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-rw-r--r--docs/reference/transform_odeparms.html527
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'>&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: Thu Nov 17 22:57:06 2016
-#&gt; Date of summary: Thu Nov 17 22:57:06 2016
+#&gt; Date of fit: Fri Nov 18 15:20:49 2016
+#&gt; Date of summary: Fri Nov 18 15:20:49 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 0.684 s
+#&gt; Fitted with method Port using 153 model solutions performed in 0.681 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -222,10 +222,220 @@
#&gt; DT50 DT90
#&gt; parent 7.023 23.33
#&gt; m1 131.761 437.70</div><div class='input'>
-<span class='co'>## Not run: ------------------------------------</span>
-<span class='co'># fit.2 &lt;- 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'>&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
+#&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;
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
+#&gt; d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 327 model solutions performed in 1.34 s
+#&gt;
+#&gt; Weighting: none
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; parent_0 100.7500 state
+#&gt; k_parent_sink 0.1000 deparm
+#&gt; k_parent_m1 0.1001 deparm
+#&gt; k_m1_sink 0.1002 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; parent_0 100.7500 -Inf Inf
+#&gt; k_parent_sink 0.1000 0 Inf
+#&gt; k_parent_m1 0.1001 0 Inf
+#&gt; k_m1_sink 0.1002 0 Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; m1_0 0 state
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.600000 1.6140000 96.330000 1.029e+02
+#&gt; k_parent_sink 0.047920 0.0037500 0.040310 5.553e-02
+#&gt; k_parent_m1 0.050780 0.0020940 0.046530 5.502e-02
+#&gt; k_m1_sink 0.005261 0.0007159 0.003809 6.713e-03
+#&gt;
+#&gt; Parameter correlation:
+#&gt; parent_0 k_parent_sink k_parent_m1 k_m1_sink
+#&gt; parent_0 1.00000 0.6075 -0.06625 -0.1701
+#&gt; k_parent_sink 0.60752 1.0000 -0.08740 -0.6253
+#&gt; k_parent_m1 -0.06625 -0.0874 1.00000 0.4716
+#&gt; k_m1_sink -0.17006 -0.6253 0.47164 1.0000
+#&gt;
+#&gt; Residual standard error: 3.211 on 36 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02
+#&gt; k_parent_sink 0.047920 12.780 3.050e-15 0.040310 5.553e-02
+#&gt; k_parent_m1 0.050780 24.250 3.407e-24 0.046530 5.502e-02
+#&gt; k_m1_sink 0.005261 7.349 5.758e-09 0.003809 6.713e-03
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 6.398 4 15
+#&gt; parent 6.827 3 6
+#&gt; m1 4.490 1 9
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; parent_sink 0.4855
+#&gt; parent_m1 0.5145
+#&gt; m1_sink 1.0000
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; parent 7.023 23.33
+#&gt; m1 131.761 437.70</div><div class='input'>
<span class='no'>initials</span> <span class='kw'>&lt;-</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'>&lt;-</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'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 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'>#&gt; parent_0 k_parent_sink k_parent_m1 k_m1_sink
#&gt; 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 &lt;- 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 &lt;- mkinfit(SFO_SFO.ff, FOCUS_2006_D)</span>
-<span class='co'># summary(fit.ff, data = FALSE)</span>
-<span class='co'># initials &lt;- c("f_parent_to_m1" = 0.5)</span>
-<span class='co'># transformed &lt;- 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 &lt;- 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 &lt;- 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'>&lt;-</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'>#&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
+#&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;
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt; d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 185 model solutions performed in 0.764 s
+#&gt;
+#&gt; Weighting: none
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; parent_0 100.7500 state
+#&gt; k_parent 0.1000 deparm
+#&gt; k_m1 0.1001 deparm
+#&gt; f_parent_to_m1 0.5000 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; parent_0 100.750000 -Inf Inf
+#&gt; log_k_parent -2.302585 -Inf Inf
+#&gt; log_k_m1 -2.301586 -Inf Inf
+#&gt; f_parent_ilr_1 0.000000 -Inf Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; m1_0 0 state
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 99.60000 1.61400 96.3300 102.9000
+#&gt; log_k_parent -2.31600 0.04187 -2.4010 -2.2310
+#&gt; log_k_m1 -5.24800 0.13610 -5.5230 -4.9720
+#&gt; f_parent_ilr_1 0.04096 0.06477 -0.0904 0.1723
+#&gt;
+#&gt; Parameter correlation:
+#&gt; parent_0 log_k_parent log_k_m1 f_parent_ilr_1
+#&gt; parent_0 1.0000 0.5178 -0.1701 -0.5489
+#&gt; log_k_parent 0.5178 1.0000 -0.3285 -0.5451
+#&gt; log_k_m1 -0.1701 -0.3285 1.0000 0.7466
+#&gt; f_parent_ilr_1 -0.5489 -0.5451 0.7466 1.0000
+#&gt;
+#&gt; Residual standard error: 3.211 on 36 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02
+#&gt; k_parent 0.098700 23.880 5.701e-24 0.090660 1.074e-01
+#&gt; k_m1 0.005261 7.349 5.758e-09 0.003992 6.933e-03
+#&gt; f_parent_to_m1 0.514500 22.490 4.374e-23 0.468100 5.606e-01
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 6.398 4 15
+#&gt; parent 6.459 2 7
+#&gt; m1 4.690 2 8
+#&gt;
+#&gt; Resulting formation fractions:
+#&gt; ff
+#&gt; parent_m1 0.5145
+#&gt; parent_sink 0.4855
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; parent 7.023 23.33
+#&gt; m1 131.761 437.70</div><div class='input'><span class='no'>initials</span> <span class='kw'>&lt;-</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'>&lt;-</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'>#&gt; f_parent_to_m1
+#&gt; 0.5 </div><div class='input'>
+<span class='co'># And without sink</span>
+<span class='no'>SFO_SFO.ff.2</span> <span class='kw'>&lt;-</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'>#&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
+#&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;
+#&gt; Equations:
+#&gt; d_parent/dt = - k_parent * parent
+#&gt; d_m1/dt = + k_parent * parent - k_m1 * m1
+#&gt;
+#&gt; Model predictions using solution type deSolve
+#&gt;
+#&gt; Fitted with method Port using 104 model solutions performed in 0.44 s
+#&gt;
+#&gt; Weighting: none
+#&gt;
+#&gt; Starting values for parameters to be optimised:
+#&gt; value type
+#&gt; parent_0 100.7500 state
+#&gt; k_parent 0.1000 deparm
+#&gt; k_m1 0.1001 deparm
+#&gt;
+#&gt; Starting values for the transformed parameters actually optimised:
+#&gt; value lower upper
+#&gt; parent_0 100.750000 -Inf Inf
+#&gt; log_k_parent -2.302585 -Inf Inf
+#&gt; log_k_m1 -2.301586 -Inf Inf
+#&gt;
+#&gt; Fixed parameter values:
+#&gt; value type
+#&gt; m1_0 0 state
+#&gt;
+#&gt; Optimised, transformed parameters with symmetric confidence intervals:
+#&gt; Estimate Std. Error Lower Upper
+#&gt; parent_0 84.790 2.96500 78.78 90.800
+#&gt; log_k_parent -2.756 0.08088 -2.92 -2.593
+#&gt; log_k_m1 -4.214 0.11150 -4.44 -3.988
+#&gt;
+#&gt; Parameter correlation:
+#&gt; parent_0 log_k_parent log_k_m1
+#&gt; parent_0 1.0000 0.11059 0.46156
+#&gt; log_k_parent 0.1106 1.00000 0.06274
+#&gt; log_k_m1 0.4616 0.06274 1.00000
+#&gt;
+#&gt; Residual standard error: 8.333 on 37 degrees of freedom
+#&gt;
+#&gt; Backtransformed parameters:
+#&gt; Confidence intervals for internally transformed parameters are asymmetric.
+#&gt; t-test (unrealistically) based on the assumption of normal distribution
+#&gt; for estimators of untransformed parameters.
+#&gt; Estimate t value Pr(&gt;t) Lower Upper
+#&gt; parent_0 84.79000 28.600 3.939e-27 78.78000 90.80000
+#&gt; k_parent 0.06352 12.360 5.237e-15 0.05392 0.07483
+#&gt; k_m1 0.01478 8.966 4.114e-11 0.01179 0.01853
+#&gt;
+#&gt; Chi2 error levels in percent:
+#&gt; err.min n.optim df
+#&gt; All data 19.66 3 16
+#&gt; parent 17.56 2 7
+#&gt; m1 18.71 1 9
+#&gt;
+#&gt; Estimated disappearance times:
+#&gt; DT50 DT90
+#&gt; parent 10.91 36.25
+#&gt; m1 46.89 155.75</div><div class='input'>
+</div></pre>
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