From 7e8d788d298b8e1492fd8f62d88456e99e0f5992 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 4 Jul 2019 08:10:33 +0200 Subject: Address failures of CRAN checks, improve NEWS 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 | 4 ++-- 5 files changed, 21 insertions(+), 21 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 3e20fc5d..0983007e 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -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 Jul 3 16:36:58 2019 -#> Date of summary: Wed Jul 3 16:36:58 2019 +#> Date of fit: Thu Jul 4 08:02:21 2019 +#> Date of summary: Thu Jul 4 08:02:21 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 0.46 s +#> Fitted using 222 model solutions performed in 0.464 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 -#> 1.497 0.000 1.499
coef(fit)
#> NULL
endpoints(fit)
#> $ff +#> 1.507 0.004 1.511
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 -#> 1.079 0.000 1.079
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff +#> 1.078 0.000 1.078
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 Jul 3 16:37:14 2019 -#> Date of summary: Wed Jul 3 16:37:14 2019 +#> Date of fit: Thu Jul 4 08:02:37 2019 +#> Date of summary: Thu Jul 4 08:02:37 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 1.107 s +#> Fitted using 421 model solutions performed in 1.096 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 Jul 3 16:37:17 2019 -#> Date of summary: Wed Jul 3 16:37:17 2019 +#> Date of fit: Thu Jul 4 08:02:40 2019 +#> Date of summary: Thu Jul 4 08:02:40 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 2.612 s +#> Fitted using 979 model solutions performed in 2.574 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 Jul 3 16:37:26 2019 -#> Date of summary: Wed Jul 3 16:37:26 2019 +#> Date of fit: Thu Jul 4 08:02:49 2019 +#> Date of summary: Thu Jul 4 08:02:49 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 9.522 s +#> Fitted using 2289 model solutions performed in 9.379 s #> #> Error model: Two-component variance function #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index f1793541..39fe631b 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 file24f24fd75f75.c 2> file24f24fd75f75.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file6e9c38dae9ed.c 2> file6e9c38dae9ed.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 9c4263b6..ef847245 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -328,7 +328,7 @@ 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 -#> 0.003 0.000 0.004
system.time( +#> 0.004 0.000 0.003
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 @@ -338,7 +338,7 @@ c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "deSolve", use_compiled = FALSE)[201,]))
#> time parent m1 #> 201 20 4.978707 27.46227
#> User System verstrichen -#> 0.022 0.000 0.022
+#> 0.022 0.000 0.021
# Predict from a fitted model f <- mkinfit(SFO_SFO, FOCUS_2006_C)
#> Ordinary least squares optimisation
#> Sum of squared residuals at call 1: 552.5739 #> Sum of squared residuals at call 3: 552.5739 diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 7a34ac7d..38c46b6e 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 -#> 0.036 0.048 5.130
time_1
#> User System verstrichen -#> 19.222 0.000 19.233
+#> 0.055 0.032 5.069
time_1
#> User System verstrichen +#> 19.260 0.000 19.271
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 4f2c9ecb..c4d2653d 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 Jul  3 16:38:45 2019 
-#> Date of summary: Wed Jul  3 16:38:45 2019 
+#> Date of fit:     Thu Jul  4 08:04:08 2019 
+#> Date of summary: Thu Jul  4 08:04:08 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
-- 
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