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 /docs/reference/mccall81_245T.html | |
| 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
Diffstat (limited to 'docs/reference/mccall81_245T.html')
| -rw-r--r-- | docs/reference/mccall81_245T.html | 164 |
1 files changed, 9 insertions, 155 deletions
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 #> |