author</h2> + + Johannes Ranke + + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html new file mode 100644 index 00000000..04550199 --- /dev/null +++ b/docs/reference/synthetic_data_for_UBA.html @@ -0,0 +1,157 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>synthetic_data_for_UBA_2014. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>The 12 datasets were generated using four different models and three different + variance components. The four models are either the SFO or the DFOP model with either + two sequential or two parallel metabolites.</p> + + <p>Variance component 'a' is based on a normal distribution with standard deviation of 3, + Variance component 'b' is also based on a normal distribution, but with a standard deviation of 7. + Variance component 'c' is based on the error model from Rocke and Lorenzato (1995), with the + minimum standard deviation (for small y values) of 0.5, and a proportionality constant of 0.07 + for the increase of the standard deviation with y.</p> + + <p>Initial concentrations for metabolites and all values where adding the variance component resulted + in a value below the assumed limit of detection of 0.1 were set to <code>NA</code>.</p> + + <p>As an example, the first dataset has the title <code>SFO_lin_a</code> and is based on the SFO model + with two sequential metabolites (linear pathway), with added variance component 'a'.</p> + + <p>Compare also the code in the example section to see the degradation models.</p> + + + <pre><span class='no'>synthetic_data_for_UBA_2014</span></pre> + + <div class="Format"> + <h2>Format</h2> + + <p>A list containing datasets in the form internally used by the 'gmkin' package. + The list has twelfe components. Each of the components is one dataset that has, + among others, the following components + <dl class='dl-horizontal'> + <dt><code>title</code></dt><dd>The name of the dataset, e.g. <code>SFO_lin_a</code></dd> + <dt><code>data</code></dt><dd>A data frame with the data in the form expected by <code>mkinfit</code></dd> + </dl></p> + </div> + + <div class="Source"> + <h2>Source</h2> + + <p>Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative + zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452</p> + <p>Rocke, David M. und Lorenzato, Stefan (1995) A two-component model for + measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class='co'>## Not run: ------------------------------------</span> +<span class='co'># m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),</span> +<span class='co'># M1 = list(type = "SFO", to = "M2"),</span> +<span class='co'># M2 = list(type = "SFO"), use_of_ff = "max")</span> +<span class='co'># </span> +<span class='co'># </span> +<span class='co'># m_synth_SFO_par <- mkinmod(parent = list(type = "SFO", to = c("M1", "M2"),</span> +<span class='co'># sink = FALSE),</span> +<span class='co'># M1 = list(type = "SFO"),</span> +<span class='co'># M2 = list(type = "SFO"), use_of_ff = "max")</span> +<span class='co'># </span> +<span class='co'># m_synth_DFOP_lin <- mkinmod(parent = list(type = "DFOP", to = "M1"),</span> +<span class='co'># M1 = list(type = "SFO", to = "M2"),</span> +<span class='co'># M2 = list(type = "SFO"), use_of_ff = "max")</span> +<span class='co'># </span> +<span class='co'># m_synth_DFOP_par <- mkinmod(parent = list(type = "DFOP", to = c("M1", "M2"),</span> +<span class='co'># sink = FALSE),</span> +<span class='co'># M1 = list(type = "SFO"),</span> +<span class='co'># M2 = list(type = "SFO"), use_of_ff = "max")</span> +<span class='co'># </span> +<span class='co'># mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data)</span> +<span class='co'>## ---------------------------------------------</span></div></pre> + </div> + <div class="col-md-3"> + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html new file mode 100644 index 00000000..3b8be856 --- /dev/null +++ b/docs/reference/transform_odeparms.html @@ -0,0 +1,276 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>transform_odeparms. mkin</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> + +<!-- Bootstrap --> +<link href="https://maxcdn.bootstrapcdn.com/bootswatch/3.3.7/cerulean/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"> + +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> + +<!--[if lt IE 9]> +<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> +<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> +<![endif]--> + </head> + + <body> + <div class="container"> + <header> + +<div class="navbar navbar-default navbar-fixed-top" role="navigation"> + <div class="container"> + <div class="navbar-header"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">mkin</a> + </div> + <div id="navbar" class="navbar-collapse collapse"> + <ul class="nav navbar-nav"> + <li> + <a href="../index.html">Home</a> +</li> +<li> + <a href="../reference/index.html">Reference</a> +</li> + </ul> + <ul class="nav navbar-nav navbar-right"> + <li> + <a href="https://github.com/jranke/mkin"> + <span class="fa fa-github fa-lg"></span> + + </a> +</li> + </ul> + </div><!--/.nav-collapse --> + </div><!--/.container --> +</div><!--/.navbar --> + + </header> + + <div class="page-header"> + <h1> +</h1> +</div> + +<div class="row"> + <div class="col-md-9"> + + <p>The transformations are intended to map parameters that should only take + on restricted values to the full scale of real numbers. For kinetic rate + constants and other paramters that can only take on positive values, a + simple log transformation is used. For compositional parameters, such as + the formations fractions that should always sum up to 1 and can not be + negative, the <code>ilr</code> transformation is used.</p> + + <p>The transformation of sets of formation fractions is fragile, as it supposes + the same ordering of the components in forward and backward transformation. + This is no problem for the internal use in <code>mkinfit</code>.</p> + + + <pre><span class='fu'>transform_odeparms</span>(<span class='no'>parms</span>, <span class='no'>mkinmod</span>, + <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='fu'>backtransform_odeparms</span>(<span class='no'>transparms</span>, <span class='no'>mkinmod</span>, + <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>transform_fractions</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</pre> + + <h2>Arguments</h2> + <dl class="dl-horizontal"> + <dt>parms</dt> + <dd> + Parameters of kinetic models as used in the differential equations. + </dd> + <dt>transparms</dt> + <dd> + Transformed parameters of kinetic models as used in the fitting procedure. + </dd> + <dt>mkinmod</dt> + <dd> + The kinetic model of class <code>mkinmod</code>, containing the names of + the model variables that are needed for grouping the formation fractions + before <code>ilr</code> transformation, the parameter names and + the information if the pathway to sink is included in the model. + </dd> + <dt>transform_rates</dt> + <dd> + Boolean specifying if kinetic rate constants should be transformed in the + model specification used in the fitting for better compliance with the + assumption of normal distribution of the estimator. If TRUE, also + alpha and beta parameters of the FOMC model are log-transformed, as well + as k1 and k2 rate constants for the DFOP and HS models and the break point tb + of the HS model. + </dd> + <dt>transform_fractions</dt> + <dd> + Boolean specifying if formation fractions constants should be transformed in the + model specification used in the fitting for better compliance with the + assumption of normal distribution of the estimator. The default (TRUE) is + to do transformations. The g parameter of the DFOP and HS models are also + transformed, as they can also be seen as compositional data. The + transformation used for these transformations is the <code>ilr</code> + transformation. + </dd> + </dl> + + <div class="Value"> + <h2>Value</h2> + + <p>A vector of transformed or backtransformed parameters with the same names + as the original parameters.</p> + </div> + + <h2 id="examples">Examples</h2> + <pre class="examples"><div class='input'><span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>( + <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> +<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='fu'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#> mkin version: 0.9.44.9000 +#> R version: 3.3.1 +#> Date of fit: Thu Oct 6 09:18:08 2016 +#> Date of summary: Thu Oct 6 09:18:08 2016 +#> +#> Equations: +#> d_parent = - k_parent_sink * parent - k_parent_m1 * parent +#> d_m1 = + k_parent_m1 * parent - k_m1_sink * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 153 model solutions performed in 0.636 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent_sink 0.1000 deparm +#> k_parent_m1 0.1001 deparm +#> k_m1_sink 0.1002 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_parent_sink -2.302585 -Inf Inf +#> log_k_parent_m1 -2.301586 -Inf Inf +#> log_k_m1_sink -2.300587 -Inf Inf +#> +#> Fixed parameter values: +#> value type +#> m1_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 99.600 1.61400 96.330 102.900 +#> log_k_parent_sink -3.038 0.07826 -3.197 -2.879 +#> log_k_parent_m1 -2.980 0.04124 -3.064 -2.897 +#> log_k_m1_sink -5.248 0.13610 -5.523 -4.972 +#> +#> Parameter correlation: +#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> parent_0 1.00000 0.6075 -0.06625 -0.1701 +#> log_k_parent_sink 0.60752 1.0000 -0.08740 -0.6253 +#> log_k_parent_m1 -0.06625 -0.0874 1.00000 0.4716 +#> log_k_m1_sink -0.17006 -0.6253 0.47163 1.0000 +#> +#> Residual standard error: 3.211 on 36 degrees of freedom +#> +#> Backtransformed parameters: +#> Confidence intervals for internally transformed parameters are asymmetric. +#> t-test (unrealistically) based on the assumption of normal distribution +#> for estimators of untransformed parameters. +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02 +#> k_parent_sink 0.047920 12.780 3.050e-15 0.040890 5.616e-02 +#> k_parent_m1 0.050780 24.250 3.407e-24 0.046700 5.521e-02 +#> k_m1_sink 0.005261 7.349 5.758e-09 0.003992 6.933e-03 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.398 4 15 +#> parent 6.827 3 6 +#> m1 4.490 1 9 +#> +#> Resulting formation fractions: +#> ff +#> parent_sink 0.4855 +#> parent_m1 0.5145 +#> m1_sink 1.0000 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 7.023 23.33 +#> m1 131.761 437.70 +#> </div><div class='input'> +<span class='co'>## Not run: ------------------------------------</span> +<span class='co'># fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE)</span> +<span class='co'># summary(fit.2, data=FALSE) </span> +<span class='co'>## ---------------------------------------------</span> + +<span class='no'>initials</span> <span class='kw'><-</span> <span class='no'>fit</span>$<span class='no'>start</span>$<span class='no'>value</span> +<span class='fu'>names</span>(<span class='no'>initials</span>) <span class='kw'><-</span> <span class='fu'>rownames</span>(<span class='no'>fit</span>$<span class='no'>start</span>) +<span class='no'>transformed</span> <span class='kw'><-</span> <span class='no'>fit</span>$<span class='no'>start_transformed</span>$<span class='no'>value</span> +<span class='fu'>names</span>(<span class='no'>transformed</span>) <span class='kw'><-</span> <span class='fu'>rownames</span>(<span class='no'>fit</span>$<span class='no'>start_transformed</span>) +<span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 100.750000 -2.302585 -2.301586 -2.300587 +#> </div><div class='input'><span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#> parent_0 k_parent_sink k_parent_m1 k_m1_sink +#> 100.7500 0.1000 0.1001 0.1002 +#> </div><div class='input'> +<span class='co'>## Not run: ------------------------------------</span> +<span class='co'># # The case of formation fractions</span> +<span class='co'># SFO_SFO.ff <- mkinmod(</span> +<span class='co'># parent = list(type = "SFO", to = "m1", sink = TRUE),</span> +<span class='co'># m1 = list(type = "SFO"),</span> +<span class='co'># use_of_ff = "max")</span> +<span class='co'># </span> +<span class='co'># fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D)</span> +<span class='co'># summary(fit.ff, data = FALSE)</span> +<span class='co'># initials <- c("f_parent_to_m1" = 0.5)</span> +<span class='co'># transformed <- transform_odeparms(initials, SFO_SFO.ff)</span> +<span class='co'># backtransform_odeparms(transformed, SFO_SFO.ff)</span> +<span class='co'># </span> +<span class='co'># # And without sink</span> +<span class='co'># SFO_SFO.ff.2 <- mkinmod(</span> +<span class='co'># parent = list(type = "SFO", to = "m1", sink = FALSE),</span> +<span class='co'># m1 = list(type = "SFO"),</span> +<span class='co'># use_of_ff = "max")</span> +<span class='co'># </span> +<span class='co'># </span> +<span class='co'># fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D)</span> +<span class='co'># summary(fit.ff.2, data = FALSE)</span> +<span class='co'>## ---------------------------------------------</span></div></pre> + </div> + <div class="col-md-3"> + <h2>Author</h2> + + Johannes Ranke + + </div> +</div> + + <footer> + <p>Built by <a href="http://hadley.github.io/pkgdown/">pkgdown</a>. Styled with <a href="http://getbootstrap.com">Bootstrap 3</a>.</p> + </footer> + </div> + + </body> +</html> diff --git a/docs/reference/unknown-10.png b/docs/reference/unknown-10.png Binary files differnew file mode 100644 index 00000000..09bb687c --- /dev/null +++ b/docs/reference/unknown-10.png diff --git a/docs/reference/unknown-2.png b/docs/reference/unknown-2.png Binary files differnew file mode 100644 index 00000000..a26e413f --- /dev/null +++ b/docs/reference/unknown-2.png diff --git a/docs/reference/unknown-4.png b/docs/reference/unknown-4.png Binary files differnew file mode 100644 index 00000000..f23ed172 --- /dev/null +++ b/docs/reference/unknown-4.png diff --git a/docs/reference/unknown-6.png b/docs/reference/unknown-6.png Binary files differnew file mode 100644 index 00000000..dc24d92f --- /dev/null +++ b/docs/reference/unknown-6.png diff --git a/docs/reference/unknown-8.png b/docs/reference/unknown-8.png Binary files differnew file mode 100644 index 00000000..e4ab674a --- /dev/null +++ b/docs/reference/unknown-8.png |
