From a4ca3451f1b5c37d10c6a41cb18a99b1631e8aa2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 2 May 2019 17:07:55 +0200 Subject: Prepare for CRAN release - Skip long running tests on CRAN as well to avoid timeout on winbuilder - Don't install benchmark results in the package, they are only needed in the git repository - Don't run example in man/add_err.Rd as it takes > 10 s on winbuilder - Rebuild docs --- docs/reference/mkinfit.html | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) (limited to 'docs/reference/mkinfit.html') diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 7693287e..cd4f91e5 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -362,8 +362,8 @@ 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: Thu May 2 12:38:56 2019 -#> Date of summary: Thu May 2 12:38:56 2019 +#> Date of fit: Thu May 2 17:41:11 2019 +#> Date of summary: Thu May 2 17:41:11 2019 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -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 -#> 1.551 0.000 1.552
coef(fit)
#> NULL
endpoints(fit)
#> $ff +#> 1.54 0.00 1.54
coef(fit)
#> NULL
endpoints(fit)
#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -520,7 +520,7 @@ Per default, parameters in the kinetic models are internally transformed in #> Negative log-likelihood at call 152: 97.22429 #> Optimisation successfully terminated. #> User System verstrichen -#> 1.152 0.000 1.153
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff +#> 1.1 0.0 1.1
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -552,8 +552,8 @@ 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: Thu May 2 12:39:13 2019 -#> Date of summary: Thu May 2 12:39:13 2019 +#> Date of fit: Thu May 2 17:41:27 2019 +#> Date of summary: Thu May 2 17:41:27 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -561,7 +561,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 404 model solutions performed in 1.178 s +#> Fitted using 404 model solutions performed in 1.067 s #> #> Error model: #> Constant variance @@ -670,8 +670,8 @@ 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: Thu May 2 12:39:14 2019 -#> Date of summary: Thu May 2 12:39:14 2019 +#> Date of fit: Thu May 2 17:41:28 2019 +#> Date of summary: Thu May 2 17:41:28 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -679,7 +679,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 558 model solutions performed in 1.518 s +#> Fitted using 558 model solutions performed in 1.447 s #> #> Error model: #> Variance unique to each observed variable @@ -800,8 +800,8 @@ 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: Thu May 2 12:39:18 2019 -#> Date of summary: Thu May 2 12:39:18 2019 +#> Date of fit: Thu May 2 17:41:32 2019 +#> Date of summary: Thu May 2 17:41:32 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -809,7 +809,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 844 model solutions performed in 3.501 s +#> Fitted using 844 model solutions performed in 3.407 s #> #> Error model: #> Two-component variance function -- cgit v1.2.1