Convert synthetic_data_for_UBA_2014 to mkinds

Static documentation except articles rebuilt by pkgdown

8 files changed, 8 insertions, 10 deletions

diff --git a/data/synthetic_data_for_UBA_2014.RData b/data/synthetic_data_for_UBA_2014.RData
deleted file mode 100644
index 12132c97..00000000
--- a/data/synthetic_data_for_UBA_2014.RData
+++ /dev/null
diff --git a/data/synthetic_data_for_UBA_2014.rda b/data/synthetic_data_for_UBA_2014.rda
new file mode 100644
index 00000000..662dc0f3
--- /dev/null
+++ b/data/synthetic_data_for_UBA_2014.rda
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index 8a148870..f9603f34 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -121,9 +121,8 @@
         
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
-    <p>A list containing datasets in the form internally used by the 'gmkin' package.
-  The list has twelve components. Each of the components is one dataset that has,
-  among others, the following components</p><dl class='dl-horizontal'>
+    <p>A list containing twelve datasets as an R6 class defined by <code><a href='mkinds.html'>mkinds</a></code>,
+  each containing, among others, the following components</p><dl class='dl-horizontal'>
     <dt><code>title</code></dt><dd><p>The name of the dataset, e.g. <code>SFO_lin_a</code></p></dd>
     <dt><code>data</code></dt><dd><p>A data frame with the data in the form expected by <code><a href='mkinfit.html'>mkinfit</a></code></p></dd>
   </dl>
diff --git a/docs/reference/test_data_from_UBA_2014-16.png b/docs/reference/test_data_from_UBA_2014-16.png
index e5346b43..6738f3a0 100644
--- a/docs/reference/test_data_from_UBA_2014-16.png
+++ b/docs/reference/test_data_from_UBA_2014-16.png
diff --git a/docs/reference/test_data_from_UBA_2014-6.png b/docs/reference/test_data_from_UBA_2014-6.png
index e7fe4f0c..8c65e604 100644
--- a/docs/reference/test_data_from_UBA_2014-6.png
+++ b/docs/reference/test_data_from_UBA_2014-6.png
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index 601f148c..e43e2cf9 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -232,7 +232,7 @@
 #&gt; Model cost at call  380 :  186.8489 
 #&gt; Model cost at call  382 :  186.8489 
 #&gt; Model cost at call  383 :  186.8489 
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'>  <span class='fu'>plot</span>(<span class='no'>f_river</span>)</div><img src='test_data_from_UBA_2014-6.png' alt='' width='540' height='400' /><div class='input'>
+#&gt; Optimisation by method Port successfully terminated.</div><div class='input'>  <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_river</span>)</div><img src='test_data_from_UBA_2014-6.png' alt='' width='540' height='400' /><div class='input'>
   <span class='fu'>summary</span>(<span class='no'>f_river</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt;                         Estimate se_notrans      t value       Pr(&gt;t) Lower
 #&gt; parent_w_0          9.598567e+01 2.33959810 4.102657e+01 9.568973e-19    NA
 #&gt; k_parent_w_sink     3.603743e-01 0.03497716 1.030313e+01 4.988281e-09    NA
@@ -355,7 +355,7 @@
 #&gt; Model cost at call  401 :  37.69197 
 #&gt; Model cost at call  420 :  37.69197 
 #&gt; Model cost at call  441 :  37.69197 
-#&gt; Optimisation by method Port successfully terminated.</div><div class='input'>  <span class='fu'>plot</span>(<span class='no'>f_soil</span>)</div><img src='test_data_from_UBA_2014-16.png' alt='' width='540' height='400' /><div class='input'>  <span class='fu'>summary</span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt;                   Estimate  se_notrans    t value       Pr(&gt;t)        Lower
+#&gt; Optimisation by method Port successfully terminated.</div><div class='input'>  <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>f_soil</span>, <span class='kw'>lpos</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"topright"</span>, <span class='st'>"bottomright"</span>))</div><img src='test_data_from_UBA_2014-16.png' alt='' width='540' height='400' /><div class='input'>  <span class='fu'>summary</span>(<span class='no'>f_soil</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt;                   Estimate  se_notrans    t value       Pr(&gt;t)        Lower
 #&gt; parent_0       76.55425583 0.943443834 81.1434164 4.422340e-30 74.602593306
 #&gt; k_parent        0.12081956 0.004815515 25.0896457 1.639665e-18  0.111257526
 #&gt; k_M1            0.84258650 0.930121206  0.9058889 1.871937e-01  0.085876305
diff --git a/man/synthetic_data_for_UBA.Rd b/man/synthetic_data_for_UBA.Rd
index fbccf6d8..a9df9767 100644
--- a/man/synthetic_data_for_UBA.Rd
+++ b/man/synthetic_data_for_UBA.Rd
@@ -25,9 +25,8 @@
 }

 \usage{synthetic_data_for_UBA_2014}

 \format{

-  A list containing datasets in the form internally used by the 'gmkin' package.

-  The list has twelve components. Each of the components is one dataset that has,

-  among others, the following components

+  A list containing twelve datasets as an R6 class defined by \code{\link{mkinds}},

+  each containing, among others, the following components

   \describe{

     \item{\code{title}}{The name of the dataset, e.g. \code{SFO_lin_a}}

     \item{\code{data}}{A data frame with the data in the form expected by \code{\link{mkinfit}}}

diff --git a/man/test_data_from_UBA_2014.Rd b/man/test_data_from_UBA_2014.Rd
index 53100d8d..a3543559 100644
--- a/man/test_data_from_UBA_2014.Rd
+++ b/man/test_data_from_UBA_2014.Rd
@@ -31,7 +31,7 @@
   m_ws <- mkinmod(parent_w = mkinsub("SFO", "parent_s"),
                   parent_s = mkinsub("SFO", "parent_w"))
   f_river <- mkinfit(m_ws, test_data_from_UBA_2014[[1]]$data)
-  plot(f_river)
+  plot_sep(f_river)
 
   summary(f_river)$bpar
   mkinerrmin(f_river)
@@ -45,7 +45,7 @@
                     use_of_ff = "max")
 
   f_soil <- mkinfit(m_soil, test_data_from_UBA_2014[[3]]$data)
-  plot(f_soil)
+  plot_sep(f_soil, lpos = c("topright", "topright", "topright", "bottomright"))
   summary(f_soil)$bpar
   mkinerrmin(f_soil)
 }