From b5ee48a86e4b1d4c05aaadb80b44954e2e994ebc Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 27 May 2020 07:12:51 +0200 Subject: Add docs generated using released version 0.9.52 --- docs/articles/FOCUS_L.html | 129 ++++++++++++++++++++++----------------------- 1 file changed, 63 insertions(+), 66 deletions(-) (limited to 'docs/articles/FOCUS_L.html') diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index df5c77c4..2a58b4e5 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -68,9 +68,6 @@
  • Example evaluation of NAFTA SOP Attachment examples
    • -
  • - Some benchmark timings -
  • @@ -100,10 +97,10 @@

    Example evaluation of FOCUS Laboratory Data L1 to L3

    Johannes Ranke

    -

    2020-05-14

    +

    2020-05-27

    - Source: vignettes/FOCUS_L.rmd - + Source: vignettes/FOCUS_L.Rmd + @@ -126,15 +123,15 @@ summary(m.L1.SFO) 
    ## mkin version used for fitting:    0.9.50.2 
 ## R version used for fitting:       4.0.0 
-## Date of fit:     Thu May 14 17:07:14 2020 
-## Date of summary: Thu May 14 17:07:14 2020 
+## Date of fit:     Wed May 27 07:05:36 2020 
+## Date of summary: Wed May 27 07:05:36 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 133 model solutions performed in 0.032 s
+## Fitted using 133 model solutions performed in 0.031 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -166,9 +163,9 @@
 ## 
 ## Parameter correlation:
 ##                     parent_0 log_k_parent_sink      sigma
-## parent_0           1.000e+00         6.186e-01 -1.516e-09
-## log_k_parent_sink  6.186e-01         1.000e+00 -3.124e-09
-## sigma             -1.516e-09        -3.124e-09  1.000e+00
+## parent_0           1.000e+00         6.186e-01 -1.712e-09
+## log_k_parent_sink  6.186e-01         1.000e+00 -3.237e-09
+## sigma             -1.712e-09        -3.237e-09  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -221,14 +218,14 @@
 
    plot(m.L1.FOMC, show_errmin = TRUE, main = "FOCUS L1 - FOMC")
    
 
    
 
    summary(m.L1.FOMC, data = FALSE)
    
-
    ## Warning in sqrt(diag(covar)): NaNs wurden erzeugt
    
-
    ## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt
    
+
    ## Warning in sqrt(diag(covar)): NaNs produced
    
+
    ## Warning in sqrt(1/diag(V)): NaNs produced
    
 
    ## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
 ## doubtful
    
 
    ## mkin version used for fitting:    0.9.50.2 
 ## R version used for fitting:       4.0.0 
-## Date of fit:     Thu May 14 17:07:14 2020 
-## Date of summary: Thu May 14 17:07:14 2020 
+## Date of fit:     Wed May 27 07:05:36 2020 
+## Date of summary: Wed May 27 07:05:36 2020 
 ## 
 ## 
 ## Warning: Optimisation did not converge:
@@ -240,7 +237,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 380 model solutions performed in 0.081 s
+## Fitted using 899 model solutions performed in 0.204 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -264,31 +261,31 @@
 ## Results:
 ## 
 ##        AIC      BIC    logLik
-##   95.88778 99.44927 -43.94389
+##   95.88835 99.44984 -43.94418
 ## 
 ## Optimised, transformed parameters with symmetric confidence intervals:
 ##           Estimate Std. Error  Lower  Upper
-## parent_0     92.47     1.2820 89.720 95.220
-## log_alpha    16.92        NaN    NaN    NaN
-## log_beta     19.26        NaN    NaN    NaN
-## sigma         2.78     0.4501  1.814  3.745
+## parent_0     92.47     1.2800 89.730 95.220
+## log_alpha    10.58        NaN    NaN    NaN
+## log_beta     12.93        NaN    NaN    NaN
+## sigma         2.78     0.4507  1.813  3.747
 ## 
 ## Parameter correlation:
-##           parent_0 log_alpha log_beta    sigma
-## parent_0  1.000000       NaN      NaN 0.002218
-## log_alpha      NaN         1      NaN      NaN
-## log_beta       NaN       NaN        1      NaN
-## sigma     0.002218       NaN      NaN 1.000000
+##           parent_0 log_alpha log_beta   sigma
+## parent_0   1.00000       NaN      NaN 0.01452
+## log_alpha      NaN         1      NaN     NaN
+## log_beta       NaN       NaN        1     NaN
+## sigma      0.01452       NaN      NaN 1.00000
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
 ## t-test (unrealistically) based on the assumption of normal distribution
 ## for estimators of untransformed parameters.
-##           Estimate t value Pr(>t)  Lower  Upper
-## parent_0 9.247e+01      NA     NA 89.720 95.220
-## alpha    2.223e+07      NA     NA     NA     NA
-## beta     2.325e+08      NA     NA     NA     NA
-## sigma    2.780e+00      NA     NA  1.814  3.745
+##           Estimate  t value    Pr(>t)  Lower  Upper
+## parent_0     92.47 72.13000 1.052e-19 89.730 95.220
+## alpha     39440.00  0.02397 4.906e-01     NA     NA
+## beta     412500.00  0.02397 4.906e-01     NA     NA
+## sigma         2.78  6.00000 1.628e-05  1.813  3.747
 ## 
 ## FOCUS Chi2 error levels in percent:
 ##          err.min n.optim df
@@ -296,8 +293,8 @@
 ## parent     3.619       3  6
 ## 
 ## Estimated disappearance times:
-##        DT50  DT90 DT50back
-## parent 7.25 24.08     7.25
    
+##         DT50  DT90 DT50back
+## parent 7.249 24.08    7.249

    We get a warning that the default optimisation algorithm Port did not converge, which is an indication that the model is overparameterised, i.e. contains too many parameters that are ill-defined as a consequence.

    And in fact, 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 parameters log_alpha and log_beta internally fitted in the model have excessive confidence intervals, that span more than 25 orders of magnitude (!) when backtransformed to the scale of alpha and beta. Also, the t-test for significant difference from zero does not indicate such a significant difference, with p-values greater than 0.1, and finally, the parameter correlation of log_alpha and log_beta is 1.000, clearly 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 and 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 was the first widely used standard package in this field. Also, the calculation of \(\chi^2\) error levels was compared with KinGUII, CAKE and DegKin manager in a project sponsored by the German Umweltbundesamt (Ranke 2014).

    @@ -335,8 +332,8 @@ 
    summary(m.L2.FOMC, data = FALSE)
    ## mkin version used for fitting:    0.9.50.2 
 ## R version used for fitting:       4.0.0 
-## Date of fit:     Thu May 14 17:07:15 2020 
-## Date of summary: Thu May 14 17:07:15 2020 
+## Date of fit:     Wed May 27 07:05:37 2020 
+## Date of summary: Wed May 27 07:05:37 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -378,10 +375,10 @@
 ## 
 ## Parameter correlation:
 ##             parent_0  log_alpha   log_beta      sigma
-## parent_0   1.000e+00 -1.151e-01 -2.085e-01 -7.436e-09
+## parent_0   1.000e+00 -1.151e-01 -2.085e-01 -7.637e-09
 ## log_alpha -1.151e-01  1.000e+00  9.741e-01 -1.617e-07
-## log_beta  -2.085e-01  9.741e-01  1.000e+00 -1.386e-07
-## sigma     -7.436e-09 -1.617e-07 -1.386e-07  1.000e+00
+## log_beta  -2.085e-01  9.741e-01  1.000e+00 -1.387e-07
+## sigma     -7.637e-09 -1.617e-07 -1.387e-07  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -414,8 +411,8 @@
 
    summary(m.L2.DFOP, data = FALSE)
    
 
    ## mkin version used for fitting:    0.9.50.2 
 ## R version used for fitting:       4.0.0 
-## Date of fit:     Thu May 14 17:07:15 2020 
-## Date of summary: Thu May 14 17:07:15 2020 
+## Date of fit:     Wed May 27 07:05:37 2020 
+## Date of summary: Wed May 27 07:05:37 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -424,7 +421,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 572 model solutions performed in 0.131 s
+## Fitted using 572 model solutions performed in 0.132 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -455,18 +452,18 @@
 ## Optimised, transformed parameters with symmetric confidence intervals:
 ##          Estimate Std. Error      Lower     Upper
 ## parent_0  93.9500  9.998e-01    91.5900   96.3100
-## log_k1     3.1370  2.376e+03 -5615.0000 5622.0000
+## log_k1     3.1370  2.376e+03 -5616.0000 5622.0000
 ## log_k2    -1.0880  6.285e-02    -1.2370   -0.9394
 ## g_ilr     -0.2821  7.033e-02    -0.4484   -0.1158
 ## sigma      1.4140  2.886e-01     0.7314    2.0960
 ## 
 ## Parameter correlation:
 ##            parent_0     log_k1     log_k2      g_ilr      sigma
-## parent_0  1.000e+00  5.157e-07  2.376e-09  2.665e-01 -6.837e-09
-## log_k1    5.157e-07  1.000e+00  8.434e-05 -1.659e-04 -7.786e-06
-## log_k2    2.376e-09  8.434e-05  1.000e+00 -7.903e-01 -1.263e-08
-## g_ilr     2.665e-01 -1.659e-04 -7.903e-01  1.000e+00  3.248e-08
-## sigma    -6.837e-09 -7.786e-06 -1.263e-08  3.248e-08  1.000e+00
+## parent_0  1.000e+00  5.155e-07  2.371e-09  2.665e-01 -6.849e-09
+## log_k1    5.155e-07  1.000e+00  8.434e-05 -1.659e-04 -7.791e-06
+## log_k2    2.371e-09  8.434e-05  1.000e+00 -7.903e-01 -1.262e-08
+## g_ilr     2.665e-01 -1.659e-04 -7.903e-01  1.000e+00  3.241e-08
+## sigma    -6.849e-09 -7.791e-06 -1.262e-08  3.241e-08  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -517,8 +514,8 @@
 
    summary(mm.L3[["DFOP", 1]])
    
 
    ## mkin version used for fitting:    0.9.50.2 
 ## R version used for fitting:       4.0.0 
-## Date of fit:     Thu May 14 17:07:16 2020 
-## Date of summary: Thu May 14 17:07:16 2020 
+## Date of fit:     Wed May 27 07:05:38 2020 
+## Date of summary: Wed May 27 07:05:38 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -565,11 +562,11 @@
 ## 
 ## Parameter correlation:
 ##            parent_0     log_k1     log_k2      g_ilr      sigma
-## parent_0  1.000e+00  1.732e-01  2.282e-02  4.009e-01 -6.868e-07
-## log_k1    1.732e-01  1.000e+00  4.945e-01 -5.809e-01  3.175e-07
-## log_k2    2.282e-02  4.945e-01  1.000e+00 -6.812e-01  7.631e-07
-## g_ilr     4.009e-01 -5.809e-01 -6.812e-01  1.000e+00 -8.694e-07
-## sigma    -6.868e-07  3.175e-07  7.631e-07 -8.694e-07  1.000e+00
+## parent_0  1.000e+00  1.732e-01  2.282e-02  4.009e-01 -6.872e-07
+## log_k1    1.732e-01  1.000e+00  4.945e-01 -5.809e-01  3.200e-07
+## log_k2    2.282e-02  4.945e-01  1.000e+00 -6.812e-01  7.673e-07
+## g_ilr     4.009e-01 -5.809e-01 -6.812e-01  1.000e+00 -8.731e-07
+## sigma    -6.872e-07  3.200e-07  7.673e-07 -8.731e-07  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -626,8 +623,8 @@
 
    summary(mm.L4[["SFO", 1]], data = FALSE)
    
 
    ## mkin version used for fitting:    0.9.50.2 
 ## R version used for fitting:       4.0.0 
-## Date of fit:     Thu May 14 17:07:16 2020 
-## Date of summary: Thu May 14 17:07:16 2020 
+## Date of fit:     Wed May 27 07:05:38 2020 
+## Date of summary: Wed May 27 07:05:38 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
@@ -666,9 +663,9 @@
 ## 
 ## Parameter correlation:
 ##                    parent_0 log_k_parent_sink     sigma
-## parent_0          1.000e+00         5.938e-01 3.387e-07
-## log_k_parent_sink 5.938e-01         1.000e+00 5.830e-07
-## sigma             3.387e-07         5.830e-07 1.000e+00
+## parent_0          1.000e+00         5.938e-01 3.440e-07
+## log_k_parent_sink 5.938e-01         1.000e+00 5.885e-07
+## sigma             3.440e-07         5.885e-07 1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -690,8 +687,8 @@
 
    summary(mm.L4[["FOMC", 1]], data = FALSE)
    
 
    ## mkin version used for fitting:    0.9.50.2 
 ## R version used for fitting:       4.0.0 
-## Date of fit:     Thu May 14 17:07:16 2020 
-## Date of summary: Thu May 14 17:07:16 2020 
+## Date of fit:     Wed May 27 07:05:38 2020 
+## Date of summary: Wed May 27 07:05:38 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -733,10 +730,10 @@
 ## 
 ## Parameter correlation:
 ##             parent_0  log_alpha   log_beta      sigma
-## parent_0   1.000e+00 -4.696e-01 -5.543e-01 -2.456e-07
-## log_alpha -4.696e-01  1.000e+00  9.889e-01  2.169e-08
-## log_beta  -5.543e-01  9.889e-01  1.000e+00  4.910e-08
-## sigma     -2.456e-07  2.169e-08  4.910e-08  1.000e+00
+## parent_0   1.000e+00 -4.696e-01 -5.543e-01 -2.563e-07
+## log_alpha -4.696e-01  1.000e+00  9.889e-01  4.066e-08
+## log_beta  -5.543e-01  9.889e-01  1.000e+00  6.818e-08
+## sigma     -2.563e-07  4.066e-08  6.818e-08  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
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