aboutsummaryrefslogtreecommitdiff
path: root/vignettes
diff options
context:
space:
mode:
authorJohannes Ranke <jranke@uni-bremen.de>2015-06-21 01:46:51 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2015-06-21 15:23:20 +0200
commit6733555d7a9315c55001770bacc4c61c4d4f39d5 (patch)
treef645a69a54fa6b58cfd65ed581d5f2b88950f6d6 /vignettes
parentf0da2e311eb33fa5851956e958e91c25b4da5c1e (diff)
Do the t-test for untransformed parametersv0.9-36
Diffstat (limited to 'vignettes')
-rw-r--r--vignettes/FOCUS_D.html50
-rw-r--r--vignettes/FOCUS_L.html357
-rw-r--r--vignettes/FOCUS_Z.Rnw2
-rw-r--r--vignettes/FOCUS_Z.pdfbin215014 -> 224256 bytes
-rw-r--r--vignettes/compiled_models.html42
-rw-r--r--vignettes/mkin.pdfbin160260 -> 160260 bytes
6 files changed, 232 insertions, 219 deletions
diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html
index 6573cc7a..b1ea64ea 100644
--- a/vignettes/FOCUS_D.html
+++ b/vignettes/FOCUS_D.html
@@ -215,13 +215,7 @@ library we look a the data. We have observed concentrations in the column named
named <code>parent</code> and <code>m1</code>.</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">print(FOCUS_2006_D)
+print(FOCUS_2006_D)
</code></pre>
<pre><code>## name time value
@@ -276,7 +270,7 @@ kinetics (SFO) to one metabolite named m1, which also degrades with SFO kinetics
<p>The call to mkinmod returns a degradation model. The differential equations represented in
R code can be found in the character vector <code>$diffs</code> of the <code>mkinmod</code> object. If
-the <code>ccSolve</code> package is installed and functional, the differential equation model
+the gcc compiler is installed and functional, the differential equation model
will be compiled from auto-generated C code.</p>
<pre><code class="r">SFO_SFO &lt;- mkinmod(parent = mkinsub(&quot;SFO&quot;, &quot;m1&quot;), m1 = mkinsub(&quot;SFO&quot;))
@@ -312,7 +306,7 @@ using the <code>plot</code> method for <code>mkinfit</code> objects.</p>
<pre><code class="r">mkinparplot(fit)
</code></pre>
-<p><img src="data:image/png;base64,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" alt="plot of chunk unnamed-chunk-6"/> </p>
+<p><img src="data:image/png;base64,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" alt="plot of chunk unnamed-chunk-6"/> </p>
<p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code>
objects.</p>
@@ -321,9 +315,9 @@ objects.</p>
</code></pre>
<pre><code>## mkin version: 0.9.36
-## R version: 3.2.0
-## Date of fit: Fri Jun 5 14:20:31 2015
-## Date of summary: Fri Jun 5 14:20:31 2015
+## R version: 3.2.1
+## Date of fit: Sun Jun 21 01:47:59 2015
+## Date of summary: Sun Jun 21 01:47:59 2015
##
## Equations:
## d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -331,7 +325,7 @@ objects.</p>
##
## Model predictions using solution type deSolve
##
-## Fitted with method Port using 153 model solutions performed in 0.621 s
+## Fitted with method Port using 153 model solutions performed in 0.698 s
##
## Weighting: none
##
@@ -353,17 +347,12 @@ objects.</p>
## value type
## m1_0 0 state
##
-## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper t value Pr(&gt;|t|)
-## parent_0 99.600 1.61400 96.330 102.900 61.72 4.048e-38
-## log_k_parent_sink -3.038 0.07826 -3.197 -2.879 -38.82 5.601e-31
-## log_k_parent_m1 -2.980 0.04124 -3.064 -2.897 -72.27 1.446e-40
-## log_k_m1_sink -5.248 0.13610 -5.523 -4.972 -38.56 7.087e-31
-## Pr(&gt;t)
-## parent_0 2.024e-38
-## log_k_parent_sink 2.800e-31
-## log_k_parent_m1 7.228e-41
-## log_k_m1_sink 3.543e-31
+## Optimised, transformed parameters with symmetric confidence intervals:
+## Estimate Std. Error Lower Upper
+## parent_0 99.600 1.61400 96.330 102.900
+## log_k_parent_sink -3.038 0.07826 -3.197 -2.879
+## log_k_parent_m1 -2.980 0.04124 -3.064 -2.897
+## log_k_m1_sink -5.248 0.13610 -5.523 -4.972
##
## Parameter correlation:
## parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
@@ -375,11 +364,14 @@ objects.</p>
## Residual standard error: 3.211 on 36 degrees of freedom
##
## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 99.600000 96.330000 1.029e+02
-## k_parent_sink 0.047920 0.040890 5.616e-02
-## k_parent_m1 0.050780 0.046700 5.521e-02
-## k_m1_sink 0.005261 0.003992 6.933e-03
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
+## Estimate t value Pr(&gt;t) Lower Upper
+## parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02
+## k_parent_sink 0.047920 12.780 3.050e-15 0.040890 5.616e-02
+## k_parent_m1 0.050780 24.250 3.407e-24 0.046700 5.521e-02
+## k_m1_sink 0.005261 7.349 5.758e-09 0.003992 6.933e-03
##
## Chi2 error levels in percent:
## err.min n.optim df
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index 96ea70ce..692caf93 100644
--- a/vignettes/FOCUS_L.html
+++ b/vignettes/FOCUS_L.html
@@ -214,13 +214,7 @@ 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,
@@ -242,17 +236,17 @@ given in the FOCUS report. </p>
summary(m.L1.SFO)
</code></pre>
-<pre><code>## mkin version: 0.9.35
-## R version: 3.1.2
-## Date of fit: Sat Feb 21 14:44:53 2015
-## Date of summary: Sat Feb 21 14:44:53 2015
+<pre><code>## mkin version: 0.9.36
+## R version: 3.2.1
+## Date of fit: Sun Jun 21 01:47:59 2015
+## Date of summary: Sun Jun 21 01:47:59 2015
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 37 model solutions performed in 0.098 s
+## Fitted with method Port using 37 model solutions performed in 0.093 s
##
## Weighting: none
##
@@ -269,13 +263,10 @@ summary(m.L1.SFO)
## Fixed parameter values:
## None
##
-## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper t value Pr(&gt;|t|)
-## parent_0 92.470 1.36800 89.570 95.370 67.58 4.339e-21
-## log_k_parent_sink -2.347 0.04057 -2.433 -2.261 -57.86 5.155e-20
-## Pr(&gt;t)
-## parent_0 2.170e-21
-## log_k_parent_sink 2.577e-20
+## Optimised, transformed parameters with symmetric confidence intervals:
+## Estimate Std. Error Lower Upper
+## parent_0 92.470 1.36800 89.570 95.370
+## log_k_parent_sink -2.347 0.04057 -2.433 -2.261
##
## Parameter correlation:
## parent_0 log_k_parent_sink
@@ -285,9 +276,12 @@ summary(m.L1.SFO)
## Residual standard error: 2.948 on 16 degrees of freedom
##
## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 92.47000 89.57000 95.3700
-## k_parent_sink 0.09561 0.08773 0.1042
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
+## Estimate t value Pr(&gt;t) Lower Upper
+## parent_0 92.47000 67.58 2.170e-21 89.57000 95.3700
+## k_parent_sink 0.09561 24.65 1.867e-14 0.08773 0.1042
##
## Chi2 error levels in percent:
## err.min n.optim df
@@ -341,20 +335,31 @@ The residual plot can be easily obtained by</p>
is checked.</p>
<pre><code class="r">m.L1.FOMC &lt;- mkinfit(&quot;FOMC&quot;, FOCUS_2006_L1_mkin, quiet=TRUE)
-summary(m.L1.FOMC, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.35
-## R version: 3.1.2
-## Date of fit: Sat Feb 21 14:44:55 2015
-## Date of summary: Sat Feb 21 14:44:55 2015
+<pre><code>## Warning in mkinfit(&quot;FOMC&quot;, FOCUS_2006_L1_mkin, quiet = TRUE): Optimisation by method Port did not converge.
+## Convergence code is 1
+</code></pre>
+
+<pre><code class="r">summary(m.L1.FOMC, data = FALSE)
+</code></pre>
+
+<pre><code>## mkin version: 0.9.36
+## R version: 3.2.1
+## Date of fit: Sun Jun 21 01:48:00 2015
+## Date of summary: Sun Jun 21 01:48:00 2015
+##
+##
+## Warning: Optimisation by method Port did not converge.
+## Convergence code is 1
+##
##
## Equations:
-## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
+## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 611 model solutions performed in 1.509 s
+## Fitted with method Port using 188 model solutions performed in 0.463 s
##
## Weighting: none
##
@@ -373,29 +378,28 @@ summary(m.L1.FOMC, data = FALSE)
## Fixed parameter values:
## None
##
-## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper t value Pr(&gt;|t|)
-## parent_0 92.47 1.482 89.31 95.63 62.39000 1.546e-19
-## log_alpha 11.25 598.200 -1264.00 1286.00 0.01880 9.852e-01
-## log_beta 13.60 598.200 -1261.00 1289.00 0.02273 9.822e-01
-## Pr(&gt;t)
-## parent_0 7.730e-20
-## log_alpha 4.926e-01
-## log_beta 4.911e-01
+## Optimised, transformed parameters with symmetric confidence intervals:
+## Estimate Std. Error Lower Upper
+## parent_0 92.47 1.422 89.44 95.50
+## log_alpha 15.43 15.080 -16.71 47.58
+## log_beta 17.78 15.090 -14.37 49.93
##
## Parameter correlation:
## parent_0 log_alpha log_beta
-## parent_0 1.0000 -0.3016 -0.3016
-## log_alpha -0.3016 1.0000 1.0000
-## log_beta -0.3016 1.0000 1.0000
+## parent_0 1.0000 0.1129 0.1112
+## log_alpha 0.1129 1.0000 1.0000
+## log_beta 0.1112 1.0000 1.0000
##
## Residual standard error: 3.045 on 15 degrees of freedom
##
## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 92.47 89.31 95.63
-## alpha 76830.00 0.00 Inf
-## beta 803500.00 0.00 Inf
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
+## Estimate t value Pr(&gt;t) Lower Upper
+## parent_0 9.247e+01 65.150 4.044e-20 8.944e+01 9.550e+01
+## alpha 5.044e+06 1.271 1.115e-01 5.510e-08 4.618e+20
+## beta 5.276e+07 1.259 1.137e-01 5.732e-07 4.857e+21
##
## Chi2 error levels in percent:
## err.min n.optim df
@@ -403,8 +407,8 @@ summary(m.L1.FOMC, data = FALSE)
## parent 3.619 3 6
##
## Estimated disappearance times:
-## DT50 DT90 DT50back
-## parent 7.249 24.08 7.249
+## DT50 DT90 DT50back
+## parent 7.25 24.08 7.25
</code></pre>
<p>Due to the higher number of parameters, and the lower number of degrees of
@@ -442,17 +446,17 @@ FOCUS_2006_L2_mkin &lt;- mkin_wide_to_long(FOCUS_2006_L2)
summary(m.L2.SFO)
</code></pre>
-<pre><code>## mkin version: 0.9.35
-## R version: 3.1.2
-## Date of fit: Sat Feb 21 14:44:55 2015
-## Date of summary: Sat Feb 21 14:44:55 2015
+<pre><code>## mkin version: 0.9.36
+## R version: 3.2.1
+## Date of fit: Sun Jun 21 01:48:00 2015
+## Date of summary: Sun Jun 21 01:48:00 2015
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 41 model solutions performed in 0.1 s
+## Fitted with method Port using 41 model solutions performed in 0.097 s
##
## Weighting: none
##
@@ -469,13 +473,10 @@ summary(m.L2.SFO)
## Fixed parameter values:
## None
##
-## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper t value Pr(&gt;|t|)
-## parent_0 91.4700 3.8070 82.9800 99.9500 24.030 3.545e-10
-## log_k_parent_sink -0.4112 0.1074 -0.6505 -0.1719 -3.828 3.329e-03
-## Pr(&gt;t)
-## parent_0 1.773e-10
-## log_k_parent_sink 1.664e-03
+## Optimised, transformed parameters with symmetric confidence intervals:
+## Estimate Std. Error Lower Upper
+## parent_0 91.4700 3.8070 82.9800 99.9500
+## log_k_parent_sink -0.4112 0.1074 -0.6505 -0.1719
##
## Parameter correlation:
## parent_0 log_k_parent_sink
@@ -485,9 +486,12 @@ summary(m.L2.SFO)
## Residual standard error: 5.51 on 10 degrees of freedom
##
## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 91.4700 82.9800 99.9500
-## k_parent_sink 0.6629 0.5218 0.8421
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
+## Estimate t value Pr(&gt;t) Lower Upper
+## parent_0 91.4700 24.03 1.773e-10 82.9800 99.9500
+## k_parent_sink 0.6629 9.31 1.525e-06 0.5218 0.8421
##
## Chi2 error levels in percent:
## err.min n.optim df
@@ -552,17 +556,17 @@ mkinresplot(m.L2.FOMC)
<pre><code class="r">summary(m.L2.FOMC, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.35
-## R version: 3.1.2
-## Date of fit: Sat Feb 21 14:44:55 2015
-## Date of summary: Sat Feb 21 14:44:55 2015
+<pre><code>## mkin version: 0.9.36
+## R version: 3.2.1
+## Date of fit: Sun Jun 21 01:48:00 2015
+## Date of summary: Sun Jun 21 01:48:00 2015
##
## Equations:
-## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
+## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 81 model solutions performed in 0.201 s
+## Fitted with method Port using 81 model solutions performed in 0.191 s
##
## Weighting: none
##
@@ -581,11 +585,11 @@ mkinresplot(m.L2.FOMC)
## Fixed parameter values:
## None
##
-## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper t value Pr(&gt;|t|) Pr(&gt;t)
-## parent_0 93.7700 1.8560 89.5700 97.9700 50.5100 2.345e-12 1.173e-12
-## log_alpha 0.3180 0.1867 -0.1044 0.7405 1.7030 1.227e-01 6.137e-02
-## log_beta 0.2102 0.2943 -0.4555 0.8759 0.7142 4.932e-01 2.466e-01
+## Optimised, transformed parameters with symmetric confidence intervals:
+## Estimate Std. Error Lower Upper
+## parent_0 93.7700 1.8560 89.5700 97.9700
+## log_alpha 0.3180 0.1867 -0.1044 0.7405
+## log_beta 0.2102 0.2943 -0.4555 0.8759
##
## Parameter correlation:
## parent_0 log_alpha log_beta
@@ -596,10 +600,13 @@ mkinresplot(m.L2.FOMC)
## Residual standard error: 2.628 on 9 degrees of freedom
##
## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 93.770 89.5700 97.970
-## alpha 1.374 0.9009 2.097
-## beta 1.234 0.6341 2.401
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
+## Estimate t value Pr(&gt;t) Lower Upper
+## parent_0 93.770 50.510 1.173e-12 89.5700 97.970
+## alpha 1.374 5.355 2.296e-04 0.9009 2.097
+## beta 1.234 3.398 3.949e-03 0.6341 2.401
##
## Chi2 error levels in percent:
## err.min n.optim df
@@ -638,10 +645,10 @@ plot(m.L2.DFOP)
<pre><code class="r">summary(m.L2.DFOP, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.35
-## R version: 3.1.2
-## Date of fit: Sat Feb 21 14:44:57 2015
-## Date of summary: Sat Feb 21 14:44:57 2015
+<pre><code>## mkin version: 0.9.36
+## R version: 3.2.1
+## Date of fit: Sun Jun 21 01:48:02 2015
+## Date of summary: Sun Jun 21 01:48:02 2015
##
## Equations:
## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -650,7 +657,7 @@ plot(m.L2.DFOP)
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 336 model solutions performed in 0.856 s
+## Fitted with method Port using 336 model solutions performed in 0.835 s
##
## Weighting: none
##
@@ -671,12 +678,12 @@ plot(m.L2.DFOP)
## Fixed parameter values:
## None
##
-## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper t value Pr(&gt;|t|) Pr(&gt;t)
-## parent_0 93.9500 NA NA NA NA NA NA
-## log_k1 3.1210 NA NA NA NA NA NA
-## log_k2 -1.0880 NA NA NA NA NA NA
-## g_ilr -0.2821 NA NA NA NA NA NA
+## Optimised, transformed parameters with symmetric confidence intervals:
+## Estimate Std. Error Lower Upper
+## parent_0 93.9500 NA NA NA
+## log_k1 3.1210 NA NA NA
+## log_k2 -1.0880 NA NA NA
+## g_ilr -0.2821 NA NA NA
##
## Parameter correlation:
## Could not estimate covariance matrix; singular system:
@@ -684,11 +691,14 @@ plot(m.L2.DFOP)
## Residual standard error: 1.732 on 8 degrees of freedom
##
## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 93.9500 NA NA
-## k1 22.6700 NA NA
-## k2 0.3369 NA NA
-## g 0.4016 NA NA
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
+## Estimate t value Pr(&gt;t) Lower Upper
+## parent_0 93.9500 NA NA NA NA
+## k1 22.6700 NA NA NA NA
+## k2 0.3369 NA NA NA NA
+## g 0.4016 NA NA NA NA
##
## Chi2 error levels in percent:
## err.min n.optim df
@@ -727,17 +737,17 @@ plot(m.L3.SFO)
<pre><code class="r">summary(m.L3.SFO)
</code></pre>
-<pre><code>## mkin version: 0.9.35
-## R version: 3.1.2
-## Date of fit: Sat Feb 21 14:44:57 2015
-## Date of summary: Sat Feb 21 14:44:57 2015
+<pre><code>## mkin version: 0.9.36
+## R version: 3.2.1
+## Date of fit: Sun Jun 21 01:48:03 2015
+## Date of summary: Sun Jun 21 01:48:03 2015
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 43 model solutions performed in 0.109 s
+## Fitted with method Port using 43 model solutions performed in 0.104 s
##
## Weighting: none
##
@@ -754,13 +764,10 @@ plot(m.L3.SFO)
## Fixed parameter values:
## None
##
-## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper t value Pr(&gt;|t|)
-## parent_0 74.870 8.4570 54.180 95.57 8.853 1.155e-04
-## log_k_parent_sink -3.678 0.3261 -4.476 -2.88 -11.280 2.903e-05
-## Pr(&gt;t)
-## parent_0 5.776e-05
-## log_k_parent_sink 1.451e-05
+## Optimised, transformed parameters with symmetric confidence intervals:
+## Estimate Std. Error Lower Upper
+## parent_0 74.870 8.4570 54.180 95.57
+## log_k_parent_sink -3.678 0.3261 -4.476 -2.88
##
## Parameter correlation:
## parent_0 log_k_parent_sink
@@ -770,9 +777,12 @@ plot(m.L3.SFO)
## Residual standard error: 12.91 on 6 degrees of freedom
##
## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 74.87000 54.18000 95.57000
-## k_parent_sink 0.02527 0.01138 0.05612
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
+## Estimate t value Pr(&gt;t) Lower Upper
+## parent_0 74.87000 8.853 5.776e-05 54.18000 95.57000
+## k_parent_sink 0.02527 3.067 1.102e-02 0.01138 0.05612
##
## Chi2 error levels in percent:
## err.min n.optim df
@@ -813,17 +823,17 @@ plot(m.L3.FOMC)
<pre><code class="r">summary(m.L3.FOMC, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.35
-## R version: 3.1.2
-## Date of fit: Sat Feb 21 14:44:58 2015
-## Date of summary: Sat Feb 21 14:44:58 2015
+<pre><code>## mkin version: 0.9.36
+## R version: 3.2.1
+## Date of fit: Sun Jun 21 01:48:03 2015
+## Date of summary: Sun Jun 21 01:48:03 2015
##
## Equations:
-## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
+## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 83 model solutions performed in 0.203 s
+## Fitted with method Port using 83 model solutions performed in 0.196 s
##
## Weighting: none
##
@@ -842,11 +852,11 @@ plot(m.L3.FOMC)
## Fixed parameter values:
## None
##
-## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper t value Pr(&gt;|t|) Pr(&gt;t)
-## parent_0 96.9700 4.5500 85.2800 108.7000 21.310 4.216e-06 2.108e-06
-## log_alpha -0.8619 0.1704 -1.3000 -0.4238 -5.057 3.911e-03 1.955e-03
-## log_beta 0.6193 0.4744 -0.6003 1.8390 1.305 2.486e-01 1.243e-01
+## Optimised, transformed parameters with symmetric confidence intervals:
+## Estimate Std. Error Lower Upper
+## parent_0 96.9700 4.5500 85.2800 108.7000
+## log_alpha -0.8619 0.1704 -1.3000 -0.4238
+## log_beta 0.6193 0.4744 -0.6003 1.8390
##
## Parameter correlation:
## parent_0 log_alpha log_beta
@@ -857,10 +867,13 @@ plot(m.L3.FOMC)
## Residual standard error: 4.572 on 5 degrees of freedom
##
## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 96.9700 85.2800 108.7000
-## alpha 0.4224 0.2725 0.6546
-## beta 1.8580 0.5487 6.2890
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
+## Estimate t value Pr(&gt;t) Lower Upper
+## parent_0 96.9700 21.310 2.108e-06 85.2800 108.7000
+## alpha 0.4224 5.867 1.020e-03 0.2725 0.6546
+## beta 1.8580 2.108 4.444e-02 0.5487 6.2890
##
## Chi2 error levels in percent:
## err.min n.optim df
@@ -886,10 +899,10 @@ plot(m.L3.DFOP)
<pre><code class="r">summary(m.L3.DFOP, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.35
-## R version: 3.1.2
-## Date of fit: Sat Feb 21 14:44:58 2015
-## Date of summary: Sat Feb 21 14:44:58 2015
+<pre><code>## mkin version: 0.9.36
+## R version: 3.2.1
+## Date of fit: Sun Jun 21 01:48:03 2015
+## Date of summary: Sun Jun 21 01:48:03 2015
##
## Equations:
## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -898,7 +911,7 @@ plot(m.L3.DFOP)
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 137 model solutions performed in 0.346 s
+## Fitted with method Port using 137 model solutions performed in 0.35 s
##
## Weighting: none
##
@@ -919,12 +932,12 @@ plot(m.L3.DFOP)
## Fixed parameter values:
## None
##
-## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper t value Pr(&gt;|t|) Pr(&gt;t)
-## parent_0 97.7500 1.43800 93.7500 101.70000 67.970 2.808e-07 1.404e-07
-## log_k1 -0.6612 0.13340 -1.0310 -0.29100 -4.958 7.715e-03 3.858e-03
-## log_k2 -4.2860 0.05902 -4.4500 -4.12200 -72.620 2.155e-07 1.077e-07
-## g_ilr -0.1229 0.05121 -0.2651 0.01925 -2.401 7.431e-02 3.716e-02
+## Optimised, transformed parameters with symmetric confidence intervals:
+## Estimate Std. Error Lower Upper
+## parent_0 97.7500 1.43800 93.7500 101.70000
+## log_k1 -0.6612 0.13340 -1.0310 -0.29100
+## log_k2 -4.2860 0.05902 -4.4500 -4.12200
+## g_ilr -0.1229 0.05121 -0.2651 0.01925
##
## Parameter correlation:
## parent_0 log_k1 log_k2 g_ilr
@@ -936,11 +949,14 @@ plot(m.L3.DFOP)
## Residual standard error: 1.439 on 4 degrees of freedom
##
## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 97.75000 93.75000 101.70000
-## k1 0.51620 0.35650 0.74750
-## k2 0.01376 0.01168 0.01621
-## g 0.45660 0.40730 0.50680
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
+## Estimate t value Pr(&gt;t) Lower Upper
+## parent_0 97.75000 67.970 1.404e-07 93.75000 101.70000
+## k1 0.51620 7.499 8.460e-04 0.35650 0.74750
+## k2 0.01376 16.940 3.557e-05 0.01168 0.01621
+## g 0.45660 25.410 7.121e-06 0.40730 0.50680
##
## Chi2 error levels in percent:
## err.min n.optim df
@@ -984,17 +1000,17 @@ plot(m.L4.SFO)
<pre><code class="r">summary(m.L4.SFO, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.35
-## R version: 3.1.2
-## Date of fit: Sat Feb 21 14:44:58 2015
-## Date of summary: Sat Feb 21 14:44:58 2015
+<pre><code>## mkin version: 0.9.36
+## R version: 3.2.1
+## Date of fit: Sun Jun 21 01:48:04 2015
+## Date of summary: Sun Jun 21 01:48:04 2015
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 46 model solutions performed in 0.109 s
+## Fitted with method Port using 46 model solutions performed in 0.105 s
##
## Weighting: none
##
@@ -1011,13 +1027,10 @@ plot(m.L4.SFO)
## Fixed parameter values:
## None
##
-## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper t value Pr(&gt;|t|)
-## parent_0 96.44 1.94900 91.670 101.200 49.49 4.566e-09
-## log_k_parent_sink -5.03 0.07999 -5.225 -4.834 -62.88 1.088e-09
-## Pr(&gt;t)
-## parent_0 2.283e-09
-## log_k_parent_sink 5.438e-10
+## Optimised, transformed parameters with symmetric confidence intervals:
+## Estimate Std. Error Lower Upper
+## parent_0 96.44 1.94900 91.670 101.200
+## log_k_parent_sink -5.03 0.07999 -5.225 -4.834
##
## Parameter correlation:
## parent_0 log_k_parent_sink
@@ -1027,9 +1040,12 @@ plot(m.L4.SFO)
## Residual standard error: 3.651 on 6 degrees of freedom
##
## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 96.440000 91.670000 1.012e+02
-## k_parent_sink 0.006541 0.005378 7.955e-03
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
+## Estimate t value Pr(&gt;t) Lower Upper
+## parent_0 96.440000 49.49 2.283e-09 91.670000 1.012e+02
+## k_parent_sink 0.006541 12.50 8.008e-06 0.005378 7.955e-03
##
## Chi2 error levels in percent:
## err.min n.optim df
@@ -1059,17 +1075,17 @@ plot(m.L4.FOMC)
<pre><code class="r">summary(m.L4.FOMC, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.35
-## R version: 3.1.2
-## Date of fit: Sat Feb 21 14:44:58 2015
-## Date of summary: Sat Feb 21 14:44:58 2015
+<pre><code>## mkin version: 0.9.36
+## R version: 3.2.1
+## Date of fit: Sun Jun 21 01:48:04 2015
+## Date of summary: Sun Jun 21 01:48:04 2015
##
## Equations:
-## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
+## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 66 model solutions performed in 0.161 s
+## Fitted with method Port using 66 model solutions performed in 0.159 s
##
## Weighting: none
##
@@ -1088,11 +1104,11 @@ plot(m.L4.FOMC)
## Fixed parameter values:
## None
##
-## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper t value Pr(&gt;|t|) Pr(&gt;t)
-## parent_0 99.1400 1.6800 94.820 103.5000 59.0200 2.643e-08 1.322e-08
-## log_alpha -0.3506 0.3725 -1.308 0.6068 -0.9414 3.897e-01 1.949e-01
-## log_beta 4.1740 0.5635 2.726 5.6230 7.4070 7.059e-04 3.530e-04
+## Optimised, transformed parameters with symmetric confidence intervals:
+## Estimate Std. Error Lower Upper
+## parent_0 99.1400 1.6800 94.820 103.5000
+## log_alpha -0.3506 0.3725 -1.308 0.6068
+## log_beta 4.1740 0.5635 2.726 5.6230
##
## Parameter correlation:
## parent_0 log_alpha log_beta
@@ -1103,10 +1119,13 @@ plot(m.L4.FOMC)
## Residual standard error: 2.315 on 5 degrees of freedom
##
## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 99.1400 94.8200 103.500
-## alpha 0.7042 0.2703 1.835
-## beta 64.9800 15.2600 276.600
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
+## Estimate t value Pr(&gt;t) Lower Upper
+## parent_0 99.1400 59.020 1.322e-08 94.8200 103.500
+## alpha 0.7042 2.685 2.178e-02 0.2703 1.835
+## beta 64.9800 1.775 6.807e-02 15.2600 276.600
##
## Chi2 error levels in percent:
## err.min n.optim df
diff --git a/vignettes/FOCUS_Z.Rnw b/vignettes/FOCUS_Z.Rnw
index 5e2e0251..1df0ee9c 100644
--- a/vignettes/FOCUS_Z.Rnw
+++ b/vignettes/FOCUS_Z.Rnw
@@ -265,11 +265,13 @@ summary(m.Z.mkin.5a, data = FALSE)$bpar
@
A graphical representation of the confidence intervals can finally be obtained.
+
<<FOCUS_2006_Z_fits_11b, echo=TRUE>>=
mkinparplot(m.Z.mkin.5a)
@
The endpoints obtained with this model are
+
<<FOCUS_2006_Z_fits_11b_endpoints, echo=TRUE>>=
endpoints(m.Z.mkin.5a)
@
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index 3174a23a..36f3dc14 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 2f2a6edb..e6f21b09 100644
--- a/vignettes/compiled_models.html
+++ b/vignettes/compiled_models.html
@@ -77,7 +77,7 @@ img {
-->
<div id="benchmark-for-a-model-that-can-also-be-solved-with-eigenvalues" class="section level1">
<h1>Benchmark for a model that can also be solved with Eigenvalues</h1>
-<p>This evaluation is taken from the example section of mkinfit. When using an mkin version greater than 0.9-36 and the ccSolve package is installed and functional, you will get a message that the model is being compiled when defining a model using mkinmod.</p>
+<p>This evaluation is taken from the example section of mkinfit. When using an mkin version equal to or greater than 0.9-36 and a compiler (gcc) is installed, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod.</p>
<pre class="r"><code>library(&quot;mkin&quot;)
SFO_SFO &lt;- mkinmod(
parent = list(type = &quot;SFO&quot;, to = &quot;m1&quot;, sink = TRUE),
@@ -94,20 +94,20 @@ mb.1 &lt;- microbenchmark(
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 6192.0125 6195.3470 6211.0309 6198.6816 6220.5401
-## Eigenvalue based 956.7604 1008.7224 1026.2572 1060.6844 1061.0055
-## deSolve, compiled 869.6880 871.9315 883.4929 874.1751 890.3953
+<pre><code>## min lq mean median uq
+## deSolve, not compiled 4969.585 5033.7311 5092.7389 5097.8773 5154.3160
+## Eigenvalue based 868.731 891.7239 909.6449 914.7169 930.1018
+## deSolve, compiled 4935.049 4935.4796 4968.2150 4935.9097 4984.7978
## max neval
-## deSolve, not compiled 6242.3986 3
-## Eigenvalue based 1061.3266 3
-## deSolve, compiled 906.6155 3</code></pre>
+## deSolve, not compiled 5210.7547 3
+## Eigenvalue based 945.4867 3
+## deSolve, compiled 5033.6858 3</code></pre>
<p>We see that using the compiled model is almost a factor of 8 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 7.120877
-## Eigenvalue based 1.205328
-## deSolve, compiled 1.000000</code></pre>
+<pre><code>## median
+## deSolve, not compiled 1.0328141
+## Eigenvalue based 0.1853188
+## deSolve, compiled 1.0000000</code></pre>
</div>
<div id="benchmark-for-a-model-that-can-not-be-solved-with-eigenvalues" class="section level1">
<h1>Benchmark for a model that can not be solved with Eigenvalues</h1>
@@ -124,16 +124,16 @@ 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 13.297283 13.427702 13.481155 13.558121 13.573092
-## deSolve, compiled 1.486926 1.526887 1.546851 1.566848 1.576813
-## max neval
-## deSolve, not compiled 13.588063 3
-## deSolve, compiled 1.586778 3</code></pre>
+## deSolve, not compiled 11.745276 11.754288 11.820726 11.763300 11.858451
+## deSolve, compiled 1.385829 1.386407 1.400841 1.386985 1.408347
+## max neval
+## deSolve, not compiled 11.95360 3
+## deSolve, compiled 1.42971 3</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 8.653119
-## deSolve, compiled 1.000000</code></pre>
-<p>Here we get a performance benefit of more than a factor of 8 using the version of the differential equation model compiled from C code using the ccSolve package!</p>
+<pre><code>## median
+## deSolve, not compiled 8.4812
+## deSolve, compiled 1.0000</code></pre>
+<p>Here we get a performance benefit of more than a factor of 10 using the version of the differential equation model compiled from C code using the inline package!</p>
</div>
diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
index 8f1e0884..5786c5bf 100644
--- a/vignettes/mkin.pdf
+++ b/vignettes/mkin.pdf
Binary files differ

Contact - Imprint