Restore NAMESPACE

which was accidentally overwritten by pkgdown -> roxygen

1 files changed, 399 insertions, 3 deletions

diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 1be9e0f1..2a1d63b5 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -166,15 +166,411 @@
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'>  <span class='co'># Only use one core, to pass R CMD check --as-cran</span>
   <span class='no'>fits</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/c'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>), <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/list'>list</a></span>(<span class='kw'>B</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_B</span>, <span class='kw'>C</span> <span class='kw'>=</span> <span class='no'>FOCUS_2006_C</span>),
-                <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='error'>Error in mmkin(c("SFO", "FOMC"), list(B = FOCUS_2006_B, C = FOCUS_2006_C),     cores = 1, quiet = TRUE): konnte Funktion "mmkin" nicht finden</span></div><div class='input'>  <span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ]</div><div class='output co'>#&gt; <span class='error'>Error in eval(expr, envir, enclos): Objekt 'fits' nicht gefunden</span></div><div class='input'>  <span class='no'>fits</span>[, <span class='st'>"B"</span>]</div><div class='output co'>#&gt; <span class='error'>Error in eval(expr, envir, enclos): Objekt 'fits' nicht gefunden</span></div><div class='input'>  <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#&gt; <span class='error'>Error in eval(expr, envir, enclos): Objekt 'fits' nicht gefunden</span></div><div class='input'>
+                <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+  <span class='no'>fits</span>[<span class='st'>"FOMC"</span>, ]</div><div class='output co'>#&gt;       dataset
+#&gt; model  B       C      
+#&gt;   FOMC List,45 List,45
+#&gt; attr(,"class")
+#&gt; [1] "mmkin"</div><div class='input'>  <span class='no'>fits</span>[, <span class='st'>"B"</span>]</div><div class='output co'>#&gt;       dataset
+#&gt; model  B      
+#&gt;   SFO  List,45
+#&gt;   FOMC List,45
+#&gt; attr(,"class")
+#&gt; [1] "mmkin"</div><div class='input'>  <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>]</div><div class='output co'>#&gt;      dataset
+#&gt; model B      
+#&gt;   SFO List,45
+#&gt; attr(,"class")
+#&gt; [1] "mmkin"</div><div class='input'>
   <span class='fu'><a href='https://www.rdocumentation.org/packages/utils/topics/head'>head</a></span>(
     <span class='co'># This extracts an mkinfit object with lots of components</span>
     <span class='no'>fits</span><span class='kw'>[[</span><span class='st'>"FOMC"</span>, <span class='st'>"B"</span>]]
-  )</div><div class='output co'>#&gt; <span class='error'>Error in head(fits[["FOMC", "B"]]): Objekt 'fits' nicht gefunden</span></div><div class='input'>
+  )</div><div class='output co'>#&gt; $par
+#&gt;  parent_0 log_alpha  log_beta 
+#&gt; 99.666193  2.549849  5.050586 
+#&gt; 
+#&gt; $ssr
+#&gt; [1] 28.58291
+#&gt; 
+#&gt; $convergence
+#&gt; [1] 0
+#&gt; 
+#&gt; $iterations
+#&gt; [1] 21
+#&gt; 
+#&gt; $evaluations
+#&gt; function gradient 
+#&gt;       25       78 
+#&gt; 
+#&gt; $counts
+#&gt; [1] "relative convergence (4)"
+#&gt; </div><div class='input'>
   <span class='fu'><a href='https://www.rdocumentation.org/packages/utils/topics/head'>head</a></span>(
   <span class='co'># The same can be achieved by</span>
     <span class='no'>fits</span>[<span class='st'>"SFO"</span>, <span class='st'>"B"</span>, <span class='kw'>drop</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>]
-  )</div><div class='output co'>#&gt; <span class='error'>Error in head(fits["SFO", "B", drop = TRUE]): Objekt 'fits' nicht gefunden</span></div></pre>
+  )</div><div class='output co'>#&gt; [[1]]
+#&gt; $par
+#&gt;          parent_0 log_k_parent_sink 
+#&gt;         99.174072         -2.549028 
+#&gt; 
+#&gt; $ssr
+#&gt; [1] 30.65564
+#&gt; 
+#&gt; $convergence
+#&gt; [1] 0
+#&gt; 
+#&gt; $iterations
+#&gt; [1] 5
+#&gt; 
+#&gt; $evaluations
+#&gt; function gradient 
+#&gt;        8       15 
+#&gt; 
+#&gt; $counts
+#&gt; [1] "relative convergence (4)"
+#&gt; 
+#&gt; $hessian
+#&gt;                     parent_0 log_k_parent_sink
+#&gt; parent_0            4.163631         -94.09343
+#&gt; log_k_parent_sink -94.093431        6311.34610
+#&gt; 
+#&gt; $residuals
+#&gt;      parent      parent      parent      parent      parent      parent 
+#&gt;  0.55407218 -2.98452128  4.20445742 -1.68599939 -0.58185357 -0.72033730 
+#&gt;      parent      parent 
+#&gt; -0.24260405 -0.07020339 
+#&gt; 
+#&gt; $ms
+#&gt; [1] 3.831956
+#&gt; 
+#&gt; $var_ms
+#&gt;   parent 
+#&gt; 3.831956 
+#&gt; 
+#&gt; $var_ms_unscaled
+#&gt;   parent 
+#&gt; 3.831956 
+#&gt; 
+#&gt; $var_ms_unweighted
+#&gt;   parent 
+#&gt; 3.831956 
+#&gt; 
+#&gt; $rank
+#&gt; [1] 2
+#&gt; 
+#&gt; $df.residual
+#&gt; [1] 6
+#&gt; 
+#&gt; $solution_type
+#&gt; [1] "analytical"
+#&gt; 
+#&gt; $transform_rates
+#&gt; [1] TRUE
+#&gt; 
+#&gt; $transform_fractions
+#&gt; [1] TRUE
+#&gt; 
+#&gt; $method.modFit
+#&gt; [1] "Port"
+#&gt; 
+#&gt; $maxit.modFit
+#&gt; [1] "auto"
+#&gt; 
+#&gt; $calls
+#&gt; [1] 29
+#&gt; 
+#&gt; $time
+#&gt;        User      System verstrichen 
+#&gt;       0.197       0.000       0.198 
+#&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: SFO; $sink: TRUE
+#&gt; Coefficient matrix $coefmat available
+#&gt; Differential equations:
+#&gt; d_parent/dt = - k_parent_sink * parent
+#&gt; 
+#&gt; $observed
+#&gt;     name time value
+#&gt; 1 parent    0 98.62
+#&gt; 2 parent    3 81.43
+#&gt; 3 parent    7 53.18
+#&gt; 4 parent   14 34.89
+#&gt; 5 parent   30 10.09
+#&gt; 6 parent   62  1.50
+#&gt; 7 parent   90  0.33
+#&gt; 8 parent  118  0.08
+#&gt; 
+#&gt; $obs_vars
+#&gt; [1] "parent"
+#&gt; 
+#&gt; $predicted
+#&gt;       name       time       value
+#&gt; 1   parent   0.000000 99.17407218
+#&gt; 2   parent   1.191919 90.35253561
+#&gt; 3   parent   2.383838 82.31567498
+#&gt; 4   parent   3.000000 78.44547872
+#&gt; 5   parent   3.575758 74.99369333
+#&gt; 6   parent   4.767677 68.32300215
+#&gt; 7   parent   5.959596 62.24566915
+#&gt; 8   parent   7.000000 57.38445742
+#&gt; 9   parent   7.151515 56.70891509
+#&gt; 10  parent   8.343434 51.66465547
+#&gt; 11  parent   9.535354 47.06908288
+#&gt; 12  parent  10.727273 42.88228661
+#&gt; 13  parent  11.919192 39.06790599
+#&gt; 14  parent  13.111111 35.59281463
+#&gt; 15  parent  14.000000 33.20400061
+#&gt; 16  parent  14.303030 32.42683275
+#&gt; 17  parent  15.494949 29.54246504
+#&gt; 18  parent  16.686869 26.91466193
+#&gt; 19  parent  17.878788 24.52060198
+#&gt; 20  parent  19.070707 22.33949373
+#&gt; 21  parent  20.262626 20.35239512
+#&gt; 22  parent  21.454545 18.54204899
+#&gt; 23  parent  22.646465 16.89273320
+#&gt; 24  parent  23.838384 15.39012410
+#&gt; 25  parent  25.030303 14.02117212
+#&gt; 26  parent  26.222222 12.77398846
+#&gt; 27  parent  27.414141 11.63774182
+#&gt; 28  parent  28.606061 10.60256435
+#&gt; 29  parent  29.797980  9.65946594
+#&gt; 30  parent  30.000000  9.50814643
+#&gt; 31  parent  30.989899  8.80025617
+#&gt; 32  parent  32.181818  8.01747313
+#&gt; 33  parent  33.373737  7.30431867
+#&gt; 34  parent  34.565657  6.65459931
+#&gt; 35  parent  35.757576  6.06267251
+#&gt; 36  parent  36.949495  5.52339762
+#&gt; 37  parent  38.141414  5.03209124
+#&gt; 38  parent  39.333333  4.58448658
+#&gt; 39  parent  40.525253  4.17669637
+#&gt; 40  parent  41.717172  3.80517911
+#&gt; 41  parent  42.909091  3.46670832
+#&gt; 42  parent  44.101010  3.15834451
+#&gt; 43  parent  45.292929  2.87740968
+#&gt; 44  parent  46.484848  2.62146400
+#&gt; 45  parent  47.676768  2.38828471
+#&gt; 46  parent  48.868687  2.17584671
+#&gt; 47  parent  50.060606  1.98230508
+#&gt; 48  parent  51.252525  1.80597899
+#&gt; 49  parent  52.444444  1.64533711
+#&gt; 50  parent  53.636364  1.49898432
+#&gt; 51  parent  54.828283  1.36564963
+#&gt; 52  parent  56.020202  1.24417505
+#&gt; 53  parent  57.212121  1.13350565
+#&gt; 54  parent  58.404040  1.03268029
+#&gt; 55  parent  59.595960  0.94082335
+#&gt; 56  parent  60.787879  0.85713708
+#&gt; 57  parent  61.979798  0.78089471
+#&gt; 58  parent  62.000000  0.77966270
+#&gt; 59  parent  63.171717  0.71143411
+#&gt; 60  parent  64.363636  0.64815202
+#&gt; 61  parent  65.555556  0.59049888
+#&gt; 62  parent  66.747475  0.53797399
+#&gt; 63  parent  67.939394  0.49012119
+#&gt; 64  parent  69.131313  0.44652489
+#&gt; 65  parent  70.323232  0.40680649
+#&gt; 66  parent  71.515152  0.37062104
+#&gt; 67  parent  72.707071  0.33765429
+#&gt; 68  parent  73.898990  0.30761993
+#&gt; 69  parent  75.090909  0.28025713
+#&gt; 70  parent  76.282828  0.25532825
+#&gt; 71  parent  77.474747  0.23261679
+#&gt; 72  parent  78.666667  0.21192552
+#&gt; 73  parent  79.858586  0.19307474
+#&gt; 74  parent  81.050505  0.17590074
+#&gt; 75  parent  82.242424  0.16025436
+#&gt; 76  parent  83.434343  0.14599973
+#&gt; 77  parent  84.626263  0.13301305
+#&gt; 78  parent  85.818182  0.12118154
+#&gt; 79  parent  87.010101  0.11040244
+#&gt; 80  parent  88.202020  0.10058214
+#&gt; 81  parent  89.393939  0.09163535
+#&gt; 82  parent  90.000000  0.08739595
+#&gt; 83  parent  90.585859  0.08348439
+#&gt; 84  parent  91.777778  0.07605845
+#&gt; 85  parent  92.969697  0.06929305
+#&gt; 86  parent  94.161616  0.06312943
+#&gt; 87  parent  95.353535  0.05751406
+#&gt; 88  parent  96.545455  0.05239819
+#&gt; 89  parent  97.737374  0.04773737
+#&gt; 90  parent  98.929293  0.04349113
+#&gt; 91  parent 100.121212  0.03962259
+#&gt; 92  parent 101.313131  0.03609816
+#&gt; 93  parent 102.505051  0.03288723
+#&gt; 94  parent 103.696970  0.02996191
+#&gt; 95  parent 104.888889  0.02729679
+#&gt; 96  parent 106.080808  0.02486874
+#&gt; 97  parent 107.272727  0.02265667
+#&gt; 98  parent 108.464646  0.02064136
+#&gt; 99  parent 109.656566  0.01880531
+#&gt; 100 parent 110.848485  0.01713257
+#&gt; 101 parent 112.040404  0.01560863
+#&gt; 102 parent 113.232323  0.01422024
+#&gt; 103 parent 114.424242  0.01295535
+#&gt; 104 parent 115.616162  0.01180297
+#&gt; 105 parent 116.808081  0.01075310
+#&gt; 106 parent 118.000000  0.00979661
+#&gt; 
+#&gt; $cost
+#&gt; function (P) 
+#&gt; {
+#&gt;     assign("calls", calls + 1, inherits = TRUE)
+#&gt;     if (trace_parms) 
+#&gt;         cat(P, "\n")
+#&gt;     if (length(state.ini.optim) &gt; 0) {
+#&gt;         odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
+#&gt;         names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
+#&gt;     }
+#&gt;     else {
+#&gt;         odeini &lt;- state.ini.fixed
+#&gt;         names(odeini) &lt;- state.ini.fixed.boxnames
+#&gt;     }
+#&gt;     odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)], 
+#&gt;         transparms.fixed)
+#&gt;     parms &lt;- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates, 
+#&gt;         transform_fractions = transform_fractions)
+#&gt;     out &lt;- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type, 
+#&gt;         use_compiled = use_compiled, method.ode = method.ode, 
+#&gt;         atol = atol, rtol = rtol, ...)
+#&gt;     assign("out_predicted", out, inherits = TRUE)
+#&gt;     mC &lt;- modCost(out, observed, y = "value", err = err, weight = weight, 
+#&gt;         scaleVar = scaleVar)
+#&gt;     if (mC$model &lt; cost.old) {
+#&gt;         if (!quiet) 
+#&gt;             cat("Model cost at call ", calls, ": ", mC$model, 
+#&gt;                 "\n")
+#&gt;         if (plot) {
+#&gt;             outtimes_plot = seq(min(observed$time), max(observed$time), 
+#&gt;                 length.out = 100)
+#&gt;             out_plot &lt;- mkinpredict(mkinmod, parms, odeini, outtimes_plot, 
+#&gt;                 solution_type = solution_type, use_compiled = use_compiled, 
+#&gt;                 method.ode = method.ode, atol = atol, rtol = rtol, 
+#&gt;                 ...)
+#&gt;             plot(0, type = "n", xlim = range(observed$time), 
+#&gt;                 ylim = c(0, max(observed$value, na.rm = TRUE)), 
+#&gt;                 xlab = "Time", ylab = "Observed")
+#&gt;             col_obs &lt;- pch_obs &lt;- 1:length(obs_vars)
+#&gt;             lty_obs &lt;- rep(1, length(obs_vars))
+#&gt;             names(col_obs) &lt;- names(pch_obs) &lt;- names(lty_obs) &lt;- obs_vars
+#&gt;             for (obs_var in obs_vars) {
+#&gt;                 points(subset(observed, name == obs_var, c(time, 
+#&gt;                   value)), pch = pch_obs[obs_var], col = col_obs[obs_var])
+#&gt;             }
+#&gt;             matlines(out_plot$time, out_plot[-1], col = col_obs, 
+#&gt;                 lty = lty_obs)
+#&gt;             legend("topright", inset = c(0.05, 0.05), legend = obs_vars, 
+#&gt;                 col = col_obs, pch = pch_obs, lty = 1:length(pch_obs))
+#&gt;         }
+#&gt;         assign("cost.old", mC$model, inherits = TRUE)
+#&gt;     }
+#&gt;     return(mC)
+#&gt; }
+#&gt; &lt;bytecode: 0x55555916c520&gt;
+#&gt; &lt;environment: 0x55555b68a808&gt;
+#&gt; 
+#&gt; $cost_notrans
+#&gt; function (P) 
+#&gt; {
+#&gt;     if (length(state.ini.optim) &gt; 0) {
+#&gt;         odeini &lt;- c(P[1:length(state.ini.optim)], state.ini.fixed)
+#&gt;         names(odeini) &lt;- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
+#&gt;     }
+#&gt;     else {
+#&gt;         odeini &lt;- state.ini.fixed
+#&gt;         names(odeini) &lt;- state.ini.fixed.boxnames
+#&gt;     }
+#&gt;     odeparms &lt;- c(P[(length(state.ini.optim) + 1):length(P)], 
+#&gt;         parms.fixed)
+#&gt;     out &lt;- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type, 
+#&gt;         use_compiled = use_compiled, method.ode = method.ode, 
+#&gt;         atol = atol, rtol = rtol, ...)
+#&gt;     mC &lt;- modCost(out, observed, y = "value", err = err, weight = weight, 
+#&gt;         scaleVar = scaleVar)
+#&gt;     return(mC)
+#&gt; }
+#&gt; &lt;bytecode: 0x55555a1242b0&gt;
+#&gt; &lt;environment: 0x55555b68a808&gt;
+#&gt; 
+#&gt; $hessian_notrans
+#&gt;                   parent_0 k_parent_sink
+#&gt; parent_0          4.163631     -1203.894
+#&gt; k_parent_sink -1203.893702   1033188.753
+#&gt; 
+#&gt; $start
+#&gt;               value   type
+#&gt; parent_0      98.62  state
+#&gt; k_parent_sink  0.10 deparm
+#&gt; 
+#&gt; $start_transformed
+#&gt;                       value lower upper
+#&gt; parent_0          98.620000  -Inf   Inf
+#&gt; log_k_parent_sink -2.302585  -Inf   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    98.62 99.17407218 -0.55407218
+#&gt; 2    3   parent    81.43 78.44547872  2.98452128
+#&gt; 3    7   parent    53.18 57.38445742 -4.20445742
+#&gt; 4   14   parent    34.89 33.20400061  1.68599939
+#&gt; 5   30   parent    10.09  9.50814643  0.58185357
+#&gt; 6   62   parent     1.50  0.77966270  0.72033730
+#&gt; 7   90   parent     0.33  0.08739595  0.24260405
+#&gt; 8  118   parent     0.08  0.00979661  0.07020339
+#&gt; 
+#&gt; $atol
+#&gt; [1] 1e-08
+#&gt; 
+#&gt; $rtol
+#&gt; [1] 1e-10
+#&gt; 
+#&gt; $weight.ini
+#&gt; [1] "none"
+#&gt; 
+#&gt; $tc.ini
+#&gt; sigma_low  rsd_high 
+#&gt;      0.50      0.07 
+#&gt; 
+#&gt; $reweight.tol
+#&gt; [1] 1e-08
+#&gt; 
+#&gt; $reweight.max.iter
+#&gt; [1] 10
+#&gt; 
+#&gt; $bparms.optim
+#&gt;      parent_0 k_parent_sink 
+#&gt;   99.17407218    0.07815759 
+#&gt; 
+#&gt; $bparms.fixed
+#&gt; numeric(0)
+#&gt; 
+#&gt; $bparms.ode
+#&gt; k_parent_sink 
+#&gt;    0.07815759 
+#&gt; 
+#&gt; $bparms.state
+#&gt;   parent 
+#&gt; 99.17407 
+#&gt; 
+#&gt; $date
+#&gt; [1] "Thu Jan 31 16:50:45 2019"
+#&gt; 
+#&gt; $version
+#&gt; [1] "0.9.47.6"
+#&gt; 
+#&gt; $Rversion
+#&gt; [1] "3.5.2"
+#&gt; 
+#&gt; attr(,"class")
+#&gt; [1] "mkinfit" "modFit" 
+#&gt; </div></pre>
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     <h2>Contents</h2>