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/transform_odeparms.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/transform_odeparms.html')
| -rw-r--r-- | docs/reference/transform_odeparms.html | 527 |
1 files changed, 497 insertions, 30 deletions
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 00af0267..08fbf368 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: Thu Nov 17 22:57:06 2016 -#> Date of summary: Thu Nov 17 22:57:06 2016 +#> Date of fit: Fri Nov 18 15:20:49 2016 +#> Date of summary: Fri Nov 18 15:20:49 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 0.684 s +#> Fitted with method Port using 153 model solutions performed in 0.681 s #> #> Weighting: none #> @@ -222,10 +222,220 @@ #> DT50 DT90 #> parent 7.023 23.33 #> m1 131.761 437.70</div><div class='input'> -<span class='co'>## Not run: ------------------------------------</span> -<span class='co'># fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE)</span> -<span class='co'># summary(fit.2, data=FALSE)</span> -<span class='co'>## ---------------------------------------------</span> + +<span class='no'>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 +#> 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 +#> +#> Equations: +#> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent +#> d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 327 model solutions performed in 1.34 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent_sink 0.1000 deparm +#> k_parent_m1 0.1001 deparm +#> k_m1_sink 0.1002 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.7500 -Inf Inf +#> k_parent_sink 0.1000 0 Inf +#> k_parent_m1 0.1001 0 Inf +#> k_m1_sink 0.1002 0 Inf +#> +#> Fixed parameter values: +#> value type +#> m1_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 99.600000 1.6140000 96.330000 1.029e+02 +#> k_parent_sink 0.047920 0.0037500 0.040310 5.553e-02 +#> k_parent_m1 0.050780 0.0020940 0.046530 5.502e-02 +#> k_m1_sink 0.005261 0.0007159 0.003809 6.713e-03 +#> +#> Parameter correlation: +#> parent_0 k_parent_sink k_parent_m1 k_m1_sink +#> parent_0 1.00000 0.6075 -0.06625 -0.1701 +#> k_parent_sink 0.60752 1.0000 -0.08740 -0.6253 +#> k_parent_m1 -0.06625 -0.0874 1.00000 0.4716 +#> k_m1_sink -0.17006 -0.6253 0.47164 1.0000 +#> +#> Residual standard error: 3.211 on 36 degrees of freedom +#> +#> Backtransformed parameters: +#> Confidence intervals for internally transformed parameters are asymmetric. +#> t-test (unrealistically) based on the assumption of normal distribution +#> for estimators of untransformed parameters. +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02 +#> k_parent_sink 0.047920 12.780 3.050e-15 0.040310 5.553e-02 +#> k_parent_m1 0.050780 24.250 3.407e-24 0.046530 5.502e-02 +#> k_m1_sink 0.005261 7.349 5.758e-09 0.003809 6.713e-03 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.398 4 15 +#> parent 6.827 3 6 +#> m1 4.490 1 9 +#> +#> Resulting formation fractions: +#> ff +#> parent_sink 0.4855 +#> parent_m1 0.5145 +#> m1_sink 1.0000 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 7.023 23.33 +#> m1 131.761 437.70</div><div class='input'> <span class='no'>initials</span> <span class='kw'><-</span> <span class='no'>fit</span>$<span class='no'>start</span>$<span class='no'>value</span> <span class='fu'>names</span>(<span class='no'>initials</span>) <span class='kw'><-</span> <span class='fu'>rownames</span>(<span class='no'>fit</span>$<span class='no'>start</span>) @@ -234,29 +444,286 @@ <span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 100.750000 -2.302585 -2.301586 -2.300587 </div><div class='input'><span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO</span>)</div><div class='output co'>#> parent_0 k_parent_sink k_parent_m1 k_m1_sink #> 100.7500 0.1000 0.1001 0.1002 </div><div class='input'> -<span class='co'>## Not run: ------------------------------------</span> -<span class='co'># # The case of formation fractions</span> -<span class='co'># SFO_SFO.ff <- mkinmod(</span> -<span class='co'># parent = list(type = "SFO", to = "m1", sink = TRUE),</span> -<span class='co'># m1 = list(type = "SFO"),</span> -<span class='co'># use_of_ff = "max")</span> -<span class='co'># </span> -<span class='co'># fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D)</span> -<span class='co'># summary(fit.ff, data = FALSE)</span> -<span class='co'># initials <- c("f_parent_to_m1" = 0.5)</span> -<span class='co'># transformed <- transform_odeparms(initials, SFO_SFO.ff)</span> -<span class='co'># backtransform_odeparms(transformed, SFO_SFO.ff)</span> -<span class='co'># </span> -<span class='co'># # And without sink</span> -<span class='co'># SFO_SFO.ff.2 <- mkinmod(</span> -<span class='co'># parent = list(type = "SFO", to = "m1", sink = FALSE),</span> -<span class='co'># m1 = list(type = "SFO"),</span> -<span class='co'># use_of_ff = "max")</span> -<span class='co'># </span> -<span class='co'># </span> -<span class='co'># fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D)</span> -<span class='co'># summary(fit.ff.2, data = FALSE)</span> -<span class='co'>## ---------------------------------------------</span></div></pre> + +<span class='co'># The case of formation fractions</span> +<span class='no'>SFO_SFO.ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( + <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>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 +#> 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 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 185 model solutions performed in 0.764 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent 0.1000 deparm +#> k_m1 0.1001 deparm +#> f_parent_to_m1 0.5000 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_m1 -2.301586 -Inf Inf +#> f_parent_ilr_1 0.000000 -Inf Inf +#> +#> Fixed parameter values: +#> value type +#> m1_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 99.60000 1.61400 96.3300 102.9000 +#> log_k_parent -2.31600 0.04187 -2.4010 -2.2310 +#> log_k_m1 -5.24800 0.13610 -5.5230 -4.9720 +#> f_parent_ilr_1 0.04096 0.06477 -0.0904 0.1723 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.0000 0.5178 -0.1701 -0.5489 +#> log_k_parent 0.5178 1.0000 -0.3285 -0.5451 +#> log_k_m1 -0.1701 -0.3285 1.0000 0.7466 +#> f_parent_ilr_1 -0.5489 -0.5451 0.7466 1.0000 +#> +#> Residual standard error: 3.211 on 36 degrees of freedom +#> +#> Backtransformed parameters: +#> Confidence intervals for internally transformed parameters are asymmetric. +#> t-test (unrealistically) based on the assumption of normal distribution +#> for estimators of untransformed parameters. +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02 +#> k_parent 0.098700 23.880 5.701e-24 0.090660 1.074e-01 +#> k_m1 0.005261 7.349 5.758e-09 0.003992 6.933e-03 +#> f_parent_to_m1 0.514500 22.490 4.374e-23 0.468100 5.606e-01 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.398 4 15 +#> parent 6.459 2 7 +#> m1 4.690 2 8 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.5145 +#> parent_sink 0.4855 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 7.023 23.33 +#> m1 131.761 437.70</div><div class='input'><span class='no'>initials</span> <span class='kw'><-</span> <span class='fu'>c</span>(<span class='st'>"f_parent_to_m1"</span> <span class='kw'>=</span> <span class='fl'>0.5</span>) +<span class='no'>transformed</span> <span class='kw'><-</span> <span class='fu'>transform_odeparms</span>(<span class='no'>initials</span>, <span class='no'>SFO_SFO.ff</span>) +<span class='fu'>backtransform_odeparms</span>(<span class='no'>transformed</span>, <span class='no'>SFO_SFO.ff</span>)</div><div class='output co'>#> f_parent_to_m1 +#> 0.5 </div><div class='input'> +<span class='co'># And without sink</span> +<span class='no'>SFO_SFO.ff.2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>( + <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>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'>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'>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 +#> 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 +#> +#> Equations: +#> d_parent/dt = - k_parent * parent +#> d_m1/dt = + k_parent * parent - k_m1 * m1 +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 104 model solutions performed in 0.44 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> parent_0 100.7500 state +#> k_parent 0.1000 deparm +#> k_m1 0.1001 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> parent_0 100.750000 -Inf Inf +#> log_k_parent -2.302585 -Inf Inf +#> log_k_m1 -2.301586 -Inf Inf +#> +#> Fixed parameter values: +#> value type +#> m1_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> parent_0 84.790 2.96500 78.78 90.800 +#> log_k_parent -2.756 0.08088 -2.92 -2.593 +#> log_k_m1 -4.214 0.11150 -4.44 -3.988 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 +#> parent_0 1.0000 0.11059 0.46156 +#> log_k_parent 0.1106 1.00000 0.06274 +#> log_k_m1 0.4616 0.06274 1.00000 +#> +#> Residual standard error: 8.333 on 37 degrees of freedom +#> +#> Backtransformed parameters: +#> Confidence intervals for internally transformed parameters are asymmetric. +#> t-test (unrealistically) based on the assumption of normal distribution +#> for estimators of untransformed parameters. +#> Estimate t value Pr(>t) Lower Upper +#> parent_0 84.79000 28.600 3.939e-27 78.78000 90.80000 +#> k_parent 0.06352 12.360 5.237e-15 0.05392 0.07483 +#> k_m1 0.01478 8.966 4.114e-11 0.01179 0.01853 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 19.66 3 16 +#> parent 17.56 2 7 +#> m1 18.71 1 9 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 10.91 36.25 +#> m1 46.89 155.75</div><div class='input'> +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> |