diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2019-01-31 16:55:20 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2019-01-31 16:55:20 +0100 |
| commit | 3eefecf0adfbb30b8fb895c244dea6903bcb3e9c (patch) | |
| tree | bb70432fd6f13ca306443047d6911a797757ee96 /docs/reference | |
| parent | e5453f4d020aa120cabea074120f587f8ea4735f (diff) | |
Restore NAMESPACE
which was accidentally overwritten by pkgdown -> roxygen
Diffstat (limited to 'docs/reference')
32 files changed, 2260 insertions, 118 deletions
diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index a90e81bb..d90b325f 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -160,12 +160,22 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='no'>f</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='st'>"FOCUS A"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_A</span>, - <span class='st'>"FOCUS C"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>))</div><div class='output co'>#> <span class='error'>Error in mmkin(c("SFO", "FOMC", "DFOP"), list(`FOCUS A` = FOCUS_2006_A, `FOCUS C` = FOCUS_2006_C)): konnte Funktion "mmkin" nicht finden</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/AIC'>AIC</a></span>(<span class='no'>f</span>[<span class='fl'>1</span>, <span class='st'>"FOCUS A"</span>]) <span class='co'># We get a single number for a single fit</span></div><div class='output co'>#> <span class='error'>Error in AIC(f[1, "FOCUS A"]): Objekt 'f' nicht gefunden</span></div><div class='input'> + <span class='st'>"FOCUS C"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>)) + <span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/AIC'>AIC</a></span>(<span class='no'>f</span>[<span class='fl'>1</span>, <span class='st'>"FOCUS A"</span>]) <span class='co'># We get a single number for a single fit</span></div><div class='output co'>#> [1] 55.32452</div><div class='input'> <span class='co'># For FOCUS A, the models fit almost equally well, so the higher the number</span> <span class='co'># of parameters, the higher (worse) the AIC</span> - <span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/AIC'>AIC</a></span>(<span class='no'>f</span>[, <span class='st'>"FOCUS A"</span>])</div><div class='output co'>#> <span class='error'>Error in AIC(f[, "FOCUS A"]): Objekt 'f' nicht gefunden</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/AIC'>AIC</a></span>(<span class='no'>f</span>[, <span class='st'>"FOCUS A"</span>], <span class='kw'>k</span> <span class='kw'>=</span> <span class='fl'>0</span>) <span class='co'># If we do not penalize additional parameters, we get nearly the same</span></div><div class='output co'>#> <span class='error'>Error in AIC(f[, "FOCUS A"], k = 0): Objekt 'f' nicht gefunden</span></div><div class='input'> + <span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/AIC'>AIC</a></span>(<span class='no'>f</span>[, <span class='st'>"FOCUS A"</span>])</div><div class='output co'>#> df AIC +#> SFO 3 55.32452 +#> FOMC 4 57.32477 +#> DFOP 5 59.32452</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/AIC'>AIC</a></span>(<span class='no'>f</span>[, <span class='st'>"FOCUS A"</span>], <span class='kw'>k</span> <span class='kw'>=</span> <span class='fl'>0</span>) <span class='co'># If we do not penalize additional parameters, we get nearly the same</span></div><div class='output co'>#> df AIC +#> SFO 3 49.32452 +#> FOMC 4 49.32477 +#> DFOP 5 49.32452</div><div class='input'> <span class='co'># For FOCUS C, the more complex models fit better</span> - <span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/AIC'>AIC</a></span>(<span class='no'>f</span>[, <span class='st'>"FOCUS C"</span>])</div><div class='output co'>#> <span class='error'>Error in AIC(f[, "FOCUS C"]): Objekt 'f' nicht gefunden</span></div></pre> + <span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/AIC'>AIC</a></span>(<span class='no'>f</span>[, <span class='st'>"FOCUS C"</span>])</div><div class='output co'>#> df AIC +#> SFO 3 59.84675 +#> FOMC 4 44.70584 +#> DFOP 5 29.08369</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index c82eb161..7f17e421 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -173,7 +173,7 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><div class='output co'>#> <span class='error'>Error in DFOP.solution(x, 100, 5, 0.5, 0.3): konnte Funktion "DFOP.solution" nicht finden</span></div></pre> + <pre class="examples"><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><div class='img'><img src='DFOP.solution-1.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 1be9e0f1..2a1d63b5 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -166,15 +166,411 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>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'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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>)</div><div class='output co'>#> <span class='error'>Error in mmkin(c("SFO", "FOMC"), list(B = FOCUS_2006_B, C = FOCUS_2006_C), cores = 1, quiet = TRUE): konnte Funktion "mmkin" nicht finden</span></div><div class='input'> <span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ]</div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'fits' nicht gefunden</span></div><div class='input'> <span class='no'>fits</span>[, <span class='st'>"B"</span>]</div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'fits' nicht gefunden</span></div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'fits' nicht gefunden</span></div><div class='input'> + <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,45 List,45 +#> 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,45 +#> FOMC List,45 +#> attr(,"class") +#> [1] "mmkin"</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,45 +#> attr(,"class") +#> [1] "mmkin"</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/utils/topics/head'>head</a></span>( <span class='co'># This extracts an mkinfit object with lots of components</span> <span class='no'>fits</span><span class='kw'>[[</span><span class='st'>"FOMC"</span>, <span class='st'>"B"</span>]] - )</div><div class='output co'>#> <span class='error'>Error in head(fits[["FOMC", "B"]]): Objekt 'fits' nicht gefunden</span></div><div class='input'> + )</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] "relative convergence (4)" +#> </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/utils/topics/head'>head</a></span>( <span class='co'># The same can be achieved by</span> <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'>#> <span class='error'>Error in head(fits["SFO", "B", drop = TRUE]): Objekt 'fits' nicht gefunden</span></div></pre> + )</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 verstrichen +#> 0.197 0.000 0.198 +#> +#> $mkinmod +#> <mkinmod> model generated with +#> Use of formation fractions $use_of_ff: min +#> Specification $spec: +#> $parent +#> $type: SFO; $sink: TRUE +#> Coefficient matrix $coefmat available +#> Differential equations: +#> d_parent/dt = - k_parent_sink * parent +#> +#> $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) +#> } +#> <bytecode: 0x55555916c520> +#> <environment: 0x55555b68a808> +#> +#> $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) +#> } +#> <bytecode: 0x55555a1242b0> +#> <environment: 0x55555b68a808> +#> +#> $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 Zeilen> (oder row.names mit Länge 0) +#> +#> $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" +#> +#> $tc.ini +#> sigma_low rsd_high +#> 0.50 0.07 +#> +#> $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 Jan 31 16:50:45 2019" +#> +#> $version +#> [1] "0.9.47.6" +#> +#> $Rversion +#> [1] "3.5.2" +#> +#> attr(,"class") +#> [1] "mkinfit" "modFit" +#> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index bbe84618..3ece2c08 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -185,7 +185,7 @@ The form given here differs slightly from the original reference by Gustafson <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><div class='output co'>#> <span class='error'>Error in FOMC.solution(x, 100, 10, 2): konnte Funktion "FOMC.solution" nicht finden</span></div></pre> + <pre class="examples"><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><div class='img'><img src='FOMC.solution-1.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index d836e8a5..0d8751e1 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -174,7 +174,7 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><div class='output co'>#> <span class='error'>Error in HS.solution(x, 100, 2, 0.3, 0.5): konnte Funktion "HS.solution" nicht finden</span></div></pre> + <pre class="examples"><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>,<span class='fl'>100</span>))</div><div class='img'><img src='HS.solution-1.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 5bc5a57d..2ad38a16 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -174,10 +174,19 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><div class='output co'>#> <span class='error'>Error in IORE.solution(x, 100, 0.2, 1.3): konnte Funktion "IORE.solution" nicht finden</span></div><div class='input'> <span class='no'>fit.fomc</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></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>)</div><div class='output co'>#> <span class='error'>Error in mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'> <span class='no'>fit.iore</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></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>)</div><div class='output co'>#> <span class='error'>Error in mkinfit("IORE", FOCUS_2006_C, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'> <span class='no'>fit.iore.deS</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></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>)</div><div class='output co'>#> <span class='error'>Error in mkinfit("IORE", FOCUS_2006_C, solution_type = "deSolve", quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'> + <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>))</div><div class='img'><img src='IORE.solution-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='no'>fit.fomc</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></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'><a href='mkinfit.html'>mkinfit</a></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'><a href='mkinfit.html'>mkinfit</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.fomc</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.iore</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.iore.deS</span>), - <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='st'>"model par"</span>, <span class='fl'>1</span>:<span class='fl'>3</span>)))</div><div class='output co'>#> <span class='error'>Error in coef(fit.fomc): Objekt 'fit.fomc' nicht gefunden</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/cbind'>rbind</a></span>(<span class='kw'>fomc</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.fomc</span>)$<span class='no'>distimes</span>, <span class='kw'>iore</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>, - <span class='kw'>iore.deS</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>))</div><div class='output co'>#> <span class='error'>Error in endpoints(fit.fomc): konnte Funktion "endpoints" nicht finden</span></div></pre> + <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></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 85.874890 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'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/cbind'>rbind</a></span>(<span class='kw'>fomc</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.fomc</span>)$<span class='no'>distimes</span>, <span class='kw'>iore</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.iore</span>)$<span class='no'>distimes</span>, + <span class='kw'>iore.deS</span> <span class='kw'>=</span> <span class='fu'><a href='endpoints.html'>endpoints</a></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 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 87ccdcf0..55ff216c 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -162,7 +162,7 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFO.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)</div><div class='output co'>#> <span class='error'>Error in SFO.solution(x, 100, 3): konnte Funktion "SFO.solution" nicht finden</span></div></pre> + <pre class="examples"><div class='input'> </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFO.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)</div><div class='img'><img src='SFO.solution-1.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 49c78dc4..81ed61aa 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -179,7 +179,7 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFORB.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.5</span>, <span class='fl'>2</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)</div><div class='output co'>#> <span class='error'>Error in SFORB.solution(x, 100, 0.5, 2, 3): konnte Funktion "SFORB.solution" nicht finden</span></div></pre> + <pre class="examples"><div class='input'> </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>SFORB.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.5</span>, <span class='fl'>2</span>, <span class='fl'>3</span>), <span class='fl'>0</span>, <span class='fl'>2</span>)</div><div class='img'><img src='SFORB.solution-1.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 78574e92..c8024d66 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -193,7 +193,7 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>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'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M1"</span>), - <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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 co'>#> <span class='error'>Error in mkinmod(parent = mkinsub("SFO", "M1"), M1 = mkinsub("SFO"), use_of_ff = "max"): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'> + <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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 co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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>) @@ -203,12 +203,15 @@ <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/Log'>log</a></span>(<span class='fl'>2</span>)/<span class='fl'>1000</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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>)</div><div class='output co'>#> <span class='error'>Error in mkinpredict(m_SFO_SFO, c(k_parent = 0.1, f_parent_to_M1 = 0.5, k_M1 = log(2)/1000), c(parent = 100, M1 = 0), sampling_times): konnte Funktion "mkinpredict" nicht finden</span></div><div class='input'> + <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> )</div><div class='output co'>#> <span class='error'>Error in add_err(d_SFO_SFO, function(x) 10, n = 3, seed = 123456789): konnte Funktion "add_err" nicht finden</span></div><div class='input'> +<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'><a href='https://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>d_SFO_SFO_err</span>) <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='st'>"Dataset"</span>, <span class='fl'>1</span>:<span class='fl'>3</span>)</div><div class='output co'>#> <span class='error'>Error in names(d_SFO_SFO_err) <- paste("Dataset", 1:3): Objekt 'd_SFO_SFO_err' nicht gefunden</span></div><div class='input'> +<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>d_SFO_SFO_err</span>) <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></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> @@ -216,15 +219,16 @@ <span class='co'># checks</span> <span class='no'>f_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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>)</div><div class='output co'>#> <span class='error'>Error in mmkin(list(`SFO-SFO` = m_SFO_SFO), d_SFO_SFO_err, cores = 1, quiet = TRUE, method.modFit = "Marq"): konnte Funktion "mmkin" nicht finden</span></div><div class='input'> -<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>f_SFO_SFO</span>)</div><div class='output co'>#> <span class='error'>Error in plot(f_SFO_SFO): Objekt 'f_SFO_SFO' nicht gefunden</span></div><div class='input'> + <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'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>f_SFO_SFO</span>)</div><div class='img'><img src='add_err-1.png' alt='' width='700' height='433' /></div><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'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></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><div class='output co'>#> <span class='error'>Error in plot(f_SFO_SFO[[3]], show_residuals = TRUE): Objekt 'f_SFO_SFO' nicht gefunden</span></div><div class='input'> +<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></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><div class='img'><img src='add_err-2.png' alt='' width='700' height='433' /></div><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'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>f_SFO_SFO</span>[<span class='fl'>1</span>, <span class='fl'>3</span>])</div><div class='output co'>#> <span class='error'>Error in plot(f_SFO_SFO[1, 3]): Objekt 'f_SFO_SFO' nicht gefunden</span></div><div class='input'> +<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>f_SFO_SFO</span>[<span class='fl'>1</span>, <span class='fl'>3</span>])</div><div class='img'><img src='add_err-3.png' alt='' width='700' height='433' /></div><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 63db2467..9952f7ad 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -156,7 +156,17 @@ with the advantage that the SFORB model can also be used for metabolites.</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></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>)</div><div class='output co'>#> <span class='error'>Error in mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'> <span class='fu'>endpoints</span>(<span class='no'>fit</span>)</div><div class='output co'>#> <span class='error'>Error in endpoints(fit): konnte Funktion "endpoints" nicht finden</span></div></pre> + <pre class="examples"><div class='input'> <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></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'>endpoints</span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff +#> logical(0) +#> +#> $SFORB +#> logical(0) +#> +#> $distimes +#> DT50 DT90 DT50back +#> parent 1.785233 15.1479 4.559973 +#> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index db737b2c..ca3d8808 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -150,7 +150,7 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>1</span>,<span class='fl'>3</span>, <span class='fl'>9</span>))</div><div class='output co'>#> <span class='error'>Error in geometric_mean(c(1, 3, 9)): konnte Funktion "geometric_mean" nicht finden</span></div><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>1</span>,<span class='fl'>3</span>, <span class='fl'>NA</span>))</div><div class='output co'>#> <span class='error'>Error in geometric_mean(c(1, 3, NA)): konnte Funktion "geometric_mean" nicht finden</span></div><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'>#> <span class='error'>Error in geometric_mean(c(1, 3, NA), na.rm = TRUE): konnte Funktion "geometric_mean" nicht finden</span></div></pre> + <pre class="examples"><div class='input'> <span class='fu'>geometric_mean</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index b75a9a91..760dd3aa 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -158,14 +158,15 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># Order matters</span> -<span class='fu'>ilr</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0.1</span>, <span class='fl'>1</span>, <span class='fl'>10</span>))</div><div class='output co'>#> <span class='error'>Error in ilr(c(0.1, 1, 10)): konnte Funktion "ilr" nicht finden</span></div><div class='input'><span class='fu'>ilr</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>10</span>, <span class='fl'>1</span>, <span class='fl'>0.1</span>))</div><div class='output co'>#> <span class='error'>Error in ilr(c(10, 1, 0.1)): konnte Funktion "ilr" nicht finden</span></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>3</span>, <span class='fl'>3</span>, <span class='fl'>3</span>))</div><div class='output co'>#> <span class='error'>Error in ilr(c(3, 3, 3)): konnte Funktion "ilr" nicht finden</span></div><div class='input'><span class='co'># Almost equal entries give small numbers</span> -<span class='fu'>ilr</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0.3</span>, <span class='fl'>0.4</span>, <span class='fl'>0.3</span>))</div><div class='output co'>#> <span class='error'>Error in ilr(c(0.3, 0.4, 0.3)): konnte Funktion "ilr" nicht finden</span></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0.7</span>, <span class='fl'>0.29</span>, <span class='fl'>0.01</span>)))</div><div class='output co'>#> <span class='error'>Error in invilr(ilr(c(0.7, 0.29, 0.01))): konnte Funktion "invilr" nicht finden</span></div><div class='input'><span class='fu'>invilr</span>(<span class='fu'>ilr</span>(<span class='fl'>2.1</span> * <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>0.7</span>, <span class='fl'>0.29</span>, <span class='fl'>0.01</span>)))</div><div class='output co'>#> <span class='error'>Error in invilr(ilr(2.1 * c(0.7, 0.29, 0.01))): konnte Funktion "invilr" nicht finden</span></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'>#> <span class='error'>Error in invilr(-10): konnte Funktion "invilr" nicht finden</span></div><div class='input'><span class='fu'>invilr</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(-<span class='fl'>10</span>, <span class='fl'>0</span>))</div><div class='output co'>#> <span class='error'>Error in invilr(c(-10, 0)): konnte Funktion "invilr" nicht finden</span></div><div class='input'><span class='co'># The sum of the elements of the inverse ilr is 1</span> -<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/sum'>sum</a></span>(<span class='fu'>invilr</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(-<span class='fl'>10</span>, <span class='fl'>0</span>)))</div><div class='output co'>#> <span class='error'>Error in invilr(c(-10, 0)): konnte Funktion "invilr" nicht finden</span></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='fu'>ilr</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/sum'>sum</a></span>(<span class='fu'>invilr</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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>)</div><div class='output co'>#> <span class='error'>Error in invilr(a): konnte Funktion "invilr" nicht finden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/length'>length</a></span>(<span class='no'>b</span>) <span class='co'># Four elements</span></div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'b' nicht gefunden</span></div><div class='input'><span class='fu'>ilr</span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='fl'>1</span> - <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/sum'>sum</a></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'>#> <span class='error'>Error in ilr(c(b[1:3], 1 - sum(b[1:3]))): konnte Funktion "ilr" nicht finden</span></div></pre> +<span class='no'>b</span> <span class='kw'><-</span> <span class='fu'>invilr</span>(<span class='no'>a</span>) +<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/length'>length</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='no'>b</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='fl'>1</span> - <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/sum'>sum</a></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 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index 303a337d..a23ea52b 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -195,10 +195,18 @@ In the case of iterative reweighting, the variances obtained by this <pre class="examples"><div class='input'> <span class='no'>sfo_sfo</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>) - )</div><div class='output co'>#> <span class='error'>Error in mkinmod(parent = mkinsub("SFO", to = "m1"), m1 = mkinsub("SFO")): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'> <span class='no'>d_t</span> <span class='kw'><-</span> <span class='no'>FOCUS_2006_D</span> + )</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='no'>d_t</span> <span class='kw'><-</span> <span class='no'>FOCUS_2006_D</span> <span class='no'>d_t</span>[<span class='fl'>23</span>:<span class='fl'>24</span>, <span class='st'>"value"</span>] <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>NA</span>, <span class='fl'>NA</span>) <span class='co'># can't cope with zero values at the moment</span> - <span class='no'>f_nw</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>sfo_sfo</span>, <span class='no'>d_t</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># no weighting (weights are unity)</span></div><div class='output co'>#> <span class='error'>Error in mkinfit(sfo_sfo, d_t, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'> <span class='no'>f_obs</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>sfo_sfo</span>, <span class='no'>d_t</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(sfo_sfo, d_t, reweight.method = "obs", quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'> <span class='no'>f_tc</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>sfo_sfo</span>, <span class='no'>d_t</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(sfo_sfo, d_t, reweight.method = "tc", quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'> <span class='no'>d_t</span>$<span class='no'>err</span> <span class='kw'><-</span> <span class='no'>d_t</span>$<span class='no'>value</span> <span class='co'># Manual weighting assuming sigma ~ y</span> - <span class='no'>f_man</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>sfo_sfo</span>, <span class='no'>d_t</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(sfo_sfo, d_t, err = "err", quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/AIC'>AIC</a></span>(<span class='no'>f_nw</span>, <span class='no'>f_obs</span>, <span class='no'>f_tc</span>, <span class='no'>f_man</span>)</div><div class='output co'>#> <span class='error'>Error in AIC(f_nw, f_obs, f_tc, f_man): Objekt 'f_nw' nicht gefunden</span></div></pre> + <span class='no'>f_nw</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>sfo_sfo</span>, <span class='no'>d_t</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># no weighting (weights are unity)</span> + <span class='no'>f_obs</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>sfo_sfo</span>, <span class='no'>d_t</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='no'>f_tc</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>sfo_sfo</span>, <span class='no'>d_t</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"tc"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='no'>d_t</span>$<span class='no'>err</span> <span class='kw'><-</span> <span class='no'>d_t</span>$<span class='no'>value</span> <span class='co'># Manual weighting assuming sigma ~ y</span> + <span class='no'>f_man</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>sfo_sfo</span>, <span class='no'>d_t</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/AIC'>AIC</a></span>(<span class='no'>f_nw</span>, <span class='no'>f_obs</span>, <span class='no'>f_tc</span>, <span class='no'>f_man</span>)</div><div class='output co'>#> df AIC +#> f_nw 5 204.4619 +#> f_obs 6 205.8727 +#> f_tc 6 143.8773 +#> f_man 4 291.8000</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index ee99d0c8..320bdd46 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -166,7 +166,9 @@ guidance.</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></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>)</div><div class='output co'>#> <span class='error'>Error in mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'> <span class='fu'>max_twa_parent</span>(<span class='no'>fit</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>7</span>, <span class='fl'>21</span>))</div><div class='output co'>#> <span class='error'>Error in max_twa_parent(fit, c(7, 21)): konnte Funktion "max_twa_parent" nicht finden</span></div></pre> + <pre class="examples"><div class='input'> <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></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'>max_twa_parent</span>(<span class='no'>fit</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='fl'>7</span>, <span class='fl'>21</span>))</div><div class='output co'>#> 7 21 +#> 34.71343 18.22124 </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 86ba7566..93d7f197 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -157,11 +157,190 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='error'>Error in mkinmod(T245 = list(type = "SFO", to = "phenol"), phenol = list(type = "SFO", to = "anisole"), anisole = list(type = "SFO")): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'> </div><div class='input'> <span class='no'>fit.1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></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>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> <span class='error'>Error in summary(fit.1, data = FALSE): Objekt 'fit.1' nicht gefunden</span></div><div class='input'> <span class='co'># No convergence, no covariance matrix ...</span> + <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> </div><div class='input'> <span class='no'>fit.1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.1</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.6 +#> R version used for fitting: 3.5.2 +#> Date of fit: Thu Jan 31 16:51:05 2019 +#> Date of summary: Thu Jan 31 16:51:05 2019 +#> +#> Equations: +#> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 +#> d_phenol/dt = + k_T245_phenol * T245 - k_phenol_sink * phenol - +#> k_phenol_anisole * phenol +#> d_anisole/dt = + k_phenol_anisole * phenol - k_anisole_sink * anisole +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 574 model solutions performed in 3.87 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_sink 0.1002 deparm +#> k_phenol_anisole 0.1003 deparm +#> k_anisole_sink 0.1004 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_sink -2.300587 -Inf Inf +#> log_k_phenol_anisole -2.299590 -Inf Inf +#> log_k_anisole_sink -2.298593 -Inf Inf +#> +#> Fixed parameter values: +#> value type +#> phenol_0 0 state +#> anisole_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> T245_0 103.9000 NA NA NA +#> log_k_T245_sink -4.1130 NA NA NA +#> log_k_T245_phenol -3.6120 NA NA NA +#> log_k_phenol_sink -25.0800 NA NA NA +#> log_k_phenol_anisole -0.9037 NA NA NA +#> log_k_anisole_sink -5.0090 NA NA NA +#> +#> Parameter correlation:</div><div class='output co'>#> <span class='warning'>Warning: Could not estimate covariance matrix; singular system:</span></div><div class='output co'>#> Could not estimate covariance matrix; singular system: +#> +#> Residual standard error: 2.78 on 18 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 4.282e+01 7.236e-20 NA NA +#> k_T245_sink 1.636e-02 8.901e-01 1.926e-01 NA NA +#> k_T245_phenol 2.701e-02 1.504e+00 7.498e-02 NA NA +#> k_phenol_sink 1.286e-11 4.575e-11 5.000e-01 NA NA +#> k_phenol_anisole 4.051e-01 2.518e+00 1.075e-02 NA NA +#> k_anisole_sink 6.679e-03 8.146e+00 9.469e-08 NA NA +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 10.070 6 16 +#> T245 7.908 3 5 +#> phenol 106.445 2 5 +#> anisole 5.379 1 6 +#> +#> Resulting formation fractions: +#> ff +#> T245_sink 3.772e-01 +#> T245_phenol 6.228e-01 +#> phenol_sink 3.175e-11 +#> phenol_anisole 1.000e+00 +#> anisole_sink 1.000e+00 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> T245 15.982 53.091 +#> phenol 1.711 5.685 +#> anisole 103.784 344.763</div><div class='input'> <span class='co'># No convergence, no covariance matrix ...</span> <span class='co'># 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'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), parms.ini = c(k_phenol_sink = 0), fixed_parms = "k_phenol_sink", quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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'>#> <span class='error'>Error in summary(fit.2, data = FALSE): Objekt 'fit.2' nicht gefunden</span></div><div class='input'> </div></pre> + <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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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 used for fitting: 0.9.47.6 +#> R version used for fitting: 3.5.2 +#> Date of fit: Thu Jan 31 16:51:07 2019 +#> Date of summary: Thu Jan 31 16:51:07 2019 +#> +#> Equations: +#> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 +#> d_phenol/dt = + k_T245_phenol * T245 - k_phenol_sink * phenol - +#> k_phenol_anisole * phenol +#> d_anisole/dt = + k_phenol_anisole * phenol - k_anisole_sink * anisole +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 246 model solutions performed in 1.618 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><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 9a7e3c61..290d3e76 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -160,7 +160,29 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>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'>#> <span class='error'>Error in mkin_long_to_wide(FOCUS_2006_D): konnte Funktion "mkin_long_to_wide" nicht finden</span></div></pre> + <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 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 5e7df90d..d7438fcf 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -154,7 +154,13 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>wide</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></span>(<span class='kw'>t</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'>#> <span class='error'>Error in mkin_wide_to_long(wide): konnte Funktion "mkin_wide_to_long" nicht finden</span></div></pre> +<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 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 1686679b..35086a61 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -175,8 +175,16 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>SFO_SFO</span> <span class='kw'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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'><a href='mkinsub.html'>mkinsub</a></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 co'>#> <span class='error'>Error in mkinmod(parent = mkinsub("SFO", to = "m1"), m1 = mkinsub("SFO"), use_of_ff = "max"): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'> -<span class='no'>fit_FOCUS_D</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></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>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/Round'>round</a></span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_D</span>), <span class='fl'>4</span>)</div><div class='output co'>#> <span class='error'>Error in mkinerrmin(fit_FOCUS_D): konnte Funktion "mkinerrmin" nicht finden</span></div><div class='input'> <span class='no'>fit_FOCUS_E</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></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>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFO_SFO, FOCUS_2006_E, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/Round'>round</a></span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_E</span>), <span class='fl'>4</span>)</div><div class='output co'>#> <span class='error'>Error in mkinerrmin(fit_FOCUS_E): konnte Funktion "mkinerrmin" nicht finden</span></div></pre> + <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> +<span class='no'>fit_FOCUS_D</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/Round'>round</a></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'><a href='mkinfit.html'>mkinfit</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/Round'>round</a></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 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index bd691770..42845d68 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -435,40 +435,914 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>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>)</div><div class='output co'>#> <span class='error'>Error in mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> <span class='error'>Error in summary(fit): Objekt 'fit' nicht gefunden</span></div><div class='input'> +<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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.6 +#> R version used for fitting: 3.5.2 +#> Date of fit: Thu Jan 31 16:51:10 2019 +#> Date of summary: Thu Jan 31 16:51:10 2019 +#> +#> Equations: +#> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent +#> +#> Model predictions using solution type analytical +#> +#> Fitted with method Port using 64 model solutions performed in 0.162 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'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='error'>Error in mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></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'>#> <span class='error'>Error in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0 0 0</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> <span class='error'>Error in coef(fit): Objekt 'fit' nicht gefunden</span></div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> <span class='error'>Error in endpoints(fit): konnte Funktion "endpoints" nicht finden</span></div><div class='input'><span class='co'># deSolve is slower when no C compiler (gcc) was available during model generation</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 verstrichen +#> 1.022 0.000 1.025 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></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'><a href='endpoints.html'>endpoints</a></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'># deSolve is slower when no C compiler (gcc) was available during model generation</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fit.deSolve</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'>"deSolve"</span>)))</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve"): konnte Funktion "mkinfit" nicht finden</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0 0 0</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> <span class='error'>Error in coef(fit.deSolve): Objekt 'fit.deSolve' nicht gefunden</span></div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#> <span class='error'>Error in endpoints(fit.deSolve): konnte Funktion "endpoints" nicht finden</span></div><div class='input'> + <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)))</div><div class='output co'>#> Model cost at call 1 : 18915.53 +#> Model cost at call 2 : 18915.53 +#> Model cost at call 6 : 11424.02 +#> Model cost at call 10 : 11424 +#> Model cost at call 12 : 4094.396 +#> Model cost at call 16 : 4094.396 +#> Model cost at call 19 : 1340.595 +#> Model cost at call 20 : 1340.593 +#> Model cost at call 25 : 1072.239 +#> Model cost at call 28 : 1072.236 +#> Model cost at call 30 : 874.2615 +#> Model cost at call 33 : 874.2611 +#> Model cost at call 35 : 616.2377 +#> Model cost at call 37 : 616.2372 +#> Model cost at call 40 : 467.4386 +#> Model cost at call 42 : 467.4381 +#> Model cost at call 46 : 398.2914 +#> Model cost at call 48 : 398.2914 +#> Model cost at call 49 : 398.2913 +#> Model cost at call 51 : 395.0712 +#> Model cost at call 54 : 395.0711 +#> Model cost at call 56 : 378.3298 +#> Model cost at call 59 : 378.3298 +#> Model cost at call 62 : 376.9812 +#> Model cost at call 64 : 376.9811 +#> Model cost at call 67 : 375.2085 +#> Model cost at call 69 : 375.2085 +#> Model cost at call 70 : 375.2085 +#> Model cost at call 71 : 375.2085 +#> Model cost at call 72 : 374.5723 +#> Model cost at call 74 : 374.5723 +#> Model cost at call 77 : 374.0075 +#> Model cost at call 79 : 374.0075 +#> Model cost at call 80 : 374.0075 +#> Model cost at call 82 : 373.1711 +#> Model cost at call 84 : 373.1711 +#> Model cost at call 87 : 372.6445 +#> Model cost at call 88 : 372.1614 +#> Model cost at call 90 : 372.1614 +#> Model cost at call 91 : 372.1614 +#> Model cost at call 94 : 371.6464 +#> Model cost at call 99 : 371.4299 +#> Model cost at call 101 : 371.4299 +#> Model cost at call 104 : 371.4071 +#> Model cost at call 106 : 371.4071 +#> Model cost at call 107 : 371.4071 +#> Model cost at call 109 : 371.2524 +#> Model cost at call 113 : 371.2524 +#> Model cost at call 114 : 371.2136 +#> Model cost at call 115 : 371.2136 +#> Model cost at call 116 : 371.2136 +#> Model cost at call 119 : 371.2134 +#> Model cost at call 120 : 371.2134 +#> Model cost at call 122 : 371.2134 +#> Model cost at call 123 : 371.2134 +#> Model cost at call 125 : 371.2134 +#> Model cost at call 126 : 371.2134 +#> Model cost at call 135 : 371.2134 +#> Model cost at call 146 : 371.2134 +#> Optimisation by method Port successfully terminated. +#> User System verstrichen +#> 0.823 0.000 0.823 </div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/stats/topics/coef'>coef</a></span>(<span class='no'>fit.deSolve</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'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</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 131.760711 437.69961 +#> </div><div class='input'> # Use stepwise fitting, using optimised parameters from parent only fit, FOMC </div><div class='input'><span class='no'>FOMC_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"FOMC"</span>, <span class='st'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='error'>Error in mkinmod(parent = mkinsub("FOMC", "m1"), m1 = mkinsub("SFO")): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> -<span class='no'>fit.FOMC_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='co'># Use starting parameters from parent only FOMC fit</span> -<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_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit("FOMC", FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='no'>fit.FOMC_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_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'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.FOMC</span>$<span class='no'>bparms.ode</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE, parms.ini = fit.FOMC$bparms.ode): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> +<span class='no'>fit.FOMC_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='co'># Use starting parameters from parent only FOMC fit</span> +<span class='no'>fit.FOMC</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='no'>fit.FOMC_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.FOMC</span>$<span class='no'>bparms.ode</span>) + <span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, SFORB</span> <span class='no'>SFORB_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFORB"</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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='error'>Error in mkinmod(parent = list(type = "SFORB", to = "m1", sink = TRUE), m1 = list(type = "SFO")): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> -<span class='no'>fit.SFORB_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFORB_SFO, FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='no'>fit.SFORB_SFO.deSolve</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</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>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFORB_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='co'># Use starting parameters from parent only SFORB fit (not really needed in this case)</span> -<span class='no'>fit.SFORB</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"SFORB"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit("SFORB", FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='no'>fit.SFORB_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.SFORB</span>$<span class='no'>bparms.ode</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='co'># Fit the model to the FOCUS example dataset D using defaults</span> +<span class='no'>fit.SFORB_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_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='no'>fit.SFORB_SFO.deSolve</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</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='co'># Use starting parameters from parent only SFORB fit (not really needed in this case)</span> +<span class='no'>fit.SFORB</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"SFORB"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='no'>fit.SFORB_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.SFORB</span>$<span class='no'>bparms.ode</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='input'> </div><div class='input'><span class='co'># Weighted fits, including IRLS</span> <span class='no'>SFO_SFO.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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 co'>#> <span class='error'>Error in mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), use_of_ff = "max"): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> <span class='error'>Error in summary(f.noweight): Objekt 'f.noweight' nicht gefunden</span></div><div class='input'><span class='no'>f.irls</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs", quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.irls</span>)</div><div class='output co'>#> <span class='error'>Error in summary(f.irls): Objekt 'f.irls' nicht gefunden</span></div><div class='input'><span class='no'>f.w.mean</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#> <span class='error'>Error in summary(f.w.mean): Objekt 'f.w.mean' nicht gefunden</span></div><div class='input'><span class='no'>f.w.value</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"value"</span>, - <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), err = "value", quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#> <span class='error'>Error in summary(f.w.value): Objekt 'f.w.value' nicht gefunden</span></div><div class='input'> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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 co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>f.noweight</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.6 +#> R version used for fitting: 3.5.2 +#> Date of fit: Thu Jan 31 16:51:22 2019 +#> Date of summary: Thu Jan 31 16:51:22 2019 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 186 model solutions performed in 0.872 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent 0.1000 deparm +#> k_m1 0.1001 deparm +#> f_parent_to_m1 0.5000 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_m1 -2.301586 -Inf Inf +#> f_parent_ilr_1 0.000000 -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 99.60000 1.61400 96.3300 102.9000 +#> log_k_parent -2.31600 0.04187 -2.4010 -2.2310 +#> log_k_m1 -5.24800 0.13610 -5.5230 -4.9720 +#> f_parent_ilr_1 0.04096 0.06477 -0.0904 0.1723 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.0000 0.5178 -0.1701 -0.5489 +#> log_k_parent 0.5178 1.0000 -0.3285 -0.5451 +#> log_k_m1 -0.1701 -0.3285 1.0000 0.7466 +#> f_parent_ilr_1 -0.5489 -0.5451 0.7466 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 0.098700 23.880 5.700e-24 0.090660 1.074e-01 +#> k_m1 0.005261 7.349 5.758e-09 0.003992 6.933e-03 +#> f_parent_to_m1 0.514500 22.490 4.375e-23 0.468100 5.606e-01 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.398 4 15 +#> parent 6.459 2 7 +#> m1 4.690 2 8 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.5145 +#> parent_sink 0.4855 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 7.023 23.33 +#> m1 131.761 437.70 +#> +#> Data: +#> time variable observed predicted residual +#> 0 parent 99.46 99.59848 -1.385e-01 +#> 0 parent 102.04 99.59848 2.442e+00 +#> 1 parent 93.50 90.23787 3.262e+00 +#> 1 parent 92.50 90.23787 2.262e+00 +#> 3 parent 63.23 74.07319 -1.084e+01 +#> 3 parent 68.99 74.07319 -5.083e+00 +#> 7 parent 52.32 49.91206 2.408e+00 +#> 7 parent 55.13 49.91206 5.218e+00 +#> 14 parent 27.27 25.01257 2.257e+00 +#> 14 parent 26.64 25.01257 1.627e+00 +#> 21 parent 11.50 12.53462 -1.035e+00 +#> 21 parent 11.64 12.53462 -8.946e-01 +#> 35 parent 2.85 3.14787 -2.979e-01 +#> 35 parent 2.91 3.14787 -2.379e-01 +#> 50 parent 0.69 0.71624 -2.624e-02 +#> 50 parent 0.63 0.71624 -8.624e-02 +#> 75 parent 0.05 0.06074 -1.074e-02 +#> 75 parent 0.06 0.06074 -7.381e-04 +#> 0 m1 0.00 0.00000 0.000e+00 +#> 0 m1 0.00 0.00000 0.000e+00 +#> 1 m1 4.84 4.80296 3.704e-02 +#> 1 m1 5.64 4.80296 8.370e-01 +#> 3 m1 12.91 13.02400 -1.140e-01 +#> 3 m1 12.96 13.02400 -6.400e-02 +#> 7 m1 22.97 25.04476 -2.075e+00 +#> 7 m1 24.47 25.04476 -5.748e-01 +#> 14 m1 41.69 36.69002 5.000e+00 +#> 14 m1 33.21 36.69002 -3.480e+00 +#> 21 m1 44.37 41.65310 2.717e+00 +#> 21 m1 46.44 41.65310 4.787e+00 +#> 35 m1 41.22 43.31312 -2.093e+00 +#> 35 m1 37.95 43.31312 -5.363e+00 +#> 50 m1 41.19 41.21831 -2.831e-02 +#> 50 m1 40.01 41.21831 -1.208e+00 +#> 75 m1 40.09 36.44703 3.643e+00 +#> 75 m1 33.85 36.44703 -2.597e+00 +#> 100 m1 31.04 31.98163 -9.416e-01 +#> 100 m1 33.13 31.98163 1.148e+00 +#> 120 m1 25.15 28.78984 -3.640e+00 +#> 120 m1 33.31 28.78984 4.520e+00</div><div class='input'><span class='no'>f.irls</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.irls</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.6 +#> R version used for fitting: 3.5.2 +#> Date of fit: Thu Jan 31 16:51:24 2019 +#> Date of summary: Thu Jan 31 16:51:24 2019 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 551 model solutions performed in 2.558 s +#> +#> Weighting: none +#> +#> Iterative reweighting with method obs +#> Final mean squared residuals of observed variables: +#> parent m1 +#> 11.573407 7.407845 +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent 0.1000 deparm +#> k_m1 0.1001 deparm +#> f_parent_to_m1 0.5000 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_m1 -2.301586 -Inf Inf +#> f_parent_ilr_1 0.000000 -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 99.67000 1.79200 96.04000 103.300 +#> log_k_parent -2.31200 0.04560 -2.40400 -2.219 +#> log_k_m1 -5.25100 0.12510 -5.50500 -4.998 +#> f_parent_ilr_1 0.03785 0.06318 -0.09027 0.166 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.0000 0.5083 -0.1979 -0.6148 +#> log_k_parent 0.5083 1.0000 -0.3894 -0.6062 +#> log_k_m1 -0.1979 -0.3894 1.0000 0.7417 +#> f_parent_ilr_1 -0.6148 -0.6062 0.7417 1.0000 +#> +#> Residual standard error: 1.054 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 99.67000 55.630 8.185e-37 96.040000 1.033e+02 +#> k_parent 0.09906 21.930 1.016e-22 0.090310 1.087e-01 +#> k_m1 0.00524 7.996 8.486e-10 0.004066 6.753e-03 +#> f_parent_to_m1 0.51340 23.000 2.038e-23 0.468100 5.584e-01 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.399 4 15 +#> parent 6.466 2 7 +#> m1 4.679 2 8 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.5134 +#> parent_sink 0.4866 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 6.997 23.24 +#> m1 132.282 439.43 +#> +#> Data: +#> time variable observed predicted residual err +#> 0 parent 99.46 99.67218 -2.122e-01 3.402 +#> 0 parent 102.04 99.67218 2.368e+00 3.402 +#> 1 parent 93.50 90.27153 3.228e+00 3.402 +#> 1 parent 92.50 90.27153 2.228e+00 3.402 +#> 3 parent 63.23 74.04648 -1.082e+01 3.402 +#> 3 parent 68.99 74.04648 -5.056e+00 3.402 +#> 7 parent 52.32 49.82092 2.499e+00 3.402 +#> 7 parent 55.13 49.82092 5.309e+00 3.402 +#> 14 parent 27.27 24.90288 2.367e+00 3.402 +#> 14 parent 26.64 24.90288 1.737e+00 3.402 +#> 21 parent 11.50 12.44765 -9.476e-01 3.402 +#> 21 parent 11.64 12.44765 -8.076e-01 3.402 +#> 35 parent 2.85 3.11002 -2.600e-01 3.402 +#> 35 parent 2.91 3.11002 -2.000e-01 3.402 +#> 50 parent 0.69 0.70374 -1.374e-02 3.402 +#> 50 parent 0.63 0.70374 -7.374e-02 3.402 +#> 75 parent 0.05 0.05913 -9.134e-03 3.402 +#> 75 parent 0.06 0.05913 8.662e-04 3.402 +#> 0 m1 0.00 0.00000 0.000e+00 2.722 +#> 0 m1 0.00 0.00000 0.000e+00 2.722 +#> 1 m1 4.84 4.81328 2.672e-02 2.722 +#> 1 m1 5.64 4.81328 8.267e-01 2.722 +#> 3 m1 12.91 13.04779 -1.378e-01 2.722 +#> 3 m1 12.96 13.04779 -8.779e-02 2.722 +#> 7 m1 22.97 25.07615 -2.106e+00 2.722 +#> 7 m1 24.47 25.07615 -6.062e-01 2.722 +#> 14 m1 41.69 36.70729 4.983e+00 2.722 +#> 14 m1 33.21 36.70729 -3.497e+00 2.722 +#> 21 m1 44.37 41.65050 2.720e+00 2.722 +#> 21 m1 46.44 41.65050 4.790e+00 2.722 +#> 35 m1 41.22 43.28866 -2.069e+00 2.722 +#> 35 m1 37.95 43.28866 -5.339e+00 2.722 +#> 50 m1 41.19 41.19339 -3.386e-03 2.722 +#> 50 m1 40.01 41.19339 -1.183e+00 2.722 +#> 75 m1 40.09 36.43820 3.652e+00 2.722 +#> 75 m1 33.85 36.43820 -2.588e+00 2.722 +#> 100 m1 31.04 31.98971 -9.497e-01 2.722 +#> 100 m1 33.13 31.98971 1.140e+00 2.722 +#> 120 m1 25.15 28.80898 -3.659e+00 2.722 +#> 120 m1 33.31 28.80898 4.501e+00 2.722</div><div class='input'><span class='no'>f.w.mean</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.6 +#> R version used for fitting: 3.5.2 +#> Date of fit: Thu Jan 31 16:51:25 2019 +#> Date of summary: Thu Jan 31 16:51:25 2019 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 155 model solutions performed in 0.711 s +#> +#> Weighting: mean +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent 0.1000 deparm +#> k_m1 0.1001 deparm +#> f_parent_to_m1 0.5000 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_m1 -2.301586 -Inf Inf +#> f_parent_ilr_1 0.000000 -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 99.7300 1.93200 95.81000 103.6000 +#> log_k_parent -2.3090 0.04837 -2.40700 -2.2110 +#> log_k_m1 -5.2550 0.12070 -5.49900 -5.0100 +#> f_parent_ilr_1 0.0354 0.06344 -0.09327 0.1641 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.0000 0.5004 -0.2143 -0.6514 +#> log_k_parent 0.5004 1.0000 -0.4282 -0.6383 +#> log_k_m1 -0.2143 -0.4282 1.0000 0.7390 +#> f_parent_ilr_1 -0.6514 -0.6383 0.7390 1.0000 +#> +#> Residual standard error: 0.09829 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 99.730000 51.630 1.166e-35 95.81000 1.036e+02 +#> k_parent 0.099360 20.670 7.304e-22 0.09007 1.096e-01 +#> k_m1 0.005224 8.287 3.649e-10 0.00409 6.672e-03 +#> f_parent_to_m1 0.512500 22.860 2.497e-23 0.46710 5.578e-01 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.401 4 15 +#> parent 6.473 2 7 +#> m1 4.671 2 8 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.5125 +#> parent_sink 0.4875 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 6.976 23.18 +#> m1 132.696 440.81 +#> +#> Data: +#> time variable observed predicted residual +#> 0 parent 99.46 99.73057 -0.270570 +#> 0 parent 102.04 99.73057 2.309430 +#> 1 parent 93.50 90.29805 3.201945 +#> 1 parent 92.50 90.29805 2.201945 +#> 3 parent 63.23 74.02503 -10.795028 +#> 3 parent 68.99 74.02503 -5.035028 +#> 7 parent 52.32 49.74838 2.571618 +#> 7 parent 55.13 49.74838 5.381618 +#> 14 parent 27.27 24.81588 2.454124 +#> 14 parent 26.64 24.81588 1.824124 +#> 21 parent 11.50 12.37885 -0.878849 +#> 21 parent 11.64 12.37885 -0.738849 +#> 35 parent 2.85 3.08022 -0.230219 +#> 35 parent 2.91 3.08022 -0.170219 +#> 50 parent 0.69 0.69396 -0.003958 +#> 50 parent 0.63 0.69396 -0.063958 +#> 75 parent 0.05 0.05789 -0.007888 +#> 75 parent 0.06 0.05789 0.002112 +#> 0 m1 0.00 0.00000 0.000000 +#> 0 m1 0.00 0.00000 0.000000 +#> 1 m1 4.84 4.82149 0.018512 +#> 1 m1 5.64 4.82149 0.818512 +#> 3 m1 12.91 13.06669 -0.156692 +#> 3 m1 12.96 13.06669 -0.106692 +#> 7 m1 22.97 25.10106 -2.131058 +#> 7 m1 24.47 25.10106 -0.631058 +#> 14 m1 41.69 36.72092 4.969077 +#> 14 m1 33.21 36.72092 -3.510923 +#> 21 m1 44.37 41.64835 2.721647 +#> 21 m1 46.44 41.64835 4.791647 +#> 35 m1 41.22 43.26923 -2.049225 +#> 35 m1 37.95 43.26923 -5.319225 +#> 50 m1 41.19 41.17364 0.016361 +#> 50 m1 40.01 41.17364 -1.163639 +#> 75 m1 40.09 36.43122 3.658776 +#> 75 m1 33.85 36.43122 -2.581224 +#> 100 m1 31.04 31.99612 -0.956124 +#> 100 m1 33.13 31.99612 1.133876 +#> 120 m1 25.15 28.82413 -3.674128 +#> 120 m1 33.31 28.82413 4.485872</div><div class='input'><span class='no'>f.w.value</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"value"</span>, + <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.6 +#> R version used for fitting: 3.5.2 +#> Date of fit: Thu Jan 31 16:51:26 2019 +#> Date of summary: Thu Jan 31 16:51:26 2019 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 174 model solutions performed in 0.807 s +#> +#> Weighting: manual +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent 0.1000 deparm +#> k_m1 0.1001 deparm +#> f_parent_to_m1 0.5000 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_m1 -2.301586 -Inf Inf +#> f_parent_ilr_1 0.000000 -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 99.6600 2.712000 94.14000 105.2000 +#> log_k_parent -2.2980 0.008118 -2.31500 -2.2820 +#> log_k_m1 -5.2410 0.096690 -5.43800 -5.0450 +#> f_parent_ilr_1 0.0231 0.057990 -0.09474 0.1409 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.00000 0.6843 -0.08687 -0.7564 +#> log_k_parent 0.68435 1.0000 -0.12695 -0.5812 +#> log_k_m1 -0.08687 -0.1269 1.00000 0.5195 +#> f_parent_ilr_1 -0.75644 -0.5812 0.51952 1.0000 +#> +#> Residual standard error: 0.08396 on 34 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 99.660000 36.75 2.957e-29 94.14000 1.052e+02 +#> k_parent 0.100400 123.20 5.927e-47 0.09878 1.021e-01 +#> k_m1 0.005295 10.34 2.447e-12 0.00435 6.444e-03 +#> f_parent_to_m1 0.508200 24.79 1.184e-23 0.46660 5.497e-01 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.461 4 15 +#> parent 6.520 2 7 +#> m1 4.744 2 8 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.5082 +#> parent_sink 0.4918 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 6.902 22.93 +#> m1 130.916 434.89 +#> +#> Data: +#> time variable observed predicted residual err +#> 0 parent 99.46 99.65571 -0.195715 99.46 +#> 0 parent 102.04 99.65571 2.384285 102.04 +#> 1 parent 93.50 90.13383 3.366170 93.50 +#> 1 parent 92.50 90.13383 2.366170 92.50 +#> 3 parent 63.23 73.73252 -10.502518 63.23 +#> 3 parent 68.99 73.73252 -4.742518 68.99 +#> 7 parent 52.32 49.34027 2.979728 52.32 +#> 7 parent 55.13 49.34027 5.789728 55.13 +#> 14 parent 27.27 24.42873 2.841271 27.27 +#> 14 parent 26.64 24.42873 2.211271 26.64 +#> 21 parent 11.50 12.09484 -0.594842 11.50 +#> 21 parent 11.64 12.09484 -0.454842 11.64 +#> 35 parent 2.85 2.96482 -0.114824 2.85 +#> 35 parent 2.91 2.96482 -0.054824 2.91 +#> 50 parent 0.69 0.65733 0.032670 0.69 +#> 50 parent 0.63 0.65733 -0.027330 0.63 +#> 75 parent 0.05 0.05339 -0.003386 0.05 +#> 75 parent 0.06 0.05339 0.006614 0.06 +#> 1 m1 4.84 4.82570 0.014301 4.84 +#> 1 m1 5.64 4.82570 0.814301 5.64 +#> 3 m1 12.91 13.06402 -0.154020 12.91 +#> 3 m1 12.96 13.06402 -0.104020 12.96 +#> 7 m1 22.97 25.04656 -2.076564 22.97 +#> 7 m1 24.47 25.04656 -0.576564 24.47 +#> 14 m1 41.69 36.53601 5.153988 41.69 +#> 14 m1 33.21 36.53601 -3.326012 33.21 +#> 21 m1 44.37 41.34639 3.023609 44.37 +#> 21 m1 46.44 41.34639 5.093609 46.44 +#> 35 m1 41.22 42.82669 -1.606690 41.22 +#> 35 m1 37.95 42.82669 -4.876690 37.95 +#> 50 m1 41.19 40.67342 0.516578 41.19 +#> 50 m1 40.01 40.67342 -0.663422 40.01 +#> 75 m1 40.09 35.91105 4.178947 40.09 +#> 75 m1 33.85 35.91105 -2.061053 33.85 +#> 100 m1 31.04 31.48161 -0.441612 31.04 +#> 100 m1 33.13 31.48161 1.648388 33.13 +#> 120 m1 25.15 28.32018 -3.170181 25.15 +#> 120 m1 33.31 28.32018 4.989819 33.31</div><div class='input'> </div><div class='input'><span class='co'># Manual weighting</span> <span class='no'>dw</span> <span class='kw'><-</span> <span class='no'>FOCUS_2006_D</span> <span class='no'>errors</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>1</span>) <span class='no'>dw</span>$<span class='no'>err.man</span> <span class='kw'><-</span> <span class='no'>errors</span>[<span class='no'>FOCUS_2006_D</span>$<span class='no'>name</span>] -<span class='no'>f.w.man</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#> <span class='error'>Error in summary(f.w.man): Objekt 'f.w.man' nicht gefunden</span></div><div class='input'><span class='no'>f.w.man.irls</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE, reweight.method = "obs"): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#> <span class='error'>Error in summary(f.w.man.irls): Objekt 'f.w.man.irls' nicht gefunden</span></div></pre> +<span class='no'>f.w.man</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.6 +#> R version used for fitting: 3.5.2 +#> Date of fit: Thu Jan 31 16:51:28 2019 +#> Date of summary: Thu Jan 31 16:51:28 2019 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 270 model solutions performed in 1.257 s +#> +#> Weighting: manual +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent 0.1000 deparm +#> k_m1 0.1001 deparm +#> f_parent_to_m1 0.5000 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_m1 -2.301586 -Inf Inf +#> f_parent_ilr_1 0.000000 -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 99.49000 1.33200 96.7800 102.2000 +#> log_k_parent -2.32100 0.03550 -2.3930 -2.2490 +#> log_k_m1 -5.24100 0.21280 -5.6730 -4.8100 +#> f_parent_ilr_1 0.04571 0.08966 -0.1361 0.2275 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.00000 0.5312 -0.09456 -0.3351 +#> log_k_parent 0.53123 1.0000 -0.17800 -0.3360 +#> log_k_m1 -0.09456 -0.1780 1.00000 0.7616 +#> f_parent_ilr_1 -0.33514 -0.3360 0.76156 1.0000 +#> +#> Residual standard error: 2.628 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 99.490000 74.69 2.221e-41 96.780000 1.022e+02 +#> k_parent 0.098140 28.17 2.012e-26 0.091320 1.055e-01 +#> k_m1 0.005292 4.70 1.873e-05 0.003437 8.148e-03 +#> f_parent_to_m1 0.516200 16.30 1.686e-18 0.452000 5.798e-01 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.400 4 15 +#> parent 6.454 2 7 +#> m1 4.708 2 8 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.5162 +#> parent_sink 0.4838 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 7.063 23.46 +#> m1 130.971 435.08 +#> +#> Data: +#> time variable observed predicted residual err +#> 0 parent 99.46 99.48598 -0.025979 1 +#> 0 parent 102.04 99.48598 2.554021 1 +#> 1 parent 93.50 90.18612 3.313880 1 +#> 1 parent 92.50 90.18612 2.313880 1 +#> 3 parent 63.23 74.11316 -10.883163 1 +#> 3 parent 68.99 74.11316 -5.123163 1 +#> 7 parent 52.32 50.05030 2.269705 1 +#> 7 parent 55.13 50.05030 5.079705 1 +#> 14 parent 27.27 25.17975 2.090250 1 +#> 14 parent 26.64 25.17975 1.460250 1 +#> 21 parent 11.50 12.66765 -1.167654 1 +#> 21 parent 11.64 12.66765 -1.027654 1 +#> 35 parent 2.85 3.20616 -0.356164 1 +#> 35 parent 2.91 3.20616 -0.296164 1 +#> 50 parent 0.69 0.73562 -0.045619 1 +#> 50 parent 0.63 0.73562 -0.105619 1 +#> 75 parent 0.05 0.06326 -0.013256 1 +#> 75 parent 0.06 0.06326 -0.003256 1 +#> 0 m1 0.00 0.00000 0.000000 2 +#> 0 m1 0.00 0.00000 0.000000 2 +#> 1 m1 4.84 4.78729 0.052713 2 +#> 1 m1 5.64 4.78729 0.852713 2 +#> 3 m1 12.91 12.98785 -0.077848 2 +#> 3 m1 12.96 12.98785 -0.027848 2 +#> 7 m1 22.97 24.99695 -2.026946 2 +#> 7 m1 24.47 24.99695 -0.526946 2 +#> 14 m1 41.69 36.66353 5.026472 2 +#> 14 m1 33.21 36.66353 -3.453528 2 +#> 21 m1 44.37 41.65681 2.713186 2 +#> 21 m1 46.44 41.65681 4.783186 2 +#> 35 m1 41.22 43.35031 -2.130314 2 +#> 35 m1 37.95 43.35031 -5.400314 2 +#> 50 m1 41.19 41.25637 -0.066368 2 +#> 50 m1 40.01 41.25637 -1.246368 2 +#> 75 m1 40.09 36.46057 3.629429 2 +#> 75 m1 33.85 36.46057 -2.610571 2 +#> 100 m1 31.04 31.96929 -0.929293 2 +#> 100 m1 33.13 31.96929 1.160707 2 +#> 120 m1 25.15 28.76062 -3.610621 2 +#> 120 m1 33.31 28.76062 4.549379 2</div><div class='input'><span class='no'>f.w.man.irls</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, + <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>) +<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.6 +#> R version used for fitting: 3.5.2 +#> Date of fit: Thu Jan 31 16:51:31 2019 +#> Date of summary: Thu Jan 31 16:51:31 2019 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 692 model solutions performed in 3.3 s +#> +#> Weighting: manual +#> +#> Iterative reweighting with method obs +#> Final mean squared residuals of observed variables: +#> parent m1 +#> 11.573406 7.407846 +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent 0.1000 deparm +#> k_m1 0.1001 deparm +#> f_parent_to_m1 0.5000 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_m1 -2.301586 -Inf Inf +#> f_parent_ilr_1 0.000000 -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 99.67000 1.79200 96.04000 103.300 +#> log_k_parent -2.31200 0.04560 -2.40400 -2.220 +#> log_k_m1 -5.25100 0.12510 -5.50500 -4.998 +#> f_parent_ilr_1 0.03785 0.06318 -0.09027 0.166 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.0000 0.5083 -0.1979 -0.6148 +#> log_k_parent 0.5083 1.0000 -0.3894 -0.6062 +#> log_k_m1 -0.1979 -0.3894 1.0000 0.7417 +#> f_parent_ilr_1 -0.6148 -0.6062 0.7417 1.0000 +#> +#> Residual standard error: 1.054 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 99.67000 55.630 8.185e-37 96.040000 1.033e+02 +#> k_parent 0.09906 21.930 1.016e-22 0.090310 1.087e-01 +#> k_m1 0.00524 7.996 8.486e-10 0.004066 6.753e-03 +#> f_parent_to_m1 0.51340 23.000 2.039e-23 0.468100 5.584e-01 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.399 4 15 +#> parent 6.466 2 7 +#> m1 4.679 2 8 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.5134 +#> parent_sink 0.4866 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 6.997 23.24 +#> m1 132.282 439.43 +#> +#> Data: +#> time variable observed predicted residual err.ini err +#> 0 parent 99.46 99.67217 -2.122e-01 1 3.402 +#> 0 parent 102.04 99.67217 2.368e+00 1 3.402 +#> 1 parent 93.50 90.27152 3.228e+00 1 3.402 +#> 1 parent 92.50 90.27152 2.228e+00 1 3.402 +#> 3 parent 63.23 74.04648 -1.082e+01 1 3.402 +#> 3 parent 68.99 74.04648 -5.056e+00 1 3.402 +#> 7 parent 52.32 49.82092 2.499e+00 1 3.402 +#> 7 parent 55.13 49.82092 5.309e+00 1 3.402 +#> 14 parent 27.27 24.90288 2.367e+00 1 3.402 +#> 14 parent 26.64 24.90288 1.737e+00 1 3.402 +#> 21 parent 11.50 12.44765 -9.477e-01 1 3.402 +#> 21 parent 11.64 12.44765 -8.077e-01 1 3.402 +#> 35 parent 2.85 3.11002 -2.600e-01 1 3.402 +#> 35 parent 2.91 3.11002 -2.000e-01 1 3.402 +#> 50 parent 0.69 0.70375 -1.375e-02 1 3.402 +#> 50 parent 0.63 0.70375 -7.375e-02 1 3.402 +#> 75 parent 0.05 0.05913 -9.134e-03 1 3.402 +#> 75 parent 0.06 0.05913 8.661e-04 1 3.402 +#> 0 m1 0.00 0.00000 0.000e+00 2 2.722 +#> 0 m1 0.00 0.00000 0.000e+00 2 2.722 +#> 1 m1 4.84 4.81328 2.672e-02 2 2.722 +#> 1 m1 5.64 4.81328 8.267e-01 2 2.722 +#> 3 m1 12.91 13.04779 -1.378e-01 2 2.722 +#> 3 m1 12.96 13.04779 -8.779e-02 2 2.722 +#> 7 m1 22.97 25.07615 -2.106e+00 2 2.722 +#> 7 m1 24.47 25.07615 -6.062e-01 2 2.722 +#> 14 m1 41.69 36.70729 4.983e+00 2 2.722 +#> 14 m1 33.21 36.70729 -3.497e+00 2 2.722 +#> 21 m1 44.37 41.65050 2.719e+00 2 2.722 +#> 21 m1 46.44 41.65050 4.789e+00 2 2.722 +#> 35 m1 41.22 43.28866 -2.069e+00 2 2.722 +#> 35 m1 37.95 43.28866 -5.339e+00 2 2.722 +#> 50 m1 41.19 41.19339 -3.387e-03 2 2.722 +#> 50 m1 40.01 41.19339 -1.183e+00 2 2.722 +#> 75 m1 40.09 36.43820 3.652e+00 2 2.722 +#> 75 m1 33.85 36.43820 -2.588e+00 2 2.722 +#> 100 m1 31.04 31.98971 -9.497e-01 2 2.722 +#> 100 m1 33.13 31.98971 1.140e+00 2 2.722 +#> 120 m1 25.15 28.80897 -3.659e+00 2 2.722 +#> 120 m1 33.31 28.80897 4.501e+00 2 2.722</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index d8114300..84b335f7 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -217,28 +217,51 @@ For the definition of model types and their parameters, the equations given <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='error'>Error in mkinmod(parent = list(type = "SFO")): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'> +<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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='error'>Error in mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> </div><div class='input'><span class='co'># The above model used to be specified like this, before the advent of mkinsub()</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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='error'>Error in mkinmod(parent = list(type = "SFO", to = "m1"), m1 = list(type = "SFO")): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='co'># Show details of creating the C function</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'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), verbose = TRUE): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> Compilation argument: +#> /usr/lib/R/bin/R CMD SHLIB file165a4bc987b7.c 2> file165a4bc987b7.c.err.txt +#> Program source: +#> 1: #include <R.h> +#> 2: +#> 3: +#> 4: static double parms [3]; +#> 5: #define k_parent_sink parms[0] +#> 6: #define k_parent_m1 parms[1] +#> 7: #define k_m1_sink parms[2] +#> 8: +#> 9: void initpar(void (* odeparms)(int *, double *)) { +#> 10: int N = 3; +#> 11: odeparms(&N, parms); +#> 12: } +#> 13: +#> 14: +#> 15: void func ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) { +#> 16: +#> 17: f[0] = - k_parent_sink * y[0] - k_parent_m1 * y[0]; +#> 18: f[1] = + k_parent_m1 * y[0] - k_m1_sink * y[1]; +#> 19: }</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <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='no'>m_synth_DFOP_par</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"DFOP"</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)), <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), - <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinmod(parent = mkinsub("DFOP", c("M1", "M2")), M1 = mkinsub("SFO"), M2 = mkinsub("SFO"), use_of_ff = "max", quiet = TRUE): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'> + <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='no'>fit_DFOP_par_c</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_DFOP_par</span>, <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>12</span>]]$<span class='no'>data</span>, - <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(m_synth_DFOP_par, synthetic_data_for_UBA_2014[[12]]$data, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div></pre> + <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 28357356..93aa4b41 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -151,7 +151,8 @@ <pre class="examples"><div class='input'><span class='no'>model</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"anisole"</span>)), - <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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 co'>#> <span class='error'>Error in mkinmod(T245 = mkinsub("SFO", to = c("phenol"), sink = FALSE), phenol = mkinsub("SFO", to = c("anisole")), anisole = mkinsub("SFO"), use_of_ff = "max"): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></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>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(model, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'>mkinparplot</span>(<span class='no'>fit</span>)</div><div class='output co'>#> <span class='error'>Error in mkinparplot(fit): konnte Funktion "mkinparplot" nicht finden</span></div></pre> + <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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 co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/subset'>subset</a></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><div class='img'><img src='mkinparplot-1.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index c126eec9..c34da511 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -208,39 +208,172 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='no'>SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='error'>Error in mkinmod(degradinol = mkinsub("SFO")): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'> <span class='co'># Compare solution types</span> + <pre class="examples"><div class='input'> <span class='no'>SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'>#> <span class='error'>Error in mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, solution_type = "analytical"): konnte Funktion "mkinpredict" nicht finden</span></div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'>#> <span class='error'>Error in mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, solution_type = "deSolve"): konnte Funktion "mkinpredict" nicht finden</span></div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'>#> <span class='error'>Error in mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, solution_type = "deSolve", use_compiled = FALSE): konnte Funktion "mkinpredict" nicht finden</span></div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'>#> <span class='error'>Error in mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, solution_type = "eigen"): konnte Funktion "mkinpredict" nicht finden</span></div><div class='input'> + <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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'>#> <span class='error'>Error in mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, solution_type = "analytical"): konnte Funktion "mkinpredict" nicht finden</span></div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'>#> <span class='error'>Error in mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, method = "lsoda"): konnte Funktion "mkinpredict" nicht finden</span></div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'>#> <span class='error'>Error in mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, method = "ode45"): konnte Funktion "mkinpredict" nicht finden</span></div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'>#> <span class='error'>Error in mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20, method = "rk4"): konnte Funktion "mkinpredict" nicht finden</span></div><div class='input'> <span class='co'># rk4 is not as precise here</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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), - <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></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'>#> <span class='error'>Error in mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), seq(0, 20, by = 0.1)): konnte Funktion "mkinpredict" nicht finden</span></div><div class='input'> <span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), - <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></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'>#> <span class='error'>Error in mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), seq(0, 20, by = 0.01)): konnte Funktion "mkinpredict" nicht finden</span></div><div class='input'> + <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), + <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></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'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='error'>Error in mkinmod(parent = list(type = "SFO", to = "m1"), m1 = list(type = "SFO")): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>( + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>( <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></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'>#> <span class='error'>Error in mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "eigen"): konnte Funktion "mkinpredict" nicht finden</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0 0 0.001</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></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 verstrichen +#> 0.003 0.000 0.003 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>( <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></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'>#> <span class='error'>Error in mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "deSolve"): konnte Funktion "mkinpredict" nicht finden</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0 0 0</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></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 verstrichen +#> 0.002 0.000 0.002 </div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>( <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/seq'>seq</a></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'>#> <span class='error'>Error in mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "deSolve", use_compiled = FALSE): konnte Funktion "mkinpredict" nicht finden</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0 0 0</span></div><div class='input'> + <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 verstrichen +#> 0.042 0.000 0.042 </div><div class='input'> </div><div class='input'> <span class='co'># Predict from a fitted model</span> - <span class='no'>f</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_C</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFO_SFO, FOCUS_2006_C): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/utils/topics/head'>head</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>f</span>))</div><div class='output co'>#> <span class='error'>Error in mkinpredict(f): konnte Funktion "mkinpredict" nicht finden</span></div><div class='input'> </div></pre> + <span class='no'>f</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_C</span>)</div><div class='output co'>#> Model cost at call 1 : 552.5739 +#> Model cost at call 3 : 552.5739 +#> Model cost at call 4 : 552.5739 +#> Model cost at call 6 : 279.9345 +#> Model cost at call 7 : 279.9344 +#> Model cost at call 8 : 279.9294 +#> Model cost at call 9 : 279.9294 +#> Model cost at call 12 : 200.3629 +#> Model cost at call 13 : 200.3629 +#> Model cost at call 18 : 197.9039 +#> Model cost at call 23 : 197.9039 +#> Model cost at call 25 : 196.6754 +#> Model cost at call 27 : 196.6754 +#> Model cost at call 32 : 196.5742 +#> Model cost at call 33 : 196.5742 +#> Model cost at call 34 : 196.5742 +#> Model cost at call 38 : 196.5361 +#> Model cost at call 40 : 196.5361 +#> Model cost at call 44 : 196.5336 +#> Model cost at call 45 : 196.5336 +#> Model cost at call 50 : 196.5334 +#> Model cost at call 51 : 196.5334 +#> Model cost at call 52 : 196.5334 +#> Model cost at call 56 : 196.5334 +#> Model cost at call 58 : 196.5334 +#> Model cost at call 59 : 196.5334 +#> Model cost at call 65 : 196.5334 +#> Model cost at call 73 : 196.5334 +#> Model cost at call 78 : 196.5334 +#> Model cost at call 80 : 196.5334 +#> Optimisation by method Port successfully terminated.</div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/utils/topics/head'>head</a></span>(<span class='fu'>mkinpredict</span>(<span class='no'>f</span>))</div><div class='output co'>#> time parent m1 +#> 1 0.0 82.49216 0.000000 +#> 2 0.1 80.00563 1.179955 +#> 3 0.2 77.59404 2.312580 +#> 4 0.3 75.25515 3.399419 +#> 5 0.4 72.98675 4.441969 +#> 6 0.5 70.78673 5.441679</div><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index f85344e2..d088cfc9 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -196,7 +196,8 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>model</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='error'>Error in mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></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>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(model, FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'>mkinresplot</span>(<span class='no'>fit</span>, <span class='st'>"m1"</span>)</div><div class='output co'>#> <span class='error'>Error in mkinresplot(fit, "m1"): konnte Funktion "mkinresplot" nicht finden</span></div></pre> + <pre class="examples"><div class='input'><span class='no'>model</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></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><div class='img'><img src='mkinresplot-1.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index c615d772..135c0325 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -169,15 +169,15 @@ <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'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='error'>Error in mkinmod(parent = list(type = "SFO", to = "m1"), m1 = list(type = "SFO")): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></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'><a href='mkinmod.html'>mkinmod</a></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 co'>#> <span class='error'>Error in mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></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'><a href='mkinmod.html'>mkinmod</a></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 co'>#> <span class='error'>Error in mkinmod(parent = mkinsub("SFO", "m1", full_name = "Test compound"), m1 = mkinsub("SFO", full_name = "Metabolite M1")): konnte Funktion "mkinmod" nicht finden</span></div></pre> + <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 co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index af0b8f6f..3fa5c9a5 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -179,22 +179,40 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>m_synth_SFO_lin</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M1"</span>), <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M2"</span>), - <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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 co'>#> <span class='error'>Error in mkinmod(parent = mkinsub("SFO", "M1"), M1 = mkinsub("SFO", "M2"), M2 = mkinsub("SFO"), use_of_ff = "max"): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'> + <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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 co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='no'>m_synth_FOMC_lin</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"FOMC"</span>, <span class='st'>"M1"</span>), <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M2"</span>), - <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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 co'>#> <span class='error'>Error in mkinmod(parent = mkinsub("FOMC", "M1"), M1 = mkinsub("SFO", "M2"), M2 = mkinsub("SFO"), use_of_ff = "max"): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'> -<span class='no'>models</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>SFO_lin</span> <span class='kw'>=</span> <span class='no'>m_synth_SFO_lin</span>, <span class='kw'>FOMC_lin</span> <span class='kw'>=</span> <span class='no'>m_synth_FOMC_lin</span>)</div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'm_synth_SFO_lin' nicht gefunden</span></div><div class='input'><span class='no'>datasets</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/lapply'>lapply</a></span>(<span class='no'>synthetic_data_for_UBA_2014</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='kw'>function</span>(<span class='no'>x</span>) <span class='no'>x</span>$<span class='no'>data</span>) + <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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 co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> +<span class='no'>models</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>SFO_lin</span> <span class='kw'>=</span> <span class='no'>m_synth_SFO_lin</span>, <span class='kw'>FOMC_lin</span> <span class='kw'>=</span> <span class='no'>m_synth_FOMC_lin</span>) +<span class='no'>datasets</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/lapply'>lapply</a></span>(<span class='no'>synthetic_data_for_UBA_2014</span>[<span class='fl'>1</span>:<span class='fl'>3</span>], <span class='kw'>function</span>(<span class='no'>x</span>) <span class='no'>x</span>$<span class='no'>data</span>) <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>datasets</span>) <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/paste'>paste</a></span>(<span class='st'>"Dataset"</span>, <span class='fl'>1</span>:<span class='fl'>3</span>) -<span class='no'>time_default</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fits.0</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> <span class='error'>Error in mmkin(models, datasets, quiet = TRUE): konnte Funktion "mmkin" nicht finden</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0 0 0</span></div><div class='input'><span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fits.4</span> <span class='kw'><-</span> <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='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> <span class='error'>Error in mmkin(models, datasets, cores = 1, quiet = TRUE): konnte Funktion "mmkin" nicht finden</span></div><div class='output co'>#> <span class='message'>Timing stopped at: 0 0 0</span></div><div class='input'> -<span class='no'>time_default</span></div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'time_default' nicht gefunden</span></div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'time_1' nicht gefunden</span></div><div class='input'> -<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#> <span class='error'>Error in endpoints(fits.0[["SFO_lin", 2]]): konnte Funktion "endpoints" nicht finden</span></div><div class='input'> +<span class='no'>time_default</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fits.0</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) +<span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/system.time'>system.time</a></span>(<span class='no'>fits.4</span> <span class='kw'><-</span> <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='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) + +<span class='no'>time_default</span></div><div class='output co'>#> User System verstrichen +#> 0.045 0.036 7.264 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen +#> 22.905 0.000 22.919 </div><div class='input'> +<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#> $ff +#> parent_M1 parent_sink M1_M2 M1_sink +#> 0.7340480 0.2659520 0.7505686 0.2494314 +#> +#> $SFORB +#> logical(0) +#> +#> $distimes +#> DT50 DT90 +#> parent 0.8777689 2.915885 +#> M1 2.3257453 7.725959 +#> M2 33.7200874 112.015706 +#> </div><div class='input'> <span class='co'># plot.mkinfit handles rows or columns of mmkin result objects</span> -<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ])</div><div class='output co'>#> <span class='error'>Error in plot(fits.0[1, ]): Objekt 'fits.0' nicht gefunden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ], <span class='kw'>obs_var</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>))</div><div class='output co'>#> <span class='error'>Error in plot(fits.0[1, ], obs_var = c("M1", "M2")): Objekt 'fits.0' nicht gefunden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits.0</span>[, <span class='fl'>1</span>])</div><div class='output co'>#> <span class='error'>Error in plot(fits.0[, 1]): Objekt 'fits.0' nicht gefunden</span></div><div class='input'><span class='co'># Use double brackets to extract a single mkinfit object, which will be plotted</span> +<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ])</div><div class='img'><img src='mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ], <span class='kw'>obs_var</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>))</div><div class='img'><img src='mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits.0</span>[, <span class='fl'>1</span>])</div><div class='img'><img src='mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># Use double brackets to extract a single mkinfit object, which will be plotted</span> <span class='co'># by plot.mkinfit and can be plotted using plot_sep</span> -<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</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'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in plot(fits.0[[1, 1]], sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE): Objekt 'fits.0' nicht gefunden</span></div><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</span>]])</div><div class='output co'>#> <span class='error'>Error in plot_sep(fits.0[[1, 1]]): konnte Funktion "plot_sep" nicht finden</span></div><div class='input'><span class='co'># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span> +<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</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'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='fl'>1</span>, <span class='fl'>1</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='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, <span class='fl'>1</span>])</div><div class='output co'>#> <span class='error'>Error in plot(fits.0[1, 1]): Objekt 'fits.0' nicht gefunden</span></div></pre> +<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, <span class='fl'>1</span>])</div><div class='img'><img src='mmkin-5.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index 0630c604..ab94d61b 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -260,14 +260,15 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, … <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'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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'><a href='mkinsub.html'>mkinsub</a></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 co'>#> <span class='error'>Error in mkinmod(parent = mkinsub("SFO", "m1", full = "Parent"), m1 = mkinsub("SFO", full = "Metabolite M1")): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></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>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, method.modFit = "Marq"): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> <span class='error'>Error in plot(fit): Objekt 'fit' nicht gefunden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in plot(fit, show_residuals = TRUE): Objekt 'fit' nicht gefunden</span></div><div class='input'> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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 co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></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'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='plot.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fit</span>, <span class='kw'>show_residuals</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># Show the observed variables separately</span> -<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='output co'>#> <span class='error'>Error in plot(fit, sep_obs = TRUE, lpos = c("topright", "bottomright")): Objekt 'fit' nicht gefunden</span></div><div class='input'> +<span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='plot.mkinfit-3.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># Show the observed variables separately, with residuals</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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><div class='output co'>#> <span class='error'>Error in plot(fit, sep_obs = TRUE, show_residuals = TRUE, lpos = c("topright", "bottomright"), show_errmin = TRUE): Objekt 'fit' nicht gefunden</span></div><div class='input'> + <span class='kw'>show_errmin</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='img'><img src='plot.mkinfit-4.png' alt='' width='700' height='433' /></div><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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='output co'>#> <span class='error'>Error in plot_sep(fit, lpos = c("topright", "bottomright")): konnte Funktion "plot_sep" nicht finden</span></div></pre> +<span class='fu'>plot_sep</span>(<span class='no'>fit</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index f7afed08..689fd488 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -187,11 +187,12 @@ If the current plot device is a tikz device, <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'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"FOMC"</span>, <span class='st'>"HS"</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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='co'># named list for titles</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>)</div><div class='output co'>#> <span class='error'>Error in mmkin(c("FOMC", "HS"), list(`FOCUS B` = FOCUS_2006_B, `FOCUS C` = FOCUS_2006_C), cores = 1, quiet = TRUE, method.modFit = "Marq"): konnte Funktion "mmkin" nicht finden</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits</span>[, <span class='st'>"FOCUS C"</span>])</div><div class='output co'>#> <span class='error'>Error in plot(fits[, "FOCUS C"]): Objekt 'fits' nicht gefunden</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ])</div><div class='output co'>#> <span class='error'>Error in plot(fits["FOMC", ]): Objekt 'fits' nicht gefunden</span></div><div class='input'> + <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'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits</span>[, <span class='st'>"FOCUS C"</span>])</div><div class='img'><img src='plot.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ])</div><div class='img'><img src='plot.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='co'># We can also plot a single fit, if we like the way plot.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 pkgdown, as far as I know).</span> - <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></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><div class='output co'>#> <span class='error'>Error in plot(fits["FOMC", "FOCUS C"]): Objekt 'fits' nicht gefunden</span></div></pre> + <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></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><div class='img'><img src='plot.mmkin-3.png' alt='' width='700' height='433' /></div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index c2cb9e19..0c78b6fb 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -149,8 +149,22 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='no'>m_synth_SFO_lin</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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'>"M2"</span>), - <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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 co'>#> <span class='error'>Error in mkinmod(parent = list(type = "SFO", to = "M1"), M1 = list(type = "SFO", to = "M2"), M2 = list(type = "SFO"), use_of_ff = "max"): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'> - <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>m_synth_SFO_lin</span>)</div><div class='output co'>#> <span class='error'>Error in print(m_synth_SFO_lin): Objekt 'm_synth_SFO_lin' nicht gefunden</span></div></pre> + <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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 co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> + <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>m_synth_SFO_lin</span>)</div><div class='output co'>#> <mkinmod> model generated with +#> Use of formation fractions $use_of_ff: max +#> Specification $spec: +#> $parent +#> $type: SFO; $to: M1; $sink: TRUE +#> $M1 +#> $type: SFO; $to: M2; $sink: TRUE +#> $M2 +#> $type: SFO; $sink: TRUE +#> Coefficient matrix $coefmat available +#> Compiled model $cf available +#> Differential equations: +#> d_parent/dt = - k_parent * parent +#> d_M1/dt = + f_parent_to_M1 * k_parent * parent - k_M1 * M1 +#> d_M2/dt = + f_M1_to_M2 * k_M1 * M1 - k_M2 * M2</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 0e20e895..d1c89770 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -155,12 +155,28 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>data</span> <span class='kw'><-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span>(<span class='no'>schaefer07_complex_case</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>)</div><div class='output co'>#> <span class='error'>Error in mkin_wide_to_long(schaefer07_complex_case, time = "time"): konnte Funktion "mkin_wide_to_long" nicht finden</span></div><div class='input'><span class='no'>model</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( + <pre class="examples"><div class='input'><span class='no'>data</span> <span class='kw'><-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></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'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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 co'>#> <span class='error'>Error in mkinmod(parent = list(type = "SFO", to = c("A1", "B1", "C1"), sink = FALSE), A1 = list(type = "SFO", to = "A2"), B1 = list(type = "SFO"), C1 = list(type = "SFO"), A2 = list(type = "SFO"), use_of_ff = "max"): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'> </div><div class='input'> <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(model, data, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> <span class='error'>Error in plot(fit): Objekt 'fit' nicht gefunden</span></div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> <span class='error'>Error in endpoints(fit): konnte Funktion "endpoints" nicht finden</span></div><div class='input'> </div><div class='input'> <span class='co'># Compare with the results obtained in the original publication</span> + <span class='kw'>A2</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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 co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> </div><div class='input'> <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='fu'><a href='https://www.rdocumentation.org/packages/graphics/topics/plot'>plot</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='schaefer07_complex_case-1.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#> $ff +#> parent_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink +#> 0.3809621 0.1954665 0.4235714 0.0000000 0.4479674 0.5520326 +#> +#> $SFORB +#> logical(0) +#> +#> $distimes +#> DT50 DT90 +#> parent 13.95078 46.34350 +#> A1 49.75342 165.27728 +#> B1 37.26913 123.80536 +#> C1 11.23133 37.30968 +#> A2 28.50591 94.69457 +#> </div><div class='input'> </div><div class='input'> <span class='co'># Compare with the results obtained in the original publication</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/print'>print</a></span>(<span class='no'>schaefer07_complex_results</span>)</div><div class='output co'>#> compound parameter KinGUI ModelMaker deviation #> 1 parent degradation rate 0.0496 0.0506 2.0 #> 2 parent DT50 13.9900 13.6900 2.2 diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index b6f6a5c7..2815eccb 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -206,7 +206,76 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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'>#> <span class='error'>Error in mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div></pre> + <pre class="examples"><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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 used for fitting: 0.9.47.6 +#> R version used for fitting: 3.5.2 +#> Date of fit: Thu Jan 31 16:52:23 2019 +#> Date of summary: Thu Jan 31 16:52:23 2019 +#> +#> Equations: +#> d_parent/dt = - k_parent_sink * parent +#> +#> Model predictions using solution type analytical +#> +#> Fitted with method Port using 35 model solutions performed in 0.085 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 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index 49e70681..1999de8d 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -155,16 +155,56 @@ <span class='co'># large parameter correlations, among other reasons (e.g. the adequacy of the</span> <span class='co'># model).</span> <span class='no'>m_ws</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent_w</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_s"</span>), - <span class='kw'>parent_s</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_w"</span>))</div><div class='output co'>#> <span class='error'>Error in mkinmod(parent_w = mkinsub("SFO", "parent_s"), parent_s = mkinsub("SFO", "parent_w")): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'> <span class='no'>f_river</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_ws</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(m_ws, test_data_from_UBA_2014[[1]]$data, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_river</span>)</div><div class='output co'>#> <span class='error'>Error in plot_sep(f_river): konnte Funktion "plot_sep" nicht finden</span></div><div class='input'> - <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f_river</span>)$<span class='no'>bpar</span></div><div class='output co'>#> <span class='error'>Error in summary(f_river): Objekt 'f_river' nicht gefunden</span></div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_river</span>)</div><div class='output co'>#> <span class='error'>Error in mkinerrmin(f_river): konnte Funktion "mkinerrmin" nicht finden</span></div><div class='input'> + <span class='kw'>parent_s</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"parent_w"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='no'>f_river</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_ws</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_river</span>)</div><div class='img'><img src='test_data_from_UBA_2014-1.png' alt='' width='700' height='433' /></div><div class='input'> + <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f_river</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower +#> parent_w_0 9.598567e+01 2.33959800 4.102657e+01 9.568967e-19 NA +#> k_parent_w_sink 3.603743e-01 0.03497750 1.030303e+01 4.989002e-09 NA +#> k_parent_w_parent_s 6.031371e-02 0.01746024 3.454346e+00 1.514723e-03 NA +#> k_parent_s_sink 5.108539e-11 0.10382001 4.920572e-10 5.000000e-01 NA +#> k_parent_s_parent_w 7.419672e-02 0.11338240 6.543936e-01 2.608069e-01 NA +#> Upper +#> parent_w_0 NA +#> k_parent_w_sink NA +#> k_parent_w_parent_s NA +#> k_parent_s_sink NA +#> k_parent_s_parent_w NA</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_river</span>)</div><div class='output co'>#> err.min n.optim df +#> All data 0.09246946 5 6 +#> parent_w 0.06377096 3 3 +#> parent_s 0.20882324 2 3</div><div class='input'> <span class='co'># This is the evaluation used for the validation of software packages</span> <span class='co'># in the expertise from 2014</span> <span class='no'>m_soil</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)), <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M3"</span>), <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M3"</span>), <span class='kw'>M3</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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 co'>#> <span class='error'>Error in mkinmod(parent = mkinsub("SFO", c("M1", "M2")), M1 = mkinsub("SFO", "M3"), M2 = mkinsub("SFO", "M3"), M3 = mkinsub("SFO"), use_of_ff = "max"): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'> - <span class='no'>f_soil</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_soil</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>3</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(m_soil, test_data_from_UBA_2014[[3]]$data, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'> <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_soil</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='output co'>#> <span class='error'>Error in plot_sep(f_soil, lpos = c("topright", "topright", "topright", "bottomright")): konnte Funktion "plot_sep" nicht finden</span></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span></div><div class='output co'>#> <span class='error'>Error in summary(f_soil): Objekt 'f_soil' nicht gefunden</span></div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_soil</span>)</div><div class='output co'>#> <span class='error'>Error in mkinerrmin(f_soil): konnte Funktion "mkinerrmin" nicht finden</span></div><div class='input'> </div></pre> + <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> + <span class='no'>f_soil</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_soil</span>, <span class='no'>test_data_from_UBA_2014</span><span class='kw'>[[</span><span class='fl'>3</span>]]$<span class='no'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_soil</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><div class='img'><img src='test_data_from_UBA_2014-2.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span></div><div class='output co'>#> Estimate se_notrans t value Pr(>t) Lower +#> parent_0 76.55425584 0.943443794 81.1434198 4.422336e-30 74.602593773 +#> k_parent 0.12081956 0.004815515 25.0896457 1.639665e-18 0.111257517 +#> k_M1 0.84258651 0.930121548 0.9058886 1.871938e-01 0.085876516 +#> k_M2 0.04210878 0.013729902 3.0669396 2.729137e-03 0.021450630 +#> k_M3 0.01122919 0.008044865 1.3958206 8.804912e-02 0.002550984 +#> f_parent_to_M1 0.32240199 0.278620579 1.1571363 1.295467e-01 NA +#> f_parent_to_M2 0.16099854 0.030548888 5.2701931 1.196190e-05 NA +#> f_M1_to_M3 0.27921500 0.314732842 0.8871492 1.920908e-01 0.015016983 +#> f_M2_to_M3 0.55641333 0.650246995 0.8556954 2.004966e-01 0.005360555 +#> Upper +#> parent_0 78.50591790 +#> k_parent 0.13120341 +#> k_M1 8.26712661 +#> k_M2 0.08266188 +#> k_M3 0.04942981 +#> f_parent_to_M1 NA +#> f_parent_to_M2 NA +#> f_M1_to_M3 0.90777163 +#> f_M2_to_M3 0.99658633</div><div class='input'> <span class='fu'><a href='mkinerrmin.html'>mkinerrmin</a></span>(<span class='no'>f_soil</span>)</div><div class='output co'>#> err.min n.optim df +#> All data 0.09649963 9 20 +#> parent 0.04721283 2 6 +#> M1 0.26551209 2 5 +#> M2 0.20327575 2 5 +#> M3 0.05196549 3 4</div><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index b9d96b1e..d3c20ed8 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -198,24 +198,320 @@ The transformation of sets of formation fractions is fragile, as it supposes <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='error'>Error in mkinmod(parent = list(type = "SFO", to = "m1", sink = TRUE), m1 = list(type = "SFO")): konnte Funktion "mkinmod" nicht finden</span></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'><a href='mkinfit.html'>mkinfit</a></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>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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'>#> <span class='error'>Error in summary(fit, data = FALSE): Objekt 'fit' nicht gefunden</span></div><div class='input'> -</div><div class='input'><span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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'>#> <span class='error'>Error in summary(fit.2, data = FALSE): Objekt 'fit.2' nicht gefunden</span></div><div class='input'> -<span class='no'>initials</span> <span class='kw'><-</span> <span class='no'>fit</span>$<span class='no'>start</span>$<span class='no'>value</span></div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'fit' nicht gefunden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>initials</span>) <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/colnames'>rownames</a></span>(<span class='no'>fit</span>$<span class='no'>start</span>)</div><div class='output co'>#> <span class='error'>Error in rownames(fit$start): Objekt 'fit' nicht gefunden</span></div><div class='input'><span class='no'>transformed</span> <span class='kw'><-</span> <span class='no'>fit</span>$<span class='no'>start_transformed</span>$<span class='no'>value</span></div><div class='output co'>#> <span class='error'>Error in eval(expr, envir, enclos): Objekt 'fit' nicht gefunden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>transformed</span>) <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/colnames'>rownames</a></span>(<span class='no'>fit</span>$<span class='no'>start_transformed</span>)</div><div class='output co'>#> <span class='error'>Error in rownames(fit$start_transformed): Objekt 'fit' nicht gefunden</span></div><div class='input'><span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#> <span class='error'>Error in transform_odeparms(initials, SFO_SFO): konnte Funktion "transform_odeparms" nicht finden</span></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'>#> <span class='error'>Error in backtransform_odeparms(transformed, SFO_SFO): konnte Funktion "backtransform_odeparms" nicht finden</span></div><div class='input'> + <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></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'><a href='mkinfit.html'>mkinfit</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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 used for fitting: 0.9.47.6 +#> R version used for fitting: 3.5.2 +#> Date of fit: Thu Jan 31 16:52:31 2019 +#> Date of summary: Thu Jan 31 16:52:31 2019 +#> +#> Equations: +#> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent +#> d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 153 model solutions performed in 0.703 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 0.47164 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'> +</div><div class='input'><span class='no'>fit.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>transform_rates</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></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 used for fitting: 0.9.47.6 +#> R version used for fitting: 3.5.2 +#> Date of fit: Thu Jan 31 16:52:33 2019 +#> Date of summary: Thu Jan 31 16:52:33 2019 +#> +#> Equations: +#> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent +#> d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 350 model solutions performed in 1.597 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_0 100.7500 -Inf Inf +#> k_parent_sink 0.1000 0 Inf +#> k_parent_m1 0.1001 0 Inf +#> k_m1_sink 0.1002 0 Inf +#> +#> Fixed parameter values: +#> value type +#> m1_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 99.600000 1.6140000 96.330000 1.029e+02 +#> k_parent_sink 0.047920 0.0037500 0.040310 5.553e-02 +#> k_parent_m1 0.050780 0.0020940 0.046530 5.502e-02 +#> k_m1_sink 0.005261 0.0007159 0.003809 6.713e-03 +#> +#> Parameter correlation: +#> parent_0 k_parent_sink k_parent_m1 k_m1_sink +#> parent_0 1.00000 0.6075 -0.06625 -0.1701 +#> k_parent_sink 0.60752 1.0000 -0.08740 -0.6253 +#> k_parent_m1 -0.06625 -0.0874 1.00000 0.4716 +#> k_m1_sink -0.17006 -0.6253 0.47164 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 0.040310 5.553e-02 +#> k_parent_m1 0.050780 24.250 3.407e-24 0.046530 5.502e-02 +#> k_m1_sink 0.005261 7.349 5.758e-09 0.003809 6.713e-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='no'>initials</span> <span class='kw'><-</span> <span class='no'>fit</span>$<span class='no'>start</span>$<span class='no'>value</span> +<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>initials</span>) <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/colnames'>rownames</a></span>(<span class='no'>fit</span>$<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'><a href='https://www.rdocumentation.org/packages/base/topics/names'>names</a></span>(<span class='no'>transformed</span>) <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/colnames'>rownames</a></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'> </div><div class='input'><span class='co'># The case of formation fractions</span> <span class='no'>SFO_SFO.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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 co'>#> <span class='error'>Error in mkinmod(parent = list(type = "SFO", to = "m1", sink = TRUE), m1 = list(type = "SFO"), use_of_ff = "max"): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'> -<span class='no'>fit.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> <span class='error'>Error in summary(fit.ff, data = FALSE): Objekt 'fit.ff' nicht gefunden</span></div><div class='input'><span class='no'>initials</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"f_parent_to_m1"</span> <span class='kw'>=</span> <span class='fl'>0.5</span>) -<span class='no'>transformed</span> <span class='kw'><-</span> <span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO.ff</span>)</div><div class='output co'>#> <span class='error'>Error in transform_odeparms(initials, SFO_SFO.ff): konnte Funktion "transform_odeparms" nicht finden</span></div><div class='input'><span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO.ff</span>)</div><div class='output co'>#> <span class='error'>Error in backtransform_odeparms(transformed, SFO_SFO.ff): konnte Funktion "backtransform_odeparms" nicht finden</span></div><div class='input'> + <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> +<span class='no'>fit.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff</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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.6 +#> R version used for fitting: 3.5.2 +#> Date of fit: Thu Jan 31 16:52:34 2019 +#> Date of summary: Thu Jan 31 16:52:34 2019 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 186 model solutions performed in 0.898 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent 0.1000 deparm +#> k_m1 0.1001 deparm +#> f_parent_to_m1 0.5000 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_m1 -2.301586 -Inf Inf +#> f_parent_ilr_1 0.000000 -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 99.60000 1.61400 96.3300 102.9000 +#> log_k_parent -2.31600 0.04187 -2.4010 -2.2310 +#> log_k_m1 -5.24800 0.13610 -5.5230 -4.9720 +#> f_parent_ilr_1 0.04096 0.06477 -0.0904 0.1723 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.0000 0.5178 -0.1701 -0.5489 +#> log_k_parent 0.5178 1.0000 -0.3285 -0.5451 +#> log_k_m1 -0.1701 -0.3285 1.0000 0.7466 +#> f_parent_ilr_1 -0.5489 -0.5451 0.7466 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 0.098700 23.880 5.700e-24 0.090660 1.074e-01 +#> k_m1 0.005261 7.349 5.758e-09 0.003992 6.933e-03 +#> f_parent_to_m1 0.514500 22.490 4.375e-23 0.468100 5.606e-01 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.398 4 15 +#> parent 6.459 2 7 +#> m1 4.690 2 8 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.5145 +#> parent_sink 0.4855 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 7.023 23.33 +#> m1 131.761 437.70</div><div class='input'><span class='no'>initials</span> <span class='kw'><-</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"f_parent_to_m1"</span> <span class='kw'>=</span> <span class='fl'>0.5</span>) +<span class='no'>transformed</span> <span class='kw'><-</span> <span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO.ff</span>) +<span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO.ff</span>)</div><div class='output co'>#> f_parent_to_m1 +#> 0.5 </div><div class='input'> <span class='co'># And without sink</span> <span class='no'>SFO_SFO.ff.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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'>FALSE</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></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 co'>#> <span class='error'>Error in mkinmod(parent = list(type = "SFO", to = "m1", sink = FALSE), m1 = list(type = "SFO"), use_of_ff = "max"): konnte Funktion "mkinmod" nicht finden</span></div><div class='input'> - -<span class='no'>fit.ff.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.2</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='error'>Error in mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden</span></div><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> <span class='error'>Error in summary(fit.ff.2, data = FALSE): Objekt 'fit.ff.2' nicht gefunden</span></div></pre> + <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> + +<span class='no'>fit.ff.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO.ff.2</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'><a href='https://www.rdocumentation.org/packages/base/topics/summary'>summary</a></span>(<span class='no'>fit.ff.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version used for fitting: 0.9.47.6 +#> R version used for fitting: 3.5.2 +#> Date of fit: Thu Jan 31 16:52:35 2019 +#> Date of summary: Thu Jan 31 16:52:35 2019 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + k_parent * parent - k_m1 * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 104 model solutions performed in 0.482 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent 0.1000 deparm +#> k_m1 0.1001 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_m1 -2.301586 -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 84.790 2.96500 78.78 90.800 +#> log_k_parent -2.756 0.08088 -2.92 -2.593 +#> log_k_m1 -4.214 0.11150 -4.44 -3.988 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 +#> parent_0 1.0000 0.11058 0.46156 +#> log_k_parent 0.1106 1.00000 0.06274 +#> log_k_m1 0.4616 0.06274 1.00000 +#> +#> Residual standard error: 8.333 on 37 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 84.79000 28.600 3.939e-27 78.78000 90.80000 +#> k_parent 0.06352 12.360 5.237e-15 0.05392 0.07483 +#> k_m1 0.01478 8.966 4.114e-11 0.01179 0.01853 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 19.66 3 16 +#> parent 17.56 2 7 +#> m1 18.71 1 9 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 10.91 36.25 +#> m1 46.89 155.75</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> |