Make the 'quadratic' the default for 'confint'

Also the documentation was improved here and there

1 files changed, 6 insertions, 344 deletions

diff --git a/docs/reference/update.mkinfit.html b/docs/reference/update.mkinfit.html
index b9f6f9a9..bb93a61e 100644
--- a/docs/reference/update.mkinfit.html
+++ b/docs/reference/update.mkinfit.html
@@ -72,7 +72,7 @@ override these starting values." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.8</span>
       </span>
     </div>
 
@@ -167,349 +167,11 @@ remove arguments given in the original call</p></td>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='co'># \dontrun{</span>
-<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"DFOP"</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></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'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-<span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>fit</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>)</div><div class='output co'>#&gt; $par
-#&gt;     parent_0       log_k1       log_k2        g_ilr    sigma_low     rsd_high 
-#&gt; 100.85489822   8.84468217  -2.29693632 -14.95263998   0.00375222   0.06763435 
-#&gt; 
-#&gt; $objective
-#&gt; [1] 19.40656
-#&gt; 
-#&gt; $convergence
-#&gt; [1] 0
-#&gt; 
-#&gt; $iterations
-#&gt; [1] 120
-#&gt; 
-#&gt; $evaluations
-#&gt; function gradient 
-#&gt;      144      847 
-#&gt; 
-#&gt; $message
-#&gt; [1] "relative convergence (4)"
-#&gt; 
-#&gt; $logLik
-#&gt; [1] -19.40656
-#&gt; 
-#&gt; $d_3_message
-#&gt;                                                            threestep 
-#&gt; "Three-step fitting yielded a higher likelihood than direct fitting" 
-#&gt; 
-#&gt; $hessian
-#&gt;                parent_0        log_k1        log_k2         g_ilr     sigma_low
-#&gt; parent_0   3.662473e-01 -2.914408e-16 -7.241561e+01 -3.021629e-08  1.923504e+01
-#&gt; log_k1    -2.914408e-16  0.000000e+00 -2.215935e-13 -7.291307e-25  3.416474e-15
-#&gt; log_k2    -7.241561e+01 -2.215935e-13  3.127457e+04  6.766544e-06 -1.495826e+04
-#&gt; g_ilr     -3.021629e-08 -7.291307e-25  6.766544e-06  3.122099e-09 -1.797429e-06
-#&gt; sigma_low  1.923504e+01  3.416474e-15 -1.495826e+04 -1.797429e-06  7.759299e+04
-#&gt; rsd_high   3.902119e+00 -1.801019e-16 -1.685343e+02 -3.750713e-07  3.984179e+03
-#&gt;                rsd_high
-#&gt; parent_0   3.902119e+00
-#&gt; log_k1    -1.801019e-16
-#&gt; log_k2    -1.685343e+02
-#&gt; g_ilr     -3.750713e-07
-#&gt; sigma_low  3.984179e+03
-#&gt; rsd_high   7.188991e+03
-#&gt; 
-#&gt; $hessian_notrans
-#&gt;                parent_0            k1            k2             g     sigma_low
-#&gt; parent_0   3.662473e-01 -3.714445e-19 -7.201669e+02 -3.261485e+01  1.923504e+01
-#&gt; k1        -3.714445e-19  0.000000e+00 -4.258512e-15  7.218123e-21  4.355854e-18
-#&gt; k2        -7.201669e+02 -4.258512e-15  3.092510e+06  7.263235e+04 -1.456870e+05
-#&gt; g         -3.261485e+01  7.218123e-21  7.263235e+04  3.291750e+03 -1.939948e+03
-#&gt; sigma_low  1.923504e+01  4.355854e-18 -1.456870e+05 -1.939948e+03  7.759299e+04
-#&gt; rsd_high   3.902119e+00 -2.259812e-19 -1.779680e+03 -4.048658e+02  3.984179e+03
-#&gt;                rsd_high
-#&gt; parent_0   3.902119e+00
-#&gt; k1        -2.259812e-19
-#&gt; k2        -1.779680e+03
-#&gt; g         -4.048658e+02
-#&gt; sigma_low  3.984179e+03
-#&gt; rsd_high   7.188991e+03
-#&gt; 
-#&gt; $call
-#&gt; mkinfit(mkinmod = "DFOP", observed = subset(FOCUS_2006_D, value != 
-#&gt;     0), parms.ini = c(k1 = 0.699298911979803, k2 = 0.0899931270871125, 
-#&gt; g = 0.0923391681138686), state.ini = c(parent = 101.948852047129), 
-#&gt;     quiet = TRUE, error_model = "tc")
-#&gt; 
-#&gt; $error_model_algorithm
-#&gt; [1] "d_3"
-#&gt; 
-#&gt; $solution_type
-#&gt; [1] "analytical"
-#&gt; 
-#&gt; $transform_rates
-#&gt; [1] TRUE
-#&gt; 
-#&gt; $transform_fractions
-#&gt; [1] TRUE
-#&gt; 
-#&gt; $reweight.tol
-#&gt; [1] 1e-08
-#&gt; 
-#&gt; $reweight.max.iter
-#&gt; [1] 10
-#&gt; 
-#&gt; $control
-#&gt; $control$eval.max
-#&gt; [1] 300
-#&gt; 
-#&gt; $control$iter.max
-#&gt; [1] 200
-#&gt; 
-#&gt; 
-#&gt; $calls
-#&gt; [1] 3105
-#&gt; 
-#&gt; $time
-#&gt;        User      System verstrichen 
-#&gt;      10.251       0.000      10.257 
-#&gt; 
-#&gt; $mkinmod
-#&gt; &lt;mkinmod&gt; model generated with
-#&gt; Use of formation fractions $use_of_ff: min 
-#&gt; Specification $spec:
-#&gt; $parent
-#&gt; $type: DFOP; $sink: TRUE
-#&gt; Differential equations:
-#&gt; d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
-#&gt;            time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time)))
-#&gt;            * parent
-#&gt; 
-#&gt; $observed
-#&gt;      name time  value
-#&gt; 1  parent    0  99.46
-#&gt; 2  parent    0 102.04
-#&gt; 3  parent    1  93.50
-#&gt; 4  parent    1  92.50
-#&gt; 5  parent    3  63.23
-#&gt; 6  parent    3  68.99
-#&gt; 7  parent    7  52.32
-#&gt; 8  parent    7  55.13
-#&gt; 9  parent   14  27.27
-#&gt; 10 parent   14  26.64
-#&gt; 11 parent   21  11.50
-#&gt; 12 parent   21  11.64
-#&gt; 13 parent   35   2.85
-#&gt; 14 parent   35   2.91
-#&gt; 15 parent   50   0.69
-#&gt; 16 parent   50   0.63
-#&gt; 17 parent   75   0.05
-#&gt; 18 parent   75   0.06
-#&gt; 
-#&gt; $obs_vars
-#&gt; [1] "parent"
-#&gt; 
-#&gt; $predicted
-#&gt;       name       time        value
-#&gt; 1   parent  0.0000000 100.85489822
-#&gt; 2   parent  0.7575758  93.45650191
-#&gt; 3   parent  1.0000000  91.20560523
-#&gt; 4   parent  1.5151515  86.60082860
-#&gt; 5   parent  2.2727273  80.24806580
-#&gt; 6   parent  3.0000000  74.58828105
-#&gt; 7   parent  3.0303030  74.36132158
-#&gt; 8   parent  3.7878788  68.90641029
-#&gt; 9   parent  4.5454545  63.85165403
-#&gt; 10  parent  5.3030303  59.16769870
-#&gt; 11  parent  6.0606061  54.82734352
-#&gt; 12  parent  6.8181818  50.80538306
-#&gt; 13  parent  7.0000000  49.88485755
-#&gt; 14  parent  7.5757576  47.07846089
-#&gt; 15  parent  8.3333333  43.62493394
-#&gt; 16  parent  9.0909091  40.42474681
-#&gt; 17  parent  9.8484848  37.45931528
-#&gt; 18  parent 10.6060606  34.71141842
-#&gt; 19  parent 11.3636364  32.16509858
-#&gt; 20  parent 12.1212121  29.80556871
-#&gt; 21  parent 12.8787879  27.61912649
-#&gt; 22  parent 13.6363636  25.59307475
-#&gt; 23  parent 14.0000000  24.67405211
-#&gt; 24  parent 14.3939394  23.71564776
-#&gt; 25  parent 15.1515152  21.97594287
-#&gt; 26  parent 15.9090909  20.36385722
-#&gt; 27  parent 16.6666667  18.87002909
-#&gt; 28  parent 17.4242424  17.48578345
-#&gt; 29  parent 18.1818182  16.20308170
-#&gt; 30  parent 18.9393939  15.01447489
-#&gt; 31  parent 19.6969697  13.91306051
-#&gt; 32  parent 20.4545455  12.89244241
-#&gt; 33  parent 21.0000000  12.20428157
-#&gt; 34  parent 21.2121212  11.94669362
-#&gt; 35  parent 21.9696970  11.07032198
-#&gt; 36  parent 22.7272727  10.25823818
-#&gt; 37  parent 23.4848485   9.50572628
-#&gt; 38  parent 24.2424242   8.80841627
-#&gt; 39  parent 25.0000000   8.16225872
-#&gt; 40  parent 25.7575758   7.56350125
-#&gt; 41  parent 26.5151515   7.00866672
-#&gt; 42  parent 27.2727273   6.49453311
-#&gt; 43  parent 28.0303030   6.01811471
-#&gt; 44  parent 28.7878788   5.57664485
-#&gt; 45  parent 29.5454545   5.16755983
-#&gt; 46  parent 30.3030303   4.78848399
-#&gt; 47  parent 31.0606061   4.43721595
-#&gt; 48  parent 31.8181818   4.11171583
-#&gt; 49  parent 32.5757576   3.81009336
-#&gt; 50  parent 33.3333333   3.53059697
-#&gt; 51  parent 34.0909091   3.27160354
-#&gt; 52  parent 34.8484848   3.03160906
-#&gt; 53  parent 35.0000000   2.98576554
-#&gt; 54  parent 35.6060606   2.80921981
-#&gt; 55  parent 36.3636364   2.60314433
-#&gt; 56  parent 37.1212121   2.41218590
-#&gt; 57  parent 37.8787879   2.23523557
-#&gt; 58  parent 38.6363636   2.07126576
-#&gt; 59  parent 39.3939394   1.91932426
-#&gt; 60  parent 40.1515152   1.77852870
-#&gt; 61  parent 40.9090909   1.64806147
-#&gt; 62  parent 41.6666667   1.52716489
-#&gt; 63  parent 42.4242424   1.41513691
-#&gt; 64  parent 43.1818182   1.31132694
-#&gt; 65  parent 43.9393939   1.21513214
-#&gt; 66  parent 44.6969697   1.12599389
-#&gt; 67  parent 45.4545455   1.04339454
-#&gt; 68  parent 46.2121212   0.96685442
-#&gt; 69  parent 46.9696970   0.89592904
-#&gt; 70  parent 47.7272727   0.83020652
-#&gt; 71  parent 48.4848485   0.76930520
-#&gt; 72  parent 49.2424242   0.71287140
-#&gt; 73  parent 50.0000000   0.66057741
-#&gt; 74  parent 50.7575758   0.61211954
-#&gt; 75  parent 51.5151515   0.56721639
-#&gt; 76  parent 52.2727273   0.52560719
-#&gt; 77  parent 53.0303030   0.48705031
-#&gt; 78  parent 53.7878788   0.45132184
-#&gt; 79  parent 54.5454545   0.41821430
-#&gt; 80  parent 55.3030303   0.38753542
-#&gt; 81  parent 56.0606061   0.35910705
-#&gt; 82  parent 56.8181818   0.33276409
-#&gt; 83  parent 57.5757576   0.30835357
-#&gt; 84  parent 58.3333333   0.28573373
-#&gt; 85  parent 59.0909091   0.26477320
-#&gt; 86  parent 59.8484848   0.24535028
-#&gt; 87  parent 60.6060606   0.22735216
-#&gt; 88  parent 61.3636364   0.21067432
-#&gt; 89  parent 62.1212121   0.19521992
-#&gt; 90  parent 62.8787879   0.18089921
-#&gt; 91  parent 63.6363636   0.16762901
-#&gt; 92  parent 64.3939394   0.15533228
-#&gt; 93  parent 65.1515152   0.14393759
-#&gt; 94  parent 65.9090909   0.13337879
-#&gt; 95  parent 66.6666667   0.12359454
-#&gt; 96  parent 67.4242424   0.11452804
-#&gt; 97  parent 68.1818182   0.10612662
-#&gt; 98  parent 68.9393939   0.09834151
-#&gt; 99  parent 69.6969697   0.09112749
-#&gt; 100 parent 70.4545455   0.08444266
-#&gt; 101 parent 71.2121212   0.07824822
-#&gt; 102 parent 71.9696970   0.07250818
-#&gt; 103 parent 72.7272727   0.06718920
-#&gt; 104 parent 73.4848485   0.06226042
-#&gt; 105 parent 74.2424242   0.05769319
-#&gt; 106 parent 75.0000000   0.05346100
-#&gt; 
-#&gt; $rss
-#&gt; function (P) 
-#&gt; cost_function(P, OLS = TRUE, update_data = FALSE)
-#&gt; &lt;bytecode: 0x555558e48258&gt;
-#&gt; &lt;environment: 0x55555caa08e0&gt;
-#&gt; 
-#&gt; $ll
-#&gt; function (P, fixed_degparms = FALSE, fixed_errparms = FALSE) 
-#&gt; {
-#&gt;     -cost_function(P, trans = FALSE, fixed_degparms = fixed_degparms, 
-#&gt;         fixed_errparms = fixed_errparms, OLS = FALSE, update_data = FALSE)
-#&gt; }
-#&gt; &lt;bytecode: 0x555558e47e30&gt;
-#&gt; &lt;environment: 0x55555caa08e0&gt;
-#&gt; 
-#&gt; $start
-#&gt;                  value   type
-#&gt; parent_0  101.94885205  state
-#&gt; k1          0.69929891 deparm
-#&gt; k2          0.08999313 deparm
-#&gt; g           0.09233917 deparm
-#&gt; sigma_low   0.10000000  error
-#&gt; rsd_high    0.10000000  error
-#&gt; 
-#&gt; $start_transformed
-#&gt;                value lower upper
-#&gt; parent_0  101.948852  -Inf   Inf
-#&gt; log_k1     -0.357677  -Inf   Inf
-#&gt; log_k2     -2.408022  -Inf   Inf
-#&gt; g_ilr      -1.616024  -Inf   Inf
-#&gt; sigma_low   0.100000     0   Inf
-#&gt; rsd_high    0.100000     0   Inf
-#&gt; 
-#&gt; $fixed
-#&gt; [1] value type 
-#&gt; &lt;0 Zeilen&gt; (oder row.names mit Länge 0)
-#&gt; 
-#&gt; $data
-#&gt;    time variable observed   predicted     residual
-#&gt; 1     0   parent    99.46 100.8548982  -1.39489822
-#&gt; 2     0   parent   102.04 100.8548982   1.18510178
-#&gt; 3     1   parent    93.50  91.2056052   2.29439477
-#&gt; 4     1   parent    92.50  91.2056052   1.29439477
-#&gt; 5     3   parent    63.23  74.5882810 -11.35828105
-#&gt; 6     3   parent    68.99  74.5882810  -5.59828105
-#&gt; 7     7   parent    52.32  49.8848576   2.43514245
-#&gt; 8     7   parent    55.13  49.8848576   5.24514245
-#&gt; 9    14   parent    27.27  24.6740521   2.59594789
-#&gt; 10   14   parent    26.64  24.6740521   1.96594789
-#&gt; 11   21   parent    11.50  12.2042816  -0.70428157
-#&gt; 12   21   parent    11.64  12.2042816  -0.56428157
-#&gt; 13   35   parent     2.85   2.9857655  -0.13576554
-#&gt; 14   35   parent     2.91   2.9857655  -0.07576554
-#&gt; 15   50   parent     0.69   0.6605774   0.02942259
-#&gt; 16   50   parent     0.63   0.6605774  -0.03057741
-#&gt; 17   75   parent     0.05   0.0534610  -0.00346100
-#&gt; 18   75   parent     0.06   0.0534610   0.00653900
-#&gt; 
-#&gt; $atol
-#&gt; [1] 1e-08
-#&gt; 
-#&gt; $rtol
-#&gt; [1] 1e-10
-#&gt; 
-#&gt; $err_mod
-#&gt; [1] "tc"
-#&gt; 
-#&gt; $bparms.optim
-#&gt;     parent_0           k1           k2            g 
-#&gt; 1.008549e+02 6.937399e+03 1.005665e-01 6.551046e-10 
-#&gt; 
-#&gt; $bparms.fixed
-#&gt; numeric(0)
-#&gt; 
-#&gt; $bparms.ode
-#&gt;           k1           k2            g 
-#&gt; 6.937399e+03 1.005665e-01 6.551046e-10 
-#&gt; 
-#&gt; $bparms.state
-#&gt;   parent 
-#&gt; 100.8549 
-#&gt; 
-#&gt; $errparms
-#&gt;  sigma_low   rsd_high 
-#&gt; 0.00375222 0.06763435 
-#&gt; 
-#&gt; $df.residual
-#&gt; [1] 12
-#&gt; 
-#&gt; $date
-#&gt; [1] "Fri Nov  1 10:10:42 2019"
-#&gt; 
-#&gt; $version
-#&gt; [1] "0.9.49.6"
-#&gt; 
-#&gt; $Rversion
-#&gt; [1] "3.6.1"
-#&gt; 
-#&gt; attr(,"class")
-#&gt; [1] "mkinfit" "modFit" </div><div class='input'># }
+<span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"SFO"</span>, <span class='fu'><a href='https://rdrr.io/r/base/subset.html'>subset</a></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'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit</span>)</div><div class='output co'>#&gt;      parent_0 k_parent_sink         sigma 
+#&gt;   99.44423886    0.09793574    3.39632469 </div><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_err</a></span>(<span class='no'>fit</span>)</div><div class='img'><img src='update.mkinfit-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='no'>fit_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span>(<span class='no'>fit</span>, <span class='kw'>error_model</span> <span class='kw'>=</span> <span class='st'>"tc"</span>)
+<span class='fu'><a href='parms.html'>parms</a></span>(<span class='no'>fit_2</span>)</div><div class='output co'>#&gt;      parent_0 k_parent_sink     sigma_low      rsd_high 
+#&gt;  1.008549e+02  1.005665e-01  3.752222e-03  6.763434e-02 </div><div class='input'><span class='fu'><a href='plot.mkinfit.html'>plot_err</a></span>(<span class='no'>fit_2</span>)</div><div class='img'><img src='update.mkinfit-2.png' alt='' width='700' height='433' /></div><div class='input'># }
 </div></pre>
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