Merge parent solutions to one file

- Combine R/*.solution.R into R/parent_solutions.R
- Create a roxygen family of related functions
- Reduce redundancy by using the inherit tag
- Change the parent.0 argument to parent_0 to match
  the corresponding parameter name used in mkinfit

1 files changed, 29 insertions, 3 deletions

diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html
index 3e87b90d..9697d420 100644
--- a/docs/reference/logistic.solution.html
+++ b/docs/reference/logistic.solution.html
@@ -234,7 +234,20 @@ an increasing rate constant, supposedly caused by microbial growth</p>
     <span class='kw'>sdfunc</span> <span class='kw'>=</span> <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='sigma_twocomp.html'>sigma_twocomp</a></span>(<span class='no'>x</span>, <span class='fl'>0.5</span>, <span class='fl'>0.07</span>),
     <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>reps</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>LOD</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456</span>)<span class='kw'>[[</span><span class='fl'>1</span>]]
 
-  <span class='no'>m</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"logistic"</span>, <span class='no'>d_2_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 (function (t, parent_0, kmax, k0, r) {    parent = parent_0 * (kmax/(kmax - k0 + k0 * exp(r * t)))^(kmax/r)})(t = c(0, 1, 1.21212121212121, 2.42424242424242, 3, 3.63636363636364, 4.84848484848485, 6.06060606060606, 7, 7.27272727272727, 8.48484848484848, 9.6969696969697, 10.9090909090909, 12.1212121212121, 13.3333333333333, 14, 14.5454545454545, 15.7575757575758, 16.969696969697, 18.1818181818182, 19.3939393939394, 20.6060606060606, 21.8181818181818, 23.030303030303, 24.2424242424242, 25.4545454545455, 26.6666666666667, 27.8787878787879, 28, 29.0909090909091, 30.3030303030303, 31.5151515151515, 32.7272727272727, 33.9393939393939, 35.1515151515152, 36.3636363636364, 37.5757575757576, 38.7878787878788, 40, 41.2121212121212, 42.4242424242424, 43.6363636363636, 44.8484848484849, 46.0606060606061, 47.2727272727273, 48.4848484848485, 49.6969696969697, 50.9090909090909, 52.1212121212121, 53.3333333333333, 54.5454545454545, 55.7575757575758, 56.969696969697, 58.1818181818182, 59.3939393939394, 60, 60.6060606060606, 61.8181818181818, 63.030303030303, 64.2424242424242, 65.4545454545455, 66.6666666666667, 67.8787878787879, 69.0909090909091, 70.3030303030303, 71.5151515151515, 72.7272727272727, 73.9393939393939, 75.1515151515152, 76.3636363636364, 77.5757575757576, 78.7878787878788, 80, 81.2121212121212, 82.4242424242424, 83.6363636363636, 84.8484848484848, 86.0606060606061, 87.2727272727273, 88.4848484848485, 89.6969696969697, 90, 90.9090909090909, 92.1212121212121, 93.3333333333333, 94.5454545454545, 95.7575757575758, 96.969696969697, 98.1818181818182, 99.3939393939394, 100.606060606061, 101.818181818182, 103.030303030303, 104.242424242424, 105.454545454545, 106.666666666667, 107.878787878788, 109.090909090909, 110.30303030303, 111.515151515152, 112.727272727273, 113.939393939394, 115.151515151515, 116.363636363636, 117.575757575758, 118.787878787879, 120), parent.0 = c(parent = 101.95687), kmax = 0.1,     k0 = 1e-04, r = 0.2): unbenutztes Argument (parent.0 = 101.95687)</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0.001 0 0.001</span></div><div class='input'>  <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>m</span>)</div><div class='output co'>#&gt; <span class='error'>Error in identical(fit$err_mod, "const"): Objekt 'm' nicht gefunden</span></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>m</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; <span class='error'>Error in summary(m): Objekt 'm' nicht gefunden</span></div><div class='input'>  <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>m</span>)$<span class='no'>distimes</span></div><div class='output co'>#&gt; <span class='error'>Error in endpoints(m): Objekt 'm' nicht gefunden</span></div><div class='input'>
+  <span class='no'>m</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"logistic"</span>, <span class='no'>d_2_1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+  <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>m</span>)</div><div class='img'><img src='logistic.solution-2.png' alt='' width='700' height='433' /></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>m</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt;              Estimate   se_notrans   t value       Pr(&gt;t)        Lower
+#&gt; parent_0 1.057896e+02 1.9023449703 55.610119 3.768361e-16 1.016451e+02
+#&gt; kmax     6.398190e-02 0.0143201031  4.467978 3.841829e-04 3.929235e-02
+#&gt; k0       1.612775e-04 0.0005866813  0.274898 3.940351e-01 5.846688e-08
+#&gt; r        2.263946e-01 0.1718110715  1.317695 1.061044e-01 4.335843e-02
+#&gt; sigma    5.332935e+00 0.9145907310  5.830952 4.036926e-05 3.340213e+00
+#&gt;                Upper
+#&gt; parent_0 109.9341588
+#&gt; kmax       0.1041853
+#&gt; k0         0.4448749
+#&gt; r          1.1821120
+#&gt; sigma      7.3256566</div><div class='input'>  <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>m</span>)$<span class='no'>distimes</span></div><div class='output co'>#&gt;            DT50     DT90  DT50_k0 DT50_kmax
+#&gt; parent 36.86533 62.41511 4297.853  10.83349</div><div class='input'>
 
   <span class='co'># Reproduce the plot on page 57 of FOCUS (2014)</span>
   <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.2</span>),
@@ -246,7 +259,7 @@ an increasing rate constant, supposedly caused by microbial growth</p>
        <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>5</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></span>(<span class='st'>"topright"</span>, <span class='kw'>inset</span> <span class='kw'>=</span> <span class='fl'>0.05</span>,
          <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='st'>"k0 = "</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.0001</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.001</span>, <span class='fl'>0.08</span>),
                          <span class='st'>", r = "</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.2</span>, <span class='fl'>0.4</span>, <span class='fl'>0.8</span>, <span class='fl'>0.2</span>, <span class='fl'>0.2</span>)),
-         <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fl'>5</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fl'>5</span>)</div><div class='img'><img src='logistic.solution-2.png' alt='' width='700' height='433' /></div><div class='input'>
+         <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fl'>5</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fl'>5</span>)</div><div class='img'><img src='logistic.solution-3.png' alt='' width='700' height='433' /></div><div class='input'>
   <span class='co'># Fit with synthetic data</span>
   <span class='no'>logistic</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'>"logistic"</span>))
 
@@ -259,7 +272,20 @@ an increasing rate constant, supposedly caused by microbial growth</p>
     <span class='kw'>sdfunc</span> <span class='kw'>=</span> <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='sigma_twocomp.html'>sigma_twocomp</a></span>(<span class='no'>x</span>, <span class='fl'>0.5</span>, <span class='fl'>0.07</span>),
     <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>reps</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>LOD</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456</span>)<span class='kw'>[[</span><span class='fl'>1</span>]]
 
-  <span class='no'>m</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"logistic"</span>, <span class='no'>d_2_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 (function (t, parent_0, kmax, k0, r) {    parent = parent_0 * (kmax/(kmax - k0 + k0 * exp(r * t)))^(kmax/r)})(t = c(0, 1, 1.21212121212121, 2.42424242424242, 3, 3.63636363636364, 4.84848484848485, 6.06060606060606, 7, 7.27272727272727, 8.48484848484848, 9.6969696969697, 10.9090909090909, 12.1212121212121, 13.3333333333333, 14, 14.5454545454545, 15.7575757575758, 16.969696969697, 18.1818181818182, 19.3939393939394, 20.6060606060606, 21.8181818181818, 23.030303030303, 24.2424242424242, 25.4545454545455, 26.6666666666667, 27.8787878787879, 28, 29.0909090909091, 30.3030303030303, 31.5151515151515, 32.7272727272727, 33.9393939393939, 35.1515151515152, 36.3636363636364, 37.5757575757576, 38.7878787878788, 40, 41.2121212121212, 42.4242424242424, 43.6363636363636, 44.8484848484849, 46.0606060606061, 47.2727272727273, 48.4848484848485, 49.6969696969697, 50.9090909090909, 52.1212121212121, 53.3333333333333, 54.5454545454545, 55.7575757575758, 56.969696969697, 58.1818181818182, 59.3939393939394, 60, 60.6060606060606, 61.8181818181818, 63.030303030303, 64.2424242424242, 65.4545454545455, 66.6666666666667, 67.8787878787879, 69.0909090909091, 70.3030303030303, 71.5151515151515, 72.7272727272727, 73.9393939393939, 75.1515151515152, 76.3636363636364, 77.5757575757576, 78.7878787878788, 80, 81.2121212121212, 82.4242424242424, 83.6363636363636, 84.8484848484848, 86.0606060606061, 87.2727272727273, 88.4848484848485, 89.6969696969697, 90, 90.9090909090909, 92.1212121212121, 93.3333333333333, 94.5454545454545, 95.7575757575758, 96.969696969697, 98.1818181818182, 99.3939393939394, 100.606060606061, 101.818181818182, 103.030303030303, 104.242424242424, 105.454545454545, 106.666666666667, 107.878787878788, 109.090909090909, 110.30303030303, 111.515151515152, 112.727272727273, 113.939393939394, 115.151515151515, 116.363636363636, 117.575757575758, 118.787878787879, 120), parent.0 = c(parent = 101.95687), kmax = 0.1,     k0 = 1e-04, r = 0.2): unbenutztes Argument (parent.0 = 101.95687)</span></div><div class='output co'>#&gt; <span class='message'>Timing stopped at: 0 0 0</span></div><div class='input'>  <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>m</span>)</div><div class='output co'>#&gt; <span class='error'>Error in identical(fit$err_mod, "const"): Objekt 'm' nicht gefunden</span></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>m</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt; <span class='error'>Error in summary(m): Objekt 'm' nicht gefunden</span></div><div class='input'>  <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>m</span>)$<span class='no'>distimes</span></div><div class='output co'>#&gt; <span class='error'>Error in endpoints(m): Objekt 'm' nicht gefunden</span></div><div class='input'>
+  <span class='no'>m</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"logistic"</span>, <span class='no'>d_2_1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+  <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>m</span>)</div><div class='img'><img src='logistic.solution-4.png' alt='' width='700' height='433' /></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>m</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt;              Estimate   se_notrans   t value       Pr(&gt;t)        Lower
+#&gt; parent_0 1.057896e+02 1.9023449703 55.610119 3.768361e-16 1.016451e+02
+#&gt; kmax     6.398190e-02 0.0143201031  4.467978 3.841829e-04 3.929235e-02
+#&gt; k0       1.612775e-04 0.0005866813  0.274898 3.940351e-01 5.846688e-08
+#&gt; r        2.263946e-01 0.1718110715  1.317695 1.061044e-01 4.335843e-02
+#&gt; sigma    5.332935e+00 0.9145907310  5.830952 4.036926e-05 3.340213e+00
+#&gt;                Upper
+#&gt; parent_0 109.9341588
+#&gt; kmax       0.1041853
+#&gt; k0         0.4448749
+#&gt; r          1.1821120
+#&gt; sigma      7.3256566</div><div class='input'>  <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>m</span>)$<span class='no'>distimes</span></div><div class='output co'>#&gt;            DT50     DT90  DT50_k0 DT50_kmax
+#&gt; parent 36.86533 62.41511 4297.853  10.83349</div><div class='input'>
 </div></pre>
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