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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/mkinfit.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/mkinfit.html')
-rw-r--r--docs/reference/mkinfit.html1372
1 files changed, 50 insertions, 1322 deletions
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index f6ffd21d..99b10f43 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -359,15 +359,15 @@
<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_C</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>)</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 15:19:37 2016
-#&gt; Date of summary: Fri Nov 18 15:19:37 2016
+#&gt; Date of fit: Fri Nov 18 15:36:12 2016
+#&gt; Date of summary: Fri Nov 18 15:36:12 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
#&gt;
#&gt; Model predictions using solution type analytical
#&gt;
-#&gt; Fitted with method Port using 64 model solutions performed in 0.152 s
+#&gt; Fitted with method Port using 64 model solutions performed in 0.157 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -436,7 +436,7 @@
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</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='co'># Fit the model to the FOCUS example dataset D using defaults</span>
<span class='fu'>print</span>(<span class='fu'>system.time</span>(<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
<span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)))</div><div class='output co'>#&gt; user system elapsed
-#&gt; 1.220 1.184 0.904 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 1.264 1.216 0.945 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
@@ -513,7 +513,7 @@
#&gt; Model cost at call 152 : 371.2134
#&gt; Optimisation by method Port successfully terminated.
#&gt; user system elapsed
-#&gt; 0.712 0.040 0.707 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+#&gt; 0.712 0.036 0.702 </div><div class='input'><span class='fu'>coef</span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
#&gt; 99.59848 -3.03822 -2.98030 -5.24750 </div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fit.deSolve</span>)</div><div class='output co'>#&gt; $ff
#&gt; parent_sink parent_m1 m1_sink
#&gt; 0.485524 0.514476 1.000000
@@ -532,735 +532,32 @@
<span class='no'>FOMC_SFO</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'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"FOMC"</span>, <span class='st'>"m1"</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</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='co'># Fit the model to the FOCUS example dataset D using defaults</span>
-<span class='no'>fit.FOMC_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 18857.28
-#&gt; Model cost at call 4 : 18857.28
-#&gt; Model cost at call 5 : 18857.28
-#&gt; Model cost at call 8 : 15273.94
-#&gt; Model cost at call 9 : 15273.93
-#&gt; Model cost at call 12 : 15273.67
-#&gt; Model cost at call 13 : 15273.64
-#&gt; Model cost at call 14 : 12764.42
-#&gt; Model cost at call 15 : 8382.7
-#&gt; Model cost at call 20 : 8382.696
-#&gt; Model cost at call 23 : 2729.177
-#&gt; Model cost at call 24 : 2729.175
-#&gt; Model cost at call 26 : 2729.164
-#&gt; Model cost at call 30 : 2299.383
-#&gt; Model cost at call 34 : 2299.379
-#&gt; Model cost at call 35 : 2299.373
-#&gt; Model cost at call 36 : 1944.782
-#&gt; Model cost at call 40 : 1944.782
-#&gt; Model cost at call 42 : 1328.087
-#&gt; Model cost at call 43 : 908.661
-#&gt; Model cost at call 44 : 908.6604
-#&gt; Model cost at call 50 : 877.3556
-#&gt; Model cost at call 51 : 877.3554
-#&gt; Model cost at call 54 : 877.3546
-#&gt; Model cost at call 56 : 769.5186
-#&gt; Model cost at call 59 : 769.5157
-#&gt; Model cost at call 62 : 690.3426
-#&gt; Model cost at call 66 : 690.3425
-#&gt; Model cost at call 68 : 608.4032
-#&gt; Model cost at call 72 : 608.4031
-#&gt; Model cost at call 73 : 608.4031
-#&gt; Model cost at call 74 : 601.5178
-#&gt; Model cost at call 78 : 601.5174
-#&gt; Model cost at call 79 : 601.5174
-#&gt; Model cost at call 80 : 459.9885
-#&gt; Model cost at call 81 : 459.9883
-#&gt; Model cost at call 83 : 459.9878
-#&gt; Model cost at call 87 : 447.0145
-#&gt; Model cost at call 91 : 447.0145
-#&gt; Model cost at call 94 : 445.7322
-#&gt; Model cost at call 97 : 445.7322
-#&gt; Model cost at call 99 : 445.7322
-#&gt; Model cost at call 100 : 444.6965
-#&gt; Model cost at call 103 : 444.6965
-#&gt; Model cost at call 106 : 442.9742
-#&gt; Model cost at call 109 : 442.9742
-#&gt; Model cost at call 112 : 439.9665
-#&gt; Model cost at call 115 : 439.9665
-#&gt; Model cost at call 116 : 439.9664
-#&gt; Model cost at call 118 : 435.0752
-#&gt; Model cost at call 121 : 435.0751
-#&gt; Model cost at call 124 : 430.4718
-#&gt; Model cost at call 127 : 430.4717
-#&gt; Model cost at call 132 : 424.7004
-#&gt; Model cost at call 134 : 424.7003
-#&gt; Model cost at call 138 : 423.6102
-#&gt; Model cost at call 141 : 423.6102
-#&gt; Model cost at call 142 : 423.6102
-#&gt; Model cost at call 144 : 421.1786
-#&gt; Model cost at call 147 : 421.1786
-#&gt; Model cost at call 148 : 421.1786
-#&gt; Model cost at call 150 : 418.1431
-#&gt; Model cost at call 151 : 412.8665
-#&gt; Model cost at call 152 : 396.6067
-#&gt; Model cost at call 154 : 396.6067
-#&gt; Model cost at call 158 : 391.0492
-#&gt; Model cost at call 160 : 391.0492
-#&gt; Model cost at call 164 : 385.8205
-#&gt; Model cost at call 165 : 385.8205
-#&gt; Model cost at call 170 : 379.7674
-#&gt; Model cost at call 171 : 379.7674
-#&gt; Model cost at call 172 : 379.7674
-#&gt; Model cost at call 176 : 374.9389
-#&gt; Model cost at call 177 : 374.9389
-#&gt; Model cost at call 182 : 372.727
-#&gt; Model cost at call 185 : 372.727
-#&gt; Model cost at call 188 : 371.5297
-#&gt; Model cost at call 194 : 370.3738
-#&gt; Model cost at call 195 : 370.3738
-#&gt; Model cost at call 200 : 370.0182
-#&gt; Model cost at call 206 : 369.8634
-#&gt; Model cost at call 212 : 369.8188
-#&gt; Model cost at call 213 : 369.8188
-#&gt; Model cost at call 219 : 369.8114
-#&gt; Model cost at call 221 : 369.8114
-#&gt; Model cost at call 224 : 369.8114
-#&gt; Model cost at call 226 : 369.8114
-#&gt; Model cost at call 230 : 369.8105
-#&gt; Model cost at call 231 : 369.8105
-#&gt; Model cost at call 235 : 369.8105
-#&gt; Model cost at call 236 : 369.8105
-#&gt; Model cost at call 237 : 369.8105
-#&gt; Model cost at call 238 : 369.8105
-#&gt; Model cost at call 249 : 369.8105
-#&gt; Model cost at call 260 : 369.8105
-#&gt; Model cost at call 275 : 369.8105
-#&gt; Model cost at call 276 : 369.8105
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='co'># Use starting parameters from parent only FOMC fit</span>
-<span class='no'>fit.FOMC</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 3237.008
-#&gt; Model cost at call 3 : 3237.007
-#&gt; Model cost at call 6 : 671.2571
-#&gt; Model cost at call 7 : 671.2559
-#&gt; Model cost at call 8 : 671.2301
-#&gt; Model cost at call 9 : 671.2249
-#&gt; Model cost at call 10 : 468.4899
-#&gt; Model cost at call 12 : 468.4899
-#&gt; Model cost at call 14 : 371.3486
-#&gt; Model cost at call 16 : 371.3485
-#&gt; Model cost at call 18 : 346.2972
-#&gt; Model cost at call 19 : 346.2971
-#&gt; Model cost at call 20 : 346.297
-#&gt; Model cost at call 21 : 346.2969
-#&gt; Model cost at call 22 : 269.7053
-#&gt; Model cost at call 23 : 269.7053
-#&gt; Model cost at call 26 : 243.9936
-#&gt; Model cost at call 27 : 235.1625
-#&gt; Model cost at call 28 : 235.1624
-#&gt; Model cost at call 30 : 235.1624
-#&gt; Model cost at call 31 : 224.2195
-#&gt; Model cost at call 35 : 218.1922
-#&gt; Model cost at call 36 : 218.1922
-#&gt; Model cost at call 38 : 218.1922
-#&gt; Model cost at call 39 : 211.5012
-#&gt; Model cost at call 41 : 211.5012
-#&gt; Model cost at call 43 : 207.9511
-#&gt; Model cost at call 44 : 207.9511
-#&gt; Model cost at call 47 : 206.5377
-#&gt; Model cost at call 51 : 205.8736
-#&gt; Model cost at call 55 : 205.5625
-#&gt; Model cost at call 59 : 205.4704
-#&gt; Model cost at call 63 : 205.4499
-#&gt; Model cost at call 67 : 205.448
-#&gt; Model cost at call 69 : 205.448
-#&gt; Model cost at call 70 : 205.448
-#&gt; Model cost at call 73 : 205.448
-#&gt; Model cost at call 74 : 205.4478
-#&gt; Model cost at call 75 : 205.4478
-#&gt; Model cost at call 77 : 205.4478
-#&gt; Model cost at call 79 : 205.4478
-#&gt; Model cost at call 84 : 205.4478
-#&gt; Model cost at call 95 : 205.4478
-#&gt; Model cost at call 98 : 205.4478
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='no'>fit.FOMC_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_SFO</span>, <span class='no'>FOCUS_2006_D</span>,
- <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.FOMC</span>$<span class='no'>bparms.ode</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 15169.96
-#&gt; Model cost at call 2 : 15169.96
-#&gt; Model cost at call 7 : 8247.462
-#&gt; Model cost at call 14 : 6734.371
-#&gt; Model cost at call 15 : 6734.339
-#&gt; Model cost at call 16 : 6734.136
-#&gt; Model cost at call 20 : 4855.056
-#&gt; Model cost at call 24 : 4855.038
-#&gt; Model cost at call 27 : 1239.986
-#&gt; Model cost at call 29 : 1239.985
-#&gt; Model cost at call 34 : 1030.523
-#&gt; Model cost at call 38 : 1030.523
-#&gt; Model cost at call 40 : 894.2766
-#&gt; Model cost at call 43 : 894.275
-#&gt; Model cost at call 46 : 750.3629
-#&gt; Model cost at call 49 : 750.3623
-#&gt; Model cost at call 52 : 627.6819
-#&gt; Model cost at call 55 : 627.6818
-#&gt; Model cost at call 58 : 546.2947
-#&gt; Model cost at call 61 : 546.2944
-#&gt; Model cost at call 65 : 502.5529
-#&gt; Model cost at call 69 : 502.5525
-#&gt; Model cost at call 70 : 502.5525
-#&gt; Model cost at call 71 : 475.2423
-#&gt; Model cost at call 72 : 465.5298
-#&gt; Model cost at call 75 : 465.5298
-#&gt; Model cost at call 76 : 465.5297
-#&gt; Model cost at call 78 : 464.9476
-#&gt; Model cost at call 81 : 464.9476
-#&gt; Model cost at call 82 : 464.9473
-#&gt; Model cost at call 84 : 426.9626
-#&gt; Model cost at call 88 : 426.9626
-#&gt; Model cost at call 90 : 414.5235
-#&gt; Model cost at call 93 : 414.5234
-#&gt; Model cost at call 96 : 412.1478
-#&gt; Model cost at call 99 : 412.1477
-#&gt; Model cost at call 100 : 412.1477
-#&gt; Model cost at call 101 : 412.1477
-#&gt; Model cost at call 102 : 394.146
-#&gt; Model cost at call 105 : 394.146
-#&gt; Model cost at call 106 : 394.146
-#&gt; Model cost at call 107 : 394.146
-#&gt; Model cost at call 108 : 384.2002
-#&gt; Model cost at call 112 : 384.2001
-#&gt; Model cost at call 113 : 384.2001
-#&gt; Model cost at call 115 : 380.5495
-#&gt; Model cost at call 119 : 380.5494
-#&gt; Model cost at call 120 : 380.5494
-#&gt; Model cost at call 121 : 378.4803
-#&gt; Model cost at call 123 : 378.4802
-#&gt; Model cost at call 124 : 378.4792
-#&gt; Model cost at call 127 : 374.8432
-#&gt; Model cost at call 129 : 374.8431
-#&gt; Model cost at call 133 : 372.8364
-#&gt; Model cost at call 136 : 372.8364
-#&gt; Model cost at call 137 : 372.8363
-#&gt; Model cost at call 138 : 372.8363
-#&gt; Model cost at call 141 : 372.668
-#&gt; Model cost at call 145 : 372.6679
-#&gt; Model cost at call 147 : 372.5882
-#&gt; Model cost at call 150 : 372.5882
-#&gt; Model cost at call 153 : 372.4828
-#&gt; Model cost at call 156 : 372.4828
-#&gt; Model cost at call 159 : 372.3639
-#&gt; Model cost at call 162 : 372.3639
-#&gt; Model cost at call 163 : 372.3639
-#&gt; Model cost at call 164 : 372.3639
-#&gt; Model cost at call 165 : 372.1959
-#&gt; Model cost at call 168 : 372.1959
-#&gt; Model cost at call 171 : 371.9627
-#&gt; Model cost at call 172 : 371.7467
-#&gt; Model cost at call 173 : 371.1161
-#&gt; Model cost at call 174 : 370.3326
-#&gt; Model cost at call 177 : 370.3326
-#&gt; Model cost at call 178 : 370.3326
-#&gt; Model cost at call 180 : 370.3267
-#&gt; Model cost at call 186 : 370.0471
-#&gt; Model cost at call 187 : 370.0471
-#&gt; Model cost at call 193 : 369.9649
-#&gt; Model cost at call 194 : 369.9649
-#&gt; Model cost at call 196 : 369.9649
-#&gt; Model cost at call 199 : 369.8684
-#&gt; Model cost at call 200 : 369.8684
-#&gt; Model cost at call 204 : 369.8684
-#&gt; Model cost at call 206 : 369.8349
-#&gt; Model cost at call 207 : 369.8349
-#&gt; Model cost at call 209 : 369.8349
-#&gt; Model cost at call 210 : 369.8349
-#&gt; Model cost at call 211 : 369.8349
-#&gt; Model cost at call 212 : 369.8105
-#&gt; Model cost at call 214 : 369.8105
-#&gt; Model cost at call 218 : 369.8105
-#&gt; Model cost at call 220 : 369.8105
-#&gt; Model cost at call 225 : 369.8105
-#&gt; Model cost at call 229 : 369.8105
-#&gt; Model cost at call 231 : 369.8105
-#&gt; Model cost at call 232 : 369.8105
-#&gt; Model cost at call 236 : 369.8105
-#&gt; Model cost at call 239 : 369.8105
-#&gt; Model cost at call 240 : 369.8105
-#&gt; Model cost at call 255 : 369.8105
-#&gt; Model cost at call 258 : 369.8105
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'>
+<span class='no'>fit.FOMC_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_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='co'># Use starting parameters from parent only FOMC fit</span>
+<span class='no'>fit.FOMC</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"FOMC"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='no'>fit.FOMC_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>FOMC_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='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.FOMC</span>$<span class='no'>bparms.ode</span>)
+
<span class='co'># Use stepwise fitting, using optimised parameters from parent only fit, SFORB</span>
<span class='no'>SFORB_SFO</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'>"SFORB"</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>))</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='co'># Fit the model to the FOCUS example dataset D using defaults</span>
-<span class='no'>fit.SFORB_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 19233.21
-#&gt; Model cost at call 2 : 19233.21
-#&gt; Model cost at call 5 : 19233.21
-#&gt; Model cost at call 8 : 14482.65
-#&gt; Model cost at call 11 : 14482.51
-#&gt; Model cost at call 13 : 14482.17
-#&gt; Model cost at call 15 : 6973.814
-#&gt; Model cost at call 16 : 5161.041
-#&gt; Model cost at call 17 : 5161.029
-#&gt; Model cost at call 22 : 5161.026
-#&gt; Model cost at call 24 : 3249.595
-#&gt; Model cost at call 26 : 3249.595
-#&gt; Model cost at call 27 : 3249.519
-#&gt; Model cost at call 31 : 2615.891
-#&gt; Model cost at call 32 : 2615.888
-#&gt; Model cost at call 39 : 989.1788
-#&gt; Model cost at call 44 : 989.1772
-#&gt; Model cost at call 45 : 989.1771
-#&gt; Model cost at call 47 : 647.4307
-#&gt; Model cost at call 50 : 647.4302
-#&gt; Model cost at call 51 : 647.4261
-#&gt; Model cost at call 54 : 626.7937
-#&gt; Model cost at call 55 : 626.7935
-#&gt; Model cost at call 56 : 626.7931
-#&gt; Model cost at call 61 : 527.9042
-#&gt; Model cost at call 62 : 527.9041
-#&gt; Model cost at call 68 : 505.8828
-#&gt; Model cost at call 70 : 505.8828
-#&gt; Model cost at call 73 : 505.8827
-#&gt; Model cost at call 75 : 452.8932
-#&gt; Model cost at call 77 : 452.893
-#&gt; Model cost at call 82 : 414.4918
-#&gt; Model cost at call 83 : 414.4918
-#&gt; Model cost at call 84 : 414.4918
-#&gt; Model cost at call 88 : 414.4917
-#&gt; Model cost at call 89 : 408.2617
-#&gt; Model cost at call 90 : 408.2616
-#&gt; Model cost at call 91 : 408.2616
-#&gt; Model cost at call 95 : 408.2615
-#&gt; Model cost at call 96 : 384.4461
-#&gt; Model cost at call 102 : 384.4461
-#&gt; Model cost at call 104 : 383.4905
-#&gt; Model cost at call 105 : 383.4905
-#&gt; Model cost at call 106 : 383.4905
-#&gt; Model cost at call 109 : 383.4904
-#&gt; Model cost at call 111 : 381.8828
-#&gt; Model cost at call 112 : 381.8827
-#&gt; Model cost at call 118 : 380.8499
-#&gt; Model cost at call 120 : 380.8499
-#&gt; Model cost at call 123 : 380.8499
-#&gt; Model cost at call 125 : 379.1403
-#&gt; Model cost at call 127 : 379.1402
-#&gt; Model cost at call 132 : 376.4962
-#&gt; Model cost at call 133 : 373.0958
-#&gt; Model cost at call 134 : 365.247
-#&gt; Model cost at call 137 : 365.2469
-#&gt; Model cost at call 142 : 360.8231
-#&gt; Model cost at call 143 : 360.8231
-#&gt; Model cost at call 146 : 360.8231
-#&gt; Model cost at call 148 : 360.8231
-#&gt; Model cost at call 149 : 358.3976
-#&gt; Model cost at call 152 : 358.3976
-#&gt; Model cost at call 154 : 358.3976
-#&gt; Model cost at call 156 : 355.9066
-#&gt; Model cost at call 157 : 355.9066
-#&gt; Model cost at call 163 : 354.3386
-#&gt; Model cost at call 164 : 353.6335
-#&gt; Model cost at call 172 : 353.2094
-#&gt; Model cost at call 173 : 353.2094
-#&gt; Model cost at call 174 : 353.2093
-#&gt; Model cost at call 177 : 353.2093
-#&gt; Model cost at call 178 : 353.2093
-#&gt; Model cost at call 179 : 352.6641
-#&gt; Model cost at call 182 : 352.6641
-#&gt; Model cost at call 183 : 352.6641
-#&gt; Model cost at call 186 : 352.4908
-#&gt; Model cost at call 187 : 352.4429
-#&gt; Model cost at call 195 : 352.3246
-#&gt; Model cost at call 203 : 352.2858
-#&gt; Model cost at call 204 : 352.2858
-#&gt; Model cost at call 205 : 352.2858
-#&gt; Model cost at call 206 : 352.2858
-#&gt; Model cost at call 207 : 352.2858
-#&gt; Model cost at call 210 : 352.2332
-#&gt; Model cost at call 211 : 352.2081
-#&gt; Model cost at call 214 : 352.2081
-#&gt; Model cost at call 216 : 352.2081
-#&gt; Model cost at call 218 : 352.2049
-#&gt; Model cost at call 219 : 352.2049
-#&gt; Model cost at call 220 : 352.2049
-#&gt; Model cost at call 226 : 352.2048
-#&gt; Model cost at call 228 : 352.2048
-#&gt; Model cost at call 231 : 352.2048
-#&gt; Model cost at call 232 : 352.2048
-#&gt; Model cost at call 238 : 352.2048
-#&gt; Model cost at call 239 : 352.2048
-#&gt; Model cost at call 251 : 352.2048
-#&gt; Model cost at call 264 : 352.2048
-#&gt; Model cost at call 283 : 352.2048
-#&gt; Model cost at call 284 : 352.2048
-#&gt; Model cost at call 285 : 352.2048
-#&gt; Model cost at call 286 : 352.2048
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='no'>fit.SFORB_SFO.deSolve</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 19233.21
-#&gt; Model cost at call 2 : 19233.21
-#&gt; Model cost at call 5 : 19233.21
-#&gt; Model cost at call 8 : 14482.65
-#&gt; Model cost at call 11 : 14482.51
-#&gt; Model cost at call 13 : 14482.17
-#&gt; Model cost at call 15 : 6973.814
-#&gt; Model cost at call 16 : 5161.041
-#&gt; Model cost at call 17 : 5161.029
-#&gt; Model cost at call 22 : 5161.026
-#&gt; Model cost at call 24 : 3249.595
-#&gt; Model cost at call 26 : 3249.595
-#&gt; Model cost at call 27 : 3249.519
-#&gt; Model cost at call 31 : 2615.891
-#&gt; Model cost at call 32 : 2615.888
-#&gt; Model cost at call 39 : 989.1788
-#&gt; Model cost at call 44 : 989.1772
-#&gt; Model cost at call 45 : 989.1771
-#&gt; Model cost at call 47 : 647.4307
-#&gt; Model cost at call 50 : 647.4302
-#&gt; Model cost at call 51 : 647.4261
-#&gt; Model cost at call 54 : 626.7937
-#&gt; Model cost at call 55 : 626.7935
-#&gt; Model cost at call 56 : 626.7931
-#&gt; Model cost at call 61 : 527.9042
-#&gt; Model cost at call 62 : 527.9041
-#&gt; Model cost at call 68 : 505.8828
-#&gt; Model cost at call 70 : 505.8828
-#&gt; Model cost at call 73 : 505.8827
-#&gt; Model cost at call 75 : 452.8932
-#&gt; Model cost at call 77 : 452.893
-#&gt; Model cost at call 82 : 414.4918
-#&gt; Model cost at call 83 : 414.4918
-#&gt; Model cost at call 84 : 414.4918
-#&gt; Model cost at call 88 : 414.4917
-#&gt; Model cost at call 89 : 408.2617
-#&gt; Model cost at call 90 : 408.2616
-#&gt; Model cost at call 91 : 408.2616
-#&gt; Model cost at call 95 : 408.2615
-#&gt; Model cost at call 96 : 384.4461
-#&gt; Model cost at call 102 : 384.4461
-#&gt; Model cost at call 104 : 383.4905
-#&gt; Model cost at call 105 : 383.4905
-#&gt; Model cost at call 106 : 383.4905
-#&gt; Model cost at call 109 : 383.4904
-#&gt; Model cost at call 111 : 381.8828
-#&gt; Model cost at call 112 : 381.8827
-#&gt; Model cost at call 118 : 380.8499
-#&gt; Model cost at call 120 : 380.8499
-#&gt; Model cost at call 123 : 380.8499
-#&gt; Model cost at call 125 : 379.1403
-#&gt; Model cost at call 127 : 379.1402
-#&gt; Model cost at call 132 : 376.4962
-#&gt; Model cost at call 133 : 373.0958
-#&gt; Model cost at call 134 : 365.247
-#&gt; Model cost at call 137 : 365.2469
-#&gt; Model cost at call 142 : 360.8231
-#&gt; Model cost at call 143 : 360.8231
-#&gt; Model cost at call 146 : 360.8231
-#&gt; Model cost at call 148 : 360.8231
-#&gt; Model cost at call 149 : 358.3976
-#&gt; Model cost at call 152 : 358.3976
-#&gt; Model cost at call 154 : 358.3976
-#&gt; Model cost at call 156 : 355.9066
-#&gt; Model cost at call 157 : 355.9066
-#&gt; Model cost at call 163 : 354.3386
-#&gt; Model cost at call 164 : 353.6335
-#&gt; Model cost at call 172 : 353.2094
-#&gt; Model cost at call 173 : 353.2094
-#&gt; Model cost at call 174 : 353.2093
-#&gt; Model cost at call 177 : 353.2093
-#&gt; Model cost at call 178 : 353.2093
-#&gt; Model cost at call 179 : 352.6641
-#&gt; Model cost at call 182 : 352.6641
-#&gt; Model cost at call 183 : 352.6641
-#&gt; Model cost at call 186 : 352.4908
-#&gt; Model cost at call 187 : 352.4429
-#&gt; Model cost at call 195 : 352.3246
-#&gt; Model cost at call 203 : 352.2858
-#&gt; Model cost at call 204 : 352.2858
-#&gt; Model cost at call 205 : 352.2858
-#&gt; Model cost at call 206 : 352.2858
-#&gt; Model cost at call 207 : 352.2858
-#&gt; Model cost at call 210 : 352.2332
-#&gt; Model cost at call 211 : 352.2081
-#&gt; Model cost at call 214 : 352.2081
-#&gt; Model cost at call 216 : 352.2081
-#&gt; Model cost at call 218 : 352.2049
-#&gt; Model cost at call 219 : 352.2049
-#&gt; Model cost at call 220 : 352.2049
-#&gt; Model cost at call 226 : 352.2048
-#&gt; Model cost at call 228 : 352.2048
-#&gt; Model cost at call 231 : 352.2048
-#&gt; Model cost at call 232 : 352.2048
-#&gt; Model cost at call 238 : 352.2048
-#&gt; Model cost at call 239 : 352.2048
-#&gt; Model cost at call 251 : 352.2048
-#&gt; Model cost at call 264 : 352.2048
-#&gt; Model cost at call 283 : 352.2048
-#&gt; Model cost at call 284 : 352.2048
-#&gt; Model cost at call 285 : 352.2048
-#&gt; Model cost at call 286 : 352.2048
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='co'># Use starting parameters from parent only SFORB fit (not really needed in this case)</span>
-<span class='no'>fit.SFORB</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"SFORB"</span>, <span class='no'>FOCUS_2006_D</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 10426.65
-#&gt; Model cost at call 3 : 10426.65
-#&gt; Model cost at call 6 : 1995.326
-#&gt; Model cost at call 7 : 1995.322
-#&gt; Model cost at call 8 : 1995.14
-#&gt; Model cost at call 11 : 718.5568
-#&gt; Model cost at call 12 : 718.5566
-#&gt; Model cost at call 13 : 718.5563
-#&gt; Model cost at call 16 : 408.9208
-#&gt; Model cost at call 17 : 408.9204
-#&gt; Model cost at call 18 : 408.9204
-#&gt; Model cost at call 20 : 408.9203
-#&gt; Model cost at call 21 : 402.7935
-#&gt; Model cost at call 22 : 402.793
-#&gt; Model cost at call 26 : 202.0443
-#&gt; Model cost at call 28 : 202.0443
-#&gt; Model cost at call 30 : 202.0443
-#&gt; Model cost at call 31 : 196.438
-#&gt; Model cost at call 36 : 196.1947
-#&gt; Model cost at call 37 : 196.1947
-#&gt; Model cost at call 41 : 192.9338
-#&gt; Model cost at call 43 : 192.9338
-#&gt; Model cost at call 45 : 192.9338
-#&gt; Model cost at call 46 : 191.6452
-#&gt; Model cost at call 47 : 191.6452
-#&gt; Model cost at call 51 : 188.9328
-#&gt; Model cost at call 54 : 188.9328
-#&gt; Model cost at call 55 : 188.9328
-#&gt; Model cost at call 56 : 183.6499
-#&gt; Model cost at call 59 : 183.6499
-#&gt; Model cost at call 62 : 181.9039
-#&gt; Model cost at call 67 : 179.0543
-#&gt; Model cost at call 68 : 179.0543
-#&gt; Model cost at call 69 : 179.0543
-#&gt; Model cost at call 70 : 179.0543
-#&gt; Model cost at call 72 : 176.749
-#&gt; Model cost at call 73 : 176.2321
-#&gt; Model cost at call 74 : 176.232
-#&gt; Model cost at call 75 : 176.232
-#&gt; Model cost at call 76 : 176.232
-#&gt; Model cost at call 78 : 175.3914
-#&gt; Model cost at call 79 : 175.3914
-#&gt; Model cost at call 81 : 175.3913
-#&gt; Model cost at call 83 : 174.6257
-#&gt; Model cost at call 84 : 174.6257
-#&gt; Model cost at call 89 : 174.1476
-#&gt; Model cost at call 92 : 174.1476
-#&gt; Model cost at call 93 : 174.1476
-#&gt; Model cost at call 94 : 173.8512
-#&gt; Model cost at call 99 : 173.6987
-#&gt; Model cost at call 104 : 173.6813
-#&gt; Model cost at call 105 : 173.6813
-#&gt; Model cost at call 106 : 173.6813
-#&gt; Model cost at call 107 : 173.6813
-#&gt; Model cost at call 108 : 173.6813
-#&gt; Model cost at call 109 : 173.6802
-#&gt; Model cost at call 110 : 173.6802
-#&gt; Model cost at call 111 : 173.6802
-#&gt; Model cost at call 112 : 173.6802
-#&gt; Model cost at call 113 : 173.6802
-#&gt; Model cost at call 114 : 173.6799
-#&gt; Model cost at call 116 : 173.6799
-#&gt; Model cost at call 118 : 173.6799
-#&gt; Model cost at call 119 : 173.6799
-#&gt; Model cost at call 120 : 173.6799
-#&gt; Model cost at call 129 : 173.6799
-#&gt; Model cost at call 141 : 173.6799
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='no'>fit.SFORB_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.SFORB</span>$<span class='no'>bparms.ode</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 18365.33
-#&gt; Model cost at call 2 : 18365.33
-#&gt; Model cost at call 8 : 11666.4
-#&gt; Model cost at call 9 : 10992.15
-#&gt; Model cost at call 10 : 10992.13
-#&gt; Model cost at call 11 : 10991.95
-#&gt; Model cost at call 12 : 10991.17
-#&gt; Model cost at call 14 : 10990.65
-#&gt; Model cost at call 17 : 3940.801
-#&gt; Model cost at call 20 : 3940.8
-#&gt; Model cost at call 22 : 3940.798
-#&gt; Model cost at call 24 : 3241.199
-#&gt; Model cost at call 27 : 3241.198
-#&gt; Model cost at call 30 : 3241.192
-#&gt; Model cost at call 31 : 1518.749
-#&gt; Model cost at call 37 : 1518.747
-#&gt; Model cost at call 39 : 1091.836
-#&gt; Model cost at call 42 : 1091.835
-#&gt; Model cost at call 43 : 1091.835
-#&gt; Model cost at call 44 : 1091.804
-#&gt; Model cost at call 46 : 927.8538
-#&gt; Model cost at call 49 : 927.8529
-#&gt; Model cost at call 53 : 638.102
-#&gt; Model cost at call 56 : 638.1019
-#&gt; Model cost at call 58 : 638.1018
-#&gt; Model cost at call 61 : 560.4352
-#&gt; Model cost at call 62 : 560.435
-#&gt; Model cost at call 63 : 560.4327
-#&gt; Model cost at call 68 : 423.9629
-#&gt; Model cost at call 69 : 423.9629
-#&gt; Model cost at call 70 : 423.9629
-#&gt; Model cost at call 71 : 423.9628
-#&gt; Model cost at call 73 : 423.9628
-#&gt; Model cost at call 75 : 395.8015
-#&gt; Model cost at call 78 : 395.8013
-#&gt; Model cost at call 79 : 395.8013
-#&gt; Model cost at call 83 : 365.6975
-#&gt; Model cost at call 84 : 365.6975
-#&gt; Model cost at call 88 : 365.6975
-#&gt; Model cost at call 91 : 362.9843
-#&gt; Model cost at call 93 : 362.9843
-#&gt; Model cost at call 98 : 361.5506
-#&gt; Model cost at call 99 : 361.5506
-#&gt; Model cost at call 100 : 361.5505
-#&gt; Model cost at call 105 : 359.0492
-#&gt; Model cost at call 106 : 359.0492
-#&gt; Model cost at call 112 : 357.6574
-#&gt; Model cost at call 113 : 357.6574
-#&gt; Model cost at call 114 : 357.6574
-#&gt; Model cost at call 115 : 357.6574
-#&gt; Model cost at call 119 : 355.4518
-#&gt; Model cost at call 120 : 355.4518
-#&gt; Model cost at call 127 : 354.9045
-#&gt; Model cost at call 129 : 354.9045
-#&gt; Model cost at call 131 : 354.9045
-#&gt; Model cost at call 134 : 354.4168
-#&gt; Model cost at call 135 : 354.4168
-#&gt; Model cost at call 137 : 354.4167
-#&gt; Model cost at call 141 : 353.7901
-#&gt; Model cost at call 142 : 353.7901
-#&gt; Model cost at call 143 : 353.7899
-#&gt; Model cost at call 149 : 353.3233
-#&gt; Model cost at call 151 : 353.3233
-#&gt; Model cost at call 154 : 353.3233
-#&gt; Model cost at call 156 : 353.2939
-#&gt; Model cost at call 158 : 353.2938
-#&gt; Model cost at call 159 : 353.2938
-#&gt; Model cost at call 160 : 353.2938
-#&gt; Model cost at call 163 : 353.0571
-#&gt; Model cost at call 165 : 353.0571
-#&gt; Model cost at call 170 : 352.9457
-#&gt; Model cost at call 171 : 352.7458
-#&gt; Model cost at call 173 : 352.7457
-#&gt; Model cost at call 178 : 352.6377
-#&gt; Model cost at call 180 : 352.6377
-#&gt; Model cost at call 183 : 352.6377
-#&gt; Model cost at call 185 : 352.5377
-#&gt; Model cost at call 187 : 352.5377
-#&gt; Model cost at call 188 : 352.5377
-#&gt; Model cost at call 191 : 352.5377
-#&gt; Model cost at call 193 : 352.4479
-#&gt; Model cost at call 195 : 352.4479
-#&gt; Model cost at call 198 : 352.4479
-#&gt; Model cost at call 200 : 352.4021
-#&gt; Model cost at call 202 : 352.4021
-#&gt; Model cost at call 205 : 352.4021
-#&gt; Model cost at call 207 : 352.3465
-#&gt; Model cost at call 210 : 352.3465
-#&gt; Model cost at call 214 : 352.3031
-#&gt; Model cost at call 216 : 352.3031
-#&gt; Model cost at call 221 : 352.2632
-#&gt; Model cost at call 223 : 352.2632
-#&gt; Model cost at call 228 : 352.2367
-#&gt; Model cost at call 230 : 352.2367
-#&gt; Model cost at call 231 : 352.2367
-#&gt; Model cost at call 233 : 352.2367
-#&gt; Model cost at call 235 : 352.215
-#&gt; Model cost at call 238 : 352.215
-#&gt; Model cost at call 239 : 352.215
-#&gt; Model cost at call 242 : 352.207
-#&gt; Model cost at call 245 : 352.207
-#&gt; Model cost at call 250 : 352.2053
-#&gt; Model cost at call 251 : 352.2053
-#&gt; Model cost at call 253 : 352.2053
-#&gt; Model cost at call 256 : 352.2053
-#&gt; Model cost at call 258 : 352.2053
-#&gt; Model cost at call 259 : 352.2052
-#&gt; Model cost at call 260 : 352.2052
-#&gt; Model cost at call 263 : 352.2052
-#&gt; Model cost at call 271 : 352.2048
-#&gt; Model cost at call 273 : 352.2048
-#&gt; Model cost at call 274 : 352.2048
-#&gt; Model cost at call 281 : 352.2048
-#&gt; Model cost at call 282 : 352.2048
-#&gt; Model cost at call 286 : 352.2048
-#&gt; Model cost at call 289 : 352.2048
-#&gt; Model cost at call 294 : 352.2048
-#&gt; Model cost at call 296 : 352.2048
-#&gt; Model cost at call 300 : 352.2048
-#&gt; Model cost at call 307 : 352.2048
-#&gt; Model cost at call 325 : 352.2048
-#&gt; Model cost at call 331 : 352.2048
-#&gt; Model cost at call 333 : 352.2048
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'>
+<span class='no'>fit.SFORB_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_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='no'>fit.SFORB_SFO.deSolve</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>,
+ <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='co'># Use starting parameters from parent only SFORB fit (not really needed in this case)</span>
+<span class='no'>fit.SFORB</span> <span class='kw'>=</span> <span class='fu'>mkinfit</span>(<span class='st'>"SFORB"</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='no'>fit.SFORB_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFORB_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='no'>fit.SFORB</span>$<span class='no'>bparms.ode</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+
<span class='co'># Weighted fits, including IRLS</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'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
- <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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'>f.noweight</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</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'>f.noweight</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></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'>f.noweight</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</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'>f.noweight</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 15:19:47 2016
-#&gt; Date of summary: Fri Nov 18 15:19:47 2016
+#&gt; Date of fit: Fri Nov 18 15:36:22 2016
+#&gt; Date of summary: Fri Nov 18 15:36:22 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1268,7 +565,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 185 model solutions performed in 0.748 s
+#&gt; Fitted with method Port using 185 model solutions performed in 0.752 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -1377,146 +674,11 @@
#&gt; 100 m1 31.04 3.198e+01 -9.416e-01
#&gt; 100 m1 33.13 3.198e+01 1.148e+00
#&gt; 120 m1 25.15 2.879e+01 -3.640e+00
-#&gt; 120 m1 33.31 2.879e+01 4.520e+00</div><div class='input'><span class='no'>f.irls</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</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; IRLS based on variance estimates for each observed variable
-#&gt; Initial variance estimates are:
-#&gt; parent m1
-#&gt; 11.552581 7.421226
-#&gt; Model cost at call 186 : 40
-#&gt; Model cost at call 188 : 40
-#&gt; Model cost at call 194 : 39.99562
-#&gt; Model cost at call 195 : 39.99562
-#&gt; Model cost at call 201 : 39.9956
-#&gt; Model cost at call 203 : 39.99528
-#&gt; Model cost at call 205 : 39.99528
-#&gt; Model cost at call 207 : 39.99528
-#&gt; Model cost at call 209 : 39.99515
-#&gt; Model cost at call 211 : 39.99515
-#&gt; Model cost at call 214 : 39.99515
-#&gt; Model cost at call 215 : 39.99505
-#&gt; Model cost at call 217 : 39.99505
-#&gt; Model cost at call 219 : 39.99505
-#&gt; Model cost at call 220 : 39.99489
-#&gt; Model cost at call 222 : 39.99489
-#&gt; Model cost at call 224 : 39.99489
-#&gt; Model cost at call 225 : 39.99479
-#&gt; Model cost at call 227 : 39.99479
-#&gt; Model cost at call 231 : 39.99467
-#&gt; Model cost at call 234 : 39.99467
-#&gt; Model cost at call 235 : 39.99467
-#&gt; Model cost at call 236 : 39.99458
-#&gt; Model cost at call 238 : 39.99458
-#&gt; Model cost at call 239 : 39.99458
-#&gt; Model cost at call 241 : 39.99452
-#&gt; Model cost at call 242 : 39.99444
-#&gt; Model cost at call 243 : 39.99433
-#&gt; Model cost at call 245 : 39.99433
-#&gt; Model cost at call 248 : 39.99383
-#&gt; Model cost at call 250 : 39.99383
-#&gt; Model cost at call 251 : 39.99383
-#&gt; Model cost at call 252 : 39.99383
-#&gt; Model cost at call 253 : 39.9935
-#&gt; Model cost at call 254 : 39.99309
-#&gt; Model cost at call 256 : 39.99309
-#&gt; Model cost at call 261 : 39.99295
-#&gt; Model cost at call 264 : 39.99295
-#&gt; Model cost at call 267 : 39.99281
-#&gt; Model cost at call 272 : 39.99281
-#&gt; Model cost at call 273 : 39.99278
-#&gt; Model cost at call 276 : 39.99278
-#&gt; Model cost at call 278 : 39.99278
-#&gt; Model cost at call 279 : 39.99278
-#&gt; Model cost at call 281 : 39.99278
-#&gt; Model cost at call 283 : 39.99278
-#&gt; Model cost at call 286 : 39.99278
-#&gt; Model cost at call 289 : 39.99278
-#&gt; Model cost at call 290 : 39.99278
-#&gt; Iteration 1 yields variance estimates:
-#&gt; parent m1
-#&gt; 11.573172 7.407968
-#&gt; Sum of squared differences to last variance estimates: 1.5e-05
-#&gt; Iteration 2 yields variance estimates:
-#&gt; parent m1
-#&gt; 11.573405 7.407846
-#&gt; Sum of squared differences to last variance estimates: 1.7e-09
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.irls</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+#&gt; 120 m1 33.31 2.879e+01 4.520e+00</div><div class='input'><span class='no'>f.irls</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'>summary</span>(<span class='no'>f.irls</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 15:19:50 2016
-#&gt; Date of summary: Fri Nov 18 15:19:50 2016
+#&gt; Date of fit: Fri Nov 18 15:36:24 2016
+#&gt; Date of summary: Fri Nov 18 15:36:24 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1524,7 +686,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 486 model solutions performed in 2.052 s
+#&gt; Fitted with method Port using 486 model solutions performed in 2.047 s
#&gt;
#&gt; Weighting: none then iterative reweighting method obs
#&gt;
@@ -1633,62 +795,11 @@
#&gt; 100 m1 31.04 3.199e+01 -9.497e-01 2.722
#&gt; 100 m1 33.13 3.199e+01 1.140e+00 2.722
#&gt; 120 m1 25.15 2.881e+01 -3.659e+00 2.722
-#&gt; 120 m1 33.31 2.881e+01 4.501e+00 2.722</div><div class='input'><span class='no'>f.w.mean</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 19.80132
-#&gt; Model cost at call 2 : 19.80132
-#&gt; Model cost at call 6 : 10.68776
-#&gt; Model cost at call 12 : 7.14353
-#&gt; Model cost at call 13 : 7.143529
-#&gt; Model cost at call 15 : 7.143511
-#&gt; Model cost at call 18 : 2.189024
-#&gt; Model cost at call 20 : 2.189019
-#&gt; Model cost at call 23 : 1.587262
-#&gt; Model cost at call 25 : 1.587261
-#&gt; Model cost at call 26 : 1.58726
-#&gt; Model cost at call 28 : 1.036794
-#&gt; Model cost at call 29 : 1.036794
-#&gt; Model cost at call 30 : 1.036793
-#&gt; Model cost at call 34 : 0.4939937
-#&gt; Model cost at call 35 : 0.4939937
-#&gt; Model cost at call 38 : 0.4939936
-#&gt; Model cost at call 39 : 0.4018506
-#&gt; Model cost at call 43 : 0.4018505
-#&gt; Model cost at call 45 : 0.3797853
-#&gt; Model cost at call 51 : 0.3669779
-#&gt; Model cost at call 55 : 0.3669778
-#&gt; Model cost at call 56 : 0.3585654
-#&gt; Model cost at call 57 : 0.3533252
-#&gt; Model cost at call 62 : 0.3502505
-#&gt; Model cost at call 64 : 0.3502505
-#&gt; Model cost at call 66 : 0.3502505
-#&gt; Model cost at call 67 : 0.3501535
-#&gt; Model cost at call 72 : 0.3501187
-#&gt; Model cost at call 74 : 0.3501187
-#&gt; Model cost at call 75 : 0.3501187
-#&gt; Model cost at call 77 : 0.3500378
-#&gt; Model cost at call 79 : 0.3500378
-#&gt; Model cost at call 83 : 0.349831
-#&gt; Model cost at call 88 : 0.3494286
-#&gt; Model cost at call 93 : 0.3488101
-#&gt; Model cost at call 98 : 0.3481444
-#&gt; Model cost at call 103 : 0.3478528
-#&gt; Model cost at call 108 : 0.3478092
-#&gt; Model cost at call 109 : 0.3478092
-#&gt; Model cost at call 113 : 0.347807
-#&gt; Model cost at call 116 : 0.347807
-#&gt; Model cost at call 117 : 0.347807
-#&gt; Model cost at call 119 : 0.347807
-#&gt; Model cost at call 120 : 0.347807
-#&gt; Model cost at call 125 : 0.347807
-#&gt; Model cost at call 126 : 0.347807
-#&gt; Model cost at call 128 : 0.347807
-#&gt; Model cost at call 137 : 0.347807
-#&gt; Model cost at call 148 : 0.347807
-#&gt; Model cost at call 152 : 0.347807
-#&gt; Model cost at call 154 : 0.347807
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.w.mean</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+#&gt; 120 m1 33.31 2.881e+01 4.501e+00 2.722</div><div class='input'><span class='no'>f.w.mean</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>weight</span> <span class='kw'>=</span> <span class='st'>"mean"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'>summary</span>(<span class='no'>f.w.mean</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 15:19:50 2016
-#&gt; Date of summary: Fri Nov 18 15:19:50 2016
+#&gt; Date of fit: Fri Nov 18 15:36:25 2016
+#&gt; Date of summary: Fri Nov 18 15:36:25 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1696,7 +807,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 155 model solutions performed in 0.636 s
+#&gt; Fitted with method Port using 155 model solutions performed in 0.653 s
#&gt;
#&gt; Weighting: mean
#&gt;
@@ -1805,68 +916,12 @@
#&gt; 100 m1 31.04 31.996124 -0.956124
#&gt; 100 m1 33.13 31.996124 1.133876
#&gt; 120 m1 25.15 28.824128 -3.674128
-#&gt; 120 m1 33.31 28.824128 4.485872</div><div class='input'><span class='no'>f.w.value</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='fu'>subset</span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"value"</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 11.21571
-#&gt; Model cost at call 2 : 11.21571
-#&gt; Model cost at call 3 : 11.21571
-#&gt; Model cost at call 8 : 11.12803
-#&gt; Model cost at call 10 : 11.128
-#&gt; Model cost at call 13 : 10.88016
-#&gt; Model cost at call 15 : 10.88016
-#&gt; Model cost at call 18 : 10.58819
-#&gt; Model cost at call 20 : 10.58819
-#&gt; Model cost at call 23 : 9.71699
-#&gt; Model cost at call 24 : 7.794026
-#&gt; Model cost at call 26 : 7.794026
-#&gt; Model cost at call 31 : 6.89734
-#&gt; Model cost at call 33 : 6.897337
-#&gt; Model cost at call 36 : 5.2239
-#&gt; Model cost at call 37 : 3.357735
-#&gt; Model cost at call 41 : 3.357733
-#&gt; Model cost at call 44 : 2.982323
-#&gt; Model cost at call 46 : 2.982322
-#&gt; Model cost at call 49 : 2.703946
-#&gt; Model cost at call 50 : 2.080395
-#&gt; Model cost at call 55 : 0.5307591
-#&gt; Model cost at call 56 : 0.5307591
-#&gt; Model cost at call 57 : 0.5307591
-#&gt; Model cost at call 59 : 0.5307584
-#&gt; Model cost at call 60 : 0.3240066
-#&gt; Model cost at call 61 : 0.3240066
-#&gt; Model cost at call 64 : 0.3240066
-#&gt; Model cost at call 65 : 0.2601108
-#&gt; Model cost at call 70 : 0.2414055
-#&gt; Model cost at call 74 : 0.2414055
-#&gt; Model cost at call 75 : 0.2404251
-#&gt; Model cost at call 80 : 0.2404087
-#&gt; Model cost at call 82 : 0.2404087
-#&gt; Model cost at call 85 : 0.2404054
-#&gt; Model cost at call 88 : 0.2404054
-#&gt; Model cost at call 92 : 0.2403931
-#&gt; Model cost at call 93 : 0.2403784
-#&gt; Model cost at call 98 : 0.2403784
-#&gt; Model cost at call 99 : 0.2403322
-#&gt; Model cost at call 104 : 0.2402188
-#&gt; Model cost at call 109 : 0.2400275
-#&gt; Model cost at call 114 : 0.239844
-#&gt; Model cost at call 119 : 0.2397153
-#&gt; Model cost at call 120 : 0.2397153
-#&gt; Model cost at call 124 : 0.2396978
-#&gt; Model cost at call 126 : 0.2396978
-#&gt; Model cost at call 130 : 0.239697
-#&gt; Model cost at call 131 : 0.2396963
-#&gt; Model cost at call 133 : 0.2396963
-#&gt; Model cost at call 138 : 0.2396962
-#&gt; Model cost at call 139 : 0.2396962
-#&gt; Model cost at call 141 : 0.2396962
-#&gt; Model cost at call 144 : 0.2396962
-#&gt; Model cost at call 147 : 0.2396962
-#&gt; Model cost at call 156 : 0.2396962
-#&gt; Model cost at call 167 : 0.2396962
-#&gt; Model cost at call 169 : 0.2396962
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.w.value</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+#&gt; 120 m1 33.31 28.824128 4.485872</div><div class='input'><span class='no'>f.w.value</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='fu'>subset</span>(<span class='no'>FOCUS_2006_D</span>, <span class='no'>value</span> <span class='kw'>!=</span> <span class='fl'>0</span>), <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"value"</span>,
+ <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'>summary</span>(<span class='no'>f.w.value</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 15:19:51 2016
-#&gt; Date of summary: Fri Nov 18 15:19:51 2016
+#&gt; Date of fit: Fri Nov 18 15:36:26 2016
+#&gt; Date of summary: Fri Nov 18 15:36:26 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -1874,7 +929,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 174 model solutions performed in 0.789 s
+#&gt; Fitted with method Port using 174 model solutions performed in 0.708 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -1984,139 +1039,11 @@
<span class='no'>dw</span> <span class='kw'>&lt;-</span> <span class='no'>FOCUS_2006_D</span>
<span class='no'>errors</span> <span class='kw'>&lt;-</span> <span class='fu'>c</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>1</span>)
<span class='no'>dw</span>$<span class='no'>err.man</span> <span class='kw'>&lt;-</span> <span class='no'>errors</span>[<span class='no'>FOCUS_2006_D</span>$<span class='no'>name</span>]
-<span class='no'>f.w.man</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 3949.676
-#&gt; Model cost at call 2 : 3949.676
-#&gt; Model cost at call 5 : 3949.676
-#&gt; Model cost at call 6 : 2252.859
-#&gt; Model cost at call 8 : 2252.858
-#&gt; Model cost at call 9 : 2252.826
-#&gt; Model cost at call 13 : 1567.343
-#&gt; Model cost at call 14 : 1567.342
-#&gt; Model cost at call 15 : 1567.333
-#&gt; Model cost at call 18 : 1041.524
-#&gt; Model cost at call 19 : 1041.522
-#&gt; Model cost at call 24 : 840.4649
-#&gt; Model cost at call 26 : 840.4646
-#&gt; Model cost at call 29 : 782.303
-#&gt; Model cost at call 31 : 782.3028
-#&gt; Model cost at call 34 : 664.539
-#&gt; Model cost at call 36 : 664.5389
-#&gt; Model cost at call 40 : 615.7908
-#&gt; Model cost at call 42 : 615.7907
-#&gt; Model cost at call 45 : 569.5971
-#&gt; Model cost at call 47 : 569.597
-#&gt; Model cost at call 50 : 517.3175
-#&gt; Model cost at call 52 : 517.3173
-#&gt; Model cost at call 56 : 464.8158
-#&gt; Model cost at call 58 : 464.8157
-#&gt; Model cost at call 62 : 433.0031
-#&gt; Model cost at call 64 : 433.003
-#&gt; Model cost at call 67 : 423.7407
-#&gt; Model cost at call 69 : 423.7406
-#&gt; Model cost at call 70 : 423.7392
-#&gt; Model cost at call 72 : 346.2781
-#&gt; Model cost at call 74 : 346.278
-#&gt; Model cost at call 75 : 346.2779
-#&gt; Model cost at call 78 : 334.5399
-#&gt; Model cost at call 80 : 334.5398
-#&gt; Model cost at call 83 : 324.139
-#&gt; Model cost at call 85 : 324.1389
-#&gt; Model cost at call 88 : 319.7514
-#&gt; Model cost at call 90 : 319.7514
-#&gt; Model cost at call 94 : 300.9426
-#&gt; Model cost at call 96 : 300.9425
-#&gt; Model cost at call 100 : 295.8803
-#&gt; Model cost at call 102 : 295.8803
-#&gt; Model cost at call 105 : 290.3288
-#&gt; Model cost at call 107 : 290.3287
-#&gt; Model cost at call 111 : 284.3257
-#&gt; Model cost at call 113 : 284.3257
-#&gt; Model cost at call 116 : 282.3972
-#&gt; Model cost at call 118 : 282.3972
-#&gt; Model cost at call 122 : 273.7385
-#&gt; Model cost at call 124 : 273.7385
-#&gt; Model cost at call 128 : 271.8379
-#&gt; Model cost at call 130 : 271.8379
-#&gt; Model cost at call 133 : 270.064
-#&gt; Model cost at call 135 : 270.064
-#&gt; Model cost at call 138 : 268.0107
-#&gt; Model cost at call 140 : 268.0107
-#&gt; Model cost at call 144 : 265.6194
-#&gt; Model cost at call 146 : 265.6194
-#&gt; Model cost at call 148 : 265.6194
-#&gt; Model cost at call 149 : 263.4825
-#&gt; Model cost at call 151 : 263.4825
-#&gt; Model cost at call 153 : 263.4824
-#&gt; Model cost at call 154 : 262.0988
-#&gt; Model cost at call 156 : 262.0988
-#&gt; Model cost at call 160 : 260.7078
-#&gt; Model cost at call 162 : 260.7078
-#&gt; Model cost at call 165 : 259.9453
-#&gt; Model cost at call 167 : 259.9453
-#&gt; Model cost at call 170 : 258.9623
-#&gt; Model cost at call 172 : 258.9623
-#&gt; Model cost at call 174 : 258.962
-#&gt; Model cost at call 176 : 258.0119
-#&gt; Model cost at call 178 : 258.0119
-#&gt; Model cost at call 180 : 258.0119
-#&gt; Model cost at call 181 : 257.8698
-#&gt; Model cost at call 183 : 257.8698
-#&gt; Model cost at call 186 : 256.8608
-#&gt; Model cost at call 188 : 256.8608
-#&gt; Model cost at call 190 : 256.8608
-#&gt; Model cost at call 191 : 256.2306
-#&gt; Model cost at call 193 : 256.2306
-#&gt; Model cost at call 195 : 256.2305
-#&gt; Model cost at call 196 : 255.7119
-#&gt; Model cost at call 198 : 255.7118
-#&gt; Model cost at call 201 : 255.3323
-#&gt; Model cost at call 203 : 255.3323
-#&gt; Model cost at call 205 : 255.3323
-#&gt; Model cost at call 206 : 254.6653
-#&gt; Model cost at call 208 : 254.6653
-#&gt; Model cost at call 211 : 254.3984
-#&gt; Model cost at call 213 : 254.3984
-#&gt; Model cost at call 216 : 253.3199
-#&gt; Model cost at call 218 : 253.3199
-#&gt; Model cost at call 220 : 253.3198
-#&gt; Model cost at call 221 : 252.4845
-#&gt; Model cost at call 223 : 252.4845
-#&gt; Model cost at call 225 : 252.4845
-#&gt; Model cost at call 226 : 251.6917
-#&gt; Model cost at call 229 : 251.6917
-#&gt; Model cost at call 230 : 251.6917
-#&gt; Model cost at call 233 : 251.0189
-#&gt; Model cost at call 235 : 251.0189
-#&gt; Model cost at call 238 : 250.6912
-#&gt; Model cost at call 240 : 250.6912
-#&gt; Model cost at call 243 : 250.5546
-#&gt; Model cost at call 245 : 250.5546
-#&gt; Model cost at call 248 : 250.466
-#&gt; Model cost at call 249 : 250.3744
-#&gt; Model cost at call 250 : 249.9681
-#&gt; Model cost at call 251 : 249.2215
-#&gt; Model cost at call 260 : 248.919
-#&gt; Model cost at call 264 : 248.919
-#&gt; Model cost at call 265 : 248.8876
-#&gt; Model cost at call 267 : 248.8876
-#&gt; Model cost at call 270 : 248.8521
-#&gt; Model cost at call 271 : 248.8178
-#&gt; Model cost at call 272 : 248.6837
-#&gt; Model cost at call 273 : 248.5989
-#&gt; Model cost at call 276 : 248.5989
-#&gt; Model cost at call 278 : 248.5935
-#&gt; Model cost at call 280 : 248.5935
-#&gt; Model cost at call 282 : 248.5935
-#&gt; Model cost at call 283 : 248.5902
-#&gt; Model cost at call 284 : 248.5902
-#&gt; Model cost at call 289 : 248.5902
-#&gt; Model cost at call 298 : 248.5902
-#&gt; Model cost at call 309 : 248.5902
-#&gt; Model cost at call 311 : 248.5902
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.w.man</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+<span class='no'>f.w.man</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'>summary</span>(<span class='no'>f.w.man</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 15:19:53 2016
-#&gt; Date of summary: Fri Nov 18 15:19:53 2016
+#&gt; Date of fit: Fri Nov 18 15:36:27 2016
+#&gt; Date of summary: Fri Nov 18 15:36:27 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -2124,7 +1051,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 316 model solutions performed in 1.337 s
+#&gt; Fitted with method Port using 316 model solutions performed in 1.288 s
#&gt;
#&gt; Weighting: manual
#&gt;
@@ -2233,211 +1160,12 @@
#&gt; 100 m1 31.04 31.969288 -0.929288 2
#&gt; 100 m1 33.13 31.969288 1.160712 2
#&gt; 120 m1 25.15 28.760615 -3.610615 2
-#&gt; 120 m1 33.31 28.760615 4.549385 2</div><div class='input'><span class='no'>f.w.man.irls</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>,
- <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>)</div><div class='output co'>#&gt; Model cost at call 1 : 3949.676
-#&gt; Model cost at call 2 : 3949.676
-#&gt; Model cost at call 5 : 3949.676
-#&gt; Model cost at call 6 : 2252.859
-#&gt; Model cost at call 8 : 2252.858
-#&gt; Model cost at call 9 : 2252.826
-#&gt; Model cost at call 13 : 1567.343
-#&gt; Model cost at call 14 : 1567.342
-#&gt; Model cost at call 15 : 1567.333
-#&gt; Model cost at call 18 : 1041.524
-#&gt; Model cost at call 19 : 1041.522
-#&gt; Model cost at call 24 : 840.4649
-#&gt; Model cost at call 26 : 840.4646
-#&gt; Model cost at call 29 : 782.303
-#&gt; Model cost at call 31 : 782.3028
-#&gt; Model cost at call 34 : 664.539
-#&gt; Model cost at call 36 : 664.5389
-#&gt; Model cost at call 40 : 615.7908
-#&gt; Model cost at call 42 : 615.7907
-#&gt; Model cost at call 45 : 569.5971
-#&gt; Model cost at call 47 : 569.597
-#&gt; Model cost at call 50 : 517.3175
-#&gt; Model cost at call 52 : 517.3173
-#&gt; Model cost at call 56 : 464.8158
-#&gt; Model cost at call 58 : 464.8157
-#&gt; Model cost at call 62 : 433.0031
-#&gt; Model cost at call 64 : 433.003
-#&gt; Model cost at call 67 : 423.7407
-#&gt; Model cost at call 69 : 423.7406
-#&gt; Model cost at call 70 : 423.7392
-#&gt; Model cost at call 72 : 346.2781
-#&gt; Model cost at call 74 : 346.278
-#&gt; Model cost at call 75 : 346.2779
-#&gt; Model cost at call 78 : 334.5399
-#&gt; Model cost at call 80 : 334.5398
-#&gt; Model cost at call 83 : 324.139
-#&gt; Model cost at call 85 : 324.1389
-#&gt; Model cost at call 88 : 319.7514
-#&gt; Model cost at call 90 : 319.7514
-#&gt; Model cost at call 94 : 300.9426
-#&gt; Model cost at call 96 : 300.9425
-#&gt; Model cost at call 100 : 295.8803
-#&gt; Model cost at call 102 : 295.8803
-#&gt; Model cost at call 105 : 290.3288
-#&gt; Model cost at call 107 : 290.3287
-#&gt; Model cost at call 111 : 284.3257
-#&gt; Model cost at call 113 : 284.3257
-#&gt; Model cost at call 116 : 282.3972
-#&gt; Model cost at call 118 : 282.3972
-#&gt; Model cost at call 122 : 273.7385
-#&gt; Model cost at call 124 : 273.7385
-#&gt; Model cost at call 128 : 271.8379
-#&gt; Model cost at call 130 : 271.8379
-#&gt; Model cost at call 133 : 270.064
-#&gt; Model cost at call 135 : 270.064
-#&gt; Model cost at call 138 : 268.0107
-#&gt; Model cost at call 140 : 268.0107
-#&gt; Model cost at call 144 : 265.6194
-#&gt; Model cost at call 146 : 265.6194
-#&gt; Model cost at call 148 : 265.6194
-#&gt; Model cost at call 149 : 263.4825
-#&gt; Model cost at call 151 : 263.4825
-#&gt; Model cost at call 153 : 263.4824
-#&gt; Model cost at call 154 : 262.0988
-#&gt; Model cost at call 156 : 262.0988
-#&gt; Model cost at call 160 : 260.7078
-#&gt; Model cost at call 162 : 260.7078
-#&gt; Model cost at call 165 : 259.9453
-#&gt; Model cost at call 167 : 259.9453
-#&gt; Model cost at call 170 : 258.9623
-#&gt; Model cost at call 172 : 258.9623
-#&gt; Model cost at call 174 : 258.962
-#&gt; Model cost at call 176 : 258.0119
-#&gt; Model cost at call 178 : 258.0119
-#&gt; Model cost at call 180 : 258.0119
-#&gt; Model cost at call 181 : 257.8698
-#&gt; Model cost at call 183 : 257.8698
-#&gt; Model cost at call 186 : 256.8608
-#&gt; Model cost at call 188 : 256.8608
-#&gt; Model cost at call 190 : 256.8608
-#&gt; Model cost at call 191 : 256.2306
-#&gt; Model cost at call 193 : 256.2306
-#&gt; Model cost at call 195 : 256.2305
-#&gt; Model cost at call 196 : 255.7119
-#&gt; Model cost at call 198 : 255.7118
-#&gt; Model cost at call 201 : 255.3323
-#&gt; Model cost at call 203 : 255.3323
-#&gt; Model cost at call 205 : 255.3323
-#&gt; Model cost at call 206 : 254.6653
-#&gt; Model cost at call 208 : 254.6653
-#&gt; Model cost at call 211 : 254.3984
-#&gt; Model cost at call 213 : 254.3984
-#&gt; Model cost at call 216 : 253.3199
-#&gt; Model cost at call 218 : 253.3199
-#&gt; Model cost at call 220 : 253.3198
-#&gt; Model cost at call 221 : 252.4845
-#&gt; Model cost at call 223 : 252.4845
-#&gt; Model cost at call 225 : 252.4845
-#&gt; Model cost at call 226 : 251.6917
-#&gt; Model cost at call 229 : 251.6917
-#&gt; Model cost at call 230 : 251.6917
-#&gt; Model cost at call 233 : 251.0189
-#&gt; Model cost at call 235 : 251.0189
-#&gt; Model cost at call 238 : 250.6912
-#&gt; Model cost at call 240 : 250.6912
-#&gt; Model cost at call 243 : 250.5546
-#&gt; Model cost at call 245 : 250.5546
-#&gt; Model cost at call 248 : 250.466
-#&gt; Model cost at call 249 : 250.3744
-#&gt; Model cost at call 250 : 249.9681
-#&gt; Model cost at call 251 : 249.2215
-#&gt; Model cost at call 260 : 248.919
-#&gt; Model cost at call 264 : 248.919
-#&gt; Model cost at call 265 : 248.8876
-#&gt; Model cost at call 267 : 248.8876
-#&gt; Model cost at call 270 : 248.8521
-#&gt; Model cost at call 271 : 248.8178
-#&gt; Model cost at call 272 : 248.6837
-#&gt; Model cost at call 273 : 248.5989
-#&gt; Model cost at call 276 : 248.5989
-#&gt; Model cost at call 278 : 248.5935
-#&gt; Model cost at call 280 : 248.5935
-#&gt; Model cost at call 282 : 248.5935
-#&gt; Model cost at call 283 : 248.5902
-#&gt; Model cost at call 284 : 248.5902
-#&gt; Model cost at call 289 : 248.5902
-#&gt; Model cost at call 298 : 248.5902
-#&gt; Model cost at call 309 : 248.5902
-#&gt; Model cost at call 311 : 248.5902
-#&gt; IRLS based on variance estimates for each observed variable
-#&gt; Initial variance estimates are:
-#&gt; parent m1
-#&gt; 11.536305 7.443046
-#&gt; Model cost at call 317 : 40
-#&gt; Model cost at call 319 : 40
-#&gt; Model cost at call 324 : 39.98891
-#&gt; Model cost at call 325 : 39.9889
-#&gt; Model cost at call 327 : 39.98886
-#&gt; Model cost at call 331 : 39.98871
-#&gt; Model cost at call 333 : 39.97254
-#&gt; Model cost at call 336 : 39.97253
-#&gt; Model cost at call 338 : 39.96929
-#&gt; Model cost at call 340 : 39.96929
-#&gt; Model cost at call 344 : 39.96849
-#&gt; Model cost at call 346 : 39.96849
-#&gt; Model cost at call 348 : 39.96849
-#&gt; Model cost at call 349 : 39.96774
-#&gt; Model cost at call 351 : 39.96774
-#&gt; Model cost at call 353 : 39.96774
-#&gt; Model cost at call 354 : 39.96714
-#&gt; Model cost at call 356 : 39.96714
-#&gt; Model cost at call 359 : 39.96617
-#&gt; Model cost at call 361 : 39.96617
-#&gt; Model cost at call 364 : 39.96606
-#&gt; Model cost at call 366 : 39.96606
-#&gt; Model cost at call 369 : 39.96551
-#&gt; Model cost at call 371 : 39.96551
-#&gt; Model cost at call 372 : 39.96551
-#&gt; Model cost at call 375 : 39.96527
-#&gt; Model cost at call 378 : 39.96527
-#&gt; Model cost at call 379 : 39.96527
-#&gt; Model cost at call 380 : 39.96525
-#&gt; Model cost at call 382 : 39.96525
-#&gt; Model cost at call 385 : 39.9651
-#&gt; Model cost at call 387 : 39.9651
-#&gt; Model cost at call 388 : 39.9651
-#&gt; Model cost at call 390 : 39.96502
-#&gt; Model cost at call 393 : 39.96502
-#&gt; Model cost at call 396 : 39.96502
-#&gt; Model cost at call 397 : 39.96467
-#&gt; Model cost at call 398 : 39.96422
-#&gt; Model cost at call 399 : 39.9624
-#&gt; Model cost at call 400 : 39.95909
-#&gt; Model cost at call 402 : 39.95909
-#&gt; Model cost at call 405 : 39.9571
-#&gt; Model cost at call 407 : 39.95709
-#&gt; Model cost at call 413 : 39.95479
-#&gt; Model cost at call 414 : 39.95479
-#&gt; Model cost at call 415 : 39.95479
-#&gt; Model cost at call 417 : 39.95479
-#&gt; Model cost at call 419 : 39.95398
-#&gt; Model cost at call 422 : 39.95398
-#&gt; Model cost at call 424 : 39.95387
-#&gt; Model cost at call 429 : 39.95384
-#&gt; Model cost at call 432 : 39.95384
-#&gt; Model cost at call 435 : 39.95384
-#&gt; Model cost at call 437 : 39.95384
-#&gt; Model cost at call 438 : 39.95384
-#&gt; Model cost at call 446 : 39.95384
-#&gt; Model cost at call 455 : 39.95384
-#&gt; Model cost at call 469 : 39.95384
-#&gt; Model cost at call 473 : 39.95384
-#&gt; Iteration 1 yields variance estimates:
-#&gt; parent m1
-#&gt; 11.572891 7.408116
-#&gt; Sum of squared differences to last variance estimates: 7e-05
-#&gt; Iteration 2 yields variance estimates:
-#&gt; parent m1
-#&gt; 11.573402 7.407847
-#&gt; Sum of squared differences to last variance estimates: 8.1e-09
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'><span class='fu'>summary</span>(<span class='no'>f.w.man.irls</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
+#&gt; 120 m1 33.31 28.760615 4.549385 2</div><div class='input'><span class='no'>f.w.man.irls</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO.ff</span>, <span class='no'>dw</span>, <span class='kw'>err</span> <span class='kw'>=</span> <span class='st'>"err.man"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
+ <span class='kw'>reweight.method</span> <span class='kw'>=</span> <span class='st'>"obs"</span>)
+<span class='fu'>summary</span>(<span class='no'>f.w.man.irls</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 15:19:55 2016
-#&gt; Date of summary: Fri Nov 18 15:19:55 2016
+#&gt; Date of fit: Fri Nov 18 15:36:30 2016
+#&gt; Date of summary: Fri Nov 18 15:36:30 2016
#&gt;
#&gt; Equations:
#&gt; d_parent/dt = - k_parent * parent
@@ -2445,7 +1173,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 648 model solutions performed in 2.716 s
+#&gt; Fitted with method Port using 648 model solutions performed in 2.694 s
#&gt;
#&gt; Weighting: manual then iterative reweighting method obs
#&gt;

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