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-rw-r--r--DESCRIPTION2
-rw-r--r--vignettes/FOCUS_L.html548
-rw-r--r--vignettes/FOCUS_Z.pdfbin220799 -> 214460 bytes
-rw-r--r--vignettes/mkin.pdfbin295336 -> 160336 bytes
4 files changed, 272 insertions, 278 deletions
diff --git a/DESCRIPTION b/DESCRIPTION
index b635102b..aa382e66 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -3,7 +3,7 @@ Type: Package
Title: Routines for Fitting Kinetic Models with One or More State
Variables to Chemical Degradation Data
Version: 0.9-34
-Date: 2014-11-13
+Date: 2014-11-21
Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"),
email = "jranke@uni-bremen.de"),
person("Katrin", "Lindenberger", role = "ctb"),
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index 82bbd2c7..8de60cdd 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,
@@ -243,16 +237,16 @@ summary(m.L1.SFO)
</code></pre>
<pre><code>## mkin version: 0.9.34
-## R version: 3.1.1
-## Date of fit: Wed Oct 15 00:58:15 2014
-## Date of summary: Wed Oct 15 00:58:15 2014
+## R version: 3.1.2
+## Date of fit: Fri Nov 21 19:16:16 2014
+## Date of summary: Fri Nov 21 19:16:16 2014
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 37 model solutions performed in 0.203 s
+## Fitted with method Port using 37 model solutions performed in 0.216 s
##
## Weighting: none
##
@@ -262,66 +256,66 @@ summary(m.L1.SFO)
## k_parent_sink 0.10 deparm
##
## Starting values for the transformed parameters actually optimised:
-## value lower upper
-## parent_0 89.850 -Inf Inf
-## log_k_parent_sink -2.303 -Inf Inf
+## value lower upper
+## parent_0 89.850000 -Inf Inf
+## log_k_parent_sink -2.302585 -Inf Inf
##
## Fixed parameter values:
## None
##
## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper t value Pr(&gt;|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
-## Pr(&gt;t)
-## parent_0 2.17e-21
-## log_k_parent_sink 2.58e-20
+## 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
##
## Parameter correlation:
## parent_0 log_k_parent_sink
-## parent_0 1.000 0.625
-## log_k_parent_sink 0.625 1.000
+## parent_0 1.0000 0.6248
+## log_k_parent_sink 0.6248 1.0000
##
-## Residual standard error: 2.95 on 16 degrees of freedom
+## Residual standard error: 2.948 on 16 degrees of freedom
##
## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 92.5000 89.6000 95.400
-## k_parent_sink 0.0956 0.0877 0.104
+## Estimate Lower Upper
+## parent_0 92.47000 89.57000 95.3700
+## k_parent_sink 0.09561 0.08773 0.1042
##
## Chi2 error levels in percent:
## err.min n.optim df
-## All data 3.42 2 7
-## parent 3.42 2 7
+## All data 3.424 2 7
+## parent 3.424 2 7
##
## Resulting formation fractions:
## ff
## parent_sink 1
##
## Estimated disappearance times:
-## DT50 DT90
-## parent 7.25 24.1
+## DT50 DT90
+## parent 7.249 24.08
##
## Data:
## time variable observed predicted residual
-## 0 parent 88.3 92.47 -4.171
-## 0 parent 91.4 92.47 -1.071
-## 1 parent 85.6 84.04 1.561
-## 1 parent 84.5 84.04 0.461
-## 2 parent 78.9 76.38 2.524
-## 2 parent 77.6 76.38 1.224
-## 3 parent 72.0 69.41 2.588
-## 3 parent 71.9 69.41 2.488
-## 5 parent 50.3 57.33 -7.030
-## 5 parent 59.4 57.33 2.070
-## 7 parent 47.0 47.35 -0.352
-## 7 parent 45.1 47.35 -2.252
-## 14 parent 27.7 24.25 3.453
-## 14 parent 27.3 24.25 3.053
-## 21 parent 10.0 12.42 -2.416
-## 21 parent 10.4 12.42 -2.016
-## 30 parent 2.9 5.25 -2.351
-## 30 parent 4.0 5.25 -1.251
+## 0 parent 88.3 92.471 -4.1710
+## 0 parent 91.4 92.471 -1.0710
+## 1 parent 85.6 84.039 1.5610
+## 1 parent 84.5 84.039 0.4610
+## 2 parent 78.9 76.376 2.5241
+## 2 parent 77.6 76.376 1.2241
+## 3 parent 72.0 69.412 2.5884
+## 3 parent 71.9 69.412 2.4884
+## 5 parent 50.3 57.330 -7.0301
+## 5 parent 59.4 57.330 2.0699
+## 7 parent 47.0 47.352 -0.3515
+## 7 parent 45.1 47.352 -2.2515
+## 14 parent 27.7 24.247 3.4528
+## 14 parent 27.3 24.247 3.0528
+## 21 parent 10.0 12.416 -2.4163
+## 21 parent 10.4 12.416 -2.0163
+## 30 parent 2.9 5.251 -2.3513
+## 30 parent 4.0 5.251 -1.2513
</code></pre>
<p>A plot of the fit is obtained with the plot function for mkinfit objects.</p>
@@ -343,7 +337,7 @@ is checked.</p>
<pre><code class="r">m.L1.FOMC &lt;- mkinfit(&quot;FOMC&quot;, FOCUS_2006_L1_mkin, quiet=TRUE)
</code></pre>
-<pre><code>## Warning: Optimisation by method Port did not converge.
+<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>
@@ -351,9 +345,9 @@ is checked.</p>
</code></pre>
<pre><code>## mkin version: 0.9.34
-## R version: 3.1.1
-## Date of fit: Wed Oct 15 00:58:16 2014
-## Date of summary: Wed Oct 15 00:58:16 2014
+## R version: 3.1.2
+## Date of fit: Fri Nov 21 19:16:19 2014
+## Date of summary: Fri Nov 21 19:16:19 2014
##
##
## Warning: Optimisation by method Port did not converge.
@@ -365,7 +359,7 @@ is checked.</p>
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 188 model solutions performed in 1.011 s
+## Fitted with method Port using 188 model solutions performed in 1.083 s
##
## Weighting: none
##
@@ -376,42 +370,42 @@ is checked.</p>
## beta 10.00 deparm
##
## Starting values for the transformed parameters actually optimised:
-## value lower upper
-## parent_0 89.850 -Inf Inf
-## log_alpha 0.000 -Inf Inf
-## log_beta 2.303 -Inf Inf
+## value lower upper
+## parent_0 89.850000 -Inf Inf
+## log_alpha 0.000000 -Inf Inf
+## log_beta 2.302585 -Inf Inf
##
## Fixed parameter values:
## None
##
## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper t value Pr(&gt;|t|) Pr(&gt;t)
-## 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
+## Estimate Std. Error Lower Upper t value Pr(&gt;|t|) Pr(&gt;t)
+## parent_0 92.47 1.422 89.44 95.50 65.030 8.317e-20 4.158e-20
+## log_alpha 15.43 15.080 -16.71 47.58 1.023 3.224e-01 1.612e-01
+## log_beta 17.78 15.090 -14.37 49.93 1.179 2.569e-01 1.284e-01
##
## Parameter correlation:
## parent_0 log_alpha log_beta
-## parent_0 1.000 0.113 0.111
-## log_alpha 0.113 1.000 1.000
-## log_beta 0.111 1.000 1.000
+## 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: 3.05 on 15 degrees of freedom
+## Residual standard error: 3.045 on 15 degrees of freedom
##
## Backtransformed parameters:
-## Estimate Lower Upper
-## 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
+## Estimate Lower Upper
+## parent_0 9.247e+01 8.944e+01 9.550e+01
+## alpha 5.044e+06 5.510e-08 4.618e+20
+## beta 5.276e+07 5.732e-07 4.857e+21
##
## Chi2 error levels in percent:
## err.min n.optim df
-## All data 3.62 3 6
-## parent 3.62 3 6
+## All data 3.619 3 6
+## parent 3.619 3 6
##
## Estimated disappearance times:
-## DT50 DT90 DT50back
-## parent 7.25 24.1 7.25
+## 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
@@ -450,16 +444,16 @@ summary(m.L2.SFO)
</code></pre>
<pre><code>## mkin version: 0.9.34
-## R version: 3.1.1
-## Date of fit: Wed Oct 15 00:58:17 2014
-## Date of summary: Wed Oct 15 00:58:17 2014
+## R version: 3.1.2
+## Date of fit: Fri Nov 21 19:18:44 2014
+## Date of summary: Fri Nov 21 19:18:44 2014
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 41 model solutions performed in 0.22 s
+## Fitted with method Port using 41 model solutions performed in 0.239 s
##
## Weighting: none
##
@@ -469,60 +463,60 @@ summary(m.L2.SFO)
## k_parent_sink 0.10 deparm
##
## Starting values for the transformed parameters actually optimised:
-## value lower upper
-## parent_0 93.950 -Inf Inf
-## log_k_parent_sink -2.303 -Inf Inf
+## value lower upper
+## parent_0 93.950000 -Inf Inf
+## log_k_parent_sink -2.302585 -Inf Inf
##
## Fixed parameter values:
## None
##
## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper t value Pr(&gt;|t|)
-## parent_0 91.500 3.810 83.000 99.900 24.00 3.55e-10
-## log_k_parent_sink -0.411 0.107 -0.651 -0.172 -3.83 3.33e-03
-## Pr(&gt;t)
-## parent_0 1.77e-10
-## log_k_parent_sink 1.66e-03
+## 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
##
## Parameter correlation:
## parent_0 log_k_parent_sink
-## parent_0 1.00 0.43
-## log_k_parent_sink 0.43 1.00
+## parent_0 1.0000 0.4295
+## log_k_parent_sink 0.4295 1.0000
##
## Residual standard error: 5.51 on 10 degrees of freedom
##
## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 91.500 83.000 99.900
-## k_parent_sink 0.663 0.522 0.842
+## Estimate Lower Upper
+## parent_0 91.4700 82.9800 99.9500
+## k_parent_sink 0.6629 0.5218 0.8421
##
## Chi2 error levels in percent:
## err.min n.optim df
-## All data 14.4 2 4
-## parent 14.4 2 4
+## All data 14.38 2 4
+## parent 14.38 2 4
##
## Resulting formation fractions:
## ff
## parent_sink 1
##
## Estimated disappearance times:
-## DT50 DT90
-## parent 1.05 3.47
+## DT50 DT90
+## parent 1.046 3.474
##
## Data:
## time variable observed predicted residual
-## 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
-## 7 parent 4.6 8.83e-01 3.717
-## 14 parent 2.6 8.53e-03 2.591
-## 14 parent 1.2 8.53e-03 1.191
-## 28 parent 0.3 7.96e-07 0.300
-## 28 parent 0.6 7.96e-07 0.600
+## 0 parent 96.1 9.147e+01 4.6343
+## 0 parent 91.8 9.147e+01 0.3343
+## 1 parent 41.4 4.714e+01 -5.7394
+## 1 parent 38.7 4.714e+01 -8.4394
+## 3 parent 19.3 1.252e+01 6.7790
+## 3 parent 22.3 1.252e+01 9.7790
+## 7 parent 4.6 8.834e-01 3.7166
+## 7 parent 4.6 8.834e-01 3.7166
+## 14 parent 2.6 8.532e-03 2.5915
+## 14 parent 1.2 8.532e-03 1.1915
+## 28 parent 0.3 7.958e-07 0.3000
+## 28 parent 0.6 7.958e-07 0.6000
</code></pre>
<p>The chi<sup>2</sup> error level of 14% suggests that the model does not fit very well.
@@ -560,16 +554,16 @@ mkinresplot(m.L2.FOMC)
</code></pre>
<pre><code>## mkin version: 0.9.34
-## R version: 3.1.1
-## Date of fit: Wed Oct 15 00:58:17 2014
-## Date of summary: Wed Oct 15 00:58:17 2014
+## R version: 3.1.2
+## Date of fit: Fri Nov 21 19:18:45 2014
+## Date of summary: Fri Nov 21 19:18:45 2014
##
## Equations:
## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 81 model solutions performed in 0.438 s
+## Fitted with method Port using 81 model solutions performed in 0.47 s
##
## Weighting: none
##
@@ -580,42 +574,42 @@ mkinresplot(m.L2.FOMC)
## beta 10.00 deparm
##
## Starting values for the transformed parameters actually optimised:
-## value lower upper
-## parent_0 93.950 -Inf Inf
-## log_alpha 0.000 -Inf Inf
-## log_beta 2.303 -Inf Inf
+## value lower upper
+## parent_0 93.950000 -Inf Inf
+## log_alpha 0.000000 -Inf Inf
+## log_beta 2.302585 -Inf Inf
##
## Fixed parameter values:
## None
##
## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper t value Pr(&gt;|t|) Pr(&gt;t)
-## parent_0 93.800 1.860 89.600 98.000 50.500 2.35e-12 1.17e-12
-## log_alpha 0.318 0.187 -0.104 0.740 1.700 1.23e-01 6.14e-02
-## log_beta 0.210 0.294 -0.456 0.876 0.714 4.93e-01 2.47e-01
+## 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
##
## Parameter correlation:
## parent_0 log_alpha log_beta
-## parent_0 1.0000 -0.0955 -0.186
-## log_alpha -0.0955 1.0000 0.976
-## log_beta -0.1863 0.9757 1.000
+## parent_0 1.00000 -0.09553 -0.1863
+## log_alpha -0.09553 1.00000 0.9757
+## log_beta -0.18628 0.97567 1.0000
##
-## Residual standard error: 2.63 on 9 degrees of freedom
+## Residual standard error: 2.628 on 9 degrees of freedom
##
## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 93.80 89.600 98.0
-## alpha 1.37 0.901 2.1
-## beta 1.23 0.634 2.4
+## 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
##
## Chi2 error levels in percent:
## err.min n.optim df
-## All data 6.2 3 3
-## parent 6.2 3 3
+## All data 6.205 3 3
+## parent 6.205 3 3
##
## Estimated disappearance times:
-## DT50 DT90 DT50back
-## parent 0.809 5.36 1.61
+## DT50 DT90 DT50back
+## parent 0.8092 5.356 1.612
</code></pre>
<p>The error level at which the chi<sup>2</sup> test passes is much lower in this case.
@@ -646,9 +640,9 @@ plot(m.L2.DFOP)
</code></pre>
<pre><code>## mkin version: 0.9.34
-## R version: 3.1.1
-## Date of fit: Wed Oct 15 00:58:21 2014
-## Date of summary: Wed Oct 15 00:58:21 2014
+## R version: 3.1.2
+## Date of fit: Fri Nov 21 19:18:49 2014
+## Date of summary: Fri Nov 21 19:18:49 2014
##
## Equations:
## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -657,7 +651,7 @@ plot(m.L2.DFOP)
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 336 model solutions performed in 1.844 s
+## Fitted with method Port using 336 model solutions performed in 2.026 s
##
## Weighting: none
##
@@ -669,33 +663,33 @@ plot(m.L2.DFOP)
## g 0.80 deparm
##
## Starting values for the transformed parameters actually optimised:
-## 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
+## value lower upper
+## parent_0 93.9500000 -Inf Inf
+## log_k1 0.0000000 -Inf Inf
+## log_k2 -4.6051702 -Inf Inf
+## g_ilr 0.9802581 -Inf Inf
##
## Fixed parameter values:
## None
##
## Optimised, transformed parameters:
## Estimate Std. Error Lower Upper t value Pr(&gt;|t|) Pr(&gt;t)
-## 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
+## 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
##
## Parameter correlation:
## Could not estimate covariance matrix; singular system:
##
-## Residual standard error: 1.73 on 8 degrees of freedom
+## Residual standard error: 1.732 on 8 degrees of freedom
##
## Backtransformed parameters:
## Estimate Lower Upper
-## parent_0 93.900 NA NA
-## k1 22.700 NA NA
-## k2 0.337 NA NA
-## g 0.402 NA NA
+## parent_0 93.9500 NA NA
+## k1 22.6700 NA NA
+## k2 0.3369 NA NA
+## g 0.4016 NA NA
##
## Chi2 error levels in percent:
## err.min n.optim df
@@ -704,7 +698,7 @@ plot(m.L2.DFOP)
##
## Estimated disappearance times:
## DT50 DT90 DT50_k1 DT50_k2
-## parent NA NA 0.0306 2.06
+## parent NA NA 0.03058 2.058
</code></pre>
<p>Here, the DFOP model is clearly the best-fit model for dataset L2 based on the
@@ -735,16 +729,16 @@ plot(m.L3.SFO)
</code></pre>
<pre><code>## mkin version: 0.9.34
-## R version: 3.1.1
-## Date of fit: Wed Oct 15 00:58:22 2014
-## Date of summary: Wed Oct 15 00:58:22 2014
+## R version: 3.1.2
+## Date of fit: Fri Nov 21 19:18:50 2014
+## Date of summary: Fri Nov 21 19:18:50 2014
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 43 model solutions performed in 0.232 s
+## Fitted with method Port using 43 model solutions performed in 0.254 s
##
## Weighting: none
##
@@ -754,56 +748,56 @@ plot(m.L3.SFO)
## k_parent_sink 0.1 deparm
##
## Starting values for the transformed parameters actually optimised:
-## value lower upper
-## parent_0 97.800 -Inf Inf
-## log_k_parent_sink -2.303 -Inf Inf
+## value lower upper
+## parent_0 97.800000 -Inf Inf
+## log_k_parent_sink -2.302585 -Inf Inf
##
## Fixed parameter values:
## None
##
## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper t value Pr(&gt;|t|)
-## parent_0 74.90 8.460 54.20 95.60 8.85 0.000116
-## log_k_parent_sink -3.68 0.326 -4.48 -2.88 -11.30 0.000029
-## Pr(&gt;t)
-## parent_0 5.78e-05
-## log_k_parent_sink 1.45e-05
+## 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
##
## Parameter correlation:
## parent_0 log_k_parent_sink
-## parent_0 1.000 0.548
-## log_k_parent_sink 0.548 1.000
+## parent_0 1.0000 0.5483
+## log_k_parent_sink 0.5483 1.0000
##
-## Residual standard error: 12.9 on 6 degrees of freedom
+## Residual standard error: 12.91 on 6 degrees of freedom
##
## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 74.9000 54.2000 95.6000
-## k_parent_sink 0.0253 0.0114 0.0561
+## Estimate Lower Upper
+## parent_0 74.87000 54.18000 95.57000
+## k_parent_sink 0.02527 0.01138 0.05612
##
## Chi2 error levels in percent:
## err.min n.optim df
-## All data 21.2 2 6
-## parent 21.2 2 6
+## All data 21.24 2 6
+## parent 21.24 2 6
##
## Resulting formation fractions:
## ff
## parent_sink 1
##
## Estimated disappearance times:
-## DT50 DT90
-## parent 27.4 91.1
+## DT50 DT90
+## parent 27.43 91.13
##
## Data:
## time variable observed predicted residual
-## 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 -9.5638
-## 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
+## 0 parent 97.8 74.872 22.9281
+## 3 parent 60.0 69.406 -9.4061
+## 7 parent 51.0 62.734 -11.7340
+## 14 parent 43.0 52.564 -9.5638
+## 30 parent 35.0 35.084 -0.0839
+## 60 parent 22.0 16.440 5.5602
+## 91 parent 15.0 7.511 7.4887
+## 120 parent 12.0 3.610 8.3903
</code></pre>
<p>The chi<sup>2</sup> error level of 21% as well as the plot suggest that the model
@@ -821,16 +815,16 @@ plot(m.L3.FOMC)
</code></pre>
<pre><code>## mkin version: 0.9.34
-## R version: 3.1.1
-## Date of fit: Wed Oct 15 00:58:22 2014
-## Date of summary: Wed Oct 15 00:58:22 2014
+## R version: 3.1.2
+## Date of fit: Fri Nov 21 19:18:50 2014
+## Date of summary: Fri Nov 21 19:18:50 2014
##
## Equations:
## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 83 model solutions performed in 0.442 s
+## Fitted with method Port using 83 model solutions performed in 0.496 s
##
## Weighting: none
##
@@ -841,33 +835,33 @@ plot(m.L3.FOMC)
## beta 10.0 deparm
##
## Starting values for the transformed parameters actually optimised:
-## value lower upper
-## parent_0 97.800 -Inf Inf
-## log_alpha 0.000 -Inf Inf
-## log_beta 2.303 -Inf Inf
+## value lower upper
+## parent_0 97.800000 -Inf Inf
+## log_alpha 0.000000 -Inf Inf
+## log_beta 2.302585 -Inf Inf
##
## Fixed parameter values:
## None
##
## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper t value Pr(&gt;|t|) Pr(&gt;t)
-## parent_0 97.000 4.550 85.3 109.000 21.30 4.22e-06 2.11e-06
-## log_alpha -0.862 0.170 -1.3 -0.424 -5.06 3.91e-03 1.96e-03
-## log_beta 0.619 0.474 -0.6 1.840 1.31 2.49e-01 1.24e-01
+## 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
##
## Parameter correlation:
## parent_0 log_alpha log_beta
-## parent_0 1.000 -0.151 -0.427
-## log_alpha -0.151 1.000 0.911
-## log_beta -0.427 0.911 1.000
+## parent_0 1.0000 -0.1512 -0.4271
+## log_alpha -0.1512 1.0000 0.9110
+## log_beta -0.4271 0.9110 1.0000
##
-## Residual standard error: 4.57 on 5 degrees of freedom
+## Residual standard error: 4.572 on 5 degrees of freedom
##
## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 97.000 85.300 109.000
-## alpha 0.422 0.273 0.655
-## beta 1.860 0.549 6.290
+## 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
##
## Chi2 error levels in percent:
## err.min n.optim df
@@ -875,8 +869,8 @@ plot(m.L3.FOMC)
## parent 7.32 3 5
##
## Estimated disappearance times:
-## DT50 DT90 DT50back
-## parent 7.73 431 130
+## DT50 DT90 DT50back
+## parent 7.729 431.2 129.8
</code></pre>
<p>The error level at which the chi<sup>2</sup> test passes is 7% in this case.</p>
@@ -894,9 +888,9 @@ plot(m.L3.DFOP)
</code></pre>
<pre><code>## mkin version: 0.9.34
-## R version: 3.1.1
-## Date of fit: Wed Oct 15 00:58:23 2014
-## Date of summary: Wed Oct 15 00:58:23 2014
+## R version: 3.1.2
+## Date of fit: Fri Nov 21 19:18:51 2014
+## Date of summary: Fri Nov 21 19:18:51 2014
##
## Equations:
## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -905,7 +899,7 @@ plot(m.L3.DFOP)
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 137 model solutions performed in 0.778 s
+## Fitted with method Port using 137 model solutions performed in 0.835 s
##
## Weighting: none
##
@@ -917,46 +911,46 @@ plot(m.L3.DFOP)
## g 0.50 deparm
##
## Starting values for the transformed parameters actually optimised:
-## 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
+## value lower upper
+## parent_0 97.800000 -Inf Inf
+## log_k1 -2.302585 -Inf Inf
+## log_k2 -4.605170 -Inf Inf
+## g_ilr 0.000000 -Inf Inf
##
## Fixed parameter values:
## None
##
## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper t value Pr(&gt;|t|) Pr(&gt;t)
-## parent_0 97.700 1.4400 93.800 102.0000 68.00 2.81e-07 1.40e-07
-## log_k1 -0.661 0.1330 -1.030 -0.2910 -4.96 7.72e-03 3.86e-03
-## log_k2 -4.290 0.0590 -4.450 -4.1200 -72.60 2.15e-07 1.08e-07
-## g_ilr -0.123 0.0512 -0.265 0.0193 -2.40 7.43e-02 3.72e-02
+## 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
##
## Parameter correlation:
-## parent_0 log_k1 log_k2 g_ilr
-## parent_0 1.0000 0.164 0.0131 0.425
-## log_k1 0.1640 1.000 0.4648 -0.553
-## log_k2 0.0131 0.465 1.0000 -0.663
-## g_ilr 0.4253 -0.553 -0.6631 1.000
+## parent_0 log_k1 log_k2 g_ilr
+## parent_0 1.00000 0.1640 0.01315 0.4253
+## log_k1 0.16400 1.0000 0.46478 -0.5526
+## log_k2 0.01315 0.4648 1.00000 -0.6631
+## g_ilr 0.42526 -0.5526 -0.66310 1.0000
##
-## Residual standard error: 1.44 on 4 degrees of freedom
+## Residual standard error: 1.439 on 4 degrees of freedom
##
## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 97.7000 93.8000 102.0000
-## k1 0.5160 0.3560 0.7480
-## k2 0.0138 0.0117 0.0162
-## g 0.4570 0.4070 0.5070
+## 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
##
## Chi2 error levels in percent:
## err.min n.optim df
-## All data 2.23 4 4
-## parent 2.23 4 4
+## All data 2.225 4 4
+## parent 2.225 4 4
##
## Estimated disappearance times:
-## DT50 DT90 DT50_k1 DT50_k2
-## parent 7.46 123 1.34 50.4
+## DT50 DT90 DT50_k1 DT50_k2
+## parent 7.464 123 1.343 50.37
</code></pre>
<p>Here, a look to the model plot, the confidence intervals of the parameters
@@ -992,16 +986,16 @@ plot(m.L4.SFO)
</code></pre>
<pre><code>## mkin version: 0.9.34
-## R version: 3.1.1
-## Date of fit: Wed Oct 15 00:58:24 2014
-## Date of summary: Wed Oct 15 00:58:24 2014
+## R version: 3.1.2
+## Date of fit: Fri Nov 21 19:18:53 2014
+## Date of summary: Fri Nov 21 19:18:53 2014
##
## Equations:
## d_parent = - k_parent_sink * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 46 model solutions performed in 0.246 s
+## Fitted with method Port using 46 model solutions performed in 0.268 s
##
## Weighting: none
##
@@ -1011,37 +1005,37 @@ plot(m.L4.SFO)
## k_parent_sink 0.1 deparm
##
## Starting values for the transformed parameters actually optimised:
-## value lower upper
-## parent_0 96.600 -Inf Inf
-## log_k_parent_sink -2.303 -Inf Inf
+## value lower upper
+## parent_0 96.600000 -Inf Inf
+## log_k_parent_sink -2.302585 -Inf Inf
##
## Fixed parameter values:
## None
##
## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper t value Pr(&gt;|t|)
-## parent_0 96.40 1.95 91.70 101.00 49.5 4.57e-09
-## log_k_parent_sink -5.03 0.08 -5.23 -4.83 -62.9 1.09e-09
-## Pr(&gt;t)
-## parent_0 2.28e-09
-## log_k_parent_sink 5.44e-10
+## 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
##
## Parameter correlation:
## parent_0 log_k_parent_sink
-## parent_0 1.000 0.587
-## log_k_parent_sink 0.587 1.000
+## parent_0 1.0000 0.5865
+## log_k_parent_sink 0.5865 1.0000
##
-## Residual standard error: 3.65 on 6 degrees of freedom
+## Residual standard error: 3.651 on 6 degrees of freedom
##
## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 96.40000 91.70000 1.01e+02
-## k_parent_sink 0.00654 0.00538 7.95e-03
+## Estimate Lower Upper
+## parent_0 96.440000 91.670000 1.012e+02
+## k_parent_sink 0.006541 0.005378 7.955e-03
##
## Chi2 error levels in percent:
## err.min n.optim df
-## All data 3.29 2 6
-## parent 3.29 2 6
+## All data 3.287 2 6
+## parent 3.287 2 6
##
## Resulting formation fractions:
## ff
@@ -1067,16 +1061,16 @@ plot(m.L4.FOMC)
</code></pre>
<pre><code>## mkin version: 0.9.34
-## R version: 3.1.1
-## Date of fit: Wed Oct 15 00:58:24 2014
-## Date of summary: Wed Oct 15 00:58:24 2014
+## R version: 3.1.2
+## Date of fit: Fri Nov 21 19:18:54 2014
+## Date of summary: Fri Nov 21 19:18:54 2014
##
## Equations:
## d_parent = - (alpha/beta) * ((time/beta) + 1)^-1 * parent
##
## Model predictions using solution type analytical
##
-## Fitted with method Port using 66 model solutions performed in 0.359 s
+## Fitted with method Port using 66 model solutions performed in 0.387 s
##
## Weighting: none
##
@@ -1087,42 +1081,42 @@ plot(m.L4.FOMC)
## beta 10.0 deparm
##
## Starting values for the transformed parameters actually optimised:
-## value lower upper
-## parent_0 96.600 -Inf Inf
-## log_alpha 0.000 -Inf Inf
-## log_beta 2.303 -Inf Inf
+## value lower upper
+## parent_0 96.600000 -Inf Inf
+## log_alpha 0.000000 -Inf Inf
+## log_beta 2.302585 -Inf Inf
##
## Fixed parameter values:
## None
##
## Optimised, transformed parameters:
-## Estimate Std. Error Lower Upper t value Pr(&gt;|t|) Pr(&gt;t)
-## parent_0 99.100 1.680 94.80 103.000 59.000 2.64e-08 1.32e-08
-## log_alpha -0.351 0.372 -1.31 0.607 -0.941 3.90e-01 1.95e-01
-## log_beta 4.170 0.564 2.73 5.620 7.410 7.06e-04 3.53e-04
+## 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
##
## Parameter correlation:
## parent_0 log_alpha log_beta
-## parent_0 1.000 -0.536 -0.608
-## log_alpha -0.536 1.000 0.991
-## log_beta -0.608 0.991 1.000
+## parent_0 1.0000 -0.5365 -0.6083
+## log_alpha -0.5365 1.0000 0.9913
+## log_beta -0.6083 0.9913 1.0000
##
-## Residual standard error: 2.31 on 5 degrees of freedom
+## Residual standard error: 2.315 on 5 degrees of freedom
##
## Backtransformed parameters:
-## Estimate Lower Upper
-## parent_0 99.100 94.80 103.00
-## alpha 0.704 0.27 1.83
-## beta 65.000 15.30 277.00
+## 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
##
## Chi2 error levels in percent:
## err.min n.optim df
-## All data 2.03 3 5
-## parent 2.03 3 5
+## All data 2.029 3 5
+## parent 2.029 3 5
##
## Estimated disappearance times:
-## DT50 DT90 DT50back
-## parent 109 1644 495
+## DT50 DT90 DT50back
+## parent 108.9 1644 494.9
</code></pre>
<p>The error level at which the chi<sup>2</sup> test passes is slightly lower for the FOMC
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index f215f306..0e2c5401 100644
--- a/vignettes/FOCUS_Z.pdf
+++ b/vignettes/FOCUS_Z.pdf
Binary files differ
diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf
index d14b86bf..d151878d 100644
--- a/vignettes/mkin.pdf
+++ b/vignettes/mkin.pdf
Binary files differ

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