diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2016-11-18 15:01:53 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2016-11-18 15:22:42 +0100 |
| commit | c6086d1dd97ad2d6420625de7b8009b1b0f85d06 (patch) | |
| tree | 1a38fd690c94a556555ec71edff443bcfe609b7b /docs/reference/schaefer07_complex_case.html | |
| parent | 9a8dfa8bd52664929fd4197f3e9c4e65b62cad53 (diff) | |
Static documentation rebuilt by pkgdown::build_site(run_dont_run = TRUE)
Using branch 'jranke' on jranke/pkgdown, fixing issues
hadley/pgkdown#178 and hadley/pkgdown#213
Remove plot=TRUE from mkinfit calls also in dontrun sections of examples
to avoid a flood png files documenting the progress of the fit.
Diffstat (limited to 'docs/reference/schaefer07_complex_case.html')
| -rw-r--r-- | docs/reference/schaefer07_complex_case.html | 1054 |
1 files changed, 1053 insertions, 1 deletions
diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index e2f845d9..9bb6d4ee 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -116,7 +116,1059 @@ <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='co'>## Not run: mkinfit(model, data, plot=TRUE)</span></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='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> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> |