Calculated the AIC for a column of an mmkin object

Date: Mon, 26 Nov 2018 11:44:27 +0100 Subject: Add AIC method for mmkin column objects Static documentation rebuilt by pkgdown --- docs/reference/AIC.mmkin.html | 211 +++++++++++++++++++++++++++++++++ docs/reference/Extract.mmkin.html | 12 +- docs/reference/logLik.mkinfit.html | 19 ++- docs/reference/mccall81_245T.html | 12 +- docs/reference/mkinfit.html | 46 +++---- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 4 +- docs/reference/mmkin.html | 4 +- docs/reference/summary.mkinfit.html | 4 +- docs/reference/transform_odeparms.html | 24 ++-- 10 files changed, 278 insertions(+), 60 deletions(-) create mode 100644 docs/reference/AIC.mmkin.html (limited to 'docs/reference') diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html new file mode 100644 index 00000000..a2ce9885 --- /dev/null +++ b/docs/reference/AIC.mmkin.html @@ -0,0 +1,211 @@ + + + + + + + + +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

+ +

+ + +

+ + + + + + diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 51da42fc..b304c2fb 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -278,7 +278,7 @@ #> #> $time #> User System verstrichen -#> 0.183 0.000 0.183 +#> 0.188 0.000 0.188 #> #> $mkinmod #> <mkinmod> model generated with @@ -467,8 +467,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555be28e50> -#> <environment: 0x55555bc4d2b0> +#> <bytecode: 0x55555bd98970> +#> <environment: 0x55555d417aa8> #> #> $cost_notrans #> function (P) @@ -490,8 +490,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555cd2fbb8> -#> <environment: 0x55555bc4d2b0> +#> <bytecode: 0x55555cd14308> +#> <environment: 0x55555d417aa8> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -558,7 +558,7 @@ #> 99.17407 #> #> $date -#> [1] "Mon Nov 26 09:45:35 2018" +#> [1] "Mon Nov 26 11:40:00 2018" #> #> $version #> [1] "0.9.47.6" diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index b1901703..33d9eb36 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -34,15 +34,15 @@ See also + +

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
 #> 
-- 
cgit v1.2.1

Calculated the AIC for a column of an mmkin object

Arguments

Value

Examples

Contents

Author

Examples

Examples