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. --- DESCRIPTION | 4 +- NEWS.md | 4 + docs/404.html | 39 +- docs/articles/FOCUS_D.html | 95 +- docs/articles/FOCUS_D_files/figure-html/plot-1.png | Bin 79834 -> 80361 bytes .../FOCUS_D_files/figure-html/plot_2-1.png | Bin 24334 -> 25051 bytes docs/articles/FOCUS_L.html | 256 +- .../figure-html/unnamed-chunk-10-1.png | Bin 42478 -> 42972 bytes .../figure-html/unnamed-chunk-12-1.png | Bin 83170 -> 83736 bytes .../figure-html/unnamed-chunk-13-1.png | Bin 33165 -> 33606 bytes .../figure-html/unnamed-chunk-15-1.png | Bin 58691 -> 58683 bytes .../figure-html/unnamed-chunk-4-1.png | Bin 35677 -> 36066 bytes .../figure-html/unnamed-chunk-5-1.png | Bin 22137 -> 22386 bytes .../figure-html/unnamed-chunk-6-1.png | Bin 36101 -> 36606 bytes .../figure-html/unnamed-chunk-8-1.png | Bin 41430 -> 41775 bytes .../figure-html/unnamed-chunk-9-1.png | Bin 40780 -> 41403 bytes docs/articles/index.html | 41 +- 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docs/articles/prebuilt/2022_dmta_pathway_files/figure-html/unnamed-chunk-4-1.png create mode 100644 docs/articles/prebuilt/2022_dmta_pathway_files/figure-html/unnamed-chunk-6-1.png create mode 100644 docs/articles/prebuilt/2022_dmta_pathway_files/figure-html/unnamed-chunk-7-1.png create mode 100644 docs/articles/prebuilt/2022_dmta_pathway_files/figure-html/unnamed-chunk-8-1.png create mode 100644 docs/reference/hierarchical_kinetics.html create mode 100644 docs/reference/mhmkin-1.png create mode 100644 docs/reference/mhmkin-2.png create mode 100644 docs/reference/summary_listing.html diff --git a/DESCRIPTION b/DESCRIPTION index 8a9836da..54df9c7e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data -Version: 1.2.3 -Date: 2023-04-16 +Version: 1.2.3.1 +Date: 2023-04-20 Authors@R: c( person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "johannes.ranke@jrwb.de", diff --git a/NEWS.md b/NEWS.md index f5820824..c42951de 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# mkin 1.2.3.1 + +- Small fixes to get the online docs right (example code in R/hierarchical_kinetics, cluster setup in cyantraniliprole and dmta pathway vignettes, graphics and model comparison in multistart vignette), rebuild online docs + # mkin 1.2.3 - 'R/{endpoints,parms,plot.mixed.mmkin,summary.saem.mmkin}.R': Calculate parameters and endpoints and plot population curves for specific covariate values, or specific percentiles of covariate values used in saem fits. diff --git a/docs/404.html b/docs/404.html index 8e7e8f45..4d888396 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,14 +32,14 @@ mkin - 1.2.1 + 1.2.3.1

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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diff --git a/docs/reference/test_data_from_UBA_2014-1.png b/docs/reference/test_data_from_UBA_2014-1.png index e4fc2a4c..a007a102 100644 Binary files a/docs/reference/test_data_from_UBA_2014-1.png and b/docs/reference/test_data_from_UBA_2014-1.png differ diff --git a/docs/reference/test_data_from_UBA_2014-2.png b/docs/reference/test_data_from_UBA_2014-2.png index 4ce36561..f460ac83 100644 Binary files a/docs/reference/test_data_from_UBA_2014-2.png and b/docs/reference/test_data_from_UBA_2014-2.png differ diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html index a76f23ab..e57141ec 100644 --- a/docs/reference/test_data_from_UBA_2014.html +++ b/docs/reference/test_data_from_UBA_2014.html @@ -18,13 +18,13 @@ mkin - 1.2.0 + 1.2.3
-

Site built with pkgdown 2.0.6.

+

Site built with pkgdown 2.0.7.

diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 66e94941..2845c6c1 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -22,13 +22,13 @@ the ilr transformation is used."> -