Update vignettes with 0.9-32 just released to CRAN

3 files changed, 33 insertions, 39 deletions

diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index 614fcf32..ab7ccaee 100644
--- a/vignettes/FOCUS_L.html
+++ b/vignettes/FOCUS_L.html
@@ -193,13 +193,7 @@ hr {
 report, p. 284:</p>
 
 <pre><code class="r">library(&quot;mkin&quot;)
-</code></pre>
-
-<pre><code>## Loading required package: minpack.lm
-## Loading required package: rootSolve
-</code></pre>
-
-<pre><code class="r">FOCUS_2006_L1 = data.frame(
+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,
@@ -223,8 +217,8 @@ summary(m.L1.SFO)
 
 <pre><code>## mkin version:    0.9.32 
 ## R version:       3.1.1 
-## Date of fit:     Mon Jul 21 09:14:29 2014 
-## Date of summary: Mon Jul 21 09:14:29 2014 
+## Date of fit:     Thu Jul 24 10:32:09 2014 
+## Date of summary: Thu Jul 24 10:32:09 2014 
 ## 
 ## Equations:
 ## [1] d_parent = - k_parent_sink * parent
@@ -315,7 +309,7 @@ summary(m.L1.SFO)
 <pre><code class="r">mkinresplot(m.L1.SFO, ylab = &quot;Observed&quot;, xlab = &quot;Time&quot;)
 </code></pre>
 
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alt="plot of chunk unnamed-chunk-5"/> </p>
+<p><img 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alt="plot of chunk unnamed-chunk-5"/> </p>
 
 <p>For comparison, the FOMC model is fitted as well, and the chi<sup>2</sup> error level
 is checked.</p>
@@ -326,15 +320,15 @@ summary(m.L1.FOMC, data = FALSE)
 
 <pre><code>## mkin version:    0.9.32 
 ## R version:       3.1.1 
-## Date of fit:     Mon Jul 21 09:14:30 2014 
-## Date of summary: Mon Jul 21 09:14:30 2014 
+## Date of fit:     Thu Jul 24 10:32:10 2014 
+## Date of summary: Thu Jul 24 10:32:11 2014 
 ## 
 ## Equations:
 ## [1] 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 0.32 s
+## Fitted with method Marq using 53 model solutions performed in 0.321 s
 ## 
 ## Weighting: none
 ## 
@@ -420,15 +414,15 @@ summary(m.L2.SFO)
 
 <pre><code>## mkin version:    0.9.32 
 ## R version:       3.1.1 
-## Date of fit:     Mon Jul 21 09:14:30 2014 
-## Date of summary: Mon Jul 21 09:14:30 2014 
+## Date of fit:     Thu Jul 24 10:32:11 2014 
+## Date of summary: Thu Jul 24 10:32:11 2014 
 ## 
 ## Equations:
 ## [1] d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 29 model solutions performed in 0.155 s
+## Fitted with method Marq using 29 model solutions performed in 0.196 s
 ## 
 ## Weighting: none
 ## 
@@ -502,7 +496,7 @@ plot(m.L2.SFO)
 mkinresplot(m.L2.SFO)
 </code></pre>
 
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alt="plot of chunk unnamed-chunk-9"/> </p>
 
 <p>In the FOCUS kinetics report, it is stated that there is no apparent systematic
 error observed from the residual plot up to the measured DT90 (approximately at
@@ -523,22 +517,22 @@ plot(m.L2.FOMC)
 mkinresplot(m.L2.FOMC)
 </code></pre>
 
-<p><img 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alt="plot of chunk unnamed-chunk-10"/> </p>
 
 <pre><code class="r">summary(m.L2.FOMC, data = FALSE)
 </code></pre>
 
 <pre><code>## mkin version:    0.9.32 
 ## R version:       3.1.1 
-## Date of fit:     Mon Jul 21 09:14:31 2014 
-## Date of summary: Mon Jul 21 09:14:31 2014 
+## Date of fit:     Thu Jul 24 10:32:11 2014 
+## Date of summary: Thu Jul 24 10:32:11 2014 
 ## 
 ## Equations:
 ## [1] 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 0.199 s
+## Fitted with method Marq using 35 model solutions performed in 0.223 s
 ## 
 ## Weighting: none
 ## 
@@ -616,15 +610,15 @@ plot(m.L2.DFOP)
 
 <pre><code>## mkin version:    0.9.32 
 ## R version:       3.1.1 
-## Date of fit:     Mon Jul 21 09:14:31 2014 
-## Date of summary: Mon Jul 21 09:14:31 2014 
+## Date of fit:     Thu Jul 24 10:32:12 2014 
+## Date of summary: Thu Jul 24 10:32:12 2014 
 ## 
 ## Equations:
 ## [1] 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 0.241 s
+## Fitted with method Marq using 43 model solutions performed in 0.271 s
 ## 
 ## Weighting: none
 ## 
@@ -703,15 +697,15 @@ plot(m.L3.SFO)
 
 <pre><code>## mkin version:    0.9.32 
 ## R version:       3.1.1 
-## Date of fit:     Mon Jul 21 09:14:32 2014 
-## Date of summary: Mon Jul 21 09:14:32 2014 
+## Date of fit:     Thu Jul 24 10:32:14 2014 
+## Date of summary: Thu Jul 24 10:32:14 2014 
 ## 
 ## Equations:
 ## [1] d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 44 model solutions performed in 0.242 s
+## Fitted with method Marq using 44 model solutions performed in 0.251 s
 ## 
 ## Weighting: none
 ## 
@@ -789,15 +783,15 @@ plot(m.L3.FOMC)
 
 <pre><code>## mkin version:    0.9.32 
 ## R version:       3.1.1 
-## Date of fit:     Mon Jul 21 09:14:32 2014 
-## Date of summary: Mon Jul 21 09:14:32 2014 
+## Date of fit:     Thu Jul 24 10:32:14 2014 
+## Date of summary: Thu Jul 24 10:32:14 2014 
 ## 
 ## Equations:
 ## [1] 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 0.143 s
+## Fitted with method Marq using 26 model solutions performed in 0.154 s
 ## 
 ## Weighting: none
 ## 
@@ -862,15 +856,15 @@ plot(m.L3.DFOP)
 
 <pre><code>## mkin version:    0.9.32 
 ## R version:       3.1.1 
-## Date of fit:     Mon Jul 21 09:14:32 2014 
-## Date of summary: Mon Jul 21 09:14:32 2014 
+## Date of fit:     Thu Jul 24 10:32:14 2014 
+## Date of summary: Thu Jul 24 10:32:14 2014 
 ## 
 ## Equations:
 ## [1] 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 0.21 s
+## Fitted with method Marq using 37 model solutions performed in 0.228 s
 ## 
 ## Weighting: none
 ## 
@@ -958,15 +952,15 @@ plot(m.L4.SFO)
 
 <pre><code>## mkin version:    0.9.32 
 ## R version:       3.1.1 
-## Date of fit:     Mon Jul 21 09:14:33 2014 
-## Date of summary: Mon Jul 21 09:14:33 2014 
+## Date of fit:     Thu Jul 24 10:32:15 2014 
+## Date of summary: Thu Jul 24 10:32:15 2014 
 ## 
 ## Equations:
 ## [1] d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Marq using 20 model solutions performed in 0.109 s
+## Fitted with method Marq using 20 model solutions performed in 0.141 s
 ## 
 ## Weighting: none
 ## 
@@ -1033,15 +1027,15 @@ plot(m.L4.FOMC)
 
 <pre><code>## mkin version:    0.9.32 
 ## R version:       3.1.1 
-## Date of fit:     Mon Jul 21 09:14:33 2014 
-## Date of summary: Mon Jul 21 09:14:33 2014 
+## Date of fit:     Thu Jul 24 10:32:15 2014 
+## Date of summary: Thu Jul 24 10:32:15 2014 
 ## 
 ## Equations:
 ## [1] 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 0.26 s
+## Fitted with method Marq using 48 model solutions performed in 0.296 s
 ## 
 ## Weighting: none
 ## 
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index 43f3e2e2..f7b0a65a 100644
--- a/vignettes/FOCUS_Z.pdf
+++ b/vignettes/FOCUS_Z.pdf
diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
index b69ddddc..0cc413a1 100644
--- a/vignettes/mkin.pdf
+++ b/vignettes/mkin.pdf