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/transform_odeparms.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/transform_odeparms.html')
| -rw-r--r-- | docs/reference/transform_odeparms.html | 297 |
1 files changed, 18 insertions, 279 deletions
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 #> |