From d185c26e4909efbae9dc4210ed9eac4b2600910e Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sun, 11 Mar 2018 22:12:51 +0100 Subject: Static docs rebuilt again, with current pkgdown --- docs/reference/DFOP.solution.html | 6 ++++++ docs/reference/Extract.mmkin.html | 17 +++++++++++------ docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 9 +++++++++ docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 9 +++++++++ docs/reference/FOCUS_2006_HS_ref_A_to_F.html | 9 +++++++++ docs/reference/FOCUS_2006_SFO_ref_A_to_F.html | 9 +++++++++ docs/reference/FOCUS_2006_datasets.html | 5 +++++ docs/reference/FOMC.solution.html | 9 +++++++++ docs/reference/HS.solution.html | 6 ++++++ docs/reference/IORE.solution.html | 6 ++++++ docs/reference/SFO.solution.html | 5 +++++ docs/reference/SFORB.solution.html | 9 +++++++++ docs/reference/add_err.html | 7 +++++++ docs/reference/endpoints.html | 8 ++++++++ docs/reference/geometric_mean.html | 5 +++++ docs/reference/ilr.html | 5 +++++ docs/reference/index.html | 2 ++ docs/reference/max_twa_parent.html | 9 +++++++++ docs/reference/mccall81_245T.html | 13 ++++++++++--- docs/reference/mkin_long_to_wide.html | 7 +++++++ docs/reference/mkin_wide_to_long.html | 6 ++++++ docs/reference/mkinds.html | 5 +++++ docs/reference/mkinerrmin.html | 6 ++++++ docs/reference/mkinfit.html | 23 +++++++++++++++++++---- docs/reference/mkinmod.html | 10 ++++++++++ docs/reference/mkinparplot.html | 6 ++++++ docs/reference/mkinplot.html | 5 +++++ docs/reference/mkinpredict.html | 13 ++++++++++--- docs/reference/mkinresplot.html | 8 ++++++++ docs/reference/mkinsub.html | 6 ++++++ docs/reference/mmkin.html | 6 ++++++ docs/reference/plot.mkinfit.html | 10 ++++++++++ docs/reference/plot.mmkin.html | 9 +++++++++ docs/reference/print.mkinds.html | 5 +++++ docs/reference/print.mkinmod.html | 5 +++++ docs/reference/schaefer07_complex_case.html | 7 +++++++ docs/reference/sigma_rl.html | 7 +++++++ docs/reference/summary.mkinfit.html | 14 +++++++++++--- docs/reference/synthetic_data_for_UBA.html | 17 +++++++++++++++++ docs/reference/test_data_from_UBA_2014.html | 6 ++++++ docs/reference/transform_odeparms.html | 19 ++++++++++++++++--- 41 files changed, 326 insertions(+), 22 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index f89a66e2..b1b3cf50 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -27,6 +27,11 @@ + + + + @@ -182,3 +187,4 @@ + diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 3b96f9ae..e554432f 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -27,6 +27,10 @@ + + + + @@ -259,7 +263,7 @@ #> #> $time #> user system elapsed -#> 0.06 0.00 0.06 +#> 0.234 0.000 0.234 #> #> $mkinmod #> <mkinmod> model generated with @@ -448,8 +452,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x5555599fd348> -#> <environment: 0x555557684190> +#> <bytecode: 0x5555578e66e0> +#> <environment: 0x555559cd9780> #> #> $cost_notrans #> function (P) @@ -471,8 +475,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x555559feb960> -#> <environment: 0x555557684190> +#> <bytecode: 0x55555acf3f50> +#> <environment: 0x555559cd9780> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -539,7 +543,7 @@ #> 99.17407 #> #> $date -#> [1] "Fri Mar 9 23:08:11 2018" +#> [1] "Sun Mar 11 22:10:21 2018" #> #> $version #> [1] "0.9.47.1" @@ -582,3 +586,4 @@ + diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html index ed5f29b3..f392bf64 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -27,6 +27,14 @@ + + + + @@ -167,3 +175,4 @@ in this fit.

+ diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html index e3e0d238..6e4c8d64 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -27,6 +27,14 @@ + + + + @@ -166,3 +174,4 @@ in this fit.

+ diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html index be785b0b..ed38ccae 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -27,6 +27,14 @@ + + + + @@ -167,3 +175,4 @@ in this fit.

+ diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html index 6ca8e78e..107f3e5f 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -27,6 +27,14 @@ + + + + @@ -165,3 +173,4 @@ in this fit.

+ diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 9ea69f23..cc310ee3 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -27,6 +27,10 @@ + + + + @@ -167,3 +171,4 @@ + diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index b5b4c87c..397dc82d 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -27,6 +27,14 @@ + + + + @@ -193,3 +201,4 @@ + diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 0dc432ef..f633aa67 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -27,6 +27,11 @@ + + + + @@ -183,3 +188,4 @@ + diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index b055534a..687dee5a 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -27,6 +27,11 @@ + + + + @@ -197,3 +202,4 @@ + diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index eda43e4d..1156c16f 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -27,6 +27,10 @@ + + + + @@ -174,3 +178,4 @@ + diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 2b6b2bc6..6901c435 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -27,6 +27,14 @@ + + + + @@ -187,3 +195,4 @@ + diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 407e1a3e..6d830113 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -27,6 +27,12 @@ + + + + @@ -241,3 +247,4 @@ + diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 4ab395cb..0f5ba0a4 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -27,6 +27,13 @@ + + + + @@ -177,3 +184,4 @@ with the advantage that the SFORB model can also be used for metabolites.

+ diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 7e27c1dc..9d91b5a8 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -27,6 +27,10 @@ + + + + @@ -158,3 +162,4 @@ + diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 7ed15db5..33d749ce 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -27,6 +27,10 @@ + + + + @@ -182,3 +186,4 @@ + diff --git a/docs/reference/index.html b/docs/reference/index.html index 157eaad3..6c05941d 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -27,6 +27,7 @@ + @@ -453,3 +454,4 @@ + diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 9e1e3974..696ca729 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -27,6 +27,14 @@ + + + + @@ -178,3 +186,4 @@ guidance.

+ diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 30aa894e..80cac442 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -27,6 +27,12 @@ + + + + @@ -145,8 +151,8 @@ fixed_parms = "k_phenol_sink", quiet = TRUE) summary(fit.2, data = FALSE)
#> mkin version used for fitting: 0.9.47.1 #> R version used for fitting: 3.4.3 -#> Date of fit: Fri Mar 9 23:08:18 2018 -#> Date of summary: Fri Mar 9 23:08:18 2018 +#> Date of fit: Sun Mar 11 22:10:30 2018 +#> Date of summary: Sun Mar 11 22:10:30 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -156,7 +162,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.359 s +#> Fitted with method Port using 246 model solutions performed in 1.318 s #> #> Weighting: none #> @@ -266,3 +272,4 @@ + diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index dc781aaf..3c498a76 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -27,6 +27,12 @@ + + + + @@ -192,3 +198,4 @@ + diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 2a8d20a3..f40cb7cf 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -27,6 +27,11 @@ + + + + @@ -171,3 +176,4 @@ + diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index fd707cfd..7f5ec78e 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -27,6 +27,10 @@ + + + + @@ -160,3 +164,4 @@ in order to be compatible with mkinfit

+ diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 045e5805..f172cba1 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -27,6 +27,11 @@ + + + + @@ -195,3 +200,4 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.

+ diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 10052053..991df1cc 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -27,6 +27,20 @@ + + + + @@ -400,15 +414,15 @@ fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)
#> mkin version used for fitting: 0.9.47.1 #> R version used for fitting: 3.4.3 -#> Date of fit: Fri Mar 9 23:08:20 2018 -#> Date of summary: Fri Mar 9 23:08:20 2018 +#> Date of fit: Sun Mar 11 22:10:32 2018 +#> Date of summary: Sun Mar 11 22:10:32 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 0.148 s +#> Fitted with method Port using 64 model solutions performed in 0.135 s #> #> Weighting: none #> @@ -477,7 +491,7 @@ 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 elapsed -#> 0.839 0.000 0.840
coef(fit)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.829 0.000 0.829
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 @@ -585,3 +599,4 @@ + diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 032fcbb6..7d3c0f94 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -27,6 +27,15 @@ + + + + @@ -255,3 +264,4 @@ + diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index e416d67c..81f52fc3 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -27,6 +27,11 @@ + + + + @@ -163,3 +168,4 @@ + diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index e1ee1607..cfd72521 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -27,6 +27,10 @@ + + + + @@ -158,3 +162,4 @@ + diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index 7354c496..044b2d92 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -27,6 +27,12 @@ + + + + @@ -300,17 +306,17 @@ 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 elapsed -#> 0.003 0.000 0.003
system.time( +#> 0.002 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 elapsed -#> 0.002 0.000 0.002
system.time( +#> 0.002 0.000 0.001
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 elapsed -#> 0.031 0.000 0.031
+#> 0.029 0.000 0.029