Update staticdocsv0.9-41

10 files changed, 62 insertions, 89 deletions

diff --git a/inst/web/Extract.mmkin.html b/inst/web/Extract.mmkin.html
index c6ae3ef7..6a175a02 100644
--- a/inst/web/Extract.mmkin.html
+++ b/inst/web/Extract.mmkin.html
@@ -181,7 +181,7 @@ $calls
 
 $time
    user  system elapsed 
-  0.260   0.000   0.262 
+  0.268   0.000   0.269 
 
 $mkinmod
 <mkinmod> model generated with
@@ -367,7 +367,7 @@ function (P)
     }
     return(mC)
 }
-<environment: 0x2a98780>
+<environment: 0x2d96b00>
 
 $cost_notrans
 function (P) 
@@ -389,7 +389,7 @@ function (P)
         scaleVar = scaleVar)
     return(mC)
 }
-<environment: 0x2a98780>
+<environment: 0x2d96b00>
 
 $hessian_notrans
            parent_0     alpha       beta
@@ -455,7 +455,7 @@ $bparms.state
 99.66619 
 
 $date
-[1] "Mon Nov  9 09:05:53 2015"
+[1] "Mon Nov  9 10:11:49 2015"
 
 attr(,"class")
 [1] "mkinfit" "modFit" 
@@ -540,7 +540,7 @@ $calls
 
 $time
    user  system elapsed 
-  0.088   0.000   0.086 
+  0.112   0.000   0.112 
 
 $mkinmod
 <mkinmod> model generated with
@@ -727,7 +727,7 @@ function (P)
     }
     return(mC)
 }
-<environment: 0x2ca6db8>
+<environment: 0x2fa3d28>
 
 $cost_notrans
 function (P) 
@@ -749,7 +749,7 @@ function (P)
         scaleVar = scaleVar)
     return(mC)
 }
-<environment: 0x2ca6db8>
+<environment: 0x2fa3d28>
 
 $hessian_notrans
                   parent_0 k_parent_sink
@@ -812,7 +812,7 @@ $bparms.state
 99.17407 
 
 $date
-[1] "Mon Nov  9 09:05:53 2015"
+[1] "Mon Nov  9 10:11:48 2015"
 
 attr(,"class")
 [1] "mkinfit" "modFit" 
@@ -890,7 +890,7 @@ $calls
 
 $time
    user  system elapsed 
-  0.088   0.000   0.086 
+  0.112   0.000   0.112 
 
 $mkinmod
 <mkinmod> model generated with
@@ -1077,7 +1077,7 @@ function (P)
     }
     return(mC)
 }
-<environment: 0x2ca6db8>
+<environment: 0x2fa3d28>
 
 $cost_notrans
 function (P) 
@@ -1099,7 +1099,7 @@ function (P)
         scaleVar = scaleVar)
     return(mC)
 }
-<environment: 0x2ca6db8>
+<environment: 0x2fa3d28>
 
 $hessian_notrans
                   parent_0 k_parent_sink
@@ -1162,7 +1162,7 @@ $bparms.state
 99.17407 
 
 $date
-[1] "Mon Nov  9 09:05:53 2015"
+[1] "Mon Nov  9 10:11:48 2015"
 
 attr(,"class")
 [1] "mkinfit" "modFit" 
diff --git a/inst/web/mccall81_245T.html b/inst/web/mccall81_245T.html
index f7a454ca..cd8d4d73 100644
--- a/inst/web/mccall81_245T.html
+++ b/inst/web/mccall81_245T.html
@@ -114,8 +114,8 @@
 </div>
 <div class='output'>mkin version:    0.9.41 
 R version:       3.2.2 
-Date of fit:     Mon Nov  9 09:06:00 2015 
-Date of summary: Mon Nov  9 09:06:00 2015 
+Date of fit:     Mon Nov  9 10:11:56 2015 
+Date of summary: Mon Nov  9 10:11:56 2015 
 
 Equations:
 d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -124,7 +124,7 @@ d_anisole = + k_phenol_anisole * phenol - k_anisole_sink * anisole
 
 Model predictions using solution type deSolve 
 
-Fitted with method Port using 246 model solutions performed in 1.372 s
+Fitted with method Port using 246 model solutions performed in 1.39 s
 
 Weighting: none
 
diff --git a/inst/web/mkinfit.html b/inst/web/mkinfit.html
index 96bdf95f..0550ee65 100644
--- a/inst/web/mkinfit.html
+++ b/inst/web/mkinfit.html
@@ -317,15 +317,15 @@ summary(fit)
 </div>
 <div class='output'>mkin version:    0.9.41 
 R version:       3.2.2 
-Date of fit:     Mon Nov  9 09:06:03 2015 
-Date of summary: Mon Nov  9 09:06:03 2015 
+Date of fit:     Mon Nov  9 10:11:58 2015 
+Date of summary: Mon Nov  9 10:11:58 2015 
 
 Equations:
 d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 
 Model predictions using solution type analytical 
 
-Fitted with method Port using 64 model solutions performed in 0.18 s
+Fitted with method Port using 64 model solutions performed in 0.194 s
 
 Weighting: none
 
@@ -401,7 +401,7 @@ print(system.time(fit &lt;- mkinfit(SFO_SFO, FOCUS_2006_D,
                            solution_type = &quot;eigen&quot;, quiet = TRUE)))
 </div>
 <div class='output'>   user  system elapsed 
-  1.180   1.196   0.889 
+  1.188   1.228   0.910 
 </div>
 <div class='input'>coef(fit)
 </div>
diff --git a/inst/web/mkinmod.html b/inst/web/mkinmod.html
index 797e96d5..7b43beb7 100644
--- a/inst/web/mkinmod.html
+++ b/inst/web/mkinmod.html
@@ -170,51 +170,24 @@ SFO_SFO &lt;- mkinmod(
 </div>
 <strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong>
 <div class='input'>
-# The above model used to be specified like this, before the advent of mkinsub()
-SFO_SFO &lt;- mkinmod(
-  parent = list(type = &quot;SFO&quot;, to = &quot;m1&quot;),
-  m1 = list(type = &quot;SFO&quot;))
-</div>
-<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong>
-<div class='input'>
-# Show details of creating the C function
-SFO_SFO &lt;- mkinmod(
-  parent = mkinsub(&quot;SFO&quot;, &quot;m1&quot;),
-  m1 = mkinsub(&quot;SFO&quot;), verbose = TRUE)
-</div>
-<div class='output'>Compilation argument:
- /usr/lib/R/bin/R CMD SHLIB file16d352645eb9.c 2&gt; file16d352645eb9.c.err.txt 
-Program source:
-  1: #include &lt;R.h&gt;
-  2: 
-  3: 
-  4: static double parms [3];
-  5: #define k_parent_sink parms[0]
-  6: #define k_parent_m1 parms[1]
-  7: #define k_m1_sink parms[2]
-  8: 
-  9: void initpar(void (* odeparms)(int *, double *)) {
- 10:     int N = 3;
- 11:     odeparms(&amp;N, parms);
- 12: }
- 13: 
- 14: 
- 15: void func ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) {
- 16: 
- 17: f[0] = - k_parent_sink * y[0] - k_parent_m1 * y[0];
- 18: f[1] = + k_parent_m1 * y[0] - k_m1_sink * y[1];
- 19: }
-</div>
-<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong>
-<div class='input'>
-# If we have several parallel metabolites 
-# (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)
-m_synth_DFOP_par &lt;- mkinmod(parent = mkinsub(&quot;DFOP&quot;, c(&quot;M1&quot;, &quot;M2&quot;)),
-                           M1 = mkinsub(&quot;SFO&quot;),
-                           M2 = mkinsub(&quot;SFO&quot;),
-                           use_of_ff = &quot;max&quot;, quiet = TRUE)
-
 ## Not run: 
+# # The above model used to be specified like this, before the advent of mkinsub()
+# SFO_SFO &lt;- mkinmod(
+#   parent = list(type = &quot;SFO&quot;, to = &quot;m1&quot;),
+#   m1 = list(type = &quot;SFO&quot;))
+# 
+# # Show details of creating the C function
+# SFO_SFO &lt;- mkinmod(
+#   parent = mkinsub(&quot;SFO&quot;, &quot;m1&quot;),
+#   m1 = mkinsub(&quot;SFO&quot;), verbose = TRUE)
+# 
+# # If we have several parallel metabolites 
+# # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)
+# m_synth_DFOP_par &lt;- mkinmod(parent = mkinsub(&quot;DFOP&quot;, c(&quot;M1&quot;, &quot;M2&quot;)),
+#                            M1 = mkinsub(&quot;SFO&quot;),
+#                            M2 = mkinsub(&quot;SFO&quot;),
+#                            use_of_ff = &quot;max&quot;, quiet = TRUE)
+# 
 # fit_DFOP_par_c &lt;- mkinfit(m_synth_DFOP_par, 
 #                           synthetic_data_for_UBA_2014[[12]]$data,
 #                           quiet = TRUE)
diff --git a/inst/web/mkinpredict.html b/inst/web/mkinpredict.html
index 3a6300d0..900ee26f 100644
--- a/inst/web/mkinpredict.html
+++ b/inst/web/mkinpredict.html
@@ -304,7 +304,7 @@
 201   20 4.978707 27.46227
 </div>
 <div class='output'>   user  system elapsed 
-  0.008   0.024   0.004 
+  0.004   0.028   0.005 
 </div>
 <div class='input'>  system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
@@ -315,7 +315,7 @@
 201   20 4.978707 27.46227
 </div>
 <div class='output'>   user  system elapsed 
-  0.004   0.020   0.002 
+  0.020   0.000   0.003 
 </div>
 <div class='input'>  system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
@@ -326,7 +326,7 @@
 201   20 4.978707 27.46227
 </div>
 <div class='output'>   user  system elapsed 
-  0.064   0.000   0.066 
+  0.092   0.000   0.092 
 </div></pre>
   </div>
   <div class="span4">
diff --git a/inst/web/summary.mkinfit.html b/inst/web/summary.mkinfit.html
index 02469bb6..2958b020 100644
--- a/inst/web/summary.mkinfit.html
+++ b/inst/web/summary.mkinfit.html
@@ -159,15 +159,15 @@
 </div>
 <div class='output'>mkin version:    0.9.41 
 R version:       3.2.2 
-Date of fit:     Mon Nov  9 09:06:13 2015 
-Date of summary: Mon Nov  9 09:06:13 2015 
+Date of fit:     Mon Nov  9 10:12:08 2015 
+Date of summary: Mon Nov  9 10:12:08 2015 
 
 Equations:
 d_parent = - k_parent_sink * parent
 
 Model predictions using solution type analytical 
 
-Fitted with method Port using 35 model solutions performed in 0.1 s
+Fitted with method Port using 35 model solutions performed in 0.105 s
 
 Weighting: none
 
diff --git a/inst/web/transform_odeparms.html b/inst/web/transform_odeparms.html
index 25dcaba9..36dfecf8 100644
--- a/inst/web/transform_odeparms.html
+++ b/inst/web/transform_odeparms.html
@@ -135,8 +135,8 @@ summary(fit, data=FALSE) # See transformed and backtransformed parameters
 </div>
 <div class='output'>mkin version:    0.9.41 
 R version:       3.2.2 
-Date of fit:     Mon Nov  9 09:06:14 2015 
-Date of summary: Mon Nov  9 09:06:14 2015 
+Date of fit:     Mon Nov  9 10:12:09 2015 
+Date of summary: Mon Nov  9 10:12:09 2015 
 
 Equations:
 d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -144,7 +144,7 @@ d_m1 = + k_parent_m1 * parent - k_m1_sink * m1
 
 Model predictions using solution type deSolve 
 
-Fitted with method Port using 153 model solutions performed in 0.619 s
+Fitted with method Port using 153 model solutions performed in 0.632 s
 
 Weighting: none
 
diff --git a/inst/web/vignettes/FOCUS_Z.pdf b/inst/web/vignettes/FOCUS_Z.pdf
index 1234de20..31480019 100644
--- a/inst/web/vignettes/FOCUS_Z.pdf
+++ b/inst/web/vignettes/FOCUS_Z.pdf
diff --git a/inst/web/vignettes/compiled_models.html b/inst/web/vignettes/compiled_models.html
index 92919da9..7722d95a 100644
--- a/inst/web/vignettes/compiled_models.html
+++ b/inst/web/vignettes/compiled_models.html
@@ -99,18 +99,18 @@ smb.1 &lt;- summary(mb.1)[-1]
 rownames(smb.1) &lt;- c(&quot;deSolve, not compiled&quot;, &quot;Eigenvalue based&quot;, &quot;deSolve, compiled&quot;)
 print(smb.1)</code></pre>
 <pre><code>##                             min        lq      mean    median        uq
-## deSolve, not compiled 9307.3194 9319.9546 9332.8171 9332.5899 9345.5659
-## Eigenvalue based       855.3608  855.8081  869.4725  856.2555  876.5283
-## deSolve, compiled      686.6143  687.9256  698.0279  689.2369  703.7346
+## deSolve, not compiled 9442.5119 9447.2060 9458.3420 9451.9001 9466.2571
+## Eigenvalue based       868.6312  872.4552  895.3422  876.2792  908.6977
+## deSolve, compiled      691.9663  697.5653  701.1004  703.1643  705.6674
 ##                             max neval cld
-## deSolve, not compiled 9358.5420     3   c
-## Eigenvalue based       896.8012     3  b 
-## deSolve, compiled      718.2324     3 a</code></pre>
-<p>We see that using the compiled model is by a factor of 13.5 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:</p>
+## deSolve, not compiled 9480.6141     3   c
+## Eigenvalue based       941.1163     3  b 
+## deSolve, compiled      708.1706     3 a</code></pre>
+<p>We see that using the compiled model is by a factor of 13.4 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:</p>
 <pre class="r"><code>smb.1[&quot;median&quot;]/smb.1[&quot;deSolve, compiled&quot;, &quot;median&quot;]</code></pre>
 <pre><code>##                          median
-## deSolve, not compiled 13.540468
-## Eigenvalue based       1.242324
+## deSolve, not compiled 13.441951
+## Eigenvalue based       1.246194
 ## deSolve, compiled      1.000000</code></pre>
 </div>
 <div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level2">
@@ -127,17 +127,17 @@ print(smb.1)</code></pre>
 smb.2 &lt;- summary(mb.2)[-1]
 rownames(smb.2) &lt;- c(&quot;deSolve, not compiled&quot;, &quot;deSolve, compiled&quot;)
 print(smb.2)</code></pre>
-<pre><code>##                             min        lq      mean    median        uq
-## deSolve, not compiled 20.130709 20.147223 20.180429 20.163737 20.205289
-## deSolve, compiled      1.235864  1.255748  1.267458  1.275632  1.283255
-##                             max neval cld
-## deSolve, not compiled 20.246841     3   b
-## deSolve, compiled      1.290878     3  a</code></pre>
+<pre><code>##                             min       lq      mean    median        uq
+## deSolve, not compiled 20.444632 20.48824 20.557595 20.531857 20.614077
+## deSolve, compiled      1.251733  1.25179  1.275227  1.251846  1.286973
+##                           max neval cld
+## deSolve, not compiled 20.6963     3   b
+## deSolve, compiled      1.3221     3  a</code></pre>
 <pre class="r"><code>smb.2[&quot;median&quot;]/smb.2[&quot;deSolve, compiled&quot;, &quot;median&quot;]</code></pre>
 <pre><code>##                         median
-## deSolve, not compiled 15.80686
+## deSolve, not compiled 16.40126
 ## deSolve, compiled      1.00000</code></pre>
-<p>Here we get a performance benefit of a factor of 15.8 using the version of the differential equation model compiled from C code using the inline package!</p>
+<p>Here we get a performance benefit of a factor of 16.4 using the version of the differential equation model compiled from C code using the inline package!</p>
 <p>This vignette was built with mkin 0.9.41 on</p>
 <pre><code>## R version 3.2.2 (2015-08-14)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/inst/web/vignettes/mkin.pdf b/inst/web/vignettes/mkin.pdf
index 9c1a03f3..9f9f9af0 100644
--- a/inst/web/vignettes/mkin.pdf
+++ b/inst/web/vignettes/mkin.pdf