Calculation of time weighted average concentrations with mkin

## mkin version used for fitting: 0.9.49.6 ## R version used for fitting: 3.6.1 -## Date of fit: Wed Sep 18 12:57:33 2019 -## Date of summary: Wed Sep 18 12:57:33 2019 +## Date of fit: Wed Sep 18 13:17:00 2019 +## Date of summary: Wed Sep 18 13:17:00 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -179,7 +179,7 @@ ## ## Model predictions using solution type deSolve ## -## Fitted using 389 model solutions performed in 1.01 s +## Fitted using 389 model solutions performed in 1.115 s ## ## Error model: Constant variance ## diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 81659030..0d5667f5 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -116,15 +116,15 @@ summary(m.L1.SFO)

## mkin version used for fitting: 0.9.49.6 ## R version used for fitting: 3.6.1 -## Date of fit: Wed Sep 18 12:57:35 2019 -## Date of summary: Wed Sep 18 12:57:35 2019 +## Date of fit: Wed Sep 18 13:17:02 2019 +## Date of summary: Wed Sep 18 13:17:02 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted using 133 model solutions performed in 0.287 s +## Fitted using 133 model solutions performed in 0.297 s ## ## Error model: Constant variance ## @@ -218,8 +218,8 @@ ## finite result is doubtful

## mkin version used for fitting: 0.9.49.6 ## R version used for fitting: 3.6.1 -## Date of fit: Wed Sep 18 12:57:37 2019 -## Date of summary: Wed Sep 18 12:57:37 2019 +## Date of fit: Wed Sep 18 13:17:05 2019 +## Date of summary: Wed Sep 18 13:17:05 2019 ## ## ## Warning: Optimisation did not converge: @@ -231,7 +231,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 899 model solutions performed in 1.921 s +## Fitted using 899 model solutions performed in 2.099 s ## ## Error model: Constant variance ## @@ -323,15 +323,15 @@ summary(m.L2.FOMC, data = FALSE) ## mkin version used for fitting: 0.9.49.6 ## R version used for fitting: 3.6.1 -## Date of fit: Wed Sep 18 12:57:38 2019 -## Date of summary: Wed Sep 18 12:57:38 2019 +## Date of fit: Wed Sep 18 13:17:06 2019 +## Date of summary: Wed Sep 18 13:17:06 2019 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted using 239 model solutions performed in 0.49 s +## Fitted using 239 model solutions performed in 0.554 s ## ## Error model: Constant variance ## @@ -399,8 +399,8 @@ summary(m.L2.DFOP, data = FALSE) ## mkin version used for fitting: 0.9.49.6 ## R version used for fitting: 3.6.1 -## Date of fit: Wed Sep 18 12:57:40 2019 -## Date of summary: Wed Sep 18 12:57:40 2019 +## Date of fit: Wed Sep 18 13:17:07 2019 +## Date of summary: Wed Sep 18 13:17:07 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -409,7 +409,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 572 model solutions performed in 1.209 s +## Fitted using 572 model solutions performed in 1.273 s ## ## Error model: Constant variance ## @@ -499,8 +499,8 @@ summary(mm.L3[["DFOP", 1]]) ## mkin version used for fitting: 0.9.49.6 ## R version used for fitting: 3.6.1 -## Date of fit: Wed Sep 18 12:57:42 2019 -## Date of summary: Wed Sep 18 12:57:42 2019 +## Date of fit: Wed Sep 18 13:17:09 2019 +## Date of summary: Wed Sep 18 13:17:09 2019 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * @@ -509,7 +509,7 @@ ## ## Model predictions using solution type analytical ## -## Fitted using 373 model solutions performed in 0.783 s +## Fitted using 373 model solutions performed in 0.792 s ## ## Error model: Constant variance ## @@ -605,15 +605,15 @@ summary(mm.L4[["SFO", 1]], data = FALSE) ## mkin version used for fitting: 0.9.49.6 ## R version used for fitting: 3.6.1 -## Date of fit: Wed Sep 18 12:57:42 2019 -## Date of summary: Wed Sep 18 12:57:43 2019 +## Date of fit: Wed Sep 18 13:17:10 2019 +## Date of summary: Wed Sep 18 13:17:11 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted using 142 model solutions performed in 0.288 s +## Fitted using 142 model solutions performed in 0.299 s ## ## Error model: Constant variance ## @@ -670,15 +670,15 @@ summary(mm.L4[["FOMC", 1]], data = FALSE) ## mkin version used for fitting: 0.9.49.6 ## R version used for fitting: 3.6.1 -## Date of fit: Wed Sep 18 12:57:43 2019 -## Date of summary: Wed Sep 18 12:57:43 2019 +## Date of fit: Wed Sep 18 13:17:10 2019 +## Date of summary: Wed Sep 18 13:17:11 2019 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## -## Fitted using 224 model solutions performed in 0.463 s +## Fitted using 224 model solutions performed in 0.488 s ## ## Error model: Constant variance ## diff --git a/docs/articles/twa.html b/docs/articles/twa.html index b15f1522..799349d9 100644 --- a/docs/articles/twa.html +++ b/docs/articles/twa.html @@ -130,7 +130,7 @@ \[f_\textrm{twa} = \frac{1}{t} \left( \frac{1}{k_1} \left( 1 - e^{- k_1 t_b} \right) + \frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)} \right) \right) \] -Note that a method for calculating maximum moving window time weighted average concentrations for a model fitted by ‘mkinfit’ is include in the ‘mkin’ package (‘max_twa_parent’. If the same is needed for metabolites, the function ‘max_twa’ can be used. +Note that a method for calculating maximum moving window time weighted average concentrations for a model fitted by ‘mkinfit’ or from parent decline model parameters is included in the ‘max_twa_parent’ function. If the same is needed for metabolites, the function ‘max_twa’ from the ‘pfm’ package can be used. FOCUS Work Group on Degradation Kinetics. 2014. Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration. 1.1 ed. http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics. diff --git a/docs/articles/web_only/benchmarks.html b/docs/articles/web_only/benchmarks.html index f1ed1f96..0c78d346 100644 --- a/docs/articles/web_only/benchmarks.html +++ b/docs/articles/web_only/benchmarks.html @@ -204,77 +204,77 @@ ## 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 0.9.49.6 5.920 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 6.106 ## 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 0.9.49.1 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 0.9.49.6 36.932 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 37.249 ## 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 0.9.49.1 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 0.9.49.6 4.519 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.739 ## 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 0.9.49.1 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 0.9.49.6 31.518 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 31.761 ## 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 0.9.49.6 10.619 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 10.794 ## 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 0.9.49.1 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 0.9.49.6 2.61 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 2.702 ## 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 0.9.49.1 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 0.9.49.6 4.312 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 4.351 ## 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 0.9.49.1 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 0.9.49.6 8.07 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 8.303 ## 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 0.9.49.1 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 0.9.49.6 16.102 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 16.339 ## 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 0.9.49.1 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 0.9.49.6 8.013 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 8.12 ## 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 0.9.49.1 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 0.9.49.6 10.805 +## Linux, AMD Ryzen 7 1700 Eight-Core Processor, mkin version 0.9.49.6 11.22 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 89977591..99b05623 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -165,9 +165,9 @@ ## 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 3.124 1.000 3.122 0 -## 1 deSolve, not compiled 3 28.822 9.226 28.807 0 -## 2 Eigenvalue based 3 4.416 1.414 4.413 0 +## 3 deSolve, compiled 3 3.153 1.000 3.152 0 +## 1 deSolve, not compiled 3 28.771 9.125 28.756 0 +## 2 Eigenvalue based 3 4.444 1.409 4.443 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 @@ -216,8 +216,8 @@ ## 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 4.878 1.000 4.875 0 -## 1 deSolve, not compiled 3 53.602 10.989 53.568 0 +## 2 deSolve, compiled 3 4.978 1.000 4.975 0.000 +## 1 deSolve, not compiled 3 54.194 10.887 54.160 0.004 ## user.child sys.child ## 2 0 0 ## 1 0 0 diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index b620f364..c1cfc228 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -408,15 +408,15 @@ Per default, parameters in the kinetic models are internally transformed in fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)#> mkin version used for fitting: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Wed Sep 18 12:55:32 2019 -#> Date of summary: Wed Sep 18 12:55:32 2019 +#> Date of fit: Wed Sep 18 13:14:54 2019 +#> Date of summary: Wed Sep 18 13:14:54 2019 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 222 model solutions performed in 0.459 s +#> Fitted using 222 model solutions performed in 0.475 s #> #> Error model: Constant variance #> @@ -490,7 +490,7 @@ Per default, parameters in the kinetic models are internally transformed in m1 = mkinsub("SFO")) #> Successfully compiled differential equation model from auto-generated C code. # Fit the model to the FOCUS example dataset D using defaults print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = TRUE))) #> Warning: Observations with value of zero were removed from the data #> User System verstrichen -#> 1.480 0.000 1.482 coef(fit) #> NULL endpoints(fit) #> $ff +#> 1.561 0.000 1.568 coef(fit) #> NULL endpoints(fit) #> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -563,7 +563,7 @@ Per default, parameters in the kinetic models are internally transformed in #> Sum of squared residuals at call 126: 371.2134 #> Sum of squared residuals at call 135: 371.2134 #> Negative log-likelihood at call 145: 97.22429 #> Optimisation successfully terminated. #> User System verstrichen -#> 1.045 0.000 1.046 coef(fit.deSolve) #> NULL endpoints(fit.deSolve) #> $ff +#> 1.06 0.00 1.06 coef(fit.deSolve) #> NULL endpoints(fit.deSolve) #> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -599,8 +599,8 @@ Per default, parameters in the kinetic models are internally transformed in SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), use_of_ff = "max") #> Successfully compiled differential equation model from auto-generated C code. f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE) #> Warning: Observations with value of zero were removed from the data summary(f.noweight) #> mkin version used for fitting: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Wed Sep 18 12:55:47 2019 -#> Date of summary: Wed Sep 18 12:55:47 2019 +#> Date of fit: Wed Sep 18 13:15:10 2019 +#> Date of summary: Wed Sep 18 13:15:10 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -608,7 +608,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 421 model solutions performed in 1.077 s +#> Fitted using 421 model solutions performed in 1.095 s #> #> Error model: Constant variance #> @@ -718,8 +718,8 @@ Per default, parameters in the kinetic models are internally transformed in #> 120 m1 25.15 28.78984 -3.640e+00 #> 120 m1 33.31 28.78984 4.520e+00 f.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE) #> Warning: Observations with value of zero were removed from the data summary(f.obs) #> mkin version used for fitting: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Wed Sep 18 12:55:50 2019 -#> Date of summary: Wed Sep 18 12:55:50 2019 +#> Date of fit: Wed Sep 18 13:15:12 2019 +#> Date of summary: Wed Sep 18 13:15:12 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -727,7 +727,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 979 model solutions performed in 2.624 s +#> Fitted using 979 model solutions performed in 2.639 s #> #> Error model: Variance unique to each observed variable #> @@ -850,8 +850,8 @@ Per default, parameters in the kinetic models are internally transformed in #> 120 m1 25.15 28.80429 -3.654e+00 #> 120 m1 33.31 28.80429 4.506e+00 f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE) #> Warning: Observations with value of zero were removed from the data summary(f.tc) #> mkin version used for fitting: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Wed Sep 18 12:55:59 2019 -#> Date of summary: Wed Sep 18 12:55:59 2019 +#> Date of fit: Wed Sep 18 13:15:22 2019 +#> Date of summary: Wed Sep 18 13:15:22 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -859,7 +859,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 2289 model solutions performed in 9.376 s +#> Fitted using 2289 model solutions performed in 9.723 s #> #> Error model: Two-component variance function #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 81fed454..ca243e3c 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -239,7 +239,7 @@ For the definition of model types and their parameters, the equations given SFO_SFO <- mkinmod( parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), verbose = TRUE) #> Compilation argument: -#> /usr/lib/R/bin/R CMD SHLIB file419a1fa6c394.c 2> file419a1fa6c394.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file4e7a49f4ff50.c 2> file4e7a49f4ff50.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index d162135a..f5401c1d 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -332,12 +332,12 @@ c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "eigen")[201,])) #> time parent m1 #> 201 20 4.978707 27.46227 #> User System verstrichen -#> 0.004 0.000 0.003 system.time( +#> 0.004 0.000 0.004 system.time( print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "deSolve")[201,])) #> time parent m1 #> 201 20 4.978707 27.46227 #> User System verstrichen -#> 0.002 0.000 0.001 system.time( +#> 0.002 0.000 0.002 system.time( print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "deSolve", use_compiled = FALSE)[201,])) #> time parent m1 diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 9bb7926b..ea695d9a 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -199,8 +199,8 @@ time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE)) time_default #> User System verstrichen -#> 0.012 0.024 5.064 time_1 #> User System verstrichen -#> 19.094 0.000 19.104 +#> 0.007 0.031 4.920 time_1 #> User System verstrichen +#> 19.290 0.000 19.301 endpoints(fits.0[["SFO_lin", 2]]) #> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340481 0.2659519 0.7505684 0.2494316 diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index fafca9ce..a10859fc 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -215,15 +215,15 @@ Examples summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE)) #> mkin version used for fitting: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Wed Sep 18 12:57:18 2019 -#> Date of summary: Wed Sep 18 12:57:18 2019 +#> Date of fit: Wed Sep 18 13:16:44 2019 +#> Date of summary: Wed Sep 18 13:16:44 2019 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 131 model solutions performed in 0.267 s +#> Fitted using 131 model solutions performed in 0.273 s #> #> Error model: Constant variance #> diff --git a/vignettes/mkin_benchmarks.rda b/vignettes/mkin_benchmarks.rda index b5132fa8..c2a5076b 100644 Binary files a/vignettes/mkin_benchmarks.rda and b/vignettes/mkin_benchmarks.rda differ diff --git a/vignettes/twa.Rmd b/vignettes/twa.Rmd index 724775bc..6ebb7b89 100644 --- a/vignettes/twa.Rmd +++ b/vignettes/twa.Rmd @@ -73,7 +73,9 @@ $$f_\textrm{twa} = \frac{1}{t} \left( \frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)} \right) \right) $$ Note that a method for calculating maximum moving window time weighted average -concentrations for a model fitted by 'mkinfit' is include in the -'mkin' package (['max_twa_parent'](https://pkgdown.jrwb.de/mkin/reference/max_twa_parent.html). +concentrations for a model fitted by 'mkinfit' or from parent decline model +parameters is included in the +['max_twa_parent'](https://pkgdown.jrwb.de/mkin/reference/max_twa_parent.html) +function. If the same is needed for metabolites, the function -['max_twa'](https://pkgdown.jrwb.de/pfm/reference/max_twa.html) can be used. +['max_twa'](https://pkgdown.jrwb.de/pfm/reference/max_twa.html) from the 'pfm' package can be used. diff --git a/vignettes/twa.html b/vignettes/twa.html index d8322bfc..0db7eeff 100644 --- a/vignettes/twa.html +++ b/vignettes/twa.html @@ -8,6 +8,7 @@ + @@ -15,349 +16,195 @@ Calculation of time weighted average concentrations with mkin - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -366,20 +213,12 @@ $(document).ready(function () { - - - - - - - Calculation of time weighted average concentrations with mkin Johannes Ranke 2019-09-18 - Since version 0.9.45.1 of the ‘mkin’ package, a function for calculating time weighted average concentrations for decline kinetics (i.e. only for the compound applied in the experiment) is included. Strictly speaking, they are maximum moving window time weighted average concentrations, i.e. the maximum time weighted average concentration that can be found when moving a time window of a specified width over the decline curve. @@ -413,7 +252,7 @@ $(document).ready(function () { \[f_\textrm{twa} = \frac{1}{t} \left( \frac{1}{k_1} \left( 1 - e^{- k_1 t_b} \right) + \frac{e^{- k_1 t_b}}{k_2} \left( 1 - e^{- k_2 (t - t_b)} \right) \right) \] -Note that a method for calculating maximum moving window time weighted average concentrations for any model fitted by ‘mkinfit’, and also for metabolites in such models, is integrated in the ‘mkin’ package, see the documentation at my website. +Note that a method for calculating maximum moving window time weighted average concentrations for a model fitted by ‘mkinfit’ or from parent decline model parameters is included in the ‘max_twa_parent’ function. If the same is needed for metabolites, the function ‘max_twa’ from the ‘pfm’ package can be used. FOCUS Work Group on Degradation Kinetics. 2014. Generic Guidance for Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in Eu Registration. 1.1 ed. http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics. @@ -422,22 +261,6 @@ $(document).ready(function () { - - - - -