diff options
Diffstat (limited to 'docs/reference/Extract.mmkin.html')
| -rw-r--r-- | docs/reference/Extract.mmkin.html | 402 |
1 files changed, 399 insertions, 3 deletions
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> |