From a401a9225d212ed4dc64e96765f04aaaf17cc8c1 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 18 Sep 2019 13:23:23 +0200 Subject: Further corrections of the twa vignette Static documentation rebuilt by pkgdown --- docs/reference/mkinfit.html | 28 ++++++++++++++-------------- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 4 ++-- docs/reference/mmkin.html | 4 ++-- docs/reference/summary.mkinfit.html | 6 +++--- 5 files changed, 22 insertions(+), 22 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index b620f364..c1cfc228 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -408,15 +408,15 @@ 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: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Wed Sep 18 12:55:32 2019 -#> Date of summary: Wed Sep 18 12:55:32 2019 +#> Date of fit: Wed Sep 18 13:14:54 2019 +#> Date of summary: Wed Sep 18 13:14:54 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 0.459 s +#> Fitted using 222 model solutions performed in 0.475 s #> #> Error model: Constant variance #> @@ -490,7 +490,7 @@ 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 -#> 1.480 0.000 1.482
coef(fit)
#> NULL
endpoints(fit)
#> $ff +#> 1.561 0.000 1.568
coef(fit)
#> NULL
endpoints(fit)
#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -563,7 +563,7 @@ 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 -#> 1.045 0.000 1.046
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff +#> 1.06 0.00 1.06
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -599,8 +599,8 @@ 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: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Wed Sep 18 12:55:47 2019 -#> Date of summary: Wed Sep 18 12:55:47 2019 +#> Date of fit: Wed Sep 18 13:15:10 2019 +#> Date of summary: Wed Sep 18 13:15:10 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -608,7 +608,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 421 model solutions performed in 1.077 s +#> Fitted using 421 model solutions performed in 1.095 s #> #> Error model: Constant variance #> @@ -718,8 +718,8 @@ 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: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Wed Sep 18 12:55:50 2019 -#> Date of summary: Wed Sep 18 12:55:50 2019 +#> Date of fit: Wed Sep 18 13:15:12 2019 +#> Date of summary: Wed Sep 18 13:15:12 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -727,7 +727,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 979 model solutions performed in 2.624 s +#> Fitted using 979 model solutions performed in 2.639 s #> #> Error model: Variance unique to each observed variable #> @@ -850,8 +850,8 @@ 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: 0.9.49.6 #> R version used for fitting: 3.6.1 -#> Date of fit: Wed Sep 18 12:55:59 2019 -#> Date of summary: Wed Sep 18 12:55:59 2019 +#> Date of fit: Wed Sep 18 13:15:22 2019 +#> Date of summary: Wed Sep 18 13:15:22 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -859,7 +859,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 2289 model solutions performed in 9.376 s +#> Fitted using 2289 model solutions performed in 9.723 s #> #> Error model: Two-component variance function #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 81fed454..ca243e3c 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -239,7 +239,7 @@ 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 file419a1fa6c394.c 2> file419a1fa6c394.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file4e7a49f4ff50.c 2> file4e7a49f4ff50.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index d162135a..f5401c1d 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -332,12 +332,12 @@ 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 -#> 0.004 0.000 0.003
system.time( +#> 0.004 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 #> 201 20 4.978707 27.46227
#> User System verstrichen -#> 0.002 0.000 0.001
system.time( +#> 0.002 0.000 0.002
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", use_compiled = FALSE)[201,]))
#> time parent m1 diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 9bb7926b..ea695d9a 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -199,8 +199,8 @@ time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE)) time_default
#> User System verstrichen -#> 0.012 0.024 5.064
time_1
#> User System verstrichen -#> 19.094 0.000 19.104
+#> 0.007 0.031 4.920
time_1
#> User System verstrichen +#> 19.290 0.000 19.301
endpoints(fits.0[["SFO_lin", 2]])
#> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340481 0.2659519 0.7505684 0.2494316 diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index fafca9ce..a10859fc 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -215,15 +215,15 @@

Examples

  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.49.6 
 #> R version used for fitting:       3.6.1 
-#> Date of fit:     Wed Sep 18 12:57:18 2019 
-#> Date of summary: Wed Sep 18 12:57:18 2019 
+#> Date of fit:     Wed Sep 18 13:16:44 2019 
+#> Date of summary: Wed Sep 18 13:16:44 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 131 model solutions performed in 0.267 s
+#> Fitted using 131 model solutions performed in 0.273 s
 #> 
 #> Error model: Constant variance 
 #> 
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