Calculated the AIC for a column of an mmkin object

## mkin version used for fitting: 0.9.47.6 ## R version used for fitting: 3.5.1 -## Date of fit: Mon Nov 26 09:47:28 2018 -## Date of summary: Mon Nov 26 09:47:29 2018 +## Date of fit: Mon Nov 26 11:41:55 2018 +## Date of summary: Mon Nov 26 11:41:56 2018 ## ## Equations: ## d_parent/dt = - k_parent_sink * parent ## ## Model predictions using solution type analytical ## -## Fitted with method Port using 46 model solutions performed in 0.107 s +## Fitted with method Port using 46 model solutions performed in 0.108 s ## ## Weighting: none ## @@ -620,15 +620,15 @@

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

## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Mon Nov 26 09:47:28 2018 
-## Date of summary: Mon Nov 26 09:47:29 2018 
+## Date of fit:     Mon Nov 26 11:41:56 2018 
+## Date of summary: Mon Nov 26 11:41:56 2018 
 ## 
 ## 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 0.168 s
+## Fitted with method Port using 66 model solutions performed in 0.16 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 083cdb79..8da95e4d 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -125,9 +125,9 @@
 }

## Lade nötiges Paket: rbenchmark

##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   2.264    1.000     2.263        0
-## 1 deSolve, not compiled            3  17.642    7.792    17.634        0
-## 2      Eigenvalue based            3   2.801    1.237     2.799        0
+## 3     deSolve, compiled            3   2.302    1.000     2.301        0
+## 1 deSolve, not compiled            3  17.754    7.712    17.743        0
+## 2      Eigenvalue based            3   2.840    1.234     2.838        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -156,8 +156,8 @@
 }

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

##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.012    1.000     4.010        0
-## 1 deSolve, not compiled            3  37.606    9.373    37.589        0
+## 2     deSolve, compiled            3   4.116    1.000     4.114        0
+## 1 deSolve, not compiled            3  37.902    9.208    37.884        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

diff --git a/docs/news/index.html b/docs/news/index.html index 9f658dad..1b2455a8 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -122,7 +122,8 @@ mkin 0.9.47.6 (2018-11-26) Unreleased

Add the function ‘logLik.mkinfit.R’ which makes it possible to calculate an AIC for mkinfit objects
Add the function ‘logLik.mkinfit’ which makes it possible to calculate an AIC for mkinfit objects
Add the function ‘AIC.mmkin’ to makeqit easy to compare columns of mmkin objects
‘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

Calculated the AIC for a column of an mmkin object — AIC.mmkin • mkin

+ + + +

+ +

+ + +

+ +

Provides a convenient way to compare different kineti models fitted to the + same dataset.

+ +

# S3 method for mmkin
+AIC(object, ..., k = 2)

+ +

Arguments

+ + + + + + + + + + + + + + +

object	An object of class `mmkin`, containing only one column.
…	For compatibility with the generic method
k	As in the generic method

+ +

Value

+ +

As in the generic method (a numeric value for single fits, or a dataframe if + there are several fits in the column).

+ + +

Examples

  f <- mmkin(c("SFO", "FOMC", "DFOP"),
+    list("FOCUS A" = FOCUS_2006_A,
+         "FOCUS C" = FOCUS_2006_C))
+  AIC(f[1, "FOCUS A"]) # We get a single number for a single fit
#> [1] 55.32452

+  # For FOCUS A, the models fit almost equally well, so the higher the number
+  # of parameters, the higher (worse) the AIC
+  AIC(f[, "FOCUS A"])
#>      df      AIC
+#> SFO   3 55.32452
+#> FOMC  4 57.32477
+#> DFOP  5 59.32452
  AIC(f[, "FOCUS A"], k = 0) # If we do not penalize additional parameters, we get nearly the same
#>      df      AIC
+#> SFO   3 49.32452
+#> FOMC  4 49.32477
+#> DFOP  5 49.32452

+  # For FOCUS C, the more complex models fit better
+  AIC(f[, "FOCUS C"])
#>      df      AIC
+#> SFO   3 59.84675
+#> FOMC  4 44.70584
+#> DFOP  5 29.08369

+ +

+ + +

Compare the AIC of columns of mmkin objects using + AIC.mmkin.

Examples

  sfo_sfo <- mkinmod(
@@ -207,6 +212,8 @@ In the case of iterative reweighting, the variances obtained by this
       Arguments
       
       Value
+
+      See also
       
       Examples

diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 981c633a..96082932 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -158,8 +158,8 @@ 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: 0.9.47.6 #> R version used for fitting: 3.5.1 -#> Date of fit: Mon Nov 26 09:45:54 2018 -#> Date of summary: Mon Nov 26 09:45:54 2018 +#> Date of fit: Mon Nov 26 11:40:20 2018 +#> Date of summary: Mon Nov 26 11:40:20 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 3.641 s +#> Fitted with method Port using 574 model solutions performed in 3.702 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: Mon Nov 26 09:45:56 2018 -#> Date of summary: Mon Nov 26 09:45:56 2018 +#> Date of fit: Mon Nov 26 11:40:22 2018 +#> Date of summary: Mon Nov 26 11:40:22 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 1.627 s +#> Fitted with method Port using 246 model solutions performed in 1.646 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 883dda22..77c69f4e 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -436,15 +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: Mon Nov 26 09:45:59 2018 -#> Date of summary: Mon Nov 26 09:45:59 2018 +#> Date of fit: Mon Nov 26 11:40:24 2018 +#> Date of summary: Mon Nov 26 11:40:24 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 0.155 s +#> Fitted with method Port using 64 model solutions performed in 0.156 s #> #> Weighting: none #> @@ -513,7 +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 -#> 0.974 0.000 0.975

coef(fit)

#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.989 0.000 0.990

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 @@ -588,7 +588,7 @@ #> Model cost at call 146 : 371.2134 #> Optimisation by method Port successfully terminated. #> User System verstrichen -#> 0.79 0.00 0.79

coef(fit.deSolve)

#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.799 0.000 0.800

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 @@ -626,8 +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: Mon Nov 26 09:46:10 2018 -#> Date of summary: Mon Nov 26 09:46:10 2018 +#> Date of fit: Mon Nov 26 11:40:36 2018 +#> Date of summary: Mon Nov 26 11:40:36 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -635,7 +635,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 186 model solutions performed in 0.889 s +#> Fitted with method Port using 186 model solutions performed in 0.839 s #> #> Weighting: none #> @@ -743,8 +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: Mon Nov 26 09:46:13 2018 -#> Date of summary: Mon Nov 26 09:46:13 2018 +#> Date of fit: Mon Nov 26 11:40:39 2018 +#> Date of summary: Mon Nov 26 11:40:39 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -752,7 +752,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 551 model solutions performed in 2.441 s +#> Fitted with method Port using 551 model solutions performed in 2.48 s #> #> Weighting: none #> @@ -865,8 +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: Mon Nov 26 09:46:14 2018 -#> Date of summary: Mon Nov 26 09:46:14 2018 +#> Date of fit: Mon Nov 26 11:40:40 2018 +#> Date of summary: Mon Nov 26 11:40:40 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -874,7 +874,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 155 model solutions performed in 0.679 s +#> Fitted with method Port using 155 model solutions performed in 0.694 s #> #> Weighting: mean #> @@ -983,8 +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: Mon Nov 26 09:46:15 2018 -#> Date of summary: Mon Nov 26 09:46:15 2018 +#> Date of fit: Mon Nov 26 11:40:41 2018 +#> Date of summary: Mon Nov 26 11:40:41 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -992,7 +992,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 174 model solutions performed in 0.771 s +#> Fitted with method Port using 174 model solutions performed in 0.778 s #> #> Weighting: manual #> @@ -1103,8 +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: Mon Nov 26 09:46:16 2018 -#> Date of summary: Mon Nov 26 09:46:16 2018 +#> Date of fit: Mon Nov 26 11:40:42 2018 +#> Date of summary: Mon Nov 26 11:40:42 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1112,7 +1112,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 270 model solutions performed in 1.2 s +#> Fitted with method Port using 270 model solutions performed in 1.225 s #> #> Weighting: manual #> @@ -1221,8 +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: Mon Nov 26 09:46:19 2018 -#> Date of summary: Mon Nov 26 09:46:19 2018 +#> Date of fit: Mon Nov 26 11:40:45 2018 +#> Date of summary: Mon Nov 26 11:40:45 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1230,7 +1230,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 692 model solutions performed in 3.079 s +#> Fitted with method Port using 692 model solutions performed in 3.119 s #> #> Weighting: manual #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index d947aff5..0d644bc4 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 file74b35b9de5b.c 2> file74b35b9de5b.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file4252799a8f5a.c 2> file4252799a8f5a.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 88858539..bfe71be5 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -323,7 +323,7 @@ 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 -#> 0.005 0.000 0.005

system.time( +#> 0.003 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 @@ -333,7 +333,7 @@ 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 -#> 0.039 0.000 0.039

+#> 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 49117199..92f12c2a 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 -#> 0.037 0.036 7.001

time_1

#> User System verstrichen -#> 21.838 0.000 21.852

+#> 0.050 0.037 6.958

time_1

#> User System verstrichen +#> 22.101 0.000 22.114

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 e63ab87e..554a28e3 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -206,8 +206,8 @@

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:     Mon Nov 26 09:47:09 2018 
-#> Date of summary: Mon Nov 26 09:47:09 2018 
+#> Date of fit:     Mon Nov 26 11:41:36 2018 
+#> Date of summary: Mon Nov 26 11:41:36 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index c0ff16fd..e6a42993 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:     Mon Nov 26 09:47:17 2018 
-#> Date of summary: Mon Nov 26 09:47:17 2018 
+#> Date of fit:     Mon Nov 26 11:41:44 2018 
+#> Date of summary: Mon Nov 26 11:41:44 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 0.673 s
+#> Fitted with method Port using 153 model solutions performed in 0.686 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:     Mon Nov 26 09:47:18 2018 
-#> Date of summary: Mon Nov 26 09:47:18 2018 
+#> Date of fit:     Mon Nov 26 11:41:45 2018 
+#> Date of summary: Mon Nov 26 11:41:45 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 1.529 s
+#> Fitted with method Port using 350 model solutions performed in 1.558 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:     Mon Nov 26 09:47:20 2018 
-#> Date of summary: Mon Nov 26 09:47:20 2018 
+#> Date of fit:     Mon Nov 26 11:41:46 2018 
+#> Date of summary: Mon Nov 26 11:41:46 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 0.847 s
+#> Fitted with method Port using 186 model solutions performed in 0.828 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:     Mon Nov 26 09:47:20 2018 
-#> Date of summary: Mon Nov 26 09:47:20 2018 
+#> Date of fit:     Mon Nov 26 11:41:47 2018 
+#> Date of summary: Mon Nov 26 11:41:47 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 0.457 s
+#> Fitted with method Port using 104 model solutions performed in 0.464 s
 #> 
 #> Weighting: none
 #> 
diff --git a/man/AIC.mmkin.Rd b/man/AIC.mmkin.Rd
new file mode 100644
index 00000000..e7f5c228
--- /dev/null
+++ b/man/AIC.mmkin.Rd
@@ -0,0 +1,44 @@
+\name{AIC.mmkin}
+\alias{AIC.mmkin}
+\title{
+  Calculated the AIC for a column of an mmkin object
+}
+\description{
+  Provides a convenient way to compare different kineti models fitted to the
+  same dataset.
+}
+\usage{
+  \method{AIC}{mmkin}(object, ..., k = 2)
+}
+\arguments{
+  \item{object}{
+    An object of class \code{\link{mmkin}}, containing only one column.
+  }
+  \item{\dots}{
+    For compatibility with the generic method
+  }
+  \item{k}{
+    As in the generic method
+  }
+}
+\value{
+  As in the generic method (a numeric value for single fits, or a dataframe if
+  there are several fits in the column).
+}
+\examples{
+  f <- mmkin(c("SFO", "FOMC", "DFOP"),
+    list("FOCUS A" = FOCUS_2006_A,
+         "FOCUS C" = FOCUS_2006_C))
+  AIC(f[1, "FOCUS A"]) # We get a single number for a single fit
+
+  # For FOCUS A, the models fit almost equally well, so the higher the number
+  # of parameters, the higher (worse) the AIC
+  AIC(f[, "FOCUS A"])
+  AIC(f[, "FOCUS A"], k = 0) # If we do not penalize additional parameters, we get nearly the same
+
+  # For FOCUS C, the more complex models fit better
+  AIC(f[, "FOCUS C"])
+}
+\author{
+  Johannes Ranke
+}
diff --git a/man/logLik.mkinfit.Rd b/man/logLik.mkinfit.Rd
index 8080f3db..fe517955 100644
--- a/man/logLik.mkinfit.Rd
+++ b/man/logLik.mkinfit.Rd
@@ -7,8 +7,8 @@
   This function simply calculates the product of the likelihood densities
   calculated using \code{\link{dnorm}}, i.e. assuming normal distribution.
 
-  The total number of estimated parameters returned with the value 
-  of the likelihood is calculated as the sum of fitted degradation 
+  The total number of estimated parameters returned with the value
+  of the likelihood is calculated as the sum of fitted degradation
   model parameters and the fitted error model parameters.
 
   For the case of unweighted least squares fitting, we calculate one
@@ -17,7 +17,7 @@
 
   For the case of manual weighting, we use the weight given for each
   observation as standard deviation in calculating its likelihood
-  and the total number of estimated parameters is equal to the 
+  and the total number of estimated parameters is equal to the
   number of fitted degradation model parameters.
 
   In the case of iterative reweighting, the variances obtained by this
@@ -28,7 +28,7 @@
   reweighting method is "tc".
 }
 \usage{
-\method{logLik}{mkinfit}(object, ...)
+  \method{logLik}{mkinfit}(object, ...)
 }
 \arguments{
   \item{object}{
@@ -43,6 +43,10 @@
   estimated parameters (degradation model parameters plus variance
   model parameters) as attribute.
 }
+\seealso{
+  Compare the AIC of columns of \code{\link{mmkin}} objects using
+  \code{\link{AIC.mmkin}}.
+}
 \examples{
   sfo_sfo <- mkinmod(
     parent = mkinsub("SFO", to = "m1"),
-- 
cgit v1.2.1

Calculated the AIC for a column of an mmkin object

Arguments

Value

Examples

Contents

Author

Examples

Examples