From bc3825ae2d12c18ea3d3caf17eb23c93fef180b8 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 8 Oct 2020 09:31:35 +0200 Subject: Fix issues for release --- docs/dev/articles/web_only/FOCUS_Z.html | 62 +-- .../figure-html/FOCUS_2006_Z_fits_10-1.png | Bin 133239 -> 133233 bytes .../figure-html/FOCUS_2006_Z_fits_11-1.png | Bin 132494 -> 132503 bytes .../figure-html/FOCUS_2006_Z_fits_11a-1.png | Bin 99564 -> 99562 bytes .../figure-html/FOCUS_2006_Z_fits_11b-1.png | Bin 22623 -> 22624 bytes .../figure-html/FOCUS_2006_Z_fits_6-1.png | Bin 133000 -> 133001 bytes .../figure-html/FOCUS_2006_Z_fits_9-1.png | Bin 110758 -> 110760 bytes docs/dev/articles/web_only/NAFTA_examples.html | 430 ++++++++++----------- docs/dev/articles/web_only/benchmarks.html | 46 ++- docs/dev/articles/web_only/compiled_models.html | 18 +- 10 files changed, 280 insertions(+), 276 deletions(-) (limited to 'docs/dev/articles/web_only') diff --git a/docs/dev/articles/web_only/FOCUS_Z.html b/docs/dev/articles/web_only/FOCUS_Z.html index 270232d7..763ca9be 100644 --- a/docs/dev/articles/web_only/FOCUS_Z.html +++ b/docs/dev/articles/web_only/FOCUS_Z.html @@ -101,7 +101,7 @@

Example evaluation of FOCUS dataset Z

Johannes Ranke

-

2020-05-27

+

2020-10-08

Source: vignettes/web_only/FOCUS_Z.rmd @@ -217,25 +217,25 @@ 
plot_sep(m.Z.FOCUS)

summary(m.Z.FOCUS, data = FALSE)$bpar
-
##             Estimate se_notrans t value     Pr(>t)     Lower     Upper
-## Z0_0       96.840695   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
+
##             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
endpoints(m.Z.FOCUS)
## $ff
 ##   Z2_Z3 Z2_sink 
-## 0.47148 0.52852 
+## 0.47151 0.52849 
 ## 
 ## $distimes
 ##        DT50    DT90
-## Z0  0.31287  1.0393
-## Z1  1.44911  4.8138
-## Z2  1.53474  5.0983
-## Z3 11.80989 39.2316
+## Z0 0.31288 1.0394 +## Z1 1.44919 4.8141 +## Z2 1.53479 5.0985 +## Z3 11.80955 39.2305

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.

@@ -277,51 +277,57 @@ quiet = TRUE)
## Warning in mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, parms.ini = m.Z.mkin.
 ## 3$bparms.ode, : Observations with value of zero were removed from the data
-
plot_sep(m.Z.mkin.4)
+
## Warning in mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, parms.ini = m.Z.mkin.
+## 3$bparms.ode, : Shapiro-Wilk test for standardized residuals: p = 0.0449
+
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),
+
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.

-
m.Z.mkin.5 <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin,
+
m.Z.mkin.5 <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin,
                       parms.ini = m.Z.mkin.4$bparms.ode[1:4],
                       quiet = TRUE)

 
## 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)

+
## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = m.Z.mkin.
+## 4$bparms.ode[1:4], : Shapiro-Wilk test for standardized residuals: p = 0.00785

+
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.

-
m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin,
+
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)

 
## 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)

+
## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = c(m.Z.mkin.
+## 5$bparms.ode[1:7], : Shapiro-Wilk test for standardized residuals: p = 0.00785

+
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   Z2_Z3 Z2_sink Z3_free 
 ## 1.00000 0.53656 0.46344 1.00000 
 ## 
 ## $SFORB
 ##     Z0_b1     Z0_b2     Z3_b1     Z3_b2 
-## 2.4471337 0.0075125 0.0800071 0.0000000 
+## 2.4471358 0.0075126 0.0800073 0.0000000 
 ## 
 ## $distimes
-##      DT50   DT90 DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2
-## Z0 0.3043 1.1848    0.28325     92.266         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

+##      DT50   DT90 DT50back DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2
+## Z0 0.3043 1.1848  0.35666    0.28325     92.265         NA         NA
+## Z1 1.5148 5.0320       NA         NA         NA         NA         NA
+## Z2 1.6414 5.4526       NA         NA         NA         NA         NA
+## Z3     NA     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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index dd5d89cd..0c698299 100644
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diff --git a/docs/dev/articles/web_only/NAFTA_examples.html b/docs/dev/articles/web_only/NAFTA_examples.html
index 12499452..09f40a7f 100644
--- a/docs/dev/articles/web_only/NAFTA_examples.html
+++ b/docs/dev/articles/web_only/NAFTA_examples.html
@@ -101,7 +101,7 @@
       
Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance

                         
Johannes Ranke

             
-            
2020-05-27

+            
2020-10-08

       
       Source: vignettes/web_only/NAFTA_examples.rmd
       
@@ -138,23 +138,23 @@
 ## 
 ## 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
+##          Estimate   Pr(>t)  Lower   Upper
+## parent_0  95.8401 4.67e-21 92.245 99.4357
+## k_parent   0.0102 3.92e-12  0.009  0.0117
+## sigma      4.8230 3.81e-06  3.214  6.4318
 ## 
 ## $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     NA 9.91e+01 1.02e+02
+## k__iore_parent 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
 ## 
 ## $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
+## k2       2.17e-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
 ## 
@@ -163,7 +163,7 @@
 ##      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 4.42e+11 2.42e+11
+## DFOP 55.5 5.83e+11 3.20e+11
 ## 
 ## Representative half-life:
 ## [1] 321.51

@@ -186,23 +186,23 @@
 ## 
 ## 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
+##          Estimate   Pr(>t)    Lower    Upper
+## parent_0   96.497 2.32e-24 94.85271 98.14155
+## k_parent    0.008 3.42e-14  0.00737  0.00869
+## sigma       2.295 1.22e-05  1.47976  3.11036
 ## 
 ## $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
+##                Estimate   Pr(>t)    Lower    Upper
+## parent_0       9.85e+01 1.17e-28 9.79e+01 9.92e+01
+## k__iore_parent 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
 ## 
 ## $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
+## k2       1.04e-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
 ## 
@@ -211,7 +211,7 @@
 ##      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 9.80e+10 5.98e+10
+## DFOP 83.6 1.09e+11 6.67e+10
 ## 
 ## Representative half-life:
 ## [1] 215.87
@@ -234,23 +234,23 @@ ## ## 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 +## Estimate Pr(>t) Lower Upper +## parent_0 94.7759 7.29e-24 92.3478 97.2039 +## k_parent 0.0179 8.02e-16 0.0166 0.0194 +## sigma 3.0696 3.81e-06 2.0456 4.0936 ## ## $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 +## Estimate Pr(>t) Lower Upper +## parent_0 97.12446 2.63e-26 95.62461 98.62431 +## k__iore_parent 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 ## ## $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 +## k2 3.88e-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 ## @@ -259,7 +259,7 @@ ## 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 6.66e+09 1.41e+10 +## DFOP 34.1 8.42e+09 1.79e+10 ## ## Representative half-life: ## [1] 53.17 @@ -282,23 +282,23 @@ ## ## 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 +## Estimate Pr(>t) Lower Upper +## parent_0 96.41796 4.80e-53 93.32245 99.51347 +## k_parent 0.00735 7.64e-21 0.00641 0.00843 +## sigma 7.94557 1.83e-15 6.46713 9.42401 ## ## $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 NA 9.55e+01 1.03e+02 +## k__iore_parent 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 ## ## $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 +## k2 2.30e-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 ## @@ -307,7 +307,7 @@ ## 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 6.97e+09 3.52e+09 +## DFOP 96.4 5.95e+09 3.01e+09 ## ## Representative half-life: ## [1] 454.55 @@ -320,7 +320,7 @@

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 = 1e-3))
## 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)
@@ -335,17 +335,17 @@ ## ## 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 6.53e-29 83.37344 92.95754 +## k_parent 0.00803 1.67e-13 0.00674 0.00957 +## sigma 7.44786 4.17e-10 5.66209 9.23363 ## ## $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 +## Estimate Pr(>t) Lower Upper +## parent_0 9.77e+01 7.03e-35 9.44e+01 1.01e+02 +## k__iore_parent 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 ## ## $DFOP ## Estimate Pr(>t) Lower Upper @@ -387,23 +387,23 @@ ## ## 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 +## Estimate Pr(>t) Lower Upper +## parent_0 88.1933 3.06e-12 79.9447 96.4419 +## k_parent 0.0409 2.07e-07 0.0324 0.0516 +## sigma 7.2429 3.92e-05 4.4768 10.0090 ## ## $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 +## Estimate Pr(>t) Lower Upper +## parent_0 9.89e+01 1.12e-16 9.54e+01 1.02e+02 +## k__iore_parent 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 ## ## $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 +## k2 6.69e-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 ## @@ -412,7 +412,7 @@ ## 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 2.07e+12 1.15e+12 +## DFOP 10.5 1.86e+12 1.04e+12 ## ## Representative half-life: ## [1] 101.43 @@ -422,16 +422,11 @@

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 
@@ -441,24 +436,24 @@
 ## 
 ## 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 2.15e-19 93.178 96.2464
+## k_parent   0.0389 4.47e-14  0.037  0.0408
+## sigma      1.5957 1.28e-04  0.932  2.2595
 ## 
 ## $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
+##                Estimate   Pr(>t)   Lower  Upper
+## parent_0         93.863 2.32e-18 92.4565 95.269
+## k__iore_parent    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
 ## 
 ## $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
+## g          0.7742 5.00e-01  0.0000  1.0000
 ## sigma      1.5957 2.50e-04  0.9135  2.2779
 ## 
 ## 
@@ -475,12 +470,12 @@
 

 

 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 
@@ -490,25 +485,25 @@
 ## 
 ## 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
+##          Estimate   Pr(>t)   Lower    Upper
+## parent_0 101.7315 6.42e-11 91.9259 111.5371
+## k_parent   0.0495 1.70e-07  0.0404   0.0607
+## sigma      8.0152 1.28e-04  4.6813  11.3491
 ## 
 ## $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
+##                Estimate   Pr(>t)  Lower   Upper
+## parent_0          96.86 3.32e-12 90.848 102.863
+## k__iore_parent     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
 ## 
 ## $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 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
 ## 
 ## 
 ## DTx values:
@@ -528,12 +523,12 @@
 

 

 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 
@@ -543,17 +538,17 @@
 ## 
 ## 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
+##          Estimate   Pr(>t)    Lower    Upper
+## parent_0 96.15820 4.83e-13 90.24934 1.02e+02
+## k_parent  0.00321 4.71e-05  0.00222 4.64e-03
+## sigma     6.43473 1.28e-04  3.75822 9.11e+00
 ## 
 ## $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
+##                Estimate Pr(>t)    Lower    Upper
+## parent_0       1.05e+02     NA 9.90e+01 1.10e+02
+## k__iore_parent 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
 ## 
 ## $DFOP
 ##          Estimate   Pr(>t)    Lower    Upper
@@ -571,7 +566,7 @@
 ## DFOP 4.21e+11 2.64e+12 9.56e+11
 ## 
 ## Representative half-life:
-## [1] 41148169

+## [1] 41148171

 
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.
@@ -582,14 +577,14 @@

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 
@@ -599,23 +594,23 @@
 ## 
 ## 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
+##          Estimate   Pr(>t)  Lower   Upper
+## parent_0  100.521 8.75e-12 92.461 108.581
+## k_parent    0.124 3.61e-08  0.104   0.148
+## sigma       7.048 1.28e-04  4.116   9.980
 ## 
 ## $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     NA    NA    NA
+## k__iore_parent    2.436     NA    NA    NA
+## N_parent          0.263     NA    NA    NA
+## sigma             3.965     NA    NA    NA
 ## 
 ## $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
+## k1          0.124 5.75e-06  0.0958   0.161
+## k2          0.124 6.72e-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
 ## 
@@ -632,7 +627,7 @@
 

 

 Example on page 12, lower panel

-
p12b <- nafta(NAFTA_SOP_Attachment[["p12b"]])

+
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

@@ -643,9 +638,9 @@
 ## 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 
@@ -655,17 +650,17 @@
 ## 
 ## 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 0.00039 85.9388 109.4292
+## k_parent   0.0589 0.00261  0.0431   0.0805
+## sigma      3.4323 0.04356 -1.2377   8.1023
 ## 
 ## $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 0.0055 74.539157 116.51
+## k__iore_parent    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
 ## 
 ## $DFOP
 ##          Estimate Pr(>t) Lower Upper
@@ -688,16 +683,12 @@
 

 

 Example on page 13

-
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

+
p13 <- nafta(NAFTA_SOP_Attachment[["p13"]])

 
## 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 
@@ -707,24 +698,24 @@
 ## 
 ## 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 5.99e-17 89.61936 95.85065
+## k_parent  0.00258 2.42e-09  0.00223  0.00299
+## sigma     3.41172 7.07e-05  2.05455  4.76888
 ## 
 ## $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 6.34e-16 88.53086 94.672
+## k__iore_parent   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
 ## 
 ## $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
+## k1        0.00258 4.28e-01 1.45e-08 4.61e+02
 ## k2        0.00258 3.69e-08 2.20e-03 3.03e-03
-## g         0.00442 5.00e-01       NA       NA
+## g         0.00442 5.00e-01 0.00e+00 1.00e+00
 ## sigma     3.41172 1.35e-04 2.02e+00 4.80e+00
 ## 
 ## 
@@ -741,16 +732,16 @@
 

 

 DT50 not observed in the study and DFOP problems in PestDF

-
p14 <- nafta(NAFTA_SOP_Attachment[["p14"]])

+
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 
@@ -760,23 +751,23 @@
 ## 
 ## 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
+##          Estimate   Pr(>t)    Lower    Upper
+## parent_0 99.47124 2.06e-30 98.42254 1.01e+02
+## k_parent  0.00279 3.75e-15  0.00256 3.04e-03
+## sigma     1.55616 3.81e-06  1.03704 2.08e+00
 ## 
 ## $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   NaN   NaN
+## k__iore_parent 9.44e-08     NA   NaN   NaN
+## N_parent       3.31e+00     NA   NaN   NaN
+## sigma          1.20e+00     NA 0.796   1.6
 ## 
 ## $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
+## k2       7.70e-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
 ## 
@@ -785,7 +776,7 @@
 ##          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 2.54e+10 2.46e+11 9.51e+10
+## DFOP 2.41e+10 2.33e+11 9.00e+10
 ## 
 ## Representative half-life:
 ## [1] 6697.44

@@ -794,17 +785,16 @@
 

 

 N is less than 1 and DFOP fraction parameter is below zero

-
p15a <- nafta(NAFTA_SOP_Attachment[["p15a"]])

+
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 
@@ -814,25 +804,25 @@
 ## 
 ## 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 2.00e-15 94.32049 101.615
+## k_parent  0.00952 4.93e-09  0.00824   0.011
+## sigma     4.18778 1.28e-04  2.44588   5.930
 ## 
 ## $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 2.94e-15 92.937 98.811
+## k__iore_parent    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
 ## 
 ## $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 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
 ## 
 ## 
 ## DTx values:
@@ -843,16 +833,16 @@
 ## 
 ## Representative half-life:
 ## [1] 41.33

-
p15b <- nafta(NAFTA_SOP_Attachment[["p15b"]])

+
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 
@@ -862,25 +852,25 @@
 ## 
 ## 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
+##          Estimate   Pr(>t)    Lower    Upper
+## parent_0 1.01e+02 3.06e-17 98.31594 1.03e+02
+## k_parent 4.86e-03 2.48e-10  0.00435 5.42e-03
+## sigma    2.76e+00 1.28e-04  1.61402 3.91e+00
 ## 
 ## $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 1.81e-16 97.51348 102.14
+## k__iore_parent     0.38 3.22e-01  0.00352  41.05
+## N_parent           0.00 5.00e-01 -1.07696   1.08
+## sigma              2.21 2.57e-04  1.23245   3.19
 ## 
 ## $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
+## 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
 ## g        1.50e-01     NA       NA       NA
-## sigma    2.76e+00     NA 1.58e+00 3.94e+00
+## sigma    2.76e+00     NA  1.58208 3.94e+00
 ## 
 ## 
 ## DTx values:
@@ -896,14 +886,14 @@
 

 

 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 
@@ -913,22 +903,22 @@
 ## 
 ## 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 2.33e-13 60.509 83.40
+## k_parent    0.159 4.86e-05  0.102  0.25
+## sigma      11.302 1.25e-08  8.308 14.30
 ## 
 ## $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
+##                Estimate   Pr(>t)    Lower    Upper
+## parent_0       8.74e+01 2.48e-16 7.72e+01 97.52972
+## k__iore_parent 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
 ## 
 ## $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
+## k1        18.5560 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/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html
index 9e53f113..30b7a879 100644
--- a/docs/dev/articles/web_only/benchmarks.html
+++ b/docs/dev/articles/web_only/benchmarks.html
@@ -101,7 +101,7 @@
       
Benchmark timings for mkin

                         
Johannes Ranke

             
-            
2020-05-27

+            
2020-10-08

       
       Source: vignettes/web_only/benchmarks.rmd
       
@@ -132,13 +132,20 @@
 DFOP_SFO <- mkinmod(
   parent = mkinsub("FOMC", "m1"),
   m1 = mkinsub("SFO"))
-t3 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D)))[["elapsed"]]
-t4 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D),
+t3 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D)))[["elapsed"]]

+
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
+## Shapiro-Wilk test for standardized residuals: p = 0.0165

+
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
+## Shapiro-Wilk test for standardized residuals: p = 0.0499
+
+## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
+## Shapiro-Wilk test for standardized residuals: p = 0.0499

+
t4 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D),
     error_model = "tc"))[["elapsed"]]
 t5 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D),
     error_model = "obs"))[["elapsed"]]

 
Two metabolites, synthetic data:

-
m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
+
m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
                            M1 = mkinsub("SFO", "M2"),
                            M2 = mkinsub("SFO"),
                            use_of_ff = "max", quiet = TRUE)
@@ -153,9 +160,10 @@
 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),
+t7 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c)))[["elapsed"]]

+
## Warning in mkinfit(models[[model_index]], datasets[[dataset_index]], ...):
+## Shapiro-Wilk test for standardized residuals: p = 0.000174

+
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"]]
@@ -164,7 +172,7 @@
     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)] <-
+
mkin_benchmarks[system_string, paste0("t", 1:11)] <-
   c(t1, t2, t3, t4, t5, t6, t7, t8, t9, t10, t11)
 save(mkin_benchmarks, file = "~/git/mkin/vignettes/web_only/mkin_benchmarks.rda")

 

@@ -216,8 +224,8 @@
 
 
 0.9.50.3
-1.746
-3.716
+1.707
+4.062
 
 
 
@@ -272,9 +280,9 @@
 
 
 0.9.50.3
-1.385
-6.562
-2.736
+1.372
+6.233
+2.779
 
 
 
@@ -350,12 +358,12 @@
 
 
 0.9.50.3
-0.760
-1.226
-1.455
-4.198
-2.007
-2.976
+0.768
+1.235
+1.302
+2.921
+2.078
+3.040
 
 
 
diff --git a/docs/dev/articles/web_only/compiled_models.html b/docs/dev/articles/web_only/compiled_models.html
index 997e90ea..055d0646 100644
--- a/docs/dev/articles/web_only/compiled_models.html
+++ b/docs/dev/articles/web_only/compiled_models.html
@@ -101,7 +101,7 @@
       
Performance benefit by using compiled model definitions in mkin

                         
Johannes Ranke

             
-            
2020-05-27

+            
2020-10-08

       
       Source: vignettes/web_only/compiled_models.rmd
       
@@ -153,10 +153,10 @@
   print("R package rbenchmark is not available")
 }

 
##                    test replications relative elapsed
-## 4            analytical            1    1.000   0.201
-## 3     deSolve, compiled            1    1.711   0.344
-## 2      Eigenvalue based            1    1.960   0.394
-## 1 deSolve, not compiled            1   39.881   8.016

+## 4            analytical            1    1.000   0.195
+## 3     deSolve, compiled            1    1.769   0.345
+## 2      Eigenvalue based            1    2.087   0.407
+## 1 deSolve, not compiled            1   42.656   8.318

 
We see that using the compiled model is by more than a factor of 10 faster than using deSolve without compiled code.

 

 

@@ -182,11 +182,11 @@
 }

 
## Successfully compiled differential equation model from auto-generated C code.

 
##                    test replications relative elapsed
-## 2     deSolve, compiled            1    1.000   0.467
-## 1 deSolve, not compiled            1   30.244  14.124

-
Here we get a performance benefit of a factor of 30 using the version of the differential equation model compiled from C code!

+## 2     deSolve, compiled            1    1.000   0.474
+## 1 deSolve, not compiled            1   30.909  14.651
+

Here we get a performance benefit of a factor of 31 using the version of the differential equation model compiled from C code!

This vignette was built with mkin 0.9.50.3 on

-
## R version 4.0.0 (2020-04-24)
+
## R version 4.0.2 (2020-06-22)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 10 (buster)

 
## CPU model: AMD Ryzen 7 1700 Eight-Core Processor

-- 
cgit v1.2.1