From 587662437bce06ea202551048226b86cff0db187 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 14 Sep 2018 21:02:46 +0200 Subject: Skip more tests on CRAN Static documentation rebuilt by pkgdown --- docs/reference/Extract.mmkin.html | 12 ++++----- docs/reference/mccall81_245T.html | 12 ++++----- docs/reference/mkinfit.html | 46 +++++++++++++++++----------------- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 6 ++--- docs/reference/mmkin.html | 4 +-- docs/reference/summary.mkinfit.html | 6 ++--- docs/reference/transform_odeparms.html | 24 +++++++++--------- 8 files changed, 56 insertions(+), 56 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 91226e69..97562d44 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -278,7 +278,7 @@ #> #> $time #> User System verstrichen -#> 0.166 0.000 0.166 +#> 0.177 0.000 0.176 #> #> $mkinmod #> <mkinmod> model generated with @@ -467,8 +467,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555bd812a0> -#> <environment: 0x55555bc871e8> +#> <bytecode: 0x55555bd7f230> +#> <environment: 0x55555bc85178> #> #> $cost_notrans #> function (P) @@ -490,8 +490,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555caa1d18> -#> <environment: 0x55555bc871e8> +#> <bytecode: 0x55555ca9fca8> +#> <environment: 0x55555bc85178> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -558,7 +558,7 @@ #> 99.17407 #> #> $date -#> [1] "Fri Sep 14 18:20:46 2018" +#> [1] "Fri Sep 14 20:58:46 2018" #> #> $version #> [1] "0.9.47.5" diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index d91431f3..52c09969 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -158,8 +158,8 @@ anisole = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE) summary(fit.1, data = FALSE)
#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 18:20:57 2018 -#> Date of summary: Fri Sep 14 18:20:57 2018 +#> Date of fit: Fri Sep 14 20:58:58 2018 +#> Date of summary: Fri Sep 14 20:58:58 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -169,7 +169,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 574 model solutions performed in 3.418 s +#> Fitted with method Port using 574 model solutions performed in 3.393 s #> #> Weighting: none #> @@ -247,8 +247,8 @@ fixed_parms = "k_phenol_sink", quiet = TRUE) summary(fit.2, data = FALSE)
#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 18:20:59 2018 -#> Date of summary: Fri Sep 14 18:20:59 2018 +#> Date of fit: Fri Sep 14 20:58:59 2018 +#> Date of summary: Fri Sep 14 20:59:00 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -258,7 +258,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.458 s +#> Fitted with method Port using 246 model solutions performed in 1.451 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 261d48fb..f3c6d595 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -434,15 +434,15 @@ fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)
#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 18:21:02 2018 -#> Date of summary: Fri Sep 14 18:21:02 2018 +#> Date of fit: Fri Sep 14 20:59:02 2018 +#> Date of summary: Fri Sep 14 20:59:02 2018 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.143 s +#> Fitted with method Port using 64 model solutions performed in 0.141 s #> #> Weighting: none #> @@ -511,7 +511,7 @@ 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)))
#> User System verstrichen -#> 0.918 0.000 0.919
coef(fit)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.895 0.000 0.897
coef(fit)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750
endpoints(fit)
#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -586,7 +586,7 @@ #> Model cost at call 146 : 371.2134 #> Optimisation by method Port successfully terminated. #> User System verstrichen -#> 0.757 0.000 0.757
coef(fit.deSolve)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.726 0.000 0.726
coef(fit.deSolve)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750
endpoints(fit.deSolve)
#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -624,8 +624,8 @@ 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) summary(f.noweight)
#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 18:21:13 2018 -#> Date of summary: Fri Sep 14 18:21:13 2018 +#> Date of fit: Fri Sep 14 20:59:13 2018 +#> Date of summary: Fri Sep 14 20:59:13 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -633,7 +633,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 186 model solutions performed in 0.775 s +#> Fitted with method Port using 186 model solutions performed in 0.757 s #> #> Weighting: none #> @@ -741,8 +741,8 @@ #> 120 m1 33.31 28.78984 4.520e+00
f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs", quiet = TRUE) summary(f.irls)
#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 18:21:15 2018 -#> Date of summary: Fri Sep 14 18:21:15 2018 +#> Date of fit: Fri Sep 14 20:59:15 2018 +#> Date of summary: Fri Sep 14 20:59:16 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -750,7 +750,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 551 model solutions performed in 2.282 s +#> Fitted with method Port using 551 model solutions performed in 2.329 s #> #> Weighting: none #> @@ -863,8 +863,8 @@ #> 120 m1 33.31 28.80898 4.501e+00 2.722
f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", quiet = TRUE) summary(f.w.mean)
#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 18:21:16 2018 -#> Date of summary: Fri Sep 14 18:21:16 2018 +#> Date of fit: Fri Sep 14 20:59:16 2018 +#> Date of summary: Fri Sep 14 20:59:16 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -872,7 +872,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 155 model solutions performed in 0.653 s +#> Fitted with method Port using 155 model solutions performed in 0.628 s #> #> Weighting: mean #> @@ -981,8 +981,8 @@ quiet = TRUE) summary(f.w.value)
#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 18:21:17 2018 -#> Date of summary: Fri Sep 14 18:21:17 2018 +#> Date of fit: Fri Sep 14 20:59:17 2018 +#> Date of summary: Fri Sep 14 20:59:17 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -990,7 +990,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 174 model solutions performed in 0.721 s +#> Fitted with method Port using 174 model solutions performed in 0.713 s #> #> Weighting: manual #> @@ -1101,8 +1101,8 @@ f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE) summary(f.w.man)
#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 18:21:18 2018 -#> Date of summary: Fri Sep 14 18:21:18 2018 +#> Date of fit: Fri Sep 14 20:59:18 2018 +#> Date of summary: Fri Sep 14 20:59:18 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1110,7 +1110,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 270 model solutions performed in 1.215 s +#> Fitted with method Port using 270 model solutions performed in 1.119 s #> #> Weighting: manual #> @@ -1219,8 +1219,8 @@ reweight.method = "obs") summary(f.w.man.irls)
#> mkin version used for fitting: 0.9.47.5 #> R version used for fitting: 3.5.1 -#> Date of fit: Fri Sep 14 18:21:22 2018 -#> Date of summary: Fri Sep 14 18:21:22 2018 +#> Date of fit: Fri Sep 14 20:59:21 2018 +#> Date of summary: Fri Sep 14 20:59:21 2018 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1228,7 +1228,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 692 model solutions performed in 3.114 s +#> Fitted with method Port using 692 model solutions performed in 2.955 s #> #> Weighting: manual #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 9048c1b1..464178bc 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -229,7 +229,7 @@ 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 file49ec17c0788e.c 2> file49ec17c0788e.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file7aee6cc2a6d.c 2> file7aee6cc2a6d.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 6c30d7a8..dfcd08a8 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -321,17 +321,17 @@ 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 0.003
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 #> 201 20 4.978707 27.46227
#> User System verstrichen -#> 0.002 0.000 0.002
system.time( +#> 0.001 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 #> 201 20 4.978707 27.46227
#> User System verstrichen -#> 0.035 0.000 0.035
+#> 0.036 0.000 0.036
#> User System verstrichen -#> 0.059 0.027 6.918
time_1
#> User System verstrichen -#> 21.127 0.000 21.141
+#> 0.056 0.024 6.712
time_1
#> User System verstrichen +#> 20.446 0.000 20.459
endpoints(fits.0[["SFO_lin", 2]])
#> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340480 0.2659520 0.7505686 0.2494314 diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index cb6beda2..317c7a87 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -206,15 +206,15 @@

Examples

  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 18:22:10 2018 
-#> Date of summary: Fri Sep 14 18:22:10 2018 
+#> Date of fit:     Fri Sep 14 21:00:08 2018 
+#> Date of summary: Fri Sep 14 21:00:08 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 35 model solutions performed in 0.076 s
+#> Fitted with method Port using 35 model solutions performed in 0.081 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index db92667c..6f7ec4a4 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -200,8 +200,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
 summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 18:22:17 2018 
-#> Date of summary: Fri Sep 14 18:22:17 2018 
+#> Date of fit:     Fri Sep 14 21:00:16 2018 
+#> Date of summary: Fri Sep 14 21:00:16 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -209,7 +209,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 153 model solutions performed in 0.701 s
+#> Fitted with method Port using 153 model solutions performed in 0.71 s
 #> 
 #> Weighting: none
 #> 
@@ -276,8 +276,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 
fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
 summary(fit.2, data=FALSE)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 18:22:19 2018 
-#> Date of summary: Fri Sep 14 18:22:19 2018 
+#> Date of fit:     Fri Sep 14 21:00:17 2018 
+#> Date of summary: Fri Sep 14 21:00:17 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -285,7 +285,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 350 model solutions performed in 1.431 s
+#> Fitted with method Port using 350 model solutions performed in 1.417 s
 #> 
 #> Weighting: none
 #> 
@@ -364,8 +364,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
 summary(fit.ff, data = FALSE)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 18:22:20 2018 
-#> Date of summary: Fri Sep 14 18:22:20 2018 
+#> Date of fit:     Fri Sep 14 21:00:18 2018 
+#> Date of summary: Fri Sep 14 21:00:18 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -373,7 +373,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 186 model solutions performed in 0.778 s
+#> Fitted with method Port using 186 model solutions performed in 0.755 s
 #> 
 #> Weighting: none
 #> 
@@ -448,8 +448,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE)
 summary(fit.ff.2, data = FALSE)
#> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 18:22:20 2018 
-#> Date of summary: Fri Sep 14 18:22:20 2018 
+#> Date of fit:     Fri Sep 14 21:00:19 2018 
+#> Date of summary: Fri Sep 14 21:00:19 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -457,7 +457,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 104 model solutions performed in 0.417 s
+#> Fitted with method Port using 104 model solutions performed in 0.416 s
 #> 
 #> Weighting: none
 #> 
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