Example datasets from the NAFTA SOP published 2015

## mkin version used for fitting: 0.9.48.1 ## R version used for fitting: 3.5.2 -## Date of fit: Mon Feb 25 15:25:09 2019 -## Date of summary: Mon Feb 25 15:25:09 2019 +## Date of fit: Tue Feb 26 09:29:10 2019 +## Date of summary: Tue Feb 26 09:29:10 2019 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent @@ -621,15 +621,15 @@

summary(mm.L4[["FOMC", 1]], data = FALSE)

## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Mon Feb 25 15:25:09 2019 
-## Date of summary: Mon Feb 25 15:25:09 2019 
+## Date of fit:     Tue Feb 26 09:29:10 2019 
+## Date of summary: Tue Feb 26 09:29:10 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.164 s
+## Fitted with method Port using 66 model solutions performed in 0.163 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 24520f74..f6e8af4d 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -85,7 +85,7 @@
       Introduction to mkin
                         Johannes Ranke
             
-            2019-02-25
+            2019-02-26
       
       
       mkin.Rmd
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index bf56eff2..c06672f1 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -85,7 +85,7 @@
       Calculation of time weighted average concentrations with mkin
                         Johannes Ranke
             
-            2019-02-25
+            2019-02-26
       
       
       twa.Rmd
diff --git a/docs/articles/web_only/FOCUS_Z.html b/docs/articles/web_only/FOCUS_Z.html
index 48f08bfc..b398733b 100644
--- a/docs/articles/web_only/FOCUS_Z.html
+++ b/docs/articles/web_only/FOCUS_Z.html
@@ -85,7 +85,7 @@
       Example evaluation of FOCUS dataset Z
                         Johannes Ranke
             
-            2019-02-25
+            2019-02-26
       
       
       FOCUS_Z.Rmd
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 16f0cc7a..6d4d1e42 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -85,7 +85,7 @@
       Performance benefit by using compiled model definitions in mkin
                         Johannes Ranke
             
-            2019-02-25
+            2019-02-26
       
       
       compiled_models.Rmd
@@ -126,9 +126,9 @@
 }

## Lade nötiges Paket: rbenchmark

##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   2.328    1.000     2.327        0
-## 1 deSolve, not compiled            3  17.641    7.578    17.633        0
-## 2      Eigenvalue based            3   2.873    1.234     2.871        0
+## 3     deSolve, compiled            3   2.323    1.000     2.321        0
+## 1 deSolve, not compiled            3  17.568    7.563    17.559        0
+## 2      Eigenvalue based            3   2.884    1.241     2.883        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -157,8 +157,8 @@
 }

## Successfully compiled differential equation model from auto-generated C code.

##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.126    1.000     4.125        0
-## 1 deSolve, not compiled            3  37.487    9.086    37.467        0
+## 2     deSolve, compiled            3   4.078    1.000     4.075        0
+## 1 deSolve, not compiled            3  37.246    9.133    37.231        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index f86ff43a..873d75bd 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -280,7 +280,7 @@ #> #> $time #> User System verstrichen -#> 0.196 0.000 0.198 +#> 0.195 0.000 0.195 #> #> $mkinmod #> <mkinmod> model generated with @@ -469,8 +469,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x5555592a5fc0> -#> <environment: 0x55555ba81950> +#> <bytecode: 0x55555925ca08> +#> <environment: 0x55555b668200> #> #> $cost_notrans #> function (P) @@ -492,8 +492,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555a5e0ee8> -#> <environment: 0x55555ba81950> +#> <bytecode: 0x55555a590818> +#> <environment: 0x55555b668200> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -560,7 +560,7 @@ #> 99.17407 #> #> $date -#> [1] "Mon Feb 25 15:23:07 2019" +#> [1] "Tue Feb 26 09:27:10 2019" #> #> $version #> [1] "0.9.48.1" diff --git a/docs/reference/NAFTA_SOP_2015-1.png b/docs/reference/NAFTA_SOP_2015-1.png new file mode 100644 index 00000000..c4f9f048 Binary files /dev/null and b/docs/reference/NAFTA_SOP_2015-1.png differ diff --git a/docs/reference/NAFTA_SOP_2015.html b/docs/reference/NAFTA_SOP_2015.html new file mode 100644 index 00000000..4a2c71a9 --- /dev/null +++ b/docs/reference/NAFTA_SOP_2015.html @@ -0,0 +1,220 @@ + + + + + + + + +Example datasets from the NAFTA SOP published 2015 — NAFTA_SOP_2015 • mkin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + +

+ +

+ + +

+ +

Data taken from US EPA (2015), p. 19 and 23.

+ +

NAFTA_SOP_2015

+ +

Format

+ +

2 datasets with observations on the following variables.

name: a factor containing the name of the observed variable
time: a numeric vector containing time points
value: a numeric vector containing concentrations

+ +

Source

+ +

NAFTA (2011) Guidance for evaluating and calculating degradation kinetics + in environmental media. NAFTA Technical Working Group on Pesticides + https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation + accessed 2019-02-22

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

+ + +

Examples

  nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D)
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The representative half-life of the IORE model is longer than the one corresponding
#> to the terminal degradation rate found with the DFOP model.
#> The representative half-life obtained from the DFOP model may be used
  print(nafta_evaluation)
#> Sums of squares:
+#>       SFO      IORE      DFOP 
+#> 1378.6832  615.7730  517.8836 
+#> 
+#> Critical sum of squares for checking the SFO model:
+#> [1] 717.4598
+#> 
+#> Parameters:
+#> $SFO
+#>                   Estimate       Pr(>t)        Lower        Upper
+#> parent_0      83.755751519 8.076390e-15 76.928220975 90.583282063
+#> k_parent_sink  0.001703321 7.452357e-05  0.001108568  0.002617164
+#> 
+#> $IORE
+#>                         Estimate Pr(>t)        Lower        Upper
+#> parent_0            9.685291e+01     NA 8.752855e+01 1.061773e+02
+#> k__iore_parent_sink 8.403374e-14     NA 1.092054e-19 6.466412e-08
+#> N_parent            6.684458e+00     NA 3.538511e+00 9.830405e+00
+#> 
+#> $DFOP
+#>              Estimate       Pr(>t)        Lower        Upper
+#> parent_0 9.755655e+01 4.439930e-13 8.884447e+01 1.062686e+02
+#> k1       4.240633e-02 3.554769e-02 1.414189e-02 1.271610e-01
+#> k2       8.237928e-04 2.060933e-02 3.172784e-04 2.138925e-03
+#> g        2.881037e-01 1.313715e-04 1.783967e-01 4.299694e-01
+#> 
+#> 
+#> DTx values:
+#>      DT50    DT90 DT50_rep
+#> SFO   407    1352      407
+#> IORE  541 5192066  1562968
+#> DFOP  429    2383      841
+#> 
+#> Representative half-life:
+#> [1] 841.4096
  plot(nafta_evaluation)

+ +

+ + +

+ + + + + + diff --git a/docs/reference/index.html b/docs/reference/index.html index 24403ad6..a251dc33 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -273,6 +273,12 @@

Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)

+ +

NAFTA_SOP_2015

+ +

Example datasets from the NAFTA SOP published 2015

+ +

mccall81_245T

@@ -308,6 +314,32 @@

Print mkinds objects

+ + + +

NAFTA guidance

+ + + + + +

nafta()

+ +

Evaluate parent kinetics using the NAFTA guidance

+ + + +

print(<nafta>)

+ +

Print nafta objects

+ + + +

plot(<nafta>)

+ +

Plot the results of the three models used in the NAFTA scheme

+ @@ -471,6 +503,7 @@

Show results

Work with mmkin objects

Datasets and known results

NAFTA guidance

Helper functions

Analytical solutions

Generate synthetic datasets

diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index d4501489..1845a31c 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -160,8 +160,8 @@ anisole = list(type = "SFO"))

#> Successfully compiled differential equation model from auto-generated C code.

fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE) summary(fit.1, data = FALSE)

#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Mon Feb 25 15:23:29 2019 -#> Date of summary: Mon Feb 25 15:23:29 2019 +#> Date of fit: Tue Feb 26 09:27:31 2019 +#> Date of summary: Tue Feb 26 09:27:31 2019 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -171,7 +171,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 574 model solutions performed in 3.852 s +#> Fitted with method Port using 574 model solutions performed in 3.812 s #> #> Weighting: none #> @@ -249,8 +249,8 @@ fixed_parms = "k_phenol_sink", quiet = TRUE) summary(fit.2, data = FALSE)

#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Mon Feb 25 15:23:31 2019 -#> Date of summary: Mon Feb 25 15:23:31 2019 +#> Date of fit: Tue Feb 26 09:27:33 2019 +#> Date of summary: Tue Feb 26 09:27:33 2019 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -260,7 +260,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.604 s +#> Fitted with method Port using 246 model solutions performed in 1.597 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index ffc87dfb..53f46988 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -438,8 +438,8 @@ fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)

#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Mon Feb 25 15:23:34 2019 -#> Date of summary: Mon Feb 25 15:23:34 2019 +#> Date of fit: Tue Feb 26 09:27:36 2019 +#> Date of summary: Tue Feb 26 09:27:36 2019 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -515,7 +515,7 @@ 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)))

#> User System verstrichen -#> 1.011 0.000 1.012

coef(fit)

#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 1.008 0.000 1.008

coef(fit)

#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750

endpoints(fit)

#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -590,7 +590,7 @@ #> Model cost at call 146 : 371.2134 #> Optimisation by method Port successfully terminated. #> User System verstrichen -#> 0.826 0.000 0.827

coef(fit.deSolve)

#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.812 0.000 0.813

coef(fit.deSolve)

#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750

endpoints(fit.deSolve)

#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -628,8 +628,8 @@ 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) summary(f.noweight)

#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Mon Feb 25 15:23:46 2019 -#> Date of summary: Mon Feb 25 15:23:46 2019 +#> Date of fit: Tue Feb 26 09:27:48 2019 +#> Date of summary: Tue Feb 26 09:27:48 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -637,7 +637,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 186 model solutions performed in 0.849 s +#> Fitted with method Port using 186 model solutions performed in 0.845 s #> #> Weighting: none #> @@ -745,8 +745,8 @@ #> 120 m1 33.31 28.78984 4.520e+00

f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs", quiet = TRUE) summary(f.irls)

#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Mon Feb 25 15:23:48 2019 -#> Date of summary: Mon Feb 25 15:23:48 2019 +#> Date of fit: Tue Feb 26 09:27:50 2019 +#> Date of summary: Tue Feb 26 09:27:50 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -754,7 +754,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 551 model solutions performed in 2.529 s +#> Fitted with method Port using 551 model solutions performed in 2.523 s #> #> Weighting: none #> @@ -867,8 +867,8 @@ #> 120 m1 33.31 28.80898 4.501e+00 2.722

f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", quiet = TRUE) summary(f.w.mean)

#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Mon Feb 25 15:23:49 2019 -#> Date of summary: Mon Feb 25 15:23:49 2019 +#> Date of fit: Tue Feb 26 09:27:51 2019 +#> Date of summary: Tue Feb 26 09:27:51 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -876,7 +876,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 155 model solutions performed in 0.707 s +#> Fitted with method Port using 155 model solutions performed in 0.705 s #> #> Weighting: mean #> @@ -985,8 +985,8 @@ quiet = TRUE) summary(f.w.value)

#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Mon Feb 25 15:23:50 2019 -#> Date of summary: Mon Feb 25 15:23:50 2019 +#> Date of fit: Tue Feb 26 09:27:52 2019 +#> Date of summary: Tue Feb 26 09:27:52 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -994,7 +994,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 174 model solutions performed in 0.803 s +#> Fitted with method Port using 174 model solutions performed in 0.8 s #> #> Weighting: manual #> @@ -1105,8 +1105,8 @@ f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE) summary(f.w.man)

#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Mon Feb 25 15:23:52 2019 -#> Date of summary: Mon Feb 25 15:23:52 2019 +#> Date of fit: Tue Feb 26 09:27:54 2019 +#> Date of summary: Tue Feb 26 09:27:54 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1114,7 +1114,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 270 model solutions performed in 1.242 s +#> Fitted with method Port using 270 model solutions performed in 1.238 s #> #> Weighting: manual #> @@ -1223,8 +1223,8 @@ reweight.method = "obs") summary(f.w.man.irls)

#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Mon Feb 25 15:23:55 2019 -#> Date of summary: Mon Feb 25 15:23:55 2019 +#> Date of fit: Tue Feb 26 09:27:57 2019 +#> Date of summary: Tue Feb 26 09:27:57 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1232,7 +1232,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 692 model solutions performed in 3.263 s +#> Fitted with method Port using 692 model solutions performed in 3.246 s #> #> Weighting: manual #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 48693b0c..bcf39e7f 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -231,7 +231,7 @@ 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 file6703f4535ea.c 2> file6703f4535ea.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file4a116f6acbf1.c 2> file4a116f6acbf1.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 5d786bac..a38de769 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -325,7 +325,7 @@ 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 -#> 0.003 0.000 0.004

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 diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 29684bad..6613f35c 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -191,8 +191,8 @@ time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE)) time_default

#> User System verstrichen -#> 0.040 0.038 7.255

time_1

#> User System verstrichen -#> 22.747 0.000 22.761

+#> 0.052 0.024 7.037

time_1

#> User System verstrichen +#> 22.463 0.000 22.476

endpoints(fits.0[["SFO_lin", 2]])

#> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340480 0.2659520 0.7505686 0.2494314 diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index 071ea132..b1d45272 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -175,9 +175,11 @@

Examples

  nafta_evaluation <- nafta(MRID_555555)
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The representative half-life of the IORE model is longer than the one corresponding
#> to the terminal degradation rate found with the DFOP model.
#> The representative half-life obtained from the DFOP model may be used
  print(nafta_evaluation)
#> Sums of squares:
+      nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D)
#> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c
#> The representative half-life of the IORE model is longer than the one corresponding
#> to the terminal degradation rate found with the DFOP model.
#> The representative half-life obtained from the DFOP model may be used
  print(nafta_evaluation)
#> Sums of squares:
 #>       SFO      IORE      DFOP 
 #> 1378.6832  615.7730  517.8836 
+#> 
+#> Critical sum of squares for checking the SFO model:
 #> [1] 717.4598
 #> 
 #> Parameters:
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 9afaf13a..ca0b1c4c 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -208,15 +208,15 @@
     Examples
       summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Mon Feb 25 15:24:48 2019 
-#> Date of summary: Mon Feb 25 15:24:48 2019 
+#> Date of fit:     Tue Feb 26 09:28:49 2019 
+#> Date of summary: Tue Feb 26 09:28:49 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 35 model solutions performed in 0.086 s
+#> Fitted with method Port using 35 model solutions performed in 0.085 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 6861f712..bcfbe975 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -202,8 +202,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
 summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Mon Feb 25 15:24:56 2019 
-#> Date of summary: Mon Feb 25 15:24:56 2019 
+#> Date of fit:     Tue Feb 26 09:28:57 2019 
+#> Date of summary: Tue Feb 26 09:28:57 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -211,7 +211,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 153 model solutions performed in 0.737 s
+#> Fitted with method Port using 153 model solutions performed in 0.7 s
 #> 
 #> Weighting: none
 #> 
@@ -278,8 +278,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 
fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
 summary(fit.2, data=FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Mon Feb 25 15:24:58 2019 
-#> Date of summary: Mon Feb 25 15:24:58 2019 
+#> Date of fit:     Tue Feb 26 09:28:59 2019 
+#> Date of summary: Tue Feb 26 09:28:59 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -287,7 +287,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 350 model solutions performed in 1.593 s
+#> Fitted with method Port using 350 model solutions performed in 1.59 s
 #> 
 #> Weighting: none
 #> 
@@ -366,8 +366,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
 summary(fit.ff, data = FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Mon Feb 25 15:24:59 2019 
-#> Date of summary: Mon Feb 25 15:24:59 2019 
+#> Date of fit:     Tue Feb 26 09:29:00 2019 
+#> Date of summary: Tue Feb 26 09:29:00 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -375,7 +375,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 186 model solutions performed in 0.858 s
+#> Fitted with method Port using 186 model solutions performed in 0.844 s
 #> 
 #> Weighting: none
 #> 
@@ -450,8 +450,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE)
 summary(fit.ff.2, data = FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Mon Feb 25 15:25:00 2019 
-#> Date of summary: Mon Feb 25 15:25:00 2019 
+#> Date of fit:     Tue Feb 26 09:29:01 2019 
+#> Date of summary: Tue Feb 26 09:29:01 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -459,7 +459,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 104 model solutions performed in 0.473 s
+#> Fitted with method Port using 104 model solutions performed in 0.467 s
 #> 
 #> Weighting: none
 #> 
-- 
cgit v1.2.1

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

2019-02-25

2019-02-26

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

2019-02-25

2019-02-26

Introduction to mkin

Johannes Ranke

2019-02-25

2019-02-26

Calculation of time weighted average concentrations with mkin

Johannes Ranke

2019-02-25

2019-02-26

Example evaluation of FOCUS dataset Z

Johannes Ranke

2019-02-25

2019-02-26

Performance benefit by using compiled model definitions in mkin

Johannes Ranke

2019-02-25

2019-02-26

Example datasets from the NAFTA SOP published 2015

Format

Source

Examples

Contents

NAFTA guidance

Examples

Examples