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authorJohannes Ranke <jranke@uni-bremen.de>2019-01-31 16:55:20 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2019-01-31 16:55:20 +0100
commit3eefecf0adfbb30b8fb895c244dea6903bcb3e9c (patch)
treebb70432fd6f13ca306443047d6911a797757ee96 /docs/reference/Extract.mmkin.html
parente5453f4d020aa120cabea074120f587f8ea4735f (diff)
Restore NAMESPACE
which was accidentally overwritten by pkgdown -> roxygen
Diffstat (limited to 'docs/reference/Extract.mmkin.html')
-rw-r--r--docs/reference/Extract.mmkin.html402
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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