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-rw-r--r--inst/web/Extract.mmkin.html24
-rw-r--r--inst/web/mccall81_245T.html6
-rw-r--r--inst/web/mkinfit.html8
-rw-r--r--inst/web/mkinmod.html61
-rw-r--r--inst/web/mkinpredict.html6
-rw-r--r--inst/web/summary.mkinfit.html6
-rw-r--r--inst/web/transform_odeparms.html6
-rw-r--r--inst/web/vignettes/FOCUS_Z.pdfbin224802 -> 224775 bytes
-rw-r--r--inst/web/vignettes/compiled_models.html34
-rw-r--r--inst/web/vignettes/mkin.pdfbin160268 -> 160268 bytes
-rw-r--r--vignettes/FOCUS_Z.pdfbin224802 -> 224775 bytes
-rw-r--r--vignettes/compiled_models.html34
-rw-r--r--vignettes/mkin.pdfbin160268 -> 160268 bytes
13 files changed, 79 insertions, 106 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
Binary files differ
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
Binary files differ
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index 1234de20..31480019 100644
--- a/vignettes/FOCUS_Z.pdf
+++ b/vignettes/FOCUS_Z.pdf
Binary files differ
diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html
index 92919da9..7722d95a 100644
--- a/vignettes/compiled_models.html
+++ b/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/vignettes/mkin.pdf b/vignettes/mkin.pdf
index 9c1a03f3..9f9f9af0 100644
--- a/vignettes/mkin.pdf
+++ b/vignettes/mkin.pdf
Binary files differ

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