From 798195d367111e592e5247309b90fac29ed7ddfd Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 3 Jul 2019 16:45:09 +0200 Subject: Update DESCRIPTION, improve NEWS Static documentation rebuilt by pkgdown --- docs/reference/index.html | 2 +- docs/reference/mkinfit.html | 30 +++++++++++++++--------------- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 4 ++-- docs/reference/mmkin.html | 4 ++-- docs/reference/summary.mkinfit.html | 4 ++-- 6 files changed, 23 insertions(+), 23 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/index.html b/docs/reference/index.html index c5ac0d72..b645ea5a 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -505,7 +505,7 @@

Deprecated functions

-

Functions that have been superseeded

+

Functions that have been superseded

diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 700b6805..3e20fc5d 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -334,7 +334,7 @@ Per default, parameters in the kinetic models are internally transformed in

The algorithm "direct" will directly minimize the negative log-likelihood.

The algorithm "twostep" will minimize the negative log-likelihood - after an initial unweighted leas squares optimisation step.

+ after an initial unweighted least squares optimisation step.

The algorithm "threestep" starts with unweighted least squares, then optimizes only the error model using the degradation model parameters found, and then minimizes the negative log-likelihood @@ -399,15 +399,15 @@ 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: 0.9.49.5 #> R version used for fitting: 3.6.0 -#> Date of fit: Wed Jun 5 15:08:20 2019 -#> Date of summary: Wed Jun 5 15:08:20 2019 +#> Date of fit: Wed Jul 3 16:36:58 2019 +#> Date of summary: Wed Jul 3 16:36:58 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 0.469 s +#> Fitted using 222 model solutions performed in 0.46 s #> #> Error model: Constant variance #> @@ -481,7 +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 -#> 1.579 0.000 1.581
coef(fit)
#> NULL
endpoints(fit)
#> $ff +#> 1.497 0.000 1.499
coef(fit)
#> NULL
endpoints(fit)
#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -553,7 +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 -#> 1.159 0.000 1.160
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff +#> 1.079 0.000 1.079
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 #> @@ -585,8 +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: Wed Jun 5 15:08:36 2019 -#> Date of summary: Wed Jun 5 15:08:36 2019 +#> Date of fit: Wed Jul 3 16:37:14 2019 +#> Date of summary: Wed Jul 3 16:37:14 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -594,7 +594,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 421 model solutions performed in 1.181 s +#> Fitted using 421 model solutions performed in 1.107 s #> #> Error model: Constant variance #> @@ -704,8 +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: Wed Jun 5 15:08:39 2019 -#> Date of summary: Wed Jun 5 15:08:39 2019 +#> Date of fit: Wed Jul 3 16:37:17 2019 +#> Date of summary: Wed Jul 3 16:37:17 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -713,7 +713,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 979 model solutions performed in 2.672 s +#> Fitted using 979 model solutions performed in 2.612 s #> #> Error model: Variance unique to each observed variable #> @@ -836,8 +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: Wed Jun 5 15:08:50 2019 -#> Date of summary: Wed Jun 5 15:08:50 2019 +#> Date of fit: Wed Jul 3 16:37:26 2019 +#> Date of summary: Wed Jul 3 16:37:26 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -845,7 +845,7 @@ Per default, parameters in the kinetic models are internally transformed in #> #> Model predictions using solution type deSolve #> -#> Fitted using 2289 model solutions performed in 10.959 s +#> Fitted using 2289 model solutions performed in 9.522 s #> #> Error model: Two-component variance function #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index ddab656c..f1793541 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -234,7 +234,7 @@ 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 file50a55c3108b2.c 2> file50a55c3108b2.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file24f24fd75f75.c 2> file24f24fd75f75.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 7e71ec27..9c4263b6 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -328,12 +328,12 @@ 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 0.004
system.time( +#> 0.003 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 -#> 0.003 0.000 0.002
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 61a029fc..7a34ac7d 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -194,8 +194,8 @@ time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE)) time_default
#> User System verstrichen -#> 0.038 0.050 6.779
time_1
#> User System verstrichen -#> 27.209 0.004 27.278
+#> 0.036 0.048 5.130
time_1
#> User System verstrichen +#> 19.222 0.000 19.233
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 68b36542..4f2c9ecb 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -211,8 +211,8 @@

Examples

  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.49.5 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Wed Jun  5 15:10:34 2019 
-#> Date of summary: Wed Jun  5 15:10:34 2019 
+#> Date of fit:     Wed Jul  3 16:38:45 2019 
+#> Date of summary: Wed Jul  3 16:38:45 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
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