From d2c1ab854491ff047135fa8377400a68499e72de Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 17 Jul 2014 12:53:30 +0200
Subject: Handle non-convergence and maximum number of iterations
For details see NEWS.md
---
vignettes/FOCUS_L.html | 118 ++++++++++++++++++++++++++++---------------------
vignettes/FOCUS_Z.pdf | Bin 212996 -> 214130 bytes
vignettes/mkin.pdf | Bin 160326 -> 160326 bytes
3 files changed, 67 insertions(+), 51 deletions(-)
(limited to 'vignettes')
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index bb02ec3e..85fadbfe 100644
--- a/vignettes/FOCUS_L.html
+++ b/vignettes/FOCUS_L.html
@@ -193,7 +193,13 @@ hr {
report, p. 284</p>
<pre><code class="r">library("mkin")
-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,
@@ -223,16 +229,17 @@ FOCUS report.</p>
summary(m.L1.SFO)
</code></pre>
-<pre><code>## mkin version: 0.9.31
+<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Mon Jul 14 20:32:20 2014
-## Date of summary: Mon Jul 14 20:32:20 2014
+## Date of fit: Thu Jul 17 12:37:41 2014
+## Date of summary: Thu Jul 17 12:37:41 2014
##
## Equations:
## [1] d_parent = - k_parent_sink * parent
##
-## Method used for solution of differential equation system:
-## analytical
+## Model predictions using solution type analytical
+##
+## Fitted with method Marq using 14 model solutions performed in 0.087 s
##
## Weighting: none
##
@@ -325,16 +332,17 @@ is checked.</p>
summary(m.L1.FOMC, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.31
+<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Mon Jul 14 20:32:20 2014
-## Date of summary: Mon Jul 14 20:32:20 2014
+## Date of fit: Thu Jul 17 12:37:42 2014
+## Date of summary: Thu Jul 17 12:37:42 2014
##
## Equations:
## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
##
-## Method used for solution of differential equation system:
-## analytical
+## Model predictions using solution type analytical
+##
+## Fitted with method Marq using 45 model solutions performed in 0.266 s
##
## Weighting: none
##
@@ -417,16 +425,17 @@ FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2)
summary(m.L2.SFO)
</code></pre>
-<pre><code>## mkin version: 0.9.31
+<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Mon Jul 14 20:32:20 2014
-## Date of summary: Mon Jul 14 20:32:20 2014
+## Date of fit: Thu Jul 17 12:37:42 2014
+## Date of summary: Thu Jul 17 12:37:42 2014
##
## Equations:
## [1] d_parent = - k_parent_sink * parent
##
-## Method used for solution of differential equation system:
-## analytical
+## Model predictions using solution type analytical
+##
+## Fitted with method Marq using 32 model solutions performed in 0.357 s
##
## Weighting: none
##
@@ -526,16 +535,17 @@ mkinresplot(m.L2.FOMC)
<pre><code class="r">summary(m.L2.FOMC, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.31
+<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Mon Jul 14 20:32:21 2014
-## Date of summary: Mon Jul 14 20:32:21 2014
+## Date of fit: Thu Jul 17 12:37:43 2014
+## Date of summary: Thu Jul 17 12:37:43 2014
##
## Equations:
## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
##
-## Method used for solution of differential equation system:
-## analytical
+## Model predictions using solution type analytical
+##
+## Fitted with method Marq using 39 model solutions performed in 0.235 s
##
## Weighting: none
##
@@ -611,16 +621,17 @@ plot(m.L2.DFOP)
<pre><code class="r">summary(m.L2.DFOP, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.31
+<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Mon Jul 14 20:32:23 2014
-## Date of summary: Mon Jul 14 20:32:23 2014
+## Date of fit: Thu Jul 17 12:37:44 2014
+## Date of summary: Thu Jul 17 12:37:44 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
##
-## Method used for solution of differential equation system:
-## analytical
+## Model predictions using solution type analytical
+##
+## Fitted with method Marq using 54 model solutions performed in 0.423 s
##
## Weighting: none
##
@@ -697,16 +708,17 @@ plot(m.L3.SFO)
<pre><code class="r">summary(m.L3.SFO)
</code></pre>
-<pre><code>## mkin version: 0.9.31
+<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Mon Jul 14 20:32:23 2014
-## Date of summary: Mon Jul 14 20:32:23 2014
+## Date of fit: Thu Jul 17 12:37:45 2014
+## Date of summary: Thu Jul 17 12:37:45 2014
##
## Equations:
## [1] d_parent = - k_parent_sink * parent
##
-## Method used for solution of differential equation system:
-## analytical
+## Model predictions using solution type analytical
+##
+## Fitted with method Marq using 44 model solutions performed in 0.241 s
##
## Weighting: none
##
@@ -782,16 +794,17 @@ plot(m.L3.FOMC)
<pre><code class="r">summary(m.L3.FOMC, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.31
+<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Mon Jul 14 20:32:24 2014
-## Date of summary: Mon Jul 14 20:32:24 2014
+## Date of fit: Thu Jul 17 12:37:45 2014
+## Date of summary: Thu Jul 17 12:37:45 2014
##
## Equations:
## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
##
-## Method used for solution of differential equation system:
-## analytical
+## Model predictions using solution type analytical
+##
+## Fitted with method Marq using 26 model solutions performed in 0.208 s
##
## Weighting: none
##
@@ -854,16 +867,17 @@ plot(m.L3.DFOP)
<pre><code class="r">summary(m.L3.DFOP, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.31
+<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Mon Jul 14 20:32:24 2014
-## Date of summary: Mon Jul 14 20:32:24 2014
+## Date of fit: Thu Jul 17 12:37:46 2014
+## Date of summary: Thu Jul 17 12:37:46 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
##
-## Method used for solution of differential equation system:
-## analytical
+## Model predictions using solution type analytical
+##
+## Fitted with method Marq using 37 model solutions performed in 0.338 s
##
## Weighting: none
##
@@ -944,16 +958,17 @@ plot(m.L4.SFO)
<pre><code class="r">summary(m.L4.SFO, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.31
+<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Mon Jul 14 20:32:27 2014
-## Date of summary: Mon Jul 14 20:32:27 2014
+## Date of fit: Thu Jul 17 12:37:46 2014
+## Date of summary: Thu Jul 17 12:37:46 2014
##
## Equations:
## [1] d_parent = - k_parent_sink * parent
##
-## Method used for solution of differential equation system:
-## analytical
+## Model predictions using solution type analytical
+##
+## Fitted with method Marq using 20 model solutions performed in 0.127 s
##
## Weighting: none
##
@@ -1018,16 +1033,17 @@ plot(m.L4.FOMC)
<pre><code class="r">summary(m.L4.FOMC, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.31
+<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Mon Jul 14 20:32:28 2014
-## Date of summary: Mon Jul 14 20:32:28 2014
+## Date of fit: Thu Jul 17 12:37:46 2014
+## Date of summary: Thu Jul 17 12:37:46 2014
##
## Equations:
## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
##
-## Method used for solution of differential equation system:
-## analytical
+## Model predictions using solution type analytical
+##
+## Fitted with method Marq using 53 model solutions performed in 0.355 s
##
## Weighting: none
##
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index 559504cc..43f3e2e2 100644
Binary files a/vignettes/FOCUS_Z.pdf and b/vignettes/FOCUS_Z.pdf differ
diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
index f06d38f9..9cf1b3e5 100644
Binary files a/vignettes/mkin.pdf and b/vignettes/mkin.pdf differ
--
cgit v1.2.1
From a1567638a3ba9f4d62fa199525097a94ddfd7912 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 21 Jul 2014 08:20:44 +0200
Subject: Bugfix, model shorthand, state.ini[[1]] from observed data
- The bug occurred when using transform_rates=FALSE for FOMC, DFOP or HS
- Make it possible to use mkinfit("SFO", ...)
- Take initial mean value at time zero for the variable with the highest
value in the observed data
- Update of vignette/FOCUS_L
- Improve the Makefile to build single vignettes
---
vignettes/FOCUS_L.Rmd | 81 ++++++------
vignettes/FOCUS_L.html | 328 ++++++++++++++++++++++++-------------------------
vignettes/mkin.pdf | Bin 160326 -> 160326 bytes
3 files changed, 200 insertions(+), 209 deletions(-)
(limited to 'vignettes')
diff --git a/vignettes/FOCUS_L.Rmd b/vignettes/FOCUS_L.Rmd
index 04d5f831..cd7711f6 100644
--- a/vignettes/FOCUS_L.Rmd
+++ b/vignettes/FOCUS_L.Rmd
@@ -13,7 +13,7 @@ opts_chunk$set(tidy = FALSE, cache = TRUE)
## Laboratory Data L1
The following code defines example dataset L1 from the FOCUS kinetics
-report, p. 284
+report, p. 284:
```{r}
library("mkin")
@@ -25,27 +25,18 @@ FOCUS_2006_L1 = data.frame(
FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)
```
-The next step is to set up the models used for the kinetic analysis. Note that
-the model definitions contain the names of the observed variables in the data.
-In this case, there is only one variable called `parent`.
+Here we use the assumptions of simple first order (SFO), the case of declining
+rate constant over time (FOMC) and the case of two different phases of the
+kinetics (DFOP). For a more detailed discussion of the models, please see the
+FOCUS kinetics report.
-```{r}
-SFO <- mkinmod(parent = list(type = "SFO"))
-FOMC <- mkinmod(parent = list(type = "FOMC"))
-DFOP <- mkinmod(parent = list(type = "DFOP"))
-```
-
-The three models cover the first assumption of simple first order (SFO),
-the case of declining rate constant over time (FOMC) and the case of two
-different phases of the kinetics (DFOP). For a more detailed discussion
-of the models, please see the FOCUS kinetics report.
-
-The following two lines fit the model and produce the summary report
-of the model fit. This covers the numerical analysis given in the
-FOCUS report.
+Since mkin version 0.9-32 (July 2014), we can use shorthand notation like `SFO`
+for parent only degradation models. The following two lines fit the model and
+produce the summary report of the model fit. This covers the numerical analysis
+given in the FOCUS report.
```{r}
-m.L1.SFO <- mkinfit(SFO, FOCUS_2006_L1_mkin, quiet=TRUE)
+m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet=TRUE)
summary(m.L1.SFO)
```
@@ -64,32 +55,30 @@ For comparison, the FOMC model is fitted as well, and the chi^2 error level
is checked.
```{r}
-m.L1.FOMC <- mkinfit(FOMC, FOCUS_2006_L1_mkin, quiet=TRUE)
+m.L1.FOMC <- mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet=TRUE)
summary(m.L1.FOMC, data = FALSE)
```
Due to the higher number of parameters, and the lower number of degrees of
freedom of the fit, the chi^2 error level is actually higher for the FOMC
-model (3.6%) than for the SFO model (3.4%). Additionally, the covariance
-matrix can not be obtained, indicating overparameterisation of the model.
-As a consequence, no standard errors for transformed parameters nor
-confidence intervals for backtransformed parameters are available.
+model (3.6%) than for the SFO model (3.4%). Additionally, the parameters
+`log_alpha` and `log_beta` internally fitted in the model have p-values for the two
+sided t-test of 0.18 and 0.125, and their correlation is 1.000, indicating that
+the model is overparameterised.
The chi^2 error levels reported in Appendix 3 and Appendix 7 to the FOCUS
kinetics report are rounded to integer percentages and partly deviate by one
percentage point from the results calculated by mkin. The reason for
this is not known. However, mkin gives the same chi^2 error levels
-as the kinfit package.
-
-Furthermore, the calculation routines of the kinfit package have been extensively
-compared to the results obtained by the KinGUI software, as documented in the
-kinfit package vignette. KinGUI is a widely used standard package in this field.
-Therefore, the reason for the difference was not investigated further.
+as the kinfit package. Furthermore, the calculation routines of the kinfit
+package have been extensively compared to the results obtained by the KinGUI
+software, as documented in the kinfit package vignette. KinGUI is a widely used
+standard package in this field.
## Laboratory Data L2
The following code defines example dataset L2 from the FOCUS kinetics
-report, p. 287
+report, p. 287:
```{r}
FOCUS_2006_L2 = data.frame(
@@ -100,10 +89,10 @@ FOCUS_2006_L2 = data.frame(
FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2)
```
-Again, the SFO model is fitted and a summary is obtained.
+Again, the SFO model is fitted and a summary is obtained:
```{r}
-m.L2.SFO <- mkinfit(SFO, FOCUS_2006_L2_mkin, quiet=TRUE)
+m.L2.SFO <- mkinfit("SFO", FOCUS_2006_L2_mkin, quiet=TRUE)
summary(m.L2.SFO)
```
@@ -130,7 +119,7 @@ For comparison, the FOMC model is fitted as well, and the chi^2 error level
is checked.
```{r fig.height = 8}
-m.L2.FOMC <- mkinfit(FOMC, FOCUS_2006_L2_mkin, quiet = TRUE)
+m.L2.FOMC <- mkinfit("FOMC", FOCUS_2006_L2_mkin, quiet = TRUE)
par(mfrow = c(2, 1))
plot(m.L2.FOMC)
mkinresplot(m.L2.FOMC)
@@ -144,7 +133,7 @@ experimental error has to be assumed in order to explain the data.
Fitting the four parameter DFOP model further reduces the chi^2 error level.
```{r fig.height = 5}
-m.L2.DFOP <- mkinfit(DFOP, FOCUS_2006_L2_mkin, quiet = TRUE)
+m.L2.DFOP <- mkinfit("DFOP", FOCUS_2006_L2_mkin, quiet = TRUE)
plot(m.L2.DFOP)
```
@@ -153,7 +142,7 @@ to a reasonable solution. Therefore the fit is repeated with different starting
parameters.
```{r fig.height = 5}
-m.L2.DFOP <- mkinfit(DFOP, FOCUS_2006_L2_mkin,
+m.L2.DFOP <- mkinfit("DFOP", FOCUS_2006_L2_mkin,
parms.ini = c(k1 = 1, k2 = 0.01, g = 0.8),
quiet=TRUE)
plot(m.L2.DFOP)
@@ -180,7 +169,7 @@ FOCUS_2006_L3_mkin <- mkin_wide_to_long(FOCUS_2006_L3)
SFO model, summary and plot:
```{r fig.height = 5}
-m.L3.SFO <- mkinfit(SFO, FOCUS_2006_L3_mkin, quiet = TRUE)
+m.L3.SFO <- mkinfit("SFO", FOCUS_2006_L3_mkin, quiet = TRUE)
plot(m.L3.SFO)
summary(m.L3.SFO)
```
@@ -191,7 +180,7 @@ does not fit very well.
The FOMC model performs better:
```{r fig.height = 5}
-m.L3.FOMC <- mkinfit(FOMC, FOCUS_2006_L3_mkin, quiet = TRUE)
+m.L3.FOMC <- mkinfit("FOMC", FOCUS_2006_L3_mkin, quiet = TRUE)
plot(m.L3.FOMC)
summary(m.L3.FOMC, data = FALSE)
```
@@ -202,7 +191,7 @@ Fitting the four parameter DFOP model further reduces the chi^2 error level
considerably:
```{r fig.height = 5}
-m.L3.DFOP <- mkinfit(DFOP, FOCUS_2006_L3_mkin, quiet = TRUE)
+m.L3.DFOP <- mkinfit("DFOP", FOCUS_2006_L3_mkin, quiet = TRUE)
plot(m.L3.DFOP)
summary(m.L3.DFOP, data = FALSE)
```
@@ -212,10 +201,15 @@ and the correlation matrix suggest that the parameter estimates are reliable, an
the DFOP model can be used as the best-fit model based on the chi^2 error
level criterion for laboratory data L3.
+This is also an example where the standard t-test for the parameter `g_ilr` is
+misleading, as it tests for a significant difference from zero. In this case,
+zero appears to be the correct value for this parameter, and the confidence
+interval for the backtransformed parameter `g` is quite narrow.
+
## Laboratory Data L4
The following code defines example dataset L4 from the FOCUS kinetics
-report, p. 293
+report, p. 293:
```{r}
FOCUS_2006_L4 = data.frame(
@@ -227,7 +221,7 @@ FOCUS_2006_L4_mkin <- mkin_wide_to_long(FOCUS_2006_L4)
SFO model, summary and plot:
```{r fig.height = 5}
-m.L4.SFO <- mkinfit(SFO, FOCUS_2006_L4_mkin, quiet = TRUE)
+m.L4.SFO <- mkinfit("SFO", FOCUS_2006_L4_mkin, quiet = TRUE)
plot(m.L4.SFO)
summary(m.L4.SFO, data = FALSE)
```
@@ -235,14 +229,13 @@ summary(m.L4.SFO, data = FALSE)
The chi^2 error level of 3.3% as well as the plot suggest that the model
fits very well.
-The FOMC model for comparison
+The FOMC model for comparison:
```{r fig.height = 5}
-m.L4.FOMC <- mkinfit(FOMC, FOCUS_2006_L4_mkin, quiet = TRUE)
+m.L4.FOMC <- mkinfit("FOMC", FOCUS_2006_L4_mkin, quiet = TRUE)
plot(m.L4.FOMC)
summary(m.L4.FOMC, data = FALSE)
```
The error level at which the chi^2 test passes is slightly lower for the FOMC
model. However, the difference appears negligible.
-
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index 85fadbfe..614fcf32 100644
--- a/vignettes/FOCUS_L.html
+++ b/vignettes/FOCUS_L.html
@@ -190,7 +190,7 @@ hr {
<h2>Laboratory Data L1</h2>
<p>The following code defines example dataset L1 from the FOCUS kinetics
-report, p. 284</p>
+report, p. 284:</p>
<pre><code class="r">library("mkin")
</code></pre>
@@ -207,51 +207,43 @@ report, p. 284</p>
FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)
</code></pre>
-<p>The next step is to set up the models used for the kinetic analysis. Note that
-the model definitions contain the names of the observed variables in the data.
-In this case, there is only one variable called <code>parent</code>.</p>
+<p>Here we use the assumptions of simple first order (SFO), the case of declining
+rate constant over time (FOMC) and the case of two different phases of the
+kinetics (DFOP). For a more detailed discussion of the models, please see the
+FOCUS kinetics report.</p>
-<pre><code class="r">SFO <- mkinmod(parent = list(type = "SFO"))
-FOMC <- mkinmod(parent = list(type = "FOMC"))
-DFOP <- mkinmod(parent = list(type = "DFOP"))
-</code></pre>
-
-<p>The three models cover the first assumption of simple first order (SFO),
-the case of declining rate constant over time (FOMC) and the case of two
-different phases of the kinetics (DFOP). For a more detailed discussion
-of the models, please see the FOCUS kinetics report.</p>
+<p>Since mkin version 0.9-32 (July 2014), we can use shorthand notation like <code>SFO</code>
+for parent only degradation models. The following two lines fit the model and
+produce the summary report of the model fit. This covers the numerical analysis
+given in the FOCUS report. </p>
-<p>The following two lines fit the model and produce the summary report
-of the model fit. This covers the numerical analysis given in the
-FOCUS report.</p>
-
-<pre><code class="r">m.L1.SFO <- mkinfit(SFO, FOCUS_2006_L1_mkin, quiet=TRUE)
+<pre><code class="r">m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet=TRUE)
summary(m.L1.SFO)
</code></pre>
<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Thu Jul 17 12:37:41 2014
-## Date of summary: Thu Jul 17 12:37:41 2014
+## Date of fit: Mon Jul 21 09:14:29 2014
+## Date of summary: Mon Jul 21 09:14:29 2014
##
## Equations:
## [1] d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 14 model solutions performed in 0.087 s
+## Fitted with method Marq using 14 model solutions performed in 0.081 s
##
## Weighting: none
##
## Starting values for parameters to be optimised:
## value type
-## parent_0 100.0 state
-## k_parent_sink 0.1 deparm
+## parent_0 89.85 state
+## k_parent_sink 0.10 deparm
##
## Starting values for the transformed parameters actually optimised:
-## value lower upper
-## parent_0 100.000 -Inf Inf
-## log_k_parent_sink -2.303 -Inf Inf
+## value lower upper
+## parent_0 89.850 -Inf Inf
+## log_k_parent_sink -2.303 -Inf Inf
##
## Fixed parameter values:
## None
@@ -259,7 +251,7 @@ summary(m.L1.SFO)
## Optimised, transformed parameters:
## Estimate Std. Error Lower Upper t value Pr(>|t|)
## parent_0 92.50 1.3700 89.60 95.40 67.6 4.34e-21
-## log_k_parent_sink -2.35 0.0406 -2.43 -2.26 -57.9 5.15e-20
+## log_k_parent_sink -2.35 0.0406 -2.43 -2.26 -57.9 5.16e-20
## Pr(>t)
## parent_0 2.17e-21
## log_k_parent_sink 2.58e-20
@@ -316,67 +308,70 @@ summary(m.L1.SFO)
<pre><code class="r">plot(m.L1.SFO)
</code></pre>
-<p><img 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alt="plot of chunk unnamed-chunk-5"/> </p>
+<p><img src="data:image/png;base64,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alt="plot of chunk unnamed-chunk-4"/> </p>
<p>The residual plot can be easily obtained by</p>
<pre><code class="r">mkinresplot(m.L1.SFO, ylab = "Observed", xlab = "Time")
</code></pre>
-<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>
-<pre><code class="r">m.L1.FOMC <- mkinfit(FOMC, FOCUS_2006_L1_mkin, quiet=TRUE)
+<pre><code class="r">m.L1.FOMC <- mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet=TRUE)
summary(m.L1.FOMC, data = FALSE)
</code></pre>
<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Thu Jul 17 12:37:42 2014
-## Date of summary: Thu Jul 17 12:37:42 2014
+## Date of fit: Mon Jul 21 09:14:30 2014
+## Date of summary: Mon Jul 21 09:14:30 2014
##
## Equations:
## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 45 model solutions performed in 0.266 s
+## Fitted with method Marq using 53 model solutions performed in 0.32 s
##
## Weighting: none
##
## Starting values for parameters to be optimised:
## value type
-## parent_0 100 state
-## alpha 1 deparm
-## beta 10 deparm
+## parent_0 89.85 state
+## alpha 1.00 deparm
+## beta 10.00 deparm
##
## Starting values for the transformed parameters actually optimised:
-## value lower upper
-## parent_0 100.000 -Inf Inf
-## log_alpha 0.000 -Inf Inf
-## log_beta 2.303 -Inf Inf
+## value lower upper
+## parent_0 89.850 -Inf Inf
+## log_alpha 0.000 -Inf Inf
+## log_beta 2.303 -Inf Inf
##
## Fixed parameter values:
## None
##
## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper t value Pr(>|t|) Pr(>t)
-## parent_0 92.5 NA NA NA NA NA NA
-## log_alpha 25.6 NA NA NA NA NA NA
-## log_beta 28.0 NA NA NA NA NA NA
+## Estimate Std. Error Lower Upper t value Pr(>|t|) Pr(>t)
+## parent_0 92.5 1.45 89.40 95.6 63.60 1.17e-19 5.85e-20
+## log_alpha 14.9 10.60 -7.75 37.5 1.40 1.82e-01 9.08e-02
+## log_beta 17.2 10.60 -5.38 39.8 1.62 1.25e-01 6.26e-02
##
## Parameter correlation:
-## Could not estimate covariance matrix; singular system:
+## parent_0 log_alpha log_beta
+## parent_0 1.000 0.24 0.238
+## log_alpha 0.240 1.00 1.000
+## log_beta 0.238 1.00 1.000
##
## Residual standard error: 3.05 on 15 degrees of freedom
##
## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 9.25e+01 NA NA
-## alpha 1.35e+11 NA NA
-## beta 1.41e+12 NA NA
+## Estimate Lower Upper
+## parent_0 9.25e+01 8.94e+01 9.56e+01
+## alpha 2.85e+06 4.32e-04 1.88e+16
+## beta 2.98e+07 4.59e-03 1.93e+17
##
## Chi2 error levels in percent:
## err.min n.optim df
@@ -390,26 +385,24 @@ summary(m.L1.FOMC, data = FALSE)
<p>Due to the higher number of parameters, and the lower number of degrees of
freedom of the fit, the chi<sup>2</sup> error level is actually higher for the FOMC
-model (3.6%) than for the SFO model (3.4%). Additionally, the covariance
-matrix can not be obtained, indicating overparameterisation of the model.
-As a consequence, no standard errors for transformed parameters nor
-confidence intervals for backtransformed parameters are available.</p>
+model (3.6%) than for the SFO model (3.4%). Additionally, the parameters
+<code>log_alpha</code> and <code>log_beta</code> internally fitted in the model have p-values for the two
+sided t-test of 0.18 and 0.125, and their correlation is 1.000, indicating that
+the model is overparameterised. </p>
<p>The chi<sup>2</sup> error levels reported in Appendix 3 and Appendix 7 to the FOCUS
kinetics report are rounded to integer percentages and partly deviate by one
percentage point from the results calculated by mkin. The reason for
this is not known. However, mkin gives the same chi<sup>2</sup> error levels
-as the kinfit package.</p>
-
-<p>Furthermore, the calculation routines of the kinfit package have been extensively
-compared to the results obtained by the KinGUI software, as documented in the
-kinfit package vignette. KinGUI is a widely used standard package in this field.
-Therefore, the reason for the difference was not investigated further.</p>
+as the kinfit package. Furthermore, the calculation routines of the kinfit
+package have been extensively compared to the results obtained by the KinGUI
+software, as documented in the kinfit package vignette. KinGUI is a widely used
+standard package in this field. </p>
<h2>Laboratory Data L2</h2>
<p>The following code defines example dataset L2 from the FOCUS kinetics
-report, p. 287</p>
+report, p. 287:</p>
<pre><code class="r">FOCUS_2006_L2 = data.frame(
t = rep(c(0, 1, 3, 7, 14, 28), each = 2),
@@ -419,35 +412,35 @@ report, p. 287</p>
FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2)
</code></pre>
-<p>Again, the SFO model is fitted and a summary is obtained.</p>
+<p>Again, the SFO model is fitted and a summary is obtained:</p>
-<pre><code class="r">m.L2.SFO <- mkinfit(SFO, FOCUS_2006_L2_mkin, quiet=TRUE)
+<pre><code class="r">m.L2.SFO <- mkinfit("SFO", FOCUS_2006_L2_mkin, quiet=TRUE)
summary(m.L2.SFO)
</code></pre>
<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Thu Jul 17 12:37:42 2014
-## Date of summary: Thu Jul 17 12:37:42 2014
+## Date of fit: Mon Jul 21 09:14:30 2014
+## Date of summary: Mon Jul 21 09:14:30 2014
##
## Equations:
## [1] d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 32 model solutions performed in 0.357 s
+## Fitted with method Marq using 29 model solutions performed in 0.155 s
##
## Weighting: none
##
## Starting values for parameters to be optimised:
## value type
-## parent_0 100.0 state
-## k_parent_sink 0.1 deparm
+## parent_0 93.95 state
+## k_parent_sink 0.10 deparm
##
## Starting values for the transformed parameters actually optimised:
-## value lower upper
-## parent_0 100.000 -Inf Inf
-## log_k_parent_sink -2.303 -Inf Inf
+## value lower upper
+## parent_0 93.950 -Inf Inf
+## log_k_parent_sink -2.303 -Inf Inf
##
## Fixed parameter values:
## None
@@ -487,8 +480,8 @@ summary(m.L2.SFO)
##
## Data:
## time variable observed predicted residual
-## 0 parent 96.1 9.15e+01 4.634
-## 0 parent 91.8 9.15e+01 0.334
+## 0 parent 96.1 9.15e+01 4.635
+## 0 parent 91.8 9.15e+01 0.335
## 1 parent 41.4 4.71e+01 -5.740
## 1 parent 38.7 4.71e+01 -8.440
## 3 parent 19.3 1.25e+01 6.779
@@ -509,7 +502,7 @@ plot(m.L2.SFO)
mkinresplot(m.L2.SFO)
</code></pre>
-<p><img 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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
@@ -524,42 +517,42 @@ models generally only implement SFO kinetics.</p>
<p>For comparison, the FOMC model is fitted as well, and the chi<sup>2</sup> error level
is checked.</p>
-<pre><code class="r">m.L2.FOMC <- mkinfit(FOMC, FOCUS_2006_L2_mkin, quiet = TRUE)
+<pre><code class="r">m.L2.FOMC <- mkinfit("FOMC", FOCUS_2006_L2_mkin, quiet = TRUE)
par(mfrow = c(2, 1))
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: Thu Jul 17 12:37:43 2014
-## Date of summary: Thu Jul 17 12:37:43 2014
+## Date of fit: Mon Jul 21 09:14:31 2014
+## Date of summary: Mon Jul 21 09:14:31 2014
##
## Equations:
## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 39 model solutions performed in 0.235 s
+## Fitted with method Marq using 35 model solutions performed in 0.199 s
##
## Weighting: none
##
## Starting values for parameters to be optimised:
## value type
-## parent_0 100 state
-## alpha 1 deparm
-## beta 10 deparm
+## parent_0 93.95 state
+## alpha 1.00 deparm
+## beta 10.00 deparm
##
## Starting values for the transformed parameters actually optimised:
-## value lower upper
-## parent_0 100.000 -Inf Inf
-## log_alpha 0.000 -Inf Inf
-## log_beta 2.303 -Inf Inf
+## value lower upper
+## parent_0 93.950 -Inf Inf
+## log_alpha 0.000 -Inf Inf
+## log_beta 2.303 -Inf Inf
##
## Fixed parameter values:
## None
@@ -600,62 +593,62 @@ experimental error has to be assumed in order to explain the data.</p>
<p>Fitting the four parameter DFOP model further reduces the chi<sup>2</sup> error level. </p>
-<pre><code class="r">m.L2.DFOP <- mkinfit(DFOP, FOCUS_2006_L2_mkin, quiet = TRUE)
+<pre><code class="r">m.L2.DFOP <- mkinfit("DFOP", FOCUS_2006_L2_mkin, quiet = TRUE)
plot(m.L2.DFOP)
</code></pre>
-<p><img 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alt="plot of chunk unnamed-chunk-11"/> </p>
<p>Here, the default starting parameters for the DFOP model obviously do not lead
to a reasonable solution. Therefore the fit is repeated with different starting
parameters.</p>
-<pre><code class="r">m.L2.DFOP <- mkinfit(DFOP, FOCUS_2006_L2_mkin,
+<pre><code class="r">m.L2.DFOP <- mkinfit("DFOP", FOCUS_2006_L2_mkin,
parms.ini = c(k1 = 1, k2 = 0.01, g = 0.8),
quiet=TRUE)
plot(m.L2.DFOP)
</code></pre>
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alt="plot of chunk unnamed-chunk-12"/> </p>
<pre><code class="r">summary(m.L2.DFOP, data = FALSE)
</code></pre>
<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Thu Jul 17 12:37:44 2014
-## Date of summary: Thu Jul 17 12:37:44 2014
+## Date of fit: Mon Jul 21 09:14:31 2014
+## Date of summary: Mon Jul 21 09:14:31 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 54 model solutions performed in 0.423 s
+## Fitted with method Marq using 43 model solutions performed in 0.241 s
##
## Weighting: none
##
## Starting values for parameters to be optimised:
## value type
-## parent_0 1e+02 state
-## k1 1e+00 deparm
-## k2 1e-02 deparm
-## g 8e-01 deparm
+## parent_0 93.95 state
+## k1 1.00 deparm
+## k2 0.01 deparm
+## g 0.80 deparm
##
## Starting values for the transformed parameters actually optimised:
-## value lower upper
-## parent_0 100.0000 -Inf Inf
-## log_k1 0.0000 -Inf Inf
-## log_k2 -4.6052 -Inf Inf
-## g_ilr 0.9803 -Inf Inf
+## value lower upper
+## parent_0 93.9500 -Inf Inf
+## log_k1 0.0000 -Inf Inf
+## log_k2 -4.6052 -Inf Inf
+## g_ilr 0.9803 -Inf Inf
##
## Fixed parameter values:
## None
##
## Optimised, transformed parameters:
## Estimate Std. Error Lower Upper t value Pr(>|t|) Pr(>t)
-## parent_0 93.900 NA NA NA NA NA NA
-## log_k1 4.960 NA NA NA NA NA NA
+## parent_0 94.000 NA NA NA NA NA NA
+## log_k1 6.160 NA NA NA NA NA NA
## log_k2 -1.090 NA NA NA NA NA NA
## g_ilr -0.282 NA NA NA NA NA NA
##
@@ -666,8 +659,8 @@ plot(m.L2.DFOP)
##
## Backtransformed parameters:
## Estimate Lower Upper
-## parent_0 93.900 NA NA
-## k1 142.000 NA NA
+## parent_0 94.000 NA NA
+## k1 476.000 NA NA
## k2 0.337 NA NA
## g 0.402 NA NA
##
@@ -678,7 +671,7 @@ plot(m.L2.DFOP)
##
## Estimated disappearance times:
## DT50 DT90 DT50_k1 DT50_k2
-## parent NA NA 0.00487 2.06
+## parent NA NA 0.00146 2.06
</code></pre>
<p>Here, the DFOP model is clearly the best-fit model for dataset L2 based on the
@@ -699,38 +692,38 @@ FOCUS_2006_L3_mkin <- mkin_wide_to_long(FOCUS_2006_L3)
<p>SFO model, summary and plot:</p>
-<pre><code class="r">m.L3.SFO <- mkinfit(SFO, FOCUS_2006_L3_mkin, quiet = TRUE)
+<pre><code class="r">m.L3.SFO <- mkinfit("SFO", FOCUS_2006_L3_mkin, quiet = TRUE)
plot(m.L3.SFO)
</code></pre>
-<p><img 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+<p><img 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alt="plot of chunk unnamed-chunk-14"/> </p>
<pre><code class="r">summary(m.L3.SFO)
</code></pre>
<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Thu Jul 17 12:37:45 2014
-## Date of summary: Thu Jul 17 12:37:45 2014
+## Date of fit: Mon Jul 21 09:14:32 2014
+## Date of summary: Mon Jul 21 09:14:32 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 0.241 s
+## Fitted with method Marq using 44 model solutions performed in 0.242 s
##
## Weighting: none
##
## Starting values for parameters to be optimised:
## value type
-## parent_0 100.0 state
+## parent_0 97.8 state
## k_parent_sink 0.1 deparm
##
## Starting values for the transformed parameters actually optimised:
-## value lower upper
-## parent_0 100.000 -Inf Inf
-## log_k_parent_sink -2.303 -Inf Inf
+## value lower upper
+## parent_0 97.800 -Inf Inf
+## log_k_parent_sink -2.303 -Inf Inf
##
## Fixed parameter values:
## None
@@ -770,7 +763,7 @@ plot(m.L3.SFO)
##
## Data:
## time variable observed predicted residual
-## 0 parent 97.8 74.87 22.9273
+## 0 parent 97.8 74.87 22.9274
## 3 parent 60.0 69.41 -9.4065
## 7 parent 51.0 62.73 -11.7340
## 14 parent 43.0 52.56 -9.5634
@@ -785,40 +778,40 @@ does not fit very well. </p>
<p>The FOMC model performs better:</p>
-<pre><code class="r">m.L3.FOMC <- mkinfit(FOMC, FOCUS_2006_L3_mkin, quiet = TRUE)
+<pre><code class="r">m.L3.FOMC <- mkinfit("FOMC", FOCUS_2006_L3_mkin, quiet = TRUE)
plot(m.L3.FOMC)
</code></pre>
-<p><img 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alt="plot of chunk unnamed-chunk-15"/> </p>
<pre><code class="r">summary(m.L3.FOMC, data = FALSE)
</code></pre>
<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Thu Jul 17 12:37:45 2014
-## Date of summary: Thu Jul 17 12:37:45 2014
+## Date of fit: Mon Jul 21 09:14:32 2014
+## Date of summary: Mon Jul 21 09:14:32 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 0.208 s
+## Fitted with method Marq using 26 model solutions performed in 0.143 s
##
## Weighting: none
##
## Starting values for parameters to be optimised:
## value type
-## parent_0 100 state
-## alpha 1 deparm
-## beta 10 deparm
+## parent_0 97.8 state
+## alpha 1.0 deparm
+## beta 10.0 deparm
##
## Starting values for the transformed parameters actually optimised:
-## value lower upper
-## parent_0 100.000 -Inf Inf
-## log_alpha 0.000 -Inf Inf
-## log_beta 2.303 -Inf Inf
+## value lower upper
+## parent_0 97.800 -Inf Inf
+## log_alpha 0.000 -Inf Inf
+## log_beta 2.303 -Inf Inf
##
## Fixed parameter values:
## None
@@ -858,42 +851,42 @@ plot(m.L3.FOMC)
<p>Fitting the four parameter DFOP model further reduces the chi<sup>2</sup> error level
considerably:</p>
-<pre><code class="r">m.L3.DFOP <- mkinfit(DFOP, FOCUS_2006_L3_mkin, quiet = TRUE)
+<pre><code class="r">m.L3.DFOP <- mkinfit("DFOP", FOCUS_2006_L3_mkin, quiet = TRUE)
plot(m.L3.DFOP)
</code></pre>
-<p><img 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alt="plot of chunk unnamed-chunk-17"/> </p>
+<p><img 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alt="plot of chunk unnamed-chunk-16"/> </p>
<pre><code class="r">summary(m.L3.DFOP, data = FALSE)
</code></pre>
<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Thu Jul 17 12:37:46 2014
-## Date of summary: Thu Jul 17 12:37:46 2014
+## Date of fit: Mon Jul 21 09:14:32 2014
+## Date of summary: Mon Jul 21 09:14:32 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 0.338 s
+## Fitted with method Marq using 37 model solutions performed in 0.21 s
##
## Weighting: none
##
## Starting values for parameters to be optimised:
## value type
-## parent_0 1e+02 state
-## k1 1e-01 deparm
-## k2 1e-02 deparm
-## g 5e-01 deparm
+## parent_0 97.80 state
+## k1 0.10 deparm
+## k2 0.01 deparm
+## g 0.50 deparm
##
## Starting values for the transformed parameters actually optimised:
-## value lower upper
-## parent_0 100.000 -Inf Inf
-## log_k1 -2.303 -Inf Inf
-## log_k2 -4.605 -Inf Inf
-## g_ilr 0.000 -Inf Inf
+## value lower upper
+## parent_0 97.800 -Inf Inf
+## log_k1 -2.303 -Inf Inf
+## log_k2 -4.605 -Inf Inf
+## g_ilr 0.000 -Inf Inf
##
## Fixed parameter values:
## None
@@ -936,10 +929,15 @@ and the correlation matrix suggest that the parameter estimates are reliable, an
the DFOP model can be used as the best-fit model based on the chi<sup>2</sup> error
level criterion for laboratory data L3.</p>
+<p>This is also an example where the standard t-test for the parameter <code>g_ilr</code> is
+misleading, as it tests for a significant difference from zero. In this case,
+zero appears to be the correct value for this parameter, and the confidence
+interval for the backtransformed parameter <code>g</code> is quite narrow.</p>
+
<h2>Laboratory Data L4</h2>
<p>The following code defines example dataset L4 from the FOCUS kinetics
-report, p. 293</p>
+report, p. 293:</p>
<pre><code class="r">FOCUS_2006_L4 = data.frame(
t = c(0, 3, 7, 14, 30, 60, 91, 120),
@@ -949,38 +947,38 @@ FOCUS_2006_L4_mkin <- mkin_wide_to_long(FOCUS_2006_L4)
<p>SFO model, summary and plot:</p>
-<pre><code class="r">m.L4.SFO <- mkinfit(SFO, FOCUS_2006_L4_mkin, quiet = TRUE)
+<pre><code class="r">m.L4.SFO <- mkinfit("SFO", FOCUS_2006_L4_mkin, quiet = TRUE)
plot(m.L4.SFO)
</code></pre>
-<p><img 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alt="plot of chunk unnamed-chunk-18"/> </p>
<pre><code class="r">summary(m.L4.SFO, data = FALSE)
</code></pre>
<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Thu Jul 17 12:37:46 2014
-## Date of summary: Thu Jul 17 12:37:46 2014
+## Date of fit: Mon Jul 21 09:14:33 2014
+## Date of summary: Mon Jul 21 09:14:33 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 0.127 s
+## Fitted with method Marq using 20 model solutions performed in 0.109 s
##
## Weighting: none
##
## Starting values for parameters to be optimised:
## value type
-## parent_0 100.0 state
+## parent_0 96.6 state
## k_parent_sink 0.1 deparm
##
## Starting values for the transformed parameters actually optimised:
-## value lower upper
-## parent_0 100.000 -Inf Inf
-## log_k_parent_sink -2.303 -Inf Inf
+## value lower upper
+## parent_0 96.600 -Inf Inf
+## log_k_parent_sink -2.303 -Inf Inf
##
## Fixed parameter values:
## None
@@ -1022,42 +1020,42 @@ plot(m.L4.SFO)
<p>The chi<sup>2</sup> error level of 3.3% as well as the plot suggest that the model
fits very well. </p>
-<p>The FOMC model for comparison</p>
+<p>The FOMC model for comparison:</p>
-<pre><code class="r">m.L4.FOMC <- mkinfit(FOMC, FOCUS_2006_L4_mkin, quiet = TRUE)
+<pre><code class="r">m.L4.FOMC <- mkinfit("FOMC", FOCUS_2006_L4_mkin, quiet = TRUE)
plot(m.L4.FOMC)
</code></pre>
-<p><img 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alt="plot of chunk unnamed-chunk-19"/> </p>
<pre><code class="r">summary(m.L4.FOMC, data = FALSE)
</code></pre>
<pre><code>## mkin version: 0.9.32
## R version: 3.1.1
-## Date of fit: Thu Jul 17 12:37:46 2014
-## Date of summary: Thu Jul 17 12:37:46 2014
+## Date of fit: Mon Jul 21 09:14:33 2014
+## Date of summary: Mon Jul 21 09:14:33 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 0.355 s
+## Fitted with method Marq using 48 model solutions performed in 0.26 s
##
## Weighting: none
##
## Starting values for parameters to be optimised:
## value type
-## parent_0 100 state
-## alpha 1 deparm
-## beta 10 deparm
+## parent_0 96.6 state
+## alpha 1.0 deparm
+## beta 10.0 deparm
##
## Starting values for the transformed parameters actually optimised:
-## value lower upper
-## parent_0 100.000 -Inf Inf
-## log_alpha 0.000 -Inf Inf
-## log_beta 2.303 -Inf Inf
+## value lower upper
+## parent_0 96.600 -Inf Inf
+## log_alpha 0.000 -Inf Inf
+## log_beta 2.303 -Inf Inf
##
## Fixed parameter values:
## None
diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
index 9cf1b3e5..b69ddddc 100644
Binary files a/vignettes/mkin.pdf and b/vignettes/mkin.pdf differ
--
cgit v1.2.1
From 4eb6682cf4e25cfe4d58a49c8632307a7cac1ca4 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Thu, 24 Jul 2014 14:42:00 +0200
Subject: Update vignettes with 0.9-32 just released to CRAN
---
vignettes/FOCUS_L.html | 72 +++++++++++++++++++++++--------------------------
vignettes/FOCUS_Z.pdf | Bin 214130 -> 214013 bytes
vignettes/mkin.pdf | Bin 160326 -> 160326 bytes
3 files changed, 33 insertions(+), 39 deletions(-)
(limited to 'vignettes')
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("mkin")
-</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 = "Observed", xlab = "Time")
</code></pre>
-<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>
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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
Binary files a/vignettes/FOCUS_Z.pdf and b/vignettes/FOCUS_Z.pdf differ
diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
index b69ddddc..0cc413a1 100644
Binary files a/vignettes/mkin.pdf and b/vignettes/mkin.pdf differ
--
cgit v1.2.1
From 37a252cb44fed78c4f7a00a2f7874f1c47456468 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Tue, 19 Aug 2014 17:55:06 +0200
Subject: Improve formatting of differential equations in output
Rebuild of FOCUS_Z vignette with improved formatting
---
vignettes/FOCUS_Z.Rnw | 1 +
vignettes/FOCUS_Z.pdf | Bin 214013 -> 220196 bytes
2 files changed, 1 insertion(+)
(limited to 'vignettes')
diff --git a/vignettes/FOCUS_Z.Rnw b/vignettes/FOCUS_Z.Rnw
index 5b0ee79e..e2a2473e 100644
--- a/vignettes/FOCUS_Z.Rnw
+++ b/vignettes/FOCUS_Z.Rnw
@@ -20,6 +20,7 @@
<<include=FALSE>>=
require(knitr)
opts_chunk$set(engine='R', tidy=FALSE)
+options(width=70)
@
\title{Example evaluation of FOCUS dataset Z}
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index f7b0a65a..210ce099 100644
Binary files a/vignettes/FOCUS_Z.pdf and b/vignettes/FOCUS_Z.pdf differ
--
cgit v1.2.1
From f30472ecd2afea6bd2153b8ad2bb2f663f3a2742 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 25 Aug 2014 10:39:40 +0200
Subject: Bug fix and unit tests for mkinerrmin
See NEWS.md for details
---
vignettes/FOCUS_L.html | 112 +++++++++++++++++++++++++++----------------------
vignettes/FOCUS_Z.pdf | Bin 220196 -> 220177 bytes
2 files changed, 61 insertions(+), 51 deletions(-)
(limited to 'vignettes')
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index ab7ccaee..2dd186de 100644
--- a/vignettes/FOCUS_L.html
+++ b/vignettes/FOCUS_L.html
@@ -193,7 +193,13 @@ hr {
report, p. 284:</p>
<pre><code class="r">library("mkin")
-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,
@@ -215,17 +221,17 @@ given in the FOCUS report. </p>
summary(m.L1.SFO)
</code></pre>
-<pre><code>## mkin version: 0.9.32
+<pre><code>## mkin version: 0.9.33
## R version: 3.1.1
-## Date of fit: Thu Jul 24 10:32:09 2014
-## Date of summary: Thu Jul 24 10:32:09 2014
+## Date of fit: Mon Aug 25 10:34:14 2014
+## Date of summary: Mon Aug 25 10:34:14 2014
##
## Equations:
-## [1] d_parent = - k_parent_sink * parent
+## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 14 model solutions performed in 0.081 s
+## Fitted with method Marq using 14 model solutions performed in 0.083 s
##
## Weighting: none
##
@@ -318,17 +324,17 @@ is checked.</p>
summary(m.L1.FOMC, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.32
+<pre><code>## mkin version: 0.9.33
## R version: 3.1.1
-## Date of fit: Thu Jul 24 10:32:10 2014
-## Date of summary: Thu Jul 24 10:32:11 2014
+## Date of fit: Mon Aug 25 10:34:17 2014
+## Date of summary: Mon Aug 25 10:34:17 2014
##
## Equations:
-## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
+## 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 0.321 s
+## Fitted with method Marq using 53 model solutions performed in 0.3 s
##
## Weighting: none
##
@@ -412,17 +418,17 @@ FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2)
summary(m.L2.SFO)
</code></pre>
-<pre><code>## mkin version: 0.9.32
+<pre><code>## mkin version: 0.9.33
## R version: 3.1.1
-## Date of fit: Thu Jul 24 10:32:11 2014
-## Date of summary: Thu Jul 24 10:32:11 2014
+## Date of fit: Mon Aug 25 10:34:17 2014
+## Date of summary: Mon Aug 25 10:34:17 2014
##
## Equations:
-## [1] d_parent = - k_parent_sink * parent
+## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 29 model solutions performed in 0.196 s
+## Fitted with method Marq using 29 model solutions performed in 0.184 s
##
## Weighting: none
##
@@ -522,17 +528,17 @@ mkinresplot(m.L2.FOMC)
<pre><code class="r">summary(m.L2.FOMC, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.32
+<pre><code>## mkin version: 0.9.33
## R version: 3.1.1
-## Date of fit: Thu Jul 24 10:32:11 2014
-## Date of summary: Thu Jul 24 10:32:11 2014
+## Date of fit: Mon Aug 25 10:34:17 2014
+## Date of summary: Mon Aug 25 10:34:17 2014
##
## Equations:
-## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
+## 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 0.223 s
+## Fitted with method Marq using 35 model solutions performed in 0.2 s
##
## Weighting: none
##
@@ -608,17 +614,19 @@ plot(m.L2.DFOP)
<pre><code class="r">summary(m.L2.DFOP, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.32
+<pre><code>## mkin version: 0.9.33
## R version: 3.1.1
-## Date of fit: Thu Jul 24 10:32:12 2014
-## Date of summary: Thu Jul 24 10:32:12 2014
+## Date of fit: Mon Aug 25 10:34:18 2014
+## Date of summary: Mon Aug 25 10:34:18 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
+## 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 0.271 s
+## Fitted with method Marq using 43 model solutions performed in 0.26 s
##
## Weighting: none
##
@@ -695,17 +703,17 @@ plot(m.L3.SFO)
<pre><code class="r">summary(m.L3.SFO)
</code></pre>
-<pre><code>## mkin version: 0.9.32
+<pre><code>## mkin version: 0.9.33
## R version: 3.1.1
-## Date of fit: Thu Jul 24 10:32:14 2014
-## Date of summary: Thu Jul 24 10:32:14 2014
+## Date of fit: Mon Aug 25 10:34:18 2014
+## Date of summary: Mon Aug 25 10:34:18 2014
##
## Equations:
-## [1] d_parent = - k_parent_sink * parent
+## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 44 model solutions performed in 0.251 s
+## Fitted with method Marq using 44 model solutions performed in 0.252 s
##
## Weighting: none
##
@@ -781,17 +789,17 @@ plot(m.L3.FOMC)
<pre><code class="r">summary(m.L3.FOMC, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.32
+<pre><code>## mkin version: 0.9.33
## R version: 3.1.1
-## Date of fit: Thu Jul 24 10:32:14 2014
-## Date of summary: Thu Jul 24 10:32:14 2014
+## Date of fit: Mon Aug 25 10:34:19 2014
+## Date of summary: Mon Aug 25 10:34:19 2014
##
## Equations:
-## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
+## 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 0.154 s
+## Fitted with method Marq using 26 model solutions performed in 0.148 s
##
## Weighting: none
##
@@ -854,17 +862,19 @@ plot(m.L3.DFOP)
<pre><code class="r">summary(m.L3.DFOP, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.32
+<pre><code>## mkin version: 0.9.33
## R version: 3.1.1
-## Date of fit: Thu Jul 24 10:32:14 2014
-## Date of summary: Thu Jul 24 10:32:14 2014
+## Date of fit: Mon Aug 25 10:34:19 2014
+## Date of summary: Mon Aug 25 10:34:19 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
+## 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 0.228 s
+## Fitted with method Marq using 37 model solutions performed in 0.236 s
##
## Weighting: none
##
@@ -950,17 +960,17 @@ plot(m.L4.SFO)
<pre><code class="r">summary(m.L4.SFO, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.32
+<pre><code>## mkin version: 0.9.33
## R version: 3.1.1
-## Date of fit: Thu Jul 24 10:32:15 2014
-## Date of summary: Thu Jul 24 10:32:15 2014
+## Date of fit: Mon Aug 25 10:34:19 2014
+## Date of summary: Mon Aug 25 10:34:19 2014
##
## Equations:
-## [1] d_parent = - k_parent_sink * parent
+## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 20 model solutions performed in 0.141 s
+## Fitted with method Marq using 20 model solutions performed in 0.123 s
##
## Weighting: none
##
@@ -1025,17 +1035,17 @@ plot(m.L4.FOMC)
<pre><code class="r">summary(m.L4.FOMC, data = FALSE)
</code></pre>
-<pre><code>## mkin version: 0.9.32
+<pre><code>## mkin version: 0.9.33
## R version: 3.1.1
-## Date of fit: Thu Jul 24 10:32:15 2014
-## Date of summary: Thu Jul 24 10:32:15 2014
+## Date of fit: Mon Aug 25 10:34:20 2014
+## Date of summary: Mon Aug 25 10:34:20 2014
##
## Equations:
-## [1] d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
+## 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 0.296 s
+## Fitted with method Marq using 48 model solutions performed in 0.281 s
##
## Weighting: none
##
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index 210ce099..ca6d2506 100644
Binary files a/vignettes/FOCUS_Z.pdf and b/vignettes/FOCUS_Z.pdf differ
--
cgit v1.2.1
From 587bdfc102dbaa2c882fb0c008d28a3aea1d74d8 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Sat, 11 Oct 2014 11:18:01 +0200
Subject: Updated vignettes by building static documentation
---
vignettes/FOCUS_L.html | 208 ++++++++++++++++++++++++++-----------------------
vignettes/FOCUS_Z.pdf | Bin 220177 -> 213325 bytes
vignettes/mkin.pdf | Bin 160326 -> 160333 bytes
3 files changed, 111 insertions(+), 97 deletions(-)
(limited to 'vignettes')
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index 2dd186de..c0430358 100644
--- a/vignettes/FOCUS_L.html
+++ b/vignettes/FOCUS_L.html
@@ -5,6 +5,18 @@
<title>Example evaluation of FOCUS Laboratory Data L1 to L3</title>
+<script type="text/javascript">
+window.onload = function() {
+ var imgs = document.getElementsByTagName('img'), i, img;
+ for (i = 0; i < imgs.length; i++) {
+ img = imgs[i];
+ // center an image if it is the only element of its parent
+ if (img.parentElement.childElementCount === 1)
+ img.parentElement.style.textAlign = 'center';
+ }
+};
+</script>
+
<!-- Styles for R syntax highlighter -->
<style type="text/css">
pre .operator,
@@ -13,19 +25,21 @@
}
pre .literal {
- color: rgb(88, 72, 246)
+ color: #990073
}
pre .number {
- color: rgb(0, 0, 205);
+ color: #099;
}
pre .comment {
- color: rgb(76, 136, 107);
+ color: #998;
+ font-style: italic
}
pre .keyword {
- color: rgb(0, 0, 255);
+ color: #900;
+ font-weight: bold
}
pre .identifier {
@@ -33,7 +47,7 @@
}
pre .string {
- color: rgb(3, 106, 7);
+ color: #d14;
}
</style>
@@ -43,64 +57,71 @@ var hljs=new function(){function m(p){return p.replace(/&/gm,"&").replace(/<
hljs.initHighlightingOnLoad();
</script>
-<!-- MathJax scripts -->
-<script type="text/javascript" src="https://c328740.ssl.cf1.rackcdn.com/mathjax/2.0-latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
-</script>
<style type="text/css">
body, td {
font-family: sans-serif;
background-color: white;
- font-size: 12px;
- margin: 8px;
+ font-size: 13px;
+}
+
+body {
+ max-width: 800px;
+ margin: auto;
+ padding: 1em;
+ line-height: 20px;
}
tt, code, pre {
font-family: 'DejaVu Sans Mono', 'Droid Sans Mono', 'Lucida Console', Consolas, Monaco, monospace;
}
-h1 {
- font-size:2.2em;
+h1 {
+ font-size:2.2em;
}
-h2 {
- font-size:1.8em;
+h2 {
+ font-size:1.8em;
}
-h3 {
- font-size:1.4em;
+h3 {
+ font-size:1.4em;
}
-h4 {
- font-size:1.0em;
+h4 {
+ font-size:1.0em;
}
-h5 {
- font-size:0.9em;
+h5 {
+ font-size:0.9em;
}
-h6 {
- font-size:0.8em;
+h6 {
+ font-size:0.8em;
}
a:visited {
color: rgb(50%, 0%, 50%);
}
-pre {
- margin-top: 0;
- max-width: 95%;
- border: 1px solid #ccc;
- white-space: pre-wrap;
+pre, img {
+ max-width: 100%;
+}
+pre {
+ overflow-x: auto;
}
-
pre code {
display: block; padding: 0.5em;
}
-code.r, code.cpp {
- background-color: #F8F8F8;
+code {
+ font-size: 92%;
+ border: 1px solid #ccc;
+}
+
+code[class] {
+ background-color: #F8F8F8;
}
table, td, th {
@@ -123,54 +144,54 @@ hr {
}
@media print {
- * {
- background: transparent !important;
- color: black !important;
- filter:none !important;
- -ms-filter: none !important;
+ * {
+ background: transparent !important;
+ color: black !important;
+ filter:none !important;
+ -ms-filter: none !important;
}
- body {
- font-size:12pt;
- max-width:100%;
+ body {
+ font-size:12pt;
+ max-width:100%;
}
-
- a, a:visited {
- text-decoration: underline;
+
+ a, a:visited {
+ text-decoration: underline;
}
- hr {
+ hr {
visibility: hidden;
page-break-before: always;
}
- pre, blockquote {
- padding-right: 1em;
- page-break-inside: avoid;
+ pre, blockquote {
+ padding-right: 1em;
+ page-break-inside: avoid;
}
- tr, img {
- page-break-inside: avoid;
+ tr, img {
+ page-break-inside: avoid;
}
- img {
- max-width: 100% !important;
+ img {
+ max-width: 100% !important;
}
- @page :left {
- margin: 15mm 20mm 15mm 10mm;
+ @page :left {
+ margin: 15mm 20mm 15mm 10mm;
}
-
- @page :right {
- margin: 15mm 10mm 15mm 20mm;
+
+ @page :right {
+ margin: 15mm 10mm 15mm 20mm;
}
- p, h2, h3 {
- orphans: 3; widows: 3;
+ p, h2, h3 {
+ orphans: 3; widows: 3;
}
- h2, h3 {
- page-break-after: avoid;
+ h2, h3 {
+ page-break-after: avoid;
}
}
</style>
@@ -193,13 +214,7 @@ hr {
report, p. 284:</p>
<pre><code class="r">library("mkin")
-</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 +238,8 @@ summary(m.L1.SFO)
<pre><code>## mkin version: 0.9.33
## R version: 3.1.1
-## Date of fit: Mon Aug 25 10:34:14 2014
-## Date of summary: Mon Aug 25 10:34:14 2014
+## Date of fit: Sat Oct 11 11:06:43 2014
+## Date of summary: Sat Oct 11 11:06:43 2014
##
## Equations:
## d_parent = - k_parent_sink * parent
@@ -308,9 +323,8 @@ summary(m.L1.SFO)
<pre><code class="r">plot(m.L1.SFO)
</code></pre>
-<p><img src="data:image/png;base64,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" alt="plot of chunk unnamed-chunk-4"/> </p>
-
-<p>The residual plot can be easily obtained by</p>
+<p><img src="data:image/png;base64,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alt="plot of chunk unnamed-chunk-4"/>
+The residual plot can be easily obtained by</p>
<pre><code class="r">mkinresplot(m.L1.SFO, ylab = "Observed", xlab = "Time")
</code></pre>
@@ -326,15 +340,15 @@ summary(m.L1.FOMC, data = FALSE)
<pre><code>## mkin version: 0.9.33
## R version: 3.1.1
-## Date of fit: Mon Aug 25 10:34:17 2014
-## Date of summary: Mon Aug 25 10:34:17 2014
+## Date of fit: Sat Oct 11 11:06:44 2014
+## Date of summary: Sat Oct 11 11:06:44 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 0.3 s
+## Fitted with method Marq using 53 model solutions performed in 0.314 s
##
## Weighting: none
##
@@ -420,15 +434,15 @@ summary(m.L2.SFO)
<pre><code>## mkin version: 0.9.33
## R version: 3.1.1
-## Date of fit: Mon Aug 25 10:34:17 2014
-## Date of summary: Mon Aug 25 10:34:17 2014
+## Date of fit: Sat Oct 11 11:06:44 2014
+## Date of summary: Sat Oct 11 11:06:44 2014
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 29 model solutions performed in 0.184 s
+## Fitted with method Marq using 29 model solutions performed in 0.173 s
##
## Weighting: none
##
@@ -530,15 +544,15 @@ mkinresplot(m.L2.FOMC)
<pre><code>## mkin version: 0.9.33
## R version: 3.1.1
-## Date of fit: Mon Aug 25 10:34:17 2014
-## Date of summary: Mon Aug 25 10:34:17 2014
+## Date of fit: Sat Oct 11 11:06:46 2014
+## Date of summary: Sat Oct 11 11:06:47 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 0.2 s
+## Fitted with method Marq using 35 model solutions performed in 0.206 s
##
## Weighting: none
##
@@ -616,8 +630,8 @@ plot(m.L2.DFOP)
<pre><code>## mkin version: 0.9.33
## R version: 3.1.1
-## Date of fit: Mon Aug 25 10:34:18 2014
-## Date of summary: Mon Aug 25 10:34:18 2014
+## Date of fit: Sat Oct 11 11:06:47 2014
+## Date of summary: Sat Oct 11 11:06:47 2014
##
## Equations:
## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -626,7 +640,7 @@ plot(m.L2.DFOP)
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 43 model solutions performed in 0.26 s
+## Fitted with method Marq using 43 model solutions performed in 0.265 s
##
## Weighting: none
##
@@ -705,15 +719,15 @@ plot(m.L3.SFO)
<pre><code>## mkin version: 0.9.33
## R version: 3.1.1
-## Date of fit: Mon Aug 25 10:34:18 2014
-## Date of summary: Mon Aug 25 10:34:18 2014
+## Date of fit: Sat Oct 11 11:06:48 2014
+## Date of summary: Sat Oct 11 11:06:48 2014
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 44 model solutions performed in 0.252 s
+## Fitted with method Marq using 44 model solutions performed in 0.261 s
##
## Weighting: none
##
@@ -791,15 +805,15 @@ plot(m.L3.FOMC)
<pre><code>## mkin version: 0.9.33
## R version: 3.1.1
-## Date of fit: Mon Aug 25 10:34:19 2014
-## Date of summary: Mon Aug 25 10:34:19 2014
+## Date of fit: Sat Oct 11 11:06:48 2014
+## Date of summary: Sat Oct 11 11:06:48 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 0.148 s
+## Fitted with method Marq using 26 model solutions performed in 0.159 s
##
## Weighting: none
##
@@ -864,8 +878,8 @@ plot(m.L3.DFOP)
<pre><code>## mkin version: 0.9.33
## R version: 3.1.1
-## Date of fit: Mon Aug 25 10:34:19 2014
-## Date of summary: Mon Aug 25 10:34:19 2014
+## Date of fit: Sat Oct 11 11:06:50 2014
+## Date of summary: Sat Oct 11 11:06:50 2014
##
## Equations:
## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -874,7 +888,7 @@ plot(m.L3.DFOP)
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 37 model solutions performed in 0.236 s
+## Fitted with method Marq using 37 model solutions performed in 0.225 s
##
## Weighting: none
##
@@ -962,15 +976,15 @@ plot(m.L4.SFO)
<pre><code>## mkin version: 0.9.33
## R version: 3.1.1
-## Date of fit: Mon Aug 25 10:34:19 2014
-## Date of summary: Mon Aug 25 10:34:19 2014
+## Date of fit: Sat Oct 11 11:06:51 2014
+## Date of summary: Sat Oct 11 11:06:51 2014
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 20 model solutions performed in 0.123 s
+## Fitted with method Marq using 20 model solutions performed in 0.119 s
##
## Weighting: none
##
@@ -1037,15 +1051,15 @@ plot(m.L4.FOMC)
<pre><code>## mkin version: 0.9.33
## R version: 3.1.1
-## Date of fit: Mon Aug 25 10:34:20 2014
-## Date of summary: Mon Aug 25 10:34:20 2014
+## Date of fit: Sat Oct 11 11:06:51 2014
+## Date of summary: Sat Oct 11 11:06:51 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 0.281 s
+## Fitted with method Marq using 48 model solutions performed in 0.283 s
##
## Weighting: none
##
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index ca6d2506..426aa0df 100644
Binary files a/vignettes/FOCUS_Z.pdf and b/vignettes/FOCUS_Z.pdf differ
diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
index 0cc413a1..83182e65 100644
Binary files a/vignettes/mkin.pdf and b/vignettes/mkin.pdf differ
--
cgit v1.2.1
From 4510a609159216041f10a33146534f5a8366ac76 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Tue, 14 Oct 2014 22:04:54 +0200
Subject: Further formatting improvement for differential equations
---
vignettes/FOCUS_L.html | 96 ++++++++++++++++++++++++++-----------------------
vignettes/FOCUS_Z.pdf | Bin 213325 -> 220198 bytes
2 files changed, 51 insertions(+), 45 deletions(-)
(limited to 'vignettes')
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("mkin")
-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 <- 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
Binary files a/vignettes/FOCUS_Z.pdf and b/vignettes/FOCUS_Z.pdf differ
--
cgit v1.2.1
From 65d31e345f9e61e9d05584b24df6a01c6c6ed18d Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Wed, 15 Oct 2014 01:13:48 +0200
Subject: Switch to using the Port algorithm per default
---
vignettes/FOCUS_L.html | 135 ++++++++++++++++++++++++++-----------------------
vignettes/FOCUS_Z.pdf | Bin 220198 -> 220189 bytes
2 files changed, 73 insertions(+), 62 deletions(-)
(limited to 'vignettes')
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index 60c5132a..82bbd2c7 100644
--- a/vignettes/FOCUS_L.html
+++ b/vignettes/FOCUS_L.html
@@ -244,15 +244,15 @@ summary(m.L1.SFO)
<pre><code>## mkin version: 0.9.34
## R version: 3.1.1
-## Date of fit: Tue Oct 14 22:03:33 2014
-## Date of summary: Tue Oct 14 22:03:33 2014
+## Date of fit: Wed Oct 15 00:58:15 2014
+## Date of summary: Wed Oct 15 00:58:15 2014
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 14 model solutions performed in 0.081 s
+## Fitted with method Port using 37 model solutions performed in 0.203 s
##
## Weighting: none
##
@@ -272,7 +272,7 @@ summary(m.L1.SFO)
## Optimised, transformed parameters:
## Estimate Std. Error Lower Upper t value Pr(>|t|)
## parent_0 92.50 1.3700 89.60 95.40 67.6 4.34e-21
-## log_k_parent_sink -2.35 0.0406 -2.43 -2.26 -57.9 5.16e-20
+## log_k_parent_sink -2.35 0.0406 -2.43 -2.26 -57.9 5.15e-20
## Pr(>t)
## parent_0 2.17e-21
## log_k_parent_sink 2.58e-20
@@ -341,20 +341,31 @@ The residual plot can be easily obtained by</p>
is checked.</p>
<pre><code class="r">m.L1.FOMC <- mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet=TRUE)
-summary(m.L1.FOMC, data = FALSE)
+</code></pre>
+
+<pre><code>## Warning: 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: 0.9.34
## R version: 3.1.1
-## Date of fit: Tue Oct 14 22:03:34 2014
-## Date of summary: Tue Oct 14 22:03:34 2014
+## Date of fit: Wed Oct 15 00:58:16 2014
+## Date of summary: Wed Oct 15 00:58:16 2014
+##
+##
+## Warning: Optimisation by method Port did not converge.
+## Convergence code is 1
+##
##
## 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 0.289 s
+## Fitted with method Port using 188 model solutions performed in 1.011 s
##
## Weighting: none
##
@@ -375,23 +386,23 @@ summary(m.L1.FOMC, data = FALSE)
##
## Optimised, transformed parameters:
## Estimate Std. Error Lower Upper t value Pr(>|t|) Pr(>t)
-## parent_0 92.5 1.45 89.40 95.6 63.60 1.17e-19 5.85e-20
-## log_alpha 14.9 10.60 -7.75 37.5 1.40 1.82e-01 9.08e-02
-## log_beta 17.2 10.60 -5.38 39.8 1.62 1.25e-01 6.26e-02
+## parent_0 92.5 1.42 89.4 95.5 65.00 8.32e-20 4.16e-20
+## log_alpha 15.4 15.10 -16.7 47.6 1.02 3.22e-01 1.61e-01
+## log_beta 17.8 15.10 -14.4 49.9 1.18 2.57e-01 1.28e-01
##
## Parameter correlation:
## parent_0 log_alpha log_beta
-## parent_0 1.000 0.24 0.238
-## log_alpha 0.240 1.00 1.000
-## log_beta 0.238 1.00 1.000
+## parent_0 1.000 0.113 0.111
+## log_alpha 0.113 1.000 1.000
+## log_beta 0.111 1.000 1.000
##
## Residual standard error: 3.05 on 15 degrees of freedom
##
## Backtransformed parameters:
## Estimate Lower Upper
-## parent_0 9.25e+01 8.94e+01 9.56e+01
-## alpha 2.85e+06 4.32e-04 1.88e+16
-## beta 2.98e+07 4.59e-03 1.93e+17
+## parent_0 9.25e+01 8.94e+01 9.55e+01
+## alpha 5.04e+06 5.51e-08 4.62e+20
+## beta 5.28e+07 5.73e-07 4.86e+21
##
## Chi2 error levels in percent:
## err.min n.optim df
@@ -440,15 +451,15 @@ summary(m.L2.SFO)
<pre><code>## mkin version: 0.9.34
## R version: 3.1.1
-## Date of fit: Tue Oct 14 22:03:35 2014
-## Date of summary: Tue Oct 14 22:03:35 2014
+## Date of fit: Wed Oct 15 00:58:17 2014
+## Date of summary: Wed Oct 15 00:58:17 2014
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 29 model solutions performed in 0.154 s
+## Fitted with method Port using 41 model solutions performed in 0.22 s
##
## Weighting: none
##
@@ -500,10 +511,10 @@ summary(m.L2.SFO)
##
## Data:
## time variable observed predicted residual
-## 0 parent 96.1 9.15e+01 4.635
-## 0 parent 91.8 9.15e+01 0.335
-## 1 parent 41.4 4.71e+01 -5.740
-## 1 parent 38.7 4.71e+01 -8.440
+## 0 parent 96.1 9.15e+01 4.634
+## 0 parent 91.8 9.15e+01 0.334
+## 1 parent 41.4 4.71e+01 -5.739
+## 1 parent 38.7 4.71e+01 -8.439
## 3 parent 19.3 1.25e+01 6.779
## 3 parent 22.3 1.25e+01 9.779
## 7 parent 4.6 8.83e-01 3.717
@@ -522,7 +533,7 @@ plot(m.L2.SFO)
mkinresplot(m.L2.SFO)
</code></pre>
-<p><img 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alt="plot of chunk unnamed-chunk-9"/> </p>
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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
@@ -543,22 +554,22 @@ 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: 0.9.34
## R version: 3.1.1
-## Date of fit: Tue Oct 14 22:03:36 2014
-## Date of summary: Tue Oct 14 22:03:36 2014
+## Date of fit: Wed Oct 15 00:58:17 2014
+## Date of summary: Wed Oct 15 00:58:17 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 0.192 s
+## Fitted with method Port using 81 model solutions performed in 0.438 s
##
## Weighting: none
##
@@ -617,7 +628,7 @@ experimental error has to be assumed in order to explain the data.</p>
plot(m.L2.DFOP)
</code></pre>
-<p><img 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alt="plot of chunk unnamed-chunk-11"/> </p>
<p>Here, the default starting parameters for the DFOP model obviously do not lead
to a reasonable solution. Therefore the fit is repeated with different starting
@@ -629,15 +640,15 @@ parameters.</p>
plot(m.L2.DFOP)
</code></pre>
-<p><img 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alt="plot of chunk unnamed-chunk-12"/> </p>
<pre><code class="r">summary(m.L2.DFOP, data = FALSE)
</code></pre>
<pre><code>## mkin version: 0.9.34
## R version: 3.1.1
-## Date of fit: Tue Oct 14 22:03:36 2014
-## Date of summary: Tue Oct 14 22:03:36 2014
+## Date of fit: Wed Oct 15 00:58:21 2014
+## Date of summary: Wed Oct 15 00:58:21 2014
##
## Equations:
## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -646,7 +657,7 @@ plot(m.L2.DFOP)
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 43 model solutions performed in 0.24 s
+## Fitted with method Port using 336 model solutions performed in 1.844 s
##
## Weighting: none
##
@@ -669,8 +680,8 @@ plot(m.L2.DFOP)
##
## Optimised, transformed parameters:
## Estimate Std. Error Lower Upper t value Pr(>|t|) Pr(>t)
-## parent_0 94.000 NA NA NA NA NA NA
-## log_k1 6.160 NA NA NA NA NA NA
+## parent_0 93.900 NA NA NA NA NA NA
+## log_k1 3.120 NA NA NA NA NA NA
## log_k2 -1.090 NA NA NA NA NA NA
## g_ilr -0.282 NA NA NA NA NA NA
##
@@ -681,8 +692,8 @@ plot(m.L2.DFOP)
##
## Backtransformed parameters:
## Estimate Lower Upper
-## parent_0 94.000 NA NA
-## k1 476.000 NA NA
+## parent_0 93.900 NA NA
+## k1 22.700 NA NA
## k2 0.337 NA NA
## g 0.402 NA NA
##
@@ -693,7 +704,7 @@ plot(m.L2.DFOP)
##
## Estimated disappearance times:
## DT50 DT90 DT50_k1 DT50_k2
-## parent NA NA 0.00146 2.06
+## parent NA NA 0.0306 2.06
</code></pre>
<p>Here, the DFOP model is clearly the best-fit model for dataset L2 based on the
@@ -718,22 +729,22 @@ FOCUS_2006_L3_mkin <- mkin_wide_to_long(FOCUS_2006_L3)
plot(m.L3.SFO)
</code></pre>
-<p><img 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alt="plot of chunk unnamed-chunk-14"/> </p>
+<p><img 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alt="plot of chunk unnamed-chunk-14"/> </p>
<pre><code class="r">summary(m.L3.SFO)
</code></pre>
<pre><code>## mkin version: 0.9.34
## R version: 3.1.1
-## Date of fit: Tue Oct 14 22:03:37 2014
-## Date of summary: Tue Oct 14 22:03:37 2014
+## Date of fit: Wed Oct 15 00:58:22 2014
+## Date of summary: Wed Oct 15 00:58:22 2014
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 44 model solutions performed in 0.237 s
+## Fitted with method Port using 43 model solutions performed in 0.232 s
##
## Weighting: none
##
@@ -785,14 +796,14 @@ plot(m.L3.SFO)
##
## Data:
## time variable observed predicted residual
-## 0 parent 97.8 74.87 22.9274
-## 3 parent 60.0 69.41 -9.4065
+## 0 parent 97.8 74.87 22.9281
+## 3 parent 60.0 69.41 -9.4061
## 7 parent 51.0 62.73 -11.7340
-## 14 parent 43.0 52.56 -9.5634
-## 30 parent 35.0 35.08 -0.0828
-## 60 parent 22.0 16.44 5.5614
-## 91 parent 15.0 7.51 7.4896
-## 120 parent 12.0 3.61 8.3908
+## 14 parent 43.0 52.56 -9.5638
+## 30 parent 35.0 35.08 -0.0839
+## 60 parent 22.0 16.44 5.5602
+## 91 parent 15.0 7.51 7.4887
+## 120 parent 12.0 3.61 8.3903
</code></pre>
<p>The chi<sup>2</sup> error level of 21% as well as the plot suggest that the model
@@ -811,15 +822,15 @@ plot(m.L3.FOMC)
<pre><code>## mkin version: 0.9.34
## R version: 3.1.1
-## Date of fit: Tue Oct 14 22:03:37 2014
-## Date of summary: Tue Oct 14 22:03:37 2014
+## Date of fit: Wed Oct 15 00:58:22 2014
+## Date of summary: Wed Oct 15 00:58:22 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 0.139 s
+## Fitted with method Port using 83 model solutions performed in 0.442 s
##
## Weighting: none
##
@@ -884,8 +895,8 @@ plot(m.L3.DFOP)
<pre><code>## mkin version: 0.9.34
## R version: 3.1.1
-## Date of fit: Tue Oct 14 22:03:37 2014
-## Date of summary: Tue Oct 14 22:03:37 2014
+## Date of fit: Wed Oct 15 00:58:23 2014
+## Date of summary: Wed Oct 15 00:58:23 2014
##
## Equations:
## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -894,7 +905,7 @@ plot(m.L3.DFOP)
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 37 model solutions performed in 0.207 s
+## Fitted with method Port using 137 model solutions performed in 0.778 s
##
## Weighting: none
##
@@ -982,15 +993,15 @@ plot(m.L4.SFO)
<pre><code>## mkin version: 0.9.34
## R version: 3.1.1
-## Date of fit: Tue Oct 14 22:03:38 2014
-## Date of summary: Tue Oct 14 22:03:38 2014
+## Date of fit: Wed Oct 15 00:58:24 2014
+## Date of summary: Wed Oct 15 00:58:24 2014
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Marq using 20 model solutions performed in 0.106 s
+## Fitted with method Port using 46 model solutions performed in 0.246 s
##
## Weighting: none
##
@@ -1057,15 +1068,15 @@ plot(m.L4.FOMC)
<pre><code>## mkin version: 0.9.34
## R version: 3.1.1
-## Date of fit: Tue Oct 14 22:03:38 2014
-## Date of summary: Tue Oct 14 22:03:38 2014
+## Date of fit: Wed Oct 15 00:58:24 2014
+## Date of summary: Wed Oct 15 00:58:24 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 0.26 s
+## Fitted with method Port using 66 model solutions performed in 0.359 s
##
## Weighting: none
##
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index b5898b7c..0013cd5e 100644
Binary files a/vignettes/FOCUS_Z.pdf and b/vignettes/FOCUS_Z.pdf differ
--
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