Improve examle code for `one_box`HEADmain

7 files changed, 36 insertions, 47 deletions

diff --git a/docs/reference/one_box-2.png b/docs/reference/one_box-2.png
index 6a4d0de..2883ca7 100644
--- a/docs/reference/one_box-2.png
+++ b/docs/reference/one_box-2.png
diff --git a/docs/reference/one_box-3.png b/docs/reference/one_box-3.png
index d659e3a..6a4d0de 100644
--- a/docs/reference/one_box-3.png
+++ b/docs/reference/one_box-3.png
diff --git a/docs/reference/one_box-4.png b/docs/reference/one_box-4.png
new file mode 100644
index 0000000..d659e3a
--- /dev/null
+++ b/docs/reference/one_box-4.png
diff --git a/docs/reference/one_box.html b/docs/reference/one_box.html
index 3410ac4..8866fcf 100644
--- a/docs/reference/one_box.html
+++ b/docs/reference/one_box.html
@@ -124,41 +124,32 @@ all observed variables.</p></dd>
 <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_0</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="one_box-1.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span></span></span>
-<span class="r-in"><span><span class="co"># Use a fitted mkinfit model</span></span></span>
+<span class="r-in"><span><span class="co"># Use a custom mkin model</span></span></span>
 <span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</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">pred_sfo_sfo</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/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">pred_sfo_sfo</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="one_box-2.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="co"># Use a fitted mkin model</span></span></span>
 <span class="r-in"><span><span class="va">fit</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">pred_1</span> <span class="op">&lt;-</span> <span class="fu">one_box</span><span class="op">(</span><span class="va">fit</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_1</span><span class="op">)</span></span></span>
-<span class="r-plt img"><img src="one_box-2.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="one_box-3.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span></span></span>
-<span class="r-in"><span><span class="co"># Use a model with more than one observed variable</span></span></span>
+<span class="r-in"><span><span class="co"># Use a fitted model with a metabolite</span></span></span>
 <span class="r-in"><span><span class="va">m_2</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>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>, <span class="st">"m1"</span><span class="op">)</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">fit_2</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://pkgdown.jrwb.de/mkin/reference/mkinfit.html" class="external-link">mkinfit</a></span><span class="op">(</span><span class="va">m_2</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Observations with value of zero were removed from the data</span>
 <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>
+<span class="r-plt img"><img src="one_box-4.png" alt="" width="700" height="433"></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 f956b8f..89ccecf 100644
--- a/docs/reference/one_box.md
+++ b/docs/reference/one_box.md
@@ -87,39 +87,29 @@ pred_0 <- one_box(10)
 plot(pred_0)
 
 
-# Use a fitted mkinfit model
+# Use a custom mkin model
 require(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)
+pred_sfo_sfo <- one_box(SFO_SFO, odeparms = deg_parms, ini = c_0)
+plot(pred_sfo_sfo)
+
+
+# Use a fitted mkin model
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
 pred_1 <- one_box(fit)
 plot(pred_1)
 
 
-# Use a model with more than one observed variable
+# Use a fitted model with a metabolite
 m_2 <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))
 #> Temporary DLL for differentials generated and loaded
 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/one_box.mkinmod.html b/docs/reference/one_box.mkinmod.html
new file mode 100644
index 0000000..b2bfb92
--- /dev/null
+++ b/docs/reference/one_box.mkinmod.html
@@ -0,0 +1,8 @@
+<html>
+  <head>
+    <meta http-equiv="refresh" content="0;URL=https://pkgdown.jrwb.de/pfm/reference/one_box.html" />
+    <meta name="robots" content="noindex">
+    <link rel="canonical" href="https://pkgdown.jrwb.de/pfm/reference/one_box.html">
+  </head>
+</html>
+
diff --git a/docs/reference/pfm_degradation-1.png b/docs/reference/pfm_degradation-1.png
new file mode 100644
index 0000000..ceb6e5e
--- /dev/null
+++ b/docs/reference/pfm_degradation-1.png