From 1195dfc8bdbf7c131d6c6ec30fedbbe746af1bee Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 6 May 2020 21:33:12 +0200 Subject: Change implementation of analytical solutions Preparing for symbolic solutions for more than one compound --- vignettes/FOCUS_D.html | 120 +++++++++++++++++++++++++------------------------ 1 file changed, 62 insertions(+), 58 deletions(-) (limited to 'vignettes') diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index 7a12d221..ff9d4596 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -1,17 +1,17 @@ - + - + - + Example evaluation of FOCUS Example Dataset D @@ -270,7 +270,6 @@ code { } img { max-width:100%; - height: auto; } .tabbed-pane { padding-top: 12px; @@ -332,6 +331,7 @@ summary { border: none; display: inline-block; border-radius: 4px; + background-color: transparent; } .tabset-dropdown > .nav-tabs.nav-tabs-open > li { @@ -344,18 +344,6 @@ summary { } - - @@ -377,7 +365,7 @@ $(document).ready(function () {

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

2019-05-02

+

2020-05-06

@@ -441,20 +429,20 @@ print(FOCUS_2006_D) ## "d_m1 = + k_parent_m1 * parent - k_m1_sink * m1"

We do the fitting without progress report (quiet = TRUE).

fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
-
## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
-## value of zero were removed from the data
+
## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with value
+## of zero were removed from the data

A plot of the fit including a residual plot for both observed variables is obtained using the plot_sep method for mkinfit objects, which shows separate graphs for all compounds and their residuals.

plot_sep(fit, lpos = c("topright", "bottomright"))
-

+

Confidence intervals for the parameter estimates are obtained using the mkinparplot function.

mkinparplot(fit)
-

+

A comprehensive report of the results is obtained using the summary method for mkinfit objects.

summary(fit)
-
## mkin version used for fitting:    0.9.49.4 
-## R version used for fitting:       3.6.0 
-## Date of fit:     Thu May  2 18:43:48 2019 
-## Date of summary: Thu May  2 18:43:49 2019 
+
## mkin version used for fitting:    0.9.49.11 
+## R version used for fitting:       4.0.0 
+## Date of fit:     Wed May  6 19:54:54 2020 
+## Date of summary: Wed May  6 19:54:54 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -462,18 +450,18 @@ print(FOCUS_2006_D)

 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted using 396 model solutions performed in 1.002 s
+## Fitted using 389 model solutions performed in 1.041 s
 ## 
-## Error model:
-## Constant variance 
+## Error model: Constant variance 
+## 
+## Error model algorithm: OLS 
 ## 
 ## Starting values for parameters to be optimised:
-##                    value   type
-## parent_0      100.750000  state
-## k_parent_sink   0.100000 deparm
-## k_parent_m1     0.100100 deparm
-## k_m1_sink       0.100200 deparm
-## sigma           3.125504  error
+##                  value   type
+## parent_0      100.7500  state
+## k_parent_sink   0.1000 deparm
+## k_parent_m1     0.1001 deparm
+## k_m1_sink       0.1002 deparm
 ## 
 ## Starting values for the transformed parameters actually optimised:
 ##                        value lower upper
@@ -481,7 +469,6 @@ print(FOCUS_2006_D)
## log_k_parent_sink -2.302585 -Inf Inf ## log_k_parent_m1 -2.301586 -Inf Inf ## log_k_m1_sink -2.300587 -Inf Inf -## sigma 3.125504 0 Inf ## ## Fixed parameter values: ## value type @@ -496,18 +483,18 @@ print(FOCUS_2006_D) ## sigma 3.126 0.35850 2.396 3.855 ## ## Parameter correlation: -## parent_0 log_k_parent_sink log_k_parent_m1 -## parent_0 1.000e+00 6.067e-01 -6.372e-02 -## log_k_parent_sink 6.067e-01 1.000e+00 -8.550e-02 -## log_k_parent_m1 -6.372e-02 -8.550e-02 1.000e+00 -## log_k_m1_sink -1.688e-01 -6.252e-01 4.731e-01 -## sigma -3.368e-07 3.365e-08 8.420e-07 -## log_k_m1_sink sigma -## parent_0 -1.688e-01 -3.368e-07 -## log_k_parent_sink -6.252e-01 3.365e-08 -## log_k_parent_m1 4.731e-01 8.420e-07 -## log_k_m1_sink 1.000e+00 1.958e-08 -## sigma 1.958e-08 1.000e+00 +## parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +## parent_0 1.000e+00 6.067e-01 -6.372e-02 -1.688e-01 +## log_k_parent_sink 6.067e-01 1.000e+00 -8.550e-02 -6.252e-01 +## log_k_parent_m1 -6.372e-02 -8.550e-02 1.000e+00 4.731e-01 +## log_k_m1_sink -1.688e-01 -6.252e-01 4.731e-01 1.000e+00 +## sigma 5.287e-10 3.306e-09 4.421e-08 -3.319e-10 +## sigma +## parent_0 5.287e-10 +## log_k_parent_sink 3.306e-09 +## log_k_parent_m1 4.421e-08 +## log_k_m1_sink -3.319e-10 +## sigma 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. @@ -543,10 +530,10 @@ print(FOCUS_2006_D) ## 0 parent 102.04 99.59848 2.442e+00 ## 1 parent 93.50 90.23787 3.262e+00 ## 1 parent 92.50 90.23787 2.262e+00 -## 3 parent 63.23 74.07319 -1.084e+01 -## 3 parent 68.99 74.07319 -5.083e+00 -## 7 parent 52.32 49.91206 2.408e+00 -## 7 parent 55.13 49.91206 5.218e+00 +## 3 parent 63.23 74.07320 -1.084e+01 +## 3 parent 68.99 74.07320 -5.083e+00 +## 7 parent 52.32 49.91207 2.408e+00 +## 7 parent 55.13 49.91207 5.218e+00 ## 14 parent 27.27 25.01257 2.257e+00 ## 14 parent 26.64 25.01257 1.627e+00 ## 21 parent 11.50 12.53462 -1.035e+00 @@ -556,23 +543,23 @@ print(FOCUS_2006_D) ## 50 parent 0.69 0.71624 -2.624e-02 ## 50 parent 0.63 0.71624 -8.624e-02 ## 75 parent 0.05 0.06074 -1.074e-02 -## 75 parent 0.06 0.06074 -7.381e-04 +## 75 parent 0.06 0.06074 -7.382e-04 ## 1 m1 4.84 4.80296 3.704e-02 ## 1 m1 5.64 4.80296 8.370e-01 ## 3 m1 12.91 13.02400 -1.140e-01 ## 3 m1 12.96 13.02400 -6.400e-02 ## 7 m1 22.97 25.04476 -2.075e+00 ## 7 m1 24.47 25.04476 -5.748e-01 -## 14 m1 41.69 36.69003 5.000e+00 -## 14 m1 33.21 36.69003 -3.480e+00 +## 14 m1 41.69 36.69002 5.000e+00 +## 14 m1 33.21 36.69002 -3.480e+00 ## 21 m1 44.37 41.65310 2.717e+00 ## 21 m1 46.44 41.65310 4.787e+00 ## 35 m1 41.22 43.31312 -2.093e+00 ## 35 m1 37.95 43.31312 -5.363e+00 -## 50 m1 41.19 41.21832 -2.832e-02 -## 50 m1 40.01 41.21832 -1.208e+00 -## 75 m1 40.09 36.44704 3.643e+00 -## 75 m1 33.85 36.44704 -2.597e+00 +## 50 m1 41.19 41.21831 -2.831e-02 +## 50 m1 40.01 41.21831 -1.208e+00 +## 75 m1 40.09 36.44703 3.643e+00 +## 75 m1 33.85 36.44703 -2.597e+00 ## 100 m1 31.04 31.98163 -9.416e-01 ## 100 m1 33.13 31.98163 1.148e+00 ## 120 m1 25.15 28.78984 -3.640e+00 @@ -596,6 +583,23 @@ $(document).ready(function () { + + + + + + +