From 9ae42bd20bc2543a94cf1581ba9820c2f9e3afbd Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 20 Apr 2023 19:53:28 +0200 Subject: Fix and rebuild documentation, see NEWS I had to fix the two pathway vignettes, as they did not work with the released version any more. So they and the multistart vignette which got some small fixes as well were rebuilt. Complete rebuild of the online docs with the released version. The documentation of the 'hierarchial_kinetics' format had to be fixed as well. --- docs/articles/web_only/FOCUS_Z.html | 176 +++++++--- .../figure-html/FOCUS_2006_Z_fits_1-1.png | Bin 66689 -> 67444 bytes .../figure-html/FOCUS_2006_Z_fits_10-1.png | Bin 105896 -> 107009 bytes .../figure-html/FOCUS_2006_Z_fits_11-1.png | Bin 104793 -> 106095 bytes .../figure-html/FOCUS_2006_Z_fits_11a-1.png | Bin 75230 -> 76831 bytes .../figure-html/FOCUS_2006_Z_fits_11b-1.png | Bin 36314 -> 37495 bytes .../figure-html/FOCUS_2006_Z_fits_2-1.png | Bin 66689 -> 67444 bytes .../figure-html/FOCUS_2006_Z_fits_3-1.png | Bin 66448 -> 67259 bytes .../figure-html/FOCUS_2006_Z_fits_5-1.png | Bin 80373 -> 81750 bytes .../figure-html/FOCUS_2006_Z_fits_6-1.png | Bin 105210 -> 106404 bytes .../figure-html/FOCUS_2006_Z_fits_7-1.png | Bin 104538 -> 105359 bytes .../figure-html/FOCUS_2006_Z_fits_9-1.png | Bin 88801 -> 89119 bytes docs/articles/web_only/NAFTA_examples.html | 184 +++++++---- .../NAFTA_examples_files/figure-html/p10-1.png | Bin 79758 -> 81540 bytes .../NAFTA_examples_files/figure-html/p11-1.png | Bin 76315 -> 77600 bytes .../NAFTA_examples_files/figure-html/p12a-1.png | Bin 81697 -> 83512 bytes .../NAFTA_examples_files/figure-html/p12b-1.png | Bin 70800 -> 71409 bytes .../NAFTA_examples_files/figure-html/p13-1.png | Bin 78121 -> 78613 bytes .../NAFTA_examples_files/figure-html/p14-1.png | Bin 80656 -> 81557 bytes .../NAFTA_examples_files/figure-html/p15a-1.png | Bin 76925 -> 77571 bytes .../NAFTA_examples_files/figure-html/p15b-1.png | Bin 78968 -> 79748 bytes .../NAFTA_examples_files/figure-html/p16-1.png | Bin 93950 -> 94540 bytes .../NAFTA_examples_files/figure-html/p5a-1.png | Bin 82665 -> 83061 bytes .../NAFTA_examples_files/figure-html/p5b-1.png | Bin 80721 -> 81186 bytes .../NAFTA_examples_files/figure-html/p6-1.png | Bin 83052 -> 83142 bytes .../NAFTA_examples_files/figure-html/p7-1.png | Bin 102568 -> 102935 bytes .../NAFTA_examples_files/figure-html/p8-1.png | Bin 92407 -> 93632 bytes .../NAFTA_examples_files/figure-html/p9a-1.png | Bin 78605 -> 78782 bytes .../NAFTA_examples_files/figure-html/p9b-1.png | Bin 76240 -> 76883 bytes docs/articles/web_only/benchmarks.html | 231 +++++++++++-- docs/articles/web_only/compiled_models.html | 119 +++++-- docs/articles/web_only/dimethenamid_2018.html | 356 +++++++++++++++------ .../figure-html/f_parent_mkin_dfop_const-1.png | Bin 58608 -> 57786 bytes .../f_parent_mkin_dfop_const_test-1.png | Bin 58777 -> 57786 bytes .../figure-html/f_parent_mkin_dfop_tc_test-1.png | Bin 60062 -> 59396 bytes .../figure-html/f_parent_mkin_sfo_const-1.png | Bin 56694 -> 55982 bytes .../figure-html/f_parent_saemix_sfo_tc-1.png | Bin 28655 -> 28538 bytes .../figure-html/plot_parent_nlme-1.png | Bin 59194 -> 59192 bytes docs/articles/web_only/multistart.html | 94 ++++-- .../figure-html/unnamed-chunk-3-1.png | Bin 60747 -> 66934 bytes .../figure-html/unnamed-chunk-4-1.png | Bin 58448 -> 53020 bytes .../figure-html/unnamed-chunk-5-1.png | Bin 21847 -> 22355 bytes .../figure-html/unnamed-chunk-6-1.png | Bin 50597 -> 53020 bytes docs/articles/web_only/saem_benchmarks.html | 285 +++++++++++++++-- 44 files changed, 1137 insertions(+), 308 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 ea20ecd9..9602adb5 100644 --- a/docs/articles/web_only/FOCUS_Z.html +++ b/docs/articles/web_only/FOCUS_Z.html @@ -33,14 +33,14 @@ mkin - 1.2.0 + 1.2.3

Example on page 9, lower panel @@ -454,12 +492,12 @@ 
## 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$covar): diag(.) had 0 or NA entries; non-finite result is
-## doubtful
+
## Warning in cov2cor(ans$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)
@@ -501,7 +539,12 @@ ## ## Representative half-life: ## [1] 14.8 -

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.

+

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 @@ -510,12 +553,12 @@ p10 <- nafta(NAFTA_SOP_Attachment[["p10"]])

## Warning in sqrt(diag(covar)): NaNs produced
## Warning in sqrt(1/diag(V)): NaNs produced
-
## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result is
-## doubtful
+
## Warning in cov2cor(ans$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(p10)
+plot(p10) 

 print(p10)
@@ -557,7 +600,11 @@ ## ## Representative half-life: ## [1] 8.86 -

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.

+

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.

@@ -571,7 +618,7 @@ 
## 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)
@@ -613,13 +660,19 @@ ## ## Representative half-life: ## [1] 41148170 -

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.

+

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.

-

N is less than 1 and the DFOP rate constants are like the SFO rate constant +

N is less than 1 and the DFOP rate constants are like the SFO rate +constant

-

In the following three examples, the same results are obtained with mkin as reported for PestDF. As in the case on page 10, the N values below 1 are deemed unrealistic and appear to be the result of an overparameterisation.

+

In the following three examples, the same results are obtained with +mkin as reported for PestDF. As in the case on page 10, the N values +below 1 are deemed unrealistic and appear to be the result of an +overparameterisation.

Example on page 12, upper panel

@@ -630,12 +683,12 @@ 
## 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$covar): diag(.) had 0 or NA entries; non-finite result is
-## doubtful
+
## Warning in cov2cor(ans$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(p12a)
+plot(p12a)

 print(p12a)
@@ -690,7 +743,7 @@ 
## 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)
@@ -741,7 +794,7 @@ 
## 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)
@@ -792,12 +845,12 @@ 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$covar): diag(.) had 0 or NA entries; non-finite result is
-## doubtful
+
## Warning in cov2cor(ans$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)
@@ -839,7 +892,9 @@ ## ## Representative half-life: ## [1] 6697.44 -

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.

+

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 @@ -849,7 +904,7 @@ 
## 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)
@@ -895,12 +950,12 @@ 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$covar): diag(.) had 0 or NA entries; non-finite result is
-## doubtful
+
## Warning in cov2cor(ans$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)
@@ -942,7 +997,10 @@ ## ## Representative half-life: ## [1] 71.18 -

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.

+

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 @@ -954,7 +1012,7 @@ 
## 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)
@@ -996,20 +1054,32 @@ ## ## Representative half-life: ## [1] 8.93 -

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.

+

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.

Conclusions

-

The results obtained with mkin deviate from the results obtained with PestDF either in cases where one of the interpretive rules would apply, i.e. the IORE parameter N is less than one or the DFOP k values obtained with PestDF are equal to the SFO k values, or in cases where the DFOP model did not converge, which often lead to negative rate constants returned by PestDF.

-

Therefore, mkin appears to suitable for kinetic evaluations according to the NAFTA guidance.

+

The results obtained with mkin deviate from the results obtained with +PestDF either in cases where one of the interpretive rules would apply, +i.e. the IORE parameter N is less than one or the DFOP k values obtained +with PestDF are equal to the SFO k values, or in cases where the DFOP +model did not converge, which often lead to negative rate constants +returned by PestDF.

+

Therefore, mkin appears to suitable for kinetic evaluations according +to the NAFTA guidance.

References

-
-
-

US EPA. 2015. “Standard Operating Procedure for Using the NAFTA Guidance to Calculate Representative Half-Life Values and Characterizing Pesticide Degradation.”

+
+
+US EPA. 2015. “Standard Operating Procedure for Using the NAFTA +Guidance to Calculate Representative Half-Life Values and Characterizing +Pesticide Degradation.” https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance.
@@ -1032,7 +1102,7 @@

-

Site built with pkgdown 2.0.6.

+

Site built with pkgdown 2.0.7.

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