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/mccall81_245T.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/mccall81_245T.html')
| -rw-r--r-- | docs/reference/mccall81_245T.html | 250 |
1 files changed, 242 insertions, 8 deletions
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 4314c84e..7b294129 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -111,19 +111,253 @@ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</span> <span class='kw'>=</span> <span class='fu'>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='co'>## Not run: ------------------------------------</span> -<span class='co'># fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"))</span> -<span class='co'># summary(fit.1, data = FALSE)</span> -<span class='co'># </span> -<span class='co'>## ---------------------------------------------</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='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 +#> +#> +#> Warning: Optimisation by method Port did not converge. +#> Convergence code is 1 +#> +#> +#> Equations: +#> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 +#> d_phenol/dt = + k_T245_phenol * T245 - k_phenol_sink * phenol - +#> k_phenol_anisole * phenol +#> d_anisole/dt = + k_phenol_anisole * phenol - k_anisole_sink * anisole +#> +#> Model predictions using solution type deSolve +#> +#> Fitted with method Port using 590 model solutions performed in 3.45 s +#> +#> Weighting: none +#> +#> Starting values for parameters to be optimised: +#> value type +#> T245_0 100.9000 state +#> k_T245_sink 0.1000 deparm +#> k_T245_phenol 0.1001 deparm +#> k_phenol_sink 0.1002 deparm +#> k_phenol_anisole 0.1003 deparm +#> k_anisole_sink 0.1004 deparm +#> +#> Starting values for the transformed parameters actually optimised: +#> value lower upper +#> T245_0 100.900000 -Inf Inf +#> log_k_T245_sink -2.302585 -Inf Inf +#> log_k_T245_phenol -2.301586 -Inf Inf +#> log_k_phenol_sink -2.300587 -Inf Inf +#> log_k_phenol_anisole -2.299590 -Inf Inf +#> log_k_anisole_sink -2.298593 -Inf Inf +#> +#> Fixed parameter values: +#> value type +#> phenol_0 0 state +#> anisole_0 0 state +#> +#> Optimised, transformed parameters with symmetric confidence intervals: +#> Estimate Std. Error Lower Upper +#> T245_0 103.9000 NA NA NA +#> log_k_T245_sink -4.1130 NA NA NA +#> log_k_T245_phenol -3.6120 NA NA NA +#> log_k_phenol_sink -26.3900 NA NA NA +#> log_k_phenol_anisole -0.9037 NA NA NA +#> log_k_anisole_sink -5.0090 NA NA NA +#> +#> Parameter correlation:</div><div class='output co'>#> <span class='warning'>Warning: Could not estimate covariance matrix; singular system:</span></div><div class='output co'>#> Could not estimate covariance matrix; singular system: +#> +#> Residual standard error: 2.78 on 18 degrees of freedom +#> +#> Backtransformed parameters: +#> Confidence intervals for internally transformed parameters are asymmetric. +#> t-test (unrealistically) based on the assumption of normal distribution +#> for estimators of untransformed parameters. +#> Estimate t value Pr(>t) Lower Upper +#> T245_0 1.039e+02 4.282e+01 7.236e-20 NA NA +#> k_T245_sink 1.636e-02 8.901e-01 1.926e-01 NA NA +#> k_T245_phenol 2.701e-02 1.504e+00 7.498e-02 NA NA +#> k_phenol_sink 3.457e-12 1.230e-11 5.000e-01 NA NA +#> k_phenol_anisole 4.051e-01 2.518e+00 1.075e-02 NA NA +#> k_anisole_sink 6.679e-03 8.146e+00 9.469e-08 NA NA +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 10.070 6 16 +#> T245 7.908 3 5 +#> phenol 106.445 2 5 +#> anisole 5.379 1 6 +#> +#> Resulting formation fractions: +#> ff +#> T245_sink 3.772e-01 +#> T245_phenol 6.228e-01 +#> phenol_sink 8.534e-12 +#> phenol_anisole 1.000e+00 +#> anisole_sink 1.000e+00 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> T245 15.982 53.091 +#> phenol 1.711 5.685 +#> anisole 103.784 344.763</div><div class='input'> <span class='co'># No covariance matrix and 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: Thu Nov 17 22:56:55 2016 -#> Date of summary: Thu Nov 17 22:56:55 2016 +#> Date of fit: Fri Nov 18 15:19:35 2016 +#> Date of summary: Fri Nov 18 15:19:35 2016 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -133,7 +367,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.457 s +#> Fitted with method Port using 246 model solutions performed in 1.477 s #> #> Weighting: none #> |