From ee8c8a53903de1a0f480060900b706022af091b6 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 17 Apr 2023 21:53:49 +0200 Subject: Post release changes to the docs The cyantraniliprole and dmta pathway vignettes were not working any more with the latest changes in deSolve and mkin. All docs need a rebuild. --- R/hierarchical_kinetics.R | 4 ++- _pkgdown.yml | 4 +-- vignettes/prebuilt/2022_cyan_pathway.rmd | 42 ++++++++++++++++++++++++-------- vignettes/prebuilt/2022_dmta_pathway.rmd | 21 +++++++++++++--- 4 files changed, 54 insertions(+), 17 deletions(-) diff --git a/R/hierarchical_kinetics.R b/R/hierarchical_kinetics.R index ae60d43c..46623356 100644 --- a/R/hierarchical_kinetics.R +++ b/R/hierarchical_kinetics.R @@ -30,7 +30,9 @@ #' #' \dontrun{ #' library(rmarkdown) -#' draft("example_analysis.rmd", template = "hierarchical_kinetics", package = "mkin") +#' # The following is now commented out after the relase of v1.2.3 for the generation +#' # of online docs, as the command creates a directory and opens an editor +#' #draft("example_analysis.rmd", template = "hierarchical_kinetics", package = "mkin") #' } #' #' @export diff --git a/_pkgdown.yml b/_pkgdown.yml index 5c67d88f..6bf7c14a 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,8 +1,8 @@ url: https://pkgdown.jrwb.de/mkin development: - mode: devel - version_label: info + mode: release + version_label: default template: bootswatch: spacelab diff --git a/vignettes/prebuilt/2022_cyan_pathway.rmd b/vignettes/prebuilt/2022_cyan_pathway.rmd index df34a6f2..d0b2c889 100644 --- a/vignettes/prebuilt/2022_cyan_pathway.rmd +++ b/vignettes/prebuilt/2022_cyan_pathway.rmd @@ -50,11 +50,19 @@ library(knitr) library(saemix) library(parallel) n_cores <- detectCores() -if (Sys.info()["sysname"] == "Windows") { - cl <- makePSOCKcluster(n_cores) -} else { - cl <- makeForkCluster(n_cores) + +# We need to start a new cluster after defining a compiled model that is +# saved as a DLL to the user directory, therefore we define a function +# This is used again after defining the pathway model +start_cluster <- function(n_cores) { + if (Sys.info()["sysname"] == "Windows") { + ret <- makePSOCKcluster(n_cores) + } else { + ret <- makeForkCluster(n_cores) + } + return(ret) } +cl <- start_cluster(n_cores) ``` \clearpage @@ -135,6 +143,10 @@ illparms(cyan_saem_reduced) anova(cyan_saem_reduced) |> kable(digits = 1) ``` +```{r} +stopCluster(cl) +``` + # Pathway fits ## Evaluations with pathway established previously @@ -178,6 +190,7 @@ cyan_path_1 <- list( JSE76 = mkinsub("SFO"), quiet = TRUE, name = "hs_path_1", dll_dir = "cyan_dlls", overwrite = TRUE) ) +cl_path_1 <- start_cluster(n_cores) ``` To obtain suitable starting values for the NLHM fits, separate pathway fits are performed for all datasets. @@ -187,7 +200,7 @@ f_sep_1_const <- mmkin( cyan_path_1, cyan_ds, error_model = "const", - cluster = cl, + cluster = cl_path_1, quiet = TRUE) status(f_sep_1_const) |> kable() @@ -209,7 +222,7 @@ currently under development. ```{r, f-saem-1, dependson = "f-sep-1"} f_saem_1 <- mhmkin(list(f_sep_1_const, f_sep_1_tc), no_random_effect = illparms(cyan_saem_full), - cluster = cl) + cluster = cl_path_1) ``` ```{r dependson = "f-saem-1"} @@ -253,6 +266,9 @@ at later time points are strongly and systematically underestimated. \clearpage +```{r} +stopCluster(cl_path_1) +``` ## Alternative pathway fits @@ -294,11 +310,13 @@ cyan_path_2 <- list( overwrite = TRUE ) ) + +cl_path_2 <- start_cluster(n_cores) f_sep_2_const <- mmkin( cyan_path_2, cyan_ds, error_model = "const", - cluster = cl, + cluster = cl_path_2, quiet = TRUE) status(f_sep_2_const) |> kable() @@ -319,7 +337,7 @@ Sassafras dataset. ```{r f-saem-2, dependson = c("f-sep-2-const", "f-sep-2-tc")} f_saem_2 <- mhmkin(list(f_sep_2_const, f_sep_2_tc), no_random_effect = illparms(cyan_saem_full[2:4, ]), - cluster = cl) + cluster = cl_path_2) ``` ```{r dependson = "f-saem-2"} @@ -384,11 +402,11 @@ no_ranef[["sforb_path_2", "const"]] <- c("cyan_free_0", "f_JCZ38_qlogis", "f_JSE76_qlogis") no_ranef[["sforb_path_2", "tc"]] <- c("cyan_free_0", "log_k_cyan_free_bound", "f_JCZ38_qlogis", "f_JSE76_qlogis") -clusterExport(cl, "no_ranef") +clusterExport(cl_path_2, "no_ranef") f_saem_3 <- update(f_saem_2, no_random_effect = no_ranef, - cluster = cl) + cluster = cl_path_2) ``` ```{r dependson = "f-saem-3"} @@ -413,6 +431,10 @@ two-component error) are lower than in the previous fits with the alternative pathway, the practical value of these refined evaluations is limited as no confidence intervals are obtained. +```{r} +stopCluster(cl_path_2) +``` + \clearpage # Conclusion diff --git a/vignettes/prebuilt/2022_dmta_pathway.rmd b/vignettes/prebuilt/2022_dmta_pathway.rmd index ff2b527c..f787daf2 100644 --- a/vignettes/prebuilt/2022_dmta_pathway.rmd +++ b/vignettes/prebuilt/2022_dmta_pathway.rmd @@ -45,10 +45,17 @@ library(knitr) library(saemix) library(parallel) n_cores <- detectCores() -if (Sys.info()["sysname"] == "Windows") { - cl <- makePSOCKcluster(n_cores) -} else { - cl <- makeForkCluster(n_cores) + +# We need to start a new cluster after defining a compiled model that is +# saved as a DLL to the user directory, therefore we define a function +# This is used again after defining the pathway model +start_cluster <- function(n_cores) { + if (Sys.info()["sysname"] == "Windows") { + ret <- makePSOCKcluster(n_cores) + } else { + ret <- makeForkCluster(n_cores) + } + return(ret) } ``` @@ -163,6 +170,8 @@ m_hs_path_1 <- mkinmod( unload = TRUE, overwrite = TRUE, quiet = TRUE ) +cl <- start_cluster(n_cores) + deg_mods_1 <- list( sfo_path_1 = m_sfo_path_1, fomc_path_1 = m_fomc_path_1, @@ -332,6 +341,10 @@ plot(saem_sforb_path_1_tc_reduced) Plots of the remaining fits and listings for all successful fits are shown in the Appendix. +```{r} +stopCluster(cl) +``` + # Conclusions -- cgit v1.2.1 From ad0efc2d16a84c674307ad2df9d44153b44a9cf8 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 20 Apr 2023 19:51:37 +0200 Subject: Small changes to the multistart vignette - Fix legend positions and y axis scaling - Include two more variants in the model comparison at the end, and fix the logic of the discussion --- vignettes/web_only/multistart.rmd | 27 +++++++++++---------------- 1 file changed, 11 insertions(+), 16 deletions(-) diff --git a/vignettes/web_only/multistart.rmd b/vignettes/web_only/multistart.rmd index 27a8a96a..2a9b3599 100644 --- a/vignettes/web_only/multistart.rmd +++ b/vignettes/web_only/multistart.rmd @@ -1,7 +1,7 @@ --- title: Short demo of the multistart method author: Johannes Ranke -date: Last change 26 September 2022 (rebuilt `r Sys.Date()`) +date: Last change 20 April 2023 (rebuilt `r Sys.Date()`) output: html_document vignette: > @@ -38,9 +38,9 @@ function tells us that the confidence interval for the standard deviation of 'log_k2' includes zero. We check this assessment using multiple runs with different starting values. -```{r} +```{r, warnings = FALSE} f_saem_full_multi <- multistart(f_saem_full, n = 16, cores = 16) -parplot(f_saem_full_multi) +parplot(f_saem_full_multi, lpos = "topleft") ``` This confirms that the variance of k2 is the most problematic parameter, so we @@ -51,7 +51,7 @@ for k2. f_saem_reduced <- update(f_saem_full, no_random_effect = "log_k2") illparms(f_saem_reduced) f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cores = 16) -parplot(f_saem_reduced_multi, lpos = "topright") +parplot(f_saem_reduced_multi, lpos = "topright", ylim = c(0.5, 2)) ``` The results confirm that all remaining parameters can be determined with sufficient @@ -63,20 +63,15 @@ We can also analyse the log-likelihoods obtained in the multiple runs: llhist(f_saem_reduced_multi) ``` -The parameter histograms can be further improved by excluding the result with -the low likelihood. - -```{r} -parplot(f_saem_reduced_multi, lpos = "topright", llmin = -326, ylim = c(0.5, 2)) -``` - -We can use the `anova` method to compare the models, including a likelihood ratio -test if the models are nested. +We can use the `anova` method to compare the models. ```{r} -anova(f_saem_full, best(f_saem_reduced_multi), test = TRUE) +anova(f_saem_full, best(f_saem_full_multi), + f_saem_reduced, best(f_saem_reduced_multi)) ``` -While AIC and BIC are lower for the reduced model, the likelihood ratio test -does not indicate a significant difference between the fits. +The reduced model gives the lowest information criteria and similar +likelihoods as the best variant of the full model. The multistart method +leads to a much lower improvement of the likelihood for the reduced model, +indicating that it converges faster. -- cgit v1.2.1 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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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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