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/404.html | 5 +- docs/articles/FOCUS_D.html | 23 +- docs/articles/FOCUS_L.html | 129 +++--- .../figure-html/unnamed-chunk-15-1.png | Bin 38622 -> 38623 bytes .../figure-html/unnamed-chunk-6-1.png | Bin 23881 -> 23884 bytes docs/articles/index.html | 7 +- docs/articles/mkin.html | 11 +- .../mkin_files/figure-html/unnamed-chunk-2-1.png | Bin 116140 -> 0 bytes docs/articles/twa.html | 9 +- docs/articles/web_only/FOCUS_Z.html | 39 +- .../figure-html/FOCUS_2006_Z_fits_10-1.png | Bin 133233 -> 133239 bytes .../figure-html/FOCUS_2006_Z_fits_11-1.png | Bin 132503 -> 132494 bytes .../figure-html/FOCUS_2006_Z_fits_11a-1.png | Bin 99562 -> 99564 bytes .../figure-html/FOCUS_2006_Z_fits_11b-1.png | Bin 22624 -> 22623 bytes .../figure-html/FOCUS_2006_Z_fits_6-1.png | Bin 133001 -> 133000 bytes .../figure-html/FOCUS_2006_Z_fits_9-1.png | Bin 110760 -> 110758 bytes docs/articles/web_only/NAFTA_examples.html | 175 ++++---- docs/articles/web_only/benchmarks.html | 335 ++++++---------- docs/articles/web_only/compiled_models.html | 81 ++-- docs/authors.html | 5 +- docs/index.html | 5 +- docs/news/index.html | 16 +- docs/pkgdown.yml | 2 +- docs/reference/AIC.mmkin.html | 6 +- docs/reference/Extract.mmkin.html | 2 +- docs/reference/NAFTA_SOP_Attachment.html | 4 +- docs/reference/confint.mkinfit.html | 78 ++-- docs/reference/create_deg_func.html | 10 +- docs/reference/experimental_data_for_UBA-1.png | Bin 107146 -> 107152 bytes docs/reference/get_deg_func.html | 5 +- docs/reference/index.html | 11 +- docs/reference/loftest-3.png | Bin 78761 -> 78754 bytes docs/reference/logistic.solution-3.png | Bin 80598 -> 0 bytes docs/reference/logistic.solution-4.png | Bin 29336 -> 0 bytes docs/reference/logistic.solution.html | 14 +- docs/reference/mccall81_245T-1.png | Bin 58310 -> 0 bytes docs/reference/mccall81_245T.html | 20 +- docs/reference/mkinfit.html | 216 +++++----- docs/reference/mkinmod.html | 2 +- docs/reference/mkinparplot-1.png | Bin 16468 -> 16468 bytes docs/reference/mkinpredict.html | 8 +- docs/reference/mmkin-3.png | Bin 100799 -> 100817 bytes docs/reference/mmkin-5.png | Bin 66958 -> 66959 bytes docs/reference/mmkin.html | 20 +- docs/reference/nlme-1.png | Bin 70555 -> 71631 bytes docs/reference/nlme.html | 31 +- docs/reference/nlme.mmkin.html | 79 ++-- docs/reference/parms.html | 105 +---- docs/reference/plot.nlme.mmkin-2.png | Bin 35346 -> 35346 bytes docs/reference/saemix-1.png | Bin 31551 -> 0 bytes docs/reference/saemix-2.png | Bin 58815 -> 0 bytes docs/reference/saemix-3.png | Bin 40023 -> 0 bytes docs/reference/saemix-4.png | Bin 37936 -> 0 bytes docs/reference/saemix-5.png | Bin 12062 -> 0 bytes docs/reference/saemix.html | 446 --------------------- docs/reference/schaefer07_complex_case-1.png | Bin 67740 -> 67741 bytes docs/reference/schaefer07_complex_case.html | 10 +- docs/reference/summary.mkinfit.html | 12 +- docs/reference/synthetic_data_for_UBA_2014.html | 36 +- docs/reference/test_data_from_UBA_2014.html | 30 +- docs/reference/transform_odeparms.html | 16 +- docs/reference/update.mkinfit.html | 2 +- docs/sitemap.xml | 3 - 63 files changed, 660 insertions(+), 1348 deletions(-) delete mode 100644 docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png delete mode 100644 docs/reference/logistic.solution-3.png delete mode 100644 docs/reference/logistic.solution-4.png delete mode 100644 docs/reference/mccall81_245T-1.png delete mode 100644 docs/reference/saemix-1.png delete mode 100644 docs/reference/saemix-2.png delete mode 100644 docs/reference/saemix-3.png delete mode 100644 docs/reference/saemix-4.png delete mode 100644 docs/reference/saemix-5.png delete mode 100644 docs/reference/saemix.html diff --git a/docs/404.html b/docs/404.html index e64d5690..29b71104 100644 --- a/docs/404.html +++ b/docs/404.html @@ -71,7 +71,7 @@ mkin - 0.9.50.3 + 0.9.50.2 @@ -108,9 +108,6 @@
  • Example evaluation of NAFTA SOP Attachment examples
    • -
  • - Some benchmark timings -
  • diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 243ebee1..cdd85f43 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -68,9 +68,6 @@
  • Example evaluation of NAFTA SOP Attachment examples
    • -
  • - Some benchmark timings -
  • @@ -100,10 +97,10 @@

    Example evaluation of FOCUS Example Dataset D

    Johannes Ranke

    -

    2020-05-14

    +

    2020-05-27

    - Source: vignettes/FOCUS_D.rmd - + Source: vignettes/FOCUS_D.Rmd + @@ -180,8 +177,8 @@ 
    summary(fit)
    ## mkin version used for fitting:    0.9.50.2 
 ## R version used for fitting:       4.0.0 
-## Date of fit:     Thu May 14 17:07:12 2020 
-## Date of summary: Thu May 14 17:07:12 2020 
+## Date of fit:     Wed May 27 07:05:33 2020 
+## Date of summary: Wed May 27 07:05:34 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent * parent
@@ -189,7 +186,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted using 421 model solutions performed in 0.167 s
+## Fitted using 421 model solutions performed in 0.166 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -228,11 +225,11 @@
 ## 
 ## Parameter correlation:
 ##                  parent_0 log_k_parent   log_k_m1 f_parent_ilr_1      sigma
-## parent_0        1.000e+00    5.174e-01 -1.688e-01     -5.471e-01 -3.214e-07
+## parent_0        1.000e+00    5.174e-01 -1.688e-01     -5.471e-01 -3.190e-07
 ## log_k_parent    5.174e-01    1.000e+00 -3.263e-01     -5.426e-01  3.168e-07
-## log_k_m1       -1.688e-01   -3.263e-01  1.000e+00      7.478e-01 -1.410e-07
-## f_parent_ilr_1 -5.471e-01   -5.426e-01  7.478e-01      1.000e+00  5.093e-10
-## sigma          -3.214e-07    3.168e-07 -1.410e-07      5.093e-10  1.000e+00
+## log_k_m1       -1.688e-01   -3.263e-01  1.000e+00      7.478e-01 -1.406e-07
+## f_parent_ilr_1 -5.471e-01   -5.426e-01  7.478e-01      1.000e+00 -1.587e-10
+## sigma          -3.190e-07    3.168e-07 -1.406e-07     -1.587e-10  1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
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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index 7b003598..6f97722c 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -71,7 +71,7 @@
       
       
         mkin
-        0.9.50.3
+        0.9.50.2
       
     
 
@@ -108,9 +108,6 @@
     
  • 
       Example evaluation of NAFTA SOP Attachment examples
     
    • 
-    
  • 
-      Some benchmark timings
-    
    •
  • @@ -157,7 +154,7 @@
    Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance
    -
    Benchmark timings for mkin
    +
    Benchmark timings for mkin on various systems
    Performance benefit by using compiled model definitions in mkin
    diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html index 37b7b1a1..5f858d57 100644 --- a/docs/articles/mkin.html +++ b/docs/articles/mkin.html @@ -68,9 +68,6 @@
  • Example evaluation of NAFTA SOP Attachment examples
    • -
  • - Some benchmark timings -
  • @@ -100,10 +97,10 @@

    Introduction to mkin

    Johannes Ranke

    -

    2020-05-14

    +

    2020-05-27

    - Source: vignettes/mkin.rmd - + Source: vignettes/mkin.Rmd + @@ -142,7 +139,7 @@ # Plot the results separately for parent and metabolites plot_sep(f_SFO_SFO_SFO, lpos = c("topright", "bottomright", "bottomright")) -

    +

    diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png deleted file mode 100644 index bdc067c1..00000000 Binary files a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png and /dev/null differ diff --git a/docs/articles/twa.html b/docs/articles/twa.html index c231e17d..e70205f2 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -68,9 +68,6 @@
  • Example evaluation of NAFTA SOP Attachment examples
    • -
  • - Some benchmark timings -

  • @@ -100,10 +97,10 @@

    Calculation of time weighted average concentrations with mkin

    Johannes Ranke

    -

    2020-05-14

    +

    2020-05-27

    - Source: vignettes/twa.rmd - + Source: vignettes/twa.Rmd + diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index 3427afb6..ccbfcc86 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -68,9 +68,6 @@
  • Example evaluation of NAFTA SOP Attachment examples
    • -
  • - Some benchmark timings -
  • @@ -100,10 +97,10 @@

    Example evaluation of FOCUS dataset Z

    Johannes Ranke

    -

    2020-05-14

    +

    2020-05-27

    - Source: vignettes/web_only/FOCUS_Z.rmd - + Source: vignettes/web_only/FOCUS_Z.Rmd + @@ -216,25 +213,25 @@ 
    plot_sep(m.Z.FOCUS)

    summary(m.Z.FOCUS, data = FALSE)$bpar
    -
    ##             Estimate se_notrans t value     Pr(>t)     Lower      Upper
-## Z0_0       96.838721   1.994275 48.5584 4.0283e-42 92.826878 100.850563
-## k_Z0        2.215400   0.118459 18.7019 1.0414e-23  1.989462   2.466998
-## k_Z1        0.478301   0.028257 16.9267 6.2411e-22  0.424705   0.538662
-## k_Z2        0.451623   0.042138 10.7176 1.6313e-14  0.374336   0.544867
-## k_Z3        0.058694   0.015246  3.8499 1.7804e-04  0.034809   0.098967
-## f_Z2_to_Z3  0.471510   0.058352  8.0804 9.6640e-11  0.357775   0.588283
-## sigma       3.984431   0.383402 10.3923 4.5575e-14  3.213126   4.755736
    +
    ##             Estimate se_notrans t value     Pr(>t)     Lower     Upper
+## Z0_0       96.840695   1.994285 48.5591 4.0254e-42 92.828744 100.85265
+## k_Z0        2.215467   0.118463 18.7018 1.0417e-23  1.989524   2.46707
+## k_Z1        0.478325   0.028259 16.9265 6.2441e-22  0.424725   0.53869
+## k_Z2        0.451638   0.042139 10.7177 1.6309e-14  0.374346   0.54489
+## k_Z3        0.058692   0.015245  3.8498 1.7807e-04  0.034806   0.09897
+## f_Z2_to_Z3  0.471484   0.058348  8.0805 9.6599e-11  0.357736   0.58827
+## sigma       3.984431   0.383402 10.3923 4.5576e-14  3.213126   4.75574
    endpoints(m.Z.FOCUS)
    ## $ff
 ##   Z2_Z3 Z2_sink 
-## 0.47151 0.52849 
+## 0.47148 0.52852 
 ## 
 ## $distimes
 ##        DT50    DT90
-## Z0  0.31288  1.0394
-## Z1  1.44919  4.8141
-## Z2  1.53479  5.0985
-## Z3 11.80955 39.2305
    +## Z0 0.31287 1.0393 +## Z1 1.44911 4.8138 +## Z2 1.53474 5.0983 +## Z3 11.80989 39.2316

    This fit corresponds to the final result chosen in Appendix 7 of the FOCUS report. Confidence intervals returned by mkin are based on internally transformed parameters, however.

    @@ -313,11 +310,11 @@ ## ## $SFORB ## Z0_b1 Z0_b2 Z3_b1 Z3_b2 -## 2.4471358 0.0075126 0.0800073 0.0000000 +## 2.4471337 0.0075125 0.0800071 0.0000000 ## ## $distimes ## DT50 DT90 DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2 -## Z0 0.3043 1.1848 0.28325 92.265 NA NA +## Z0 0.3043 1.1848 0.28325 92.266 NA NA ## Z1 1.5148 5.0320 NA NA NA NA ## Z2 1.6414 5.4526 NA NA NA NA ## Z3 NA NA NA NA 8.6636 Inf diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png index d3702fb6..96738dd0 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_10-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png index 4a6fce4f..4f3c2554 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png index dd6537b7..b8c3ed26 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11a-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png index b986c30b..132a7317 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_11b-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png index 47d806c0..b25bf26a 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_6-1.png differ diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png index 0c698299..dd5d89cd 100644 Binary files a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png and b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_9-1.png differ diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html index 46cb7aa5..b91e7ee7 100644 --- a/docs/articles/web_only/NAFTA_examples.html +++ b/docs/articles/web_only/NAFTA_examples.html @@ -68,9 +68,6 @@
  • Example evaluation of NAFTA SOP Attachment examples
    • -
  • - Some benchmark timings -
  • @@ -100,10 +97,10 @@

    Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance

    Johannes Ranke

    -

    2020-05-14

    +

    2020-05-27

    - Source: vignettes/web_only/NAFTA_examples.rmd - + Source: vignettes/web_only/NAFTA_examples.Rmd + @@ -153,7 +150,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.99e+01 1.41e-26 98.8116 101.0810 ## k1 2.67e-02 5.05e-06 0.0243 0.0295 -## k2 2.17e-12 5.00e-01 0.0000 Inf +## k2 2.86e-12 5.00e-01 0.0000 Inf ## g 6.47e-01 3.67e-06 0.6248 0.6677 ## sigma 1.27e+00 8.91e-06 0.8395 1.6929 ## @@ -162,7 +159,7 @@ ## DT50 DT90 DT50_rep ## SFO 67.7 2.25e+02 6.77e+01 ## IORE 58.2 1.07e+03 3.22e+02 -## DFOP 55.5 5.83e+11 3.20e+11 +## DFOP 55.5 4.42e+11 2.42e+11 ## ## Representative half-life: ## [1] 321.51 @@ -201,7 +198,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.84e+01 1.24e-27 97.8078 98.9187 ## k1 1.55e-02 4.10e-04 0.0143 0.0167 -## k2 1.04e-11 5.00e-01 0.0000 Inf +## k2 1.16e-11 5.00e-01 0.0000 Inf ## g 6.89e-01 2.92e-03 0.6626 0.7142 ## sigma 6.48e-01 2.38e-05 0.4147 0.8813 ## @@ -210,7 +207,7 @@ ## DT50 DT90 DT50_rep ## SFO 86.6 2.88e+02 8.66e+01 ## IORE 85.5 7.17e+02 2.16e+02 -## DFOP 83.6 1.09e+11 6.67e+10 +## DFOP 83.6 9.80e+10 5.98e+10 ## ## Representative half-life: ## [1] 215.87 @@ -249,7 +246,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.66e+01 1.57e-25 95.3476 97.8979 ## k1 2.55e-02 7.33e-06 0.0233 0.0278 -## k2 3.88e-11 5.00e-01 0.0000 Inf +## k2 4.90e-11 5.00e-01 0.0000 Inf ## g 8.61e-01 7.55e-06 0.8314 0.8867 ## sigma 1.46e+00 6.93e-06 0.9661 1.9483 ## @@ -258,7 +255,7 @@ ## DT50 DT90 DT50_rep ## SFO 38.6 1.28e+02 3.86e+01 ## IORE 34.0 1.77e+02 5.32e+01 -## DFOP 34.1 8.42e+09 1.79e+10 +## DFOP 34.1 6.66e+09 1.41e+10 ## ## Representative half-life: ## [1] 53.17 @@ -297,7 +294,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.89e+01 9.44e-49 95.4640 102.2573 ## k1 1.81e-02 1.75e-01 0.0116 0.0281 -## k2 2.30e-10 5.00e-01 0.0000 Inf +## k2 1.97e-10 5.00e-01 0.0000 Inf ## g 6.06e-01 2.19e-01 0.4826 0.7178 ## sigma 7.40e+00 2.97e-15 6.0201 8.7754 ## @@ -306,7 +303,7 @@ ## DT50 DT90 DT50_rep ## SFO 94.3 3.13e+02 9.43e+01 ## IORE 96.7 1.51e+03 4.55e+02 -## DFOP 96.4 5.95e+09 3.01e+09 +## DFOP 96.4 6.97e+09 3.52e+09 ## ## Representative half-life: ## [1] 454.55 @@ -402,7 +399,7 @@ ## Estimate Pr(>t) Lower Upper ## parent_0 9.85e+01 2.54e-20 97.390 99.672 ## k1 1.38e-01 3.52e-05 0.131 0.146 -## k2 6.69e-13 5.00e-01 0.000 Inf +## k2 6.02e-13 5.00e-01 0.000 Inf ## g 6.52e-01 8.13e-06 0.642 0.661 ## sigma 7.88e-01 6.13e-02 0.481 1.095 ## @@ -411,7 +408,7 @@ ## DT50 DT90 DT50_rep ## SFO 16.9 5.63e+01 1.69e+01 ## IORE 11.6 3.37e+02 1.01e+02 -## DFOP 10.5 1.86e+12 1.04e+12 +## DFOP 10.5 2.07e+12 1.15e+12 ## ## Representative half-life: ## [1] 101.43 @@ -421,11 +418,16 @@

    Example on page 9, lower panel

    p9b <- nafta(NAFTA_SOP_Attachment[["p9b"]])
    +
    ## Warning in sqrt(diag(covar)): NaNs produced
    +
    ## Warning in sqrt(diag(covar_notrans)): 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
    ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
    ## The half-life obtained from the IORE model may be used
    -
    plot(p9b)
    +
    plot(p9b)

    -
    print(p9b)
    +
    print(p9b)
    ## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 35.64867 23.22334 35.64867 
@@ -452,7 +454,7 @@
 ## parent_0  94.7123 1.61e-16 93.1355 96.2891
 ## k1         0.0389 1.43e-06  0.0312  0.0485
 ## k2         0.0389 6.67e-03  0.0186  0.0812
-## g          0.7742 5.00e-01  0.0000  1.0000
+## g          0.7742      NaN      NA      NA
 ## sigma      1.5957 2.50e-04  0.9135  2.2779
 ## 
 ## 
@@ -469,12 +471,12 @@
 
    
 
    
 Example on page 10
    
-
    p10 <- nafta(NAFTA_SOP_Attachment[["p10"]])
    
+
    p10 <- nafta(NAFTA_SOP_Attachment[["p10"]])
    
 
    ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
    
 
    ## The half-life obtained from the IORE model may be used
    
-
    plot(p10)
    
+
    plot(p10)
    
 
    
-
    print(p10)
    
+
    print(p10)
    
 
    ## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 899.4089 336.4348 899.4089 
@@ -497,12 +499,12 @@
 ## sigma                   4.90 1.77e-04  2.837   6.968
 ## 
 ## $DFOP
-##          Estimate   Pr(>t)   Lower   Upper
-## parent_0 101.7315 1.41e-09 91.6534 111.810
-## k1         0.0495 6.48e-04  0.0303   0.081
-## k2         0.0495 1.67e-02  0.0201   0.122
-## g          0.6634 5.00e-01  0.0000   1.000
-## sigma      8.0152 2.50e-04  4.5886  11.442
+##          Estimate   Pr(>t)   Lower    Upper
+## parent_0 101.7315 1.41e-09 91.6534 111.8097
+## k1         0.0495 6.42e-04  0.0301   0.0814
+## k2         0.0495 1.66e-02  0.0200   0.1225
+## g          0.6634 5.00e-01  0.0000   1.0000
+## sigma      8.0152 2.50e-04  4.5886  11.4418
 ## 
 ## 
 ## DTx values:
@@ -522,12 +524,12 @@
 
    
 
    
 Example on page 11
    
-
    p11 <- nafta(NAFTA_SOP_Attachment[["p11"]])
    
+
    p11 <- nafta(NAFTA_SOP_Attachment[["p11"]])
    
 
    ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
    
 
    ## The half-life obtained from the IORE model may be used
    
-
    plot(p11)
    
+
    plot(p11)
    
 
    
-
    print(p11)
    
+
    print(p11)
    
 
    ## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 579.6805 204.7932 144.7783 
@@ -565,7 +567,7 @@
 ## DFOP 4.21e+11 2.64e+12 9.56e+11
 ## 
 ## Representative half-life:
-## [1] 41148171
    
+## [1] 41148169
    
 
    In this case, the DFOP fit reported for PestDF resulted in a negative value for the slower rate constant, which is not possible in mkin. The other results are in agreement.
    
 
    
 
@@ -576,14 +578,14 @@
 
    
 
    
 Example on page 12, upper panel
    
-
    p12a <- nafta(NAFTA_SOP_Attachment[["p12a"]])
    
+
    p12a <- nafta(NAFTA_SOP_Attachment[["p12a"]])
    
 
    ## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance
 ## matrix
    
 
    ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
    
 
    ## The half-life obtained from the IORE model may be used
    
-
    plot(p12a)
    
+
    plot(p12a)
    
 
    
-
    print(p12a)
    
+
    print(p12a)
    
 
    ## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 695.4440 220.0685 695.4440 
@@ -608,8 +610,8 @@
 ## $DFOP
 ##          Estimate   Pr(>t)   Lower   Upper
 ## parent_0  100.521 2.74e-10 92.2366 108.805
-## k1          0.124 5.75e-06  0.0958   0.161
-## k2          0.124 6.72e-02  0.0319   0.484
+## k1          0.124 5.74e-06  0.0958   0.161
+## k2          0.124 6.61e-02  0.0319   0.484
 ## g           0.877 5.00e-01  0.0000   1.000
 ## sigma       7.048 2.50e-04  4.0349  10.061
 ## 
@@ -626,20 +628,20 @@
 
    
 
    
 Example on page 12, lower panel
    
-
    p12b <- nafta(NAFTA_SOP_Attachment[["p12b"]])
    
-
    ## Warning in sqrt(diag(covar)): NaNs wurden erzeugt
    
-
    ## Warning in qt(alpha/2, rdf): NaNs wurden erzeugt
    
-
    ## Warning in qt(1 - alpha/2, rdf): NaNs wurden erzeugt
    
-
    ## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt
    
-
    ## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs wurden erzeugt
    
-
    ## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt
    
+
    p12b <- nafta(NAFTA_SOP_Attachment[["p12b"]])
    
+
    ## Warning in sqrt(diag(covar)): NaNs produced
    
+
    ## Warning in qt(alpha/2, rdf): NaNs produced
    
+
    ## Warning in qt(1 - alpha/2, rdf): NaNs produced
    
+
    ## Warning in sqrt(diag(covar_notrans)): NaNs produced
    
+
    ## Warning in pt(abs(tval), rdf, lower.tail = FALSE): 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
    
 
    ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
    
 
    ## The half-life obtained from the IORE model may be used
    
-
    plot(p12b)
    
+
    plot(p12b)
    
 
    
-
    print(p12b)
    
+
    print(p12b)
    
 
    ## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 58.90242 19.06353 58.90242 
@@ -682,12 +684,16 @@
 
    
 
    
 Example on page 13
    
-
    p13 <- nafta(NAFTA_SOP_Attachment[["p13"]])
    
+
    p13 <- nafta(NAFTA_SOP_Attachment[["p13"]])
    
+
    ## 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
    
 
    ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
    
 
    ## The half-life obtained from the IORE model may be used
    
-
    plot(p13)
    
+
    plot(p13)
    
 
    
-
    print(p13)
    
+
    print(p13)
    
 
    ## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 174.5971 142.3951 174.5971 
@@ -712,9 +718,9 @@
 ## $DFOP
 ##          Estimate   Pr(>t)    Lower    Upper
 ## parent_0 92.73500 9.25e-15 8.95e+01 9.59e+01
-## k1        0.00258 4.28e-01 1.45e-08 4.61e+02
+## k1        0.00258 4.28e-01 1.70e-08 3.92e+02
 ## k2        0.00258 3.69e-08 2.20e-03 3.03e-03
-## g         0.00442 5.00e-01 0.00e+00 1.00e+00
+## g         0.00442 5.00e-01       NA       NA
 ## sigma     3.41172 1.35e-04 2.02e+00 4.80e+00
 ## 
 ## 
@@ -731,16 +737,16 @@
 
    
 
    
 DT50 not observed in the study and DFOP problems in PestDF
    
-
    p14 <- nafta(NAFTA_SOP_Attachment[["p14"]])
    
-
    ## Warning in sqrt(diag(covar)): NaNs wurden erzeugt
    
-
    ## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt
    
+
    p14 <- nafta(NAFTA_SOP_Attachment[["p14"]])
    
+
    ## 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
    
 
    ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
    
 
    ## The half-life obtained from the IORE model may be used
    
-
    plot(p14)
    
+
    plot(p14)
    
 
    
-
    print(p14)
    
+
    print(p14)
    
 
    ## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 48.43249 28.67746 27.26248 
@@ -766,7 +772,7 @@
 ##          Estimate   Pr(>t)    Lower    Upper
 ## parent_0 1.00e+02 2.96e-28 99.40280 101.2768
 ## k1       9.53e-03 1.20e-01  0.00638   0.0143
-## k2       7.70e-12 5.00e-01  0.00000      Inf
+## k2       7.29e-12 5.00e-01  0.00000      Inf
 ## g        3.98e-01 2.19e-01  0.30481   0.4998
 ## sigma    1.17e+00 7.68e-06  0.77406   1.5610
 ## 
@@ -775,7 +781,7 @@
 ##          DT50     DT90 DT50_rep
 ## SFO  2.48e+02 8.25e+02 2.48e+02
 ## IORE 4.34e+02 2.22e+04 6.70e+03
-## DFOP 2.41e+10 2.33e+11 9.00e+10
+## DFOP 2.54e+10 2.46e+11 9.51e+10
 ## 
 ## Representative half-life:
 ## [1] 6697.44
    
@@ -784,16 +790,17 @@
 
    
 
    
 N is less than 1 and DFOP fraction parameter is below zero
    
-
    p15a <- nafta(NAFTA_SOP_Attachment[["p15a"]])
    
-
    ## Warning in sqrt(diag(covar)): NaNs wurden erzeugt
    
-
    ## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt
    
+
    p15a <- nafta(NAFTA_SOP_Attachment[["p15a"]])
    
+
    ## Warning in sqrt(diag(covar)): NaNs produced
    
+
    ## Warning in sqrt(diag(covar_notrans)): 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
    
 
    ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
    
 
    ## The half-life obtained from the IORE model may be used
    
-
    plot(p15a)
    
+
    plot(p15a)
    
 
    
-
    print(p15a)
    
+
    print(p15a)
    
 
    ## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 245.5248 135.0132 245.5248 
@@ -816,12 +823,12 @@
 ## sigma                  3.105 1.78e-04  1.795  4.416
 ## 
 ## $DFOP
-##          Estimate Pr(>t)    Lower    Upper
-## parent_0 97.96752     NA 94.21914 101.7159
-## k1        0.00952     NA  0.00241   0.0377
-## k2        0.00952     NA  0.00747   0.0121
-## g         0.17247     NA       NA       NA
-## sigma     4.18778     NA  2.39747   5.9781
+##          Estimate   Pr(>t)    Lower    Upper
+## parent_0 97.96752 2.85e-13 94.21914 101.7159
+## k1        0.00952 6.80e-02  0.00277   0.0327
+## k2        0.00952 3.82e-06  0.00902   0.0100
+## g         0.17247      NaN       NA       NA
+## sigma     4.18778 2.50e-04  2.39747   5.9781
 ## 
 ## 
 ## DTx values:
@@ -832,16 +839,16 @@
 ## 
 ## Representative half-life:
 ## [1] 41.33
    
-
    p15b <- nafta(NAFTA_SOP_Attachment[["p15b"]])
    
-
    ## Warning in sqrt(diag(covar)): NaNs wurden erzeugt
    
-
    ## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt
    
+
    p15b <- nafta(NAFTA_SOP_Attachment[["p15b"]])
    
+
    ## 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
    
 
    ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
    
 
    ## The half-life obtained from the IORE model may be used
    
-
    plot(p15b)
    
+
    plot(p15b)
    
 
    
-
    print(p15b)
    
+
    print(p15b)
    
 
    ## Sums of squares:
 ##       SFO      IORE      DFOP 
 ## 106.91629  68.55574 106.91629 
@@ -858,18 +865,18 @@
 ## 
 ## $IORE
 ##                     Estimate   Pr(>t)    Lower  Upper
-## parent_0               99.83 1.81e-16 97.51348 102.14
+## parent_0               99.83 1.81e-16 97.51349 102.14
 ## k__iore_parent_sink     0.38 3.22e-01  0.00352  41.05
-## N_parent                0.00 5.00e-01 -1.07696   1.08
+## N_parent                0.00 5.00e-01 -1.07695   1.08
 ## sigma                   2.21 2.57e-04  1.23245   3.19
 ## 
 ## $DFOP
 ##          Estimate Pr(>t)    Lower    Upper
-## parent_0 1.01e+02     NA 98.24464 1.04e+02
-## k1       4.86e-03     NA  0.00068 3.47e-02
-## k2       4.86e-03     NA  0.00338 6.99e-03
+## parent_0 1.01e+02     NA 9.82e+01 1.04e+02
+## k1       4.86e-03     NA 6.75e-04 3.49e-02
+## k2       4.86e-03     NA 3.37e-03 6.99e-03
 ## g        1.50e-01     NA       NA       NA
-## sigma    2.76e+00     NA  1.58208 3.94e+00
+## sigma    2.76e+00     NA 1.58e+00 3.94e+00
 ## 
 ## 
 ## DTx values:
@@ -885,14 +892,14 @@
 
    
 
    
 The DFOP fraction parameter is greater than 1
    
-
    p16 <- nafta(NAFTA_SOP_Attachment[["p16"]])
    
+
    p16 <- nafta(NAFTA_SOP_Attachment[["p16"]])
    
 
    ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
    
 
    ## The representative half-life of the IORE model is longer than the one corresponding
    
 
    ## to the terminal degradation rate found with the DFOP model.
    
 
    ## The representative half-life obtained from the DFOP model may be used
    
-
    plot(p16)
    
+
    plot(p16)
    
 
    
-
    print(p16)
    
+
    print(p16)
    
 
    ## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 3831.804 2062.008 1550.980 
@@ -917,7 +924,7 @@
 ## $DFOP
 ##          Estimate   Pr(>t)   Lower  Upper
 ## parent_0  88.5333 7.40e-18 79.9836 97.083
-## k1        18.5560 5.00e-01  0.0000    Inf
+## k1        18.5561 5.00e-01  0.0000    Inf
 ## k2         0.0776 1.41e-05  0.0518  0.116
 ## g          0.4733 1.41e-09  0.3674  0.582
 ## sigma      7.1902 2.11e-08  5.2785  9.102
diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html
index 97e22303..0698baf6 100644
--- a/docs/articles/web_only/benchmarks.html
+++ b/docs/articles/web_only/benchmarks.html
@@ -5,13 +5,13 @@
 
 
 
-Benchmark timings for mkin • mkin
+Benchmark timings for mkin on various systems • mkin
 
 
 
 
 
-
+
 
 
-
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-  
-  
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-
-
-Create saemix models from mmkin row objects — saemix_model • mkin
-
-
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-
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-
-
-
-
-
-
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-
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-    
    
-    
    Create saemix models from mmkin row objects
    
-    Source: R/saemix.R
-    
-    
    
-
-    
    
-    
    This function sets up a nonlinear mixed effects model for an mmkin row
-object for use with the saemix package. An mmkin row object is essentially a
-list of mkinfit objects that have been obtained by fitting the same model to
-a list of datasets.
    
-    
    
-
-    
    saemix_model(object, cores = parallel::detectCores())
-
-saemix_data(object, ...)
    
-
-    
    Arguments
    
-    
-    
-    
-      
-      
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-      
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    object
    An mmkin row object containing several fits of the same model to different datasets
    cores
    The number of cores to be used for multicore processing.
-On Windows machines, cores > 1 is currently not supported.
    ...
    Further parameters passed to saemix::saemixData
    
-
-    
    Value
    
-
-    
    An saemix::SaemixModel object.
    
-
    An saemix::SaemixData object.
    
-    
    Details
    
-
-    
    Starting values for the fixed effects (population mean parameters, argument psi0 of
-saemix::saemixModel() are the mean values of the parameters found using
-mmkin. Starting variances of the random effects (argument omega.init) are the
-variances of the deviations of the parameters from these mean values.
    
-
-    
    Examples
    
-    
    ds <- lapply(experimental_data_for_UBA_2019[6:10],
- function(x) subset(x$data[c("name", "time", "value")]))
-names(ds) <- paste("Dataset", 6:10)
-sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"),
-  A1 = mkinsub("SFO"))
    #> Successfully compiled differential equation model from auto-generated C code.
    # \dontrun{
-f_mmkin <- mmkin(list("SFO-SFO" = sfo_sfo), ds, quiet = TRUE)
-library(saemix)
    #> Package saemix, version 3.1.9000
-#>   please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr
    m_saemix <- saemix_model(f_mmkin)
    #> 
-#> 
-#> The following SaemixModel object was successfully created:
-#> 
-#> Nonlinear mixed-effects model
-#>   Model function:  Mixed model generated from mmkin object  Model type:  structural
-#> function (psi, id, xidep) 
-#> {
-#>     uid <- unique(id)
-#>     res_list <- parallel::mclapply(uid, function(i) {
-#>         transparms_optim <- psi[i, ]
-#>         names(transparms_optim) <- names(degparms_optim)
-#>         odeini_optim <- transparms_optim[odeini_optim_parm_names]
-#>         names(odeini_optim) <- gsub("_0$", "", odeini_optim_parm_names)
-#>         odeini <- c(odeini_optim, odeini_fixed)[names(mkin_model$diffs)]
-#>         ode_transparms_optim_names <- setdiff(names(transparms_optim), 
-#>             odeini_optim_parm_names)
-#>         odeparms_optim <- backtransform_odeparms(transparms_optim[ode_transparms_optim_names], 
-#>             mkin_model, transform_rates = object[[1]]$transform_rates, 
-#>             transform_fractions = object[[1]]$transform_fractions)
-#>         odeparms <- c(odeparms_optim, odeparms_fixed)
-#>         xidep_i <- subset(xidep, id == i)
-#>         if (analytical) {
-#>             out_values <- mkin_model$deg_func(xidep_i, odeini, 
-#>                 odeparms)
-#>         }
-#>         else {
-#>             i_time <- xidep_i$time
-#>             i_name <- xidep_i$name
-#>             out_wide <- mkinpredict(mkin_model, odeparms = odeparms, 
-#>                 odeini = odeini, solution_type = object[[1]]$solution_type, 
-#>                 outtimes = sort(unique(i_time)))
-#>             out_index <- cbind(as.character(i_time), as.character(i_name))
-#>             out_values <- out_wide[out_index]
-#>         }
-#>         return(out_values)
-#>     }, mc.cores = cores)
-#>     res <- unlist(res_list)
-#>     return(res)
-#> }
-#> <bytecode: 0x555559668108>
-#> <environment: 0x555559677c08>
-#>   Nb of parameters: 4 
-#>       parameter names:  parent_0 log_k_parent log_k_A1 f_parent_ilr_1 
-#>       distribution:
-#>      Parameter      Distribution Estimated
-#> [1,] parent_0       normal       Estimated
-#> [2,] log_k_parent   normal       Estimated
-#> [3,] log_k_A1       normal       Estimated
-#> [4,] f_parent_ilr_1 normal       Estimated
-#>   Variance-covariance matrix:
-#>                parent_0 log_k_parent log_k_A1 f_parent_ilr_1
-#> parent_0              1            0        0              0
-#> log_k_parent          0            1        0              0
-#> log_k_A1              0            0        1              0
-#> f_parent_ilr_1        0            0        0              1
-#>   Error model: constant , initial values: a.1=1 
-#>     No covariate in the model.
-#>     Initial values
-#>              parent_0 log_k_parent  log_k_A1 f_parent_ilr_1
-#> Pop.CondInit 86.53449    -3.207005 -3.060308      -1.920449
    d_saemix <- saemix_data(f_mmkin)
    #> 
-#> 
-#> The following SaemixData object was successfully created:
-#> 
-#> Object of class SaemixData
-#>     longitudinal data for use with the SAEM algorithm
-#> Dataset ds_saemix 
-#>     Structured data: value ~ time + name | ds 
-#>     X variable for graphs: time () 
    saemix_options <- list(seed = 123456,
-  save = FALSE, save.graphs = FALSE, displayProgress = FALSE,
-  nbiter.saemix = c(200, 80))
-f_saemix <- saemix(m_saemix, d_saemix, saemix_options)
    #> Running main SAEM algorithm
-#> [1] "Tue May 26 18:25:16 2020"
-#> ..
-#>     Minimisation finished
-#> [1] "Tue May 26 18:31:09 2020"
    #> Nonlinear mixed-effects model fit by the SAEM algorithm
-#> -----------------------------------
-#> ----          Data             ----
-#> -----------------------------------
-#> Object of class SaemixData
-#>     longitudinal data for use with the SAEM algorithm
-#> Dataset ds_saemix 
-#>     Structured data: value ~ time + name | ds 
-#>     X variable for graphs: time () 
-#> Dataset characteristics:
-#>     number of subjects:     5 
-#>     number of observations: 170 
-#>     average/min/max nb obs: 34.00  /  30  /  38 
-#> First 10 lines of data:
-#>           ds time   name value mdv cens occ ytype
-#> 1  Dataset 6    0 parent  97.2   0    0   1     1
-#> 2  Dataset 6    0 parent  96.4   0    0   1     1
-#> 3  Dataset 6    3 parent  71.1   0    0   1     1
-#> 4  Dataset 6    3 parent  69.2   0    0   1     1
-#> 5  Dataset 6    6 parent  58.1   0    0   1     1
-#> 6  Dataset 6    6 parent  56.6   0    0   1     1
-#> 7  Dataset 6   10 parent  44.4   0    0   1     1
-#> 8  Dataset 6   10 parent  43.4   0    0   1     1
-#> 9  Dataset 6   20 parent  33.3   0    0   1     1
-#> 10 Dataset 6   20 parent  29.2   0    0   1     1
-#> -----------------------------------
-#> ----          Model            ----
-#> -----------------------------------
-#> Nonlinear mixed-effects model
-#>   Model function:  Mixed model generated from mmkin object  Model type:  structural
-#> function (psi, id, xidep) 
-#> {
-#>     uid <- unique(id)
-#>     res_list <- parallel::mclapply(uid, function(i) {
-#>         transparms_optim <- psi[i, ]
-#>         names(transparms_optim) <- names(degparms_optim)
-#>         odeini_optim <- transparms_optim[odeini_optim_parm_names]
-#>         names(odeini_optim) <- gsub("_0$", "", odeini_optim_parm_names)
-#>         odeini <- c(odeini_optim, odeini_fixed)[names(mkin_model$diffs)]
-#>         ode_transparms_optim_names <- setdiff(names(transparms_optim), 
-#>             odeini_optim_parm_names)
-#>         odeparms_optim <- backtransform_odeparms(transparms_optim[ode_transparms_optim_names], 
-#>             mkin_model, transform_rates = object[[1]]$transform_rates, 
-#>             transform_fractions = object[[1]]$transform_fractions)
-#>         odeparms <- c(odeparms_optim, odeparms_fixed)
-#>         xidep_i <- subset(xidep, id == i)
-#>         if (analytical) {
-#>             out_values <- mkin_model$deg_func(xidep_i, odeini, 
-#>                 odeparms)
-#>         }
-#>         else {
-#>             i_time <- xidep_i$time
-#>             i_name <- xidep_i$name
-#>             out_wide <- mkinpredict(mkin_model, odeparms = odeparms, 
-#>                 odeini = odeini, solution_type = object[[1]]$solution_type, 
-#>                 outtimes = sort(unique(i_time)))
-#>             out_index <- cbind(as.character(i_time), as.character(i_name))
-#>             out_values <- out_wide[out_index]
-#>         }
-#>         return(out_values)
-#>     }, mc.cores = cores)
-#>     res <- unlist(res_list)
-#>     return(res)
-#> }
-#> <bytecode: 0x555559668108>
-#> <environment: 0x555559677c08>
-#>   Nb of parameters: 4 
-#>       parameter names:  parent_0 log_k_parent log_k_A1 f_parent_ilr_1 
-#>       distribution:
-#>      Parameter      Distribution Estimated
-#> [1,] parent_0       normal       Estimated
-#> [2,] log_k_parent   normal       Estimated
-#> [3,] log_k_A1       normal       Estimated
-#> [4,] f_parent_ilr_1 normal       Estimated
-#>   Variance-covariance matrix:
-#>                parent_0 log_k_parent log_k_A1 f_parent_ilr_1
-#> parent_0              1            0        0              0
-#> log_k_parent          0            1        0              0
-#> log_k_A1              0            0        1              0
-#> f_parent_ilr_1        0            0        0              1
-#>   Error model: constant , initial values: a.1=1 
-#>     No covariate in the model.
-#>     Initial values
-#>              parent_0 log_k_parent  log_k_A1 f_parent_ilr_1
-#> Pop.CondInit 86.53449    -3.207005 -3.060308      -1.920449
-#> -----------------------------------
-#> ----    Key algorithm options  ----
-#> -----------------------------------
-#>     Estimation of individual parameters (MAP)
-#>     Estimation of standard errors and linearised log-likelihood
-#>     Estimation of log-likelihood by importance sampling
-#>     Number of iterations:  K1=200, K2=80 
-#>     Number of chains:  10 
-#>     Seed:  123456 
-#>     Number of MCMC iterations for IS:  5000 
-#>     Simulations:
-#>         nb of simulated datasets used for npde:  1000 
-#>         nb of simulated datasets used for VPC:  100 
-#>     Input/output
-#>         save the results to a file:  FALSE 
-#>         save the graphs to files:  FALSE 
-#> ----------------------------------------------------
-#> ----                  Results                   ----
-#> ----------------------------------------------------
-#> -----------------  Fixed effects  ------------------
-#> ----------------------------------------------------
-#>      Parameter      Estimate SE   CV(%)
-#> [1,] parent_0       86.14    1.61  1.9 
-#> [2,] log_k_parent   -3.21    0.59 18.5 
-#> [3,] log_k_A1       -4.66    0.30  6.4 
-#> [4,] f_parent_ilr_1 -0.33    0.30 91.7 
-#> [5,] a.1             4.68    0.27  5.8 
-#> ----------------------------------------------------
-#> -----------  Variance of random effects  -----------
-#> ----------------------------------------------------
-#>                Parameter             Estimate SE   CV(%)
-#> parent_0       omega2.parent_0       7.71     8.14 106  
-#> log_k_parent   omega2.log_k_parent   1.76     1.12  63  
-#> log_k_A1       omega2.log_k_A1       0.26     0.26 101  
-#> f_parent_ilr_1 omega2.f_parent_ilr_1 0.39     0.28  71  
-#> ----------------------------------------------------
-#> ------  Correlation matrix of random effects  ------
-#> ----------------------------------------------------
-#>                       omega2.parent_0 omega2.log_k_parent omega2.log_k_A1
-#> omega2.parent_0       1               0                   0              
-#> omega2.log_k_parent   0               1                   0              
-#> omega2.log_k_A1       0               0                   1              
-#> omega2.f_parent_ilr_1 0               0                   0              
-#>                       omega2.f_parent_ilr_1
-#> omega2.parent_0       0                    
-#> omega2.log_k_parent   0                    
-#> omega2.log_k_A1       0                    
-#> omega2.f_parent_ilr_1 1                    
-#> ----------------------------------------------------
-#> ---------------  Statistical criteria  -------------
-#> ----------------------------------------------------
-#> Likelihood computed by linearisation
-#>       -2LL= 1064.364 
-#>       AIC = 1082.364 
-#>       BIC = 1078.848 
-#> 
-#> Likelihood computed by importance sampling
-#>       -2LL= 1063.462 
-#>       AIC = 1081.462 
-#>       BIC = 1077.947 
-#> ----------------------------------------------------
    plot(f_saemix, plot.type = "convergence")
    #> Plotting convergence plots
    # }
-
    
-  
    
-  
-
    
-
-
-      
    
-      
    
-  
    Developed by Johannes Ranke.
    
-
    
-
-
    
-  
    Site built with pkgdown 1.5.1.
    
-
    
-
-      
    
-   
    
-
-  
-
-
-  
-
-
-
diff --git a/docs/reference/schaefer07_complex_case-1.png b/docs/reference/schaefer07_complex_case-1.png
index 40a1ed45..7cf7484d 100644
Binary files a/docs/reference/schaefer07_complex_case-1.png and b/docs/reference/schaefer07_complex_case-1.png differ
diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index dcecc9b5..70f1ee9a 100644
--- a/docs/reference/schaefer07_complex_case.html
+++ b/docs/reference/schaefer07_complex_case.html
@@ -180,15 +180,15 @@
     fit <- mkinfit(model, data, quiet = TRUE)
     plot(fit)
        endpoints(fit)
    #> $ff
 #>   parent_A1   parent_B1   parent_C1 parent_sink       A1_A2     A1_sink 
-#>   0.3809618   0.1954667   0.4235715   0.0000000   0.4479625   0.5520375 
+#>   0.3809619   0.1954667   0.4235714   0.0000000   0.4479609   0.5520391 
 #> 
 #> $distimes
 #>            DT50      DT90
 #> parent 13.95078  46.34350
-#> A1     49.75346 165.27741
-#> B1     37.26904 123.80508
-#> C1     11.23130  37.30958
-#> A2     28.50628  94.69580
+#> A1     49.75343 165.27733
+#> B1     37.26907 123.80517
+#> C1     11.23131  37.30959
+#> A2     28.50638  94.69614
 #> 
      # }
  # Compare with the results obtained in the original publication
  print(schaefer07_complex_results)
    #>         compound          parameter  KinGUI ModelMaker deviation
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 55ce22cf..ad6217e6 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -231,15 +231,15 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
     
    
   summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
    #> mkin version used for fitting:    0.9.50.2 
 #> R version used for fitting:       4.0.0 
-#> Date of fit:     Tue May 12 15:31:20 2020 
-#> Date of summary: Tue May 12 15:31:20 2020 
+#> Date of fit:     Wed May 27 07:05:18 2020 
+#> Date of summary: Wed May 27 07:05:18 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 131 model solutions performed in 0.027 s
+#> Fitted using 131 model solutions performed in 0.026 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -271,9 +271,9 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
 #> 
 #> Parameter correlation:
 #>               parent_0 log_k_parent     sigma
-#> parent_0     1.000e+00    5.428e-01 1.642e-07
-#> log_k_parent 5.428e-01    1.000e+00 2.507e-07
-#> sigma        1.642e-07    2.507e-07 1.000e+00
+#> parent_0     1.000e+00    5.428e-01 1.648e-07
+#> log_k_parent 5.428e-01    1.000e+00 2.513e-07
+#> sigma        1.648e-07    2.513e-07 1.000e+00
 #> 
 #> Backtransformed parameters:
 #> Confidence intervals for internally transformed parameters are asymmetric.
diff --git a/docs/reference/synthetic_data_for_UBA_2014.html b/docs/reference/synthetic_data_for_UBA_2014.html
index 17d2f973..1444be76 100644
--- a/docs/reference/synthetic_data_for_UBA_2014.html
+++ b/docs/reference/synthetic_data_for_UBA_2014.html
@@ -290,8 +290,8 @@ Compare also the code in the example section to see the degradation models." />
                  quiet = TRUE)
   plot_sep(fit)
      summary(fit)
    #> mkin version used for fitting:    0.9.50.2 
 #> R version used for fitting:       4.0.0 
-#> Date of fit:     Tue May 12 15:31:29 2020 
-#> Date of summary: Tue May 12 15:31:29 2020 
+#> Date of fit:     Wed May 27 07:05:27 2020 
+#> Date of summary: Wed May 27 07:05:27 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -300,7 +300,7 @@ Compare also the code in the example section to see the degradation models." />
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 819 model solutions performed in 0.619 s
+#> Fitted using 817 model solutions performed in 0.627 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -352,15 +352,15 @@ Compare also the code in the example section to see the degradation models." />
 #> log_k_M2        2.819e-02    7.166e-02 -3.929e-01  1.000e+00     -2.658e-01
 #> f_parent_ilr_1 -4.624e-01   -5.682e-01  7.478e-01 -2.658e-01      1.000e+00
 #> f_M1_ilr_1      1.614e-01    4.102e-01 -8.109e-01  5.419e-01     -8.605e-01
-#> sigma           1.285e-07    1.054e-07 -1.671e-07  3.644e-08     -2.503e-07
+#> sigma          -1.384e-07   -2.581e-07  9.499e-08  1.518e-07      1.236e-07
 #>                f_M1_ilr_1      sigma
-#> parent_0        1.614e-01  1.285e-07
-#> log_k_parent    4.102e-01  1.054e-07
-#> log_k_M1       -8.109e-01 -1.671e-07
-#> log_k_M2        5.419e-01  3.644e-08
-#> f_parent_ilr_1 -8.605e-01 -2.503e-07
-#> f_M1_ilr_1      1.000e+00  2.636e-07
-#> sigma           2.636e-07  1.000e+00
+#> parent_0        1.614e-01 -1.384e-07
+#> log_k_parent    4.102e-01 -2.581e-07
+#> log_k_M1       -8.109e-01  9.499e-08
+#> log_k_M2        5.419e-01  1.518e-07
+#> f_parent_ilr_1 -8.605e-01  1.236e-07
+#> f_M1_ilr_1      1.000e+00  8.795e-09
+#> sigma           8.795e-09  1.000e+00
 #> 
 #> Backtransformed parameters:
 #> Confidence intervals for internally transformed parameters are asymmetric.
@@ -397,8 +397,8 @@ Compare also the code in the example section to see the degradation models." />
 #> 
 #> Data:
 #>  time variable observed  predicted residual
-#>     0   parent    101.5  1.021e+02 -0.56249
-#>     0   parent    101.2  1.021e+02 -0.86249
+#>     0   parent    101.5  1.021e+02 -0.56248
+#>     0   parent    101.2  1.021e+02 -0.86248
 #>     1   parent     53.9  4.873e+01  5.17118
 #>     1   parent     47.5  4.873e+01 -1.22882
 #>     3   parent     10.4  1.111e+01 -0.70773
@@ -407,8 +407,8 @@ Compare also the code in the example section to see the degradation models." />
 #>     7   parent      0.3  5.772e-01 -0.27717
 #>    14   parent      3.5  3.264e-03  3.49674
 #>    28   parent      3.2  1.045e-07  3.20000
-#>    90   parent      0.6  9.531e-10  0.60000
-#>   120   parent      3.5 -5.940e-10  3.50000
+#>    90   parent      0.6  9.535e-10  0.60000
+#>   120   parent      3.5 -5.941e-10  3.50000
 #>     1       M1     36.4  3.479e+01  1.61088
 #>     1       M1     37.4  3.479e+01  2.61088
 #>     3       M1     34.3  3.937e+01 -5.07027
@@ -418,9 +418,9 @@ Compare also the code in the example section to see the degradation models." />
 #>    14       M1      5.8  1.995e+00  3.80469
 #>    14       M1      1.2  1.995e+00 -0.79531
 #>    60       M1      0.5  2.111e-06  0.50000
-#>    90       M1      3.2 -9.670e-10  3.20000
-#>   120       M1      1.5  7.670e-10  1.50000
-#>   120       M1      0.6  7.670e-10  0.60000
+#>    90       M1      3.2 -9.676e-10  3.20000
+#>   120       M1      1.5  7.671e-10  1.50000
+#>   120       M1      0.6  7.671e-10  0.60000
 #>     1       M2      4.8  4.455e+00  0.34517
 #>     3       M2     20.9  2.153e+01 -0.62527
 #>     3       M2     19.3  2.153e+01 -2.22527
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index 237149a5..6059a4d2 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -191,26 +191,26 @@
                     M3 = mkinsub("SFO"),
                     use_of_ff = "max")
    #> Successfully compiled differential equation model from auto-generated C code.
    
   f_soil <- mkinfit(m_soil, test_data_from_UBA_2014[[3]]$data, quiet = TRUE)
    #> Warning: Observations with value of zero were removed from the data
      plot_sep(f_soil, lpos = c("topright", "topright", "topright", "bottomright"))
      summary(f_soil)$bpar
    #>                   Estimate  se_notrans    t value       Pr(>t)        Lower
-#> parent_0       76.55425585 0.859186419 89.1008682 1.113862e-26 74.755958727
-#> k_parent        0.12081956 0.004601919 26.2541704 1.077361e-16  0.111561576
-#> k_M1            0.84258631 0.806165101  1.0451783 1.545282e-01  0.113778787
-#> k_M2            0.04210878 0.017083048  2.4649453 1.170195e-02  0.018013823
-#> k_M3            0.01122919 0.007245869  1.5497365 6.885076e-02  0.002909418
-#> f_parent_to_M1  0.32240194 0.240785506  1.3389591 9.819219e-02           NA
-#> f_parent_to_M2  0.16099854 0.033691990  4.7785405 6.531222e-05           NA
-#> f_M1_to_M3      0.27921506 0.269425556  1.0363347 1.565282e-01  0.022977927
-#> f_M2_to_M3      0.55641328 0.595121733  0.9349571 1.807710e-01  0.008002321
+#> parent_0       76.55425584 0.859186419 89.1008681 1.113862e-26 74.755958720
+#> k_parent        0.12081956 0.004601919 26.2541703 1.077361e-16  0.111561576
+#> k_M1            0.84258629 0.806165149  1.0451783 1.545282e-01  0.113778910
+#> k_M2            0.04210878 0.017083049  2.4649452 1.170195e-02  0.018013823
+#> k_M3            0.01122919 0.007245870  1.5497364 6.885076e-02  0.002909418
+#> f_parent_to_M1  0.32240193 0.240785518  1.3389590 9.819221e-02           NA
+#> f_parent_to_M2  0.16099854 0.033691991  4.7785404 6.531224e-05           NA
+#> f_M1_to_M3      0.27921506 0.269425582  1.0363346 1.565282e-01  0.022977955
+#> f_M2_to_M3      0.55641331 0.595121774  0.9349571 1.807710e-01  0.008002320
 #> sigma           1.14005399 0.149696423  7.6157731 1.727024e-07  0.826735778
 #>                      Upper
-#> parent_0       78.35255298
+#> parent_0       78.35255297
 #> k_parent        0.13084582
-#> k_M1            6.23975442
-#> k_M2            0.09843270
-#> k_M3            0.04334016
+#> k_M1            6.23974738
+#> k_M2            0.09843271
+#> k_M3            0.04334017
 #> f_parent_to_M1          NA
 #> f_parent_to_M2          NA
-#> f_M1_to_M3      0.86450919
-#> f_M2_to_M3      0.99489910
+#> f_M1_to_M3      0.86450905
+#> f_M2_to_M3      0.99489911
 #> sigma           1.45337221
      mkinerrmin(f_soil)
    #>             err.min n.optim df
 #> All data 0.09649963       9 20
 #> parent   0.04721283       2  6
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 7a9198de..9b84d6bf 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -77,7 +77,7 @@ the ilr transformation is used." />
       
       
         mkin
-        0.9.50.3
+        0.9.50.2
       
     
    
 
@@ -114,9 +114,6 @@ the ilr transformation is used." />
     
  • 
       Example evaluation of NAFTA SOP Attachment examples
     
    • 
-    
  • 
-      Some benchmark timings
-    
    •
  • @@ -214,12 +211,19 @@ fitting procedure.

    Value

    -

    A vector of transformed or backtransformed parameters

    +

    A vector of transformed or backtransformed parameters with the same +names as the original parameters.

    Details

    The transformation of sets of formation fractions is fragile, as it supposes the same ordering of the components in forward and backward transformation. This is no problem for the internal use in mkinfit.

    +

    Functions

    + + +
      +

    • backtransform_odeparms: Backtransform the set of transformed parameters

      • +

    Examples

    
@@ -241,7 +245,7 @@ This is no problem for the internal use in mkinfit<
 #> sigma           3.12550    0.35852    8.72 2.24e-10  2.39609   3.8549
    
 # \dontrun{
 # Compare to the version without transforming rate parameters
-fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
    #> Warning: Observations with value of zero were removed from the data
    #> Error in if (cost < cost.current) {    assign("cost.current", cost, inherits = TRUE)    if (!quiet)         cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"),             " at call ", calls, ": ", cost.current, "\n", sep = "")}: missing value where TRUE/FALSE needed
    #> Timing stopped at: 0.002 0.001 0.002
    fit.2.s <- summary(fit.2)
    #> Error in summary(fit.2): object 'fit.2' not found
    print(fit.2.s$par, 3)
    #> Error in print(fit.2.s$par, 3): object 'fit.2.s' not found
    print(fit.2.s$bpar, 3)
    #> Error in print(fit.2.s$bpar, 3): object 'fit.2.s' not found
    # }
+fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
    #> Warning: Observations with value of zero were removed from the data
    #> Error in if (cost < cost.current) {    assign("cost.current", cost, inherits = TRUE)    if (!quiet)         cat(ifelse(OLS, "Sum of squared residuals", "Negative log-likelihood"),             " at call ", calls, ": ", cost.current, "\n", sep = "")}: missing value where TRUE/FALSE needed
    #> Timing stopped at: 0.002 0 0.002
    fit.2.s <- summary(fit.2)
    #> Error in summary(fit.2): object 'fit.2' not found
    print(fit.2.s$par, 3)
    #> Error in print(fit.2.s$par, 3): object 'fit.2.s' not found
    print(fit.2.s$bpar, 3)
    #> Error in print(fit.2.s$bpar, 3): object 'fit.2.s' not found
    # }
 
 initials <- fit$start$value
 names(initials) <- rownames(fit$start)
diff --git a/docs/reference/update.mkinfit.html b/docs/reference/update.mkinfit.html
index f958fc14..83b8c466 100644
--- a/docs/reference/update.mkinfit.html
+++ b/docs/reference/update.mkinfit.html
@@ -177,7 +177,7 @@ remove arguments given in the original call
    
     
    # \dontrun{
 fit <- mkinfit("SFO", subset(FOCUS_2006_D, value != 0), quiet = TRUE)
 parms(fit)
    #>      parent_0 k_parent_sink         sigma 
-#>   99.44423885    0.09793574    3.39632469 
    plot_err(fit)
    fit_2 <- update(fit, error_model = "tc")
+#>   99.44423886    0.09793574    3.39632469 
    plot_err(fit)
    fit_2 <- update(fit, error_model = "tc")
 parms(fit_2)
    #>      parent_0 k_parent_sink     sigma_low      rsd_high 
 #>  1.008549e+02  1.005665e-01  3.752222e-03  6.763434e-02 
    plot_err(fit_2)
    # }
 
    
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index e284abf6..81368436 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -171,9 +171,6 @@
   
     https://pkgdown.jrwb.de/mkin/reference/residuals.mkinfit.html
   
-  
-    https://pkgdown.jrwb.de/mkin/reference/saemix.html
-  
   
     https://pkgdown.jrwb.de/mkin/reference/schaefer07_complex_case.html
   
-- 
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