From 20d7834a633d32b663c6bcc1a7f7b0300aa65d5b Mon Sep 17 00:00:00 2001
From: Johannes Ranke
Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: A new model based on spatial variability. Environmental Science and Technology 24, 1032-1038
diff --git a/docs/reference/HS.solution-2.png b/docs/reference/HS.solution-2.png index 0bdb37a9..2e516447 100644 Binary files a/docs/reference/HS.solution-2.png and b/docs/reference/HS.solution-2.png differ diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 3d608a2f..8f6bbbe2 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -147,7 +147,7 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.europa.eu/projects/degradation-kinetics + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics+#> 0.032 0.000 0.032# Use shorthand notation for parent only degradation fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) -summary(fit)#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:45:06 2017 -#> Date of summary: Fri May 5 12:45:06 2017 +summary(fit)#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:14:18 2017 +#> Date of summary: Sat Jul 29 15:14:18 2017 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.206 s +#> Fitted with method Port using 64 model solutions performed in 0.141 s #> #> Weighting: none #> @@ -456,7 +456,7 @@ m1 = mkinsub("SFO"))#># 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)))#> user system elapsed -#> 0.912 0.000 0.915coef(fit)#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.888 0.000 0.890coef(fit)#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750endpoints(fit)#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -535,7 +535,7 @@ #> Model cost at call 153 : 371.2134 #> Optimisation by method Port successfully terminated. #> user system elapsed -#> 0.792 0.000 0.793coef(fit.deSolve)#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.728 0.000 0.729coef(fit.deSolve)#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750endpoints(fit.deSolve)#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -576,10 +576,10 @@ # Weighted fits, including IRLS SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), use_of_ff = "max")#>f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE) -summary(f.noweight)#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:45:17 2017 -#> Date of summary: Fri May 5 12:45:17 2017 +summary(f.noweight)#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:14:28 2017 +#> Date of summary: Sat Jul 29 15:14:28 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -697,10 +697,10 @@ #> 100 m1 33.13 3.198e+01 1.148e+00 #> 120 m1 25.15 2.879e+01 -3.640e+00 #> 120 m1 33.31 2.879e+01 4.520e+00f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs", quiet = TRUE) -summary(f.irls)#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:45:19 2017 -#> Date of summary: Fri May 5 12:45:19 2017 +summary(f.irls)#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:14:30 2017 +#> Date of summary: Sat Jul 29 15:14:30 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -708,7 +708,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 468 model solutions performed in 1.925 s +#> Fitted with method Port using 468 model solutions performed in 1.914 s #> #> Weighting: none then iterative reweighting method obs #> @@ -818,10 +818,10 @@ #> 100 m1 33.13 3.199e+01 1.140e+00 2.722 #> 120 m1 25.15 2.881e+01 -3.659e+00 2.722 #> 120 m1 33.31 2.881e+01 4.501e+00 2.722f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", quiet = TRUE) -summary(f.w.mean)#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:45:20 2017 -#> Date of summary: Fri May 5 12:45:20 2017 +summary(f.w.mean)#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:14:31 2017 +#> Date of summary: Sat Jul 29 15:14:31 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -829,7 +829,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 155 model solutions performed in 0.699 s +#> Fitted with method Port using 155 model solutions performed in 0.692 s #> #> Weighting: mean #> @@ -940,10 +940,10 @@ #> 120 m1 25.15 28.824128 -3.674128 #> 120 m1 33.31 28.824128 4.485872f.w.value <- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), err = "value", quiet = TRUE) -summary(f.w.value)#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:45:21 2017 -#> Date of summary: Fri May 5 12:45:21 2017 +summary(f.w.value)#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:14:32 2017 +#> Date of summary: Sat Jul 29 15:14:32 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -951,7 +951,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 174 model solutions performed in 0.767 s +#> Fitted with method Port using 174 model solutions performed in 0.701 s #> #> Weighting: manual #> @@ -1062,10 +1062,10 @@ errors <- c(parent = 2, m1 = 1) dw$err.man <- errors[FOCUS_2006_D$name] f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE) -summary(f.w.man)#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:45:22 2017 -#> Date of summary: Fri May 5 12:45:22 2017 +summary(f.w.man)#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:14:33 2017 +#> Date of summary: Sat Jul 29 15:14:33 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1073,7 +1073,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 297 model solutions performed in 1.276 s +#> Fitted with method Port using 297 model solutions performed in 1.223 s #> #> Weighting: manual #> @@ -1184,10 +1184,10 @@ #> 120 m1 25.15 28.760616 -3.610616 2 #> 120 m1 33.31 28.760616 4.549384 2f.w.man.irls <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE, reweight.method = "obs") -summary(f.w.man.irls)#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:45:25 2017 -#> Date of summary: Fri May 5 12:45:25 2017 +summary(f.w.man.irls)#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:14:36 2017 +#> Date of summary: Sat Jul 29 15:14:36 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1195,7 +1195,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 628 model solutions performed in 2.626 s +#> Fitted with method Port using 628 model solutions performed in 2.578 s #> #> Weighting: manual then iterative reweighting method obs #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index de9815d4..5703b188 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -182,7 +182,7 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.europa.eu/projects/degradation-kinetics + http://esdac.jrc.ec.europa.eu/projects/degradation-kineticsNAFTA Technical Working Group on Pesticides (not dated) Guidance for Evaluating and Calculating Degradation Kinetics in Environmental Media
@@ -205,7 +205,7 @@ SFO_SFO <- mkinmod( parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), verbose = TRUE)#> Compilation argument: -#> /usr/lib/R/bin/R CMD SHLIB file70ea30edf42a.c 2> file70ea30edf42a.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file519167a14b3a.c 2> file519167a14b3a.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinparplot-4.png b/docs/reference/mkinparplot-4.png index 8b32f554..c9f4aadb 100644 Binary files a/docs/reference/mkinparplot-4.png and b/docs/reference/mkinparplot-4.png differ diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 327a7d8d..b3453e6c 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -299,17 +299,17 @@ 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 elapsed -#> 0.004 0.000 0.004system.time( +#> 0.004 0.000 0.003system.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 elapsed -#> 0.004 0.000 0.002system.time( +#> 0.000 0.000 0.001system.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 #> 201 20 4.978707 27.46227#> user system elapsed -#> 0.032 0.000 0.033
#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:46:20 2017 -#> Date of summary: Fri May 5 12:46:20 2017 +#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:15:30 2017 +#> Date of summary: Sat Jul 29 15:15:30 2017 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 35 model solutions performed in 0.082 s +#> Fitted with method Port using 35 model solutions performed in 0.084 s #> #> Weighting: none #> diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index d8ff3a1e..173af92e 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -156,10 +156,10 @@ M1 = list(type = "SFO"), M2 = list(type = "SFO"), use_of_ff = "max")#>summary(fit)#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:46:23 2017 -#> Date of summary: Fri May 5 12:46:23 2017 +plot_sep(fit)summary(fit)#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:15:33 2017 +#> Date of summary: Sat Jul 29 15:15:34 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -168,7 +168,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 381 model solutions performed in 2.203 s +#> Fitted with method Port using 381 model solutions performed in 2.241 s #> #> Weighting: none #> diff --git a/docs/reference/synthetic_data_for_UBA_2014-10.png b/docs/reference/synthetic_data_for_UBA_2014-10.png index b98940ff..7e15e1b3 100644 Binary files a/docs/reference/synthetic_data_for_UBA_2014-10.png and b/docs/reference/synthetic_data_for_UBA_2014-10.png differ diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index c14740c2..bbf15a41 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -170,10 +170,10 @@ parent = list(type = "SFO", to = "m1", sink = TRUE), m1 = list(type = "SFO"))#># Fit the model to the FOCUS example dataset D using defaults fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE) -summary(fit, data=FALSE) # See transformed and backtransformed parameters#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:46:24 2017 -#> Date of summary: Fri May 5 12:46:24 2017 +summary(fit, data=FALSE) # See transformed and backtransformed parameters#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:15:35 2017 +#> Date of summary: Sat Jul 29 15:15:35 2017 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -181,7 +181,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.61 s +#> Fitted with method Port using 153 model solutions performed in 0.608 s #> #> Weighting: none #> @@ -247,10 +247,10 @@ #> m1 131.761 437.70fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE) -summary(fit.2, data=FALSE)#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:46:26 2017 -#> Date of summary: Fri May 5 12:46:26 2017 +summary(fit.2, data=FALSE)#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:15:36 2017 +#> Date of summary: Sat Jul 29 15:15:36 2017 #> #> Equations: #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent @@ -258,7 +258,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 352 model solutions performed in 1.437 s +#> Fitted with method Port using 352 model solutions performed in 1.401 s #> #> Weighting: none #> @@ -337,10 +337,10 @@ m1 = list(type = "SFO"), use_of_ff = "max")#>#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:46:27 2017 -#> Date of summary: Fri May 5 12:46:27 2017 +summary(fit.ff, data = FALSE)#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:15:37 2017 +#> Date of summary: Sat Jul 29 15:15:37 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -348,7 +348,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 185 model solutions performed in 0.776 s +#> Fitted with method Port using 185 model solutions performed in 0.772 s #> #> Weighting: none #> @@ -421,10 +421,10 @@ use_of_ff = "max")#>#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:46:28 2017 -#> Date of summary: Fri May 5 12:46:28 2017 +summary(fit.ff.2, data = FALSE)#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:15:38 2017 +#> Date of summary: Sat Jul 29 15:15:38 2017 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -432,7 +432,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 104 model solutions performed in 0.433 s +#> Fitted with method Port using 104 model solutions performed in 0.416 s #> #> Weighting: none #> -- cgit v1.2.1