From b4ac7f030fdb467ee995a7e12314d80633a72668 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 6 Sep 2018 11:53:38 +0200 Subject: Static documentation rebuilt by pkgdown --- docs/reference/Extract.mmkin.html | 12 ++++++------ docs/reference/mccall81_245T.html | 6 +++--- docs/reference/mkinfit.html | 19 ++++++++++--------- docs/reference/mkinpredict.html | 4 ++-- docs/reference/summary.mkinfit.html | 6 +++--- docs/reference/transform_odeparms.html | 6 +++--- 6 files changed, 27 insertions(+), 26 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 5bc23d98..982363a1 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -278,7 +278,7 @@ #> #> $time #> User System verstrichen -#> 0.167 0.000 0.168 +#> 0.183 0.000 0.184 #> #> $mkinmod #> <mkinmod> model generated with @@ -467,8 +467,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x55555bcec700> -#> <environment: 0x55555bc44168> +#> <bytecode: 0x55555bd7d1a0> +#> <environment: 0x55555bc8d4d8> #> #> $cost_notrans #> function (P) @@ -490,8 +490,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555c9d13a8> -#> <environment: 0x55555bc44168> +#> <bytecode: 0x55555ca81b68> +#> <environment: 0x55555bc8d4d8> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -558,7 +558,7 @@ #> 99.17407 #> #> $date -#> [1] "Wed Jul 18 15:15:52 2018" +#> [1] "Thu Sep 6 11:50:56 2018" #> #> $version #> [1] "0.9.47.2" diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index aacdec88..cdfc4b5d 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -166,8 +166,8 @@ fixed_parms = "k_phenol_sink", quiet = TRUE) summary(fit.2, data = FALSE)
#> mkin version used for fitting: 0.9.47.2 #> R version used for fitting: 3.5.1 -#> Date of fit: Wed Jul 18 15:16:02 2018 -#> Date of summary: Wed Jul 18 15:16:02 2018 +#> Date of fit: Thu Sep 6 11:51:05 2018 +#> Date of summary: Thu Sep 6 11:51:05 2018 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -177,7 +177,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.416 s +#> Fitted with method Port using 246 model solutions performed in 1.51 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 9e59c7e6..e99e7d9e 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -325,13 +325,13 @@ weight

only if err=NULL: how to weight the residuals, one of "none", - "std", "mean", see details of modCost, or "tc" for the - two component error model of Rocke and Lorenzato.

+ "std", "mean", see details of modCost, or "tc" for the + two component error model.

tc -

The two components of the Rocke and Lorenzato error model as used - for (initial) weighting

+

The two components of the error model as used for (initial) + weighting

scaleVar @@ -367,7 +367,8 @@ reweight.tol or up to the maximum number of iterations specified by reweight.max.iter. The second reweighting method is called "tc" (two-component error model). - When using this method, the two components an error model similar to + When using this method, the two components of an error model similar to + the one described by Rocke and Lorenzato (1995) are estimated from the fit and the resulting variances are used for weighting the residuals in each iteration until convergence of these components or up to the maximum number of iterations @@ -432,15 +433,15 @@ fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)
#> mkin version used for fitting: 0.9.47.2 #> R version used for fitting: 3.5.1 -#> Date of fit: Wed Jul 18 15:16:04 2018 -#> Date of summary: Wed Jul 18 15:16:04 2018 +#> Date of fit: Thu Sep 6 11:51:08 2018 +#> Date of summary: Thu Sep 6 11:51:08 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 0.134 s +#> Fitted with method Port using 64 model solutions performed in 0.142 s #> #> Weighting: none #> @@ -509,7 +510,7 @@ 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 -#> 0.863 0.000 0.864
coef(fit)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.895 0.000 0.898
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 diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index d5357ef6..5e2e5449 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -326,12 +326,12 @@ 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( +#> 0.002 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 verstrichen -#> 0.035 0.000 0.035
+#> 0.035 0.000 0.034