Further formatting improvement for differential equations

5 files changed, 57 insertions, 47 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 6c4545c4..a984391c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -3,7 +3,7 @@ Type: Package
 Title: Routines for Fitting Kinetic Models with One or More State
   Variables to Chemical Degradation Data
 Version: 0.9-34
-Date: 2014-10-11
+Date: 2014-10-14
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), 
                     email = "jranke@uni-bremen.de"),
              person("Katrin", "Lindenberger", role = "ctb"),
diff --git a/NEWS.md b/NEWS.md
index 55a11818..4478be6b 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,5 +1,9 @@
 # CHANGES in mkin VERSION 0.9-34
 
+## MINOR CHANGES
+
+- The formatting of differential equations in the summary was further improved
+
 # CHANGES in mkin VERSION 0.9-33
 
 ## NEW FEATURES
diff --git a/R/mkinfit.R b/R/mkinfit.R
index 5c1de846..a966cea6 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -567,7 +567,7 @@ print.summary.mkinfit <- function(x, digits = max(3, getOption("digits") - 3), .
   if (!is.null(x$warning)) cat("\n\nWarning:", x$warning, "\n\n")

 

   cat("\nEquations:\n")

-  cat(noquote(strwrap(x[["diffs"]], exdent = 11)), fill = TRUE)

+  writeLines(strwrap(x[["diffs"]], exdent = 11))

   df  <- x$df

   rdf <- df[2]

 

diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index c0430358..60c5132a 100644
--- a/vignettes/FOCUS_L.html
+++ b/vignettes/FOCUS_L.html
@@ -214,7 +214,13 @@ hr {
 report, p. 284:</p>
 
 <pre><code class="r">library(&quot;mkin&quot;)
-FOCUS_2006_L1 = data.frame(
+</code></pre>
+
+<pre><code>## Loading required package: minpack.lm
+## Loading required package: rootSolve
+</code></pre>
+
+<pre><code class="r">FOCUS_2006_L1 = data.frame(
   t = rep(c(0, 1, 2, 3, 5, 7, 14, 21, 30), each = 2),
   parent = c(88.3, 91.4, 85.6, 84.5, 78.9, 77.6, 
              72.0, 71.9, 50.3, 59.4, 47.0, 45.1,
@@ -236,17 +242,17 @@ given in the FOCUS report. </p>
 summary(m.L1.SFO)
 </code></pre>
 
-<pre><code>## mkin version:    0.9.33 
+<pre><code>## mkin version:    0.9.34 
 ## R version:       3.1.1 
-## Date of fit:     Sat Oct 11 11:06:43 2014 
-## Date of summary: Sat Oct 11 11:06:43 2014 
+## Date of fit:     Tue Oct 14 22:03:33 2014 
+## Date of summary: Tue Oct 14 22:03:33 2014 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 14 model solutions performed in 0.083 s
+## Fitted with method Marq using 14 model solutions performed in 0.081 s
 ## 
 ## Weighting: none
 ## 
@@ -338,17 +344,17 @@ is checked.</p>
 summary(m.L1.FOMC, data = FALSE)
 </code></pre>
 
-<pre><code>## mkin version:    0.9.33 
+<pre><code>## mkin version:    0.9.34 
 ## R version:       3.1.1 
-## Date of fit:     Sat Oct 11 11:06:44 2014 
-## Date of summary: Sat Oct 11 11:06:44 2014 
+## Date of fit:     Tue Oct 14 22:03:34 2014 
+## Date of summary: Tue Oct 14 22:03:34 2014 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 53 model solutions performed in 0.314 s
+## Fitted with method Marq using 53 model solutions performed in 0.289 s
 ## 
 ## Weighting: none
 ## 
@@ -432,17 +438,17 @@ FOCUS_2006_L2_mkin &lt;- mkin_wide_to_long(FOCUS_2006_L2)
 summary(m.L2.SFO)
 </code></pre>
 
-<pre><code>## mkin version:    0.9.33 
+<pre><code>## mkin version:    0.9.34 
 ## R version:       3.1.1 
-## Date of fit:     Sat Oct 11 11:06:44 2014 
-## Date of summary: Sat Oct 11 11:06:44 2014 
+## Date of fit:     Tue Oct 14 22:03:35 2014 
+## Date of summary: Tue Oct 14 22:03:35 2014 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 29 model solutions performed in 0.173 s
+## Fitted with method Marq using 29 model solutions performed in 0.154 s
 ## 
 ## Weighting: none
 ## 
@@ -542,17 +548,17 @@ mkinresplot(m.L2.FOMC)
 <pre><code class="r">summary(m.L2.FOMC, data = FALSE)
 </code></pre>
 
-<pre><code>## mkin version:    0.9.33 
+<pre><code>## mkin version:    0.9.34 
 ## R version:       3.1.1 
-## Date of fit:     Sat Oct 11 11:06:46 2014 
-## Date of summary: Sat Oct 11 11:06:47 2014 
+## Date of fit:     Tue Oct 14 22:03:36 2014 
+## Date of summary: Tue Oct 14 22:03:36 2014 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 35 model solutions performed in 0.206 s
+## Fitted with method Marq using 35 model solutions performed in 0.192 s
 ## 
 ## Weighting: none
 ## 
@@ -628,19 +634,19 @@ plot(m.L2.DFOP)
 <pre><code class="r">summary(m.L2.DFOP, data = FALSE)
 </code></pre>
 
-<pre><code>## mkin version:    0.9.33 
+<pre><code>## mkin version:    0.9.34 
 ## R version:       3.1.1 
-## Date of fit:     Sat Oct 11 11:06:47 2014 
-## Date of summary: Sat Oct 11 11:06:47 2014 
+## Date of fit:     Tue Oct 14 22:03:36 2014 
+## Date of summary: Tue Oct 14 22:03:36 2014 
 ## 
 ## Equations:
-## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * 
-##            time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * 
+## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
+##            time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 *
 ##            time))) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 43 model solutions performed in 0.265 s
+## Fitted with method Marq using 43 model solutions performed in 0.24 s
 ## 
 ## Weighting: none
 ## 
@@ -717,17 +723,17 @@ plot(m.L3.SFO)
 <pre><code class="r">summary(m.L3.SFO)
 </code></pre>
 
-<pre><code>## mkin version:    0.9.33 
+<pre><code>## mkin version:    0.9.34 
 ## R version:       3.1.1 
-## Date of fit:     Sat Oct 11 11:06:48 2014 
-## Date of summary: Sat Oct 11 11:06:48 2014 
+## Date of fit:     Tue Oct 14 22:03:37 2014 
+## Date of summary: Tue Oct 14 22:03:37 2014 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 44 model solutions performed in 0.261 s
+## Fitted with method Marq using 44 model solutions performed in 0.237 s
 ## 
 ## Weighting: none
 ## 
@@ -803,17 +809,17 @@ plot(m.L3.FOMC)
 <pre><code class="r">summary(m.L3.FOMC, data = FALSE)
 </code></pre>
 
-<pre><code>## mkin version:    0.9.33 
+<pre><code>## mkin version:    0.9.34 
 ## R version:       3.1.1 
-## Date of fit:     Sat Oct 11 11:06:48 2014 
-## Date of summary: Sat Oct 11 11:06:48 2014 
+## Date of fit:     Tue Oct 14 22:03:37 2014 
+## Date of summary: Tue Oct 14 22:03:37 2014 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 26 model solutions performed in 0.159 s
+## Fitted with method Marq using 26 model solutions performed in 0.139 s
 ## 
 ## Weighting: none
 ## 
@@ -876,19 +882,19 @@ plot(m.L3.DFOP)
 <pre><code class="r">summary(m.L3.DFOP, data = FALSE)
 </code></pre>
 
-<pre><code>## mkin version:    0.9.33 
+<pre><code>## mkin version:    0.9.34 
 ## R version:       3.1.1 
-## Date of fit:     Sat Oct 11 11:06:50 2014 
-## Date of summary: Sat Oct 11 11:06:50 2014 
+## Date of fit:     Tue Oct 14 22:03:37 2014 
+## Date of summary: Tue Oct 14 22:03:37 2014 
 ## 
 ## Equations:
-## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * 
-##            time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * 
+## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
+##            time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 *
 ##            time))) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 37 model solutions performed in 0.225 s
+## Fitted with method Marq using 37 model solutions performed in 0.207 s
 ## 
 ## Weighting: none
 ## 
@@ -974,17 +980,17 @@ plot(m.L4.SFO)
 <pre><code class="r">summary(m.L4.SFO, data = FALSE)
 </code></pre>
 
-<pre><code>## mkin version:    0.9.33 
+<pre><code>## mkin version:    0.9.34 
 ## R version:       3.1.1 
-## Date of fit:     Sat Oct 11 11:06:51 2014 
-## Date of summary: Sat Oct 11 11:06:51 2014 
+## Date of fit:     Tue Oct 14 22:03:38 2014 
+## Date of summary: Tue Oct 14 22:03:38 2014 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 20 model solutions performed in 0.119 s
+## Fitted with method Marq using 20 model solutions performed in 0.106 s
 ## 
 ## Weighting: none
 ## 
@@ -1049,17 +1055,17 @@ plot(m.L4.FOMC)
 <pre><code class="r">summary(m.L4.FOMC, data = FALSE)
 </code></pre>
 
-<pre><code>## mkin version:    0.9.33 
+<pre><code>## mkin version:    0.9.34 
 ## R version:       3.1.1 
-## Date of fit:     Sat Oct 11 11:06:51 2014 
-## Date of summary: Sat Oct 11 11:06:51 2014 
+## Date of fit:     Tue Oct 14 22:03:38 2014 
+## Date of summary: Tue Oct 14 22:03:38 2014 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 48 model solutions performed in 0.283 s
+## Fitted with method Marq using 48 model solutions performed in 0.26 s
 ## 
 ## Weighting: none
 ## 
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index 426aa0df..b5898b7c 100644
--- a/vignettes/FOCUS_Z.pdf
+++ b/vignettes/FOCUS_Z.pdf