From 4596667b19f032232ceb8f3f762aaad5d69c15be Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 5 Jul 2019 15:57:24 +0200 Subject: Static documentation rebuilt by pkgdown --- docs/articles/web_only/FOCUS_Z.html | 251 ++++----- .../figure-html/FOCUS_2006_Z_fits_1-1.png | Bin 84962 -> 85687 bytes .../figure-html/FOCUS_2006_Z_fits_10-1.png | Bin 127841 -> 129144 bytes .../figure-html/FOCUS_2006_Z_fits_11-1.png | Bin 127069 -> 128685 bytes .../figure-html/FOCUS_2006_Z_fits_11a-1.png | Bin 95832 -> 96948 bytes .../figure-html/FOCUS_2006_Z_fits_11b-1.png | Bin 22086 -> 22115 bytes .../figure-html/FOCUS_2006_Z_fits_2-1.png | Bin 85657 -> 86379 bytes .../figure-html/FOCUS_2006_Z_fits_3-1.png | Bin 85239 -> 85961 bytes .../figure-html/FOCUS_2006_Z_fits_5-1.png | Bin 101416 -> 102300 bytes .../figure-html/FOCUS_2006_Z_fits_6-1.png | Bin 128185 -> 129356 bytes .../figure-html/FOCUS_2006_Z_fits_7-1.png | Bin 127782 -> 129340 bytes .../figure-html/FOCUS_2006_Z_fits_9-1.png | Bin 107730 -> 108583 bytes docs/articles/web_only/NAFTA_examples.html | 589 ++++++++++----------- .../NAFTA_examples_files/figure-html/p13-1.png | Bin 51343 -> 51344 bytes .../NAFTA_examples_files/figure-html/p5a-1.png | Bin 55286 -> 55292 bytes .../NAFTA_examples_files/figure-html/p8-1.png | Bin 61400 -> 61447 bytes .../NAFTA_examples_files/figure-html/p9a-1.png | Bin 53005 -> 53005 bytes .../NAFTA_examples_files/figure-html/p9b-1.png | Bin 49914 -> 49912 bytes docs/articles/web_only/benchmarks.html | 144 +++-- docs/articles/web_only/compiled_models.html | 106 +--- 20 files changed, 463 insertions(+), 627 deletions(-) (limited to 'docs/articles/web_only') diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html index 4a856b71..2a59b69d 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -30,7 +30,7 @@ mkin - 0.9.49.5 + 0.9.49.6 @@ -88,7 +88,7 @@

Example evaluation of FOCUS dataset Z

Johannes Ranke

-

2019-07-04

+

2019-07-05

@@ -125,92 +125,82 @@ 
Z.2a <- mkinmod(Z0 = mkinsub("SFO", "Z1"),
                 Z1 = mkinsub("SFO"))
## Successfully compiled differential equation model from auto-generated C code.
-
m.Z.2a <- mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE)
-
## Warning in mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE): Observations
-## with value of zero were removed from the data
-
plot_sep(m.Z.2a)
+
m.Z.2a <- mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE)
+plot_sep(m.Z.2a)

-
summary(m.Z.2a, data = FALSE)$bpar
-
##             Estimate se_notrans    t value     Pr(>t)    Lower    Upper
-## Z0_0      9.7015e+01   3.393176 2.8591e+01 6.4352e-21 91.66556 102.3642
-## k_Z0_sink 7.2231e-10   0.225254 3.2067e-09 5.0000e-01  0.00000      Inf
-## k_Z0_Z1   2.2360e+00   0.159134 1.4051e+01 1.1369e-13  1.95303   2.5600
-## k_Z1_sink 4.8212e-01   0.065454 7.3658e+00 5.1186e-08  0.40341   0.5762
-## sigma     4.8041e+00   0.637618 7.5345e+00 3.4431e-08  3.52677   6.0815
+
summary(m.Z.2a, data = FALSE)$bpar
+
##             Estimate se_notrans    t value     Pr(>t)   Lower     Upper
+## Z0_0      9.7015e+01   3.553140 2.7304e+01 1.6792e-21 91.4112 102.61853
+## k_Z0_sink 7.2008e-10   0.226895 3.1736e-09 5.0000e-01  0.0000       Inf
+## k_Z0_Z1   2.2360e+00   0.165074 1.3545e+01 7.3943e-14  1.8393   2.71827
+## k_Z1_sink 4.8212e-01   0.065854 7.3212e+00 3.5520e-08  0.4006   0.58023

As obvious from the parameter summary (the component of the summary), the kinetic rate constant from parent compound Z to sink is very small and the t-test for this parameter suggests that it is not significantly different from zero. This suggests, in agreement with the analysis in the FOCUS kinetics report, to simplify the model by removing the pathway to sink.

A similar result can be obtained when formation fractions are used in the model formulation:

-
Z.2a.ff <- mkinmod(Z0 = mkinsub("SFO", "Z1"),
-                   Z1 = mkinsub("SFO"),
-                   use_of_ff = "max")
+
Z.2a.ff <- mkinmod(Z0 = mkinsub("SFO", "Z1"),
+                   Z1 = mkinsub("SFO"),
+                   use_of_ff = "max")
## Successfully compiled differential equation model from auto-generated C code.
-
m.Z.2a.ff <- mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE)
-
## Warning in mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE): Observations
-## with value of zero were removed from the data
-
plot_sep(m.Z.2a.ff)
+
m.Z.2a.ff <- mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE)
+plot_sep(m.Z.2a.ff)

-
summary(m.Z.2a.ff, data = FALSE)$bpar
-
##            Estimate se_notrans t value     Pr(>t)    Lower    Upper
-## Z0_0       97.01488   3.301084 29.3888 3.2971e-21 91.66556 102.3642
-## k_Z0        2.23601   0.207078 10.7979 3.3309e-11  1.95303   2.5600
-## k_Z1        0.48212   0.063265  7.6207 2.8155e-08  0.40341   0.5762
-## f_Z0_to_Z1  1.00000   0.094764 10.5525 5.3560e-11  0.00000   1.0000
-## sigma       4.80411   0.635638  7.5579 3.2592e-08  3.52677   6.0815
+
summary(m.Z.2a.ff, data = FALSE)$bpar
+
## Warning in summary.mkinfit(m.Z.2a.ff, data = FALSE): Could not estimate
+## covariance matrix; singular system.
+
##            Estimate se_notrans t value     Pr(>t) Lower Upper
+## Z0_0       97.01488   3.553145 27.3040 1.6793e-21    NA    NA
+## k_Z0        2.23601   0.216848 10.3114 3.6620e-11    NA    NA
+## k_Z1        0.48212   0.065854  7.3211 3.5520e-08    NA    NA
+## f_Z0_to_Z1  1.00000   0.101473  9.8548 9.7068e-11    NA    NA

Here, the ilr transformed formation fraction fitted in the model takes a very large value, and the backtransformed formation fraction from parent Z to Z1 is practically unity. Here, the covariance matrix used for the calculation of confidence intervals is not returned as the model is overparameterised.

A simplified model is obtained by removing the pathway to the sink.

In the following, we use the parameterisation with formation fractions in order to be able to compare with the results in the FOCUS guidance, and as it makes it easier to use parameters obtained in a previous fit when adding a further metabolite.

-
Z.3 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
-               Z1 = mkinsub("SFO"), use_of_ff = "max")
+
Z.3 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
+               Z1 = mkinsub("SFO"), use_of_ff = "max")
## Successfully compiled differential equation model from auto-generated C code.
-
m.Z.3 <- mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE)
-
## Warning in mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
-## value of zero were removed from the data
-
plot_sep(m.Z.3)
+
m.Z.3 <- mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE)
+plot_sep(m.Z.3)

-
summary(m.Z.3, data = FALSE)$bpar
-
##       Estimate se_notrans t value     Pr(>t)    Lower    Upper
-## Z0_0  97.01488   2.597342  37.352 2.0106e-24 91.67597 102.3538
-## k_Z0   2.23601   0.146904  15.221 9.1477e-15  1.95354   2.5593
-## k_Z1   0.48212   0.041727  11.554 4.8268e-12  0.40355   0.5760
-## sigma  4.80411   0.620208   7.746 1.6110e-08  3.52925   6.0790
+
summary(m.Z.3, data = FALSE)$bpar
+
##      Estimate se_notrans t value     Pr(>t)    Lower   Upper
+## Z0_0 97.01488   2.681770  36.176 2.3636e-25 91.52153 102.508
+## k_Z0  2.23601   0.146862  15.225 2.2469e-15  1.95453   2.558
+## k_Z1  0.48212   0.042687  11.294 3.0685e-12  0.40216   0.578

As there is only one transformation product for Z0 and no pathway to sink, the formation fraction is internally fixed to unity.

Metabolites Z2 and Z3

As suggested in the FOCUS report, the pathway to sink was removed for metabolite Z1 as well in the next step. While this step appears questionable on the basis of the above results, it is followed here for the purpose of comparison. Also, in the FOCUS report, it is assumed that there is additional empirical evidence that Z1 quickly and exclusively hydrolyses to Z2.

-
Z.5 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
-               Z1 = mkinsub("SFO", "Z2", sink = FALSE),
-               Z2 = mkinsub("SFO"), use_of_ff = "max")
+
Z.5 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
+               Z1 = mkinsub("SFO", "Z2", sink = FALSE),
+               Z2 = mkinsub("SFO"), use_of_ff = "max")
## Successfully compiled differential equation model from auto-generated C code.
-
m.Z.5 <- mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE)
-
## Warning in mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with
-## value of zero were removed from the data
-
plot_sep(m.Z.5)
+
m.Z.5 <- mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE)
+plot_sep(m.Z.5)

Finally, metabolite Z3 is added to the model. We use the optimised differential equation parameter values from the previous fit in order to accelerate the optimization.

-
Z.FOCUS <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
-                   Z1 = mkinsub("SFO", "Z2", sink = FALSE),
-                   Z2 = mkinsub("SFO", "Z3"),
-                   Z3 = mkinsub("SFO"),
-                   use_of_ff = "max")
+
Z.FOCUS <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
+                   Z1 = mkinsub("SFO", "Z2", sink = FALSE),
+                   Z2 = mkinsub("SFO", "Z3"),
+                   Z3 = mkinsub("SFO"),
+                   use_of_ff = "max")
## Successfully compiled differential equation model from auto-generated C code.
- -
## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.
-## 5$bparms.ode, : Observations with value of zero were removed from the data
-
plot_sep(m.Z.FOCUS)
+ +
## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : Optimisation by method Port did not converge:
+## false convergence (8)
+
plot_sep(m.Z.FOCUS)

-
summary(m.Z.FOCUS, data = FALSE)$bpar
-
##             Estimate se_notrans t value     Pr(>t)     Lower      Upper
-## Z0_0       96.838607   1.994273 48.5584 4.0283e-42 92.826626 100.850589
-## k_Z0        2.215405   0.118459 18.7018 1.0415e-23  1.989465   2.467003
-## k_Z1        0.478300   0.028257 16.9267 6.2408e-22  0.424701   0.538662
-## k_Z2        0.451618   0.042138 10.7177 1.6308e-14  0.374328   0.544867
-## k_Z3        0.058693   0.015246  3.8498 1.7806e-04  0.034805   0.098978
-## f_Z2_to_Z3  0.471508   0.058352  8.0804 9.6648e-11  0.357735   0.588320
-## sigma       3.984431   0.383402 10.3923 4.5575e-14  3.213126   4.755736
-
endpoints(m.Z.FOCUS)
+
summary(m.Z.FOCUS, data = FALSE)$bpar
+
##             Estimate se_notrans t value     Pr(>t)     Lower     Upper
+## Z0_0       96.838695   2.058856 47.0352 5.5825e-44 92.705465 100.97192
+## k_Z0        2.215407   0.118130 18.7540 7.7427e-25  1.990629   2.46557
+## k_Z1        0.478300   0.029289 16.3305 3.3382e-22  0.422974   0.54086
+## k_Z2        0.451619   0.044213 10.2146 3.1113e-14  0.371037   0.54970
+## k_Z3        0.058693   0.014295  4.1058 7.2882e-05  0.035996   0.09570
+## f_Z2_to_Z3  0.471507   0.057053  8.2643 2.8118e-11  0.360388   0.58552
+
endpoints(m.Z.FOCUS)
## $ff
 ##   Z2_Z3 Z2_sink 
 ## 0.47151 0.52849 
@@ -222,8 +212,8 @@
 ##        DT50    DT90
 ## Z0  0.31288  1.0394
 ## Z1  1.44919  4.8141
-## Z2  1.53481  5.0985
-## Z3 11.80965 39.2308
+## Z2 1.53480 5.0985 +## Z3 11.80969 39.2310

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.

@@ -231,116 +221,77 @@ Using the SFORB model

As the FOCUS report states, there is a certain tailing of the time course of metabolite Z3. Also, the time course of the parent compound is not fitted very well using the SFO model, as residues at a certain low level remain.

Therefore, an additional model is offered here, using the single first-order reversible binding (SFORB) model for metabolite Z3. As expected, the \(\chi^2\) error level is lower for metabolite Z3 using this model and the graphical fit for Z3 is improved. However, the covariance matrix is not returned.

-
Z.mkin.1 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
-                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
-                    Z2 = mkinsub("SFO", "Z3"),
-                    Z3 = mkinsub("SFORB"))
+
Z.mkin.1 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
+                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
+                    Z2 = mkinsub("SFO", "Z3"),
+                    Z3 = mkinsub("SFORB"))
## Successfully compiled differential equation model from auto-generated C code.
-
m.Z.mkin.1 <- mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE)
-
## Warning in mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE): Observations
-## with value of zero were removed from the data
-
plot_sep(m.Z.mkin.1)
+
m.Z.mkin.1 <- mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE)
+plot_sep(m.Z.mkin.1)

-
summary(m.Z.mkin.1, data = FALSE)$cov.unscaled
-
##                            Z0_0 log_k_Z0_Z1 log_k_Z1_Z2 log_k_Z2_sink
-## Z0_0                 3.8375e+00  5.4918e-03  3.0584e-02    1.2969e-01
-## log_k_Z0_Z1          5.4918e-03  2.7613e-03 -1.8820e-04    2.6634e-04
-## log_k_Z1_Z2          3.0584e-02 -1.8820e-04  3.3807e-03    3.2177e-03
-## log_k_Z2_sink        1.2969e-01  2.6634e-04  3.2177e-03    3.4256e-02
-## log_k_Z2_Z3_free    -2.4223e-02 -2.6169e-04 -1.1845e-03   -8.1134e-03
-## log_k_Z3_free_sink  -6.5467e-02 -4.0815e-04 -3.2978e-03   -3.6010e-02
-## log_k_Z3_free_bound -6.0659e-02 -4.4768e-04 -3.0588e-03   -3.9074e-02
-## log_k_Z3_bound_free  5.2844e-01  4.5458e-03  7.9800e-03    4.6274e-02
-## sigma                2.0366e-10 -3.4658e-10  8.9910e-11   -2.5946e-10
-##                     log_k_Z2_Z3_free log_k_Z3_free_sink
-## Z0_0                     -2.4223e-02        -6.5467e-02
-## log_k_Z0_Z1              -2.6169e-04        -4.0815e-04
-## log_k_Z1_Z2              -1.1845e-03        -3.2978e-03
-## log_k_Z2_sink            -8.1134e-03        -3.6010e-02
-## log_k_Z2_Z3_free          1.5500e-02         2.1583e-02
-## log_k_Z3_free_sink        2.1583e-02         7.5705e-02
-## log_k_Z3_free_bound       2.5836e-02         1.1964e-01
-## log_k_Z3_bound_free       5.2534e-02         2.9441e-01
-## sigma                     1.3063e-10         3.4170e-10
-##                     log_k_Z3_free_bound log_k_Z3_bound_free       sigma
-## Z0_0                        -6.0659e-02          5.2844e-01  2.0366e-10
-## log_k_Z0_Z1                 -4.4768e-04          4.5458e-03 -3.4658e-10
-## log_k_Z1_Z2                 -3.0588e-03          7.9800e-03  8.9910e-11
-## log_k_Z2_sink               -3.9074e-02          4.6274e-02 -2.5946e-10
-## log_k_Z2_Z3_free             2.5836e-02          5.2534e-02  1.3063e-10
-## log_k_Z3_free_sink           1.1964e-01          2.9441e-01  3.4170e-10
-## log_k_Z3_free_bound          6.5902e-01          5.4737e+00 -6.7704e-10
-## log_k_Z3_bound_free          5.4737e+00          2.8722e+08  7.2421e-02
-## sigma                       -6.7704e-10          7.2421e-02  1.4170e-01
+
summary(m.Z.mkin.1, data = FALSE)$cov.unscaled
+
## Warning in summary.mkinfit(m.Z.mkin.1, data = FALSE): Could not estimate
+## covariance matrix; singular system.
+
## NULL

Therefore, a further stepwise model building is performed starting from the stage of parent and two metabolites, starting from the assumption that the model fit for the parent compound can be improved by using the SFORB model.

-
Z.mkin.3 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
-                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
-                    Z2 = mkinsub("SFO"))
+
Z.mkin.3 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
+                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
+                    Z2 = mkinsub("SFO"))
## Successfully compiled differential equation model from auto-generated C code.
-
m.Z.mkin.3 <- mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE)
-
## Warning in mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations
-## with value of zero were removed from the data
-
plot_sep(m.Z.mkin.3)
+
m.Z.mkin.3 <- mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE)
+plot_sep(m.Z.mkin.3)

This results in a much better representation of the behaviour of the parent compound Z0.

Finally, Z3 is added as well. These models appear overparameterised (no covariance matrix returned) if the sink for Z1 is left in the models.

-
Z.mkin.4 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
-                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
-                    Z2 = mkinsub("SFO", "Z3"),
-                    Z3 = mkinsub("SFO"))
+
Z.mkin.4 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
+                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
+                    Z2 = mkinsub("SFO", "Z3"),
+                    Z3 = mkinsub("SFO"))
## Successfully compiled differential equation model from auto-generated C code.
- -
## Warning in mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, parms.ini = m.Z.mkin.
-## 3$bparms.ode, : Observations with value of zero were removed from the data
-
plot_sep(m.Z.mkin.4)
+

The error level of the fit, but especially of metabolite Z3, can be improved if the SFORB model is chosen for this metabolite, as this model is capable of representing the tailing of the metabolite decline phase.

-
Z.mkin.5 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
-                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
-                    Z2 = mkinsub("SFO", "Z3"),
-                    Z3 = mkinsub("SFORB"))
+
Z.mkin.5 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
+                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
+                    Z2 = mkinsub("SFO", "Z3"),
+                    Z3 = mkinsub("SFORB"))
## Successfully compiled differential equation model from auto-generated C code.
- -
## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = m.Z.mkin.
-## 4$bparms.ode[1:4], : Observations with value of zero were removed from the
-## data
-
plot_sep(m.Z.mkin.5)
+

The summary view of the backtransformed parameters shows that we get no confidence intervals due to overparameterisation. As the optimized is excessively small, it seems reasonable to fix it to zero.

- -
## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = c(m.Z.mkin.
-## 5$bparms.ode[1:7], : Observations with value of zero were removed from the
-## data
-
plot_sep(m.Z.mkin.5a)
+
m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin,
+                       parms.ini = c(m.Z.mkin.5$bparms.ode[1:7],
+                                     k_Z3_bound_free = 0),
+                       fixed_parms = "k_Z3_bound_free",
+                       quiet = TRUE)
+plot_sep(m.Z.mkin.5a)

As expected, the residual plots for Z0 and Z3 are more random than in the case of the all SFO model for which they were shown above. In conclusion, the model is proposed as the best-fit model for the dataset from Appendix 7 of the FOCUS report.

A graphical representation of the confidence intervals can finally be obtained.

-
mkinparplot(m.Z.mkin.5a)
+
mkinparplot(m.Z.mkin.5a)

The endpoints obtained with this model are

-
endpoints(m.Z.mkin.5a)
+
endpoints(m.Z.mkin.5a)
## $ff
 ##   Z0_free_Z1        Z1_Z2      Z2_sink   Z2_Z3_free Z3_free_sink 
 ##      1.00000      1.00000      0.46344      0.53656      1.00000 
 ## 
 ## $SFORB
 ##     Z0_b1     Z0_b2     Z3_b1     Z3_b2 
-## 2.4471381 0.0075124 0.0800075 0.0000000 
+## 2.4471359 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     92.267         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     8.6635        Inf
+## Z3 NA NA NA NA 8.6636 Inf

It is clear the degradation rate of Z3 towards the end of the experiment is very low as DT50_Z3_b2 (the second Eigenvalue of the system of two differential equations representing the SFORB system for Z3, corresponding to the slower rate constant of the DFOP model) is reported to be infinity. However, this appears to be a feature of the data.

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@@ -88,7 +88,7 @@

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

Johannes Ranke

-

2019-07-04

+

2019-07-05

@@ -111,11 +111,13 @@

Example on page 5, upper panel

p5a <- nafta(NAFTA_SOP_Attachment[["p5a"]])
+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.
## 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(p5a)
+
plot(p5a)

-
print(p5a)
+
print(p5a)
## Sums of squares:
 ##       SFO      IORE      DFOP 
 ## 465.21753  56.27506  32.06401 
@@ -126,24 +128,21 @@
 ## Parameters:
 ## $SFO
 ##               Estimate   Pr(>t)  Lower   Upper
-## parent_0       95.8401 4.67e-21 92.245 99.4357
-## k_parent_sink   0.0102 3.92e-12  0.009  0.0117
-## sigma           4.8230 3.81e-06  3.214  6.4318
+## parent_0       95.8401 1.10e-21 92.121 99.5597
+## k_parent_sink   0.0102 1.71e-12  0.009  0.0117
 ## 
 ## $IORE
-##                     Estimate Pr(>t)    Lower    Upper
-## parent_0            1.01e+02     NA 9.91e+01 1.02e+02
-## k__iore_parent_sink 1.54e-05     NA 4.08e-06 5.84e-05
-## N_parent            2.57e+00     NA 2.25e+00 2.89e+00
-## sigma               1.68e+00     NA 1.12e+00 2.24e+00
+##                     Estimate   Pr(>t)    Lower    Upper
+## parent_0            1.01e+02 2.37e-26 9.89e+01 1.03e+02
+## k__iore_parent_sink 1.54e-05 8.73e-02 3.48e-06 6.85e-05
+## N_parent            2.57e+00 1.14e-11 2.22e+00 2.92e+00
 ## 
 ## $DFOP
-##          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       2.86e-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
+##          Estimate   Pr(>t) Lower Upper
+## parent_0 9.99e+01 4.33e-27    NA    NA
+## k1       2.67e-02 3.17e-05    NA    NA
+## k2       2.86e-12 5.00e-01    NA    NA
+## g        6.47e-01 2.13e-05    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -153,17 +152,19 @@
 ## DFOP 55.5 4.42e+11 2.42e+11
 ## 
 ## Representative half-life:
-## [1] 321.51
+## [1] 321.5119

Example on page 5, lower panel

-
p5b <- nafta(NAFTA_SOP_Attachment[["p5b"]])
+
p5b <- nafta(NAFTA_SOP_Attachment[["p5b"]])
+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.
## 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(p5b)
+
plot(p5b)

-
print(p5b)
+
print(p5b)
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 94.81123 10.10936  7.55871 
@@ -174,24 +175,21 @@
 ## Parameters:
 ## $SFO
 ##               Estimate   Pr(>t)    Lower    Upper
-## parent_0        96.497 2.32e-24 94.85271 98.14155
-## k_parent_sink    0.008 3.42e-14  0.00737  0.00869
-## sigma            2.295 1.22e-05  1.47976  3.11036
+## parent_0        96.497 2.62e-25 94.77653 98.21774
+## k_parent_sink    0.008 1.35e-14  0.00736  0.00871
 ## 
 ## $IORE
 ##                     Estimate   Pr(>t)    Lower    Upper
-## parent_0            9.85e+01 1.17e-28 9.79e+01 9.92e+01
-## k__iore_parent_sink 1.53e-04 6.50e-03 7.21e-05 3.26e-04
-## N_parent            1.94e+00 5.88e-13 1.76e+00 2.12e+00
-## sigma               7.49e-01 1.63e-05 4.82e-01 1.02e+00
+## parent_0            9.85e+01 1.02e-29 9.78e+01 9.93e+01
+## k__iore_parent_sink 1.53e-04 1.15e-02 6.60e-05 3.56e-04
+## N_parent            1.94e+00 8.18e-13 1.74e+00 2.14e+00
 ## 
 ## $DFOP
-##          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       1.16e-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
+##          Estimate   Pr(>t) Lower Upper
+## parent_0 9.84e+01 1.90e-28    NA    NA
+## k1       1.55e-02 2.83e-03    NA    NA
+## k2       1.16e-11 5.00e-01    NA    NA
+## g        6.89e-01 1.31e-02    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -201,17 +199,19 @@
 ## DFOP 83.6 9.80e+10 5.98e+10
 ## 
 ## Representative half-life:
-## [1] 215.87
+## [1] 215.8655

Example on page 6

-
p6 <- nafta(NAFTA_SOP_Attachment[["p6"]])
+
p6 <- nafta(NAFTA_SOP_Attachment[["p6"]])
+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.
## 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(p6)
+
plot(p6)

-
print(p6)
+
print(p6)
## Sums of squares:
 ##       SFO      IORE      DFOP 
 ## 188.45361  51.00699  42.46931 
@@ -222,24 +222,21 @@
 ## Parameters:
 ## $SFO
 ##               Estimate   Pr(>t)   Lower   Upper
-## parent_0       94.7759 7.29e-24 92.3478 97.2039
-## k_parent_sink   0.0179 8.02e-16  0.0166  0.0194
-## sigma           3.0696 3.81e-06  2.0456  4.0936
+## parent_0       94.7759 1.25e-24 92.2558 97.2960
+## k_parent_sink   0.0179 2.35e-16  0.0166  0.0194
 ## 
 ## $IORE
 ##                     Estimate   Pr(>t)    Lower    Upper
-## parent_0            97.12446 2.63e-26 95.62461 98.62431
-## k__iore_parent_sink  0.00252 1.95e-03  0.00134  0.00472
-## N_parent             1.49587 4.07e-13  1.33896  1.65279
-## sigma                1.59698 5.05e-06  1.06169  2.13227
+## parent_0            97.12446 5.62e-27 95.49343 98.75549
+## k__iore_parent_sink  0.00252 3.54e-03  0.00126  0.00502
+## N_parent             1.49587 6.13e-13  1.32380  1.66794
 ## 
 ## $DFOP
-##          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       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
+##          Estimate   Pr(>t) Lower Upper
+## parent_0 9.66e+01 4.17e-26    NA    NA
+## k1       2.55e-02 2.12e-05    NA    NA
+## k2       4.90e-11 5.00e-01    NA    NA
+## g        8.61e-01 2.10e-05    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -249,17 +246,19 @@
 ## DFOP 34.1 6.66e+09 1.41e+10
 ## 
 ## Representative half-life:
-## [1] 53.17
+## [1] 53.16582

Example on page 7

-
p7 <- nafta(NAFTA_SOP_Attachment[["p7"]])
+
p7 <- nafta(NAFTA_SOP_Attachment[["p7"]])
+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.
## 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(p7)
+
plot(p7)

-
print(p7)
+
print(p7)
## Sums of squares:
 ##      SFO     IORE     DFOP 
 ## 3661.661 3195.030 3174.145 
@@ -270,24 +269,21 @@
 ## Parameters:
 ## $SFO
 ##               Estimate   Pr(>t)    Lower    Upper
-## parent_0      96.41796 4.80e-53 93.32245 99.51347
-## k_parent_sink  0.00735 7.64e-21  0.00641  0.00843
-## sigma          7.94557 1.83e-15  6.46713  9.42401
+## parent_0      96.41796 1.52e-53 93.29554 99.54038
+## k_parent_sink  0.00735 3.59e-21  0.00641  0.00842
 ## 
 ## $IORE
-##                     Estimate Pr(>t)    Lower    Upper
-## parent_0            9.92e+01     NA 9.55e+01 1.03e+02
-## k__iore_parent_sink 1.60e-05     NA 1.45e-07 1.77e-03
-## N_parent            2.45e+00     NA 1.35e+00 3.54e+00
-## sigma               7.42e+00     NA 6.04e+00 8.80e+00
+##                     Estimate   Pr(>t)    Lower    Upper
+## parent_0            9.92e+01 7.33e-49 9.53e+01 1.03e+02
+## k__iore_parent_sink 1.60e-05 3.47e-01 9.98e-08 2.57e-03
+## N_parent            2.45e+00 6.14e-05 1.26e+00 3.63e+00
 ## 
 ## $DFOP
-##          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       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
+##          Estimate   Pr(>t) Lower Upper
+## parent_0 9.89e+01 8.13e-48    NA    NA
+## k1       1.81e-02 2.20e-01    NA    NA
+## k2       1.97e-10 5.00e-01    NA    NA
+## g        6.06e-01 2.60e-01    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -297,7 +293,7 @@
 ## DFOP 96.4 6.97e+09 3.52e+09
 ## 
 ## Representative half-life:
-## [1] 454.55
+## [1] 454.5528
@@ -307,12 +303,17 @@

Example on page 8

For this dataset, the IORE fit does not converge when the default starting values used by mkin for the IORE model are used. Therefore, a lower value for the rate constant is used here.

-
p8 <- nafta(NAFTA_SOP_Attachment[["p8"]], parms.ini = c(k__iore_parent_sink = 1e-3))
+
p8 <- nafta(NAFTA_SOP_Attachment[["p8"]], parms.ini = c(k__iore_parent_sink = 1e-3))
+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.
+
+## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.
## 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(p8)
+
plot(p8)

-
print(p8)
+
print(p8)
## Sums of squares:
 ##       SFO      IORE      DFOP 
 ## 1996.9408  444.9237  547.5616 
@@ -322,25 +323,24 @@
 ## 
 ## Parameters:
 ## $SFO
-##               Estimate   Pr(>t)    Lower    Upper
-## parent_0      88.16549 6.53e-29 83.37344 92.95754
-## k_parent_sink  0.00803 1.67e-13  0.00674  0.00957
-## sigma          7.44786 4.17e-10  5.66209  9.23363
+##                     Estimate Pr(>t) Lower Upper
+## parent_0            88.16549     NA    NA    NA
+## k__iore_parent_sink  0.00100     NA    NA    NA
+## k_parent_sink        0.00803     NA    NA    NA
 ## 
 ## $IORE
 ##                     Estimate   Pr(>t)    Lower    Upper
-## parent_0            9.77e+01 7.03e-35 9.44e+01 1.01e+02
-## k__iore_parent_sink 6.14e-05 3.20e-02 2.12e-05 1.78e-04
-## N_parent            2.27e+00 4.23e-18 2.00e+00 2.54e+00
-## sigma               3.52e+00 5.36e-10 2.67e+00 4.36e+00
+## parent_0            9.77e+01 1.05e-35 9.44e+01 1.01e+02
+## k__iore_parent_sink 6.14e-05 2.76e-02 2.21e-05 1.71e-04
+## N_parent            2.27e+00 6.00e-19 2.02e+00 2.53e+00
 ## 
 ## $DFOP
-##          Estimate   Pr(>t)    Lower    Upper
-## parent_0 95.70619 8.99e-32 91.87941 99.53298
-## k1        0.02500 5.25e-04  0.01422  0.04394
-## k2        0.00273 6.84e-03  0.00125  0.00597
-## g         0.58835 2.84e-06  0.36595  0.77970
-## sigma     3.90001 6.94e-10  2.96260  4.83741
+##                     Estimate Pr(>t) Lower Upper
+## parent_0            95.70619     NA    NA    NA
+## k__iore_parent_sink  0.00100     NA    NA    NA
+## k1                   0.02500     NA    NA    NA
+## k2                   0.00273     NA    NA    NA
+## g                    0.58835     NA    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -350,7 +350,7 @@
 ## DFOP 55.6  517    253.0
 ## 
 ## Representative half-life:
-## [1] 201.03
+## [1] 201.0316
@@ -359,12 +359,14 @@

Example on page 9, upper panel

-
p9a <- nafta(NAFTA_SOP_Attachment[["p9a"]])
+
p9a <- nafta(NAFTA_SOP_Attachment[["p9a"]])
+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.
## 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(p9a)
+
plot(p9a)

-
print(p9a)
+
print(p9a)
## Sums of squares:
 ##       SFO      IORE      DFOP 
 ## 839.35238  88.57064   9.93363 
@@ -375,24 +377,21 @@
 ## Parameters:
 ## $SFO
 ##               Estimate   Pr(>t)   Lower   Upper
-## parent_0       88.1933 3.06e-12 79.9447 96.4419
-## k_parent_sink   0.0409 2.07e-07  0.0324  0.0516
-## sigma           7.2429 3.92e-05  4.4768 10.0090
+## parent_0       88.1933 1.12e-12 79.7671 96.6195
+## k_parent_sink   0.0409 9.50e-08  0.0326  0.0513
 ## 
 ## $IORE
 ##                     Estimate   Pr(>t)    Lower    Upper
-## parent_0            9.89e+01 1.12e-16 9.54e+01 1.02e+02
-## k__iore_parent_sink 1.93e-05 1.13e-01 3.49e-06 1.06e-04
-## N_parent            2.91e+00 1.45e-09 2.50e+00 3.32e+00
-## sigma               2.35e+00 5.31e-05 1.45e+00 3.26e+00
+## parent_0            9.89e+01 5.16e-17 9.50e+01 1.03e+02
+## k__iore_parent_sink 1.93e-05 1.48e-01 2.65e-06 1.40e-04
+## N_parent            2.91e+00 3.74e-09 2.43e+00 3.39e+00
 ## 
 ## $DFOP
-##          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       6.02e-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
+##          Estimate   Pr(>t) Lower Upper
+## parent_0 9.85e+01 1.31e-21    NA    NA
+## k1       1.38e-01 3.63e-09    NA    NA
+## k2       6.02e-13 5.00e-01    NA    NA
+## g        6.52e-01 1.50e-10    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -402,23 +401,20 @@
 ## DFOP 10.5 2.07e+12 1.15e+12
 ## 
 ## Representative half-life:
-## [1] 101.43
+## [1] 101.4264

In this example, the residuals of the SFO indicate a lack of fit of this model, so even if it was an abiotic experiment, the data do not suggest a simple exponential decline.

Example on page 9, lower panel

-
p9b <- nafta(NAFTA_SOP_Attachment[["p9b"]])
-
## Warning in sqrt(diag(covar)): NaNs wurden erzeugt
-
## Warning in sqrt(diag(covar_notrans)): NaNs wurden erzeugt
-
## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt
-
## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non-
-## finite result is doubtful
+
p9b <- nafta(NAFTA_SOP_Attachment[["p9b"]])
+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.
## 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 
@@ -428,25 +424,22 @@
 ## 
 ## Parameters:
 ## $SFO
-##               Estimate   Pr(>t)  Lower   Upper
-## parent_0       94.7123 2.15e-19 93.178 96.2464
-## k_parent_sink   0.0389 4.47e-14  0.037  0.0408
-## sigma           1.5957 1.28e-04  0.932  2.2595
+##               Estimate   Pr(>t)   Lower  Upper
+## parent_0       94.7123 2.21e-20 93.0673 96.357
+## k_parent_sink   0.0389 1.48e-14  0.0369  0.041
 ## 
 ## $IORE
 ##                     Estimate   Pr(>t)   Lower  Upper
-## parent_0              93.863 2.32e-18 92.4565 95.269
-## k__iore_parent_sink    0.127 1.85e-02  0.0504  0.321
-## N_parent               0.711 1.88e-05  0.4843  0.937
-## sigma                  1.288 1.76e-04  0.7456  1.830
+## parent_0              93.863 2.91e-19 92.2996 95.426
+## k__iore_parent_sink    0.127 2.73e-02  0.0457  0.354
+## N_parent               0.711 3.13e-05  0.4605  0.961
 ## 
 ## $DFOP
-##          Estimate   Pr(>t)   Lower   Upper
-## 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      NaN      NA      NA
-## sigma      1.5957 2.50e-04  0.9135  2.2779
+##          Estimate Pr(>t) Lower Upper
+## parent_0  94.7123     NA    NA    NA
+## k1         0.0389     NA    NA    NA
+## k2         0.0389     NA    NA    NA
+## g          0.7742     NA    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -456,18 +449,20 @@
 ## DFOP 17.8 59.2     17.8
 ## 
 ## Representative half-life:
-## [1] 14.8
+## [1] 14.80012

Here, mkin gives a longer slow DT50 for the DFOP model (17.8 days) than PestDF (13.5 days). Presumably, this is related to the fact that PestDF gives a negative value for the proportion of the fast degradation which should be between 0 and 1, inclusive. This parameter is called f in PestDF and g in mkin. In mkin, it is restricted to the interval from 0 to 1.

Example on page 10

-
p10 <- nafta(NAFTA_SOP_Attachment[["p10"]])
+
p10 <- nafta(NAFTA_SOP_Attachment[["p10"]])
+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.
## 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 
@@ -478,24 +473,21 @@
 ## Parameters:
 ## $SFO
 ##               Estimate   Pr(>t)   Lower    Upper
-## parent_0      101.7315 6.42e-11 91.9259 111.5371
-## k_parent_sink   0.0495 1.70e-07  0.0404   0.0607
-## sigma           8.0152 1.28e-04  4.6813  11.3491
+## parent_0      101.7315 4.95e-11 90.9683 112.4947
+## k_parent_sink   0.0495 3.40e-07  0.0393   0.0624
 ## 
 ## $IORE
 ##                     Estimate   Pr(>t)  Lower   Upper
-## parent_0               96.86 3.32e-12 90.848 102.863
-## k__iore_parent_sink     2.96 7.91e-02  0.687  12.761
-## N_parent                0.00 5.00e-01 -0.372   0.372
-## sigma                   4.90 1.77e-04  2.837   6.968
+## parent_0               96.86 2.71e-12 89.884 103.826
+## k__iore_parent_sink     2.96 1.31e-01  0.461  19.020
+## N_parent                0.00 5.00e-01 -0.473   0.473
 ## 
 ## $DFOP
-##          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
+##          Estimate Pr(>t) Lower Upper
+## parent_0 101.7315     NA    NA    NA
+## k1         0.0495     NA    NA    NA
+## k2         0.0495     NA    NA    NA
+## g          0.6634     NA    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -505,7 +497,7 @@
 ## DFOP 14.0 46.5    14.00
 ## 
 ## Representative half-life:
-## [1] 8.86
+## [1] 8.862193

Here, a value below N is given for the IORE model, because the data suggests a faster decline towards the end of the experiment, which appears physically rather unlikely in the case of a photolysis study. It seems PestDF does not constrain N to values above zero, thus the slight difference in IORE model parameters between PestDF and mkin.

@@ -515,12 +507,14 @@

Example on page 11

-
p11 <- nafta(NAFTA_SOP_Attachment[["p11"]])
+
p11 <- nafta(NAFTA_SOP_Attachment[["p11"]])
+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.
## 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 
@@ -531,24 +525,21 @@
 ## Parameters:
 ## $SFO
 ##               Estimate   Pr(>t)    Lower    Upper
-## parent_0      96.15820 4.83e-13 90.24934 1.02e+02
-## k_parent_sink  0.00321 4.71e-05  0.00222 4.64e-03
-## sigma          6.43473 1.28e-04  3.75822 9.11e+00
+## parent_0      96.15820 1.56e-13 89.91373 1.02e+02
+## k_parent_sink  0.00321 5.27e-05  0.00218 4.71e-03
 ## 
 ## $IORE
 ##                     Estimate Pr(>t)    Lower    Upper
-## parent_0            1.05e+02     NA 9.90e+01 1.10e+02
-## k__iore_parent_sink 3.11e-17     NA 1.35e-20 7.18e-14
-## N_parent            8.36e+00     NA 6.62e+00 1.01e+01
-## sigma               3.82e+00     NA 2.21e+00 5.44e+00
+## parent_0            1.05e+02     NA 9.80e+01 1.11e+02
+## k__iore_parent_sink 3.11e-17     NA 6.88e-25 1.41e-09
+## N_parent            8.36e+00     NA 4.40e+00 1.23e+01
 ## 
 ## $DFOP
-##          Estimate   Pr(>t)    Lower    Upper
-## parent_0 1.05e+02 9.47e-13  99.9990 109.1224
-## k1       4.41e-02 5.95e-03   0.0296   0.0658
-## k2       7.25e-13 5.00e-01   0.0000      Inf
-## g        3.22e-01 1.45e-03   0.2814   0.3650
-## sigma    3.22e+00 3.52e-04   1.8410   4.5906
+##          Estimate   Pr(>t) Lower Upper
+## parent_0 1.05e+02 7.50e-13    NA    NA
+## k1       4.41e-02 3.34e-02    NA    NA
+## k2       7.25e-13 5.00e-01    NA    NA
+## g        3.22e-01 7.87e-03    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -569,14 +560,14 @@
 

 

 Example on page 12, upper panel

-
p12a <- nafta(NAFTA_SOP_Attachment[["p12a"]])

-
## Warning in summary.mkinfit(x): Could not calculate correlation; no
-## covariance matrix

+
p12a <- nafta(NAFTA_SOP_Attachment[["p12a"]])

+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.

 
## 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 
@@ -587,24 +578,21 @@
 ## Parameters:
 ## $SFO
 ##               Estimate   Pr(>t)  Lower   Upper
-## parent_0       100.521 8.75e-12 92.461 108.581
-## k_parent_sink    0.124 3.61e-08  0.104   0.148
-## sigma            7.048 1.28e-04  4.116   9.980
+## parent_0       100.521 5.61e-12 91.687 109.355
+## k_parent_sink    0.124 7.24e-08  0.102   0.152
 ## 
 ## $IORE
-##                     Estimate Pr(>t) Lower Upper
-## parent_0              96.823     NA    NA    NA
-## k__iore_parent_sink    2.436     NA    NA    NA
-## N_parent               0.263     NA    NA    NA
-## sigma                  3.965     NA    NA    NA
+##                     Estimate   Pr(>t)   Lower   Upper
+## parent_0              96.823 1.24e-13 91.5691 102.078
+## k__iore_parent_sink    2.436 3.89e-02  0.7854   7.556
+## N_parent               0.263 3.64e-02 -0.0288   0.554
 ## 
 ## $DFOP
-##          Estimate   Pr(>t)   Lower   Upper
-## parent_0  100.521 2.74e-10 92.2366 108.805
-## 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
+##          Estimate Pr(>t) Lower Upper
+## parent_0  100.521     NA    NA    NA
+## k1          0.124     NA    NA    NA
+## k2          0.124     NA    NA    NA
+## g           0.877     NA    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -614,25 +602,19 @@
 ## DFOP 5.58 18.5     5.58
 ## 
 ## Representative half-life:
-## [1] 3.99

+## [1] 3.987308

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
-
## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non-
-## finite result is doubtful
+
p12b <- nafta(NAFTA_SOP_Attachment[["p12b"]])
+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.
## 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 
@@ -642,25 +624,22 @@
 ## 
 ## Parameters:
 ## $SFO
-##               Estimate  Pr(>t)   Lower    Upper
-## parent_0       97.6840 0.00039 85.9388 109.4292
-## k_parent_sink   0.0589 0.00261  0.0431   0.0805
-## sigma           3.4323 0.04356 -1.2377   8.1023
+##               Estimate   Pr(>t)   Lower    Upper
+## parent_0       97.6840 5.36e-05 86.3205 109.0475
+## k_parent_sink   0.0589 9.87e-04  0.0432   0.0803
 ## 
 ## $IORE
-##                     Estimate Pr(>t)     Lower  Upper
-## parent_0              95.523 0.0055 74.539157 116.51
-## k__iore_parent_sink    0.333 0.1433  0.000717 154.57
-## N_parent               0.568 0.0677 -0.989464   2.13
-## sigma                  1.953 0.0975 -5.893100   9.80
+##                     Estimate   Pr(>t)   Lower  Upper
+## parent_0              95.523 0.000386 84.0963 106.95
+## k__iore_parent_sink    0.333 0.170886  0.0103  10.80
+## N_parent               0.568 0.054881 -0.3161   1.45
 ## 
 ## $DFOP
 ##          Estimate Pr(>t) Lower Upper
-## parent_0  97.6840    NaN   NaN   NaN
-## k1         0.0589    NaN    NA    NA
-## k2         0.0589    NaN    NA    NA
-## g          0.6902    NaN    NA    NA
-## sigma      3.4323    NaN   NaN   NaN
+## parent_0  97.6840     NA    NA    NA
+## k1         0.0589     NA    NA    NA
+## k2         0.0589     NA    NA    NA
+## g          0.6902     NA    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -670,21 +649,19 @@
 ## DFOP 11.8 39.1    11.80
 ## 
 ## Representative half-life:
-## [1] 9.46
+## [1] 9.461912

Example on page 13

-
p13 <- nafta(NAFTA_SOP_Attachment[["p13"]])
-
## Warning in sqrt(diag(covar)): NaNs wurden erzeugt
-
## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt
-
## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non-
-## finite result is doubtful
+
p13 <- nafta(NAFTA_SOP_Attachment[["p13"]])
+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.
## 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 
@@ -694,25 +671,22 @@
 ## 
 ## Parameters:
 ## $SFO
-##               Estimate   Pr(>t)    Lower    Upper
-## parent_0      92.73500 5.99e-17 89.61936 95.85065
-## k_parent_sink  0.00258 2.42e-09  0.00223  0.00299
-## sigma          3.41172 7.07e-05  2.05455  4.76888
+##               Estimate   Pr(>t)   Lower    Upper
+## parent_0      92.73500 1.45e-17 89.3891 96.08094
+## k_parent_sink  0.00258 2.63e-09  0.0022  0.00303
 ## 
 ## $IORE
-##                     Estimate   Pr(>t)    Lower  Upper
-## parent_0             91.6016 6.34e-16 88.53086 94.672
-## k__iore_parent_sink   0.0396 2.36e-01  0.00207  0.759
-## N_parent              0.3541 1.46e-01 -0.35153  1.060
-## sigma                 3.0811 9.64e-05  1.84296  4.319
+##                     Estimate   Pr(>t)    Lower Upper
+## parent_0             91.6016 2.93e-16 88.08711 95.12
+## k__iore_parent_sink   0.0396 2.81e-01  0.00102  1.53
+## N_parent              0.3541 1.97e-01 -0.51943  1.23
 ## 
 ## $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 1.70e-08 3.92e+02
-## k2        0.00258 3.69e-08 2.20e-03 3.03e-03
-## g         0.00442 5.00e-01       NA       NA
-## sigma     3.41172 1.35e-04 2.02e+00 4.80e+00
+##          Estimate Pr(>t) Lower Upper
+## parent_0 92.73500     NA    NA    NA
+## k1        0.00258     NA    NA    NA
+## k2        0.00258     NA    NA    NA
+## g         0.00442     NA    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -722,22 +696,20 @@
 ## DFOP  269  892      269
 ## 
 ## Representative half-life:
-## [1] 168.51
+## [1] 168.5123

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
-
## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non-
-## finite result is doubtful
+
p14 <- nafta(NAFTA_SOP_Attachment[["p14"]])
+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.
## 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 
@@ -748,24 +720,21 @@
 ## Parameters:
 ## $SFO
 ##               Estimate   Pr(>t)    Lower    Upper
-## parent_0      99.47124 2.06e-30 98.42254 1.01e+02
-## k_parent_sink  0.00279 3.75e-15  0.00256 3.04e-03
-## sigma          1.55616 3.81e-06  1.03704 2.08e+00
+## parent_0      99.47124 1.71e-31 98.37313 1.01e+02
+## k_parent_sink  0.00279 2.22e-15  0.00255 3.05e-03
 ## 
 ## $IORE
-##                     Estimate Pr(>t) Lower Upper
-## parent_0            1.00e+02     NA   NaN   NaN
-## k__iore_parent_sink 9.44e-08     NA   NaN   NaN
-## N_parent            3.31e+00     NA   NaN   NaN
-## sigma               1.20e+00     NA 0.796   1.6
+##                     Estimate Pr(>t)    Lower    Upper
+## parent_0            1.00e+02     NA 9.93e+01 1.01e+02
+## k__iore_parent_sink 9.44e-08     NA 6.81e-11 1.31e-04
+## N_parent            3.31e+00     NA 1.69e+00 4.93e+00
 ## 
 ## $DFOP
-##          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       7.29e-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
+##          Estimate   Pr(>t) Lower Upper
+## parent_0 1.00e+02 2.70e-28    NA    NA
+## k1       9.53e-03 3.39e-01    NA    NA
+## k2       7.29e-12 5.00e-01    NA    NA
+## g        3.98e-01 3.92e-01    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -775,23 +744,20 @@
 ## DFOP 2.54e+10 2.46e+11 9.51e+10
 ## 
 ## Representative half-life:
-## [1] 6697.44
+## [1] 6697.437

The slower rate constant reported by PestDF is negative, which is not physically realistic, and not possible in mkin. The other fits give the same results in mkin and PestDF.

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(diag(covar_notrans)): NaNs wurden erzeugt
-
## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt
-
## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non-
-## finite result is doubtful
+
p15a <- nafta(NAFTA_SOP_Attachment[["p15a"]])
+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.
## 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 
@@ -801,25 +767,22 @@
 ## 
 ## Parameters:
 ## $SFO
-##               Estimate   Pr(>t)    Lower   Upper
-## parent_0      97.96751 2.00e-15 94.32049 101.615
-## k_parent_sink  0.00952 4.93e-09  0.00824   0.011
-## sigma          4.18778 1.28e-04  2.44588   5.930
+##               Estimate   Pr(>t)    Lower    Upper
+## parent_0      97.96751 4.98e-16 94.03829 101.8967
+## k_parent_sink  0.00952 5.24e-09  0.00813   0.0112
 ## 
 ## $IORE
-##                     Estimate   Pr(>t)  Lower  Upper
-## parent_0              95.874 2.94e-15 92.937 98.811
-## k__iore_parent_sink    0.629 2.11e-01  0.044  8.982
-## N_parent               0.000 5.00e-01 -0.642  0.642
-## sigma                  3.105 1.78e-04  1.795  4.416
+##                     Estimate   Pr(>t)   Lower  Upper
+## parent_0              95.874 8.30e-16 92.5802 99.167
+## k__iore_parent_sink    0.629 2.39e-01  0.0316 12.519
+## N_parent               0.000 5.00e-01 -0.7219  0.722
 ## 
 ## $DFOP
-##          Estimate   Pr(>t)    Lower    Upper
-## parent_0 97.96752 2.85e-13 94.21914 101.7159
-## k1        0.00952 6.80e-02  0.00277   0.0327
-## k2        0.00952 3.82e-06  0.00902   0.0100
-## g         0.17247      NaN       NA       NA
-## sigma     4.18778 2.50e-04  2.39747   5.9781
+##          Estimate Pr(>t) Lower Upper
+## parent_0 97.96752     NA    NA    NA
+## k1        0.00952     NA    NA    NA
+## k2        0.00952     NA    NA    NA
+## g         0.17247     NA    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -829,17 +792,15 @@
 ## DFOP 72.8  242     72.8
 ## 
 ## Representative half-life:
-## [1] 41.33
-
p15b <- nafta(NAFTA_SOP_Attachment[["p15b"]])
-
## Warning in sqrt(diag(covar)): NaNs wurden erzeugt
-
## Warning in sqrt(1/diag(V)): NaNs wurden erzeugt
-
## Warning in cov2cor(ans$cov.unscaled): diag(.) had 0 or NA entries; non-
-## finite result is doubtful
+## [1] 41.32749 +
p15b <- nafta(NAFTA_SOP_Attachment[["p15b"]])
+
## Warning in summary.mkinfit(x): Could not estimate covariance matrix;
+## singular system.
## 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 
@@ -850,24 +811,21 @@
 ## Parameters:
 ## $SFO
 ##               Estimate   Pr(>t)    Lower    Upper
-## parent_0      1.01e+02 3.06e-17 98.31594 1.03e+02
-## k_parent_sink 4.86e-03 2.48e-10  0.00435 5.42e-03
-## sigma         2.76e+00 1.28e-04  1.61402 3.91e+00
+## parent_0      1.01e+02 4.99e-18 98.12761 1.04e+02
+## k_parent_sink 4.86e-03 1.76e-10  0.00432 5.46e-03
 ## 
 ## $IORE
-##                     Estimate   Pr(>t)    Lower  Upper
-## 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 -1.07695   1.08
-## sigma                   2.21 2.57e-04  1.23245   3.19
+##                     Estimate   Pr(>t)    Lower Upper
+## parent_0               99.83 4.49e-17 97.19753 102.5
+## k__iore_parent_sink     0.38 3.41e-01  0.00206  70.0
+## N_parent                0.00 5.00e-01 -1.20105   1.2
 ## 
 ## $DFOP
-##          Estimate Pr(>t)    Lower    Upper
-## 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 1.58e+00 3.94e+00
+##          Estimate Pr(>t) Lower Upper
+## parent_0 1.01e+02     NA    NA    NA
+## k1       4.86e-03     NA    NA    NA
+## k2       4.86e-03     NA    NA    NA
+## g        1.50e-01     NA    NA    NA
 ## 
 ## 
 ## DTx values:
@@ -877,20 +835,20 @@
 ## DFOP  143  474    143.0
 ## 
 ## Representative half-life:
-## [1] 71.18
+## [1] 71.18014

In mkin, only the IORE fit is affected (deemed unrealistic), as the fraction parameter of the DFOP model is restricted to the interval between 0 and 1 in mkin. The SFO fits give the same results for both mkin and PestDF.

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 
@@ -900,25 +858,22 @@
 ## 
 ## Parameters:
 ## $SFO
-##               Estimate   Pr(>t)  Lower Upper
-## parent_0        71.953 2.33e-13 60.509 83.40
-## k_parent_sink    0.159 4.86e-05  0.102  0.25
-## sigma           11.302 1.25e-08  8.308 14.30
+##               Estimate   Pr(>t)  Lower  Upper
+## parent_0        71.953 3.92e-14 61.087 82.819
+## k_parent_sink    0.159 2.27e-06  0.111  0.229
 ## 
 ## $IORE
 ##                     Estimate   Pr(>t)    Lower    Upper
-## parent_0            8.74e+01 2.48e-16 7.72e+01 97.52972
-## k__iore_parent_sink 4.55e-04 2.16e-01 3.48e-05  0.00595
-## N_parent            2.70e+00 1.21e-08 1.99e+00  3.40046
-## sigma               8.29e+00 1.61e-08 6.09e+00 10.49062
+## parent_0            8.74e+01 1.74e-16 7.71e+01 97.70701
+## k__iore_parent_sink 4.55e-04 2.28e-01 3.01e-05  0.00688
+## N_parent            2.70e+00 1.87e-08 1.97e+00  3.42611
 ## 
 ## $DFOP
-##          Estimate   Pr(>t)   Lower  Upper
-## parent_0  88.5333 7.40e-18 79.9836 97.083
-## 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
+##          Estimate Pr(>t)   Lower  Upper
+## parent_0  88.5333     NA 79.3673 97.699
+## k1        18.5561     NA  0.0000    Inf
+## k2         0.0776     NA  0.0471  0.128
+## g          0.4733     NA  0.3138  0.639
 ## 
 ## 
 ## DTx values:
@@ -928,7 +883,7 @@
 ## DFOP 0.67 21.4     8.93
 ## 
 ## Representative half-life:
-## [1] 8.93
+## [1] 8.932679

In PestDF, the DFOP fit seems to have stuck in a local minimum, as mkin finds a solution with a much lower \(\chi^2\) error level. As the half-life from the slower rate constant of the DFOP model is larger than the IORE derived half-life, the NAFTA recommendation obtained with mkin is to use the DFOP representative half-life of 8.9 days.

diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png index d0f89858..4cf9c8ea 100644 Binary files a/docs/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png and b/docs/articles/web_only/NAFTA_examples_files/figure-html/p13-1.png differ diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p5a-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p5a-1.png index 596a33b2..c1f61bab 100644 Binary files a/docs/articles/web_only/NAFTA_examples_files/figure-html/p5a-1.png and b/docs/articles/web_only/NAFTA_examples_files/figure-html/p5a-1.png differ diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p8-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p8-1.png index fa8621e7..2747b2d6 100644 Binary files a/docs/articles/web_only/NAFTA_examples_files/figure-html/p8-1.png and b/docs/articles/web_only/NAFTA_examples_files/figure-html/p8-1.png differ diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png index aac3600b..32b3bf29 100644 Binary files a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png and b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9a-1.png differ diff --git a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png index cb52aecd..8b8ea5aa 100644 Binary files a/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png and b/docs/articles/web_only/NAFTA_examples_files/figure-html/p9b-1.png differ diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html index 005834cc..eacecc2f 100644 --- a/docs/articles/web_only/benchmarks.html +++ b/docs/articles/web_only/benchmarks.html @@ -30,7 +30,7 @@ mkin - 0.9.49.5 + 0.9.49.6
@@ -88,7 +88,7 @@

Benchmark timings for mkin on various systems

Johannes Ranke

-

2019-07-04

+

2019-07-05

@@ -116,8 +116,17 @@ 
# Parent only
 t1 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_2006_C, FOCUS_2006_D)))[["elapsed"]]
 t2 <- system.time(mmkin_bench(c("SFO", "FOMC", "DFOP", "HS"), list(FOCUS_2006_C, FOCUS_2006_D), error_model = "tc"))[["elapsed"]]
-
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation did not converge:
-## iteration limit reached without convergence (10)
+
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation by method Port did not converge:
+## false convergence (8)
+
+## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation by method Port did not converge:
+## false convergence (8)
+
+## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation by method Port did not converge:
+## false convergence (8)
+
+## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation by method Port did not converge:
+## false convergence (8)
# One metabolite
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
@@ -131,149 +140,124 @@
   parent = mkinsub("FOMC", "m1"),
   m1 = mkinsub("SFO"))
## Successfully compiled differential equation model from auto-generated C code.
-
t3 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D)))[["elapsed"]]
-
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
-## Observations with value of zero were removed from the data
-
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
-## Observations with value of zero were removed from the data
-
-## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
-## Observations with value of zero were removed from the data
-
t4 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(subset(FOCUS_2006_D, value != 0)), error_model = "tc"))[["elapsed"]]
-t5 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D), error_model = "obs"))[["elapsed"]]
-
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
-## Observations with value of zero were removed from the data
-
-## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
-## Observations with value of zero were removed from the data
-
-## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
-## Observations with value of zero were removed from the data
-
# Two metabolites, synthetic data
-m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
-                           M1 = mkinsub("SFO", "M2"),
-                           M2 = mkinsub("SFO"),
-                           use_of_ff = "max", quiet = TRUE)
-
-m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
-                           M1 = mkinsub("SFO"),
-                           M2 = mkinsub("SFO"),
-                           use_of_ff = "max", quiet = TRUE)
-
-SFO_lin_a <- synthetic_data_for_UBA_2014[[1]]$data
-
-DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data
-
-t6 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a)))["elapsed"]
-t7 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c)))["elapsed"]
-
-t8 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), error_model = "tc"))["elapsed"]
-t9 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), error_model = "tc"))["elapsed"]
-
-t10 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), error_model = "obs"))["elapsed"]
-t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), error_model = "obs"))["elapsed"]
-
-mkin_benchmarks[system_string, paste0("t", 1:11)] <- c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)
-mkin_benchmarks
+
t3 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D)))[["elapsed"]]
+t4 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(subset(FOCUS_2006_D, value != 0)), error_model = "tc"))[["elapsed"]]
+t5 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_2006_D), error_model = "obs"))[["elapsed"]]
+
+# Two metabolites, synthetic data
+m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
+                           M1 = mkinsub("SFO", "M2"),
+                           M2 = mkinsub("SFO"),
+                           use_of_ff = "max", quiet = TRUE)
+
+m_synth_DFOP_par <- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),
+                           M1 = mkinsub("SFO"),
+                           M2 = mkinsub("SFO"),
+                           use_of_ff = "max", quiet = TRUE)
+
+SFO_lin_a <- synthetic_data_for_UBA_2014[[1]]$data
+
+DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data
+
+t6 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a)))["elapsed"]
+t7 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c)))["elapsed"]
+
+t8 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), error_model = "tc"))["elapsed"]
+
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation by method Port did not converge:
+## false convergence (8)
+
t9 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), error_model = "tc"))["elapsed"]
+
+t10 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), error_model = "obs"))["elapsed"]
+t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), error_model = "obs"))["elapsed"]
+
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...): Optimisation by method Port did not converge:
+## false convergence (8)
+
mkin_benchmarks[system_string, paste0("t", 1:11)] <- c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)
+mkin_benchmarks
##                                                                                                       CPU
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 AMD Ryzen 7 1700 Eight-Core Processor
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 AMD Ryzen 7 1700 Eight-Core Processor
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 AMD Ryzen 7 1700 Eight-Core Processor
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 AMD Ryzen 7 1700 Eight-Core Processor
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 AMD Ryzen 7 1700 Eight-Core Processor
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 AMD Ryzen 7 1700 Eight-Core Processor
 ##                                                                        OS
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 Linux
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 Linux
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 Linux
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 Linux
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 Linux
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 Linux
 ##                                                                         mkin
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 0.9.48.1
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 0.9.49.1
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 0.9.49.2
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 0.9.49.3
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 0.9.49.4
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 0.9.49.5
 ##                                                                        t1
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.610
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.107
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 8.184
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 7.064
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.296
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.936
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 5.843
 ##                                                                         t2
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 11.019
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 10.105
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 22.889
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 12.558
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 21.239
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 20.545
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 35.863
 ##                                                                        t3
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.764
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 3.415
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.649
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.786
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.510
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.446
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.417
 ##                                                                         t4
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 14.347
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 13.228
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 13.789
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  8.461
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 13.805
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 15.335
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 30.484
-##                                                                         t5
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1  9.495
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  6.395
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  5.675
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3  7.386
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  6.002
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.307
+##                                                                        t5
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 8.511
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 6.395
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 5.675
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 7.386
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 6.002
 ##                                                                        t6
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 2.623
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 2.368
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 2.542
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 2.723
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 2.643
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 2.635
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 2.538
 ##                                                                        t7
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 4.587
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1  4.12
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.128
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.478
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 4.374
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.259
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 4.196
 ##                                                                        t8
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 7.525
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 6.357
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 4.632
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 4.862
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3  7.02
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 4.737
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.853
 ##                                                                         t9
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 16.621
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1  15.42
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  8.171
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  7.618
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 11.124
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  7.763
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 15.643
 ##                                                                       t10
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 8.576
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 7.868
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1 3.676
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2 3.579
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3 5.388
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 3.427
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 7.733
 ##                                                                        t11
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 31.267
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.48.1 28.858
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.1  5.636
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.2  5.574
 ## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.3  7.365
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4  5.626
-## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.5 10.511
-
save(mkin_benchmarks, file = "~/git/mkin/vignettes/mkin_benchmarks.rda")
+## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.4 5.626 +
save(mkin_benchmarks, file = "~/git/mkin/vignettes/mkin_benchmarks.rda")
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 3fc54cfa..ca883f17 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -30,7 +30,7 @@ mkin - 0.9.49.5 + 0.9.49.6 @@ -88,7 +88,7 @@

Performance benefit by using compiled model definitions in mkin

Johannes Ranke

-

2019-07-04

+

2019-07-05

@@ -128,99 +128,45 @@ print("R package rbenchmark is not available") } 
## Lade nötiges Paket: rbenchmark
-
## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve",
-## use_compiled = FALSE, : Observations with value of zero were removed from
-## the data
-
## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet =
-## TRUE): Observations with value of zero were removed from the data
-
## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet
-## = TRUE): Observations with value of zero were removed from the data
-
## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve",
-## use_compiled = FALSE, : Observations with value of zero were removed from
-## the data
-
-## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve",
-## use_compiled = FALSE, : Observations with value of zero were removed from
-## the data
-
-## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve",
-## use_compiled = FALSE, : Observations with value of zero were removed from
-## the data
-
## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet =
-## TRUE): Observations with value of zero were removed from the data
-
-## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet =
-## TRUE): Observations with value of zero were removed from the data
-
-## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet =
-## TRUE): Observations with value of zero were removed from the data
-
## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet
-## = TRUE): Observations with value of zero were removed from the data
-
-## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet
-## = TRUE): Observations with value of zero were removed from the data
-
-## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet
-## = TRUE): Observations with value of zero were removed from the data
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   3.061    1.000     3.059        0
-## 1 deSolve, not compiled            3  28.502    9.311    28.487        0
-## 2      Eigenvalue based            3   4.321    1.412     4.318        0
+## 3     deSolve, compiled            3   2.147    1.000     2.145        0
+## 1 deSolve, not compiled            3  12.653    5.893    12.646        0
+## 2      Eigenvalue based            3   2.690    1.253     2.688        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
 ## 2          0         0
-

We see that using the compiled model is by a factor of around 9 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs.

+

We see that using the compiled model is by a factor of around 6 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs.

Model that can not be solved with Eigenvalues

This evaluation is also taken from the example section of mkinfit.

-
if (require(rbenchmark)) {
-  FOMC_SFO <- mkinmod(
-    parent = mkinsub("FOMC", "m1"),
-    m1 = mkinsub( "SFO"))
-
-  b.2 <- benchmark(
-    "deSolve, not compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D,
-                                      use_compiled = FALSE, quiet = TRUE),
-    "deSolve, compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE),
-    replications = 3)
-  print(b.2)
-  factor_FOMC_SFO <- round(b.2["1", "relative"])
-} else {
-  factor_FOMC_SFO <- NA
-  print("R package benchmark is not available")
-}
+
if (require(rbenchmark)) {
+  FOMC_SFO <- mkinmod(
+    parent = mkinsub("FOMC", "m1"),
+    m1 = mkinsub( "SFO"))
+
+  b.2 <- benchmark(
+    "deSolve, not compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D,
+                                      use_compiled = FALSE, quiet = TRUE),
+    "deSolve, compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE),
+    replications = 3)
+  print(b.2)
+  factor_FOMC_SFO <- round(b.2["1", "relative"])
+} else {
+  factor_FOMC_SFO <- NA
+  print("R package benchmark is not available")
+}
## Successfully compiled differential equation model from auto-generated C code.
-
## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet =
-## TRUE): Observations with value of zero were removed from the data
-
## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
-## value of zero were removed from the data
-
## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet =
-## TRUE): Observations with value of zero were removed from the data
-
-## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet =
-## TRUE): Observations with value of zero were removed from the data
-
-## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet =
-## TRUE): Observations with value of zero were removed from the data
-
## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
-## value of zero were removed from the data
-
-## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
-## value of zero were removed from the data
-
-## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
-## value of zero were removed from the data
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.818    1.000     4.814        0
-## 1 deSolve, not compiled            3  53.275   11.057    53.249        0
+## 2     deSolve, compiled            3   3.773    1.000     3.770        0
+## 1 deSolve, not compiled            3  27.812    7.371    27.798        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0
-

Here we get a performance benefit of a factor of 11 using the version of the differential equation model compiled from C code!

-

This vignette was built with mkin 0.9.49.5 on

+

Here we get a performance benefit of a factor of 7 using the version of the differential equation model compiled from C code!

+

This vignette was built with mkin 0.9.48.1 on

## R version 3.6.0 (2019-04-26)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 10 (buster)
-- cgit v1.2.1