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/add_err.html | 6 ++---- docs/reference/mkinfit.html | 26 +++++++++++++------------- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 2 +- docs/reference/mmkin.html | 4 ++-- docs/reference/summary.mkinfit.html | 4 ++-- 6 files changed, 21 insertions(+), 23 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 2eee6131..63aa358c 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -217,8 +217,7 @@ # Name the model in the list of models (with only one member in this case) for # nicer plotting later on. Be quiet and use only one core not to offend CRAN -# checks -f_SFO_SFO <- mmkin(list("SFO-SFO" = m_SFO_SFO), +# checks
f_SFO_SFO <- mmkin(list("SFO-SFO" = m_SFO_SFO), d_SFO_SFO_err, cores = 1, quiet = TRUE) @@ -229,8 +228,7 @@ plot(f_SFO_SFO[[3]], show_residuals = TRUE)
# If we use single brackets, we should give two indices (model and dataset), # and plot.mmkin is used -plot(f_SFO_SFO[1, 3])
-
+plot(f_SFO_SFO[1, 3])
#> 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 diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index b545dad1..0b96c6cb 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 file35fe67db2b2a.c 2> file35fe67db2b2a.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file7e6c2d3bf9bc.c 2> file7e6c2d3bf9bc.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 4b75603f..e3e17e78 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -333,7 +333,7 @@ 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 a16cb6d7..d61c0565 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 -#> 0.040 0.035 7.515
time_1
#> User System verstrichen -#> 21.597 0.000 21.609
+#> 0.044 0.026 7.470
time_1
#> User System verstrichen +#> 21.144 0.004 21.161
endpoints(fits.0[["SFO_lin", 2]])
#> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340481 0.2659519 0.7505683 0.2494317 diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 1a08132f..7e767ab3 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:    0.9.49.4 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Thu May  2 12:40:14 2019 
-#> Date of summary: Thu May  2 12:40:14 2019 
+#> Date of fit:     Thu May  2 17:42:27 2019 
+#> Date of summary: Thu May  2 17:42:27 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
-- 
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