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authorJohannes Ranke <jranke@uni-bremen.de>2016-11-18 16:28:49 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2016-11-18 16:28:49 +0100
commite7b2d16306b7d03cde66223c9b27abde928f9447 (patch)
tree85d650cfb8e071b00a1228566ec788dc1b477809 /docs/reference/transform_odeparms.html
parent8bdb67360502bd1a8eb5317d287b094510b4a02c (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.html297
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'>&lt;-</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'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 18 15:20:49 2016
-#&gt; Date of summary: Fri Nov 18 15:20:49 2016
+#&gt; Date of fit: Fri Nov 18 16:24:02 2016
+#&gt; Date of summary: Fri Nov 18 16:24:02 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -158,7 +158,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 153 model solutions performed in 0.681 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.708 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -223,148 +223,11 @@
#&gt; parent 7.023 23.33
#&gt; m1 131.761 437.70</div><div class='input'>
-<span class='no'>fit.2</span> <span class='kw'>&lt;-</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'>#&gt; Model cost at call 1 : 18915.53
-#&gt; Model cost at call 2 : 18915.53
-#&gt; Model cost at call 7 : 10205.88
-#&gt; Model cost at call 10 : 10205.05
-#&gt; Model cost at call 13 : 8136.609
-#&gt; Model cost at call 18 : 2504.352
-#&gt; Model cost at call 20 : 2504.35
-#&gt; Model cost at call 22 : 2504.285
-#&gt; Model cost at call 25 : 1747.542
-#&gt; Model cost at call 27 : 1745.941
-#&gt; Model cost at call 29 : 1745.431
-#&gt; Model cost at call 30 : 1341.034
-#&gt; Model cost at call 34 : 1341.034
-#&gt; Model cost at call 35 : 1032.65
-#&gt; Model cost at call 39 : 1032.649
-#&gt; Model cost at call 40 : 919.9522
-#&gt; Model cost at call 42 : 919.952
-#&gt; Model cost at call 44 : 919.9518
-#&gt; Model cost at call 45 : 903.8272
-#&gt; Model cost at call 47 : 903.827
-#&gt; Model cost at call 49 : 903.8268
-#&gt; Model cost at call 50 : 780.8699
-#&gt; Model cost at call 52 : 780.8698
-#&gt; Model cost at call 54 : 780.8697
-#&gt; Model cost at call 55 : 734.3043
-#&gt; Model cost at call 57 : 734.3036
-#&gt; Model cost at call 60 : 717.8438
-#&gt; Model cost at call 67 : 676.3908
-#&gt; Model cost at call 68 : 676.3907
-#&gt; Model cost at call 69 : 676.3906
-#&gt; Model cost at call 71 : 676.3885
-#&gt; Model cost at call 72 : 642.2738
-#&gt; Model cost at call 73 : 642.2738
-#&gt; Model cost at call 76 : 642.2738
-#&gt; Model cost at call 77 : 604.7128
-#&gt; Model cost at call 78 : 604.7126
-#&gt; Model cost at call 82 : 560.1285
-#&gt; Model cost at call 83 : 560.1285
-#&gt; Model cost at call 86 : 560.1285
-#&gt; Model cost at call 87 : 521.6932
-#&gt; Model cost at call 88 : 521.6932
-#&gt; Model cost at call 91 : 521.6931
-#&gt; Model cost at call 92 : 453.6483
-#&gt; Model cost at call 93 : 453.6483
-#&gt; Model cost at call 96 : 453.6483
-#&gt; Model cost at call 98 : 422.5498
-#&gt; Model cost at call 102 : 422.5497
-#&gt; Model cost at call 106 : 413.6426
-#&gt; Model cost at call 108 : 413.6416
-#&gt; Model cost at call 111 : 407.4639
-#&gt; Model cost at call 113 : 407.4639
-#&gt; Model cost at call 115 : 407.4639
-#&gt; Model cost at call 116 : 403.6974
-#&gt; Model cost at call 118 : 403.6973
-#&gt; Model cost at call 120 : 403.6973
-#&gt; Model cost at call 121 : 396.004
-#&gt; Model cost at call 123 : 396.004
-#&gt; Model cost at call 126 : 391.2533
-#&gt; Model cost at call 128 : 391.2533
-#&gt; Model cost at call 130 : 391.2533
-#&gt; Model cost at call 131 : 388.4056
-#&gt; Model cost at call 133 : 388.4056
-#&gt; Model cost at call 135 : 388.4055
-#&gt; Model cost at call 137 : 384.0739
-#&gt; Model cost at call 139 : 384.0734
-#&gt; Model cost at call 143 : 383.6352
-#&gt; Model cost at call 145 : 383.635
-#&gt; Model cost at call 148 : 381.1342
-#&gt; Model cost at call 152 : 381.1342
-#&gt; Model cost at call 153 : 380.1443
-#&gt; Model cost at call 157 : 380.1443
-#&gt; Model cost at call 158 : 378.5615
-#&gt; Model cost at call 162 : 378.5614
-#&gt; Model cost at call 164 : 378.4583
-#&gt; Model cost at call 168 : 378.4583
-#&gt; Model cost at call 169 : 377.7047
-#&gt; Model cost at call 173 : 377.7047
-#&gt; Model cost at call 175 : 377.7042
-#&gt; Model cost at call 178 : 377.7042
-#&gt; Model cost at call 179 : 377.7042
-#&gt; Model cost at call 180 : 377.1553
-#&gt; Model cost at call 182 : 377.1553
-#&gt; Model cost at call 183 : 377.1553
-#&gt; Model cost at call 185 : 377.0866
-#&gt; Model cost at call 187 : 377.0866
-#&gt; Model cost at call 190 : 377.0288
-#&gt; Model cost at call 194 : 377.0288
-#&gt; Model cost at call 196 : 376.9814
-#&gt; Model cost at call 200 : 376.9814
-#&gt; Model cost at call 201 : 376.9488
-#&gt; Model cost at call 203 : 376.9488
-#&gt; Model cost at call 205 : 376.9488
-#&gt; Model cost at call 206 : 376.9184
-#&gt; Model cost at call 208 : 376.9184
-#&gt; Model cost at call 211 : 376.9095
-#&gt; Model cost at call 213 : 376.9095
-#&gt; Model cost at call 215 : 376.9095
-#&gt; Model cost at call 216 : 376.901
-#&gt; Model cost at call 218 : 376.901
-#&gt; Model cost at call 221 : 376.8936
-#&gt; Model cost at call 225 : 376.8936
-#&gt; Model cost at call 226 : 376.8848
-#&gt; Model cost at call 227 : 376.8608
-#&gt; Model cost at call 228 : 376.7665
-#&gt; Model cost at call 229 : 376.4162
-#&gt; Model cost at call 230 : 375.4439
-#&gt; Model cost at call 235 : 375.4439
-#&gt; Model cost at call 237 : 375.2281
-#&gt; Model cost at call 241 : 375.2281
-#&gt; Model cost at call 242 : 374.3381
-#&gt; Model cost at call 244 : 374.3381
-#&gt; Model cost at call 251 : 374.2632
-#&gt; Model cost at call 253 : 374.2632
-#&gt; Model cost at call 256 : 374.2391
-#&gt; Model cost at call 257 : 374.2247
-#&gt; Model cost at call 259 : 374.2247
-#&gt; Model cost at call 261 : 374.2247
-#&gt; Model cost at call 263 : 374.2024
-#&gt; Model cost at call 266 : 374.2024
-#&gt; Model cost at call 270 : 374.1952
-#&gt; Model cost at call 274 : 374.1952
-#&gt; Model cost at call 275 : 374.186
-#&gt; Model cost at call 279 : 374.186
-#&gt; Model cost at call 280 : 374.1724
-#&gt; Model cost at call 281 : 374.156
-#&gt; Model cost at call 282 : 374.0763
-#&gt; Model cost at call 283 : 373.7692
-#&gt; Model cost at call 284 : 372.729
-#&gt; Model cost at call 285 : 371.4251
-#&gt; Model cost at call 287 : 371.4251
-#&gt; Model cost at call 290 : 371.2142
-#&gt; Model cost at call 291 : 371.2142
-#&gt; Model cost at call 292 : 371.2142
-#&gt; Model cost at call 295 : 371.2134
-#&gt; Model cost at call 298 : 371.2134
-#&gt; Model cost at call 300 : 371.2134
-#&gt; Model cost at call 309 : 371.2134
-#&gt; Model cost at call 320 : 371.2134
-#&gt; 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'>#&gt; mkin version: 0.9.44.9000
+<span class='no'>fit.2</span> <span class='kw'>&lt;-</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'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 18 15:20:51 2016
-#&gt; Date of summary: Fri Nov 18 15:20:51 2016
+#&gt; Date of fit: Fri Nov 18 16:24:03 2016
+#&gt; Date of summary: Fri Nov 18 16:24:03 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -372,7 +235,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 327 model solutions performed in 1.34 s
+#&gt; Fitted with method Port using 327 model solutions performed in 1.341 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -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'>#&gt; <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'>&lt;-</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'>#&gt; Model cost at call 1 : 15156.12
-#&gt; Model cost at call 2 : 15156.12
-#&gt; Model cost at call 6 : 8243.644
-#&gt; Model cost at call 12 : 6290.714
-#&gt; Model cost at call 13 : 6290.684
-#&gt; Model cost at call 15 : 6290.453
-#&gt; Model cost at call 18 : 1700.75
-#&gt; Model cost at call 20 : 1700.612
-#&gt; Model cost at call 24 : 1190.923
-#&gt; Model cost at call 26 : 1190.922
-#&gt; Model cost at call 29 : 1017.417
-#&gt; Model cost at call 31 : 1017.417
-#&gt; Model cost at call 33 : 1017.416
-#&gt; Model cost at call 34 : 644.0471
-#&gt; Model cost at call 36 : 644.0469
-#&gt; Model cost at call 38 : 644.0468
-#&gt; Model cost at call 39 : 590.5024
-#&gt; Model cost at call 41 : 590.5021
-#&gt; Model cost at call 43 : 590.5015
-#&gt; Model cost at call 44 : 543.2187
-#&gt; Model cost at call 45 : 543.2183
-#&gt; Model cost at call 46 : 543.2182
-#&gt; Model cost at call 50 : 391.348
-#&gt; Model cost at call 51 : 391.3479
-#&gt; Model cost at call 56 : 386.4789
-#&gt; Model cost at call 58 : 386.4789
-#&gt; Model cost at call 60 : 386.4779
-#&gt; Model cost at call 61 : 384.0686
-#&gt; Model cost at call 63 : 384.0686
-#&gt; Model cost at call 66 : 382.7812
-#&gt; Model cost at call 68 : 382.7812
-#&gt; Model cost at call 70 : 382.7812
-#&gt; Model cost at call 71 : 378.9272
-#&gt; Model cost at call 73 : 378.9272
-#&gt; Model cost at call 75 : 378.9272
-#&gt; Model cost at call 76 : 377.4846
-#&gt; Model cost at call 78 : 377.4846
-#&gt; Model cost at call 81 : 375.9738
-#&gt; Model cost at call 83 : 375.9738
-#&gt; Model cost at call 86 : 375.3387
-#&gt; Model cost at call 88 : 375.3387
-#&gt; Model cost at call 91 : 374.5774
-#&gt; Model cost at call 93 : 374.5774
-#&gt; Model cost at call 95 : 374.5774
-#&gt; Model cost at call 96 : 373.5447
-#&gt; Model cost at call 100 : 373.5446
-#&gt; Model cost at call 102 : 373.2643
-#&gt; Model cost at call 104 : 373.2643
-#&gt; Model cost at call 107 : 372.6799
-#&gt; Model cost at call 111 : 372.6798
-#&gt; Model cost at call 114 : 372.6325
-#&gt; Model cost at call 116 : 372.6325
-#&gt; Model cost at call 119 : 372.6159
-#&gt; Model cost at call 121 : 372.6159
-#&gt; Model cost at call 123 : 372.6159
-#&gt; Model cost at call 124 : 372.5845
-#&gt; Model cost at call 126 : 372.5845
-#&gt; Model cost at call 129 : 372.5375
-#&gt; Model cost at call 130 : 372.4771
-#&gt; Model cost at call 131 : 372.2008
-#&gt; Model cost at call 132 : 371.4923
-#&gt; Model cost at call 134 : 371.4923
-#&gt; Model cost at call 137 : 371.3022
-#&gt; Model cost at call 139 : 371.3022
-#&gt; Model cost at call 143 : 371.2271
-#&gt; Model cost at call 144 : 371.2271
-#&gt; Model cost at call 148 : 371.2202
-#&gt; Model cost at call 149 : 371.215
-#&gt; Model cost at call 152 : 371.215
-#&gt; Model cost at call 154 : 371.2136
-#&gt; Model cost at call 155 : 371.2136
-#&gt; Model cost at call 156 : 371.2136
-#&gt; Model cost at call 160 : 371.2134
-#&gt; Model cost at call 164 : 371.2134
-#&gt; Model cost at call 167 : 371.2134
-#&gt; 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'>#&gt; mkin version: 0.9.44.9000
+<span class='no'>fit.ff</span> <span class='kw'>&lt;-</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'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 18 15:20:52 2016
-#&gt; Date of summary: Fri Nov 18 15:20:52 2016
+#&gt; Date of fit: Fri Nov 18 16:24:04 2016
+#&gt; Date of summary: Fri Nov 18 16:24:04 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -536,7 +325,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 185 model solutions performed in 0.764 s
+#&gt; Fitted with method Port using 185 model solutions performed in 0.756 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -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'>#&gt; <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'>&lt;-</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'>#&gt; Model cost at call 1 : 12435.14
-#&gt; Model cost at call 2 : 12435.14
-#&gt; Model cost at call 5 : 8276.306
-#&gt; Model cost at call 6 : 8276.294
-#&gt; Model cost at call 7 : 8275.676
-#&gt; Model cost at call 9 : 5256.953
-#&gt; Model cost at call 11 : 5256.951
-#&gt; Model cost at call 12 : 5256.943
-#&gt; Model cost at call 14 : 4469.745
-#&gt; Model cost at call 18 : 4462.927
-#&gt; Model cost at call 21 : 4462.925
-#&gt; Model cost at call 22 : 4376.059
-#&gt; Model cost at call 24 : 4376.058
-#&gt; Model cost at call 27 : 4366.956
-#&gt; Model cost at call 29 : 4366.956
-#&gt; Model cost at call 31 : 4365.275
-#&gt; Model cost at call 33 : 4365.275
-#&gt; Model cost at call 35 : 4351.877
-#&gt; Model cost at call 37 : 4351.877
-#&gt; Model cost at call 39 : 4338.109
-#&gt; Model cost at call 41 : 4338.109
-#&gt; Model cost at call 43 : 4297.053
-#&gt; Model cost at call 44 : 4218.591
-#&gt; Model cost at call 45 : 3940.397
-#&gt; Model cost at call 46 : 3690.395
-#&gt; Model cost at call 48 : 3690.395
-#&gt; Model cost at call 49 : 3690.385
-#&gt; Model cost at call 50 : 3038.366
-#&gt; Model cost at call 53 : 3038.365
-#&gt; Model cost at call 54 : 2637.866
-#&gt; Model cost at call 57 : 2637.865
-#&gt; Model cost at call 59 : 2588.01
-#&gt; Model cost at call 60 : 2588.009
-#&gt; Model cost at call 63 : 2576.742
-#&gt; Model cost at call 66 : 2576.742
-#&gt; Model cost at call 67 : 2574
-#&gt; Model cost at call 68 : 2574
-#&gt; Model cost at call 69 : 2574
-#&gt; Model cost at call 71 : 2569.76
-#&gt; Model cost at call 73 : 2569.76
-#&gt; Model cost at call 74 : 2569.76
-#&gt; Model cost at call 75 : 2569.403
-#&gt; Model cost at call 76 : 2569.403
-#&gt; Model cost at call 79 : 2569.4
-#&gt; Model cost at call 80 : 2569.4
-#&gt; Model cost at call 81 : 2569.4
-#&gt; Model cost at call 83 : 2569.4
-#&gt; Model cost at call 86 : 2569.4
-#&gt; Model cost at call 90 : 2569.4
-#&gt; Model cost at call 99 : 2569.4
-#&gt; Model cost at call 100 : 2569.4
-#&gt; 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'>#&gt; mkin version: 0.9.44.9000
+<span class='no'>fit.ff.2</span> <span class='kw'>&lt;-</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'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.2
-#&gt; Date of fit: Fri Nov 18 15:20:52 2016
-#&gt; Date of summary: Fri Nov 18 15:20:52 2016
+#&gt; Date of fit: Fri Nov 18 16:24:05 2016
+#&gt; Date of summary: Fri Nov 18 16:24:05 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -670,7 +409,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 104 model solutions performed in 0.44 s
+#&gt; Fitted with method Port using 104 model solutions performed in 0.416 s
#&gt;
#&gt; Weighting: none
#&gt;

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