From 7091d3738e7e55acb20edb88772b228f6f5b6c98 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 31 Oct 2019 01:55:01 +0100 Subject: Add likelihood ratio test and other methods, fixes The likelihood ratio test method is lrtest, in addition, methods for update and residuals were added. --- docs/reference/mkinfit.html | 32 +++++++++++++++++--------------- 1 file changed, 17 insertions(+), 15 deletions(-) (limited to 'docs/reference/mkinfit.html') diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 6c98bc38..c72d1cd0 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -218,7 +218,9 @@ must be given.

fixed_parms

The names of parameters that should not be optimised but -rather kept at the values specified in parms.ini.

+rather kept at the values specified in parms.ini. Alternatively, +a named numeric vector of parameters to be fixed, regardless of the values +in parms.ini.

fixed_initials @@ -400,15 +402,15 @@ estimators.

fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)
#> mkin version used for fitting: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Fri Oct 25 02:08:07 2019 -#> Date of summary: Fri Oct 25 02:08:07 2019 +#> Date of fit: Thu Oct 31 01:48:29 2019 +#> Date of summary: Thu Oct 31 01:48:29 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 0.453 s +#> Fitted using 222 model solutions performed in 0.455 s #> #> Error model: Constant variance #> @@ -480,7 +482,7 @@ estimators.

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 -#> 1.447 0.000 1.448
coef(fit)
#> NULL
endpoints(fit)
#> $ff +#> 1.464 0.000 1.465
coef(fit)
#> NULL
endpoints(fit)
#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -553,7 +555,7 @@ estimators.

#> 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 -#> 1.032 0.000 1.032
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff +#> 1.047 0.000 1.047
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -589,8 +591,8 @@ estimators.

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: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Fri Oct 25 02:08:22 2019 -#> Date of summary: Fri Oct 25 02:08:22 2019 +#> Date of fit: Thu Oct 31 01:48:44 2019 +#> Date of summary: Thu Oct 31 01:48:44 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -598,7 +600,7 @@ estimators.

#> #> Model predictions using solution type deSolve #> -#> Fitted using 421 model solutions performed in 1.062 s +#> Fitted using 421 model solutions performed in 1.136 s #> #> Error model: Constant variance #> @@ -706,8 +708,8 @@ estimators.

#> 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: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Fri Oct 25 02:08:25 2019 -#> Date of summary: Fri Oct 25 02:08:25 2019 +#> Date of fit: Thu Oct 31 01:48:47 2019 +#> Date of summary: Thu Oct 31 01:48:47 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -715,7 +717,7 @@ estimators.

#> #> Model predictions using solution type deSolve #> -#> Fitted using 978 model solutions performed in 2.523 s +#> Fitted using 978 model solutions performed in 2.512 s #> #> Error model: Variance unique to each observed variable #> @@ -838,8 +840,8 @@ estimators.

#> 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: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Fri Oct 25 02:08:34 2019 -#> Date of summary: Fri Oct 25 02:08:34 2019 +#> Date of fit: Thu Oct 31 01:48:56 2019 +#> Date of summary: Thu Oct 31 01:48:56 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -847,7 +849,7 @@ estimators.

#> #> Model predictions using solution type deSolve #> -#> Fitted using 2289 model solutions performed in 9.136 s +#> Fitted using 2289 model solutions performed in 9.124 s #> #> Error model: Two-component variance function #> -- cgit v1.2.1