4 files changed, 138 insertions, 2 deletions
diff --git a/docs/reference/one_box.html b/docs/reference/one_box.html
index 4987f15..3410ac4 100644
--- a/docs/reference/one_box.html
+++ b/docs/reference/one_box.html
@@ -53,6 +53,17 @@
 <span><span class="co"># S3 method for class 'character'</span></span>
 <span><span class="fu">one_box</span><span class="op">(</span><span class="va">x</span>, ini <span class="op">=</span> <span class="fl">1</span>, <span class="va">parms</span>, <span class="va">...</span>, t_end <span class="op">=</span> <span class="fl">100</span>, res <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span></span>
 <span></span>
+<span><span class="co"># S3 method for class 'mkinmod'</span></span>
+<span><span class="fu">one_box</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  ini <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>, <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fu"><a href="https://rdrr.io/r/base/length.html" class="external-link">length</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">diffs</span><span class="op">)</span> <span class="op">-</span> <span class="fl">1</span><span class="op">)</span><span class="op">)</span>,</span>
+<span>  <span class="va">odeparms</span>,</span>
+<span>  solution_type <span class="op">=</span> <span class="st">"deSolve"</span>,</span>
+<span>  <span class="va">...</span>,</span>
+<span>  t_end <span class="op">=</span> <span class="fl">100</span>,</span>
+<span>  res <span class="op">=</span> <span class="fl">0.01</span></span>
+<span><span class="op">)</span></span>
+<span></span>
 <span><span class="co"># S3 method for class 'mkinfit'</span></span>
 <span><span class="fu">one_box</span><span class="op">(</span><span class="va">x</span>, ini <span class="op">=</span> <span class="st">"model"</span>, <span class="va">...</span>, t_end <span class="op">=</span> <span class="fl">100</span>, res <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span></span></code></pre></div>
     </div>
@@ -92,6 +103,14 @@ all observed variables.</p></dd>
 <dt id="arg-parms">parms<a class="anchor" aria-label="anchor" href="#arg-parms"></a></dt>
 <dd><p>A named numeric vector containing the model parameters</p></dd>
 
+
+<dt id="arg-odeparms">odeparms<a class="anchor" aria-label="anchor" href="#arg-odeparms"></a></dt>
+<dd><p>Will be passed to <a href="https://pkgdown.jrwb.de/mkin/reference/mkinpredict.html" class="external-link">mkinpredict</a></p></dd>
+
+
+<dt id="arg-solution-type">solution_type<a class="anchor" aria-label="anchor" href="#arg-solution-type"></a></dt>
+<dd><p>Will be passed to <a href="https://pkgdown.jrwb.de/mkin/reference/mkinpredict.html" class="external-link">mkinpredict</a></p></dd>
+
 </dl></div>
     <div class="section level2">
     <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
@@ -120,6 +139,26 @@ all observed variables.</p></dd>
 <span class="r-in"><span><span class="va">pred_2</span> <span class="op">&lt;-</span> <span class="fu">one_box</span><span class="op">(</span><span class="va">fit_2</span>, ini <span class="op">=</span> <span class="st">"model"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">pred_2</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="one_box-3.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pkgdown.jrwb.de/mkin/" class="external-link">mkin</a></span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinmod</a></span><span class="op">(</span></span></span>
+<span class="r-in"><span>  parent <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  m1 <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
+<span class="r-in"><span><span class="va">c_0</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">deg_parms</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.15</span>, f_parent_to_m1 <span class="op">=</span> <span class="fl">0.5</span>, k_m1 <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">sfo_sfo_box</span> <span class="op">&lt;-</span> <span class="fu">one_box</span><span class="op">(</span><span class="va">SFO_SFO</span>, odeparms <span class="op">=</span> <span class="va">deg_parms</span>, ini <span class="op">=</span> <span class="va">c_0</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">sfo_sfo_box</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Time Series:</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Start = c(0, 1) </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> End = c(0, 6) </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Frequency = 100 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>         parent         m1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 0.00 100.00000 0.00000000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 0.01  99.85011 0.07494003</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 0.02  99.70045 0.14976024</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 0.03  99.55101 0.22446081</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 0.04  99.40180 0.29904192</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 0.05  99.25281 0.37350376</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
diff --git a/docs/reference/one_box.md b/docs/reference/one_box.md
index 0c93346..f956b8f 100644
--- a/docs/reference/one_box.md
+++ b/docs/reference/one_box.md
@@ -13,6 +13,17 @@ one_box(x, ini = 1, ..., t_end = 100, res = 0.01)
 # S3 method for class 'character'
 one_box(x, ini = 1, parms, ..., t_end = 100, res = 0.01)
 
+# S3 method for class 'mkinmod'
+one_box(
+  x,
+  ini = c(1, rep(0, length(x$diffs) - 1)),
+  odeparms,
+  solution_type = "deSolve",
+  ...,
+  t_end = 100,
+  res = 0.01
+)
+
 # S3 method for class 'mkinfit'
 one_box(x, ini = "model", ..., t_end = 100, res = 0.01)
 ```
@@ -53,6 +64,16 @@ one_box(x, ini = "model", ..., t_end = 100, res = 0.01)
 
   A named numeric vector containing the model parameters
 
+- odeparms:
+
+  Will be passed to
+  [mkinpredict](https://pkgdown.jrwb.de/mkin/reference/mkinpredict.html)
+
+- solution_type:
+
+  Will be passed to
+  [mkinpredict](https://pkgdown.jrwb.de/mkin/reference/mkinpredict.html)
+
 ## Value
 
 An object of class `one_box`, inheriting from
@@ -80,4 +101,25 @@ fit_2 <- mkinfit(m_2, FOCUS_2006_D, quiet = TRUE)
 #> Warning: Observations with value of zero were removed from the data
 pred_2 <- one_box(fit_2, ini = "model")
 plot(pred_2)
+
+library(mkin)
+SFO_SFO <- mkinmod(
+  parent = mkinsub("SFO", to = "m1"),
+  m1 = mkinsub("SFO"))
+#> Temporary DLL for differentials generated and loaded
+c_0 = c(parent = 100, m1 = 0)
+deg_parms = c(k_parent = 0.15, f_parent_to_m1 = 0.5, k_m1 = 0.01)
+sfo_sfo_box <- one_box(SFO_SFO, odeparms = deg_parms, ini = c_0)
+head(sfo_sfo_box)
+#> Time Series:
+#> Start = c(0, 1) 
+#> End = c(0, 6) 
+#> Frequency = 100 
+#>         parent         m1
+#> 0.00 100.00000 0.00000000
+#> 0.01  99.85011 0.07494003
+#> 0.02  99.70045 0.14976024
+#> 0.03  99.55101 0.22446081
+#> 0.04  99.40180 0.29904192
+#> 0.05  99.25281 0.37350376
 ```
diff --git a/docs/reference/pfm_degradation.html b/docs/reference/pfm_degradation.html
index b4f3279..22d90ca 100644
--- a/docs/reference/pfm_degradation.html
+++ b/docs/reference/pfm_degradation.html
@@ -86,13 +86,21 @@ is calculated (SFO model).</p></dd>
 
 </dl></div>
     <div class="section level2">
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <p>A data frame containing the output times and the concentrations
+assuming initial concentrations of 1 for the parent and zero for
+metabolites, if any.</p>
+    </div>
+    <div class="section level2">
     <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
     <p>Johannes Ranke</p>
     </div>
 
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="fu">pfm_degradation</span><span class="op">(</span><span class="st">"SFO"</span>, DT50 <span class="op">=</span> <span class="fl">10</span><span class="op">)</span><span class="op">)</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Simple example of an SFO decline curve</span></span></span>
+<span class="r-in"><span><span class="va">sfo_out</span> <span class="op">&lt;-</span> <span class="fu">pfm_degradation</span><span class="op">(</span><span class="st">"SFO"</span>, DT50 <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">sfo_out</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   time    parent</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 0    0 1.0000000</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1    1 0.9330330</span>
@@ -100,6 +108,26 @@ is calculated (SFO model).</p></dd>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 3    3 0.8122524</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 4    4 0.7578583</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 5    5 0.7071068</span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># Fictive example with a metabolite where we first generate an SFO-SFO model</span></span></span>
+<span class="r-in"><span><span class="va">sfo_sfo</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinmod</a></span><span class="op">(</span></span></span>
+<span class="r-in"><span>  parent <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"metabolite"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  metabolite <span class="op">=</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinmod.html" class="external-link">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="va">sfo_sfo_out</span> <span class="op">&lt;-</span> <span class="fu">pfm_degradation</span><span class="op">(</span><span class="va">sfo_sfo</span>,</span></span>
+<span class="r-in"><span>  parms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k_parent <span class="op">=</span> <span class="fl">0.1</span>, f_parent_to_metabolite <span class="op">=</span> <span class="fl">0.5</span>, k_metabolite <span class="op">=</span> <span class="fl">0.02</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span></span></span>
+<span class="r-in"><span>  <span class="va">sfo_sfo_out</span><span class="op">[</span>, <span class="st">"time"</span><span class="op">]</span>,</span></span>
+<span class="r-in"><span>  <span class="va">sfo_sfo_out</span><span class="op">[</span>, <span class="st">"parent"</span><span class="op">]</span>, type <span class="op">=</span> <span class="st">"l"</span>,</span></span>
+<span class="r-in"><span>  xlab <span class="op">=</span> <span class="st">"Time"</span>, ylab <span class="op">=</span> <span class="st">"Relative concentration"</span>,</span></span>
+<span class="r-in"><span>  xlim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">100</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/lines.html" class="external-link">lines</a></span><span class="op">(</span></span></span>
+<span class="r-in"><span>  <span class="va">sfo_sfo_out</span><span class="op">[</span>, <span class="st">"time"</span><span class="op">]</span>,</span></span>
+<span class="r-in"><span>  <span class="va">sfo_sfo_out</span><span class="op">[</span>, <span class="st">"metabolite"</span><span class="op">]</span>, lty <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="pfm_degradation-1.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span></span></span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
diff --git a/docs/reference/pfm_degradation.md b/docs/reference/pfm_degradation.md
index fb241ff..7dba450 100644
--- a/docs/reference/pfm_degradation.md
+++ b/docs/reference/pfm_degradation.md
@@ -44,6 +44,12 @@ pfm_degradation(
 
   The output times
 
+## Value
+
+A data frame containing the output times and the concentrations assuming
+initial concentrations of 1 for the parent and zero for metabolites, if
+any.
+
 ## Author
 
 Johannes Ranke
@@ -51,7 +57,9 @@ Johannes Ranke
 ## Examples
 
 ``` r
-head(pfm_degradation("SFO", DT50 = 10))
+# Simple example of an SFO decline curve
+sfo_out <- pfm_degradation("SFO", DT50 = 10)
+head(sfo_out)
 #>   time    parent
 #> 0    0 1.0000000
 #> 1    1 0.9330330
@@ -59,4 +67,23 @@ head(pfm_degradation("SFO", DT50 = 10))
 #> 3    3 0.8122524
 #> 4    4 0.7578583
 #> 5    5 0.7071068
+
+# Fictive example with a metabolite where we first generate an SFO-SFO model
+sfo_sfo <- mkinmod(
+  parent = mkinsub("SFO", to = "metabolite"),
+  metabolite = mkinsub("SFO"))
+#> Temporary DLL for differentials generated and loaded
+
+sfo_sfo_out <- pfm_degradation(sfo_sfo,
+  parms = c(k_parent = 0.1, f_parent_to_metabolite = 0.5, k_metabolite = 0.02))
+
+plot(
+  sfo_sfo_out[, "time"],
+  sfo_sfo_out[, "parent"], type = "l",
+  xlab = "Time", ylab = "Relative concentration",
+  xlim = c(0, 100))
+lines(
+  sfo_sfo_out[, "time"],
+  sfo_sfo_out[, "metabolite"], lty = 2)
+
 ```