diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2016-11-18 16:28:49 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2016-11-18 16:28:49 +0100 |
| commit | e7b2d16306b7d03cde66223c9b27abde928f9447 (patch) | |
| tree | 85d650cfb8e071b00a1228566ec788dc1b477809 | |
| parent | 8bdb67360502bd1a8eb5317d287b094510b4a02c (diff) | |
Improve examples for showing with pkgdown
- Use quiet= TRUE in dontrun sections
- Use mkinsub in model definitions
- Avoid \code{\link{}} in titles
35 files changed, 424 insertions, 5464 deletions
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 09d7513c..6a75a530 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -120,7 +120,20 @@ #> SFO List,42 #> FOMC List,42 #> attr(,"class") -#> [1] "mmkin"</div><div class='input'> <span class='no'>fits</span>[, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]$<span class='no'>FOMC</span></div><div class='output co'>#> $par +#> [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,42 +#> attr(,"class") +#> [1] "mmkin"</div><div class='input'> + <span class='fu'>head</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='message'></span> +#> <span class='message'>Attaching package: ‘utils’</span></div><div class='output co'>#> <span class='message'>The following objects are masked from ‘devtools_shims’:</span> +#> <span class='message'></span> +#> <span class='message'> ?, help</span></div><div class='output co'>#> <span class='message'>The following object is masked from ‘package:inline’:</span> +#> <span class='message'></span> +#> <span class='message'> package.skeleton</span></div><div class='output co'>#> $par #> parent_0 log_alpha log_beta #> 99.666193 2.549849 5.050586 #> @@ -139,689 +152,11 @@ #> #> $counts #> [1] "both X-convergence and relative convergence (5)" -#> -#> $hessian -#> parent_0 log_alpha log_beta -#> parent_0 4.123033 -95.69983 93.17699 -#> log_alpha -95.699832 6618.85833 -6352.46648 -#> log_beta 93.176993 -6352.46648 6101.23483 -#> -#> $residuals -#> parent parent parent parent parent parent -#> 1.046192647 -3.322396479 3.655156669 -1.705316770 0.406306255 -0.123734689 -#> parent parent -#> -0.036886982 -0.006240458 -#> -#> $ms -#> [1] 3.572863 -#> -#> $var_ms -#> parent -#> 3.572863 -#> -#> $var_ms_unscaled -#> parent -#> 3.572863 -#> -#> $var_ms_unweighted -#> parent -#> 3.572863 -#> -#> $rank -#> [1] 3 -#> -#> $df.residual -#> [1] 5 -#> -#> $solution_type -#> [1] "analytical" -#> -#> $transform_rates -#> [1] TRUE -#> -#> $transform_fractions -#> [1] TRUE -#> -#> $method.modFit -#> [1] "Port" -#> -#> $maxit.modFit -#> [1] "auto" -#> -#> $calls -#> [1] 111 -#> -#> $time -#> user system elapsed -#> 0.256 0.000 0.255 -#> -#> $mkinmod -#> <mkinmod> model generated with -#> Use of formation fractions $use_of_ff: min -#> Specification $spec: -#> $parent -#> $type: FOMC; $sink: TRUE -#> -#> $observed -#> name time value -#> 1 parent 0 98.62 -#> 2 parent 3 81.43 -#> 3 parent 7 53.18 -#> 4 parent 14 34.89 -#> 5 parent 30 10.09 -#> 6 parent 62 1.50 -#> 7 parent 90 0.33 -#> 8 parent 118 0.08 -#> -#> $obs_vars -#> [1] "parent" -#> -#> $predicted -#> name time value -#> 1 parent 0.000000 99.66619265 -#> 2 parent 1.191919 90.41690342 -#> 3 parent 2.383838 82.08630014 -#> 4 parent 3.000000 78.10760352 -#> 5 parent 3.575758 74.57722848 -#> 6 parent 4.767677 67.80342415 -#> 7 parent 5.959596 61.68822425 -#> 8 parent 7.000000 56.83515667 -#> 9 parent 7.151515 56.16343898 -#> 10 parent 8.343434 51.16836285 -#> 11 parent 9.535354 46.64890734 -#> 12 parent 10.727273 42.55683931 -#> 13 parent 11.919192 38.84911158 -#> 14 parent 13.111111 35.48727414 -#> 15 parent 14.000000 33.18468323 -#> 16 parent 14.303030 32.43695565 -#> 17 parent 15.494949 29.66740651 -#> 18 parent 16.686869 27.15109578 -#> 19 parent 17.878788 24.86335532 -#> 20 parent 19.070707 22.78206538 -#> 21 parent 20.262626 20.88737647 -#> 22 parent 21.454545 19.16146324 -#> 23 parent 22.646465 17.58830644 -#> 24 parent 23.838384 16.15349953 -#> 25 parent 25.030303 14.84407724 -#> 26 parent 26.222222 13.64836315 -#> 27 parent 27.414141 12.55583436 -#> 28 parent 28.606061 11.55700107 -#> 29 parent 29.797980 10.64329940 -#> 30 parent 30.000000 10.49630626 -#> 31 parent 30.989899 9.80699593 -#> 32 parent 32.181818 9.04110261 -#> 33 parent 33.373737 8.33930082 -#> 34 parent 34.565657 7.69587362 -#> 35 parent 35.757576 7.10564515 -#> 36 parent 36.949495 6.56392657 -#> 37 parent 38.141414 6.06646759 -#> 38 parent 39.333333 5.60941311 -#> 39 parent 40.525253 5.18926438 -#> 40 parent 41.717172 4.80284421 -#> 41 parent 42.909091 4.44726569 -#> 42 parent 44.101010 4.11990420 -#> 43 parent 45.292929 3.81837216 -#> 44 parent 46.484848 3.54049644 -#> 45 parent 47.676768 3.28429799 -#> 46 parent 48.868687 3.04797350 -#> 47 parent 50.060606 2.82987892 -#> 48 parent 51.252525 2.62851456 -#> 49 parent 52.444444 2.44251172 -#> 50 parent 53.636364 2.27062056 -#> 51 parent 54.828283 2.11169922 -#> 52 parent 56.020202 1.96470393 -#> 53 parent 57.212121 1.82868009 -#> 54 parent 58.404040 1.70275424 -#> 55 parent 59.595960 1.58612677 -#> 56 parent 60.787879 1.47806529 -#> 57 parent 61.979798 1.37789865 -#> 58 parent 62.000000 1.37626531 -#> 59 parent 63.171717 1.28501157 -#> 60 parent 64.363636 1.19883967 -#> 61 parent 65.555556 1.11886504 -#> 62 parent 66.747475 1.04461220 -#> 63 parent 67.939394 0.97564441 -#> 64 parent 69.131313 0.91156031 -#> 65 parent 70.323232 0.85199096 -#> 66 parent 71.515152 0.79659697 -#> 67 parent 72.707071 0.74506609 -#> 68 parent 73.898990 0.69711084 -#> 69 parent 75.090909 0.65246649 -#> 70 parent 76.282828 0.61088912 -#> 71 parent 77.474747 0.57215389 -#> 72 parent 78.666667 0.53605348 -#> 73 parent 79.858586 0.50239663 -#> 74 parent 81.050505 0.47100683 -#> 75 parent 82.242424 0.44172111 -#> 76 parent 83.434343 0.41438896 -#> 77 parent 84.626263 0.38887128 -#> 78 parent 85.818182 0.36503953 -#> 79 parent 87.010101 0.34277481 -#> 80 parent 88.202020 0.32196716 -#> 81 parent 89.393939 0.30251479 -#> 82 parent 90.000000 0.29311302 -#> 83 parent 90.585859 0.28432347 -#> 84 parent 91.777778 0.26730596 -#> 85 parent 92.969697 0.25138141 -#> 86 parent 94.161616 0.23647487 -#> 87 parent 95.353535 0.22251689 -#> 88 parent 96.545455 0.20944302 -#> 89 parent 97.737374 0.19719349 -#> 90 parent 98.929293 0.18571281 -#> 91 parent 100.121212 0.17494947 -#> 92 parent 101.313131 0.16485560 -#> 93 parent 102.505051 0.15538676 -#> 94 parent 103.696970 0.14650163 -#> 95 parent 104.888889 0.13816179 -#> 96 parent 106.080808 0.13033150 -#> 97 parent 107.272727 0.12297753 -#> 98 parent 108.464646 0.11606895 -#> 99 parent 109.656566 0.10957695 -#> 100 parent 110.848485 0.10347470 -#> 101 parent 112.040404 0.09773723 -#> 102 parent 113.232323 0.09234125 -#> 103 parent 114.424242 0.08726506 -#> 104 parent 115.616162 0.08248842 -#> 105 parent 116.808081 0.07799245 -#> 106 parent 118.000000 0.07375954 -#> -#> $cost -#> function (P) -#> { -#> assign("calls", calls + 1, inherits = TRUE) -#> if (trace_parms) -#> cat(P, "\n") -#> if (length(state.ini.optim) > 0) { -#> odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed) -#> names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames) -#> } -#> else { -#> odeini <- state.ini.fixed -#> names(odeini) <- state.ini.fixed.boxnames -#> } -#> odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], -#> transparms.fixed) -#> parms <- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates, -#> transform_fractions = transform_fractions) -#> out <- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type, -#> use_compiled = use_compiled, method.ode = method.ode, -#> atol = atol, rtol = rtol, ...) -#> assign("out_predicted", out, inherits = TRUE) -#> mC <- modCost(out, observed, y = "value", err = err, weight = weight, -#> scaleVar = scaleVar) -#> if (mC$model < cost.old) { -#> if (!quiet) -#> cat("Model cost at call ", calls, ": ", mC$model, -#> "\n") -#> if (plot) { -#> outtimes_plot = seq(min(observed$time), max(observed$time), -#> length.out = 100) -#> out_plot <- mkinpredict(mkinmod, parms, odeini, outtimes_plot, -#> solution_type = solution_type, use_compiled = use_compiled, -#> method.ode = method.ode, atol = atol, rtol = rtol, -#> ...) -#> plot(0, type = "n", xlim = range(observed$time), -#> ylim = c(0, max(observed$value, na.rm = TRUE)), -#> xlab = "Time", ylab = "Observed") -#> col_obs <- pch_obs <- 1:length(obs_vars) -#> lty_obs <- rep(1, length(obs_vars)) -#> names(col_obs) <- names(pch_obs) <- names(lty_obs) <- obs_vars -#> for (obs_var in obs_vars) { -#> points(subset(observed, name == obs_var, c(time, -#> value)), pch = pch_obs[obs_var], col = col_obs[obs_var]) -#> } -#> matlines(out_plot$time, out_plot[-1], col = col_obs, -#> lty = lty_obs) -#> legend("topright", inset = c(0.05, 0.05), legend = obs_vars, -#> col = col_obs, pch = pch_obs, lty = 1:length(pch_obs)) -#> } -#> assign("cost.old", mC$model, inherits = TRUE) -#> } -#> return(mC) -#> } -#> <environment: 0x3fc5fa0> -#> -#> $cost_notrans -#> function (P) -#> { -#> if (length(state.ini.optim) > 0) { -#> odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed) -#> names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames) -#> } -#> else { -#> odeini <- state.ini.fixed -#> names(odeini) <- state.ini.fixed.boxnames -#> } -#> odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], -#> parms.fixed) -#> out <- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type, -#> use_compiled = use_compiled, method.ode = method.ode, -#> atol = atol, rtol = rtol, ...) -#> mC <- modCost(out, observed, y = "value", err = err, weight = weight, -#> scaleVar = scaleVar) -#> return(mC) -#> } -#> <environment: 0x3fc5fa0> -#> -#> $hessian_notrans -#> parent_0 alpha beta -#> parent_0 4.1230329 -7.473531 0.5968527 -#> alpha -7.4735307 40.365690 -3.1777189 -#> beta 0.5968527 -3.177719 0.2503425 -#> -#> $start -#> value type -#> parent_0 98.62 state -#> alpha 1.00 deparm -#> beta 10.00 deparm -#> -#> $start_transformed -#> value lower upper -#> parent_0 98.620000 -Inf Inf -#> log_alpha 0.000000 -Inf Inf -#> log_beta 2.302585 -Inf Inf -#> -#> $fixed -#> [1] value type -#> <0 rows> (or 0-length row.names) -#> -#> $data -#> time variable observed predicted residual -#> 1 0 parent 98.62 99.66619265 -1.046192647 -#> 2 3 parent 81.43 78.10760352 3.322396479 -#> 3 7 parent 53.18 56.83515667 -3.655156669 -#> 4 14 parent 34.89 33.18468323 1.705316770 -#> 5 30 parent 10.09 10.49630626 -0.406306255 -#> 6 62 parent 1.50 1.37626531 0.123734689 -#> 7 90 parent 0.33 0.29311302 0.036886982 -#> 8 118 parent 0.08 0.07375954 0.006240458 -#> -#> $atol -#> [1] 1e-08 -#> -#> $rtol -#> [1] 1e-10 -#> -#> $weight.ini -#> [1] "none" -#> -#> $reweight.tol -#> [1] 1e-08 -#> -#> $reweight.max.iter -#> [1] 10 -#> -#> $bparms.optim -#> parent_0 alpha beta -#> 99.66619 12.80517 156.11390 -#> -#> $bparms.fixed -#> numeric(0) -#> -#> $bparms.ode -#> alpha beta -#> 12.80517 156.11390 -#> -#> $bparms.state -#> parent -#> 99.66619 -#> -#> $date -#> [1] "Fri Nov 18 15:19:25 2016" -#> -#> attr(,"class") -#> [1] "mkinfit" "modFit" </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#> dataset -#> model B -#> SFO List,42 -#> attr(,"class") -#> [1] "mmkin"</div><div class='input'> <span class='no'>fits</span><span class='kw'>[[</span><span class='st'>"SFO"</span>, <span class='st'>"B"</span>]] <span class='co'># This is equivalent to</span></div><div class='output co'>#> $par -#> parent_0 log_k_parent_sink -#> 99.174072 -2.549028 -#> -#> $ssr -#> [1] 30.65564 -#> -#> $convergence -#> [1] 0 -#> -#> $iterations -#> [1] 5 -#> -#> $evaluations -#> function gradient -#> 8 15 -#> -#> $counts -#> [1] "relative convergence (4)" -#> -#> $hessian -#> parent_0 log_k_parent_sink -#> parent_0 4.163631 -94.09343 -#> log_k_parent_sink -94.093431 6311.34610 -#> -#> $residuals -#> parent parent parent parent parent parent -#> 0.55407218 -2.98452128 4.20445742 -1.68599939 -0.58185357 -0.72033730 -#> parent parent -#> -0.24260405 -0.07020339 -#> -#> $ms -#> [1] 3.831956 -#> -#> $var_ms -#> parent -#> 3.831956 -#> -#> $var_ms_unscaled -#> parent -#> 3.831956 -#> -#> $var_ms_unweighted -#> parent -#> 3.831956 -#> -#> $rank -#> [1] 2 -#> -#> $df.residual -#> [1] 6 -#> -#> $solution_type -#> [1] "analytical" -#> -#> $transform_rates -#> [1] TRUE -#> -#> $transform_fractions -#> [1] TRUE -#> -#> $method.modFit -#> [1] "Port" -#> -#> $maxit.modFit -#> [1] "auto" -#> -#> $calls -#> [1] 29 -#> -#> $time -#> user system elapsed -#> 0.064 0.000 0.066 -#> -#> $mkinmod -#> <mkinmod> model generated with -#> Use of formation fractions $use_of_ff: min -#> Specification $spec: -#> $parent -#> $type: SFO; $sink: TRUE -#> Coefficient matrix $coefmat available -#> -#> $observed -#> name time value -#> 1 parent 0 98.62 -#> 2 parent 3 81.43 -#> 3 parent 7 53.18 -#> 4 parent 14 34.89 -#> 5 parent 30 10.09 -#> 6 parent 62 1.50 -#> 7 parent 90 0.33 -#> 8 parent 118 0.08 -#> -#> $obs_vars -#> [1] "parent" -#> -#> $predicted -#> name time value -#> 1 parent 0.000000 99.17407218 -#> 2 parent 1.191919 90.35253561 -#> 3 parent 2.383838 82.31567498 -#> 4 parent 3.000000 78.44547872 -#> 5 parent 3.575758 74.99369333 -#> 6 parent 4.767677 68.32300215 -#> 7 parent 5.959596 62.24566915 -#> 8 parent 7.000000 57.38445742 -#> 9 parent 7.151515 56.70891509 -#> 10 parent 8.343434 51.66465547 -#> 11 parent 9.535354 47.06908288 -#> 12 parent 10.727273 42.88228661 -#> 13 parent 11.919192 39.06790599 -#> 14 parent 13.111111 35.59281463 -#> 15 parent 14.000000 33.20400061 -#> 16 parent 14.303030 32.42683275 -#> 17 parent 15.494949 29.54246504 -#> 18 parent 16.686869 26.91466193 -#> 19 parent 17.878788 24.52060198 -#> 20 parent 19.070707 22.33949373 -#> 21 parent 20.262626 20.35239512 -#> 22 parent 21.454545 18.54204899 -#> 23 parent 22.646465 16.89273320 -#> 24 parent 23.838384 15.39012410 -#> 25 parent 25.030303 14.02117212 -#> 26 parent 26.222222 12.77398846 -#> 27 parent 27.414141 11.63774182 -#> 28 parent 28.606061 10.60256435 -#> 29 parent 29.797980 9.65946594 -#> 30 parent 30.000000 9.50814643 -#> 31 parent 30.989899 8.80025617 -#> 32 parent 32.181818 8.01747313 -#> 33 parent 33.373737 7.30431867 -#> 34 parent 34.565657 6.65459931 -#> 35 parent 35.757576 6.06267251 -#> 36 parent 36.949495 5.52339762 -#> 37 parent 38.141414 5.03209124 -#> 38 parent 39.333333 4.58448658 -#> 39 parent 40.525253 4.17669637 -#> 40 parent 41.717172 3.80517911 -#> 41 parent 42.909091 3.46670832 -#> 42 parent 44.101010 3.15834451 -#> 43 parent 45.292929 2.87740968 -#> 44 parent 46.484848 2.62146400 -#> 45 parent 47.676768 2.38828471 -#> 46 parent 48.868687 2.17584671 -#> 47 parent 50.060606 1.98230508 -#> 48 parent 51.252525 1.80597899 -#> 49 parent 52.444444 1.64533711 -#> 50 parent 53.636364 1.49898432 -#> 51 parent 54.828283 1.36564963 -#> 52 parent 56.020202 1.24417505 -#> 53 parent 57.212121 1.13350565 -#> 54 parent 58.404040 1.03268029 -#> 55 parent 59.595960 0.94082335 -#> 56 parent 60.787879 0.85713708 -#> 57 parent 61.979798 0.78089471 -#> 58 parent 62.000000 0.77966270 -#> 59 parent 63.171717 0.71143411 -#> 60 parent 64.363636 0.64815202 -#> 61 parent 65.555556 0.59049888 -#> 62 parent 66.747475 0.53797399 -#> 63 parent 67.939394 0.49012119 -#> 64 parent 69.131313 0.44652489 -#> 65 parent 70.323232 0.40680649 -#> 66 parent 71.515152 0.37062104 -#> 67 parent 72.707071 0.33765429 -#> 68 parent 73.898990 0.30761993 -#> 69 parent 75.090909 0.28025713 -#> 70 parent 76.282828 0.25532825 -#> 71 parent 77.474747 0.23261679 -#> 72 parent 78.666667 0.21192552 -#> 73 parent 79.858586 0.19307474 -#> 74 parent 81.050505 0.17590074 -#> 75 parent 82.242424 0.16025436 -#> 76 parent 83.434343 0.14599973 -#> 77 parent 84.626263 0.13301305 -#> 78 parent 85.818182 0.12118154 -#> 79 parent 87.010101 0.11040244 -#> 80 parent 88.202020 0.10058214 -#> 81 parent 89.393939 0.09163535 -#> 82 parent 90.000000 0.08739595 -#> 83 parent 90.585859 0.08348439 -#> 84 parent 91.777778 0.07605845 -#> 85 parent 92.969697 0.06929305 -#> 86 parent 94.161616 0.06312943 -#> 87 parent 95.353535 0.05751406 -#> 88 parent 96.545455 0.05239819 -#> 89 parent 97.737374 0.04773737 -#> 90 parent 98.929293 0.04349113 -#> 91 parent 100.121212 0.03962259 -#> 92 parent 101.313131 0.03609816 -#> 93 parent 102.505051 0.03288723 -#> 94 parent 103.696970 0.02996191 -#> 95 parent 104.888889 0.02729679 -#> 96 parent 106.080808 0.02486874 -#> 97 parent 107.272727 0.02265667 -#> 98 parent 108.464646 0.02064136 -#> 99 parent 109.656566 0.01880531 -#> 100 parent 110.848485 0.01713257 -#> 101 parent 112.040404 0.01560863 -#> 102 parent 113.232323 0.01422024 -#> 103 parent 114.424242 0.01295535 -#> 104 parent 115.616162 0.01180297 -#> 105 parent 116.808081 0.01075310 -#> 106 parent 118.000000 0.00979661 -#> -#> $cost -#> function (P) -#> { -#> assign("calls", calls + 1, inherits = TRUE) -#> if (trace_parms) -#> cat(P, "\n") -#> if (length(state.ini.optim) > 0) { -#> odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed) -#> names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames) -#> } -#> else { -#> odeini <- state.ini.fixed -#> names(odeini) <- state.ini.fixed.boxnames -#> } -#> odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], -#> transparms.fixed) -#> parms <- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates, -#> transform_fractions = transform_fractions) -#> out <- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type, -#> use_compiled = use_compiled, method.ode = method.ode, -#> atol = atol, rtol = rtol, ...) -#> assign("out_predicted", out, inherits = TRUE) -#> mC <- modCost(out, observed, y = "value", err = err, weight = weight, -#> scaleVar = scaleVar) -#> if (mC$model < cost.old) { -#> if (!quiet) -#> cat("Model cost at call ", calls, ": ", mC$model, -#> "\n") -#> if (plot) { -#> outtimes_plot = seq(min(observed$time), max(observed$time), -#> length.out = 100) -#> out_plot <- mkinpredict(mkinmod, parms, odeini, outtimes_plot, -#> solution_type = solution_type, use_compiled = use_compiled, -#> method.ode = method.ode, atol = atol, rtol = rtol, -#> ...) -#> plot(0, type = "n", xlim = range(observed$time), -#> ylim = c(0, max(observed$value, na.rm = TRUE)), -#> xlab = "Time", ylab = "Observed") -#> col_obs <- pch_obs <- 1:length(obs_vars) -#> lty_obs <- rep(1, length(obs_vars)) -#> names(col_obs) <- names(pch_obs) <- names(lty_obs) <- obs_vars -#> for (obs_var in obs_vars) { -#> points(subset(observed, name == obs_var, c(time, -#> value)), pch = pch_obs[obs_var], col = col_obs[obs_var]) -#> } -#> matlines(out_plot$time, out_plot[-1], col = col_obs, -#> lty = lty_obs) -#> legend("topright", inset = c(0.05, 0.05), legend = obs_vars, -#> col = col_obs, pch = pch_obs, lty = 1:length(pch_obs)) -#> } -#> assign("cost.old", mC$model, inherits = TRUE) -#> } -#> return(mC) -#> } -#> <environment: 0x3b66828> -#> -#> $cost_notrans -#> function (P) -#> { -#> if (length(state.ini.optim) > 0) { -#> odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed) -#> names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames) -#> } -#> else { -#> odeini <- state.ini.fixed -#> names(odeini) <- state.ini.fixed.boxnames -#> } -#> odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], -#> parms.fixed) -#> out <- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type, -#> use_compiled = use_compiled, method.ode = method.ode, -#> atol = atol, rtol = rtol, ...) -#> mC <- modCost(out, observed, y = "value", err = err, weight = weight, -#> scaleVar = scaleVar) -#> return(mC) -#> } -#> <environment: 0x3b66828> -#> -#> $hessian_notrans -#> parent_0 k_parent_sink -#> parent_0 4.163631 -1203.894 -#> k_parent_sink -1203.893702 1033188.753 -#> -#> $start -#> value type -#> parent_0 98.62 state -#> k_parent_sink 0.10 deparm -#> -#> $start_transformed -#> value lower upper -#> parent_0 98.620000 -Inf Inf -#> log_k_parent_sink -2.302585 -Inf Inf -#> -#> $fixed -#> [1] value type -#> <0 rows> (or 0-length row.names) -#> -#> $data -#> time variable observed predicted residual -#> 1 0 parent 98.62 99.17407218 -0.55407218 -#> 2 3 parent 81.43 78.44547872 2.98452128 -#> 3 7 parent 53.18 57.38445742 -4.20445742 -#> 4 14 parent 34.89 33.20400061 1.68599939 -#> 5 30 parent 10.09 9.50814643 0.58185357 -#> 6 62 parent 1.50 0.77966270 0.72033730 -#> 7 90 parent 0.33 0.08739595 0.24260405 -#> 8 118 parent 0.08 0.00979661 0.07020339 -#> -#> $atol -#> [1] 1e-08 -#> -#> $rtol -#> [1] 1e-10 -#> -#> $weight.ini -#> [1] "none" -#> -#> $reweight.tol -#> [1] 1e-08 -#> -#> $reweight.max.iter -#> [1] 10 -#> -#> $bparms.optim -#> parent_0 k_parent_sink -#> 99.17407218 0.07815759 -#> -#> $bparms.fixed -#> numeric(0) -#> -#> $bparms.ode -#> k_parent_sink -#> 0.07815759 -#> -#> $bparms.state -#> parent -#> 99.17407 -#> -#> $date -#> [1] "Fri Nov 18 15:19:25 2016" -#> -#> attr(,"class") -#> [1] "mkinfit" "modFit" </div><div class='input'> <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]</div><div class='output co'>#> [[1]] +#> </div><div class='input'> + <span class='fu'>head</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'>#> [[1]] #> $par #> parent_0 log_k_parent_sink #> 99.174072 -2.549028 @@ -894,7 +229,7 @@ #> #> $time #> user system elapsed -#> 0.064 0.000 0.066 +#> 0.068 0.000 0.070 #> #> $mkinmod #> <mkinmod> model generated with @@ -1081,7 +416,7 @@ #> } #> return(mC) #> } -#> <environment: 0x3b66828> +#> <environment: 0x3a3e8a8> #> #> $cost_notrans #> function (P) @@ -1103,7 +438,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x3b66828> +#> <environment: 0x3a3e8a8> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -1166,7 +501,7 @@ #> 99.17407 #> #> $date -#> [1] "Fri Nov 18 15:19:25 2016" +#> [1] "Fri Nov 18 16:03:57 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 990ceadf..7e3455c9 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -106,6 +106,18 @@ with the advantage that the SFORB model can also be used for metabolites.</p> <p>A list with the components mentioned above.</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>) + <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> @@ -115,7 +127,9 @@ with the advantage that the SFORB model can also be used for metabolites.</p> <li><a href="#note">Note</a></li> <li><a href="#value">Value</a></li> - </ul> + + <li><a href="#examples">Examples</a></li> + </ul> <h2>Author</h2> diff --git a/docs/reference/index.html b/docs/reference/index.html index 2d052a80..eff83260 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -119,8 +119,7 @@ <li><code><a href="mkinresplot.html">mkinresplot</a></code></li> </ul> - <p><a href="mkinparplot.html">Function to plot the confidence intervals obtained using - list(list("mkinfit"))</a></p> + <p><a href="mkinparplot.html">Function to plot the confidence intervals obtained using mkinfit</a></p> <ul> <li><code><a href="mkinparplot.html">mkinparplot</a></code></li> </ul> @@ -247,9 +246,9 @@ <p class="section-desc"><p>Parent only model solutions</p></p> - <p><a href="DFOP.solution.html">Double First-Order in Parallel kinetics</a></p> + <p><a href="SFO.solution.html">Single First-Order kinetics</a></p> <ul> - <li><code><a href="DFOP.solution.html">DFOP.solution</a></code></li> + <li><code><a href="SFO.solution.html">SFO.solution</a></code></li> </ul> <p><a href="FOMC.solution.html">First-Order Multi-Compartment kinetics</a></p> @@ -257,24 +256,24 @@ <li><code><a href="FOMC.solution.html">FOMC.solution</a></code></li> </ul> - <p><a href="HS.solution.html">Hockey-Stick kinetics</a></p> + <p><a href="DFOP.solution.html">Double First-Order in Parallel kinetics</a></p> <ul> - <li><code><a href="HS.solution.html">HS.solution</a></code></li> + <li><code><a href="DFOP.solution.html">DFOP.solution</a></code></li> </ul> - <p><a href="IORE.solution.html">Indeterminate order rate equation kinetics</a></p> + <p><a href="SFORB.solution.html">Single First-Order Reversible Binding kinetics</a></p> <ul> - <li><code><a href="IORE.solution.html">IORE.solution</a></code></li> + <li><code><a href="SFORB.solution.html">SFORB.solution</a></code></li> </ul> - <p><a href="SFO.solution.html">Single First-Order kinetics</a></p> + <p><a href="HS.solution.html">Hockey-Stick kinetics</a></p> <ul> - <li><code><a href="SFO.solution.html">SFO.solution</a></code></li> + <li><code><a href="HS.solution.html">HS.solution</a></code></li> </ul> - <p><a href="SFORB.solution.html">Single First-Order Reversible Binding kinetics</a></p> + <p><a href="IORE.solution.html">Indeterminate order rate equation kinetics</a></p> <ul> - <li><code><a href="SFORB.solution.html">SFORB.solution</a></code></li> + <li><code><a href="IORE.solution.html">IORE.solution</a></code></li> </ul> <h2 id="section-generate-synthetic-datasets" class="hasAnchor"><a href="#section-generate-synthetic-datasets" class="anchor"></a>Generate synthetic datasets</h2> <p class="section-desc"></p> diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 7b294129..baf452d0 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -112,158 +112,11 @@ <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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"phenol"</span>), <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"anisole"</span>), <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></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'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>))</div><div class='output co'>#> Model cost at call 1 : 13655.2 -#> Model cost at call 2 : 13655.2 -#> Model cost at call 8 : 9191.59 -#> Model cost at call 16 : 5663.584 -#> Model cost at call 17 : 5663.582 -#> Model cost at call 18 : 5663.566 -#> Model cost at call 19 : 5663.55 -#> Model cost at call 23 : 3035.567 -#> Model cost at call 24 : 3035.566 -#> Model cost at call 26 : 3035.561 -#> Model cost at call 27 : 3035.559 -#> Model cost at call 28 : 3035.558 -#> Model cost at call 30 : 2252.97 -#> Model cost at call 31 : 2252.965 -#> Model cost at call 32 : 2252.965 -#> Model cost at call 36 : 2252.958 -#> Model cost at call 37 : 1220.201 -#> Model cost at call 38 : 1220.2 -#> Model cost at call 39 : 1220.199 -#> Model cost at call 41 : 1220.183 -#> Model cost at call 45 : 507.1358 -#> Model cost at call 48 : 507.1353 -#> Model cost at call 52 : 198.5695 -#> Model cost at call 55 : 198.5694 -#> Model cost at call 60 : 175.8239 -#> Model cost at call 63 : 175.8239 -#> Model cost at call 67 : 170.6316 -#> Model cost at call 69 : 170.6316 -#> Model cost at call 74 : 165.881 -#> Model cost at call 77 : 165.881 -#> Model cost at call 81 : 161.6423 -#> Model cost at call 84 : 161.6423 -#> Model cost at call 88 : 158.2953 -#> Model cost at call 91 : 158.2953 -#> Model cost at call 95 : 156.7311 -#> Model cost at call 97 : 156.731 -#> Model cost at call 103 : 155.998 -#> Model cost at call 106 : 155.998 -#> Model cost at call 110 : 155.6263 -#> Model cost at call 113 : 155.6262 -#> Model cost at call 116 : 155.6262 -#> Model cost at call 117 : 155.1202 -#> Model cost at call 120 : 155.1202 -#> Model cost at call 124 : 154.4133 -#> Model cost at call 125 : 153.8489 -#> Model cost at call 126 : 152.7413 -#> Model cost at call 129 : 152.7413 -#> Model cost at call 132 : 152.7413 -#> Model cost at call 133 : 150.3995 -#> Model cost at call 134 : 148.7256 -#> Model cost at call 135 : 147.2618 -#> Model cost at call 137 : 147.2618 -#> Model cost at call 139 : 147.2618 -#> Model cost at call 142 : 145.115 -#> Model cost at call 144 : 145.115 -#> Model cost at call 145 : 145.115 -#> Model cost at call 146 : 145.115 -#> Model cost at call 147 : 145.115 -#> Model cost at call 150 : 143.7878 -#> Model cost at call 157 : 142.8531 -#> Model cost at call 160 : 142.8531 -#> Model cost at call 164 : 142.7325 -#> Model cost at call 167 : 142.7325 -#> Model cost at call 169 : 142.7325 -#> Model cost at call 172 : 141.8393 -#> Model cost at call 173 : 141.8393 -#> Model cost at call 174 : 141.8393 -#> Model cost at call 179 : 141.3446 -#> Model cost at call 180 : 141.3446 -#> Model cost at call 181 : 141.3446 -#> Model cost at call 186 : 141.1111 -#> Model cost at call 193 : 140.7786 -#> Model cost at call 200 : 140.451 -#> Model cost at call 207 : 140.1395 -#> Model cost at call 214 : 139.7903 -#> Model cost at call 221 : 139.5476 -#> Model cost at call 228 : 139.4441 -#> Model cost at call 235 : 139.3204 -#> Model cost at call 242 : 139.2508 -#> Model cost at call 249 : 139.1891 -#> Model cost at call 256 : 139.1561 -#> Model cost at call 263 : 139.137 -#> Model cost at call 270 : 139.1278 -#> Model cost at call 271 : 139.1278 -#> Model cost at call 279 : 139.1211 -#> Model cost at call 280 : 139.1211 -#> Model cost at call 281 : 139.1211 -#> Model cost at call 282 : 139.1211 -#> Model cost at call 286 : 139.1179 -#> Model cost at call 287 : 139.1179 -#> Model cost at call 291 : 139.1179 -#> Model cost at call 294 : 139.1179 -#> Model cost at call 298 : 139.1158 -#> Model cost at call 299 : 139.1158 -#> Model cost at call 302 : 139.1158 -#> Model cost at call 310 : 139.1148 -#> Model cost at call 311 : 139.1148 -#> Model cost at call 315 : 139.1148 -#> Model cost at call 322 : 139.1143 -#> Model cost at call 323 : 139.1143 -#> Model cost at call 326 : 139.1143 -#> Model cost at call 334 : 139.114 -#> Model cost at call 335 : 139.114 -#> Model cost at call 338 : 139.114 -#> Model cost at call 339 : 139.114 -#> Model cost at call 346 : 139.1139 -#> Model cost at call 347 : 139.1139 -#> Model cost at call 350 : 139.1139 -#> Model cost at call 351 : 139.1139 -#> Model cost at call 358 : 139.1139 -#> Model cost at call 359 : 139.1139 -#> Model cost at call 362 : 139.1139 -#> Model cost at call 363 : 139.1139 -#> Model cost at call 370 : 139.1138 -#> Model cost at call 382 : 139.1138 -#> Model cost at call 390 : 139.1138 -#> Model cost at call 395 : 139.1138 -#> Model cost at call 403 : 139.1138 -#> Model cost at call 408 : 139.1138 -#> Model cost at call 416 : 139.1138 -#> Model cost at call 421 : 139.1138 -#> Model cost at call 429 : 139.1138 -#> Model cost at call 434 : 139.1138 -#> Model cost at call 442 : 139.1138 -#> Model cost at call 447 : 139.1138 -#> Model cost at call 455 : 139.1138 -#> Model cost at call 460 : 139.1138 -#> Model cost at call 468 : 139.1138 -#> Model cost at call 473 : 139.1138 -#> Model cost at call 481 : 139.1138 -#> Model cost at call 486 : 139.1138 -#> Model cost at call 494 : 139.1138 -#> Model cost at call 499 : 139.1138 -#> Model cost at call 507 : 139.1138 -#> Model cost at call 512 : 139.1138 -#> Model cost at call 519 : 139.1138 -#> Model cost at call 520 : 139.1138 -#> Model cost at call 525 : 139.1138 -#> Model cost at call 538 : 139.1138 -#> Model cost at call 545 : 139.1138 -#> Model cost at call 546 : 139.1138 -#> Model cost at call 551 : 139.1138 -#> Model cost at call 558 : 139.1138 -#> Model cost at call 559 : 139.1138 -#> Model cost at call 564 : 139.1138 -#> Model cost at call 571 : 139.1138 -#> Model cost at call 580 : 139.1138 -#> Model cost at call 588 : 139.1138 </div><div class='output co'>#> <span class='warning'>Warning: Optimisation by method Port did not converge.</span> + <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'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> <span class='warning'>Warning: Optimisation by method Port did not converge.</span> #> <span class='warning'>Convergence code is 1</span></div><div class='input'> <span class='fu'>summary</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: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 18 15:19:33 2016 -#> Date of summary: Fri Nov 18 15:19:33 2016 +#> Date of fit: Fri Nov 18 16:08:19 2016 +#> Date of summary: Fri Nov 18 16:08:19 2016 #> #> #> Warning: Optimisation by method Port did not converge. @@ -278,7 +131,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 590 model solutions performed in 3.45 s +#> Fitted with method Port using 590 model solutions performed in 3.568 s #> #> Weighting: none #> @@ -350,14 +203,15 @@ #> T245 15.982 53.091 #> phenol 1.711 5.685 #> anisole 103.784 344.763</div><div class='input'> - <span class='co'># No covariance matrix and k_phenol_sink is really small, therefore fix it to zero</span> + <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'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 18 15:19:35 2016 -#> Date of summary: Fri Nov 18 15:19:35 2016 +#> Date of fit: Fri Nov 18 16:08:21 2016 +#> Date of summary: Fri Nov 18 16:08:21 2016 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -367,7 +221,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.477 s +#> Fitted with method Port using 246 model solutions performed in 1.408 s #> #> Weighting: none #> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index d212e3b2..a8557261 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -81,9 +81,8 @@ </div> - <p>This function uses <code>optimize</code> in order to iteratively find the -smallest relative error still resulting in passing the chi-squared test -as defined in the FOCUS kinetics report from 2006.</p> + <p>This function finds the smallest relative error still resulting in passing the +chi-squared test as defined in the FOCUS kinetics report from 2006.</p> <pre><span class='fu'>mkinerrmin</span>(<span class='no'>fit</span>, <span class='kw'>alpha</span> <span class='kw'>=</span> <span class='fl'>0.05</span>)</pre> @@ -120,8 +119,8 @@ 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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>), - <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), + <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='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'>round</span>(<span class='fu'>mkinerrmin</span>(<span class='no'>fit_FOCUS_D</span>), <span class='fl'>4</span>)</div><div class='output co'>#> err.min n.optim df diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index f6ffd21d..99b10f43 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -359,15 +359,15 @@ <span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 18 15:19:37 2016 -#> Date of summary: Fri Nov 18 15:19:37 2016 +#> Date of fit: Fri Nov 18 15:36:12 2016 +#> Date of summary: Fri Nov 18 15:36:12 2016 #> #> 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 0.152 s +#> Fitted with method Port using 64 model solutions performed in 0.157 s #> #> Weighting: none #> @@ -436,7 +436,7 @@ <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'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#> user system elapsed -#> 1.220 1.184 0.904 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 1.264 1.216 0.945 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><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 @@ -513,7 +513,7 @@ #> Model cost at call 152 : 371.2134 #> Optimisation by method Port successfully terminated. #> user system elapsed -#> 0.712 0.040 0.707 </div><div class='input'><span class='fu'>coef</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 +#> 0.712 0.036 0.702 </div><div class='input'><span class='fu'>coef</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 @@ -532,735 +532,32 @@ <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='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>)</div><div class='output co'>#> Model cost at call 1 : 18857.28 -#> Model cost at call 4 : 18857.28 -#> Model cost at call 5 : 18857.28 -#> Model cost at call 8 : 15273.94 -#> Model cost at call 9 : 15273.93 -#> Model cost at call 12 : 15273.67 -#> Model cost at call 13 : 15273.64 -#> Model cost at call 14 : 12764.42 -#> Model cost at call 15 : 8382.7 -#> Model cost at call 20 : 8382.696 -#> Model cost at call 23 : 2729.177 -#> Model cost at call 24 : 2729.175 -#> Model cost at call 26 : 2729.164 -#> Model cost at call 30 : 2299.383 -#> Model cost at call 34 : 2299.379 -#> Model cost at call 35 : 2299.373 -#> Model cost at call 36 : 1944.782 -#> Model cost at call 40 : 1944.782 -#> Model cost at call 42 : 1328.087 -#> Model cost at call 43 : 908.661 -#> Model cost at call 44 : 908.6604 -#> Model cost at call 50 : 877.3556 -#> Model cost at call 51 : 877.3554 -#> Model cost at call 54 : 877.3546 -#> Model cost at call 56 : 769.5186 -#> Model cost at call 59 : 769.5157 -#> Model cost at call 62 : 690.3426 -#> Model cost at call 66 : 690.3425 -#> Model cost at call 68 : 608.4032 -#> Model cost at call 72 : 608.4031 -#> Model cost at call 73 : 608.4031 -#> Model cost at call 74 : 601.5178 -#> Model cost at call 78 : 601.5174 -#> Model cost at call 79 : 601.5174 -#> Model cost at call 80 : 459.9885 -#> Model cost at call 81 : 459.9883 -#> Model cost at call 83 : 459.9878 -#> Model cost at call 87 : 447.0145 -#> Model cost at call 91 : 447.0145 -#> Model cost at call 94 : 445.7322 -#> Model cost at call 97 : 445.7322 -#> Model cost at call 99 : 445.7322 -#> Model cost at call 100 : 444.6965 -#> Model cost at call 103 : 444.6965 -#> Model cost at call 106 : 442.9742 -#> Model cost at call 109 : 442.9742 -#> Model cost at call 112 : 439.9665 -#> Model cost at call 115 : 439.9665 -#> Model cost at call 116 : 439.9664 -#> Model cost at call 118 : 435.0752 -#> Model cost at call 121 : 435.0751 -#> Model cost at call 124 : 430.4718 -#> Model cost at call 127 : 430.4717 -#> Model cost at call 132 : 424.7004 -#> Model cost at call 134 : 424.7003 -#> Model cost at call 138 : 423.6102 -#> Model cost at call 141 : 423.6102 -#> Model cost at call 142 : 423.6102 -#> Model cost at call 144 : 421.1786 -#> Model cost at call 147 : 421.1786 -#> Model cost at call 148 : 421.1786 -#> Model cost at call 150 : 418.1431 -#> Model cost at call 151 : 412.8665 -#> Model cost at call 152 : 396.6067 -#> Model cost at call 154 : 396.6067 -#> Model cost at call 158 : 391.0492 -#> Model cost at call 160 : 391.0492 -#> Model cost at call 164 : 385.8205 -#> Model cost at call 165 : 385.8205 -#> Model cost at call 170 : 379.7674 -#> Model cost at call 171 : 379.7674 -#> Model cost at call 172 : 379.7674 -#> Model cost at call 176 : 374.9389 -#> Model cost at call 177 : 374.9389 -#> Model cost at call 182 : 372.727 -#> Model cost at call 185 : 372.727 -#> Model cost at call 188 : 371.5297 -#> Model cost at call 194 : 370.3738 -#> Model cost at call 195 : 370.3738 -#> Model cost at call 200 : 370.0182 -#> Model cost at call 206 : 369.8634 -#> Model cost at call 212 : 369.8188 -#> Model cost at call 213 : 369.8188 -#> Model cost at call 219 : 369.8114 -#> Model cost at call 221 : 369.8114 -#> Model cost at call 224 : 369.8114 -#> Model cost at call 226 : 369.8114 -#> Model cost at call 230 : 369.8105 -#> Model cost at call 231 : 369.8105 -#> Model cost at call 235 : 369.8105 -#> Model cost at call 236 : 369.8105 -#> Model cost at call 237 : 369.8105 -#> Model cost at call 238 : 369.8105 -#> Model cost at call 249 : 369.8105 -#> Model cost at call 260 : 369.8105 -#> Model cost at call 275 : 369.8105 -#> Model cost at call 276 : 369.8105 -#> Optimisation by method Port successfully terminated.</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>)</div><div class='output co'>#> Model cost at call 1 : 3237.008 -#> Model cost at call 3 : 3237.007 -#> Model cost at call 6 : 671.2571 -#> Model cost at call 7 : 671.2559 -#> Model cost at call 8 : 671.2301 -#> Model cost at call 9 : 671.2249 -#> Model cost at call 10 : 468.4899 -#> Model cost at call 12 : 468.4899 -#> Model cost at call 14 : 371.3486 -#> Model cost at call 16 : 371.3485 -#> Model cost at call 18 : 346.2972 -#> Model cost at call 19 : 346.2971 -#> Model cost at call 20 : 346.297 -#> Model cost at call 21 : 346.2969 -#> Model cost at call 22 : 269.7053 -#> Model cost at call 23 : 269.7053 -#> Model cost at call 26 : 243.9936 -#> Model cost at call 27 : 235.1625 -#> Model cost at call 28 : 235.1624 -#> Model cost at call 30 : 235.1624 -#> Model cost at call 31 : 224.2195 -#> Model cost at call 35 : 218.1922 -#> Model cost at call 36 : 218.1922 -#> Model cost at call 38 : 218.1922 -#> Model cost at call 39 : 211.5012 -#> Model cost at call 41 : 211.5012 -#> Model cost at call 43 : 207.9511 -#> Model cost at call 44 : 207.9511 -#> Model cost at call 47 : 206.5377 -#> Model cost at call 51 : 205.8736 -#> Model cost at call 55 : 205.5625 -#> Model cost at call 59 : 205.4704 -#> Model cost at call 63 : 205.4499 -#> Model cost at call 67 : 205.448 -#> Model cost at call 69 : 205.448 -#> Model cost at call 70 : 205.448 -#> Model cost at call 73 : 205.448 -#> Model cost at call 74 : 205.4478 -#> Model cost at call 75 : 205.4478 -#> Model cost at call 77 : 205.4478 -#> Model cost at call 79 : 205.4478 -#> Model cost at call 84 : 205.4478 -#> Model cost at call 95 : 205.4478 -#> Model cost at call 98 : 205.4478 -#> Optimisation by method Port successfully terminated.</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'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.FOMC</span>$<span class='no'>bparms.ode</span>)</div><div class='output co'>#> Model cost at call 1 : 15169.96 -#> Model cost at call 2 : 15169.96 -#> Model cost at call 7 : 8247.462 -#> Model cost at call 14 : 6734.371 -#> Model cost at call 15 : 6734.339 -#> Model cost at call 16 : 6734.136 -#> Model cost at call 20 : 4855.056 -#> Model cost at call 24 : 4855.038 -#> Model cost at call 27 : 1239.986 -#> Model cost at call 29 : 1239.985 -#> Model cost at call 34 : 1030.523 -#> Model cost at call 38 : 1030.523 -#> Model cost at call 40 : 894.2766 -#> Model cost at call 43 : 894.275 -#> Model cost at call 46 : 750.3629 -#> Model cost at call 49 : 750.3623 -#> Model cost at call 52 : 627.6819 -#> Model cost at call 55 : 627.6818 -#> Model cost at call 58 : 546.2947 -#> Model cost at call 61 : 546.2944 -#> Model cost at call 65 : 502.5529 -#> Model cost at call 69 : 502.5525 -#> Model cost at call 70 : 502.5525 -#> Model cost at call 71 : 475.2423 -#> Model cost at call 72 : 465.5298 -#> Model cost at call 75 : 465.5298 -#> Model cost at call 76 : 465.5297 -#> Model cost at call 78 : 464.9476 -#> Model cost at call 81 : 464.9476 -#> Model cost at call 82 : 464.9473 -#> Model cost at call 84 : 426.9626 -#> Model cost at call 88 : 426.9626 -#> Model cost at call 90 : 414.5235 -#> Model cost at call 93 : 414.5234 -#> Model cost at call 96 : 412.1478 -#> Model cost at call 99 : 412.1477 -#> Model cost at call 100 : 412.1477 -#> Model cost at call 101 : 412.1477 -#> Model cost at call 102 : 394.146 -#> Model cost at call 105 : 394.146 -#> Model cost at call 106 : 394.146 -#> Model cost at call 107 : 394.146 -#> Model cost at call 108 : 384.2002 -#> Model cost at call 112 : 384.2001 -#> Model cost at call 113 : 384.2001 -#> Model cost at call 115 : 380.5495 -#> Model cost at call 119 : 380.5494 -#> Model cost at call 120 : 380.5494 -#> Model cost at call 121 : 378.4803 -#> Model cost at call 123 : 378.4802 -#> Model cost at call 124 : 378.4792 -#> Model cost at call 127 : 374.8432 -#> Model cost at call 129 : 374.8431 -#> Model cost at call 133 : 372.8364 -#> Model cost at call 136 : 372.8364 -#> Model cost at call 137 : 372.8363 -#> Model cost at call 138 : 372.8363 -#> Model cost at call 141 : 372.668 -#> Model cost at call 145 : 372.6679 -#> Model cost at call 147 : 372.5882 -#> Model cost at call 150 : 372.5882 -#> Model cost at call 153 : 372.4828 -#> Model cost at call 156 : 372.4828 -#> Model cost at call 159 : 372.3639 -#> Model cost at call 162 : 372.3639 -#> Model cost at call 163 : 372.3639 -#> Model cost at call 164 : 372.3639 -#> Model cost at call 165 : 372.1959 -#> Model cost at call 168 : 372.1959 -#> Model cost at call 171 : 371.9627 -#> Model cost at call 172 : 371.7467 -#> Model cost at call 173 : 371.1161 -#> Model cost at call 174 : 370.3326 -#> Model cost at call 177 : 370.3326 -#> Model cost at call 178 : 370.3326 -#> Model cost at call 180 : 370.3267 -#> Model cost at call 186 : 370.0471 -#> Model cost at call 187 : 370.0471 -#> Model cost at call 193 : 369.9649 -#> Model cost at call 194 : 369.9649 -#> Model cost at call 196 : 369.9649 -#> Model cost at call 199 : 369.8684 -#> Model cost at call 200 : 369.8684 -#> Model cost at call 204 : 369.8684 -#> Model cost at call 206 : 369.8349 -#> Model cost at call 207 : 369.8349 -#> Model cost at call 209 : 369.8349 -#> Model cost at call 210 : 369.8349 -#> Model cost at call 211 : 369.8349 -#> Model cost at call 212 : 369.8105 -#> Model cost at call 214 : 369.8105 -#> Model cost at call 218 : 369.8105 -#> Model cost at call 220 : 369.8105 -#> Model cost at call 225 : 369.8105 -#> Model cost at call 229 : 369.8105 -#> Model cost at call 231 : 369.8105 -#> Model cost at call 232 : 369.8105 -#> Model cost at call 236 : 369.8105 -#> Model cost at call 239 : 369.8105 -#> Model cost at call 240 : 369.8105 -#> Model cost at call 255 : 369.8105 -#> Model cost at call 258 : 369.8105 -#> Optimisation by method Port successfully terminated.</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='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'>list</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'>list</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>)</div><div class='output co'>#> Model cost at call 1 : 19233.21 -#> Model cost at call 2 : 19233.21 -#> Model cost at call 5 : 19233.21 -#> Model cost at call 8 : 14482.65 -#> Model cost at call 11 : 14482.51 -#> Model cost at call 13 : 14482.17 -#> Model cost at call 15 : 6973.814 -#> Model cost at call 16 : 5161.041 -#> Model cost at call 17 : 5161.029 -#> Model cost at call 22 : 5161.026 -#> Model cost at call 24 : 3249.595 -#> Model cost at call 26 : 3249.595 -#> Model cost at call 27 : 3249.519 -#> Model cost at call 31 : 2615.891 -#> Model cost at call 32 : 2615.888 -#> Model cost at call 39 : 989.1788 -#> Model cost at call 44 : 989.1772 -#> Model cost at call 45 : 989.1771 -#> Model cost at call 47 : 647.4307 -#> Model cost at call 50 : 647.4302 -#> Model cost at call 51 : 647.4261 -#> Model cost at call 54 : 626.7937 -#> Model cost at call 55 : 626.7935 -#> Model cost at call 56 : 626.7931 -#> Model cost at call 61 : 527.9042 -#> Model cost at call 62 : 527.9041 -#> Model cost at call 68 : 505.8828 -#> Model cost at call 70 : 505.8828 -#> Model cost at call 73 : 505.8827 -#> Model cost at call 75 : 452.8932 -#> Model cost at call 77 : 452.893 -#> Model cost at call 82 : 414.4918 -#> Model cost at call 83 : 414.4918 -#> Model cost at call 84 : 414.4918 -#> Model cost at call 88 : 414.4917 -#> Model cost at call 89 : 408.2617 -#> Model cost at call 90 : 408.2616 -#> Model cost at call 91 : 408.2616 -#> Model cost at call 95 : 408.2615 -#> Model cost at call 96 : 384.4461 -#> Model cost at call 102 : 384.4461 -#> Model cost at call 104 : 383.4905 -#> Model cost at call 105 : 383.4905 -#> Model cost at call 106 : 383.4905 -#> Model cost at call 109 : 383.4904 -#> Model cost at call 111 : 381.8828 -#> Model cost at call 112 : 381.8827 -#> Model cost at call 118 : 380.8499 -#> Model cost at call 120 : 380.8499 -#> Model cost at call 123 : 380.8499 -#> Model cost at call 125 : 379.1403 -#> Model cost at call 127 : 379.1402 -#> Model cost at call 132 : 376.4962 -#> Model cost at call 133 : 373.0958 -#> Model cost at call 134 : 365.247 -#> Model cost at call 137 : 365.2469 -#> Model cost at call 142 : 360.8231 -#> Model cost at call 143 : 360.8231 -#> Model cost at call 146 : 360.8231 -#> Model cost at call 148 : 360.8231 -#> Model cost at call 149 : 358.3976 -#> Model cost at call 152 : 358.3976 -#> Model cost at call 154 : 358.3976 -#> Model cost at call 156 : 355.9066 -#> Model cost at call 157 : 355.9066 -#> Model cost at call 163 : 354.3386 -#> Model cost at call 164 : 353.6335 -#> Model cost at call 172 : 353.2094 -#> Model cost at call 173 : 353.2094 -#> Model cost at call 174 : 353.2093 -#> Model cost at call 177 : 353.2093 -#> Model cost at call 178 : 353.2093 -#> Model cost at call 179 : 352.6641 -#> Model cost at call 182 : 352.6641 -#> Model cost at call 183 : 352.6641 -#> Model cost at call 186 : 352.4908 -#> Model cost at call 187 : 352.4429 -#> Model cost at call 195 : 352.3246 -#> Model cost at call 203 : 352.2858 -#> Model cost at call 204 : 352.2858 -#> Model cost at call 205 : 352.2858 -#> Model cost at call 206 : 352.2858 -#> Model cost at call 207 : 352.2858 -#> Model cost at call 210 : 352.2332 -#> Model cost at call 211 : 352.2081 -#> Model cost at call 214 : 352.2081 -#> Model cost at call 216 : 352.2081 -#> Model cost at call 218 : 352.2049 -#> Model cost at call 219 : 352.2049 -#> Model cost at call 220 : 352.2049 -#> Model cost at call 226 : 352.2048 -#> Model cost at call 228 : 352.2048 -#> Model cost at call 231 : 352.2048 -#> Model cost at call 232 : 352.2048 -#> Model cost at call 238 : 352.2048 -#> Model cost at call 239 : 352.2048 -#> Model cost at call 251 : 352.2048 -#> Model cost at call 264 : 352.2048 -#> Model cost at call 283 : 352.2048 -#> Model cost at call 284 : 352.2048 -#> Model cost at call 285 : 352.2048 -#> Model cost at call 286 : 352.2048 -#> Optimisation by method Port successfully terminated.</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>)</div><div class='output co'>#> Model cost at call 1 : 19233.21 -#> Model cost at call 2 : 19233.21 -#> Model cost at call 5 : 19233.21 -#> Model cost at call 8 : 14482.65 -#> Model cost at call 11 : 14482.51 -#> Model cost at call 13 : 14482.17 -#> Model cost at call 15 : 6973.814 -#> Model cost at call 16 : 5161.041 -#> Model cost at call 17 : 5161.029 -#> Model cost at call 22 : 5161.026 -#> Model cost at call 24 : 3249.595 -#> Model cost at call 26 : 3249.595 -#> Model cost at call 27 : 3249.519 -#> Model cost at call 31 : 2615.891 -#> Model cost at call 32 : 2615.888 -#> Model cost at call 39 : 989.1788 -#> Model cost at call 44 : 989.1772 -#> Model cost at call 45 : 989.1771 -#> Model cost at call 47 : 647.4307 -#> Model cost at call 50 : 647.4302 -#> Model cost at call 51 : 647.4261 -#> Model cost at call 54 : 626.7937 -#> Model cost at call 55 : 626.7935 -#> Model cost at call 56 : 626.7931 -#> Model cost at call 61 : 527.9042 -#> Model cost at call 62 : 527.9041 -#> Model cost at call 68 : 505.8828 -#> Model cost at call 70 : 505.8828 -#> Model cost at call 73 : 505.8827 -#> Model cost at call 75 : 452.8932 -#> Model cost at call 77 : 452.893 -#> Model cost at call 82 : 414.4918 -#> Model cost at call 83 : 414.4918 -#> Model cost at call 84 : 414.4918 -#> Model cost at call 88 : 414.4917 -#> Model cost at call 89 : 408.2617 -#> Model cost at call 90 : 408.2616 -#> Model cost at call 91 : 408.2616 -#> Model cost at call 95 : 408.2615 -#> Model cost at call 96 : 384.4461 -#> Model cost at call 102 : 384.4461 -#> Model cost at call 104 : 383.4905 -#> Model cost at call 105 : 383.4905 -#> Model cost at call 106 : 383.4905 -#> Model cost at call 109 : 383.4904 -#> Model cost at call 111 : 381.8828 -#> Model cost at call 112 : 381.8827 -#> Model cost at call 118 : 380.8499 -#> Model cost at call 120 : 380.8499 -#> Model cost at call 123 : 380.8499 -#> Model cost at call 125 : 379.1403 -#> Model cost at call 127 : 379.1402 -#> Model cost at call 132 : 376.4962 -#> Model cost at call 133 : 373.0958 -#> Model cost at call 134 : 365.247 -#> Model cost at call 137 : 365.2469 -#> Model cost at call 142 : 360.8231 -#> Model cost at call 143 : 360.8231 -#> Model cost at call 146 : 360.8231 -#> Model cost at call 148 : 360.8231 -#> Model cost at call 149 : 358.3976 -#> Model cost at call 152 : 358.3976 -#> Model cost at call 154 : 358.3976 -#> Model cost at call 156 : 355.9066 -#> Model cost at call 157 : 355.9066 -#> Model cost at call 163 : 354.3386 -#> Model cost at call 164 : 353.6335 -#> Model cost at call 172 : 353.2094 -#> Model cost at call 173 : 353.2094 -#> Model cost at call 174 : 353.2093 -#> Model cost at call 177 : 353.2093 -#> Model cost at call 178 : 353.2093 -#> Model cost at call 179 : 352.6641 -#> Model cost at call 182 : 352.6641 -#> Model cost at call 183 : 352.6641 -#> Model cost at call 186 : 352.4908 -#> Model cost at call 187 : 352.4429 -#> Model cost at call 195 : 352.3246 -#> Model cost at call 203 : 352.2858 -#> Model cost at call 204 : 352.2858 -#> Model cost at call 205 : 352.2858 -#> Model cost at call 206 : 352.2858 -#> Model cost at call 207 : 352.2858 -#> Model cost at call 210 : 352.2332 -#> Model cost at call 211 : 352.2081 -#> Model cost at call 214 : 352.2081 -#> Model cost at call 216 : 352.2081 -#> Model cost at call 218 : 352.2049 -#> Model cost at call 219 : 352.2049 -#> Model cost at call 220 : 352.2049 -#> Model cost at call 226 : 352.2048 -#> Model cost at call 228 : 352.2048 -#> Model cost at call 231 : 352.2048 -#> Model cost at call 232 : 352.2048 -#> Model cost at call 238 : 352.2048 -#> Model cost at call 239 : 352.2048 -#> Model cost at call 251 : 352.2048 -#> Model cost at call 264 : 352.2048 -#> Model cost at call 283 : 352.2048 -#> Model cost at call 284 : 352.2048 -#> Model cost at call 285 : 352.2048 -#> Model cost at call 286 : 352.2048 -#> Optimisation by method Port successfully terminated.</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>)</div><div class='output co'>#> Model cost at call 1 : 10426.65 -#> Model cost at call 3 : 10426.65 -#> Model cost at call 6 : 1995.326 -#> Model cost at call 7 : 1995.322 -#> Model cost at call 8 : 1995.14 -#> Model cost at call 11 : 718.5568 -#> Model cost at call 12 : 718.5566 -#> Model cost at call 13 : 718.5563 -#> Model cost at call 16 : 408.9208 -#> Model cost at call 17 : 408.9204 -#> Model cost at call 18 : 408.9204 -#> Model cost at call 20 : 408.9203 -#> Model cost at call 21 : 402.7935 -#> Model cost at call 22 : 402.793 -#> Model cost at call 26 : 202.0443 -#> Model cost at call 28 : 202.0443 -#> Model cost at call 30 : 202.0443 -#> Model cost at call 31 : 196.438 -#> Model cost at call 36 : 196.1947 -#> Model cost at call 37 : 196.1947 -#> Model cost at call 41 : 192.9338 -#> Model cost at call 43 : 192.9338 -#> Model cost at call 45 : 192.9338 -#> Model cost at call 46 : 191.6452 -#> Model cost at call 47 : 191.6452 -#> Model cost at call 51 : 188.9328 -#> Model cost at call 54 : 188.9328 -#> Model cost at call 55 : 188.9328 -#> Model cost at call 56 : 183.6499 -#> Model cost at call 59 : 183.6499 -#> Model cost at call 62 : 181.9039 -#> Model cost at call 67 : 179.0543 -#> Model cost at call 68 : 179.0543 -#> Model cost at call 69 : 179.0543 -#> Model cost at call 70 : 179.0543 -#> Model cost at call 72 : 176.749 -#> Model cost at call 73 : 176.2321 -#> Model cost at call 74 : 176.232 -#> Model cost at call 75 : 176.232 -#> Model cost at call 76 : 176.232 -#> Model cost at call 78 : 175.3914 -#> Model cost at call 79 : 175.3914 -#> Model cost at call 81 : 175.3913 -#> Model cost at call 83 : 174.6257 -#> Model cost at call 84 : 174.6257 -#> Model cost at call 89 : 174.1476 -#> Model cost at call 92 : 174.1476 -#> Model cost at call 93 : 174.1476 -#> Model cost at call 94 : 173.8512 -#> Model cost at call 99 : 173.6987 -#> Model cost at call 104 : 173.6813 -#> Model cost at call 105 : 173.6813 -#> Model cost at call 106 : 173.6813 -#> Model cost at call 107 : 173.6813 -#> Model cost at call 108 : 173.6813 -#> Model cost at call 109 : 173.6802 -#> Model cost at call 110 : 173.6802 -#> Model cost at call 111 : 173.6802 -#> Model cost at call 112 : 173.6802 -#> Model cost at call 113 : 173.6802 -#> Model cost at call 114 : 173.6799 -#> Model cost at call 116 : 173.6799 -#> Model cost at call 118 : 173.6799 -#> Model cost at call 119 : 173.6799 -#> Model cost at call 120 : 173.6799 -#> Model cost at call 129 : 173.6799 -#> Model cost at call 141 : 173.6799 -#> Optimisation by method Port successfully terminated.</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>)</div><div class='output co'>#> Model cost at call 1 : 18365.33 -#> Model cost at call 2 : 18365.33 -#> Model cost at call 8 : 11666.4 -#> Model cost at call 9 : 10992.15 -#> Model cost at call 10 : 10992.13 -#> Model cost at call 11 : 10991.95 -#> Model cost at call 12 : 10991.17 -#> Model cost at call 14 : 10990.65 -#> Model cost at call 17 : 3940.801 -#> Model cost at call 20 : 3940.8 -#> Model cost at call 22 : 3940.798 -#> Model cost at call 24 : 3241.199 -#> Model cost at call 27 : 3241.198 -#> Model cost at call 30 : 3241.192 -#> Model cost at call 31 : 1518.749 -#> Model cost at call 37 : 1518.747 -#> Model cost at call 39 : 1091.836 -#> Model cost at call 42 : 1091.835 -#> Model cost at call 43 : 1091.835 -#> Model cost at call 44 : 1091.804 -#> Model cost at call 46 : 927.8538 -#> Model cost at call 49 : 927.8529 -#> Model cost at call 53 : 638.102 -#> Model cost at call 56 : 638.1019 -#> Model cost at call 58 : 638.1018 -#> Model cost at call 61 : 560.4352 -#> Model cost at call 62 : 560.435 -#> Model cost at call 63 : 560.4327 -#> Model cost at call 68 : 423.9629 -#> Model cost at call 69 : 423.9629 -#> Model cost at call 70 : 423.9629 -#> Model cost at call 71 : 423.9628 -#> Model cost at call 73 : 423.9628 -#> Model cost at call 75 : 395.8015 -#> Model cost at call 78 : 395.8013 -#> Model cost at call 79 : 395.8013 -#> Model cost at call 83 : 365.6975 -#> Model cost at call 84 : 365.6975 -#> Model cost at call 88 : 365.6975 -#> Model cost at call 91 : 362.9843 -#> Model cost at call 93 : 362.9843 -#> Model cost at call 98 : 361.5506 -#> Model cost at call 99 : 361.5506 -#> Model cost at call 100 : 361.5505 -#> Model cost at call 105 : 359.0492 -#> Model cost at call 106 : 359.0492 -#> Model cost at call 112 : 357.6574 -#> Model cost at call 113 : 357.6574 -#> Model cost at call 114 : 357.6574 -#> Model cost at call 115 : 357.6574 -#> Model cost at call 119 : 355.4518 -#> Model cost at call 120 : 355.4518 -#> Model cost at call 127 : 354.9045 -#> Model cost at call 129 : 354.9045 -#> Model cost at call 131 : 354.9045 -#> Model cost at call 134 : 354.4168 -#> Model cost at call 135 : 354.4168 -#> Model cost at call 137 : 354.4167 -#> Model cost at call 141 : 353.7901 -#> Model cost at call 142 : 353.7901 -#> Model cost at call 143 : 353.7899 -#> Model cost at call 149 : 353.3233 -#> Model cost at call 151 : 353.3233 -#> Model cost at call 154 : 353.3233 -#> Model cost at call 156 : 353.2939 -#> Model cost at call 158 : 353.2938 -#> Model cost at call 159 : 353.2938 -#> Model cost at call 160 : 353.2938 -#> Model cost at call 163 : 353.0571 -#> Model cost at call 165 : 353.0571 -#> Model cost at call 170 : 352.9457 -#> Model cost at call 171 : 352.7458 -#> Model cost at call 173 : 352.7457 -#> Model cost at call 178 : 352.6377 -#> Model cost at call 180 : 352.6377 -#> Model cost at call 183 : 352.6377 -#> Model cost at call 185 : 352.5377 -#> Model cost at call 187 : 352.5377 -#> Model cost at call 188 : 352.5377 -#> Model cost at call 191 : 352.5377 -#> Model cost at call 193 : 352.4479 -#> Model cost at call 195 : 352.4479 -#> Model cost at call 198 : 352.4479 -#> Model cost at call 200 : 352.4021 -#> Model cost at call 202 : 352.4021 -#> Model cost at call 205 : 352.4021 -#> Model cost at call 207 : 352.3465 -#> Model cost at call 210 : 352.3465 -#> Model cost at call 214 : 352.3031 -#> Model cost at call 216 : 352.3031 -#> Model cost at call 221 : 352.2632 -#> Model cost at call 223 : 352.2632 -#> Model cost at call 228 : 352.2367 -#> Model cost at call 230 : 352.2367 -#> Model cost at call 231 : 352.2367 -#> Model cost at call 233 : 352.2367 -#> Model cost at call 235 : 352.215 -#> Model cost at call 238 : 352.215 -#> Model cost at call 239 : 352.215 -#> Model cost at call 242 : 352.207 -#> Model cost at call 245 : 352.207 -#> Model cost at call 250 : 352.2053 -#> Model cost at call 251 : 352.2053 -#> Model cost at call 253 : 352.2053 -#> Model cost at call 256 : 352.2053 -#> Model cost at call 258 : 352.2053 -#> Model cost at call 259 : 352.2052 -#> Model cost at call 260 : 352.2052 -#> Model cost at call 263 : 352.2052 -#> Model cost at call 271 : 352.2048 -#> Model cost at call 273 : 352.2048 -#> Model cost at call 274 : 352.2048 -#> Model cost at call 281 : 352.2048 -#> Model cost at call 282 : 352.2048 -#> Model cost at call 286 : 352.2048 -#> Model cost at call 289 : 352.2048 -#> Model cost at call 294 : 352.2048 -#> Model cost at call 296 : 352.2048 -#> Model cost at call 300 : 352.2048 -#> Model cost at call 307 : 352.2048 -#> Model cost at call 325 : 352.2048 -#> Model cost at call 331 : 352.2048 -#> Model cost at call 333 : 352.2048 -#> Optimisation by method Port successfully terminated.</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'>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>) + <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='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>)</div><div class='output co'>#> Model cost at call 1 : 15156.12 -#> Model cost at call 2 : 15156.12 -#> Model cost at call 6 : 8243.644 -#> Model cost at call 12 : 6290.714 -#> Model cost at call 13 : 6290.684 -#> Model cost at call 15 : 6290.453 -#> Model cost at call 18 : 1700.75 -#> Model cost at call 20 : 1700.612 -#> Model cost at call 24 : 1190.923 -#> Model cost at call 26 : 1190.922 -#> Model cost at call 29 : 1017.417 -#> Model cost at call 31 : 1017.417 -#> Model cost at call 33 : 1017.416 -#> Model cost at call 34 : 644.0471 -#> Model cost at call 36 : 644.0469 -#> Model cost at call 38 : 644.0468 -#> Model cost at call 39 : 590.5024 -#> Model cost at call 41 : 590.5021 -#> Model cost at call 43 : 590.5015 -#> Model cost at call 44 : 543.2187 -#> Model cost at call 45 : 543.2183 -#> Model cost at call 46 : 543.2182 -#> Model cost at call 50 : 391.348 -#> Model cost at call 51 : 391.3479 -#> Model cost at call 56 : 386.4789 -#> Model cost at call 58 : 386.4789 -#> Model cost at call 60 : 386.4779 -#> Model cost at call 61 : 384.0686 -#> Model cost at call 63 : 384.0686 -#> Model cost at call 66 : 382.7812 -#> Model cost at call 68 : 382.7812 -#> Model cost at call 70 : 382.7812 -#> Model cost at call 71 : 378.9272 -#> Model cost at call 73 : 378.9272 -#> Model cost at call 75 : 378.9272 -#> Model cost at call 76 : 377.4846 -#> Model cost at call 78 : 377.4846 -#> Model cost at call 81 : 375.9738 -#> Model cost at call 83 : 375.9738 -#> Model cost at call 86 : 375.3387 -#> Model cost at call 88 : 375.3387 -#> Model cost at call 91 : 374.5774 -#> Model cost at call 93 : 374.5774 -#> Model cost at call 95 : 374.5774 -#> Model cost at call 96 : 373.5447 -#> Model cost at call 100 : 373.5446 -#> Model cost at call 102 : 373.2643 -#> Model cost at call 104 : 373.2643 -#> Model cost at call 107 : 372.6799 -#> Model cost at call 111 : 372.6798 -#> Model cost at call 114 : 372.6325 -#> Model cost at call 116 : 372.6325 -#> Model cost at call 119 : 372.6159 -#> Model cost at call 121 : 372.6159 -#> Model cost at call 123 : 372.6159 -#> Model cost at call 124 : 372.5845 -#> Model cost at call 126 : 372.5845 -#> Model cost at call 129 : 372.5375 -#> Model cost at call 130 : 372.4771 -#> Model cost at call 131 : 372.2008 -#> Model cost at call 132 : 371.4923 -#> Model cost at call 134 : 371.4923 -#> Model cost at call 137 : 371.3022 -#> Model cost at call 139 : 371.3022 -#> Model cost at call 143 : 371.2271 -#> Model cost at call 144 : 371.2271 -#> Model cost at call 148 : 371.2202 -#> Model cost at call 149 : 371.215 -#> Model cost at call 152 : 371.215 -#> Model cost at call 154 : 371.2136 -#> Model cost at call 155 : 371.2136 -#> Model cost at call 156 : 371.2136 -#> Model cost at call 160 : 371.2134 -#> Model cost at call 164 : 371.2134 -#> Model cost at call 167 : 371.2134 -#> Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 + <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'>summary</span>(<span class='no'>f.noweight</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 18 15:19:47 2016 -#> Date of summary: Fri Nov 18 15:19:47 2016 +#> Date of fit: Fri Nov 18 15:36:22 2016 +#> Date of summary: Fri Nov 18 15:36:22 2016 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1268,7 +565,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 185 model solutions performed in 0.748 s +#> Fitted with method Port using 185 model solutions performed in 0.752 s #> #> Weighting: none #> @@ -1377,146 +674,11 @@ #> 100 m1 31.04 3.198e+01 -9.416e-01 #> 100 m1 33.13 3.198e+01 1.148e+00 #> 120 m1 25.15 2.879e+01 -3.640e+00 -#> 120 m1 33.31 2.879e+01 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>)</div><div class='output co'>#> Model cost at call 1 : 15156.12 -#> Model cost at call 2 : 15156.12 -#> Model cost at call 6 : 8243.644 -#> Model cost at call 12 : 6290.714 -#> Model cost at call 13 : 6290.684 -#> Model cost at call 15 : 6290.453 -#> Model cost at call 18 : 1700.75 -#> Model cost at call 20 : 1700.612 -#> Model cost at call 24 : 1190.923 -#> Model cost at call 26 : 1190.922 -#> Model cost at call 29 : 1017.417 -#> Model cost at call 31 : 1017.417 -#> Model cost at call 33 : 1017.416 -#> Model cost at call 34 : 644.0471 -#> Model cost at call 36 : 644.0469 -#> Model cost at call 38 : 644.0468 -#> Model cost at call 39 : 590.5024 -#> Model cost at call 41 : 590.5021 -#> Model cost at call 43 : 590.5015 -#> Model cost at call 44 : 543.2187 -#> Model cost at call 45 : 543.2183 -#> Model cost at call 46 : 543.2182 -#> Model cost at call 50 : 391.348 -#> Model cost at call 51 : 391.3479 -#> Model cost at call 56 : 386.4789 -#> Model cost at call 58 : 386.4789 -#> Model cost at call 60 : 386.4779 -#> Model cost at call 61 : 384.0686 -#> Model cost at call 63 : 384.0686 -#> Model cost at call 66 : 382.7812 -#> Model cost at call 68 : 382.7812 -#> Model cost at call 70 : 382.7812 -#> Model cost at call 71 : 378.9272 -#> Model cost at call 73 : 378.9272 -#> Model cost at call 75 : 378.9272 -#> Model cost at call 76 : 377.4846 -#> Model cost at call 78 : 377.4846 -#> Model cost at call 81 : 375.9738 -#> Model cost at call 83 : 375.9738 -#> Model cost at call 86 : 375.3387 -#> Model cost at call 88 : 375.3387 -#> Model cost at call 91 : 374.5774 -#> Model cost at call 93 : 374.5774 -#> Model cost at call 95 : 374.5774 -#> Model cost at call 96 : 373.5447 -#> Model cost at call 100 : 373.5446 -#> Model cost at call 102 : 373.2643 -#> Model cost at call 104 : 373.2643 -#> Model cost at call 107 : 372.6799 -#> Model cost at call 111 : 372.6798 -#> Model cost at call 114 : 372.6325 -#> Model cost at call 116 : 372.6325 -#> Model cost at call 119 : 372.6159 -#> Model cost at call 121 : 372.6159 -#> Model cost at call 123 : 372.6159 -#> Model cost at call 124 : 372.5845 -#> Model cost at call 126 : 372.5845 -#> Model cost at call 129 : 372.5375 -#> Model cost at call 130 : 372.4771 -#> Model cost at call 131 : 372.2008 -#> Model cost at call 132 : 371.4923 -#> Model cost at call 134 : 371.4923 -#> Model cost at call 137 : 371.3022 -#> Model cost at call 139 : 371.3022 -#> Model cost at call 143 : 371.2271 -#> Model cost at call 144 : 371.2271 -#> Model cost at call 148 : 371.2202 -#> Model cost at call 149 : 371.215 -#> Model cost at call 152 : 371.215 -#> Model cost at call 154 : 371.2136 -#> Model cost at call 155 : 371.2136 -#> Model cost at call 156 : 371.2136 -#> Model cost at call 160 : 371.2134 -#> Model cost at call 164 : 371.2134 -#> Model cost at call 167 : 371.2134 -#> IRLS based on variance estimates for each observed variable -#> Initial variance estimates are: -#> parent m1 -#> 11.552581 7.421226 -#> Model cost at call 186 : 40 -#> Model cost at call 188 : 40 -#> Model cost at call 194 : 39.99562 -#> Model cost at call 195 : 39.99562 -#> Model cost at call 201 : 39.9956 -#> Model cost at call 203 : 39.99528 -#> Model cost at call 205 : 39.99528 -#> Model cost at call 207 : 39.99528 -#> Model cost at call 209 : 39.99515 -#> Model cost at call 211 : 39.99515 -#> Model cost at call 214 : 39.99515 -#> Model cost at call 215 : 39.99505 -#> Model cost at call 217 : 39.99505 -#> Model cost at call 219 : 39.99505 -#> Model cost at call 220 : 39.99489 -#> Model cost at call 222 : 39.99489 -#> Model cost at call 224 : 39.99489 -#> Model cost at call 225 : 39.99479 -#> Model cost at call 227 : 39.99479 -#> Model cost at call 231 : 39.99467 -#> Model cost at call 234 : 39.99467 -#> Model cost at call 235 : 39.99467 -#> Model cost at call 236 : 39.99458 -#> Model cost at call 238 : 39.99458 -#> Model cost at call 239 : 39.99458 -#> Model cost at call 241 : 39.99452 -#> Model cost at call 242 : 39.99444 -#> Model cost at call 243 : 39.99433 -#> Model cost at call 245 : 39.99433 -#> Model cost at call 248 : 39.99383 -#> Model cost at call 250 : 39.99383 -#> Model cost at call 251 : 39.99383 -#> Model cost at call 252 : 39.99383 -#> Model cost at call 253 : 39.9935 -#> Model cost at call 254 : 39.99309 -#> Model cost at call 256 : 39.99309 -#> Model cost at call 261 : 39.99295 -#> Model cost at call 264 : 39.99295 -#> Model cost at call 267 : 39.99281 -#> Model cost at call 272 : 39.99281 -#> Model cost at call 273 : 39.99278 -#> Model cost at call 276 : 39.99278 -#> Model cost at call 278 : 39.99278 -#> Model cost at call 279 : 39.99278 -#> Model cost at call 281 : 39.99278 -#> Model cost at call 283 : 39.99278 -#> Model cost at call 286 : 39.99278 -#> Model cost at call 289 : 39.99278 -#> Model cost at call 290 : 39.99278 -#> Iteration 1 yields variance estimates: -#> parent m1 -#> 11.573172 7.407968 -#> Sum of squared differences to last variance estimates: 1.5e-05 -#> Iteration 2 yields variance estimates: -#> parent m1 -#> 11.573405 7.407846 -#> Sum of squared differences to last variance estimates: 1.7e-09 -#> Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 +#> 120 m1 33.31 2.879e+01 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'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 18 15:19:50 2016 -#> Date of summary: Fri Nov 18 15:19:50 2016 +#> Date of fit: Fri Nov 18 15:36:24 2016 +#> Date of summary: Fri Nov 18 15:36:24 2016 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1524,7 +686,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 486 model solutions performed in 2.052 s +#> Fitted with method Port using 486 model solutions performed in 2.047 s #> #> Weighting: none then iterative reweighting method obs #> @@ -1633,62 +795,11 @@ #> 100 m1 31.04 3.199e+01 -9.497e-01 2.722 #> 100 m1 33.13 3.199e+01 1.140e+00 2.722 #> 120 m1 25.15 2.881e+01 -3.659e+00 2.722 -#> 120 m1 33.31 2.881e+01 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>)</div><div class='output co'>#> Model cost at call 1 : 19.80132 -#> Model cost at call 2 : 19.80132 -#> Model cost at call 6 : 10.68776 -#> Model cost at call 12 : 7.14353 -#> Model cost at call 13 : 7.143529 -#> Model cost at call 15 : 7.143511 -#> Model cost at call 18 : 2.189024 -#> Model cost at call 20 : 2.189019 -#> Model cost at call 23 : 1.587262 -#> Model cost at call 25 : 1.587261 -#> Model cost at call 26 : 1.58726 -#> Model cost at call 28 : 1.036794 -#> Model cost at call 29 : 1.036794 -#> Model cost at call 30 : 1.036793 -#> Model cost at call 34 : 0.4939937 -#> Model cost at call 35 : 0.4939937 -#> Model cost at call 38 : 0.4939936 -#> Model cost at call 39 : 0.4018506 -#> Model cost at call 43 : 0.4018505 -#> Model cost at call 45 : 0.3797853 -#> Model cost at call 51 : 0.3669779 -#> Model cost at call 55 : 0.3669778 -#> Model cost at call 56 : 0.3585654 -#> Model cost at call 57 : 0.3533252 -#> Model cost at call 62 : 0.3502505 -#> Model cost at call 64 : 0.3502505 -#> Model cost at call 66 : 0.3502505 -#> Model cost at call 67 : 0.3501535 -#> Model cost at call 72 : 0.3501187 -#> Model cost at call 74 : 0.3501187 -#> Model cost at call 75 : 0.3501187 -#> Model cost at call 77 : 0.3500378 -#> Model cost at call 79 : 0.3500378 -#> Model cost at call 83 : 0.349831 -#> Model cost at call 88 : 0.3494286 -#> Model cost at call 93 : 0.3488101 -#> Model cost at call 98 : 0.3481444 -#> Model cost at call 103 : 0.3478528 -#> Model cost at call 108 : 0.3478092 -#> Model cost at call 109 : 0.3478092 -#> Model cost at call 113 : 0.347807 -#> Model cost at call 116 : 0.347807 -#> Model cost at call 117 : 0.347807 -#> Model cost at call 119 : 0.347807 -#> Model cost at call 120 : 0.347807 -#> Model cost at call 125 : 0.347807 -#> Model cost at call 126 : 0.347807 -#> Model cost at call 128 : 0.347807 -#> Model cost at call 137 : 0.347807 -#> Model cost at call 148 : 0.347807 -#> Model cost at call 152 : 0.347807 -#> Model cost at call 154 : 0.347807 -#> Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 +#> 120 m1 33.31 2.881e+01 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'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 18 15:19:50 2016 -#> Date of summary: Fri Nov 18 15:19:50 2016 +#> Date of fit: Fri Nov 18 15:36:25 2016 +#> Date of summary: Fri Nov 18 15:36:25 2016 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1696,7 +807,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 155 model solutions performed in 0.636 s +#> Fitted with method Port using 155 model solutions performed in 0.653 s #> #> Weighting: mean #> @@ -1805,68 +916,12 @@ #> 100 m1 31.04 31.996124 -0.956124 #> 100 m1 33.13 31.996124 1.133876 #> 120 m1 25.15 28.824128 -3.674128 -#> 120 m1 33.31 28.824128 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'>subset</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>)</div><div class='output co'>#> Model cost at call 1 : 11.21571 -#> Model cost at call 2 : 11.21571 -#> Model cost at call 3 : 11.21571 -#> Model cost at call 8 : 11.12803 -#> Model cost at call 10 : 11.128 -#> Model cost at call 13 : 10.88016 -#> Model cost at call 15 : 10.88016 -#> Model cost at call 18 : 10.58819 -#> Model cost at call 20 : 10.58819 -#> Model cost at call 23 : 9.71699 -#> Model cost at call 24 : 7.794026 -#> Model cost at call 26 : 7.794026 -#> Model cost at call 31 : 6.89734 -#> Model cost at call 33 : 6.897337 -#> Model cost at call 36 : 5.2239 -#> Model cost at call 37 : 3.357735 -#> Model cost at call 41 : 3.357733 -#> Model cost at call 44 : 2.982323 -#> Model cost at call 46 : 2.982322 -#> Model cost at call 49 : 2.703946 -#> Model cost at call 50 : 2.080395 -#> Model cost at call 55 : 0.5307591 -#> Model cost at call 56 : 0.5307591 -#> Model cost at call 57 : 0.5307591 -#> Model cost at call 59 : 0.5307584 -#> Model cost at call 60 : 0.3240066 -#> Model cost at call 61 : 0.3240066 -#> Model cost at call 64 : 0.3240066 -#> Model cost at call 65 : 0.2601108 -#> Model cost at call 70 : 0.2414055 -#> Model cost at call 74 : 0.2414055 -#> Model cost at call 75 : 0.2404251 -#> Model cost at call 80 : 0.2404087 -#> Model cost at call 82 : 0.2404087 -#> Model cost at call 85 : 0.2404054 -#> Model cost at call 88 : 0.2404054 -#> Model cost at call 92 : 0.2403931 -#> Model cost at call 93 : 0.2403784 -#> Model cost at call 98 : 0.2403784 -#> Model cost at call 99 : 0.2403322 -#> Model cost at call 104 : 0.2402188 -#> Model cost at call 109 : 0.2400275 -#> Model cost at call 114 : 0.239844 -#> Model cost at call 119 : 0.2397153 -#> Model cost at call 120 : 0.2397153 -#> Model cost at call 124 : 0.2396978 -#> Model cost at call 126 : 0.2396978 -#> Model cost at call 130 : 0.239697 -#> Model cost at call 131 : 0.2396963 -#> Model cost at call 133 : 0.2396963 -#> Model cost at call 138 : 0.2396962 -#> Model cost at call 139 : 0.2396962 -#> Model cost at call 141 : 0.2396962 -#> Model cost at call 144 : 0.2396962 -#> Model cost at call 147 : 0.2396962 -#> Model cost at call 156 : 0.2396962 -#> Model cost at call 167 : 0.2396962 -#> Model cost at call 169 : 0.2396962 -#> Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 +#> 120 m1 33.31 28.824128 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'>subset</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'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 18 15:19:51 2016 -#> Date of summary: Fri Nov 18 15:19:51 2016 +#> Date of fit: Fri Nov 18 15:36:26 2016 +#> Date of summary: Fri Nov 18 15:36:26 2016 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1874,7 +929,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 174 model solutions performed in 0.789 s +#> Fitted with method Port using 174 model solutions performed in 0.708 s #> #> Weighting: manual #> @@ -1984,139 +1039,11 @@ <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'>c</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>)</div><div class='output co'>#> Model cost at call 1 : 3949.676 -#> Model cost at call 2 : 3949.676 -#> Model cost at call 5 : 3949.676 -#> Model cost at call 6 : 2252.859 -#> Model cost at call 8 : 2252.858 -#> Model cost at call 9 : 2252.826 -#> Model cost at call 13 : 1567.343 -#> Model cost at call 14 : 1567.342 -#> Model cost at call 15 : 1567.333 -#> Model cost at call 18 : 1041.524 -#> Model cost at call 19 : 1041.522 -#> Model cost at call 24 : 840.4649 -#> Model cost at call 26 : 840.4646 -#> Model cost at call 29 : 782.303 -#> Model cost at call 31 : 782.3028 -#> Model cost at call 34 : 664.539 -#> Model cost at call 36 : 664.5389 -#> Model cost at call 40 : 615.7908 -#> Model cost at call 42 : 615.7907 -#> Model cost at call 45 : 569.5971 -#> Model cost at call 47 : 569.597 -#> Model cost at call 50 : 517.3175 -#> Model cost at call 52 : 517.3173 -#> Model cost at call 56 : 464.8158 -#> Model cost at call 58 : 464.8157 -#> Model cost at call 62 : 433.0031 -#> Model cost at call 64 : 433.003 -#> Model cost at call 67 : 423.7407 -#> Model cost at call 69 : 423.7406 -#> Model cost at call 70 : 423.7392 -#> Model cost at call 72 : 346.2781 -#> Model cost at call 74 : 346.278 -#> Model cost at call 75 : 346.2779 -#> Model cost at call 78 : 334.5399 -#> Model cost at call 80 : 334.5398 -#> Model cost at call 83 : 324.139 -#> Model cost at call 85 : 324.1389 -#> Model cost at call 88 : 319.7514 -#> Model cost at call 90 : 319.7514 -#> Model cost at call 94 : 300.9426 -#> Model cost at call 96 : 300.9425 -#> Model cost at call 100 : 295.8803 -#> Model cost at call 102 : 295.8803 -#> Model cost at call 105 : 290.3288 -#> Model cost at call 107 : 290.3287 -#> Model cost at call 111 : 284.3257 -#> Model cost at call 113 : 284.3257 -#> Model cost at call 116 : 282.3972 -#> Model cost at call 118 : 282.3972 -#> Model cost at call 122 : 273.7385 -#> Model cost at call 124 : 273.7385 -#> Model cost at call 128 : 271.8379 -#> Model cost at call 130 : 271.8379 -#> Model cost at call 133 : 270.064 -#> Model cost at call 135 : 270.064 -#> Model cost at call 138 : 268.0107 -#> Model cost at call 140 : 268.0107 -#> Model cost at call 144 : 265.6194 -#> Model cost at call 146 : 265.6194 -#> Model cost at call 148 : 265.6194 -#> Model cost at call 149 : 263.4825 -#> Model cost at call 151 : 263.4825 -#> Model cost at call 153 : 263.4824 -#> Model cost at call 154 : 262.0988 -#> Model cost at call 156 : 262.0988 -#> Model cost at call 160 : 260.7078 -#> Model cost at call 162 : 260.7078 -#> Model cost at call 165 : 259.9453 -#> Model cost at call 167 : 259.9453 -#> Model cost at call 170 : 258.9623 -#> Model cost at call 172 : 258.9623 -#> Model cost at call 174 : 258.962 -#> Model cost at call 176 : 258.0119 -#> Model cost at call 178 : 258.0119 -#> Model cost at call 180 : 258.0119 -#> Model cost at call 181 : 257.8698 -#> Model cost at call 183 : 257.8698 -#> Model cost at call 186 : 256.8608 -#> Model cost at call 188 : 256.8608 -#> Model cost at call 190 : 256.8608 -#> Model cost at call 191 : 256.2306 -#> Model cost at call 193 : 256.2306 -#> Model cost at call 195 : 256.2305 -#> Model cost at call 196 : 255.7119 -#> Model cost at call 198 : 255.7118 -#> Model cost at call 201 : 255.3323 -#> Model cost at call 203 : 255.3323 -#> Model cost at call 205 : 255.3323 -#> Model cost at call 206 : 254.6653 -#> Model cost at call 208 : 254.6653 -#> Model cost at call 211 : 254.3984 -#> Model cost at call 213 : 254.3984 -#> Model cost at call 216 : 253.3199 -#> Model cost at call 218 : 253.3199 -#> Model cost at call 220 : 253.3198 -#> Model cost at call 221 : 252.4845 -#> Model cost at call 223 : 252.4845 -#> Model cost at call 225 : 252.4845 -#> Model cost at call 226 : 251.6917 -#> Model cost at call 229 : 251.6917 -#> Model cost at call 230 : 251.6917 -#> Model cost at call 233 : 251.0189 -#> Model cost at call 235 : 251.0189 -#> Model cost at call 238 : 250.6912 -#> Model cost at call 240 : 250.6912 -#> Model cost at call 243 : 250.5546 -#> Model cost at call 245 : 250.5546 -#> Model cost at call 248 : 250.466 -#> Model cost at call 249 : 250.3744 -#> Model cost at call 250 : 249.9681 -#> Model cost at call 251 : 249.2215 -#> Model cost at call 260 : 248.919 -#> Model cost at call 264 : 248.919 -#> Model cost at call 265 : 248.8876 -#> Model cost at call 267 : 248.8876 -#> Model cost at call 270 : 248.8521 -#> Model cost at call 271 : 248.8178 -#> Model cost at call 272 : 248.6837 -#> Model cost at call 273 : 248.5989 -#> Model cost at call 276 : 248.5989 -#> Model cost at call 278 : 248.5935 -#> Model cost at call 280 : 248.5935 -#> Model cost at call 282 : 248.5935 -#> Model cost at call 283 : 248.5902 -#> Model cost at call 284 : 248.5902 -#> Model cost at call 289 : 248.5902 -#> Model cost at call 298 : 248.5902 -#> Model cost at call 309 : 248.5902 -#> Model cost at call 311 : 248.5902 -#> Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 +<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'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 18 15:19:53 2016 -#> Date of summary: Fri Nov 18 15:19:53 2016 +#> Date of fit: Fri Nov 18 15:36:27 2016 +#> Date of summary: Fri Nov 18 15:36:27 2016 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -2124,7 +1051,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 316 model solutions performed in 1.337 s +#> Fitted with method Port using 316 model solutions performed in 1.288 s #> #> Weighting: manual #> @@ -2233,211 +1160,12 @@ #> 100 m1 31.04 31.969288 -0.929288 2 #> 100 m1 33.13 31.969288 1.160712 2 #> 120 m1 25.15 28.760615 -3.610615 2 -#> 120 m1 33.31 28.760615 4.549385 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'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>)</div><div class='output co'>#> Model cost at call 1 : 3949.676 -#> Model cost at call 2 : 3949.676 -#> Model cost at call 5 : 3949.676 -#> Model cost at call 6 : 2252.859 -#> Model cost at call 8 : 2252.858 -#> Model cost at call 9 : 2252.826 -#> Model cost at call 13 : 1567.343 -#> Model cost at call 14 : 1567.342 -#> Model cost at call 15 : 1567.333 -#> Model cost at call 18 : 1041.524 -#> Model cost at call 19 : 1041.522 -#> Model cost at call 24 : 840.4649 -#> Model cost at call 26 : 840.4646 -#> Model cost at call 29 : 782.303 -#> Model cost at call 31 : 782.3028 -#> Model cost at call 34 : 664.539 -#> Model cost at call 36 : 664.5389 -#> Model cost at call 40 : 615.7908 -#> Model cost at call 42 : 615.7907 -#> Model cost at call 45 : 569.5971 -#> Model cost at call 47 : 569.597 -#> Model cost at call 50 : 517.3175 -#> Model cost at call 52 : 517.3173 -#> Model cost at call 56 : 464.8158 -#> Model cost at call 58 : 464.8157 -#> Model cost at call 62 : 433.0031 -#> Model cost at call 64 : 433.003 -#> Model cost at call 67 : 423.7407 -#> Model cost at call 69 : 423.7406 -#> Model cost at call 70 : 423.7392 -#> Model cost at call 72 : 346.2781 -#> Model cost at call 74 : 346.278 -#> Model cost at call 75 : 346.2779 -#> Model cost at call 78 : 334.5399 -#> Model cost at call 80 : 334.5398 -#> Model cost at call 83 : 324.139 -#> Model cost at call 85 : 324.1389 -#> Model cost at call 88 : 319.7514 -#> Model cost at call 90 : 319.7514 -#> Model cost at call 94 : 300.9426 -#> Model cost at call 96 : 300.9425 -#> Model cost at call 100 : 295.8803 -#> Model cost at call 102 : 295.8803 -#> Model cost at call 105 : 290.3288 -#> Model cost at call 107 : 290.3287 -#> Model cost at call 111 : 284.3257 -#> Model cost at call 113 : 284.3257 -#> Model cost at call 116 : 282.3972 -#> Model cost at call 118 : 282.3972 -#> Model cost at call 122 : 273.7385 -#> Model cost at call 124 : 273.7385 -#> Model cost at call 128 : 271.8379 -#> Model cost at call 130 : 271.8379 -#> Model cost at call 133 : 270.064 -#> Model cost at call 135 : 270.064 -#> Model cost at call 138 : 268.0107 -#> Model cost at call 140 : 268.0107 -#> Model cost at call 144 : 265.6194 -#> Model cost at call 146 : 265.6194 -#> Model cost at call 148 : 265.6194 -#> Model cost at call 149 : 263.4825 -#> Model cost at call 151 : 263.4825 -#> Model cost at call 153 : 263.4824 -#> Model cost at call 154 : 262.0988 -#> Model cost at call 156 : 262.0988 -#> Model cost at call 160 : 260.7078 -#> Model cost at call 162 : 260.7078 -#> Model cost at call 165 : 259.9453 -#> Model cost at call 167 : 259.9453 -#> Model cost at call 170 : 258.9623 -#> Model cost at call 172 : 258.9623 -#> Model cost at call 174 : 258.962 -#> Model cost at call 176 : 258.0119 -#> Model cost at call 178 : 258.0119 -#> Model cost at call 180 : 258.0119 -#> Model cost at call 181 : 257.8698 -#> Model cost at call 183 : 257.8698 -#> Model cost at call 186 : 256.8608 -#> Model cost at call 188 : 256.8608 -#> Model cost at call 190 : 256.8608 -#> Model cost at call 191 : 256.2306 -#> Model cost at call 193 : 256.2306 -#> Model cost at call 195 : 256.2305 -#> Model cost at call 196 : 255.7119 -#> Model cost at call 198 : 255.7118 -#> Model cost at call 201 : 255.3323 -#> Model cost at call 203 : 255.3323 -#> Model cost at call 205 : 255.3323 -#> Model cost at call 206 : 254.6653 -#> Model cost at call 208 : 254.6653 -#> Model cost at call 211 : 254.3984 -#> Model cost at call 213 : 254.3984 -#> Model cost at call 216 : 253.3199 -#> Model cost at call 218 : 253.3199 -#> Model cost at call 220 : 253.3198 -#> Model cost at call 221 : 252.4845 -#> Model cost at call 223 : 252.4845 -#> Model cost at call 225 : 252.4845 -#> Model cost at call 226 : 251.6917 -#> Model cost at call 229 : 251.6917 -#> Model cost at call 230 : 251.6917 -#> Model cost at call 233 : 251.0189 -#> Model cost at call 235 : 251.0189 -#> Model cost at call 238 : 250.6912 -#> Model cost at call 240 : 250.6912 -#> Model cost at call 243 : 250.5546 -#> Model cost at call 245 : 250.5546 -#> Model cost at call 248 : 250.466 -#> Model cost at call 249 : 250.3744 -#> Model cost at call 250 : 249.9681 -#> Model cost at call 251 : 249.2215 -#> Model cost at call 260 : 248.919 -#> Model cost at call 264 : 248.919 -#> Model cost at call 265 : 248.8876 -#> Model cost at call 267 : 248.8876 -#> Model cost at call 270 : 248.8521 -#> Model cost at call 271 : 248.8178 -#> Model cost at call 272 : 248.6837 -#> Model cost at call 273 : 248.5989 -#> Model cost at call 276 : 248.5989 -#> Model cost at call 278 : 248.5935 -#> Model cost at call 280 : 248.5935 -#> Model cost at call 282 : 248.5935 -#> Model cost at call 283 : 248.5902 -#> Model cost at call 284 : 248.5902 -#> Model cost at call 289 : 248.5902 -#> Model cost at call 298 : 248.5902 -#> Model cost at call 309 : 248.5902 -#> Model cost at call 311 : 248.5902 -#> IRLS based on variance estimates for each observed variable -#> Initial variance estimates are: -#> parent m1 -#> 11.536305 7.443046 -#> Model cost at call 317 : 40 -#> Model cost at call 319 : 40 -#> Model cost at call 324 : 39.98891 -#> Model cost at call 325 : 39.9889 -#> Model cost at call 327 : 39.98886 -#> Model cost at call 331 : 39.98871 -#> Model cost at call 333 : 39.97254 -#> Model cost at call 336 : 39.97253 -#> Model cost at call 338 : 39.96929 -#> Model cost at call 340 : 39.96929 -#> Model cost at call 344 : 39.96849 -#> Model cost at call 346 : 39.96849 -#> Model cost at call 348 : 39.96849 -#> Model cost at call 349 : 39.96774 -#> Model cost at call 351 : 39.96774 -#> Model cost at call 353 : 39.96774 -#> Model cost at call 354 : 39.96714 -#> Model cost at call 356 : 39.96714 -#> Model cost at call 359 : 39.96617 -#> Model cost at call 361 : 39.96617 -#> Model cost at call 364 : 39.96606 -#> Model cost at call 366 : 39.96606 -#> Model cost at call 369 : 39.96551 -#> Model cost at call 371 : 39.96551 -#> Model cost at call 372 : 39.96551 -#> Model cost at call 375 : 39.96527 -#> Model cost at call 378 : 39.96527 -#> Model cost at call 379 : 39.96527 -#> Model cost at call 380 : 39.96525 -#> Model cost at call 382 : 39.96525 -#> Model cost at call 385 : 39.9651 -#> Model cost at call 387 : 39.9651 -#> Model cost at call 388 : 39.9651 -#> Model cost at call 390 : 39.96502 -#> Model cost at call 393 : 39.96502 -#> Model cost at call 396 : 39.96502 -#> Model cost at call 397 : 39.96467 -#> Model cost at call 398 : 39.96422 -#> Model cost at call 399 : 39.9624 -#> Model cost at call 400 : 39.95909 -#> Model cost at call 402 : 39.95909 -#> Model cost at call 405 : 39.9571 -#> Model cost at call 407 : 39.95709 -#> Model cost at call 413 : 39.95479 -#> Model cost at call 414 : 39.95479 -#> Model cost at call 415 : 39.95479 -#> Model cost at call 417 : 39.95479 -#> Model cost at call 419 : 39.95398 -#> Model cost at call 422 : 39.95398 -#> Model cost at call 424 : 39.95387 -#> Model cost at call 429 : 39.95384 -#> Model cost at call 432 : 39.95384 -#> Model cost at call 435 : 39.95384 -#> Model cost at call 437 : 39.95384 -#> Model cost at call 438 : 39.95384 -#> Model cost at call 446 : 39.95384 -#> Model cost at call 455 : 39.95384 -#> Model cost at call 469 : 39.95384 -#> Model cost at call 473 : 39.95384 -#> Iteration 1 yields variance estimates: -#> parent m1 -#> 11.572891 7.408116 -#> Sum of squared differences to last variance estimates: 7e-05 -#> Iteration 2 yields variance estimates: -#> parent m1 -#> 11.573402 7.407847 -#> Sum of squared differences to last variance estimates: 8.1e-09 -#> Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 +#> 120 m1 33.31 28.760615 4.549385 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'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 18 15:19:55 2016 -#> Date of summary: Fri Nov 18 15:19:55 2016 +#> Date of fit: Fri Nov 18 15:36:30 2016 +#> Date of summary: Fri Nov 18 15:36:30 2016 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -2445,7 +1173,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 648 model solutions performed in 2.716 s +#> Fitted with method Port using 648 model solutions performed in 2.694 s #> #> Weighting: manual then iterative reweighting method obs #> diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 764f1ab4..acc21bd4 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -6,8 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Function to plot the confidence intervals obtained using - list(list("mkinfit")) — mkinparplot • mkin</title> +<title>Function to plot the confidence intervals obtained using mkinfit — mkinparplot • mkin</title> <!-- jquery --> <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> @@ -78,8 +77,7 @@ <div class="row"> <div class="col-md-9 contents"> <div class="page-header"> - <h1>Function to plot the confidence intervals obtained using - list(list("mkinfit"))</h1> + <h1>Function to plot the confidence intervals obtained using mkinfit</h1> </div> @@ -104,9 +102,9 @@ <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'>T245</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"phenol"</span>), <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>), - <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"anisole"</span>)), - <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output 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'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='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'>c</span>(<span class='st'>"phenol"</span>), <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>), + <span class='kw'>phenol</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"anisole"</span>)), + <span class='kw'>anisole</span> <span class='kw'>=</span> <span class='fu'><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'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>), <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='fu'>mkinparplot</span>(<span class='no'>fit</span>)</div><img src='mkinparplot-4.png' alt='' width='540' height='400' /></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> diff --git a/docs/reference/mmkin-10.png b/docs/reference/mmkin-10.png Binary files differnew file mode 100644 index 00000000..9e40d451 --- /dev/null +++ b/docs/reference/mmkin-10.png diff --git a/docs/reference/mmkin-12.png b/docs/reference/mmkin-12.png Binary files differnew file mode 100644 index 00000000..9e40d451 --- /dev/null +++ b/docs/reference/mmkin-12.png diff --git a/docs/reference/mmkin-14.png b/docs/reference/mmkin-14.png Binary files differindex 9e40d451..72cfc5e7 100644 --- a/docs/reference/mmkin-14.png +++ b/docs/reference/mmkin-14.png diff --git a/docs/reference/mmkin-16.png b/docs/reference/mmkin-16.png Binary files differindex 72cfc5e7..0b315b1a 100644 --- a/docs/reference/mmkin-16.png +++ b/docs/reference/mmkin-16.png diff --git a/docs/reference/mmkin-18.png b/docs/reference/mmkin-18.png Binary files differindex 0b315b1a..b98940ff 100644 --- a/docs/reference/mmkin-18.png +++ b/docs/reference/mmkin-18.png diff --git a/docs/reference/mmkin-20.png b/docs/reference/mmkin-20.png Binary files differindex b98940ff..c2e9e5ae 100644 --- a/docs/reference/mmkin-20.png +++ b/docs/reference/mmkin-20.png diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 0e39dac0..45a246f9 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -139,1091 +139,32 @@ <span class='no'>datasets</span> <span class='kw'><-</span> <span class='fu'>lapply</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'>names</span>(<span class='no'>datasets</span>) <span class='kw'><-</span> <span class='fu'>paste</span>(<span class='st'>"Dataset"</span>, <span class='fl'>1</span>:<span class='fl'>3</span>) -<span class='no'>time_default</span> <span class='kw'><-</span> <span class='fu'>system.time</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='no'>time_1</span> <span class='kw'><-</span> <span class='fu'>system.time</span>(<span class='no'>fits.1</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>))</div><div class='output co'>#> Model cost at call 1 : 31054.59 -#> Model cost at call 3 : 31054.59 -#> Model cost at call 8 : 15089.57 -#> Model cost at call 9 : 11464.3 -#> Model cost at call 11 : 11464.1 -#> Model cost at call 16 : 5723.32 -#> Model cost at call 17 : 5723.318 -#> Model cost at call 19 : 5723.304 -#> Model cost at call 21 : 5723.304 -#> Model cost at call 24 : 3968.126 -#> Model cost at call 25 : 3968.124 -#> Model cost at call 28 : 3968.119 -#> Model cost at call 31 : 3416.421 -#> Model cost at call 32 : 3416.42 -#> Model cost at call 36 : 3416.418 -#> Model cost at call 38 : 866.5564 -#> Model cost at call 42 : 866.5557 -#> Model cost at call 45 : 670.4833 -#> Model cost at call 47 : 670.476 -#> Model cost at call 53 : 312.9905 -#> Model cost at call 57 : 312.9904 -#> Model cost at call 58 : 312.9904 -#> Model cost at call 61 : 287.8916 -#> Model cost at call 63 : 287.8916 -#> Model cost at call 66 : 287.8916 -#> Model cost at call 69 : 284.5441 -#> Model cost at call 71 : 284.5441 -#> Model cost at call 73 : 284.5441 -#> Model cost at call 76 : 283.4533 -#> Model cost at call 78 : 283.4533 -#> Model cost at call 83 : 282.1356 -#> Model cost at call 85 : 282.1356 -#> Model cost at call 88 : 282.1356 -#> Model cost at call 90 : 280.7846 -#> Model cost at call 92 : 280.7846 -#> Model cost at call 95 : 280.7846 -#> Model cost at call 97 : 278.4856 -#> Model cost at call 98 : 274.5025 -#> Model cost at call 99 : 269.2866 -#> Model cost at call 101 : 269.2866 -#> Model cost at call 102 : 269.2866 -#> Model cost at call 103 : 269.2866 -#> Model cost at call 106 : 254.1284 -#> Model cost at call 108 : 254.1283 -#> Model cost at call 109 : 254.1283 -#> Model cost at call 112 : 254.128 -#> Model cost at call 114 : 233.1376 -#> Model cost at call 116 : 233.1376 -#> Model cost at call 118 : 233.1375 -#> Model cost at call 121 : 227.5879 -#> Model cost at call 124 : 227.5879 -#> Model cost at call 125 : 227.5878 -#> Model cost at call 129 : 217.0041 -#> Model cost at call 133 : 217.0041 -#> Model cost at call 135 : 217.0041 -#> Model cost at call 136 : 215.1367 -#> Model cost at call 138 : 215.1367 -#> Model cost at call 143 : 213.3794 -#> Model cost at call 145 : 213.3794 -#> Model cost at call 150 : 211.0201 -#> Model cost at call 152 : 211.0201 -#> Model cost at call 154 : 211.0201 -#> Model cost at call 155 : 211.0201 -#> Model cost at call 157 : 210.6426 -#> Model cost at call 159 : 210.6426 -#> Model cost at call 160 : 210.6425 -#> Model cost at call 164 : 207.6331 -#> Model cost at call 167 : 207.6331 -#> Model cost at call 171 : 206.2366 -#> Model cost at call 173 : 206.2366 -#> Model cost at call 174 : 206.2366 -#> Model cost at call 178 : 204.8117 -#> Model cost at call 180 : 204.8117 -#> Model cost at call 185 : 204.7988 -#> Model cost at call 187 : 204.7988 -#> Model cost at call 190 : 204.7988 -#> Model cost at call 192 : 203.5122 -#> Model cost at call 194 : 203.5122 -#> Model cost at call 197 : 203.5122 -#> Model cost at call 198 : 203.5122 -#> Model cost at call 199 : 203.354 -#> Model cost at call 201 : 203.354 -#> Model cost at call 204 : 203.354 -#> Model cost at call 206 : 202.6825 -#> Model cost at call 208 : 202.6825 -#> Model cost at call 209 : 202.6825 -#> Model cost at call 212 : 202.6825 -#> Model cost at call 213 : 202.4582 -#> Model cost at call 215 : 202.4582 -#> Model cost at call 220 : 202.3261 -#> Model cost at call 222 : 202.3261 -#> Model cost at call 227 : 202.2306 -#> Model cost at call 229 : 202.2306 -#> Model cost at call 231 : 202.2306 -#> Model cost at call 234 : 202.115 -#> Model cost at call 236 : 202.115 -#> Model cost at call 238 : 202.115 -#> Model cost at call 241 : 202.0397 -#> Model cost at call 243 : 202.0397 -#> Model cost at call 248 : 201.8989 -#> Model cost at call 249 : 201.8551 -#> Model cost at call 252 : 201.8551 -#> Model cost at call 257 : 201.676 -#> Model cost at call 259 : 201.676 -#> Model cost at call 264 : 201.6285 -#> Model cost at call 266 : 201.6285 -#> Model cost at call 270 : 201.6284 -#> Model cost at call 271 : 201.5876 -#> Model cost at call 272 : 201.5876 -#> Model cost at call 278 : 201.5317 -#> Model cost at call 279 : 201.5317 -#> Model cost at call 286 : 201.5207 -#> Model cost at call 287 : 201.5207 -#> Model cost at call 289 : 201.5207 -#> Model cost at call 293 : 201.5207 -#> Model cost at call 294 : 201.5207 -#> Model cost at call 296 : 201.5174 -#> Model cost at call 301 : 201.5174 -#> Model cost at call 304 : 201.5169 -#> Model cost at call 305 : 201.5169 -#> Model cost at call 306 : 201.5169 -#> Model cost at call 309 : 201.5169 -#> Model cost at call 312 : 201.5169 -#> Model cost at call 314 : 201.5169 -#> Model cost at call 322 : 201.5169 -#> Model cost at call 325 : 201.5169 -#> Model cost at call 340 : 201.5169 -#> Optimisation by method Port successfully terminated. -#> Model cost at call 1 : 35974.4 -#> Model cost at call 3 : 35974.4 -#> Model cost at call 5 : 35974.4 -#> Model cost at call 7 : 35974.4 -#> Model cost at call 9 : 13270.14 -#> Model cost at call 10 : 12432.22 -#> Model cost at call 14 : 12432.12 -#> Model cost at call 16 : 12431.88 -#> Model cost at call 18 : 5356.271 -#> Model cost at call 19 : 5356.268 -#> Model cost at call 20 : 5356.251 -#> Model cost at call 22 : 5356.245 -#> Model cost at call 27 : 1507.839 -#> Model cost at call 33 : 1507.839 -#> Model cost at call 35 : 582.0818 -#> Model cost at call 36 : 582.0813 -#> Model cost at call 38 : 582.0802 -#> Model cost at call 40 : 582.0799 -#> Model cost at call 44 : 328.9337 -#> Model cost at call 45 : 328.9335 -#> Model cost at call 51 : 328.9328 -#> Model cost at call 53 : 313.4901 -#> Model cost at call 59 : 313.49 -#> Model cost at call 60 : 313.4899 -#> Model cost at call 61 : 308.6268 -#> Model cost at call 63 : 308.6267 -#> Model cost at call 69 : 302.4454 -#> Model cost at call 73 : 302.4453 -#> Model cost at call 77 : 298.0751 -#> Model cost at call 79 : 298.075 -#> Model cost at call 85 : 293.1404 -#> Model cost at call 86 : 289.6645 -#> Model cost at call 88 : 289.6645 -#> Model cost at call 95 : 288.1617 -#> Model cost at call 101 : 288.1616 -#> Model cost at call 102 : 288.1615 -#> Model cost at call 103 : 286.7649 -#> Model cost at call 109 : 286.7649 -#> Model cost at call 111 : 284.5224 -#> Model cost at call 117 : 284.5224 -#> Model cost at call 118 : 284.5224 -#> Model cost at call 119 : 281.3466 -#> Model cost at call 125 : 281.3466 -#> Model cost at call 127 : 274.0924 -#> Model cost at call 128 : 264.929 -#> Model cost at call 133 : 264.929 -#> Model cost at call 136 : 251.3329 -#> Model cost at call 137 : 251.3329 -#> Model cost at call 140 : 251.3329 -#> Model cost at call 141 : 251.3329 -#> Model cost at call 146 : 247.7019 -#> Model cost at call 147 : 247.7019 -#> Model cost at call 149 : 247.7018 -#> Model cost at call 154 : 247.3465 -#> Model cost at call 158 : 247.3465 -#> Model cost at call 160 : 247.3464 -#> Model cost at call 162 : 244.622 -#> Model cost at call 166 : 244.622 -#> Model cost at call 170 : 242.5961 -#> Model cost at call 171 : 241.6973 -#> Model cost at call 173 : 241.6973 -#> Model cost at call 174 : 241.6973 -#> Model cost at call 175 : 241.6973 -#> Model cost at call 179 : 238.8924 -#> Model cost at call 181 : 238.8923 -#> Model cost at call 187 : 236.0921 -#> Model cost at call 190 : 236.0921 -#> Model cost at call 192 : 236.092 -#> Model cost at call 195 : 233.9082 -#> Model cost at call 197 : 233.9082 -#> Model cost at call 201 : 233.9082 -#> Model cost at call 202 : 233.9082 -#> Model cost at call 203 : 228.1486 -#> Model cost at call 205 : 228.1486 -#> Model cost at call 206 : 228.1485 -#> Model cost at call 207 : 228.1485 -#> Model cost at call 211 : 225.0879 -#> Model cost at call 214 : 225.0879 -#> Model cost at call 216 : 225.0879 -#> Model cost at call 218 : 225.0879 -#> Model cost at call 219 : 220.9928 -#> Model cost at call 221 : 220.9928 -#> Model cost at call 227 : 219.1889 -#> Model cost at call 229 : 219.1888 -#> Model cost at call 233 : 219.1888 -#> Model cost at call 235 : 218.6966 -#> Model cost at call 238 : 218.6966 -#> Model cost at call 239 : 218.6966 -#> Model cost at call 240 : 218.6966 -#> Model cost at call 241 : 218.6966 -#> Model cost at call 242 : 218.6966 -#> Model cost at call 243 : 214.4307 -#> Model cost at call 247 : 214.4307 -#> Model cost at call 251 : 213.6076 -#> Model cost at call 253 : 213.6076 -#> Model cost at call 254 : 213.6076 -#> Model cost at call 256 : 213.6076 -#> Model cost at call 259 : 211.0287 -#> Model cost at call 262 : 211.0287 -#> Model cost at call 263 : 211.0287 -#> Model cost at call 267 : 209.6141 -#> Model cost at call 270 : 209.6141 -#> Model cost at call 271 : 209.6141 -#> Model cost at call 276 : 207.896 -#> Model cost at call 278 : 207.896 -#> Model cost at call 284 : 206.4468 -#> Model cost at call 286 : 206.4468 -#> Model cost at call 289 : 206.4468 -#> Model cost at call 292 : 205.8789 -#> Model cost at call 296 : 205.8789 -#> Model cost at call 298 : 205.8789 -#> Model cost at call 299 : 205.8789 -#> Model cost at call 300 : 204.2634 -#> Model cost at call 301 : 204.2634 -#> Model cost at call 303 : 204.2634 -#> Model cost at call 305 : 204.2634 -#> Model cost at call 308 : 203.5453 -#> Model cost at call 309 : 203.338 -#> Model cost at call 310 : 203.338 -#> Model cost at call 313 : 203.338 -#> Model cost at call 314 : 203.338 -#> Model cost at call 316 : 203.338 -#> Model cost at call 318 : 202.797 -#> Model cost at call 321 : 202.797 -#> Model cost at call 326 : 202.4377 -#> Model cost at call 327 : 202.4377 -#> Model cost at call 334 : 202.0027 -#> Model cost at call 335 : 202.0027 -#> Model cost at call 342 : 201.8249 -#> Model cost at call 344 : 201.8249 -#> Model cost at call 349 : 201.8249 -#> Model cost at call 351 : 201.7123 -#> Model cost at call 352 : 201.7123 -#> Model cost at call 359 : 201.6476 -#> Model cost at call 361 : 201.6476 -#> Model cost at call 365 : 201.6476 -#> Model cost at call 368 : 201.5827 -#> Model cost at call 371 : 201.5827 -#> Model cost at call 378 : 201.5531 -#> Model cost at call 379 : 201.5531 -#> Model cost at call 386 : 201.5531 -#> Model cost at call 390 : 201.537 -#> Model cost at call 391 : 201.537 -#> Model cost at call 401 : 201.5281 -#> Model cost at call 402 : 201.5281 -#> Model cost at call 404 : 201.5281 -#> Model cost at call 407 : 201.5281 -#> Model cost at call 413 : 201.5231 -#> Model cost at call 417 : 201.5231 -#> Model cost at call 418 : 201.5231 -#> Model cost at call 420 : 201.5231 -#> Model cost at call 426 : 201.5199 -#> Model cost at call 428 : 201.5199 -#> Model cost at call 439 : 201.5184 -#> Model cost at call 443 : 201.5184 -#> Model cost at call 444 : 201.5184 -#> Model cost at call 446 : 201.5184 -#> Model cost at call 454 : 201.5177 -#> Model cost at call 457 : 201.5177 -#> Model cost at call 469 : 201.5174 -#> Model cost at call 473 : 201.5174 -#> Model cost at call 476 : 201.5174 -#> Model cost at call 480 : 201.5174 -#> Model cost at call 483 : 201.5174 -#> Model cost at call 484 : 201.5171 -#> Model cost at call 487 : 201.5171 -#> Model cost at call 499 : 201.517 -#> Model cost at call 506 : 201.517 -#> Model cost at call 510 : 201.517 -#> Model cost at call 514 : 201.517 -#> Model cost at call 522 : 201.517 -#> Model cost at call 526 : 201.517 -#> Model cost at call 527 : 201.517 -#> Model cost at call 529 : 201.5169 -#> Model cost at call 536 : 201.5169 -#> Model cost at call 540 : 201.5169 -#> Model cost at call 544 : 201.5169 -#> Model cost at call 556 : 201.5169 -#> Model cost at call 557 : 201.5169 -#> Model cost at call 559 : 201.5169 -#> Model cost at call 574 : 201.5169 -#> Model cost at call 575 : 201.5169 -#> Model cost at call 578 : 201.5169 -#> Model cost at call 582 : 201.5169 -#> Model cost at call 586 : 201.5169 -#> Model cost at call 589 : 201.5169 -#> Model cost at call 590 : 201.5169 -#> Model cost at call 601 : 201.5169 -#> Model cost at call 604 : 201.5169 -#> Model cost at call 617 : 201.5169 -#> Model cost at call 632 : 201.5169 -#> Model cost at call 647 : 201.5169 -#> Model cost at call 662 : 201.5169 -#> Model cost at call 680 : 201.5169 -#> Optimisation by method Port successfully terminated. -#> Model cost at call 1 : 30689.89 -#> Model cost at call 3 : 30689.89 -#> Model cost at call 8 : 16294.04 -#> Model cost at call 9 : 12699.33 -#> Model cost at call 11 : 12699.26 -#> Model cost at call 14 : 12699.05 -#> Model cost at call 17 : 9202.163 -#> Model cost at call 18 : 9202.16 -#> Model cost at call 20 : 9202.147 -#> Model cost at call 22 : 9202.147 -#> Model cost at call 25 : 6601.043 -#> Model cost at call 26 : 6601.041 -#> Model cost at call 30 : 6601.04 -#> Model cost at call 32 : 4223.705 -#> Model cost at call 34 : 4223.703 -#> Model cost at call 39 : 4223.703 -#> Model cost at call 40 : 1443.507 -#> Model cost at call 45 : 1443.507 -#> Model cost at call 49 : 1191.267 -#> Model cost at call 51 : 1191.267 -#> Model cost at call 56 : 1186.498 -#> Model cost at call 57 : 1186.498 -#> Model cost at call 58 : 1186.497 -#> Model cost at call 59 : 1186.497 -#> Model cost at call 61 : 1186.496 -#> Model cost at call 62 : 1186.494 -#> Model cost at call 63 : 1130.799 -#> Model cost at call 64 : 1130.799 -#> Model cost at call 71 : 1126.363 -#> Model cost at call 73 : 1126.363 -#> Model cost at call 78 : 1122.848 -#> Model cost at call 80 : 1122.848 -#> Model cost at call 82 : 1122.848 -#> Model cost at call 85 : 1120.954 -#> Model cost at call 87 : 1120.954 -#> Model cost at call 88 : 1120.954 -#> Model cost at call 89 : 1120.954 -#> Model cost at call 92 : 1117.156 -#> Model cost at call 95 : 1117.156 -#> Model cost at call 96 : 1117.156 -#> Model cost at call 99 : 1116.894 -#> Model cost at call 101 : 1116.894 -#> Model cost at call 104 : 1116.894 -#> Model cost at call 106 : 1113.955 -#> Model cost at call 108 : 1113.955 -#> Model cost at call 112 : 1113.955 -#> Model cost at call 113 : 1113.03 -#> Model cost at call 115 : 1113.03 -#> Model cost at call 120 : 1111.643 -#> Model cost at call 122 : 1111.643 -#> Model cost at call 127 : 1109.657 -#> Model cost at call 129 : 1109.657 -#> Model cost at call 131 : 1109.657 -#> Model cost at call 134 : 1106.725 -#> Model cost at call 136 : 1106.725 -#> Model cost at call 137 : 1106.725 -#> Model cost at call 142 : 1106.005 -#> Model cost at call 144 : 1106.005 -#> Model cost at call 145 : 1106.005 -#> Model cost at call 147 : 1106.005 -#> Model cost at call 149 : 1105.268 -#> Model cost at call 151 : 1105.268 -#> Model cost at call 153 : 1105.268 -#> Model cost at call 156 : 1104.247 -#> Model cost at call 158 : 1104.247 -#> Model cost at call 159 : 1104.247 -#> Model cost at call 161 : 1104.247 -#> Model cost at call 163 : 1103.813 -#> Model cost at call 165 : 1103.813 -#> Model cost at call 167 : 1103.813 -#> Model cost at call 170 : 1103.075 -#> Model cost at call 172 : 1103.075 -#> Model cost at call 173 : 1103.075 -#> Model cost at call 177 : 1102.447 -#> Model cost at call 179 : 1102.447 -#> Model cost at call 180 : 1102.447 -#> Model cost at call 183 : 1102.447 -#> Model cost at call 184 : 1102.038 -#> Model cost at call 185 : 1101.712 -#> Model cost at call 186 : 1101.337 -#> Model cost at call 188 : 1101.337 -#> Model cost at call 193 : 1100.37 -#> Model cost at call 195 : 1100.37 -#> Model cost at call 197 : 1100.37 -#> Model cost at call 200 : 1099.46 -#> Model cost at call 202 : 1099.46 -#> Model cost at call 207 : 1099.262 -#> Model cost at call 209 : 1099.262 -#> Model cost at call 211 : 1099.262 -#> Model cost at call 212 : 1099.261 -#> Model cost at call 214 : 1099.227 -#> Model cost at call 216 : 1099.227 -#> Model cost at call 217 : 1099.227 -#> Model cost at call 218 : 1099.227 -#> Model cost at call 221 : 1098.331 -#> Model cost at call 223 : 1098.331 -#> Model cost at call 224 : 1098.331 -#> Model cost at call 230 : 1098.24 -#> Model cost at call 235 : 1098.24 -#> Model cost at call 236 : 1098.24 -#> Model cost at call 238 : 1098.231 -#> Model cost at call 240 : 1098.231 -#> Model cost at call 245 : 1098.228 -#> Model cost at call 247 : 1098.228 -#> Model cost at call 252 : 1098.221 -#> Model cost at call 254 : 1098.221 -#> Model cost at call 255 : 1098.221 -#> Model cost at call 258 : 1098.221 -#> Model cost at call 261 : 1098.214 -#> Model cost at call 263 : 1098.214 -#> Model cost at call 268 : 1098.204 -#> Model cost at call 269 : 1098.196 -#> Model cost at call 270 : 1098.187 -#> Model cost at call 272 : 1098.187 -#> Model cost at call 273 : 1098.187 -#> Model cost at call 279 : 1098.181 -#> Model cost at call 281 : 1098.181 -#> Model cost at call 282 : 1098.181 -#> Model cost at call 284 : 1098.181 -#> Model cost at call 285 : 1098.181 -#> Model cost at call 287 : 1098.172 -#> Model cost at call 291 : 1098.172 -#> Model cost at call 293 : 1098.172 -#> Model cost at call 294 : 1098.169 -#> Model cost at call 295 : 1098.169 -#> Model cost at call 296 : 1098.169 -#> Model cost at call 301 : 1098.169 -#> Model cost at call 305 : 1098.169 -#> Model cost at call 306 : 1098.169 -#> Model cost at call 309 : 1098.169 -#> Model cost at call 314 : 1098.169 -#> Model cost at call 318 : 1098.169 -#> Model cost at call 319 : 1098.169 -#> Model cost at call 321 : 1098.169 -#> Model cost at call 324 : 1098.169 -#> Model cost at call 325 : 1098.169 -#> Model cost at call 331 : 1098.169 -#> Model cost at call 333 : 1098.169 -#> Model cost at call 336 : 1098.169 -#> Model cost at call 342 : 1098.169 -#> Model cost at call 344 : 1098.169 -#> Model cost at call 348 : 1098.169 -#> Model cost at call 352 : 1098.169 -#> Model cost at call 357 : 1098.169 -#> Model cost at call 370 : 1098.169 -#> Model cost at call 385 : 1098.169 -#> Model cost at call 386 : 1098.169 -#> Optimisation by method Port successfully terminated. -#> Model cost at call 1 : 34499.23 -#> Model cost at call 3 : 34499.23 -#> Model cost at call 5 : 34499.23 -#> Model cost at call 7 : 34499.23 -#> Model cost at call 9 : 14274.95 -#> Model cost at call 10 : 14162.89 -#> Model cost at call 14 : 14162.68 -#> Model cost at call 18 : 13341.49 -#> Model cost at call 19 : 13341.48 -#> Model cost at call 20 : 13341.47 -#> Model cost at call 22 : 13341.44 -#> Model cost at call 27 : 10055.95 -#> Model cost at call 28 : 10055.95 -#> Model cost at call 30 : 10055.95 -#> Model cost at call 35 : 7732.384 -#> Model cost at call 36 : 7732.381 -#> Model cost at call 39 : 7732.381 -#> Model cost at call 44 : 6325.124 -#> Model cost at call 45 : 6325.122 -#> Model cost at call 47 : 6325.117 -#> Model cost at call 52 : 3732.612 -#> Model cost at call 54 : 3732.611 -#> Model cost at call 61 : 1371.768 -#> Model cost at call 64 : 1371.768 -#> Model cost at call 67 : 1371.768 -#> Model cost at call 70 : 1302.633 -#> Model cost at call 74 : 1302.633 -#> Model cost at call 75 : 1302.633 -#> Model cost at call 78 : 1298.854 -#> Model cost at call 82 : 1298.854 -#> Model cost at call 84 : 1298.854 -#> Model cost at call 86 : 1245.775 -#> Model cost at call 91 : 1245.775 -#> Model cost at call 94 : 1230.679 -#> Model cost at call 96 : 1230.679 -#> Model cost at call 100 : 1230.679 -#> Model cost at call 103 : 1227.471 -#> Model cost at call 105 : 1227.471 -#> Model cost at call 109 : 1227.471 -#> Model cost at call 111 : 1225.318 -#> Model cost at call 113 : 1225.318 -#> Model cost at call 117 : 1225.318 -#> Model cost at call 118 : 1225.318 -#> Model cost at call 119 : 1221.478 -#> Model cost at call 121 : 1221.478 -#> Model cost at call 127 : 1214.191 -#> Model cost at call 128 : 1203.986 -#> Model cost at call 129 : 1164.433 -#> Model cost at call 135 : 1164.433 -#> Model cost at call 140 : 1158.843 -#> Model cost at call 145 : 1158.843 -#> Model cost at call 148 : 1156.585 -#> Model cost at call 154 : 1156.585 -#> Model cost at call 156 : 1155.177 -#> Model cost at call 159 : 1155.177 -#> Model cost at call 161 : 1155.176 -#> Model cost at call 164 : 1151.603 -#> Model cost at call 166 : 1151.603 -#> Model cost at call 167 : 1151.603 -#> Model cost at call 169 : 1151.603 -#> Model cost at call 173 : 1150.467 -#> Model cost at call 175 : 1150.467 -#> Model cost at call 176 : 1150.467 -#> Model cost at call 181 : 1150.117 -#> Model cost at call 184 : 1150.117 -#> Model cost at call 185 : 1150.117 -#> Model cost at call 187 : 1150.117 -#> Model cost at call 188 : 1150.117 -#> Model cost at call 189 : 1149.03 -#> Model cost at call 193 : 1149.03 -#> Model cost at call 195 : 1149.03 -#> Model cost at call 197 : 1148.468 -#> Model cost at call 199 : 1148.468 -#> Model cost at call 205 : 1147.297 -#> Model cost at call 207 : 1147.297 -#> Model cost at call 211 : 1147.297 -#> Model cost at call 213 : 1146.841 -#> Model cost at call 216 : 1146.841 -#> Model cost at call 217 : 1146.841 -#> Model cost at call 219 : 1146.841 -#> Model cost at call 221 : 1144.548 -#> Model cost at call 223 : 1144.548 -#> Model cost at call 229 : 1143.258 -#> Model cost at call 231 : 1143.258 -#> Model cost at call 237 : 1141.772 -#> Model cost at call 239 : 1141.772 -#> Model cost at call 240 : 1141.772 -#> Model cost at call 241 : 1141.772 -#> Model cost at call 243 : 1141.772 -#> Model cost at call 245 : 1140.849 -#> Model cost at call 251 : 1140.849 -#> Model cost at call 252 : 1140.849 -#> Model cost at call 253 : 1139.456 -#> Model cost at call 259 : 1139.456 -#> Model cost at call 261 : 1137.678 -#> Model cost at call 263 : 1137.678 -#> Model cost at call 269 : 1135.358 -#> Model cost at call 270 : 1134.128 -#> Model cost at call 272 : 1134.128 -#> Model cost at call 280 : 1133.342 -#> Model cost at call 283 : 1133.342 -#> Model cost at call 286 : 1133.342 -#> Model cost at call 288 : 1133.229 -#> Model cost at call 292 : 1133.229 -#> Model cost at call 294 : 1133.229 -#> Model cost at call 295 : 1133.229 -#> Model cost at call 296 : 1132.641 -#> Model cost at call 300 : 1132.641 -#> Model cost at call 304 : 1132.126 -#> Model cost at call 310 : 1132.126 -#> Model cost at call 312 : 1131.169 -#> Model cost at call 318 : 1131.169 -#> Model cost at call 320 : 1130.405 -#> Model cost at call 324 : 1130.405 -#> Model cost at call 328 : 1129.635 -#> Model cost at call 330 : 1129.635 -#> Model cost at call 332 : 1129.635 -#> Model cost at call 334 : 1129.635 -#> Model cost at call 336 : 1128.526 -#> Model cost at call 338 : 1128.526 -#> Model cost at call 343 : 1128.526 -#> Model cost at call 344 : 1127.498 -#> Model cost at call 346 : 1127.498 -#> Model cost at call 350 : 1127.498 -#> Model cost at call 352 : 1126.06 -#> Model cost at call 353 : 1124.911 -#> Model cost at call 356 : 1124.911 -#> Model cost at call 362 : 1120.309 -#> Model cost at call 366 : 1120.309 -#> Model cost at call 368 : 1120.308 -#> Model cost at call 369 : 1120.308 -#> Model cost at call 370 : 1117.687 -#> Model cost at call 374 : 1117.687 -#> Model cost at call 375 : 1117.687 -#> Model cost at call 378 : 1112.013 -#> Model cost at call 379 : 1112.013 -#> Model cost at call 381 : 1112.013 -#> Model cost at call 386 : 1108.648 -#> Model cost at call 387 : 1108.251 -#> Model cost at call 388 : 1108.251 -#> Model cost at call 391 : 1108.251 -#> Model cost at call 392 : 1108.251 -#> Model cost at call 395 : 1104.73 -#> Model cost at call 396 : 1104.73 -#> Model cost at call 397 : 1104.73 -#> Model cost at call 403 : 1103.277 -#> Model cost at call 404 : 1103.277 -#> Model cost at call 411 : 1101.351 -#> Model cost at call 414 : 1101.351 -#> Model cost at call 416 : 1101.351 -#> Model cost at call 417 : 1101.351 -#> Model cost at call 419 : 1100.36 -#> Model cost at call 420 : 1100.36 -#> Model cost at call 421 : 1100.36 -#> Model cost at call 427 : 1099.596 -#> Model cost at call 431 : 1099.596 -#> Model cost at call 432 : 1099.596 -#> Model cost at call 435 : 1099.029 -#> Model cost at call 437 : 1099.029 -#> Model cost at call 444 : 1098.722 -#> Model cost at call 447 : 1098.722 -#> Model cost at call 448 : 1098.722 -#> Model cost at call 453 : 1098.441 -#> Model cost at call 455 : 1098.441 -#> Model cost at call 458 : 1098.441 -#> Model cost at call 463 : 1098.314 -#> Model cost at call 464 : 1098.314 -#> Model cost at call 469 : 1098.314 -#> Model cost at call 471 : 1098.314 -#> Model cost at call 475 : 1098.245 -#> Model cost at call 477 : 1098.245 -#> Model cost at call 480 : 1098.245 -#> Model cost at call 486 : 1098.209 -#> Model cost at call 487 : 1098.209 -#> Model cost at call 489 : 1098.209 -#> Model cost at call 493 : 1098.209 -#> Model cost at call 505 : 1098.209 -#> Model cost at call 506 : 1098.209 -#> Model cost at call 510 : 1098.209 -#> Model cost at call 518 : 1098.209 -#> Model cost at call 519 : 1098.209 -#> Model cost at call 522 : 1098.209 -#> Model cost at call 526 : 1098.209 -#> Model cost at call 528 : 1098.209 -#> Model cost at call 530 : 1098.209 -#> Model cost at call 533 : 1098.209 -#> Model cost at call 534 : 1098.209 -#> Model cost at call 536 : 1098.209 -#> Model cost at call 542 : 1098.209 -#> Model cost at call 549 : 1098.207 -#> Model cost at call 551 : 1098.207 -#> Model cost at call 552 : 1098.207 -#> Model cost at call 555 : 1098.207 -#> Model cost at call 564 : 1098.205 -#> Model cost at call 566 : 1098.205 -#> Model cost at call 567 : 1098.205 -#> Model cost at call 570 : 1098.205 -#> Model cost at call 579 : 1098.2 -#> Model cost at call 580 : 1098.191 -#> Model cost at call 581 : 1098.191 -#> Model cost at call 583 : 1098.191 -#> Model cost at call 586 : 1098.191 -#> Model cost at call 587 : 1098.191 -#> Model cost at call 589 : 1098.191 -#> Model cost at call 595 : 1098.186 -#> Model cost at call 596 : 1098.186 -#> Model cost at call 606 : 1098.18 -#> Model cost at call 609 : 1098.18 -#> Model cost at call 610 : 1098.18 -#> Model cost at call 616 : 1098.177 -#> Model cost at call 619 : 1098.177 -#> Model cost at call 620 : 1098.177 -#> Model cost at call 627 : 1098.173 -#> Model cost at call 630 : 1098.173 -#> Model cost at call 631 : 1098.173 -#> Model cost at call 636 : 1098.173 -#> Model cost at call 641 : 1098.172 -#> Model cost at call 642 : 1098.172 -#> Model cost at call 653 : 1098.172 -#> Model cost at call 654 : 1098.172 -#> Model cost at call 664 : 1098.172 -#> Model cost at call 669 : 1098.172 -#> Model cost at call 671 : 1098.172 -#> Model cost at call 675 : 1098.172 -#> Model cost at call 678 : 1098.172 -#> Model cost at call 680 : 1098.172 -#> Model cost at call 683 : 1098.172 -#> Model cost at call 684 : 1098.172 -#> Model cost at call 686 : 1098.172 -#> Model cost at call 690 : 1098.172 -#> Model cost at call 702 : 1098.172 -#> Model cost at call 704 : 1098.172 -#> Model cost at call 708 : 1098.172 -#> Model cost at call 721 : 1098.172 -#> Model cost at call 723 : 1098.172 -#> Model cost at call 736 : 1098.172 -#> Model cost at call 738 : 1098.172 -#> Model cost at call 751 : 1098.172 -#> Model cost at call 753 : 1098.172 -#> Model cost at call 766 : 1098.172 -#> Model cost at call 767 : 1098.172 -#> Model cost at call 768 : 1098.172 -#> Model cost at call 770 : 1098.172 -#> Model cost at call 783 : 1098.172 -#> Model cost at call 784 : 1098.172 -#> Model cost at call 785 : 1098.172 -#> Model cost at call 799 : 1098.172 -#> Model cost at call 800 : 1098.172 -#> Model cost at call 814 : 1098.172 -#> Model cost at call 815 : 1098.172 -#> Model cost at call 816 : 1098.172 -#> Model cost at call 822 : 1098.172 -#> Model cost at call 830 : 1098.172 -#> Model cost at call 831 : 1098.172 -#> Model cost at call 834 : 1098.172 -#> Model cost at call 845 : 1098.172 -#> Model cost at call 846 : 1098.172 -#> Model cost at call 849 : 1098.172 -#> Model cost at call 860 : 1098.171 -#> Model cost at call 861 : 1098.171 -#> Model cost at call 864 : 1098.171 -#> Model cost at call 875 : 1098.171 -#> Model cost at call 876 : 1098.171 -#> Model cost at call 879 : 1098.171 -#> Model cost at call 890 : 1098.17 -#> Model cost at call 891 : 1098.17 -#> Model cost at call 894 : 1098.17 -#> Model cost at call 904 : 1098.169 -#> Model cost at call 905 : 1098.169 -#> Model cost at call 908 : 1098.169 -#> Model cost at call 909 : 1098.169 -#> Model cost at call 919 : 1098.169 -#> Model cost at call 921 : 1098.169 -#> Model cost at call 931 : 1098.169 -#> Model cost at call 932 : 1098.169 -#> Model cost at call 934 : 1098.169 -#> Model cost at call 936 : 1098.169 -#> Model cost at call 937 : 1098.169 -#> Model cost at call 944 : 1098.169 -#> Model cost at call 947 : 1098.169 -#> Model cost at call 949 : 1098.169 -#> Model cost at call 951 : 1098.169 -#> Model cost at call 952 : 1098.169 -#> Model cost at call 954 : 1098.169 -#> Model cost at call 964 : 1098.169 -#> Model cost at call 967 : 1098.169 -#> Model cost at call 969 : 1098.169 -#> Model cost at call 982 : 1098.169 -#> Model cost at call 1017 : 1098.169 -#> Model cost at call 1018 : 1098.169 -#> Model cost at call 1022 : 1098.169 -#> Model cost at call 1029 : 1098.169 -#> Model cost at call 1033 : 1098.169 -#> Model cost at call 1038 : 1098.169 -#> Model cost at call 1048 : 1098.169 -#> Model cost at call 1049 : 1098.169 -#> Model cost at call 1055 : 1098.169 -#> Model cost at call 1063 : 1098.169 -#> Model cost at call 1074 : 1098.169 -#> Model cost at call 1079 : 1098.169 -#> Model cost at call 1089 : 1098.169 -#> Model cost at call 1120 : 1098.169 -#> Model cost at call 1124 : 1098.169 -#> Model cost at call 1139 : 1098.169 -#> Model cost at call 1154 : 1098.169 -#> Model cost at call 1170 : 1098.169 -#> Model cost at call 1185 : 1098.169 -#> Model cost at call 1200 : 1098.169 -#> Model cost at call 1215 : 1098.169 -#> Model cost at call 1231 : 1098.169 -#> Model cost at call 1246 : 1098.169 -#> Model cost at call 1247 : 1098.169 -#> Model cost at call 1248 : 1098.169 -#> Model cost at call 1258 : 1098.169 -#> Model cost at call 1263 : 1098.169 -#> Model cost at call 1278 : 1098.169 -#> Model cost at call 1295 : 1098.169 -#> Model cost at call 1296 : 1098.169 -#> Model cost at call 1297 : 1098.169 -#> Model cost at call 1298 : 1098.169 -#> Model cost at call 1306 : 1098.169 -#> Model cost at call 1308 : 1098.169 -#> Optimisation by method Port successfully terminated. -#> Model cost at call 1 : 31389.19 -#> Model cost at call 3 : 31389.19 -#> Model cost at call 8 : 15003.41 -#> Model cost at call 9 : 11136.21 -#> Model cost at call 11 : 11135.87 -#> Model cost at call 16 : 4800.182 -#> Model cost at call 17 : 4800.181 -#> Model cost at call 19 : 4800.163 -#> Model cost at call 24 : 3036.068 -#> Model cost at call 25 : 3036.068 -#> Model cost at call 26 : 3036.052 -#> Model cost at call 31 : 1361.371 -#> Model cost at call 33 : 1361.371 -#> Model cost at call 40 : 494.6738 -#> Model cost at call 41 : 494.6736 -#> Model cost at call 45 : 494.6734 -#> Model cost at call 48 : 260.2631 -#> Model cost at call 49 : 260.2629 -#> Model cost at call 55 : 248.3035 -#> Model cost at call 56 : 248.3034 -#> Model cost at call 57 : 248.3023 -#> Model cost at call 62 : 171.6337 -#> Model cost at call 63 : 171.6337 -#> Model cost at call 70 : 167.3473 -#> Model cost at call 72 : 167.3473 -#> Model cost at call 73 : 167.3473 -#> Model cost at call 78 : 165.9868 -#> Model cost at call 80 : 165.9868 -#> Model cost at call 83 : 165.9868 -#> Model cost at call 85 : 165.2025 -#> Model cost at call 87 : 165.2024 -#> Model cost at call 92 : 163.5932 -#> Model cost at call 94 : 163.5932 -#> Model cost at call 96 : 163.5932 -#> Model cost at call 99 : 159.4289 -#> Model cost at call 100 : 147.5939 -#> Model cost at call 105 : 147.5939 -#> Model cost at call 108 : 139.3925 -#> Model cost at call 113 : 139.3925 -#> Model cost at call 115 : 139.392 -#> Model cost at call 116 : 123.9799 -#> Model cost at call 117 : 123.9798 -#> Model cost at call 118 : 123.9795 -#> Model cost at call 124 : 103.8653 -#> Model cost at call 125 : 103.8653 -#> Model cost at call 126 : 103.8652 -#> Model cost at call 131 : 96.14276 -#> Model cost at call 134 : 96.14275 -#> Model cost at call 135 : 96.14274 -#> Model cost at call 139 : 95.96056 -#> Model cost at call 141 : 95.96056 -#> Model cost at call 142 : 95.96056 -#> Model cost at call 145 : 95.96056 -#> Model cost at call 146 : 95.90851 -#> Model cost at call 148 : 95.9085 -#> Model cost at call 153 : 95.84671 -#> Model cost at call 155 : 95.8467 -#> Model cost at call 161 : 95.82479 -#> Model cost at call 163 : 95.82479 -#> Model cost at call 166 : 95.82479 -#> Model cost at call 168 : 95.81938 -#> Model cost at call 170 : 95.81938 -#> Model cost at call 174 : 95.81938 -#> Model cost at call 175 : 95.81558 -#> Model cost at call 177 : 95.81558 -#> Model cost at call 178 : 95.81558 -#> Model cost at call 180 : 95.81558 -#> Model cost at call 181 : 95.81558 -#> Model cost at call 183 : 95.81558 -#> Model cost at call 184 : 95.8118 -#> Model cost at call 186 : 95.8118 -#> Model cost at call 188 : 95.8118 -#> Model cost at call 191 : 95.80885 -#> Model cost at call 192 : 95.80353 -#> Model cost at call 193 : 95.78121 -#> Model cost at call 194 : 95.72164 -#> Model cost at call 197 : 95.72164 -#> Model cost at call 201 : 95.72163 -#> Model cost at call 206 : 95.71206 -#> Model cost at call 208 : 95.71205 -#> Model cost at call 213 : 95.70874 -#> Model cost at call 215 : 95.70874 -#> Model cost at call 219 : 95.70874 -#> Model cost at call 221 : 95.70751 -#> Model cost at call 222 : 95.70404 -#> Model cost at call 223 : 95.69259 -#> Model cost at call 224 : 95.68092 -#> Model cost at call 226 : 95.68092 -#> Model cost at call 227 : 95.68092 -#> Model cost at call 233 : 95.67595 -#> Model cost at call 235 : 95.67595 -#> Model cost at call 236 : 95.67595 -#> Model cost at call 242 : 95.67219 -#> Model cost at call 244 : 95.67219 -#> Model cost at call 245 : 95.67219 -#> Model cost at call 249 : 95.66939 -#> Model cost at call 251 : 95.66939 -#> Model cost at call 253 : 95.66939 -#> Model cost at call 254 : 95.66939 -#> Model cost at call 256 : 95.66904 -#> Model cost at call 257 : 95.66904 -#> Model cost at call 260 : 95.66904 -#> Model cost at call 265 : 95.66857 -#> Model cost at call 267 : 95.66856 -#> Model cost at call 273 : 95.66822 -#> Model cost at call 275 : 95.66822 -#> Model cost at call 276 : 95.66822 -#> Model cost at call 282 : 95.66809 -#> Model cost at call 283 : 95.66809 -#> Model cost at call 291 : 95.66805 -#> Model cost at call 293 : 95.66805 -#> Model cost at call 295 : 95.66805 -#> Model cost at call 297 : 95.66805 -#> Model cost at call 298 : 95.66805 -#> Model cost at call 302 : 95.66805 -#> Model cost at call 304 : 95.66805 -#> Model cost at call 306 : 95.66805 -#> Model cost at call 309 : 95.66805 -#> Model cost at call 314 : 95.66805 -#> Model cost at call 315 : 95.66805 -#> Model cost at call 328 : 95.66805 -#> Optimisation by method Port successfully terminated. -#> Model cost at call 1 : 36597.78 -#> Model cost at call 3 : 36597.78 -#> Model cost at call 5 : 36597.78 -#> Model cost at call 7 : 36597.78 -#> Model cost at call 9 : 13188.26 -#> Model cost at call 10 : 12648.25 -#> Model cost at call 14 : 12648.13 -#> Model cost at call 16 : 12647.92 -#> Model cost at call 18 : 6148.715 -#> Model cost at call 19 : 6148.712 -#> Model cost at call 20 : 6148.695 -#> Model cost at call 22 : 6148.683 -#> Model cost at call 27 : 1490.597 -#> Model cost at call 33 : 1490.597 -#> Model cost at call 35 : 594.2031 -#> Model cost at call 36 : 594.2023 -#> Model cost at call 38 : 594.201 -#> Model cost at call 40 : 594.2009 -#> Model cost at call 44 : 230.6504 -#> Model cost at call 45 : 230.6503 -#> Model cost at call 48 : 230.6503 -#> Model cost at call 50 : 230.6495 -#> Model cost at call 51 : 230.6494 -#> Model cost at call 53 : 186.2336 -#> Model cost at call 57 : 186.2336 -#> Model cost at call 59 : 186.2336 -#> Model cost at call 60 : 186.2336 -#> Model cost at call 62 : 181.3507 -#> Model cost at call 66 : 181.3507 -#> Model cost at call 70 : 180.733 -#> Model cost at call 74 : 180.733 -#> Model cost at call 76 : 180.7329 -#> Model cost at call 77 : 180.7329 -#> Model cost at call 78 : 175.5254 -#> Model cost at call 80 : 175.5253 -#> Model cost at call 86 : 173.1139 -#> Model cost at call 88 : 173.1139 -#> Model cost at call 94 : 168.0503 -#> Model cost at call 96 : 168.0502 -#> Model cost at call 102 : 164.9084 -#> Model cost at call 104 : 164.9084 -#> Model cost at call 105 : 164.9084 -#> Model cost at call 110 : 159.7912 -#> Model cost at call 112 : 159.7912 -#> Model cost at call 113 : 159.7912 -#> Model cost at call 116 : 159.7911 -#> Model cost at call 117 : 159.7911 -#> Model cost at call 118 : 158.6003 -#> Model cost at call 122 : 158.6002 -#> Model cost at call 124 : 158.6002 -#> Model cost at call 126 : 150.4132 -#> Model cost at call 132 : 150.4132 -#> Model cost at call 133 : 150.4132 -#> Model cost at call 134 : 146.5123 -#> Model cost at call 140 : 146.5122 -#> Model cost at call 142 : 136.6018 -#> Model cost at call 145 : 136.6018 -#> Model cost at call 149 : 136.6018 -#> Model cost at call 150 : 133.91 -#> Model cost at call 153 : 133.91 -#> Model cost at call 155 : 133.91 -#> Model cost at call 156 : 133.91 -#> Model cost at call 158 : 124.7878 -#> Model cost at call 162 : 124.7878 -#> Model cost at call 163 : 124.7878 -#> Model cost at call 167 : 124.2615 -#> Model cost at call 169 : 124.2614 -#> Model cost at call 170 : 124.2614 -#> Model cost at call 175 : 123.2425 -#> Model cost at call 179 : 123.2425 -#> Model cost at call 180 : 123.2425 -#> Model cost at call 181 : 123.2425 -#> Model cost at call 182 : 123.2425 -#> Model cost at call 183 : 120.7214 -#> Model cost at call 185 : 120.7214 -#> Model cost at call 191 : 119.2706 -#> Model cost at call 192 : 117.872 -#> Model cost at call 193 : 114.6257 -#> Model cost at call 198 : 114.6257 -#> Model cost at call 201 : 111.8985 -#> Model cost at call 203 : 111.8985 -#> Model cost at call 206 : 111.8984 -#> Model cost at call 209 : 111.6987 -#> Model cost at call 212 : 111.6987 -#> Model cost at call 213 : 111.6986 -#> Model cost at call 217 : 107.9995 -#> Model cost at call 219 : 107.9995 -#> Model cost at call 225 : 106.1322 -#> Model cost at call 226 : 104.6907 -#> Model cost at call 227 : 104.6316 -#> Model cost at call 229 : 104.6316 -#> Model cost at call 232 : 104.6315 -#> Model cost at call 239 : 103.3421 -#> Model cost at call 245 : 103.3421 -#> Model cost at call 246 : 103.3421 -#> Model cost at call 247 : 103.1772 -#> Model cost at call 248 : 103.1772 -#> Model cost at call 249 : 103.1772 -#> Model cost at call 250 : 103.1772 -#> Model cost at call 253 : 103.1772 -#> Model cost at call 255 : 102.8623 -#> Model cost at call 256 : 102.8623 -#> Model cost at call 262 : 102.8623 -#> Model cost at call 263 : 102.6013 -#> Model cost at call 266 : 102.6013 -#> Model cost at call 271 : 102.0341 -#> Model cost at call 272 : 101.25 -#> Model cost at call 273 : 99.17557 -#> Model cost at call 274 : 99.17556 -#> Model cost at call 282 : 99.06481 -#> Model cost at call 284 : 99.06479 -#> Model cost at call 290 : 98.57515 -#> Model cost at call 294 : 98.57514 -#> Model cost at call 296 : 98.57514 -#> Model cost at call 298 : 98.05781 -#> Model cost at call 304 : 98.05781 -#> Model cost at call 305 : 98.05781 -#> Model cost at call 306 : 97.81766 -#> Model cost at call 307 : 97.63972 -#> Model cost at call 308 : 97.63971 -#> Model cost at call 315 : 97.15447 -#> Model cost at call 317 : 97.15447 -#> Model cost at call 321 : 97.15446 -#> Model cost at call 323 : 96.25231 -#> Model cost at call 324 : 96.25231 -#> Model cost at call 328 : 96.25231 -#> Model cost at call 331 : 95.48051 -#> Model cost at call 334 : 95.4805 -#> Model cost at call 339 : 95.08754 -#> Model cost at call 341 : 95.08754 -#> Model cost at call 347 : 94.9916 -#> Model cost at call 348 : 94.9916 -#> Model cost at call 350 : 94.9916 -#> Model cost at call 355 : 94.93856 -#> Model cost at call 356 : 94.93856 -#> Model cost at call 357 : 94.93856 -#> Model cost at call 363 : 94.92067 -#> Model cost at call 366 : 94.92067 -#> Model cost at call 367 : 94.92067 -#> Model cost at call 369 : 94.92067 -#> Model cost at call 370 : 94.92067 -#> Model cost at call 371 : 94.91762 -#> Model cost at call 372 : 94.91762 -#> Model cost at call 373 : 94.91762 -#> Model cost at call 379 : 94.91744 -#> Model cost at call 380 : 94.91744 -#> Model cost at call 385 : 94.91744 -#> Model cost at call 387 : 94.91744 -#> Model cost at call 393 : 94.91743 -#> Model cost at call 394 : 94.91743 -#> Model cost at call 404 : 94.91743 -#> Model cost at call 407 : 94.91743 -#> Model cost at call 408 : 94.91743 -#> Model cost at call 423 : 94.91743 -#> Model cost at call 442 : 94.91743 -#> Model cost at call 446 : 94.91743 -#> Model cost at call 447 : 94.91743 -#> Optimisation by method Port successfully terminated.</div><div class='input'> +<span class='no'>time_default</span> <span class='kw'><-</span> <span class='fu'>system.time</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'>system.time</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 elapsed -#> 16.180 0.132 9.130 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> user system elapsed -#> 22.856 0.000 22.858 </div><div class='input'> -<span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits</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[["SFO_lin", 2]]): Objekt 'fits' nicht gefunden</span></div><div class='input'> -<span class='co'># Plot.mkinfit handles rows or columns of mmkin result objects</span> -<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ])</div><img src='mmkin-14.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</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'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>))</div><img src='mmkin-16.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fits.0</span>[, <span class='fl'>1</span>])</div><img src='mmkin-18.png' alt='' width='540' height='400' /><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</span> -<span class='fu'>plot</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><img src='mmkin-20.png' alt='' width='540' height='400' /><div class='input'><span class='co'># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span> +#> 17.340 0.088 9.561 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> user system elapsed +#> 22.868 0.000 22.866 </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 +#> 0.7340479 0.2659521 0.7505687 0.2494313 +#> +#> $SFORB +#> logical(0) +#> +#> $distimes +#> DT50 DT90 +#> parent 0.8777688 2.915885 +#> M1 2.3257456 7.725960 +#> M2 33.7200881 112.015708 +#> </div><div class='input'> +<span class='co'># plot.mkinfit handles rows or columns of mmkin result objects</span> +<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, ])</div><img src='mmkin-12.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</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'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>))</div><img src='mmkin-14.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>plot</span>(<span class='no'>fits.0</span>[, <span class='fl'>1</span>])</div><img src='mmkin-16.png' alt='' width='540' height='400' /><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'>plot</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><img src='mmkin-18.png' alt='' width='540' height='400' /><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'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, <span class='fl'>1</span>])</div><img src='mmkin-22.png' alt='' width='540' height='400' /><div class='input'> +<span class='fu'>plot</span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, <span class='fl'>1</span>])</div><img src='mmkin-20.png' alt='' width='540' height='400' /><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index f171ab5b..0fc7a05a 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -133,12 +133,13 @@ <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 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'>c</span>(<span class='st'>"FOMC"</span>, <span class='st'>"HS"</span>), <span class='fu'>list</span>(<span class='st'>"FOCUS B"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='st'>"FOCUS C"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>), + <span class='no'>fits</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'>c</span>(<span class='st'>"FOMC"</span>, <span class='st'>"HS"</span>), + <span class='fu'>list</span>(<span class='st'>"FOCUS B"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='st'>"FOCUS C"</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>), <span class='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>) <span class='fu'>plot</span>(<span class='no'>fits</span>[, <span class='st'>"FOCUS C"</span>])</div><img src='plot.mmkin-2.png' alt='' width='540' height='400' /><div class='input'> <span class='fu'>plot</span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ])</div><img src='plot.mmkin-4.png' alt='' width='540' height='400' /><div class='input'> - <span class='co'># We can also plot a single fit, if we like the way mmkin works, but then the plot</span> + <span class='co'># 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 staticdocs, as far as I know).</span> + <span class='co'># generated by pkgdown, as far as I know).</span> <span class='fu'>plot</span>(<span class='no'>fits</span>[<span class='st'>"FOMC"</span>, <span class='st'>"FOCUS C"</span>]) <span class='co'># same as plot(fits[1, 2])</span></div><img src='plot.mmkin-6.png' alt='' width='540' height='400' /></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index 2034ea10..ab10b0b2 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -100,12 +100,33 @@ </dl> + <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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M1"</span>), + <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"M2"</span>), + <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> + <span class='fu'>print</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> <ul class="nav nav-pills nav-stacked"> <li><a href="#arguments">Arguments</a></li> - </ul> + + <li><a href="#examples">Examples</a></li> + </ul> </div> </div> diff --git a/docs/reference/schaefer07_complex_case-4.png b/docs/reference/schaefer07_complex_case-4.png Binary files differnew file mode 100644 index 00000000..b87ccb82 --- /dev/null +++ b/docs/reference/schaefer07_complex_case-4.png diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index 9bb6d4ee..1bcc1826 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -116,1059 +116,39 @@ <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"A2"</span>), <span class='kw'>B1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>C1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), - <span class='kw'>A2</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>model</span>, <span class='no'>data</span>)</div><div class='output co'>#> Model cost at call 1 : 2511.655 -#> Model cost at call 2 : 2511.655 -#> Model cost at call 11 : 1436.639 -#> Model cost at call 12 : 1436.638 -#> Model cost at call 13 : 1436.566 -#> Model cost at call 21 : 643.6583 -#> Model cost at call 22 : 643.6583 -#> Model cost at call 23 : 643.6582 -#> Model cost at call 29 : 643.6576 -#> Model cost at call 31 : 454.0244 -#> Model cost at call 32 : 454.0241 -#> Model cost at call 34 : 454.0229 -#> Model cost at call 43 : 378.1144 -#> Model cost at call 45 : 378.1143 -#> Model cost at call 53 : 357.245 -#> Model cost at call 55 : 357.2449 -#> Model cost at call 56 : 357.2447 -#> Model cost at call 63 : 354.3415 -#> Model cost at call 64 : 354.3415 -#> Model cost at call 65 : 354.3413 -#> Model cost at call 73 : 332.49 -#> Model cost at call 74 : 332.49 -#> Model cost at call 81 : 332.4899 -#> Model cost at call 83 : 315.2962 -#> Model cost at call 84 : 306.3085 -#> Model cost at call 86 : 306.3084 -#> Model cost at call 87 : 306.3084 -#> Model cost at call 92 : 306.3083 -#> Model cost at call 94 : 290.6377 -#> Model cost at call 96 : 290.6375 -#> Model cost at call 98 : 290.6375 -#> Model cost at call 101 : 290.6371 -#> Model cost at call 105 : 269.09 -#> Model cost at call 107 : 269.0899 -#> Model cost at call 115 : 259.7551 -#> Model cost at call 120 : 259.7549 -#> Model cost at call 123 : 259.7547 -#> Model cost at call 126 : 253.7973 -#> Model cost at call 128 : 253.7972 -#> Model cost at call 137 : 251.7358 -#> Model cost at call 139 : 251.7358 -#> Model cost at call 147 : 250.7394 -#> Model cost at call 149 : 250.7393 -#> Model cost at call 157 : 249.1148 -#> Model cost at call 159 : 249.1148 -#> Model cost at call 167 : 246.8768 -#> Model cost at call 169 : 246.8768 -#> Model cost at call 177 : 244.9758 -#> Model cost at call 179 : 244.9758 -#> Model cost at call 187 : 243.2914 -#> Model cost at call 189 : 243.2914 -#> Model cost at call 190 : 243.2914 -#> Model cost at call 194 : 243.2914 -#> Model cost at call 199 : 242.9202 -#> Model cost at call 201 : 242.9202 -#> Model cost at call 202 : 242.9202 -#> Model cost at call 209 : 242.7695 -#> Model cost at call 211 : 242.7695 -#> Model cost at call 216 : 242.7695 -#> Model cost at call 219 : 242.5771 -#> Model cost at call 221 : 242.5771 -#> Model cost at call 229 : 242.4402 -#> Model cost at call 231 : 242.4402 -#> Model cost at call 239 : 242.1878 -#> Model cost at call 241 : 242.1878 -#> Model cost at call 249 : 242.0553 -#> Model cost at call 251 : 242.0553 -#> Model cost at call 256 : 242.0553 -#> Model cost at call 259 : 241.8761 -#> Model cost at call 260 : 241.7412 -#> Model cost at call 261 : 241.6954 -#> Model cost at call 264 : 241.6954 -#> Model cost at call 275 : 241.5982 -#> Model cost at call 277 : 241.5982 -#> Model cost at call 285 : 241.5459 -#> Model cost at call 287 : 241.5459 -#> Model cost at call 295 : 241.4837 -#> Model cost at call 297 : 241.4837 -#> Model cost at call 305 : 241.3882 -#> Model cost at call 306 : 241.3161 -#> Model cost at call 307 : 241.2315 -#> Model cost at call 309 : 241.2315 -#> Model cost at call 314 : 241.2315 -#> Model cost at call 317 : 240.9738 -#> Model cost at call 322 : 240.9738 -#> Model cost at call 327 : 240.8244 -#> Model cost at call 329 : 240.8244 -#> Model cost at call 337 : 240.7005 -#> Model cost at call 339 : 240.7005 -#> Model cost at call 342 : 240.7005 -#> Model cost at call 347 : 240.629 -#> Model cost at call 350 : 240.629 -#> Model cost at call 357 : 240.6193 -#> Model cost at call 358 : 240.6193 -#> Model cost at call 364 : 240.6193 -#> Model cost at call 367 : 240.6193 -#> Model cost at call 369 : 240.5873 -#> Model cost at call 374 : 240.5873 -#> Model cost at call 380 : 240.578 -#> Model cost at call 382 : 240.578 -#> Model cost at call 390 : 240.5723 -#> Model cost at call 393 : 240.5723 -#> Model cost at call 403 : 240.569 -#> Model cost at call 404 : 240.569 -#> Model cost at call 413 : 240.569 -#> Model cost at call 415 : 240.5688 -#> Model cost at call 416 : 240.5688 -#> Model cost at call 417 : 240.5688 -#> Model cost at call 431 : 240.5686 -#> Model cost at call 432 : 240.5686 -#> Model cost at call 434 : 240.5686 -#> Model cost at call 443 : 240.5686 -#> Model cost at call 444 : 240.5686 -#> Model cost at call 447 : 240.5686 -#> Model cost at call 449 : 240.5686 -#> Model cost at call 450 : 240.5686 -#> Model cost at call 466 : 240.5686 -#> Model cost at call 470 : 240.5686 -#> Model cost at call 485 : 240.5686 -#> Model cost at call 509 : 240.5686 -#> Optimisation by method Port successfully terminated.</div><div class='output co'>#> $par -#> parent_0 log_k_parent log_k_A1 log_k_B1 log_k_C1 -#> 91.9181598 -3.0020485 -4.2735924 -3.9846764 -2.7852180 -#> log_k_A2 f_parent_ilr_1 f_parent_ilr_2 f_A1_ilr_1 -#> -3.7166415 0.4718588 -0.3589948 -0.1477244 -#> -#> $ssr -#> [1] 240.5686 -#> -#> $convergence -#> [1] 0 -#> -#> $iterations -#> [1] 43 -#> -#> $evaluations -#> function gradient -#> 62 441 -#> -#> $counts -#> [1] "relative convergence (4)" -#> -#> $hessian -#> parent_0 log_k_parent log_k_A1 log_k_B1 -#> parent_0 7.3650812 -92.141920 -1.001134e+01 -2.432415e+00 -#> log_k_parent -92.1419204 6632.673492 -4.316240e+01 -1.320833e+01 -#> log_k_A1 -10.0113364 -43.162398 6.071628e+02 0.000000e+00 -#> log_k_B1 -2.4324147 -13.208329 0.000000e+00 1.572303e+02 -#> log_k_C1 -4.7153201 -118.288037 -5.878291e-05 -3.073041e-06 -#> log_k_A2 -0.4360727 -5.304259 -1.977980e+01 0.000000e+00 -#> f_parent_ilr_1 10.5460899 271.145438 -5.299954e+02 1.874235e+02 -#> f_parent_ilr_2 11.6409409 222.570696 -4.773816e+02 -1.159875e+02 -#> f_A1_ilr_1 0.5572072 10.374810 2.850173e+01 0.000000e+00 -#> log_k_C1 log_k_A2 f_parent_ilr_1 f_parent_ilr_2 -#> parent_0 -4.715320e+00 -4.360727e-01 10.54609 11.64094 -#> log_k_parent -1.182880e+02 -5.304259e+00 271.14544 222.57070 -#> log_k_A1 -5.878291e-05 -1.977980e+01 -529.99537 -477.38164 -#> log_k_B1 -3.073041e-06 0.000000e+00 187.42348 -115.98754 -#> log_k_C1 3.372749e+02 -2.395674e-06 56.85184 305.98862 -#> log_k_A2 -2.395674e-06 2.749192e+01 -23.08549 -20.79373 -#> f_parent_ilr_1 5.685184e+01 -2.308549e+01 1256.24941 632.09769 -#> f_parent_ilr_2 3.059886e+02 -2.079373e+01 632.09769 1250.65147 -#> f_A1_ilr_1 3.158891e-06 -3.129286e+01 29.49830 26.56991 -#> f_A1_ilr_1 -#> parent_0 5.572072e-01 -#> log_k_parent 1.037481e+01 -#> log_k_A1 2.850173e+01 -#> log_k_B1 0.000000e+00 -#> log_k_C1 3.158891e-06 -#> log_k_A2 -3.129286e+01 -#> f_parent_ilr_1 2.949830e+01 -#> f_parent_ilr_2 2.656991e+01 -#> f_A1_ilr_1 3.998554e+01 -#> -#> $residuals -#> parent parent parent parent parent parent parent -#> -1.2818402 -1.9372115 -0.5105519 3.8165318 -2.3531716 4.8043342 -2.2775432 -#> parent A1 A1 A1 A1 A1 A1 -#> -5.3608524 4.1967522 2.9032987 -1.3124875 -0.6021093 2.5092324 -1.8861396 -#> B1 B1 B1 B1 B1 C1 C1 -#> 4.3801768 5.5002481 -5.7917184 1.3852658 0.5313301 1.2796458 1.7105311 -#> C1 C1 C1 C1 C1 A2 A2 -#> 3.7116712 -0.1182953 0.5228429 -0.8570298 -3.5476556 -0.5447276 -1.3652404 -#> A2 A2 A2 A2 A2 -#> -0.3330261 -0.5802059 0.1285850 0.2119280 -0.1381990 -#> -#> $ms -#> [1] 7.289956 -#> -#> $var_ms -#> parent A1 B1 C1 A2 -#> 10.3459333 6.3301336 17.0367907 4.5639474 0.3841002 -#> -#> $var_ms_unscaled -#> parent A1 B1 C1 A2 -#> 10.3459333 6.3301336 17.0367907 4.5639474 0.3841002 -#> -#> $var_ms_unweighted -#> parent A1 B1 C1 A2 -#> 10.3459333 6.3301336 17.0367907 4.5639474 0.3841002 -#> -#> $rank -#> [1] 9 -#> -#> $df.residual -#> [1] 24 -#> -#> $solution_type -#> [1] "deSolve" -#> -#> $transform_rates -#> [1] TRUE -#> -#> $transform_fractions -#> [1] TRUE -#> -#> $method.modFit -#> [1] "Port" -#> -#> $maxit.modFit -#> [1] "auto" -#> -#> $calls -#> [1] 523 -#> -#> $time -#> user system elapsed -#> 5.004 0.000 5.004 -#> -#> $mkinmod -#> <mkinmod> model generated with -#> Use of formation fractions $use_of_ff: max -#> Specification $spec: -#> $parent -#> $type: SFO; $to: A1, B1, C1; $sink: FALSE -#> $A1 -#> $type: SFO; $to: A2; $sink: TRUE -#> $B1 -#> $type: SFO; $sink: TRUE -#> $C1 -#> $type: SFO; $sink: TRUE -#> $A2 -#> $type: SFO; $sink: TRUE -#> Coefficient matrix $coefmat available -#> Compiled model $cf available -#> -#> $observed -#> name time value -#> 1 parent 0 93.20 -#> 2 parent 1 89.40 -#> 3 parent 3 79.70 -#> 4 parent 7 61.10 -#> 5 parent 14 48.20 -#> 6 parent 30 15.90 -#> 7 parent 62 6.50 -#> 8 parent 100 6.00 -#> 9 A1 0 NA -#> 10 A1 1 NA -#> 11 A1 3 0.55 -#> 12 A1 7 6.87 -#> 13 A1 14 17.08 -#> 14 A1 30 21.68 -#> 15 A1 62 15.77 -#> 16 A1 100 13.63 -#> 17 B1 0 NA -#> 18 B1 1 NA -#> 19 B1 3 NA -#> 20 B1 7 0.55 -#> 21 B1 14 2.31 -#> 22 B1 30 15.76 -#> 23 B1 62 6.36 -#> 24 B1 100 3.74 -#> 25 C1 0 NA -#> 26 C1 1 0.55 -#> 27 C1 3 3.20 -#> 28 C1 7 5.46 -#> 29 C1 14 12.55 -#> 30 C1 30 10.45 -#> 31 C1 62 4.74 -#> 32 C1 100 4.33 -#> 33 A2 0 NA -#> 34 A2 1 0.55 -#> 35 A2 3 1.41 -#> 36 A2 7 0.55 -#> 37 A2 14 1.29 -#> 38 A2 30 1.95 -#> 39 A2 62 3.54 -#> 40 A2 100 3.86 -#> -#> $obs_vars -#> [1] "parent" "A1" "B1" "C1" "A2" -#> -#> $predicted -#> name time value -#> 1 parent 0.000000 91.918159794 -#> 2 parent 1.000000 87.462788491 -#> 3 parent 1.010101 87.418904506 -#> 4 parent 2.020202 83.139880984 -#> 5 parent 3.000000 79.189448055 -#> 6 parent 3.030303 79.070309209 -#> 7 parent 4.040404 75.199936833 -#> 8 parent 5.050505 71.519013349 -#> 9 parent 6.060606 68.018265517 -#> 10 parent 7.000000 64.916531757 -#> 11 parent 7.070707 64.688874011 -#> 12 parent 8.080808 61.522451197 -#> 13 parent 9.090909 58.511020005 -#> 14 parent 10.101010 55.646993828 -#> 15 parent 11.111111 52.923157412 -#> 16 parent 12.121212 50.332648680 -#> 17 parent 13.131313 47.868941444 -#> 18 parent 14.000000 45.846828365 -#> 19 parent 14.141414 45.525828960 -#> 20 parent 15.151515 43.297408299 -#> 21 parent 16.161616 41.178065468 -#> 22 parent 17.171717 39.162461272 -#> 23 parent 18.181818 37.245517861 -#> 24 parent 19.191919 35.422405939 -#> 25 parent 20.202020 33.688532595 -#> 26 parent 21.212121 32.039529737 -#> 27 parent 22.222222 30.471243081 -#> 28 parent 23.232323 28.979721692 -#> 29 parent 24.242424 27.561208025 -#> 30 parent 25.252525 26.212128463 -#> 31 parent 26.262626 24.929084310 -#> 32 parent 27.272727 23.708843233 -#> 33 parent 28.282828 22.548331117 -#> 34 parent 29.292929 21.444624318 -#> 35 parent 30.000000 20.704334210 -#> 36 parent 30.303030 20.394942302 -#> 37 parent 31.313131 19.396640638 -#> 38 parent 32.323232 18.447204335 -#> 39 parent 33.333333 17.544241506 -#> 40 parent 34.343434 16.685477346 -#> 41 parent 35.353535 15.868748397 -#> 42 parent 36.363636 15.091997098 -#> 43 parent 37.373737 14.353266603 -#> 44 parent 38.383838 13.650695852 -#> 45 parent 39.393939 12.982514879 -#> 46 parent 40.404040 12.347040357 -#> 47 parent 41.414141 11.742671354 -#> 48 parent 42.424242 11.167885303 -#> 49 parent 43.434343 10.621234162 -#> 50 parent 44.444444 10.101340770 -#> 51 parent 45.454545 9.606895375 -#> 52 parent 46.464646 9.136652336 -#> 53 parent 47.474747 8.689426985 -#> 54 parent 48.484848 8.264092640 -#> 55 parent 49.494949 7.859577770 -#> 56 parent 50.505051 7.474863293 -#> 57 parent 51.515152 7.108980009 -#> 58 parent 52.525253 6.761006160 -#> 59 parent 53.535354 6.430065106 -#> 60 parent 54.545455 6.115323117 -#> 61 parent 55.555556 5.815987274 -#> 62 parent 56.565657 5.531303470 -#> 63 parent 57.575758 5.260554508 -#> 64 parent 58.585859 5.003058299 -#> 65 parent 59.595960 4.758166141 -#> 66 parent 60.606061 4.525261085 -#> 67 parent 61.616162 4.303756381 -#> 68 parent 62.000000 4.222456793 -#> 69 parent 62.626263 4.093093997 -#> 70 parent 63.636364 3.892743220 -#> 71 parent 64.646465 3.702199310 -#> 72 parent 65.656566 3.520982238 -#> 73 parent 66.666667 3.348635468 -#> 74 parent 67.676768 3.184724813 -#> 75 parent 68.686869 3.028837337 -#> 76 parent 69.696970 2.880580317 -#> 77 parent 70.707071 2.739580256 -#> 78 parent 71.717172 2.605481934 -#> 79 parent 72.727273 2.477947523 -#> 80 parent 73.737374 2.356655730 -#> 81 parent 74.747475 2.241300986 -#> 82 parent 75.757576 2.131592683 -#> 83 parent 76.767677 2.027254437 -#> 84 parent 77.777778 1.928023390 -#> 85 parent 78.787879 1.833649553 -#> 86 parent 79.797980 1.743895173 -#> 87 parent 80.808081 1.658534134 -#> 88 parent 81.818182 1.577351390 -#> 89 parent 82.828283 1.500142419 -#> 90 parent 83.838384 1.426712710 -#> 91 parent 84.848485 1.356877275 -#> 92 parent 85.858586 1.290460179 -#> 93 parent 86.868687 1.227294099 -#> 94 parent 87.878788 1.167219904 -#> 95 parent 88.888889 1.110086250 -#> 96 parent 89.898990 1.055749203 -#> 97 parent 90.909091 1.004071872 -#> 98 parent 91.919192 0.954924068 -#> 99 parent 92.929293 0.908181975 -#> 100 parent 93.939394 0.863727837 -#> 101 parent 94.949495 0.821449662 -#> 102 parent 95.959596 0.781240940 -#> 103 parent 96.969697 0.743000375 -#> 104 parent 97.979798 0.706631627 -#> 105 parent 98.989899 0.672043075 -#> 106 parent 100.000000 0.639147580 -#> 107 A1 0.000000 0.000000000 -#> 108 A1 1.000000 1.685461006 -#> 109 A1 1.010101 1.701940789 -#> 110 A1 2.020202 3.296791533 -#> 111 A1 3.000000 4.746752202 -#> 112 A1 3.030303 4.790126465 -#> 113 A1 4.040404 6.187242320 -#> 114 A1 5.050505 7.493171988 -#> 115 A1 6.060606 8.712697491 -#> 116 A1 7.000000 9.773298725 -#> 117 A1 7.070707 9.850362326 -#> 118 A1 8.080808 10.910483202 -#> 119 A1 9.090909 11.897161206 -#> 120 A1 10.101010 12.814292412 -#> 121 A1 11.111111 13.665577981 -#> 122 A1 12.121212 14.454533757 -#> 123 A1 13.131313 15.184499397 -#> 124 A1 14.000000 15.767512526 -#> 125 A1 14.141414 15.858647054 -#> 126 A1 15.151515 16.479989628 -#> 127 A1 16.161616 17.051388624 -#> 128 A1 17.171717 17.575561608 -#> 129 A1 18.181818 18.055089316 -#> 130 A1 19.191919 18.492422399 -#> 131 A1 20.202020 18.889887843 -#> 132 A1 21.212121 19.249695079 -#> 133 A1 22.222222 19.573941783 -#> 134 A1 23.232323 19.864619397 -#> 135 A1 24.242424 20.123618383 -#> 136 A1 25.252525 20.352733211 -#> 137 A1 26.262626 20.553667106 -#> 138 A1 27.272727 20.728036563 -#> 139 A1 28.282828 20.877375640 -#> 140 A1 29.292929 21.003140039 -#> 141 A1 30.000000 21.077890710 -#> 142 A1 30.303030 21.106710984 -#> 143 A1 31.313131 21.189398917 -#> 144 A1 32.323232 21.252447002 -#> 145 A1 33.333333 21.297034466 -#> 146 A1 34.343434 21.324279770 -#> 147 A1 35.353535 21.335243623 -#> 148 A1 36.363636 21.330931858 -#> 149 A1 37.373737 21.312298151 -#> 150 A1 38.383838 21.280246621 -#> 151 A1 39.393939 21.235634295 -#> 152 A1 40.404040 21.179273450 -#> 153 A1 41.414141 21.111933845 -#> 154 A1 42.424242 21.034344838 -#> 155 A1 43.434343 20.947197407 -#> 156 A1 44.444444 20.851146060 -#> 157 A1 45.454545 20.746810660 -#> 158 A1 46.464646 20.634778158 -#> 159 A1 47.474747 20.515604239 -#> 160 A1 48.484848 20.389814887 -#> 161 A1 49.494949 20.257907875 -#> 162 A1 50.505051 20.120354180 -#> 163 A1 51.515152 19.977599327 -#> 164 A1 52.525253 19.830064674 -#> 165 A1 53.535354 19.678148618 -#> 166 A1 54.545455 19.522227762 -#> 167 A1 55.555556 19.362658007 -#> 168 A1 56.565657 19.199775600 -#> 169 A1 57.575758 19.033898126 -#> 170 A1 58.585859 18.865325451 -#> 171 A1 59.595960 18.694340625 -#> 172 A1 60.606061 18.521210729 -#> 173 A1 61.616162 18.346187688 -#> 174 A1 62.000000 18.279232408 -#> 175 A1 62.626263 18.169509043 -#> 176 A1 63.636364 17.991398686 -#> 177 A1 64.646465 17.812067549 -#> 178 A1 65.656566 17.631714275 -#> 179 A1 66.666667 17.450525840 -#> 180 A1 67.676768 17.268678156 -#> 181 A1 68.686869 17.086336636 -#> 182 A1 69.696970 16.903656738 -#> 183 A1 70.707071 16.720784474 -#> 184 A1 71.717172 16.537856901 -#> 185 A1 72.727273 16.355002582 -#> 186 A1 73.737374 16.172342031 -#> 187 A1 74.747475 15.989988127 -#> 188 A1 75.757576 15.808046514 -#> 189 A1 76.767677 15.626615980 -#> 190 A1 77.777778 15.445788814 -#> 191 A1 78.787879 15.265651148 -#> 192 A1 79.797980 15.086283284 -#> 193 A1 80.808081 14.907759996 -#> 194 A1 81.818182 14.730150830 -#> 195 A1 82.828283 14.553520376 -#> 196 A1 83.838384 14.377928535 -#> 197 A1 84.848485 14.203430771 -#> 198 A1 85.858586 14.030078345 -#> 199 A1 86.868687 13.857918547 -#> 200 A1 87.878788 13.686994907 -#> 201 A1 88.888889 13.517347398 -#> 202 A1 89.898990 13.349012635 -#> 203 A1 90.909091 13.182024056 -#> 204 A1 91.919192 13.016412097 -#> 205 A1 92.929293 12.852204356 -#> 206 A1 93.939394 12.689425755 -#> 207 A1 94.949495 12.528098688 -#> 208 A1 95.959596 12.368243159 -#> 209 A1 96.969697 12.209876925 -#> 210 A1 97.979798 12.053015616 -#> 211 A1 98.989899 11.897672861 -#> 212 A1 100.000000 11.743860400 -#> 213 B1 0.000000 0.000000000 -#> 214 B1 1.000000 0.862762059 -#> 215 B1 1.010101 0.871177048 -#> 216 B1 2.020202 1.683497848 -#> 217 B1 3.000000 2.418226457 -#> 218 B1 3.030303 2.440145075 -#> 219 B1 4.040404 3.144139999 -#> 220 B1 5.050505 3.798350490 -#> 221 B1 6.060606 4.405498633 -#> 222 B1 7.000000 4.930176837 -#> 223 B1 7.070707 4.968167964 -#> 224 B1 8.080808 5.488810347 -#> 225 B1 9.090909 5.969752521 -#> 226 B1 10.101010 6.413202316 -#> 227 B1 11.111111 6.821254568 -#> 228 B1 12.121212 7.195896744 -#> 229 B1 13.131313 7.539014282 -#> 230 B1 14.000000 7.810248132 -#> 231 B1 14.141414 7.852395679 -#> 232 B1 15.151515 8.137737320 -#> 233 B1 16.161616 8.396648072 -#> 234 B1 17.171717 8.630653651 -#> 235 B1 18.181818 8.841200774 -#> 236 B1 19.191919 9.029661109 -#> 237 B1 20.202020 9.197335022 -#> 238 B1 21.212121 9.345455150 -#> 239 B1 22.222222 9.475189788 -#> 240 B1 23.232323 9.587646116 -#> 241 B1 24.242424 9.683873262 -#> 242 B1 25.252525 9.764865214 -#> 243 B1 26.262626 9.831563593 -#> 244 B1 27.272727 9.884860284 -#> 245 B1 28.282828 9.925599936 -#> 246 B1 29.292929 9.954582344 -#> 247 B1 30.000000 9.968281596 -#> 248 B1 30.303030 9.972564708 -#> 249 B1 31.313131 9.980263783 -#> 250 B1 32.323232 9.978357919 -#> 251 B1 33.333333 9.967489009 -#> 252 B1 34.343434 9.948264327 -#> 253 B1 35.353535 9.921258285 -#> 254 B1 36.363636 9.887014102 -#> 255 B1 37.373737 9.846045383 -#> 256 B1 38.383838 9.798837632 -#> 257 B1 39.393939 9.745849674 -#> 258 B1 40.404040 9.687515023 -#> 259 B1 41.414141 9.624243169 -#> 260 B1 42.424242 9.556420809 -#> 261 B1 43.434343 9.484413012 -#> 262 B1 44.444444 9.408564328 -#> 263 B1 45.454545 9.329199843 -#> 264 B1 46.464646 9.246626179 -#> 265 B1 47.474747 9.161132446 -#> 266 B1 48.484848 9.072991146 -#> 267 B1 49.494949 8.982459028 -#> 268 B1 50.505051 8.889777910 -#> 269 B1 51.515152 8.795175451 -#> 270 B1 52.525253 8.698865886 -#> 271 B1 53.535354 8.601050726 -#> 272 B1 54.545455 8.501919425 -#> 273 B1 55.555556 8.401650008 -#> 274 B1 56.565657 8.300409672 -#> 275 B1 57.575758 8.198355355 -#> 276 B1 58.585859 8.095634277 -#> 277 B1 59.595960 7.992384454 -#> 278 B1 60.606061 7.888735183 -#> 279 B1 61.616162 7.784807509 -#> 280 B1 62.000000 7.745265792 -#> 281 B1 62.626263 7.680714664 -#> 282 B1 63.636364 7.576562482 -#> 283 B1 64.646465 7.472449799 -#> 284 B1 65.656566 7.368468826 -#> 285 B1 66.666667 7.264705509 -#> 286 B1 67.676768 7.161239868 -#> 287 B1 68.686869 7.058146319 -#> 288 B1 69.696970 6.955493978 -#> 289 B1 70.707071 6.853346953 -#> 290 B1 71.717172 6.751764620 -#> 291 B1 72.727273 6.650801882 -#> 292 B1 73.737374 6.550509419 -#> 293 B1 74.747475 6.450933922 -#> 294 B1 75.757576 6.352118318 -#> 295 B1 76.767677 6.254101979 -#> 296 B1 77.777778 6.156920928 -#> 297 B1 78.787879 6.060608023 -#> 298 B1 79.797980 5.965193142 -#> 299 B1 80.808081 5.870703355 -#> 300 B1 81.818182 5.777163083 -#> 301 B1 82.828283 5.684594257 -#> 302 B1 83.838384 5.593016458 -#> 303 B1 84.848485 5.502447062 -#> 304 B1 85.858586 5.412901366 -#> 305 B1 86.868687 5.324392718 -#> 306 B1 87.878788 5.236932630 -#> 307 B1 88.888889 5.150530889 -#> 308 B1 89.898990 5.065195670 -#> 309 B1 90.909091 4.980933628 -#> 310 B1 91.919192 4.897749999 -#> 311 B1 92.929293 4.815648688 -#> 312 B1 93.939394 4.734632351 -#> 313 B1 94.949495 4.654702481 -#> 314 B1 95.959596 4.575859481 -#> 315 B1 96.969697 4.498102737 -#> 316 B1 97.979798 4.421430686 -#> 317 B1 98.989899 4.345840882 -#> 318 B1 100.000000 4.271330056 -#> 319 C1 0.000000 0.000000000 -#> 320 C1 1.000000 1.829645786 -#> 321 C1 1.010101 1.847087763 -#> 322 C1 2.020202 3.492133303 -#> 323 C1 3.000000 4.910531064 -#> 324 C1 3.030303 4.951772742 -#> 325 C1 4.040404 6.241420142 -#> 326 C1 5.050505 7.375351980 -#> 327 C1 6.060606 8.366785999 -#> 328 C1 7.000000 9.171671206 -#> 329 C1 7.070707 9.227954769 -#> 330 C1 8.080808 9.970174354 -#> 331 C1 9.090909 10.603908370 -#> 332 C1 10.101010 11.138827767 -#> 333 C1 11.111111 11.583866567 -#> 334 C1 12.121212 11.947273869 -#> 335 C1 13.131313 12.236662337 -#> 336 C1 14.000000 12.431704739 -#> 337 C1 14.141414 12.459053419 -#> 338 C1 15.151515 12.620919488 -#> 339 C1 16.161616 12.728223141 -#> 340 C1 17.171717 12.786453805 -#> 341 C1 18.181818 12.800661859 -#> 342 C1 19.191919 12.775490422 -#> 343 C1 20.202020 12.715204956 -#> 344 C1 21.212121 12.623720845 -#> 345 C1 22.222222 12.504629065 -#> 346 C1 23.232323 12.361220091 -#> 347 C1 24.242424 12.196506142 -#> 348 C1 25.252525 12.013241882 -#> 349 C1 26.262626 11.813943686 -#> 350 C1 27.272727 11.600907551 -#> 351 C1 28.282828 11.376225763 -#> 352 C1 29.292929 11.141802382 -#> 353 C1 30.000000 10.972842888 -#> 354 C1 30.303030 10.899367648 -#> 355 C1 31.313131 10.650491354 -#> 356 C1 32.323232 10.396595286 -#> 357 C1 33.333333 10.138964763 -#> 358 C1 34.343434 9.878759358 -#> 359 C1 35.353535 9.617022857 -#> 360 C1 36.363636 9.354692485 -#> 361 C1 37.373737 9.092607481 -#> 362 C1 38.383838 8.831517041 -#> 363 C1 39.393939 8.572087685 -#> 364 C1 40.404040 8.314910084 -#> 365 C1 41.414141 8.060505385 -#> 366 C1 42.424242 7.809331068 -#> 367 C1 43.434343 7.561786371 -#> 368 C1 44.444444 7.318217302 -#> 369 C1 45.454545 7.078921287 -#> 370 C1 46.464646 6.844151456 -#> 371 C1 47.474747 6.614120611 -#> 372 C1 48.484848 6.389004885 -#> 373 C1 49.494949 6.168947129 -#> 374 C1 50.505051 5.954060026 -#> 375 C1 51.515152 5.744428970 -#> 376 C1 52.525253 5.540114721 -#> 377 C1 53.535354 5.341155842 -#> 378 C1 54.545455 5.147570951 -#> 379 C1 55.555556 4.959360784 -#> 380 C1 56.565657 4.776510102 -#> 381 C1 57.575758 4.598989433 -#> 382 C1 58.585859 4.426756673 -#> 383 C1 59.595960 4.259758556 -#> 384 C1 60.606061 4.097932000 -#> 385 C1 61.616162 3.941205338 -#> 386 C1 62.000000 3.882970158 -#> 387 C1 62.626263 3.789499444 -#> 388 C1 63.636364 3.642728760 -#> 389 C1 64.646465 3.500802233 -#> 390 C1 65.656566 3.363624171 -#> 391 C1 66.666667 3.231095021 -#> 392 C1 67.676768 3.103112069 -#> 393 C1 68.686869 2.979570086 -#> 394 C1 69.696970 2.860361903 -#> 395 C1 70.707071 2.745378939 -#> 396 C1 71.717172 2.634511667 -#> 397 C1 72.727273 2.527650041 -#> 398 C1 73.737374 2.424683880 -#> 399 C1 74.747475 2.325503203 -#> 400 C1 75.757576 2.229998536 -#> 401 C1 76.767677 2.138061182 -#> 402 C1 77.777778 2.049583458 -#> 403 C1 78.787879 1.964458908 -#> 404 C1 79.797980 1.882582485 -#> 405 C1 80.808081 1.803850715 -#> 406 C1 81.818182 1.728161832 -#> 407 C1 82.828283 1.655415900 -#> 408 C1 83.838384 1.585514911 -#> 409 C1 84.848485 1.518362874 -#> 410 C1 85.858586 1.453865880 -#> 411 C1 86.868687 1.391932162 -#> 412 C1 87.878788 1.332472134 -#> 413 C1 88.888889 1.275398429 -#> 414 C1 89.898990 1.220625918 -#> 415 C1 90.909091 1.168071723 -#> 416 C1 91.919192 1.117655227 -#> 417 C1 92.929293 1.069298066 -#> 418 C1 93.939394 1.022924125 -#> 419 C1 94.949495 0.978459525 -#> 420 C1 95.959596 0.935832597 -#> 421 C1 96.969697 0.894973866 -#> 422 C1 97.979798 0.855816021 -#> 423 C1 98.989899 0.818293881 -#> 424 C1 100.000000 0.782344364 -#> 425 A2 0.000000 0.000000000 -#> 426 A2 1.000000 0.005272357 -#> 427 A2 1.010101 0.005377817 -#> 428 A2 2.020202 0.020885524 -#> 429 A2 3.000000 0.044759575 -#> 430 A2 3.030303 0.045628064 -#> 431 A2 4.040404 0.078765936 -#> 432 A2 5.050505 0.119512155 -#> 433 A2 6.060606 0.167129381 -#> 434 A2 7.000000 0.216973934 -#> 435 A2 7.070707 0.220927189 -#> 436 A2 8.080808 0.280259484 -#> 437 A2 9.090909 0.344522046 -#> 438 A2 10.101010 0.413150206 -#> 439 A2 11.111111 0.485616641 -#> 440 A2 12.121212 0.561429288 -#> 441 A2 13.131313 0.640129357 -#> 442 A2 14.000000 0.709794102 -#> 443 A2 14.141414 0.721289460 -#> 444 A2 15.151515 0.804511827 -#> 445 A2 16.161616 0.889426625 -#> 446 A2 17.171717 0.975690359 -#> 447 A2 18.181818 1.062984358 -#> 448 A2 19.191919 1.151013342 -#> 449 A2 20.202020 1.239504068 -#> 450 A2 21.212121 1.328204041 -#> 451 A2 22.222222 1.416880297 -#> 452 A2 23.232323 1.505318253 -#> 453 A2 24.242424 1.593320615 -#> 454 A2 25.252525 1.680706344 -#> 455 A2 26.262626 1.767309680 -#> 456 A2 27.272727 1.852979219 -#> 457 A2 28.282828 1.937577034 -#> 458 A2 29.292929 2.020977853 -#> 459 A2 30.000000 2.078585030 -#> 460 A2 30.303030 2.103068270 -#> 461 A2 31.313131 2.183746011 -#> 462 A2 32.323232 2.262919231 -#> 463 A2 33.333333 2.340505852 -#> 464 A2 34.343434 2.416432940 -#> 465 A2 35.353535 2.490636111 -#> 466 A2 36.363636 2.563058979 -#> 467 A2 37.373737 2.633652622 -#> 468 A2 38.383838 2.702375089 -#> 469 A2 39.393939 2.769190926 -#> 470 A2 40.404040 2.834070737 -#> 471 A2 41.414141 2.896990764 -#> 472 A2 42.424242 2.957932489 -#> 473 A2 43.434343 3.016882265 -#> 474 A2 44.444444 3.073830964 -#> 475 A2 45.454545 3.128773647 -#> 476 A2 46.464646 3.181709250 -#> 477 A2 47.474747 3.232640290 -#> 478 A2 48.484848 3.281572591 -#> 479 A2 49.494949 3.328515022 -#> 480 A2 50.505051 3.373479253 -#> 481 A2 51.515152 3.416479521 -#> 482 A2 52.525253 3.457532417 -#> 483 A2 53.535354 3.496656681 -#> 484 A2 54.545455 3.533873012 -#> 485 A2 55.555556 3.569203883 -#> 486 A2 56.565657 3.602673379 -#> 487 A2 57.575758 3.634307034 -#> 488 A2 58.585859 3.664131686 -#> 489 A2 59.595960 3.692175334 -#> 490 A2 60.606061 3.718467012 -#> 491 A2 61.616162 3.743036663 -#> 492 A2 62.000000 3.751927986 -#> 493 A2 62.626263 3.765915028 -#> 494 A2 63.636364 3.787133539 -#> 495 A2 64.646465 3.806724217 -#> 496 A2 65.656566 3.824719582 -#> 497 A2 66.666667 3.841152565 -#> 498 A2 67.676768 3.856056426 -#> 499 A2 68.686869 3.869464684 -#> 500 A2 69.696970 3.881411040 -#> 501 A2 70.707071 3.891929316 -#> 502 A2 71.717172 3.901053396 -#> 503 A2 72.727273 3.908817168 -#> 504 A2 73.737374 3.915254472 -#> 505 A2 74.747475 3.920399054 -#> 506 A2 75.757576 3.924284521 -#> 507 A2 76.767677 3.926944303 -#> 508 A2 77.777778 3.928411610 -#> 509 A2 78.787879 3.928719404 -#> 510 A2 79.797980 3.927900364 -#> 511 A2 80.808081 3.925986861 -#> 512 A2 81.818182 3.923010926 -#> 513 A2 82.828283 3.919004234 -#> 514 A2 83.838384 3.913998077 -#> 515 A2 84.848485 3.908023347 -#> 516 A2 85.858586 3.901110518 -#> 517 A2 86.868687 3.893289633 -#> 518 A2 87.878788 3.884590288 -#> 519 A2 88.888889 3.875041619 -#> 520 A2 89.898990 3.864672297 -#> 521 A2 90.909091 3.853510511 -#> 522 A2 91.919192 3.841583970 -#> 523 A2 92.929293 3.828919886 -#> 524 A2 93.939394 3.815544978 -#> 525 A2 94.949495 3.801485462 -#> 526 A2 95.959596 3.786767051 -#> 527 A2 96.969697 3.771414951 -#> 528 A2 97.979798 3.755453860 -#> 529 A2 98.989899 3.738907968 -#> 530 A2 100.000000 3.721800959 -#> -#> $cost -#> function (P) -#> { -#> assign("calls", calls + 1, inherits = TRUE) -#> if (trace_parms) -#> cat(P, "\n") -#> if (length(state.ini.optim) > 0) { -#> odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed) -#> names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames) -#> } -#> else { -#> odeini <- state.ini.fixed -#> names(odeini) <- state.ini.fixed.boxnames -#> } -#> odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], -#> transparms.fixed) -#> parms <- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates, -#> transform_fractions = transform_fractions) -#> out <- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type, -#> use_compiled = use_compiled, method.ode = method.ode, -#> atol = atol, rtol = rtol, ...) -#> assign("out_predicted", out, inherits = TRUE) -#> mC <- modCost(out, observed, y = "value", err = err, weight = weight, -#> scaleVar = scaleVar) -#> if (mC$model < cost.old) { -#> if (!quiet) -#> cat("Model cost at call ", calls, ": ", mC$model, -#> "\n") -#> if (plot) { -#> outtimes_plot = seq(min(observed$time), max(observed$time), -#> length.out = 100) -#> out_plot <- mkinpredict(mkinmod, parms, odeini, outtimes_plot, -#> solution_type = solution_type, use_compiled = use_compiled, -#> method.ode = method.ode, atol = atol, rtol = rtol, -#> ...) -#> plot(0, type = "n", xlim = range(observed$time), -#> ylim = c(0, max(observed$value, na.rm = TRUE)), -#> xlab = "Time", ylab = "Observed") -#> col_obs <- pch_obs <- 1:length(obs_vars) -#> lty_obs <- rep(1, length(obs_vars)) -#> names(col_obs) <- names(pch_obs) <- names(lty_obs) <- obs_vars -#> for (obs_var in obs_vars) { -#> points(subset(observed, name == obs_var, c(time, -#> value)), pch = pch_obs[obs_var], col = col_obs[obs_var]) -#> } -#> matlines(out_plot$time, out_plot[-1], col = col_obs, -#> lty = lty_obs) -#> legend("topright", inset = c(0.05, 0.05), legend = obs_vars, -#> col = col_obs, pch = pch_obs, lty = 1:length(pch_obs)) -#> } -#> assign("cost.old", mC$model, inherits = TRUE) -#> } -#> return(mC) -#> } -#> <environment: 0x36a83b0> -#> -#> $cost_notrans -#> function (P) -#> { -#> if (length(state.ini.optim) > 0) { -#> odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed) -#> names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames) -#> } -#> else { -#> odeini <- state.ini.fixed -#> names(odeini) <- state.ini.fixed.boxnames -#> } -#> odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], -#> parms.fixed) -#> out <- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type, -#> use_compiled = use_compiled, method.ode = method.ode, -#> atol = atol, rtol = rtol, ...) -#> mC <- modCost(out, observed, y = "value", err = err, weight = weight, -#> scaleVar = scaleVar) -#> return(mC) -#> } -#> <environment: 0x36a83b0> -#> -#> $hessian_notrans -#> parent_0 k_parent k_A1 k_B1 -#> parent_0 7.365081 -1854.5113 -7.186039e+02 -1.307858e+02 -#> k_parent -1854.511330 2686790.7676 -6.235542e+04 -1.429363e+04 -#> k_A1 -718.603865 -62355.4211 3.128242e+06 0.000000e+00 -#> k_B1 -130.785796 -14293.6348 0.000000e+00 4.545506e+05 -#> k_C1 -76.404274 -38575.9391 1.190516e-02 -9.422820e-04 -#> k_A2 -17.933942 -4390.5079 -5.838973e+04 0.000000e+00 -#> f_parent_to_A1 75.150866 43257.2599 -1.733841e+05 0.000000e+00 -#> f_parent_to_B1 29.265575 17940.1132 0.000000e+00 -6.150198e+04 -#> f_parent_to_C1 20.661354 19692.5582 -6.146186e-05 -1.990817e-03 -#> f_A1_to_A2 1.593279 597.0744 5.849840e+03 0.000000e+00 -#> k_C1 k_A2 f_parent_to_A1 f_parent_to_B1 -#> parent_0 -7.640427e+01 -1.793394e+01 7.515087e+01 2.926558e+01 -#> k_parent -3.857594e+04 -4.390508e+03 4.325726e+04 1.794011e+04 -#> k_A1 1.190516e-02 -5.838973e+04 -1.733841e+05 0.000000e+00 -#> k_B1 -9.422820e-04 0.000000e+00 0.000000e+00 -6.150198e+04 -#> k_C1 8.855106e+04 4.105787e-04 -1.354551e-03 5.852620e-04 -#> k_A2 4.105787e-04 4.649850e+04 -4.327086e+03 0.000000e+00 -#> f_parent_to_A1 -1.354551e-03 -4.327086e+03 1.813234e+04 0.000000e+00 -#> f_parent_to_B1 5.852620e-04 0.000000e+00 0.000000e+00 1.376213e+04 -#> f_parent_to_C1 -1.658031e+04 2.903794e-04 1.946385e-03 1.325258e-03 -#> f_A1_to_A2 -4.367402e-05 -3.679910e+03 3.844249e+02 0.000000e+00 -#> f_parent_to_C1 f_A1_to_A2 -#> parent_0 2.066135e+01 1.593279e+00 -#> k_parent 1.969256e+04 5.970744e+02 -#> k_A1 -6.146186e-05 5.849840e+03 -#> k_B1 -1.990817e-03 0.000000e+00 -#> k_C1 -1.658031e+04 -4.367402e-05 -#> k_A2 2.903794e-04 -3.679910e+03 -#> f_parent_to_A1 1.946385e-03 3.844249e+02 -#> f_parent_to_B1 1.325258e-03 0.000000e+00 -#> f_parent_to_C1 4.483759e+03 -3.796730e-05 -#> f_A1_to_A2 -3.796730e-05 3.269288e+02 -#> -#> $start -#> value type -#> parent_0 93.2000000 state -#> k_parent 0.1000000 deparm -#> k_A1 0.1001000 deparm -#> k_B1 0.1002000 deparm -#> k_C1 0.1003000 deparm -#> k_A2 0.1004000 deparm -#> f_parent_to_A1 0.3333333 deparm -#> f_parent_to_B1 0.3333333 deparm -#> f_parent_to_C1 0.3333333 deparm -#> f_A1_to_A2 0.5000000 deparm -#> -#> $start_transformed -#> value lower upper -#> parent_0 93.200000 -Inf Inf -#> log_k_parent -2.302585 -Inf Inf -#> log_k_A1 -2.301586 -Inf Inf -#> log_k_B1 -2.300587 -Inf Inf -#> log_k_C1 -2.299590 -Inf Inf -#> log_k_A2 -2.298593 -Inf Inf -#> f_parent_ilr_1 0.000000 -Inf Inf -#> f_parent_ilr_2 0.000000 -Inf Inf -#> f_A1_ilr_1 0.000000 -Inf Inf -#> -#> $fixed -#> value type -#> A1_0 0 state -#> B1_0 0 state -#> C1_0 0 state -#> A2_0 0 state -#> -#> $data -#> time variable observed predicted residual -#> 1 0 parent 93.20 91.918159794 1.2818402 -#> 2 1 parent 89.40 87.462788491 1.9372115 -#> 3 3 parent 79.70 79.189448055 0.5105519 -#> 4 7 parent 61.10 64.916531757 -3.8165318 -#> 5 14 parent 48.20 45.846828365 2.3531716 -#> 6 30 parent 15.90 20.704334210 -4.8043342 -#> 7 62 parent 6.50 4.222456793 2.2775432 -#> 8 100 parent 6.00 0.639147580 5.3608524 -#> 9 0 A1 NA 0.000000000 NA -#> 10 1 A1 NA 1.685461006 NA -#> 11 3 A1 0.55 4.746752202 -4.1967522 -#> 12 7 A1 6.87 9.773298725 -2.9032987 -#> 13 14 A1 17.08 15.767512526 1.3124875 -#> 14 30 A1 21.68 21.077890710 0.6021093 -#> 15 62 A1 15.77 18.279232408 -2.5092324 -#> 16 100 A1 13.63 11.743860400 1.8861396 -#> 17 0 B1 NA 0.000000000 NA -#> 18 1 B1 NA 0.862762059 NA -#> 19 3 B1 NA 2.418226457 NA -#> 20 7 B1 0.55 4.930176837 -4.3801768 -#> 21 14 B1 2.31 7.810248132 -5.5002481 -#> 22 30 B1 15.76 9.968281596 5.7917184 -#> 23 62 B1 6.36 7.745265792 -1.3852658 -#> 24 100 B1 3.74 4.271330056 -0.5313301 -#> 25 0 C1 NA 0.000000000 NA -#> 26 1 C1 0.55 1.829645786 -1.2796458 -#> 27 3 C1 3.20 4.910531064 -1.7105311 -#> 28 7 C1 5.46 9.171671206 -3.7116712 -#> 29 14 C1 12.55 12.431704739 0.1182953 -#> 30 30 C1 10.45 10.972842888 -0.5228429 -#> 31 62 C1 4.74 3.882970158 0.8570298 -#> 32 100 C1 4.33 0.782344364 3.5476556 -#> 33 0 A2 NA 0.000000000 NA -#> 34 1 A2 0.55 0.005272357 0.5447276 -#> 35 3 A2 1.41 0.044759575 1.3652404 -#> 36 7 A2 0.55 0.216973934 0.3330261 -#> 37 14 A2 1.29 0.709794102 0.5802059 -#> 38 30 A2 1.95 2.078585030 -0.1285850 -#> 39 62 A2 3.54 3.751927986 -0.2119280 -#> 40 100 A2 3.86 3.721800959 0.1381990 -#> -#> $atol -#> [1] 1e-08 -#> -#> $rtol -#> [1] 1e-10 -#> -#> $weight.ini -#> [1] "none" -#> -#> $reweight.tol -#> [1] 1e-08 -#> -#> $reweight.max.iter -#> [1] 10 -#> -#> $bparms.optim -#> parent_0 k_parent k_A1 k_B1 k_C1 -#> 91.91815979 0.04968519 0.01393165 0.01859846 0.06171564 -#> k_A2 f_parent_to_A1 f_parent_to_B1 f_parent_to_C1 f_A1_to_A2 -#> 0.02431549 0.38096192 0.19546676 0.42357132 0.44796066 -#> -#> $bparms.fixed -#> A1_0 B1_0 C1_0 A2_0 -#> 0 0 0 0 -#> -#> $bparms.ode -#> k_parent f_parent_to_A1 f_parent_to_B1 f_parent_to_C1 k_A1 -#> 0.04968519 0.38096192 0.19546676 0.42357132 0.01393165 -#> f_A1_to_A2 k_B1 k_C1 k_A2 -#> 0.44796066 0.01859846 0.06171564 0.02431549 -#> -#> $bparms.state -#> parent A1 B1 C1 A2 -#> 91.91816 0.00000 0.00000 0.00000 0.00000 -#> -#> $date -#> [1] "Fri Nov 18 15:20:45 2016" -#> -#> attr(,"class") -#> [1] "mkinfit" "modFit" </div></pre> + <span class='kw'>A2</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output 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'>data</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) + <span class='fu'>plot</span>(<span class='no'>fit</span>)</div><img src='schaefer07_complex_case-4.png' alt='' width='540' height='400' /><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 +#> 0.3809619 0.1954668 0.4235713 0.0000000 0.4479607 0.5520393 +#> +#> $SFORB +#> logical(0) +#> +#> $distimes +#> DT50 DT90 +#> parent 13.95078 46.34349 +#> A1 49.75343 165.27732 +#> B1 37.26906 123.80513 +#> C1 11.23131 37.30959 +#> A2 28.50640 94.69621 +#> </div><div class='input'> + <span class='co'># Compare with the results obtained in the original publication</span> + <span class='fu'>print</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 +#> 3 metabolite A1 formation fraction 0.3803 0.3696 2.9 +#> 4 metabolite A1 degradation rate 0.0139 0.0136 2.2 +#> 5 metabolite A1 DT50 49.9600 50.8900 1.8 +#> 6 metabolite B1 formation fraction 0.1866 0.1818 2.6 +#> 7 metabolite B1 degradation rate 0.0175 0.0172 1.7 +#> 8 metabolite B1 DT50 39.6100 40.2400 1.6 +#> 9 metabolite C1 formation fraction 0.4331 0.4486 3.5 +#> 10 metabolite C1 degradation rate 0.0638 0.0700 8.9 +#> 11 metabolite C1 DT50 10.8700 9.9000 9.8 +#> 12 metabolite A2 formation fraction 0.4529 0.4559 0.7 +#> 13 metabolite A2 degradation rate 0.0245 0.0244 0.4 +#> 14 metabolite A2 DT50 28.2400 28.4500 0.7</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index b334b3aa..8adb5aff 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -140,17 +140,17 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='fu'>summary</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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>)), <span class='no'>FOCUS_2006_A</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))</div><div class='output co'>#> mkin version: 0.9.44.9000 + <pre class="examples"><div class='input'> <span class='fu'>summary</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: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 18 15:20:45 2016 -#> Date of summary: Fri Nov 18 15:20:45 2016 +#> Date of fit: Fri Nov 18 15:44:43 2016 +#> Date of summary: Fri Nov 18 15:44:43 2016 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.081 s +#> Fitted with method Port using 35 model solutions performed in 0.085 s #> #> Weighting: none #> diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index 97407402..c2794427 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -137,722 +137,24 @@ <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'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> -<span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_SFO_lin</span>, <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<span class='no'>data</span>)</div><div class='output co'>#> Model cost at call 1 : 31054.59 -#> Model cost at call 3 : 31054.59 -#> Model cost at call 8 : 15089.57 -#> Model cost at call 9 : 11464.3 -#> Model cost at call 11 : 11464.1 -#> Model cost at call 16 : 5723.32 -#> Model cost at call 17 : 5723.318 -#> Model cost at call 19 : 5723.304 -#> Model cost at call 21 : 5723.304 -#> Model cost at call 24 : 3968.126 -#> Model cost at call 25 : 3968.124 -#> Model cost at call 28 : 3968.119 -#> Model cost at call 31 : 3416.421 -#> Model cost at call 32 : 3416.42 -#> Model cost at call 36 : 3416.418 -#> Model cost at call 38 : 866.5564 -#> Model cost at call 42 : 866.5557 -#> Model cost at call 45 : 670.4833 -#> Model cost at call 47 : 670.476 -#> Model cost at call 53 : 312.9905 -#> Model cost at call 57 : 312.9904 -#> Model cost at call 58 : 312.9904 -#> Model cost at call 61 : 287.8916 -#> Model cost at call 63 : 287.8916 -#> Model cost at call 66 : 287.8916 -#> Model cost at call 69 : 284.5441 -#> Model cost at call 71 : 284.5441 -#> Model cost at call 73 : 284.5441 -#> Model cost at call 76 : 283.4533 -#> Model cost at call 78 : 283.4533 -#> Model cost at call 83 : 282.1356 -#> Model cost at call 85 : 282.1356 -#> Model cost at call 88 : 282.1356 -#> Model cost at call 90 : 280.7846 -#> Model cost at call 92 : 280.7846 -#> Model cost at call 95 : 280.7846 -#> Model cost at call 97 : 278.4856 -#> Model cost at call 98 : 274.5025 -#> Model cost at call 99 : 269.2866 -#> Model cost at call 101 : 269.2866 -#> Model cost at call 102 : 269.2866 -#> Model cost at call 103 : 269.2866 -#> Model cost at call 106 : 254.1284 -#> Model cost at call 108 : 254.1283 -#> Model cost at call 109 : 254.1283 -#> Model cost at call 112 : 254.128 -#> Model cost at call 114 : 233.1376 -#> Model cost at call 116 : 233.1376 -#> Model cost at call 118 : 233.1375 -#> Model cost at call 121 : 227.5879 -#> Model cost at call 124 : 227.5879 -#> Model cost at call 125 : 227.5878 -#> Model cost at call 129 : 217.0041 -#> Model cost at call 133 : 217.0041 -#> Model cost at call 135 : 217.0041 -#> Model cost at call 136 : 215.1367 -#> Model cost at call 138 : 215.1367 -#> Model cost at call 143 : 213.3794 -#> Model cost at call 145 : 213.3794 -#> Model cost at call 150 : 211.0201 -#> Model cost at call 152 : 211.0201 -#> Model cost at call 154 : 211.0201 -#> Model cost at call 155 : 211.0201 -#> Model cost at call 157 : 210.6426 -#> Model cost at call 159 : 210.6426 -#> Model cost at call 160 : 210.6425 -#> Model cost at call 164 : 207.6331 -#> Model cost at call 167 : 207.6331 -#> Model cost at call 171 : 206.2366 -#> Model cost at call 173 : 206.2366 -#> Model cost at call 174 : 206.2366 -#> Model cost at call 178 : 204.8117 -#> Model cost at call 180 : 204.8117 -#> Model cost at call 185 : 204.7988 -#> Model cost at call 187 : 204.7988 -#> Model cost at call 190 : 204.7988 -#> Model cost at call 192 : 203.5122 -#> Model cost at call 194 : 203.5122 -#> Model cost at call 197 : 203.5122 -#> Model cost at call 198 : 203.5122 -#> Model cost at call 199 : 203.354 -#> Model cost at call 201 : 203.354 -#> Model cost at call 204 : 203.354 -#> Model cost at call 206 : 202.6825 -#> Model cost at call 208 : 202.6825 -#> Model cost at call 209 : 202.6825 -#> Model cost at call 212 : 202.6825 -#> Model cost at call 213 : 202.4582 -#> Model cost at call 215 : 202.4582 -#> Model cost at call 220 : 202.3261 -#> Model cost at call 222 : 202.3261 -#> Model cost at call 227 : 202.2306 -#> Model cost at call 229 : 202.2306 -#> Model cost at call 231 : 202.2306 -#> Model cost at call 234 : 202.115 -#> Model cost at call 236 : 202.115 -#> Model cost at call 238 : 202.115 -#> Model cost at call 241 : 202.0397 -#> Model cost at call 243 : 202.0397 -#> Model cost at call 248 : 201.8989 -#> Model cost at call 249 : 201.8551 -#> Model cost at call 252 : 201.8551 -#> Model cost at call 257 : 201.676 -#> Model cost at call 259 : 201.676 -#> Model cost at call 264 : 201.6285 -#> Model cost at call 266 : 201.6285 -#> Model cost at call 270 : 201.6284 -#> Model cost at call 271 : 201.5876 -#> Model cost at call 272 : 201.5876 -#> Model cost at call 278 : 201.5317 -#> Model cost at call 279 : 201.5317 -#> Model cost at call 286 : 201.5207 -#> Model cost at call 287 : 201.5207 -#> Model cost at call 289 : 201.5207 -#> Model cost at call 293 : 201.5207 -#> Model cost at call 294 : 201.5207 -#> Model cost at call 296 : 201.5174 -#> Model cost at call 301 : 201.5174 -#> Model cost at call 304 : 201.5169 -#> Model cost at call 305 : 201.5169 -#> Model cost at call 306 : 201.5169 -#> Model cost at call 309 : 201.5169 -#> Model cost at call 312 : 201.5169 -#> Model cost at call 314 : 201.5169 -#> Model cost at call 322 : 201.5169 -#> Model cost at call 325 : 201.5169 -#> Model cost at call 340 : 201.5169 -#> Optimisation by method Port successfully terminated.</div><div class='output co'>#> $par -#> parent_0 log_k_parent log_k_M1 log_k_M2 f_parent_ilr_1 -#> 102.0624835 -0.3020316 -1.2067882 -3.9007519 0.8491684 -#> f_M1_ilr_1 -#> 0.6780411 +<span class='no'>fit</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_SFO_lin</span>, <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>1</span>]]$<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'>fit</span>)</div><img src='synthetic_data_for_UBA_2014-10.png' alt='' width='540' height='400' /><div class='input'><span class='fu'>summary</span>(<span class='no'>fit</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 +#> R version: 3.3.2 +#> Date of fit: Fri Nov 18 16:16:12 2016 +#> Date of summary: Fri Nov 18 16:16:12 2016 #> -#> $ssr -#> [1] 201.5169 +#> 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 #> -#> $convergence -#> [1] 0 +#> Model predictions using solution type deSolve #> -#> $iterations -#> [1] 43 +#> Fitted with method Port using 351 model solutions performed in 2.193 s #> -#> $evaluations -#> function gradient -#> 56 281 +#> Weighting: none #> -#> $counts -#> [1] "relative convergence (4)" -#> -#> $hessian -#> parent_0 log_k_parent log_k_M1 log_k_M2 f_parent_ilr_1 -#> parent_0 8.433594 -29.66715 -18.40708 -68.90161 115.9976 -#> log_k_parent -29.667146 10561.33531 675.33998 55.94284 1666.8940 -#> log_k_M1 -18.407082 675.33998 6274.11801 44.01714 -614.5674 -#> log_k_M2 -68.901614 55.94284 44.01714 5021.66991 -2300.4467 -#> f_parent_ilr_1 115.997604 1666.89403 -614.56735 -2300.44667 3872.8569 -#> f_M1_ilr_1 92.819176 604.06870 1483.45826 -2755.79082 3098.9947 -#> f_M1_ilr_1 -#> parent_0 92.81918 -#> log_k_parent 604.06870 -#> log_k_M1 1483.45826 -#> log_k_M2 -2755.79082 -#> f_parent_ilr_1 3098.99466 -#> f_M1_ilr_1 3712.39824 -#> -#> $residuals -#> parent parent parent parent parent parent -#> 0.56248353 0.86248353 -5.17118695 1.22881305 0.70772795 3.50772795 -#> parent parent parent parent parent parent -#> -0.52282962 0.27717038 -3.49673606 -3.19999990 -0.60000000 -3.50000000 -#> M1 M1 M1 M1 M1 M1 -#> -1.61088639 -2.61088639 5.07026619 -0.42973381 0.38714436 -2.31285564 -#> M1 M1 M1 M1 M1 M1 -#> -3.80468869 0.79531131 -0.49999789 -3.20000000 -1.50000000 -0.60000000 -#> M2 M2 M2 M2 M2 M2 -#> -0.34517017 0.62526794 2.22526794 -0.07941701 -1.17941701 -3.83353798 -#> M2 M2 M2 M2 M2 M2 -#> 1.26646202 0.87274743 2.47274743 -0.21837410 0.98162590 -0.47130583 -#> M2 M2 M2 -#> -0.67130583 -4.27893112 2.22106888 -#> -#> $ms -#> [1] 5.1671 -#> -#> $var_ms -#> parent M1 M2 -#> 6.461983 5.750942 3.664121 -#> -#> $var_ms_unscaled -#> parent M1 M2 -#> 6.461983 5.750942 3.664121 -#> -#> $var_ms_unweighted -#> parent M1 M2 -#> 6.461983 5.750942 3.664121 -#> -#> $rank -#> [1] 6 -#> -#> $df.residual -#> [1] 33 -#> -#> $solution_type -#> [1] "deSolve" -#> -#> $transform_rates -#> [1] TRUE -#> -#> $transform_fractions -#> [1] TRUE -#> -#> $method.modFit -#> [1] "Port" -#> -#> $maxit.modFit -#> [1] "auto" -#> -#> $calls -#> [1] 351 -#> -#> $time -#> user system elapsed -#> 2.116 0.000 2.113 -#> -#> $mkinmod -#> <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 -#> -#> $observed -#> name time value override err -#> 1 parent 0 101.5 NA 1 -#> 2 parent 0 101.2 NA 1 -#> 3 parent 1 53.9 NA 1 -#> 4 parent 1 47.5 NA 1 -#> 5 parent 3 10.4 NA 1 -#> 6 parent 3 7.6 NA 1 -#> 7 parent 7 1.1 NA 1 -#> 8 parent 7 0.3 NA 1 -#> 9 parent 14 NA NA 1 -#> 10 parent 14 3.5 NA 1 -#> 11 parent 28 NA NA 1 -#> 12 parent 28 3.2 NA 1 -#> 13 parent 60 NA NA 1 -#> 14 parent 60 NA NA 1 -#> 15 parent 90 0.6 NA 1 -#> 16 parent 90 NA NA 1 -#> 17 parent 120 NA NA 1 -#> 18 parent 120 3.5 NA 1 -#> 19 M1 0 NA NA 1 -#> 20 M1 0 NA NA 1 -#> 21 M1 1 36.4 NA 1 -#> 22 M1 1 37.4 NA 1 -#> 23 M1 3 34.3 NA 1 -#> 24 M1 3 39.8 NA 1 -#> 25 M1 7 15.1 NA 1 -#> 26 M1 7 17.8 NA 1 -#> 27 M1 14 5.8 NA 1 -#> 28 M1 14 1.2 NA 1 -#> 29 M1 28 NA NA 1 -#> 30 M1 28 NA NA 1 -#> 31 M1 60 0.5 NA 1 -#> 32 M1 60 NA NA 1 -#> 33 M1 90 NA NA 1 -#> 34 M1 90 3.2 NA 1 -#> 35 M1 120 1.5 NA 1 -#> 36 M1 120 0.6 NA 1 -#> 37 M2 0 NA NA 1 -#> 38 M2 0 NA NA 1 -#> 39 M2 1 NA NA 1 -#> 40 M2 1 4.8 NA 1 -#> 41 M2 3 20.9 NA 1 -#> 42 M2 3 19.3 NA 1 -#> 43 M2 7 42.0 NA 1 -#> 44 M2 7 43.1 NA 1 -#> 45 M2 14 49.4 NA 1 -#> 46 M2 14 44.3 NA 1 -#> 47 M2 28 34.6 NA 1 -#> 48 M2 28 33.0 NA 1 -#> 49 M2 60 18.8 NA 1 -#> 50 M2 60 17.6 NA 1 -#> 51 M2 90 10.6 NA 1 -#> 52 M2 90 10.8 NA 1 -#> 53 M2 120 9.8 NA 1 -#> 54 M2 120 3.3 NA 1 -#> -#> $obs_vars -#> [1] "parent" "M1" "M2" -#> -#> $predicted -#> name time value -#> 1 parent 0.000000 1.020625e+02 -#> 2 parent 1.000000 4.872881e+01 -#> 3 parent 1.212121 4.165603e+01 -#> 4 parent 2.424242 1.700159e+01 -#> 5 parent 3.000000 1.110773e+01 -#> 6 parent 3.636364 6.939072e+00 -#> 7 parent 4.848485 2.832130e+00 -#> 8 parent 6.060606 1.155912e+00 -#> 9 parent 7.000000 5.771704e-01 -#> 10 parent 7.272727 4.717769e-01 -#> 11 parent 8.484848 1.925522e-01 -#> 12 parent 9.696970 7.858872e-02 -#> 13 parent 10.909091 3.207539e-02 -#> 14 parent 12.121212 1.309133e-02 -#> 15 parent 13.333333 5.343128e-03 -#> 16 parent 14.000000 3.263939e-03 -#> 17 parent 14.545455 2.180757e-03 -#> 18 parent 15.757576 8.900590e-04 -#> 19 parent 16.969697 3.632705e-04 -#> 20 parent 18.181818 1.482660e-04 -#> 21 parent 19.393939 6.051327e-05 -#> 22 parent 20.606061 2.469808e-05 -#> 23 parent 21.818182 1.008035e-05 -#> 24 parent 23.030303 4.114467e-06 -#> 25 parent 24.242424 1.679140e-06 -#> 26 parent 25.454545 6.853728e-07 -#> 27 parent 26.666667 2.797450e-07 -#> 28 parent 27.878788 1.142138e-07 -#> 29 parent 28.000000 1.044512e-07 -#> 30 parent 29.090909 4.657425e-08 -#> 31 parent 30.303030 1.900245e-08 -#> 32 parent 31.515152 7.760238e-09 -#> 33 parent 32.727273 3.164577e-09 -#> 34 parent 33.939394 1.291779e-09 -#> 35 parent 35.151515 5.261577e-10 -#> 36 parent 36.363636 2.132915e-10 -#> 37 parent 37.575758 8.767818e-11 -#> 38 parent 38.787879 3.442792e-11 -#> 39 parent 40.000000 1.827291e-11 -#> 40 parent 41.212121 3.771071e-12 -#> 41 parent 42.424242 6.084856e-12 -#> 42 parent 43.636364 -3.377858e-12 -#> 43 parent 44.848485 5.870338e-12 -#> 44 parent 46.060606 -6.263257e-12 -#> 45 parent 47.272727 8.743492e-12 -#> 46 parent 48.484848 -9.381771e-12 -#> 47 parent 49.696970 1.403389e-11 -#> 48 parent 50.909091 -3.592528e-11 -#> 49 parent 52.121212 -8.487459e-11 -#> 50 parent 53.333333 -3.309153e-12 -#> 51 parent 54.545455 -2.966799e-11 -#> 52 parent 55.757576 -4.723329e-11 -#> 53 parent 56.969697 7.635833e-11 -#> 54 parent 58.181818 -1.887064e-11 -#> 55 parent 59.393939 -1.548352e-10 -#> 56 parent 60.000000 -1.053819e-10 -#> 57 parent 60.606061 5.780435e-12 -#> 58 parent 61.818182 9.056244e-11 -#> 59 parent 63.030303 -8.889581e-11 -#> 60 parent 64.242424 -6.653389e-11 -#> 61 parent 65.454545 1.181114e-10 -#> 62 parent 66.666667 -9.226329e-12 -#> 63 parent 67.878788 -8.897326e-11 -#> 64 parent 69.090909 1.984998e-10 -#> 65 parent 70.303030 3.255550e-11 -#> 66 parent 71.515152 -2.991002e-10 -#> 67 parent 72.727273 2.254268e-10 -#> 68 parent 73.939394 2.696039e-10 -#> 69 parent 75.151515 1.226806e-10 -#> 70 parent 76.363636 3.447399e-11 -#> 71 parent 77.575758 2.048902e-11 -#> 72 parent 78.787879 6.830755e-12 -#> 73 parent 80.000000 8.242171e-13 -#> 74 parent 81.212121 -5.357740e-12 -#> 75 parent 82.424242 2.198907e-11 -#> 76 parent 83.636364 3.739511e-11 -#> 77 parent 84.848485 -6.616091e-12 -#> 78 parent 86.060606 -2.562689e-12 -#> 79 parent 87.272727 4.089395e-11 -#> 80 parent 88.484848 -2.042159e-11 -#> 81 parent 89.696970 -4.088127e-11 -#> 82 parent 90.000000 -1.874889e-11 -#> 83 parent 90.909091 4.225747e-11 -#> 84 parent 92.121212 8.054402e-12 -#> 85 parent 93.333333 3.917595e-12 -#> 86 parent 94.545455 6.591454e-12 -#> 87 parent 95.757576 2.790958e-11 -#> 88 parent 96.969697 2.720721e-12 -#> 89 parent 98.181818 -1.304470e-12 -#> 90 parent 99.393939 1.345055e-11 -#> 91 parent 100.606061 -9.662077e-12 -#> 92 parent 101.818182 -2.086798e-11 -#> 93 parent 103.030303 9.332507e-12 -#> 94 parent 104.242424 -6.752606e-12 -#> 95 parent 105.454545 -3.326620e-11 -#> 96 parent 106.666667 2.500680e-11 -#> 97 parent 107.878788 2.184148e-11 -#> 98 parent 109.090909 -5.985657e-11 -#> 99 parent 110.303030 -8.750836e-14 -#> 100 parent 111.515152 1.820588e-12 -#> 101 parent 112.727273 -1.261472e-11 -#> 102 parent 113.939394 1.455439e-11 -#> 103 parent 115.151515 1.945812e-12 -#> 104 parent 116.363636 9.598249e-13 -#> 105 parent 117.575758 1.724679e-12 -#> 106 parent 118.787879 -1.334504e-12 -#> 107 parent 120.000000 -2.804801e-11 -#> 108 M1 0.000000 0.000000e+00 -#> 109 M1 1.000000 3.478911e+01 -#> 110 M1 1.212121 3.791354e+01 -#> 111 M1 2.424242 4.185645e+01 -#> 112 M1 3.000000 3.937027e+01 -#> 113 M1 3.636364 3.544167e+01 -#> 114 M1 4.848485 2.723995e+01 -#> 115 M1 6.060606 2.000711e+01 -#> 116 M1 7.000000 1.548714e+01 -#> 117 M1 7.272727 1.435144e+01 -#> 118 M1 8.484848 1.016177e+01 -#> 119 M1 9.696970 7.142649e+00 -#> 120 M1 10.909091 4.999441e+00 -#> 121 M1 12.121212 3.490801e+00 -#> 122 M1 13.333333 2.433954e+00 -#> 123 M1 14.000000 1.995311e+00 -#> 124 M1 14.545455 1.695664e+00 -#> 125 M1 15.757576 1.180746e+00 -#> 126 M1 16.969697 8.219589e-01 -#> 127 M1 18.181818 5.720991e-01 -#> 128 M1 19.393939 3.981531e-01 -#> 129 M1 20.606061 2.770793e-01 -#> 130 M1 21.818182 1.928162e-01 -#> 131 M1 23.030303 1.341758e-01 -#> 132 M1 24.242424 9.336844e-02 -#> 133 M1 25.454545 6.497152e-02 -#> 134 M1 26.666667 4.521101e-02 -#> 135 M1 27.878788 3.146041e-02 -#> 136 M1 28.000000 3.034005e-02 -#> 137 M1 29.090909 2.189192e-02 -#> 138 M1 30.303030 1.523362e-02 -#> 139 M1 31.515152 1.060040e-02 -#> 140 M1 32.727273 7.376345e-03 -#> 141 M1 33.939394 5.132870e-03 -#> 142 M1 35.151515 3.571730e-03 -#> 143 M1 36.363636 2.485406e-03 -#> 144 M1 37.575758 1.729482e-03 -#> 145 M1 38.787879 1.203467e-03 -#> 146 M1 40.000000 8.374380e-04 -#> 147 M1 41.212121 5.827347e-04 -#> 148 M1 42.424242 4.054989e-04 -#> 149 M1 43.636364 2.821681e-04 -#> 150 M1 44.848485 1.963481e-04 -#> 151 M1 46.060606 1.366297e-04 -#> 152 M1 47.272727 9.507439e-05 -#> 153 M1 48.484848 6.615797e-05 -#> 154 M1 49.696970 4.603629e-05 -#> 155 M1 50.909091 3.203434e-05 -#> 156 M1 52.121212 2.229196e-05 -#> 157 M1 53.333333 1.551223e-05 -#> 158 M1 54.545455 1.079420e-05 -#> 159 M1 55.757576 7.511255e-06 -#> 160 M1 56.969697 5.226640e-06 -#> 161 M1 58.181818 3.636450e-06 -#> 162 M1 59.393939 2.530191e-06 -#> 163 M1 60.000000 2.110651e-06 -#> 164 M1 60.606061 1.760625e-06 -#> 165 M1 61.818182 1.225095e-06 -#> 166 M1 63.030303 8.527010e-07 -#> 167 M1 64.242424 5.934161e-07 -#> 168 M1 65.454545 4.127474e-07 -#> 169 M1 66.666667 2.874114e-07 -#> 170 M1 67.878788 2.001921e-07 -#> 171 M1 69.090909 1.389331e-07 -#> 172 M1 70.303030 9.678549e-08 -#> 173 M1 71.515152 6.777214e-08 -#> 174 M1 72.727273 4.658761e-08 -#> 175 M1 73.939394 3.226837e-08 -#> 176 M1 75.151515 2.253752e-08 -#> 177 M1 76.363636 1.574843e-08 -#> 178 M1 77.575758 1.096303e-08 -#> 179 M1 78.787879 7.638209e-09 -#> 180 M1 80.000000 5.319996e-09 -#> 181 M1 81.212121 3.709993e-09 -#> 182 M1 82.424242 2.548810e-09 -#> 183 M1 83.636364 1.744629e-09 -#> 184 M1 84.848485 1.256081e-09 -#> 185 M1 86.060606 8.714672e-10 -#> 186 M1 87.272727 5.511830e-10 -#> 187 M1 88.484848 4.466725e-10 -#> 188 M1 89.696970 3.452654e-10 -#> 189 M1 90.000000 2.913252e-10 -#> 190 M1 90.909091 1.489262e-10 -#> 191 M1 92.121212 1.311985e-10 -#> 192 M1 93.333333 9.347248e-11 -#> 193 M1 94.545455 6.004640e-11 -#> 194 M1 95.757576 1.166926e-11 -#> 195 M1 96.969697 2.968203e-11 -#> 196 M1 98.181818 2.478228e-11 -#> 197 M1 99.393939 -1.291838e-12 -#> 198 M1 100.606061 2.366481e-11 -#> 199 M1 101.818182 3.472871e-11 -#> 200 M1 103.030303 -6.633877e-12 -#> 201 M1 104.242424 1.248743e-11 -#> 202 M1 105.454545 4.557313e-11 -#> 203 M1 106.666667 -3.046261e-11 -#> 204 M1 107.878788 -2.693037e-11 -#> 205 M1 109.090909 7.816593e-11 -#> 206 M1 110.303030 7.276098e-13 -#> 207 M1 111.515152 -1.922924e-12 -#> 208 M1 112.727273 1.658481e-11 -#> 209 M1 113.939394 -1.858452e-11 -#> 210 M1 115.151515 -2.368198e-12 -#> 211 M1 116.363636 -1.138989e-12 -#> 212 M1 117.575758 -2.157011e-12 -#> 213 M1 118.787879 1.771568e-12 -#> 214 M1 120.000000 3.624738e-11 -#> 215 M2 0.000000 0.000000e+00 -#> 216 M2 1.000000 4.454830e+00 -#> 217 M2 1.212121 6.103803e+00 -#> 218 M2 2.424242 1.667567e+01 -#> 219 M2 3.000000 2.152527e+01 -#> 220 M2 3.636364 2.637280e+01 -#> 221 M2 4.848485 3.384106e+01 -#> 222 M2 6.060606 3.910279e+01 -#> 223 M2 7.000000 4.192058e+01 -#> 224 M2 7.272727 4.256708e+01 -#> 225 M2 8.484848 4.467909e+01 -#> 226 M2 9.696970 4.581396e+01 -#> 227 M2 10.909091 4.625927e+01 -#> 228 M2 12.121212 4.622588e+01 -#> 229 M2 13.333333 4.586473e+01 -#> 230 M2 14.000000 4.556646e+01 -#> 231 M2 14.545455 4.528249e+01 -#> 232 M2 15.757576 4.455394e+01 -#> 233 M2 16.969697 4.373119e+01 -#> 234 M2 18.181818 4.285048e+01 -#> 235 M2 19.393939 4.193685e+01 -#> 236 M2 20.606061 4.100759e+01 -#> 237 M2 21.818182 4.007456e+01 -#> 238 M2 23.030303 3.914584e+01 -#> 239 M2 24.242424 3.822688e+01 -#> 240 M2 25.454545 3.732133e+01 -#> 241 M2 26.666667 3.643154e+01 -#> 242 M2 27.878788 3.555901e+01 -#> 243 M2 28.000000 3.547275e+01 -#> 244 M2 29.090909 3.470463e+01 -#> 245 M2 30.303030 3.386887e+01 -#> 246 M2 31.515152 3.305190e+01 -#> 247 M2 32.727273 3.225371e+01 -#> 248 M2 33.939394 3.147416e+01 -#> 249 M2 35.151515 3.071300e+01 -#> 250 M2 36.363636 2.996993e+01 -#> 251 M2 37.575758 2.924463e+01 -#> 252 M2 38.787879 2.853672e+01 -#> 253 M2 40.000000 2.784585e+01 -#> 254 M2 41.212121 2.717163e+01 -#> 255 M2 42.424242 2.651368e+01 -#> 256 M2 43.636364 2.587163e+01 -#> 257 M2 44.848485 2.524511e+01 -#> 258 M2 46.060606 2.463374e+01 -#> 259 M2 47.272727 2.403716e+01 -#> 260 M2 48.484848 2.345502e+01 -#> 261 M2 49.696970 2.288698e+01 -#> 262 M2 50.909091 2.233268e+01 -#> 263 M2 52.121212 2.179181e+01 -#> 264 M2 53.333333 2.126404e+01 -#> 265 M2 54.545455 2.074905e+01 -#> 266 M2 55.757576 2.024653e+01 -#> 267 M2 56.969697 1.975618e+01 -#> 268 M2 58.181818 1.927770e+01 -#> 269 M2 59.393939 1.881081e+01 -#> 270 M2 60.000000 1.858163e+01 -#> 271 M2 60.606061 1.835523e+01 -#> 272 M2 61.818182 1.791068e+01 -#> 273 M2 63.030303 1.747690e+01 -#> 274 M2 64.242424 1.705363e+01 -#> 275 M2 65.454545 1.664061e+01 -#> 276 M2 66.666667 1.623759e+01 -#> 277 M2 67.878788 1.584433e+01 -#> 278 M2 69.090909 1.546059e+01 -#> 279 M2 70.303030 1.508615e+01 -#> 280 M2 71.515152 1.472078e+01 -#> 281 M2 72.727273 1.436425e+01 -#> 282 M2 73.939394 1.401636e+01 -#> 283 M2 75.151515 1.367690e+01 -#> 284 M2 76.363636 1.334566e+01 -#> 285 M2 77.575758 1.302244e+01 -#> 286 M2 78.787879 1.270705e+01 -#> 287 M2 80.000000 1.239929e+01 -#> 288 M2 81.212121 1.209899e+01 -#> 289 M2 82.424242 1.180597e+01 -#> 290 M2 83.636364 1.152004e+01 -#> 291 M2 84.848485 1.124103e+01 -#> 292 M2 86.060606 1.096878e+01 -#> 293 M2 87.272727 1.070313e+01 -#> 294 M2 88.484848 1.044391e+01 -#> 295 M2 89.696970 1.019097e+01 -#> 296 M2 90.000000 1.012869e+01 -#> 297 M2 90.909091 9.944151e+00 -#> 298 M2 92.121212 9.703312e+00 -#> 299 M2 93.333333 9.468307e+00 -#> 300 M2 94.545455 9.238993e+00 -#> 301 M2 95.757576 9.015233e+00 -#> 302 M2 96.969697 8.796892e+00 -#> 303 M2 98.181818 8.583839e+00 -#> 304 M2 99.393939 8.375946e+00 -#> 305 M2 100.606061 8.173088e+00 -#> 306 M2 101.818182 7.975143e+00 -#> 307 M2 103.030303 7.781992e+00 -#> 308 M2 104.242424 7.593520e+00 -#> 309 M2 105.454545 7.409611e+00 -#> 310 M2 106.666667 7.230157e+00 -#> 311 M2 107.878788 7.055049e+00 -#> 312 M2 109.090909 6.884182e+00 -#> 313 M2 110.303030 6.717454e+00 -#> 314 M2 111.515152 6.554763e+00 -#> 315 M2 112.727273 6.396012e+00 -#> 316 M2 113.939394 6.241107e+00 -#> 317 M2 115.151515 6.089953e+00 -#> 318 M2 116.363636 5.942460e+00 -#> 319 M2 117.575758 5.798538e+00 -#> 320 M2 118.787879 5.658103e+00 -#> 321 M2 120.000000 5.521069e+00 -#> -#> $cost -#> function (P) -#> { -#> assign("calls", calls + 1, inherits = TRUE) -#> if (trace_parms) -#> cat(P, "\n") -#> if (length(state.ini.optim) > 0) { -#> odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed) -#> names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames) -#> } -#> else { -#> odeini <- state.ini.fixed -#> names(odeini) <- state.ini.fixed.boxnames -#> } -#> odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], -#> transparms.fixed) -#> parms <- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates, -#> transform_fractions = transform_fractions) -#> out <- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type, -#> use_compiled = use_compiled, method.ode = method.ode, -#> atol = atol, rtol = rtol, ...) -#> assign("out_predicted", out, inherits = TRUE) -#> mC <- modCost(out, observed, y = "value", err = err, weight = weight, -#> scaleVar = scaleVar) -#> if (mC$model < cost.old) { -#> if (!quiet) -#> cat("Model cost at call ", calls, ": ", mC$model, -#> "\n") -#> if (plot) { -#> outtimes_plot = seq(min(observed$time), max(observed$time), -#> length.out = 100) -#> out_plot <- mkinpredict(mkinmod, parms, odeini, outtimes_plot, -#> solution_type = solution_type, use_compiled = use_compiled, -#> method.ode = method.ode, atol = atol, rtol = rtol, -#> ...) -#> plot(0, type = "n", xlim = range(observed$time), -#> ylim = c(0, max(observed$value, na.rm = TRUE)), -#> xlab = "Time", ylab = "Observed") -#> col_obs <- pch_obs <- 1:length(obs_vars) -#> lty_obs <- rep(1, length(obs_vars)) -#> names(col_obs) <- names(pch_obs) <- names(lty_obs) <- obs_vars -#> for (obs_var in obs_vars) { -#> points(subset(observed, name == obs_var, c(time, -#> value)), pch = pch_obs[obs_var], col = col_obs[obs_var]) -#> } -#> matlines(out_plot$time, out_plot[-1], col = col_obs, -#> lty = lty_obs) -#> legend("topright", inset = c(0.05, 0.05), legend = obs_vars, -#> col = col_obs, pch = pch_obs, lty = 1:length(pch_obs)) -#> } -#> assign("cost.old", mC$model, inherits = TRUE) -#> } -#> return(mC) -#> } -#> <environment: 0x3ff8420> -#> -#> $cost_notrans -#> function (P) -#> { -#> if (length(state.ini.optim) > 0) { -#> odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed) -#> names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames) -#> } -#> else { -#> odeini <- state.ini.fixed -#> names(odeini) <- state.ini.fixed.boxnames -#> } -#> odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], -#> parms.fixed) -#> out <- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type, -#> use_compiled = use_compiled, method.ode = method.ode, -#> atol = atol, rtol = rtol, ...) -#> mC <- modCost(out, observed, y = "value", err = err, weight = weight, -#> scaleVar = scaleVar) -#> return(mC) -#> } -#> <environment: 0x3ff8420> -#> -#> $hessian_notrans -#> parent_0 k_parent k_M1 k_M2 f_parent_to_M1 -#> parent_0 8.433594 -40.12785 -61.53042 -3406.469 461.2995 -#> k_parent -40.127847 19322.43697 3053.54654 3740.691 8966.4055 -#> k_M1 -61.530424 3053.54654 70106.05907 7274.316 -8169.6841 -#> k_M2 -3406.468786 3740.69112 7274.31610 12274341.595 -452294.7998 -#> f_parent_to_M1 461.299501 8966.40549 -8169.68407 -452294.800 61249.1755 -#> f_M1_to_M2 327.648696 2884.22668 17504.38651 -480941.198 43503.6440 -#> f_M1_to_M2 -#> parent_0 327.6487 -#> k_parent 2884.2267 -#> k_M1 17504.3865 -#> k_M2 -480941.1983 -#> f_parent_to_M1 43503.6440 -#> f_M1_to_M2 46258.9775 -#> -#> $start +#> Starting values for parameters to be optimised: #> value type #> parent_0 101.3500 state #> k_parent 0.1000 deparm @@ -861,7 +163,7 @@ #> f_parent_to_M1 0.5000 deparm #> f_M1_to_M2 0.5000 deparm #> -#> $start_transformed +#> Starting values for the transformed parameters actually optimised: #> value lower upper #> parent_0 101.350000 -Inf Inf #> log_k_parent -2.302585 -Inf Inf @@ -870,106 +172,126 @@ #> f_parent_ilr_1 0.000000 -Inf Inf #> f_M1_ilr_1 0.000000 -Inf Inf #> -#> $fixed +#> Fixed parameter values: #> value type #> M1_0 0 state #> M2_0 0 state #> -#> $data -#> time variable observed predicted residual -#> 1 0 parent 101.5 1.020625e+02 -0.56248353 -#> 2 0 parent 101.2 1.020625e+02 -0.86248353 -#> 3 1 parent 53.9 4.872881e+01 5.17118695 -#> 4 1 parent 47.5 4.872881e+01 -1.22881305 -#> 5 3 parent 10.4 1.110773e+01 -0.70772795 -#> 6 3 parent 7.6 1.110773e+01 -3.50772795 -#> 7 7 parent 1.1 5.771704e-01 0.52282962 -#> 8 7 parent 0.3 5.771704e-01 -0.27717038 -#> 9 14 parent NA 3.263939e-03 NA -#> 10 14 parent 3.5 3.263939e-03 3.49673606 -#> 11 28 parent NA 1.044512e-07 NA -#> 12 28 parent 3.2 1.044512e-07 3.19999990 -#> 13 60 parent NA -1.053819e-10 NA -#> 14 60 parent NA -1.053819e-10 NA -#> 15 90 parent 0.6 -1.874889e-11 0.60000000 -#> 16 90 parent NA -1.874889e-11 NA -#> 17 120 parent NA -2.804801e-11 NA -#> 18 120 parent 3.5 -2.804801e-11 3.50000000 -#> 19 0 M1 NA 0.000000e+00 NA -#> 20 0 M1 NA 0.000000e+00 NA -#> 21 1 M1 36.4 3.478911e+01 1.61088639 -#> 22 1 M1 37.4 3.478911e+01 2.61088639 -#> 23 3 M1 34.3 3.937027e+01 -5.07026619 -#> 24 3 M1 39.8 3.937027e+01 0.42973381 -#> 25 7 M1 15.1 1.548714e+01 -0.38714436 -#> 26 7 M1 17.8 1.548714e+01 2.31285564 -#> 27 14 M1 5.8 1.995311e+00 3.80468869 -#> 28 14 M1 1.2 1.995311e+00 -0.79531131 -#> 29 28 M1 NA 3.034005e-02 NA -#> 30 28 M1 NA 3.034005e-02 NA -#> 31 60 M1 0.5 2.110651e-06 0.49999789 -#> 32 60 M1 NA 2.110651e-06 NA -#> 33 90 M1 NA 2.913252e-10 NA -#> 34 90 M1 3.2 2.913252e-10 3.20000000 -#> 35 120 M1 1.5 3.624738e-11 1.50000000 -#> 36 120 M1 0.6 3.624738e-11 0.60000000 -#> 37 0 M2 NA 0.000000e+00 NA -#> 38 0 M2 NA 0.000000e+00 NA -#> 39 1 M2 NA 4.454830e+00 NA -#> 40 1 M2 4.8 4.454830e+00 0.34517017 -#> 41 3 M2 20.9 2.152527e+01 -0.62526794 -#> 42 3 M2 19.3 2.152527e+01 -2.22526794 -#> 43 7 M2 42.0 4.192058e+01 0.07941701 -#> 44 7 M2 43.1 4.192058e+01 1.17941701 -#> 45 14 M2 49.4 4.556646e+01 3.83353798 -#> 46 14 M2 44.3 4.556646e+01 -1.26646202 -#> 47 28 M2 34.6 3.547275e+01 -0.87274743 -#> 48 28 M2 33.0 3.547275e+01 -2.47274743 -#> 49 60 M2 18.8 1.858163e+01 0.21837410 -#> 50 60 M2 17.6 1.858163e+01 -0.98162590 -#> 51 90 M2 10.6 1.012869e+01 0.47130583 -#> 52 90 M2 10.8 1.012869e+01 0.67130583 -#> 53 120 M2 9.8 5.521069e+00 4.27893112 -#> 54 120 M2 3.3 5.521069e+00 -2.22106888 -#> -#> $atol -#> [1] 1e-08 -#> -#> $rtol -#> [1] 1e-10 -#> -#> $weight.ini -#> [1] "none" -#> -#> $reweight.tol -#> [1] 1e-08 -#> -#> $reweight.max.iter -#> [1] 10 -#> -#> $bparms.optim -#> parent_0 k_parent k_M1 k_M2 f_parent_to_M1 -#> 102.0624835 0.7393147 0.2991566 0.0202267 0.7686858 -#> f_M1_to_M2 -#> 0.7229005 -#> -#> $bparms.fixed -#> M1_0 M2_0 -#> 0 0 -#> -#> $bparms.ode -#> k_parent f_parent_to_M1 k_M1 f_M1_to_M2 k_M2 -#> 0.7393147 0.7686858 0.2991566 0.7229005 0.0202267 -#> -#> $bparms.state -#> parent M1 M2 -#> 102.0625 0.0000 0.0000 -#> -#> $date -#> [1] "Fri Nov 18 15:20:48 2016" -#> -#> attr(,"class") -#> [1] "mkinfit" "modFit" </div><div class='input'> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 102.1000 1.71400 98.5800 105.5000 +#> log_k_parent -0.3020 0.04294 -0.3894 -0.2147 +#> log_k_M1 -1.2070 0.07599 -1.3610 -1.0520 +#> log_k_M2 -3.9010 0.06952 -4.0420 -3.7590 +#> f_parent_ilr_1 0.8492 0.18090 0.4812 1.2170 +#> f_M1_ilr_1 0.6780 0.18860 0.2943 1.0620 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_M1 log_k_M2 f_parent_ilr_1 +#> parent_0 1.00000 0.40213 -0.1693 0.02912 -0.4726 +#> log_k_parent 0.40213 1.00000 -0.4210 0.07241 -0.5837 +#> log_k_M1 -0.16931 -0.42102 1.0000 -0.37657 0.7438 +#> log_k_M2 0.02912 0.07241 -0.3766 1.00000 -0.2518 +#> f_parent_ilr_1 -0.47263 -0.58367 0.7438 -0.25177 1.0000 +#> f_M1_ilr_1 0.17148 0.42642 -0.8054 0.52648 -0.8602 +#> f_M1_ilr_1 +#> parent_0 0.1715 +#> log_k_parent 0.4264 +#> log_k_M1 -0.8054 +#> log_k_M2 0.5265 +#> f_parent_ilr_1 -0.8602 +#> f_M1_ilr_1 1.0000 +#> +#> Residual standard error: 2.471 on 33 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_0 102.10000 59.55 1.815e-35 98.58000 105.5000 +#> k_parent 0.73930 23.29 2.337e-22 0.67750 0.8068 +#> k_M1 0.29920 13.16 5.552e-15 0.25630 0.3492 +#> k_M2 0.02023 14.38 4.497e-16 0.01756 0.0233 +#> f_parent_to_M1 0.76870 16.90 4.093e-18 0.66380 0.8483 +#> f_M1_to_M2 0.72290 13.53 2.557e-15 0.60260 0.8178 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 8.454 6 17 +#> parent 8.660 2 6 +#> M1 10.583 2 5 +#> M2 3.586 2 6 +#> +#> Resulting formation fractions: +#> ff +#> parent_M1 0.7687 +#> parent_sink 0.2313 +#> M1_M2 0.7229 +#> M1_sink 0.2771 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 0.9376 3.114 +#> M1 2.3170 7.697 +#> M2 34.2689 113.839 +#> +#> Data: +#> time variable observed predicted residual +#> 0 parent 101.5 1.021e+02 -0.56248 +#> 0 parent 101.2 1.021e+02 -0.86248 +#> 1 parent 53.9 4.873e+01 5.17119 +#> 1 parent 47.5 4.873e+01 -1.22881 +#> 3 parent 10.4 1.111e+01 -0.70773 +#> 3 parent 7.6 1.111e+01 -3.50773 +#> 7 parent 1.1 5.772e-01 0.52283 +#> 7 parent 0.3 5.772e-01 -0.27717 +#> 14 parent NA 3.264e-03 NA +#> 14 parent 3.5 3.264e-03 3.49674 +#> 28 parent NA 1.045e-07 NA +#> 28 parent 3.2 1.045e-07 3.20000 +#> 60 parent NA -1.054e-10 NA +#> 60 parent NA -1.054e-10 NA +#> 90 parent 0.6 -1.875e-11 0.60000 +#> 90 parent NA -1.875e-11 NA +#> 120 parent NA -2.805e-11 NA +#> 120 parent 3.5 -2.805e-11 3.50000 +#> 0 M1 NA 0.000e+00 NA +#> 0 M1 NA 0.000e+00 NA +#> 1 M1 36.4 3.479e+01 1.61089 +#> 1 M1 37.4 3.479e+01 2.61089 +#> 3 M1 34.3 3.937e+01 -5.07027 +#> 3 M1 39.8 3.937e+01 0.42973 +#> 7 M1 15.1 1.549e+01 -0.38714 +#> 7 M1 17.8 1.549e+01 2.31286 +#> 14 M1 5.8 1.995e+00 3.80469 +#> 14 M1 1.2 1.995e+00 -0.79531 +#> 28 M1 NA 3.034e-02 NA +#> 28 M1 NA 3.034e-02 NA +#> 60 M1 0.5 2.111e-06 0.50000 +#> 60 M1 NA 2.111e-06 NA +#> 90 M1 NA 2.913e-10 NA +#> 90 M1 3.2 2.913e-10 3.20000 +#> 120 M1 1.5 3.625e-11 1.50000 +#> 120 M1 0.6 3.625e-11 0.60000 +#> 0 M2 NA 0.000e+00 NA +#> 0 M2 NA 0.000e+00 NA +#> 1 M2 NA 4.455e+00 NA +#> 1 M2 4.8 4.455e+00 0.34517 +#> 3 M2 20.9 2.153e+01 -0.62527 +#> 3 M2 19.3 2.153e+01 -2.22527 +#> 7 M2 42.0 4.192e+01 0.07942 +#> 7 M2 43.1 4.192e+01 1.17942 +#> 14 M2 49.4 4.557e+01 3.83354 +#> 14 M2 44.3 4.557e+01 -1.26646 +#> 28 M2 34.6 3.547e+01 -0.87275 +#> 28 M2 33.0 3.547e+01 -2.47275 +#> 60 M2 18.8 1.858e+01 0.21837 +#> 60 M2 17.6 1.858e+01 -0.98163 +#> 90 M2 10.6 1.013e+01 0.47131 +#> 90 M2 10.8 1.013e+01 0.67131 +#> 120 M2 9.8 5.521e+00 4.27893 +#> 120 M2 3.3 5.521e+00 -2.22107</div><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> diff --git a/docs/reference/synthetic_data_for_UBA_2014-10.png b/docs/reference/synthetic_data_for_UBA_2014-10.png Binary files differnew file mode 100644 index 00000000..b98940ff --- /dev/null +++ b/docs/reference/synthetic_data_for_UBA_2014-10.png diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 08fbf368..2aff0468 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -149,8 +149,8 @@ <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'>summary</span>(<span class='no'>fit</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>) <span class='co'># See transformed and backtransformed parameters</span></div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 18 15:20:49 2016 -#> Date of summary: Fri Nov 18 15:20:49 2016 +#> Date of fit: Fri Nov 18 16:24:02 2016 +#> Date of summary: Fri Nov 18 16:24:02 2016 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -158,7 +158,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.681 s +#> Fitted with method Port using 153 model solutions performed in 0.708 s #> #> Weighting: none #> @@ -223,148 +223,11 @@ #> parent 7.023 23.33 #> m1 131.761 437.70</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>)</div><div class='output co'>#> Model cost at call 1 : 18915.53 -#> Model cost at call 2 : 18915.53 -#> Model cost at call 7 : 10205.88 -#> Model cost at call 10 : 10205.05 -#> Model cost at call 13 : 8136.609 -#> Model cost at call 18 : 2504.352 -#> Model cost at call 20 : 2504.35 -#> Model cost at call 22 : 2504.285 -#> Model cost at call 25 : 1747.542 -#> Model cost at call 27 : 1745.941 -#> Model cost at call 29 : 1745.431 -#> Model cost at call 30 : 1341.034 -#> Model cost at call 34 : 1341.034 -#> Model cost at call 35 : 1032.65 -#> Model cost at call 39 : 1032.649 -#> Model cost at call 40 : 919.9522 -#> Model cost at call 42 : 919.952 -#> Model cost at call 44 : 919.9518 -#> Model cost at call 45 : 903.8272 -#> Model cost at call 47 : 903.827 -#> Model cost at call 49 : 903.8268 -#> Model cost at call 50 : 780.8699 -#> Model cost at call 52 : 780.8698 -#> Model cost at call 54 : 780.8697 -#> Model cost at call 55 : 734.3043 -#> Model cost at call 57 : 734.3036 -#> Model cost at call 60 : 717.8438 -#> Model cost at call 67 : 676.3908 -#> Model cost at call 68 : 676.3907 -#> Model cost at call 69 : 676.3906 -#> Model cost at call 71 : 676.3885 -#> Model cost at call 72 : 642.2738 -#> Model cost at call 73 : 642.2738 -#> Model cost at call 76 : 642.2738 -#> Model cost at call 77 : 604.7128 -#> Model cost at call 78 : 604.7126 -#> Model cost at call 82 : 560.1285 -#> Model cost at call 83 : 560.1285 -#> Model cost at call 86 : 560.1285 -#> Model cost at call 87 : 521.6932 -#> Model cost at call 88 : 521.6932 -#> Model cost at call 91 : 521.6931 -#> Model cost at call 92 : 453.6483 -#> Model cost at call 93 : 453.6483 -#> Model cost at call 96 : 453.6483 -#> Model cost at call 98 : 422.5498 -#> Model cost at call 102 : 422.5497 -#> Model cost at call 106 : 413.6426 -#> Model cost at call 108 : 413.6416 -#> Model cost at call 111 : 407.4639 -#> Model cost at call 113 : 407.4639 -#> Model cost at call 115 : 407.4639 -#> Model cost at call 116 : 403.6974 -#> Model cost at call 118 : 403.6973 -#> Model cost at call 120 : 403.6973 -#> Model cost at call 121 : 396.004 -#> Model cost at call 123 : 396.004 -#> Model cost at call 126 : 391.2533 -#> Model cost at call 128 : 391.2533 -#> Model cost at call 130 : 391.2533 -#> Model cost at call 131 : 388.4056 -#> Model cost at call 133 : 388.4056 -#> Model cost at call 135 : 388.4055 -#> Model cost at call 137 : 384.0739 -#> Model cost at call 139 : 384.0734 -#> Model cost at call 143 : 383.6352 -#> Model cost at call 145 : 383.635 -#> Model cost at call 148 : 381.1342 -#> Model cost at call 152 : 381.1342 -#> Model cost at call 153 : 380.1443 -#> Model cost at call 157 : 380.1443 -#> Model cost at call 158 : 378.5615 -#> Model cost at call 162 : 378.5614 -#> Model cost at call 164 : 378.4583 -#> Model cost at call 168 : 378.4583 -#> Model cost at call 169 : 377.7047 -#> Model cost at call 173 : 377.7047 -#> Model cost at call 175 : 377.7042 -#> Model cost at call 178 : 377.7042 -#> Model cost at call 179 : 377.7042 -#> Model cost at call 180 : 377.1553 -#> Model cost at call 182 : 377.1553 -#> Model cost at call 183 : 377.1553 -#> Model cost at call 185 : 377.0866 -#> Model cost at call 187 : 377.0866 -#> Model cost at call 190 : 377.0288 -#> Model cost at call 194 : 377.0288 -#> Model cost at call 196 : 376.9814 -#> Model cost at call 200 : 376.9814 -#> Model cost at call 201 : 376.9488 -#> Model cost at call 203 : 376.9488 -#> Model cost at call 205 : 376.9488 -#> Model cost at call 206 : 376.9184 -#> Model cost at call 208 : 376.9184 -#> Model cost at call 211 : 376.9095 -#> Model cost at call 213 : 376.9095 -#> Model cost at call 215 : 376.9095 -#> Model cost at call 216 : 376.901 -#> Model cost at call 218 : 376.901 -#> Model cost at call 221 : 376.8936 -#> Model cost at call 225 : 376.8936 -#> Model cost at call 226 : 376.8848 -#> Model cost at call 227 : 376.8608 -#> Model cost at call 228 : 376.7665 -#> Model cost at call 229 : 376.4162 -#> Model cost at call 230 : 375.4439 -#> Model cost at call 235 : 375.4439 -#> Model cost at call 237 : 375.2281 -#> Model cost at call 241 : 375.2281 -#> Model cost at call 242 : 374.3381 -#> Model cost at call 244 : 374.3381 -#> Model cost at call 251 : 374.2632 -#> Model cost at call 253 : 374.2632 -#> Model cost at call 256 : 374.2391 -#> Model cost at call 257 : 374.2247 -#> Model cost at call 259 : 374.2247 -#> Model cost at call 261 : 374.2247 -#> Model cost at call 263 : 374.2024 -#> Model cost at call 266 : 374.2024 -#> Model cost at call 270 : 374.1952 -#> Model cost at call 274 : 374.1952 -#> Model cost at call 275 : 374.186 -#> Model cost at call 279 : 374.186 -#> Model cost at call 280 : 374.1724 -#> Model cost at call 281 : 374.156 -#> Model cost at call 282 : 374.0763 -#> Model cost at call 283 : 373.7692 -#> Model cost at call 284 : 372.729 -#> Model cost at call 285 : 371.4251 -#> Model cost at call 287 : 371.4251 -#> Model cost at call 290 : 371.2142 -#> Model cost at call 291 : 371.2142 -#> Model cost at call 292 : 371.2142 -#> Model cost at call 295 : 371.2134 -#> Model cost at call 298 : 371.2134 -#> Model cost at call 300 : 371.2134 -#> Model cost at call 309 : 371.2134 -#> Model cost at call 320 : 371.2134 -#> Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 +<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'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><div class='output co'>#> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 18 15:20:51 2016 -#> Date of summary: Fri Nov 18 15:20:51 2016 +#> Date of fit: Fri Nov 18 16:24:03 2016 +#> Date of summary: Fri Nov 18 16:24:03 2016 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -372,7 +235,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 327 model solutions performed in 1.34 s +#> Fitted with method Port using 327 model solutions performed in 1.341 s #> #> Weighting: none #> @@ -450,85 +313,11 @@ <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>, <span class='kw'>sink</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>), <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <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>)</div><div class='output co'>#> Model cost at call 1 : 15156.12 -#> Model cost at call 2 : 15156.12 -#> Model cost at call 6 : 8243.644 -#> Model cost at call 12 : 6290.714 -#> Model cost at call 13 : 6290.684 -#> Model cost at call 15 : 6290.453 -#> Model cost at call 18 : 1700.75 -#> Model cost at call 20 : 1700.612 -#> Model cost at call 24 : 1190.923 -#> Model cost at call 26 : 1190.922 -#> Model cost at call 29 : 1017.417 -#> Model cost at call 31 : 1017.417 -#> Model cost at call 33 : 1017.416 -#> Model cost at call 34 : 644.0471 -#> Model cost at call 36 : 644.0469 -#> Model cost at call 38 : 644.0468 -#> Model cost at call 39 : 590.5024 -#> Model cost at call 41 : 590.5021 -#> Model cost at call 43 : 590.5015 -#> Model cost at call 44 : 543.2187 -#> Model cost at call 45 : 543.2183 -#> Model cost at call 46 : 543.2182 -#> Model cost at call 50 : 391.348 -#> Model cost at call 51 : 391.3479 -#> Model cost at call 56 : 386.4789 -#> Model cost at call 58 : 386.4789 -#> Model cost at call 60 : 386.4779 -#> Model cost at call 61 : 384.0686 -#> Model cost at call 63 : 384.0686 -#> Model cost at call 66 : 382.7812 -#> Model cost at call 68 : 382.7812 -#> Model cost at call 70 : 382.7812 -#> Model cost at call 71 : 378.9272 -#> Model cost at call 73 : 378.9272 -#> Model cost at call 75 : 378.9272 -#> Model cost at call 76 : 377.4846 -#> Model cost at call 78 : 377.4846 -#> Model cost at call 81 : 375.9738 -#> Model cost at call 83 : 375.9738 -#> Model cost at call 86 : 375.3387 -#> Model cost at call 88 : 375.3387 -#> Model cost at call 91 : 374.5774 -#> Model cost at call 93 : 374.5774 -#> Model cost at call 95 : 374.5774 -#> Model cost at call 96 : 373.5447 -#> Model cost at call 100 : 373.5446 -#> Model cost at call 102 : 373.2643 -#> Model cost at call 104 : 373.2643 -#> Model cost at call 107 : 372.6799 -#> Model cost at call 111 : 372.6798 -#> Model cost at call 114 : 372.6325 -#> Model cost at call 116 : 372.6325 -#> Model cost at call 119 : 372.6159 -#> Model cost at call 121 : 372.6159 -#> Model cost at call 123 : 372.6159 -#> Model cost at call 124 : 372.5845 -#> Model cost at call 126 : 372.5845 -#> Model cost at call 129 : 372.5375 -#> Model cost at call 130 : 372.4771 -#> Model cost at call 131 : 372.2008 -#> Model cost at call 132 : 371.4923 -#> Model cost at call 134 : 371.4923 -#> Model cost at call 137 : 371.3022 -#> Model cost at call 139 : 371.3022 -#> Model cost at call 143 : 371.2271 -#> Model cost at call 144 : 371.2271 -#> Model cost at call 148 : 371.2202 -#> Model cost at call 149 : 371.215 -#> Model cost at call 152 : 371.215 -#> Model cost at call 154 : 371.2136 -#> Model cost at call 155 : 371.2136 -#> Model cost at call 156 : 371.2136 -#> Model cost at call 160 : 371.2134 -#> Model cost at call 164 : 371.2134 -#> Model cost at call 167 : 371.2134 -#> Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</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: 0.9.44.9000 +<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'>summary</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: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 18 15:20:52 2016 -#> Date of summary: Fri Nov 18 15:20:52 2016 +#> Date of fit: Fri Nov 18 16:24:04 2016 +#> Date of summary: Fri Nov 18 16:24:04 2016 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -536,7 +325,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 185 model solutions performed in 0.764 s +#> Fitted with method Port using 185 model solutions performed in 0.756 s #> #> Weighting: none #> @@ -608,61 +397,11 @@ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output 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>)</div><div class='output co'>#> Model cost at call 1 : 12435.14 -#> Model cost at call 2 : 12435.14 -#> Model cost at call 5 : 8276.306 -#> Model cost at call 6 : 8276.294 -#> Model cost at call 7 : 8275.676 -#> Model cost at call 9 : 5256.953 -#> Model cost at call 11 : 5256.951 -#> Model cost at call 12 : 5256.943 -#> Model cost at call 14 : 4469.745 -#> Model cost at call 18 : 4462.927 -#> Model cost at call 21 : 4462.925 -#> Model cost at call 22 : 4376.059 -#> Model cost at call 24 : 4376.058 -#> Model cost at call 27 : 4366.956 -#> Model cost at call 29 : 4366.956 -#> Model cost at call 31 : 4365.275 -#> Model cost at call 33 : 4365.275 -#> Model cost at call 35 : 4351.877 -#> Model cost at call 37 : 4351.877 -#> Model cost at call 39 : 4338.109 -#> Model cost at call 41 : 4338.109 -#> Model cost at call 43 : 4297.053 -#> Model cost at call 44 : 4218.591 -#> Model cost at call 45 : 3940.397 -#> Model cost at call 46 : 3690.395 -#> Model cost at call 48 : 3690.395 -#> Model cost at call 49 : 3690.385 -#> Model cost at call 50 : 3038.366 -#> Model cost at call 53 : 3038.365 -#> Model cost at call 54 : 2637.866 -#> Model cost at call 57 : 2637.865 -#> Model cost at call 59 : 2588.01 -#> Model cost at call 60 : 2588.009 -#> Model cost at call 63 : 2576.742 -#> Model cost at call 66 : 2576.742 -#> Model cost at call 67 : 2574 -#> Model cost at call 68 : 2574 -#> Model cost at call 69 : 2574 -#> Model cost at call 71 : 2569.76 -#> Model cost at call 73 : 2569.76 -#> Model cost at call 74 : 2569.76 -#> Model cost at call 75 : 2569.403 -#> Model cost at call 76 : 2569.403 -#> Model cost at call 79 : 2569.4 -#> Model cost at call 80 : 2569.4 -#> Model cost at call 81 : 2569.4 -#> Model cost at call 83 : 2569.4 -#> Model cost at call 86 : 2569.4 -#> Model cost at call 90 : 2569.4 -#> Model cost at call 99 : 2569.4 -#> Model cost at call 100 : 2569.4 -#> Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</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: 0.9.44.9000 +<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'>summary</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: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 18 15:20:52 2016 -#> Date of summary: Fri Nov 18 15:20:52 2016 +#> Date of fit: Fri Nov 18 16:24:05 2016 +#> Date of summary: Fri Nov 18 16:24:05 2016 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -670,7 +409,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 104 model solutions performed in 0.44 s +#> Fitted with method Port using 104 model solutions performed in 0.416 s #> #> Weighting: none #> diff --git a/man/Extract.mmkin.Rd b/man/Extract.mmkin.Rd index 6e0c84e3..e27e83a0 100644 --- a/man/Extract.mmkin.Rd +++ b/man/Extract.mmkin.Rd @@ -31,8 +31,15 @@ cores = 1, quiet = TRUE) fits["FOMC", ] fits[, "B"] - fits[, "B", drop = TRUE]$FOMC fits["SFO", "B"] - fits[["SFO", "B"]] # This is equivalent to - fits["SFO", "B", drop = TRUE] + + head( + # This extracts an mkinfit object with lots of components + fits[["FOMC", "B"]] + ) + + head( + # The same can be achieved by + fits["SFO", "B", drop = TRUE] + ) } diff --git a/man/endpoints.Rd b/man/endpoints.Rd index 08773c3e..55a4cb0a 100644 --- a/man/endpoints.Rd +++ b/man/endpoints.Rd @@ -23,6 +23,10 @@ endpoints(fit) \value{ A list with the components mentioned above. } +\examples{ + fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) + endpoints(fit) +} \author{ Johannes Ranke } diff --git a/man/mccall81_245T.Rd b/man/mccall81_245T.Rd index 7cc5c363..656ca33f 100644 --- a/man/mccall81_245T.Rd +++ b/man/mccall81_245T.Rd @@ -32,10 +32,11 @@ phenol = list(type = "SFO", to = "anisole"),
anisole = list(type = "SFO"))
\dontrun{
- fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"))
+ fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
summary(fit.1, data = FALSE)
}
- # No covariance matrix and k_phenol_sink is really small, therefore fix it to zero
+ # No convergence, no covariance matrix ...
+ # k_phenol_sink is really small, therefore fix it to zero
fit.2 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"),
parms.ini = c(k_phenol_sink = 0),
fixed_parms = "k_phenol_sink", quiet = TRUE)
diff --git a/man/mkinerrmin.Rd b/man/mkinerrmin.Rd index 12c9ebd4..9229fc7f 100644 --- a/man/mkinerrmin.Rd +++ b/man/mkinerrmin.Rd @@ -4,9 +4,8 @@ Calculate the minimum error to assume in order to pass the variance test
}
\description{
-This function uses \code{\link{optimize}} in order to iteratively find the
-smallest relative error still resulting in passing the chi-squared test
-as defined in the FOCUS kinetics report from 2006.
+This function finds the smallest relative error still resulting in passing the
+chi-squared test as defined in the FOCUS kinetics report from 2006.
}
\usage{
mkinerrmin(fit, alpha = 0.05)
@@ -34,8 +33,8 @@ mkinerrmin(fit, alpha = 0.05) This function is used internally by \code{\link{summary.mkinfit}}.
}
\examples{
-SFO_SFO = mkinmod(parent = list(type = "SFO", to = "m1"),
- m1 = list(type = "SFO"),
+SFO_SFO = mkinmod(parent = mkinsub("SFO", to = "m1"),
+ m1 = mkinsub("SFO"),
use_of_ff = "max")
fit_FOCUS_D = mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index aa38b462..8e2fbeb1 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -275,10 +275,10 @@ FOMC_SFO <- mkinmod( parent = mkinsub("FOMC", "m1"), m1 = mkinsub("SFO")) # Fit the model to the FOCUS example dataset D using defaults -fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D) +fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE) # Use starting parameters from parent only FOMC fit -fit.FOMC = mkinfit("FOMC", FOCUS_2006_D) -fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, +fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, quiet = TRUE) +fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE, parms.ini = fit.FOMC$bparms.ode) # Use stepwise fitting, using optimised parameters from parent only fit, SFORB @@ -286,24 +286,26 @@ SFORB_SFO <- mkinmod( parent = list(type = "SFORB", to = "m1", sink = TRUE), m1 = list(type = "SFO")) # Fit the model to the FOCUS example dataset D using defaults -fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D) -fit.SFORB_SFO.deSolve <- mkinfit(SFORB_SFO, FOCUS_2006_D, solution_type = "deSolve") +fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, quiet = TRUE) +fit.SFORB_SFO.deSolve <- mkinfit(SFORB_SFO, FOCUS_2006_D, solution_type = "deSolve", + quiet = TRUE) # Use starting parameters from parent only SFORB fit (not really needed in this case) -fit.SFORB = mkinfit("SFORB", FOCUS_2006_D) -fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode) +fit.SFORB = mkinfit("SFORB", FOCUS_2006_D, quiet = TRUE) +fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode, quiet = TRUE) } \dontrun{ # Weighted fits, including IRLS SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), use_of_ff = "max") -f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D) +f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE) summary(f.noweight) -f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs") +f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs", quiet = TRUE) summary(f.irls) -f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean") +f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", quiet = TRUE) summary(f.w.mean) -f.w.value <- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), err = "value") +f.w.value <- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), err = "value", + quiet = TRUE) summary(f.w.value) } @@ -312,9 +314,9 @@ summary(f.w.value) dw <- FOCUS_2006_D errors <- c(parent = 2, m1 = 1) dw$err.man <- errors[FOCUS_2006_D$name] -f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man") +f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE) summary(f.w.man) -f.w.man.irls <- mkinfit(SFO_SFO.ff, dw, err = "err.man", +f.w.man.irls <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE, reweight.method = "obs") summary(f.w.man.irls) } diff --git a/man/mkinparplot.Rd b/man/mkinparplot.Rd index 3eda08d2..34b06963 100644 --- a/man/mkinparplot.Rd +++ b/man/mkinparplot.Rd @@ -1,8 +1,7 @@ \name{mkinparplot}
\alias{mkinparplot}
\title{
- Function to plot the confidence intervals obtained using
- \code{\link{mkinfit}}
+ Function to plot the confidence intervals obtained using mkinfit
}
\description{
This function plots the confidence intervals for the parameters
@@ -25,9 +24,9 @@ \examples{
model <- mkinmod(
- T245 = list(type = "SFO", to = c("phenol"), sink = FALSE),
- phenol = list(type = "SFO", to = c("anisole")),
- anisole = list(type = "SFO"), use_of_ff = "max")
+ T245 = mkinsub("SFO", to = c("phenol"), sink = FALSE),
+ phenol = mkinsub("SFO", to = c("anisole")),
+ anisole = mkinsub("SFO"), use_of_ff = "max")
fit <- mkinfit(model, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
mkinparplot(fit)
}
diff --git a/man/mmkin.Rd b/man/mmkin.Rd index 3a8d4a1f..eb6d05eb 100644 --- a/man/mmkin.Rd +++ b/man/mmkin.Rd @@ -57,21 +57,22 @@ models <- list(SFO_lin = m_synth_SFO_lin, FOMC_lin = m_synth_FOMC_lin) datasets <- lapply(synthetic_data_for_UBA_2014[1:3], function(x) x$data) names(datasets) <- paste("Dataset", 1:3) -time_default <- system.time(fits.0 <- mmkin(models, datasets)) -time_1 <- system.time(fits.1 <- mmkin(models, datasets, cores = 1)) +time_default <- system.time(fits.0 <- mmkin(models, datasets, quiet = TRUE)) +time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE)) time_default time_1 -endpoints(fits[["SFO_lin", 2]]) +endpoints(fits.0[["SFO_lin", 2]]) -# Plot.mkinfit handles rows or columns of mmkin result objects +# plot.mkinfit handles rows or columns of mmkin result objects plot(fits.0[1, ]) plot(fits.0[1, ], obs_var = c("M1", "M2")) plot(fits.0[, 1]) # Use double brackets to extract a single mkinfit object, which will be plotted -# by plot.mkinfit +# by plot.mkinfit and can be plotted using plot_sep plot(fits.0[[1, 1]], sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE) +plot_sep(fits.0[[1, 1]]) # Plotting with mmkin (single brackets, extracting an mmkin object) does not # allow to plot the observed variables separately plot(fits.0[1, 1]) diff --git a/man/plot.mmkin.Rd b/man/plot.mmkin.Rd index 57f69c90..7f3460d3 100644 --- a/man/plot.mmkin.Rd +++ b/man/plot.mmkin.Rd @@ -46,13 +46,14 @@ } \examples{ # Only use one core not to offend CRAN checks, use Levenberg-Marquardt for speed - fits <- mmkin(c("FOMC", "HS"), list("FOCUS B" = FOCUS_2006_B, "FOCUS C" = FOCUS_2006_C), + fits <- mmkin(c("FOMC", "HS"), + list("FOCUS B" = FOCUS_2006_B, "FOCUS C" = FOCUS_2006_C), # named list for titles cores = 1, quiet = TRUE, method.modFit = "Marq") plot(fits[, "FOCUS C"]) plot(fits["FOMC", ]) - # We can also plot a single fit, if we like the way mmkin works, but then the plot + # We can also plot a single fit, if we like the way plot.mmkin works, but then the plot # height should be smaller than the plot width (this is not possible for the html pages - # generated by staticdocs, as far as I know). + # generated by pkgdown, as far as I know). plot(fits["FOMC", "FOCUS C"]) # same as plot(fits[1, 2]) } diff --git a/man/print.mkinmod.Rd b/man/print.mkinmod.Rd index fa02c1cb..24555def 100644 --- a/man/print.mkinmod.Rd +++ b/man/print.mkinmod.Rd @@ -7,7 +7,7 @@ Print mkinmod objects in a way that the user finds his way to get to its components. } \usage{ -\method{print}{mkinmod}(x, ...) + \method{print}{mkinmod}(x, ...) } \arguments{ \item{x}{ @@ -17,3 +17,10 @@ Not used. } } +\examples{ + m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"), + M1 = list(type = "SFO", to = "M2"), + M2 = list(type = "SFO"), use_of_ff = "max") + + print(m_synth_SFO_lin) +} diff --git a/man/schaefer07_complex_case.Rd b/man/schaefer07_complex_case.Rd index c666d08b..50272f4e 100644 --- a/man/schaefer07_complex_case.Rd +++ b/man/schaefer07_complex_case.Rd @@ -36,6 +36,12 @@ model <- mkinmod( B1 = list(type = "SFO"),
C1 = list(type = "SFO"),
A2 = list(type = "SFO"), use_of_ff = "max")
-\dontrun{mkinfit(model, data)}
+ \dontrun{
+ fit <- mkinfit(model, data, quiet = TRUE)
+ plot(fit)
+ endpoints(fit)
+ }
+ # Compare with the results obtained in the original publication
+ print(schaefer07_complex_results)
}
\keyword{datasets}
diff --git a/man/summary.mkinfit.Rd b/man/summary.mkinfit.Rd index af09e86a..876fc362 100644 --- a/man/summary.mkinfit.Rd +++ b/man/summary.mkinfit.Rd @@ -70,6 +70,6 @@ Johannes Ranke
}
\examples{
- summary(mkinfit(mkinmod(parent = list(type = "SFO")), FOCUS_2006_A, quiet = TRUE))
+ summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
}
\keyword{ utilities }
diff --git a/man/synthetic_data_for_UBA.Rd b/man/synthetic_data_for_UBA.Rd index 468e3731..a9739d55 100644 --- a/man/synthetic_data_for_UBA.Rd +++ b/man/synthetic_data_for_UBA.Rd @@ -61,7 +61,9 @@ m_synth_DFOP_par <- mkinmod(parent = list(type = "DFOP", to = c("M1", "M2"), M1 = list(type = "SFO"),
M2 = list(type = "SFO"), use_of_ff = "max")
-mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data)
+fit <- mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data, quiet = TRUE)
+plot_sep(fit)
+summary(fit)
}
}
\keyword{datasets}
diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd index 71c179d7..a1ccdf26 100644 --- a/man/transform_odeparms.Rd +++ b/man/transform_odeparms.Rd @@ -69,7 +69,7 @@ fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE) summary(fit, data=FALSE) # See transformed and backtransformed parameters \dontrun{ -fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE) +fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE) summary(fit.2, data=FALSE) } @@ -87,7 +87,7 @@ SFO_SFO.ff <- mkinmod( m1 = list(type = "SFO"), use_of_ff = "max") -fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D) +fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE) summary(fit.ff, data = FALSE) initials <- c("f_parent_to_m1" = 0.5) transformed <- transform_odeparms(initials, SFO_SFO.ff) @@ -100,7 +100,7 @@ SFO_SFO.ff.2 <- mkinmod( use_of_ff = "max") -fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D) +fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE) summary(fit.ff.2, data = FALSE) } } |
