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| -rw-r--r-- | DESCRIPTION | 2 | ||||
| -rw-r--r-- | vignettes/FOCUS_L.html | 548 | ||||
| -rw-r--r-- | vignettes/FOCUS_Z.pdf | bin | 220799 -> 214460 bytes | |||
| -rw-r--r-- | vignettes/mkin.pdf | bin | 295336 -> 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("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, @@ -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(>|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(>t) -## parent_0 2.17e-21 -## log_k_parent_sink 2.58e-20 +## Estimate Std. Error Lower Upper t value Pr(>|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(>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 <- mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet=TRUE) </code></pre> -<pre><code>## Warning: Optimisation by method Port did not converge. +<pre><code>## Warning in mkinfit("FOMC", 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(>|t|) Pr(>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(>|t|) Pr(>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(>|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(>t) -## parent_0 1.77e-10 -## log_k_parent_sink 1.66e-03 +## Estimate Std. Error Lower Upper t value Pr(>|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(>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(>|t|) Pr(>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(>|t|) Pr(>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(>|t|) Pr(>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(>|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(>t) -## parent_0 5.78e-05 -## log_k_parent_sink 1.45e-05 +## Estimate Std. Error Lower Upper t value Pr(>|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(>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(>|t|) Pr(>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(>|t|) Pr(>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(>|t|) Pr(>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(>|t|) Pr(>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(>|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(>t) -## parent_0 2.28e-09 -## log_k_parent_sink 5.44e-10 +## Estimate Std. Error Lower Upper t value Pr(>|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(>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(>|t|) Pr(>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(>|t|) Pr(>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 Binary files differindex f215f306..0e2c5401 100644 --- a/vignettes/FOCUS_Z.pdf +++ b/vignettes/FOCUS_Z.pdf diff --git a/vignettes/mkin.pdf b/vignettes/mkin.pdf Binary files differindex d14b86bf..d151878d 100644 --- a/vignettes/mkin.pdf +++ b/vignettes/mkin.pdf |