From 5181a55b1619c153b690db97ee82698bf76525ff Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 21 Feb 2019 16:16:21 +0100 Subject: Static documentation rebuilt by pkgdown to get the codecov badge into the docs --- 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 | 2 +- docs/reference/mmkin.html | 4 +-- docs/reference/summary.mkinfit.html | 6 ++--- docs/reference/transform_odeparms.html | 24 +++++++++--------- 8 files changed, 54 insertions(+), 54 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 39228ba7..8e018e96 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -280,7 +280,7 @@ #> #> $time #> User System verstrichen -#> 0.197 0.000 0.197 +#> 0.198 0.000 0.198 #> #> $mkinmod #> <mkinmod> model generated with @@ -469,8 +469,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555920c328> -#> <environment: 0x555555b0eb48> +#> <bytecode: 0x55555920cdf0> +#> <environment: 0x5555562c5500> #> #> $cost_notrans #> function (P) @@ -492,8 +492,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555a39faa0> -#> <environment: 0x555555b0eb48> +#> <bytecode: 0x55555a399838> +#> <environment: 0x5555562c5500> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -560,7 +560,7 @@ #> 99.17407 #> #> $date -#> [1] "Thu Feb 21 15:11:41 2019" +#> [1] "Thu Feb 21 16:11:47 2019" #> #> $version #> [1] "0.9.48.1" diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index ce1c88e9..7d865dcf 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -160,8 +160,8 @@ 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: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Feb 21 15:12:02 2019 -#> Date of summary: Thu Feb 21 15:12:02 2019 +#> Date of fit: Thu Feb 21 16:12:08 2019 +#> Date of summary: Thu Feb 21 16:12:08 2019 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -171,7 +171,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 574 model solutions performed in 3.856 s +#> Fitted with method Port using 574 model solutions performed in 3.846 s #> #> Weighting: none #> @@ -249,8 +249,8 @@ fixed_parms = "k_phenol_sink", quiet = TRUE) summary(fit.2, data = FALSE)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Feb 21 15:12:04 2019 -#> Date of summary: Thu Feb 21 15:12:04 2019 +#> Date of fit: Thu Feb 21 16:12:10 2019 +#> Date of summary: Thu Feb 21 16:12:10 2019 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -260,7 +260,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.607 s +#> Fitted with method Port using 246 model solutions performed in 1.602 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 369d7bbe..5f57189c 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -438,15 +438,15 @@ fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Feb 21 15:12:07 2019 -#> Date of summary: Thu Feb 21 15:12:07 2019 +#> Date of fit: Thu Feb 21 16:12:13 2019 +#> Date of summary: Thu Feb 21 16:12:13 2019 #> #> 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 0.164 s +#> Fitted with method Port using 64 model solutions performed in 0.16 s #> #> Weighting: none #> @@ -515,7 +515,7 @@ 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 -#> 1.045 0.000 1.046
coef(fit)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 1.035 0.004 1.040
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 @@ -590,7 +590,7 @@ #> Model cost at call 146 : 371.2134 #> Optimisation by method Port successfully terminated. #> User System verstrichen -#> 0.835 0.000 0.835
coef(fit.deSolve)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.819 0.000 0.819
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 @@ -628,8 +628,8 @@ 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: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Feb 21 15:12:19 2019 -#> Date of summary: Thu Feb 21 15:12:19 2019 +#> Date of fit: Thu Feb 21 16:12:25 2019 +#> Date of summary: Thu Feb 21 16:12:25 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -637,7 +637,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 186 model solutions performed in 0.853 s +#> Fitted with method Port using 186 model solutions performed in 0.877 s #> #> Weighting: none #> @@ -745,8 +745,8 @@ #> 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: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Feb 21 15:12:22 2019 -#> Date of summary: Thu Feb 21 15:12:22 2019 +#> Date of fit: Thu Feb 21 16:12:28 2019 +#> Date of summary: Thu Feb 21 16:12:28 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -754,7 +754,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 551 model solutions performed in 2.573 s +#> Fitted with method Port using 551 model solutions performed in 2.574 s #> #> Weighting: none #> @@ -867,8 +867,8 @@ #> 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: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Feb 21 15:12:22 2019 -#> Date of summary: Thu Feb 21 15:12:22 2019 +#> Date of fit: Thu Feb 21 16:12:29 2019 +#> Date of summary: Thu Feb 21 16:12:29 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -876,7 +876,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 155 model solutions performed in 0.718 s +#> Fitted with method Port using 155 model solutions performed in 0.756 s #> #> Weighting: mean #> @@ -985,8 +985,8 @@ quiet = TRUE) summary(f.w.value)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Feb 21 15:12:23 2019 -#> Date of summary: Thu Feb 21 15:12:23 2019 +#> Date of fit: Thu Feb 21 16:12:30 2019 +#> Date of summary: Thu Feb 21 16:12:30 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -994,7 +994,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 174 model solutions performed in 0.802 s +#> Fitted with method Port using 174 model solutions performed in 0.864 s #> #> Weighting: manual #> @@ -1105,8 +1105,8 @@ f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE) summary(f.w.man)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Feb 21 15:12:25 2019 -#> Date of summary: Thu Feb 21 15:12:25 2019 +#> Date of fit: Thu Feb 21 16:12:31 2019 +#> Date of summary: Thu Feb 21 16:12:31 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1114,7 +1114,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 270 model solutions performed in 1.251 s +#> Fitted with method Port using 270 model solutions performed in 1.306 s #> #> Weighting: manual #> @@ -1223,8 +1223,8 @@ reweight.method = "obs") summary(f.w.man.irls)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Thu Feb 21 15:12:28 2019 -#> Date of summary: Thu Feb 21 15:12:28 2019 +#> Date of fit: Thu Feb 21 16:12:35 2019 +#> Date of summary: Thu Feb 21 16:12:35 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1232,7 +1232,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 692 model solutions performed in 3.31 s +#> Fitted with method Port using 692 model solutions performed in 3.309 s #> #> Weighting: manual #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index e4509e8a..79eb89d3 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -231,7 +231,7 @@ 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 file6490632228a0.c 2> file6490632228a0.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB file23f474fcf31d.c 2> file23f474fcf31d.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index deb1335a..02b809a0 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -325,7 +325,7 @@ 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 -#> 0.004 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 diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index af52e38a..71c347fd 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -191,8 +191,8 @@ time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE)) time_default
#> User System verstrichen -#> 0.036 0.050 7.160
time_1
#> User System verstrichen -#> 22.888 0.000 22.902
+#> 0.051 0.032 7.366
time_1
#> User System verstrichen +#> 23.290 0.000 23.305
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 80298bb4..3b55635c 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -208,15 +208,15 @@

Examples

  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 15:13:20 2019 
-#> Date of summary: Thu Feb 21 15:13:20 2019 
+#> Date of fit:     Thu Feb 21 16:13:27 2019 
+#> Date of summary: Thu Feb 21 16:13:27 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 35 model solutions performed in 0.087 s
+#> Fitted with method Port using 35 model solutions performed in 0.086 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 088ea9d0..d15b0213 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -202,8 +202,8 @@ 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:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 15:13:29 2019 
-#> Date of summary: Thu Feb 21 15:13:29 2019 
+#> Date of fit:     Thu Feb 21 16:13:35 2019 
+#> Date of summary: Thu Feb 21 16:13:35 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -211,7 +211,7 @@ 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 0.84 s
+#> Fitted with method Port using 153 model solutions performed in 0.782 s
 #> 
 #> Weighting: none
 #> 
@@ -278,8 +278,8 @@ 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:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 15:13:30 2019 
-#> Date of summary: Thu Feb 21 15:13:30 2019 
+#> Date of fit:     Thu Feb 21 16:13:37 2019 
+#> Date of summary: Thu Feb 21 16:13:37 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -287,7 +287,7 @@ 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 1.631 s
+#> Fitted with method Port using 350 model solutions performed in 1.579 s
 #> 
 #> Weighting: none
 #> 
@@ -366,8 +366,8 @@ 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:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 15:13:32 2019 
-#> Date of summary: Thu Feb 21 15:13:32 2019 
+#> Date of fit:     Thu Feb 21 16:13:38 2019 
+#> Date of summary: Thu Feb 21 16:13:38 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -375,7 +375,7 @@ 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 0.852 s
+#> Fitted with method Port using 186 model solutions performed in 0.859 s
 #> 
 #> Weighting: none
 #> 
@@ -450,8 +450,8 @@ 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:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 15:13:32 2019 
-#> Date of summary: Thu Feb 21 15:13:32 2019 
+#> Date of fit:     Thu Feb 21 16:13:39 2019 
+#> Date of summary: Thu Feb 21 16:13:39 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -459,7 +459,7 @@ 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 0.473 s
+#> Fitted with method Port using 104 model solutions performed in 0.47 s
 #> 
 #> Weighting: none
 #> 
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