Calculated the log-likelihood of a fitted mkinfit object

‘add_err’: Respect the argument giving the number of replicates in the synthetic dataset
‘max_twa_parent’: Support maximum time weighted average concentration calculations for the hockey stick (HS) model
‘mkinpredict’: Make the function generic and create a method for mkinfit objects
‘mkinfit’: Improve the correctness of the fitted two component error model by fitting the mean absolute deviance at each observation against the observed values, weighting with the current two-component error model
‘tests/testthat/test_irls.R’: Test if the components of the error model used to generate the data can be reproduced with moderate accuracy

@@ -668,7 +670,7 @@

0.9.47.6
0.9.47.6
0.9.47.5
0.9.47.3
0.9.47.2

mkinerrmin()

Calculate the minimum error to assume in order to pass the variance test

logLik(<mkinfit>)

Calculated the log-likelihood of a fitted mkinfit object

Calculated the log-likelihood of a fitted mkinfit object — logLik.mkinfit • mkin

+ + + +

+ +

+ + +

+ +

This function simply calculates the product of the likelihood densities + calc

+ +

# S3 method for mkinfit
+logLik(object, ...)

+ +

Arguments

+ + + + + + + + + + +

object	An object of class `mkinfit`.
…	For compatibility with the generic method

+ +

Value

+ +

An object of class logLik with the number of + estimated parameters (degradation model parameters plus variance + model parameters) as attribute.

+ + +

Examples

  sfo_sfo <- mkinmod(
+    parent = mkinsub("SFO", to = "m1"),
+    m1 = mkinsub("SFO")
+  )
#> Successfully compiled differential equation model from auto-generated C code.
  d_t <- FOCUS_2006_D
+  d_t[23:24, "value"] <- c(NA, NA) # can't cope with zero values at the moment
+  f_nw <- mkinfit(sfo_sfo, d_t, quiet = TRUE)
+  f_obs <- mkinfit(sfo_sfo, d_t, reweight.method = "obs", quiet = TRUE)
+  f_tc <- mkinfit(sfo_sfo, d_t, reweight.method = "tc", quiet = TRUE)
+  AIC(f_nw, f_obs, f_tc)
#>       df      AIC
+#> f_nw   5 204.4619
+#> f_obs  6 205.8727
+#> f_tc   6 143.8773

+ +

+ + +

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: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:16:48 2018 -#> Date of summary: Tue Sep 18 15:16:48 2018 +#> Date of fit: Fri Nov 23 19:57:18 2018 +#> Date of summary: Fri Nov 23 19:57:18 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -169,7 +169,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 574 model solutions performed in 3.602 s +#> Fitted with method Port using 574 model solutions performed in 3.661 s #> #> Weighting: none #> @@ -247,8 +247,8 @@ fixed_parms = "k_phenol_sink", quiet = TRUE) summary(fit.2, data = FALSE)

#> mkin version used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:16:50 2018 -#> Date of summary: Tue Sep 18 15:16:50 2018 +#> Date of fit: Fri Nov 23 19:57:19 2018 +#> Date of summary: Fri Nov 23 19:57:19 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -258,7 +258,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.513 s +#> Fitted with method Port using 246 model solutions performed in 1.549 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 3c8442b6..9bbe3900 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -326,7 +326,7 @@ weight

only if err=NULL: how to weight the residuals, one of "none", "std", "mean", see details of modCost, or "tc" for the - two component error model. The option "manual" is available for + two component error model. The option "manual" is available for the case that err!=NULL, but it is not necessary to specify it.

@@ -406,6 +406,8 @@

Plotting methods plot.mkinfit and mkinparplot.

Comparisons of models fitted to the same data can be made using AIC + by virtue of the method logLik.mkinfit.

Fitting of several models to several datasets in a single call to mmkin.

@@ -434,15 +436,15 @@ fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)

#> mkin version used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:16:52 2018 -#> Date of summary: Tue Sep 18 15:16:52 2018 +#> Date of fit: Fri Nov 23 19:57:22 2018 +#> Date of summary: Fri Nov 23 19:57:22 2018 #> #> 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 0.158 s +#> Fitted with method Port using 64 model solutions performed in 0.155 s #> #> Weighting: none #> @@ -511,7 +513,7 @@ 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 +#> 0.995 0.000 0.995

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 @@ -586,7 +588,7 @@ #> Model cost at call 146 : 371.2134 #> Optimisation by method Port successfully terminated. #> User System verstrichen -#> 0.755 0.000 0.755

coef(fit.deSolve)

#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.789 0.000 0.790

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 @@ -624,8 +626,8 @@ 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: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:17:04 2018 -#> Date of summary: Tue Sep 18 15:17:04 2018 +#> Date of fit: Fri Nov 23 19:57:34 2018 +#> Date of summary: Fri Nov 23 19:57:34 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -633,7 +635,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 186 model solutions performed in 0.823 s +#> Fitted with method Port using 186 model solutions performed in 0.825 s #> #> Weighting: none #> @@ -741,8 +743,8 @@ #> 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: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:17:06 2018 -#> Date of summary: Tue Sep 18 15:17:06 2018 +#> Date of fit: Fri Nov 23 19:57:36 2018 +#> Date of summary: Fri Nov 23 19:57:36 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -750,7 +752,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 551 model solutions performed in 2.374 s +#> Fitted with method Port using 551 model solutions performed in 2.528 s #> #> Weighting: none #> @@ -863,8 +865,8 @@ #> 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: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:17:07 2018 -#> Date of summary: Tue Sep 18 15:17:07 2018 +#> Date of fit: Fri Nov 23 19:57:37 2018 +#> Date of summary: Fri Nov 23 19:57:37 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -872,7 +874,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 155 model solutions performed in 0.636 s +#> Fitted with method Port using 155 model solutions performed in 0.687 s #> #> Weighting: mean #> @@ -981,8 +983,8 @@ quiet = TRUE) summary(f.w.value)

#> mkin version used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:17:08 2018 -#> Date of summary: Tue Sep 18 15:17:08 2018 +#> Date of fit: Fri Nov 23 19:57:38 2018 +#> Date of summary: Fri Nov 23 19:57:38 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -990,7 +992,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 174 model solutions performed in 0.717 s +#> Fitted with method Port using 174 model solutions performed in 0.781 s #> #> Weighting: manual #> @@ -1101,8 +1103,8 @@ f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE) summary(f.w.man)

#> mkin version used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:17:09 2018 -#> Date of summary: Tue Sep 18 15:17:09 2018 +#> Date of fit: Fri Nov 23 19:57:39 2018 +#> Date of summary: Fri Nov 23 19:57:39 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1110,7 +1112,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 270 model solutions performed in 1.181 s +#> Fitted with method Port using 270 model solutions performed in 1.201 s #> #> Weighting: manual #> @@ -1219,8 +1221,8 @@ reweight.method = "obs") summary(f.w.man.irls)

#> mkin version used for fitting: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Tue Sep 18 15:17:13 2018 -#> Date of summary: Tue Sep 18 15:17:13 2018 +#> Date of fit: Fri Nov 23 19:57:43 2018 +#> Date of summary: Fri Nov 23 19:57:43 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1228,7 +1230,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 692 model solutions performed in 3.077 s +#> Fitted with method Port using 692 model solutions performed in 3.087 s #> #> Weighting: manual #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index af364403..3148efd8 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -229,7 +229,7 @@ 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 file20267955fc75.c 2> file20267955fc75.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file140043d42642.c 2> file140043d42642.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 91e9289d..baa67000 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -323,17 +323,17 @@ 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 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 #> 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 #> 201 20 4.978707 27.46227

#> User System verstrichen -#> 0.034 0.000 0.034

+#> 0.039 0.000 0.040

# Predict from a fitted model f <- mkinfit(SFO_SFO, FOCUS_2006_C)

#> Model cost at call 1 : 552.5739 #> Model cost at call 3 : 552.5739 diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index ad011b75..8bc7b18c 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -189,8 +189,8 @@ time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE)) time_default

#> User System verstrichen -#> 0.054 0.027 6.836

time_1

#> User System verstrichen -#> 20.444 0.000 20.459

+#> 0.029 0.039 6.854

time_1

#> User System verstrichen +#> 22.091 0.000 22.106

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/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index f8e09b45..9428f187 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -206,15 +206,15 @@

Examples

  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Tue Sep 18 15:17:59 2018 
-#> Date of summary: Tue Sep 18 15:17:59 2018 
+#> Date of fit:     Fri Nov 23 19:58:33 2018 
+#> Date of summary: Fri Nov 23 19:58:33 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 35 model solutions performed in 0.071 s
+#> Fitted with method Port using 35 model solutions performed in 0.081 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index f2602792..aa82269a 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -200,8 +200,8 @@ 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:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Tue Sep 18 15:18:06 2018 
-#> Date of summary: Tue Sep 18 15:18:06 2018 
+#> Date of fit:     Fri Nov 23 19:58:40 2018 
+#> Date of summary: Fri Nov 23 19:58:40 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -209,7 +209,7 @@ 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 0.662 s
+#> Fitted with method Port using 153 model solutions performed in 0.688 s
 #> 
 #> Weighting: none
 #> 
@@ -276,8 +276,8 @@ 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:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Tue Sep 18 15:18:08 2018 
-#> Date of summary: Tue Sep 18 15:18:08 2018 
+#> Date of fit:     Fri Nov 23 19:58:42 2018 
+#> Date of summary: Fri Nov 23 19:58:42 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -285,7 +285,7 @@ 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 1.342 s
+#> Fitted with method Port using 350 model solutions performed in 1.608 s
 #> 
 #> Weighting: none
 #> 
@@ -364,8 +364,8 @@ 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:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Tue Sep 18 15:18:09 2018 
-#> Date of summary: Tue Sep 18 15:18:09 2018 
+#> Date of fit:     Fri Nov 23 19:58:43 2018 
+#> Date of summary: Fri Nov 23 19:58:43 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -373,7 +373,7 @@ 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 0.737 s
+#> Fitted with method Port using 186 model solutions performed in 0.821 s
 #> 
 #> Weighting: none
 #> 
@@ -448,8 +448,8 @@ 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:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Tue Sep 18 15:18:10 2018 
-#> Date of summary: Tue Sep 18 15:18:10 2018 
+#> Date of fit:     Fri Nov 23 19:58:44 2018 
+#> Date of summary: Fri Nov 23 19:58:44 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -457,7 +457,7 @@ 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 0.414 s
+#> Fitted with method Port using 104 model solutions performed in 0.46 s
 #> 
 #> Weighting: none
 #> 
-- 
cgit v1.2.1

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

2018-09-18

2018-11-23

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

2018-09-18

2018-11-23

Introduction to mkin

Johannes Ranke

2018-09-18

2018-11-23

Calculation of time weighted average concentrations with mkin

Johannes Ranke

2018-09-18

2018-11-23

Example evaluation of FOCUS dataset Z

Johannes Ranke

2018-09-18

2018-11-23

Performance benefit by using compiled model definitions in mkin

Johannes Ranke

2018-09-18

2018-11-23

-mkin 0.9.47.6 (2018-09-18) Unreleased +mkin 0.9.47.6 (2018-09-21) Unreleased

Contents

Calculated the log-likelihood of a fitted mkinfit object

Arguments

Value

Examples

Contents

Author

Examples