From c6079a807e2b400fe0c772603392aeacd887da2f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 8 May 2019 20:57:48 +0200 Subject: Add functionality to plot the error model by plotting squared residuals against predicted values, and showing the variance function used in the fitted error model. Rebuild docs --- docs/reference/mkinfit.html | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) (limited to 'docs/reference/mkinfit.html') diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 09329a86..bfca44fc 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -362,15 +362,15 @@ 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: 0.9.49.4 #> R version used for fitting: 3.6.0 -#> Date of fit: Tue May 7 08:36:16 2019 -#> Date of summary: Tue May 7 08:36:16 2019 +#> Date of fit: Wed May 8 20:50:50 2019 +#> Date of summary: Wed May 8 20:50:50 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 0.89 s +#> Fitted using 222 model solutions performed in 0.456 s #> #> Error model: #> Constant variance @@ -443,7 +443,7 @@ 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 -#> 2.251 0.000 2.253
coef(fit)
#> NULL
endpoints(fit)
#> $ff +#> 1.488 0.000 1.488
coef(fit)
#> NULL
endpoints(fit)
#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -515,7 +515,7 @@ 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 -#> 1.151 0.000 1.152
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff +#> 1.086 0.000 1.087
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -547,8 +547,8 @@ 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: 0.9.49.4 #> R version used for fitting: 3.6.0 -#> Date of fit: Tue May 7 08:36:33 2019 -#> Date of summary: Tue May 7 08:36:33 2019 +#> Date of fit: Wed May 8 20:51:06 2019 +#> Date of summary: Wed May 8 20:51:06 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -556,7 +556,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 421 model solutions performed in 1.1 s +#> Fitted using 421 model solutions performed in 1.082 s #> #> Error model: #> Constant variance @@ -665,8 +665,8 @@ 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: 0.9.49.4 #> R version used for fitting: 3.6.0 -#> Date of fit: Tue May 7 08:36:35 2019 -#> Date of summary: Tue May 7 08:36:35 2019 +#> Date of fit: Wed May 8 20:51:08 2019 +#> Date of summary: Wed May 8 20:51:08 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -674,7 +674,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 758 model solutions performed in 1.991 s +#> Fitted using 758 model solutions performed in 1.971 s #> #> Error model: #> Variance unique to each observed variable @@ -795,8 +795,8 @@ Per default, parameters in the kinetic models are internally transformed in #> 120 m1 25.15 28.80430 -3.654e+00 #> 120 m1 33.31 28.80430 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: 0.9.49.4 #> R version used for fitting: 3.6.0 -#> Date of fit: Tue May 7 08:36:39 2019 -#> Date of summary: Tue May 7 08:36:39 2019 +#> Date of fit: Wed May 8 20:51:11 2019 +#> Date of summary: Wed May 8 20:51:11 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -804,7 +804,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 821 model solutions performed in 3.304 s +#> Fitted using 821 model solutions performed in 3.29 s #> #> Error model: #> Two-component variance function -- cgit v1.2.1