From b6027bbd157734e1c7f8c3ba6373451f5c85fc38 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 5 Jun 2019 15:16:59 +0200 Subject: Add error model algorithm to output --- docs/reference/mkinfit.html | 50 +++++++++++++++++++++++++-------------------- 1 file changed, 28 insertions(+), 22 deletions(-) (limited to 'docs/reference/mkinfit.html') diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 8cabcb21..700b6805 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -399,18 +399,19 @@ Per default, parameters in the kinetic models are internally transformed in fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)
#> mkin version used for fitting: 0.9.49.5 #> R version used for fitting: 3.6.0 -#> Date of fit: Tue Jun 4 15:01:15 2019 -#> Date of summary: Tue Jun 4 15:01:15 2019 +#> Date of fit: Wed Jun 5 15:08:20 2019 +#> Date of summary: Wed Jun 5 15:08:20 2019 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 222 model solutions performed in 0.461 s +#> Fitted using 222 model solutions performed in 0.469 s #> -#> Error model: -#> Constant variance +#> Error model: Constant variance +#> +#> Error model algorithm: d_3 #> #> Starting values for parameters to be optimised: #> value type @@ -480,7 +481,7 @@ Per default, parameters in the kinetic models are internally transformed in 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)))
#> Warning: Observations with value of zero were removed from the data
#> User System verstrichen -#> 1.521 0.000 1.526
coef(fit)
#> NULL
endpoints(fit)
#> $ff +#> 1.579 0.000 1.581
coef(fit)
#> NULL
endpoints(fit)
#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -552,7 +553,7 @@ Per default, parameters in the kinetic models are internally transformed in #> Sum of squared residuals at call 126: 371.2134 #> Sum of squared residuals at call 135: 371.2134 #> Negative log-likelihood at call 145: 97.22429
#> Optimisation successfully terminated.
#> User System verstrichen -#> 1.093 0.000 1.093
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff +#> 1.159 0.000 1.160
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -584,8 +585,8 @@ Per default, parameters in the kinetic models are internally transformed in SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"), 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)
#> Warning: Observations with value of zero were removed from the data
summary(f.noweight)
#> mkin version used for fitting: 0.9.49.5 #> R version used for fitting: 3.6.0 -#> Date of fit: Tue Jun 4 15:01:31 2019 -#> Date of summary: Tue Jun 4 15:01:31 2019 +#> Date of fit: Wed Jun 5 15:08:36 2019 +#> Date of summary: Wed Jun 5 15:08:36 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -593,10 +594,11 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 421 model solutions performed in 1.096 s +#> Fitted using 421 model solutions performed in 1.181 s +#> +#> Error model: Constant variance #> -#> Error model: -#> Constant variance +#> Error model algorithm: d_3 #> #> Starting values for parameters to be optimised: #> value type @@ -702,8 +704,8 @@ Per default, parameters in the kinetic models are internally transformed in #> 120 m1 25.15 28.78984 -3.640e+00 #> 120 m1 33.31 28.78984 4.520e+00
f.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.obs)
#> mkin version used for fitting: 0.9.49.5 #> R version used for fitting: 3.6.0 -#> Date of fit: Tue Jun 4 15:01:34 2019 -#> Date of summary: Tue Jun 4 15:01:34 2019 +#> Date of fit: Wed Jun 5 15:08:39 2019 +#> Date of summary: Wed Jun 5 15:08:39 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -711,10 +713,12 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 979 model solutions performed in 2.603 s +#> Fitted using 979 model solutions performed in 2.672 s #> -#> Error model: -#> Variance unique to each observed variable +#> Error model: Variance unique to each observed variable +#> +#> Error model algorithm: d_3 +#> Direct fitting and three-step fitting yield approximately the same likelihood #> #> Starting values for parameters to be optimised: #> value type @@ -832,8 +836,8 @@ Per default, parameters in the kinetic models are internally transformed in #> 120 m1 25.15 28.80429 -3.654e+00 #> 120 m1 33.31 28.80429 4.506e+00
f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.tc)
#> mkin version used for fitting: 0.9.49.5 #> R version used for fitting: 3.6.0 -#> Date of fit: Tue Jun 4 15:01:43 2019 -#> Date of summary: Tue Jun 4 15:01:43 2019 +#> Date of fit: Wed Jun 5 15:08:50 2019 +#> Date of summary: Wed Jun 5 15:08:50 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -841,10 +845,12 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 2289 model solutions performed in 9.499 s +#> Fitted using 2289 model solutions performed in 10.959 s +#> +#> Error model: Two-component variance function #> -#> Error model: -#> Two-component variance function +#> Error model algorithm: d_3 +#> Direct fitting and three-step fitting yield approximately the same likelihood #> #> Starting values for parameters to be optimised: #> value type -- cgit v1.2.1