From d106bebafe070cb803dd7205b1581b20eaf61cb5 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 6 Oct 2016 10:47:45 +0200 Subject: Static documentation rebuilt by pkgdown::build_site() --- GNUmakefile | 2 +- docs/reference/Extract.mmkin.html | 24 ++++++++++++------------ docs/reference/mccall81_245T.html | 6 +++--- docs/reference/mkinfit.html | 8 ++++---- docs/reference/mkinpredict.html | 6 +++--- docs/reference/summary.mkinfit.html | 6 +++--- docs/reference/transform_odeparms.html | 6 +++--- 7 files changed, 29 insertions(+), 29 deletions(-) diff --git a/GNUmakefile b/GNUmakefile index 7cddc15d..3cb2e40f 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -92,7 +92,7 @@ sd: git commit -m 'Static documentation rebuilt by staticdocs::build_site()' -e pd: - "$(RBIN)/Rscript" -e "pkgdown::build_site()" + "$(RBIN)/Rscript" -e "pkgdown::build_site(articles = FALSE)" git add -A git commit -m 'Static documentation rebuilt by pkgdown::build_site()' -e diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 1802e260..b513fac1 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -192,7 +192,7 @@ #> #> $time #> user system elapsed -#> 0.256 0.000 0.256 +#> 0.252 0.000 0.253 #> #> $mkinmod #> <mkinmod> model generated with @@ -378,7 +378,7 @@ #> } #> return(mC) #> } -#> <environment: 0x435ac28> +#> <environment: 0x3e9c368> #> #> $cost_notrans #> function (P) @@ -400,7 +400,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x435ac28> +#> <environment: 0x3e9c368> #> #> $hessian_notrans #> parent_0 alpha beta @@ -466,7 +466,7 @@ #> 99.66619 #> #> $date -#> [1] "Thu Oct 6 09:39:06 2016" +#> [1] "Thu Oct 6 10:47:28 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" @@ -547,7 +547,7 @@ #> #> $time #> user system elapsed -#> 0.068 0.000 0.068 +#> 0.064 0.000 0.067 #> #> $mkinmod #> <mkinmod> model generated with @@ -734,7 +734,7 @@ #> } #> return(mC) #> } -#> <environment: 0x4da08d0> +#> <environment: 0x3c1a660> #> #> $cost_notrans #> function (P) @@ -756,7 +756,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x4da08d0> +#> <environment: 0x3c1a660> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -819,7 +819,7 @@ #> 99.17407 #> #> $date -#> [1] "Thu Oct 6 09:39:06 2016" +#> [1] "Thu Oct 6 10:47:28 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" @@ -896,7 +896,7 @@ #> #> $time #> user system elapsed -#> 0.068 0.000 0.068 +#> 0.064 0.000 0.067 #> #> $mkinmod #> <mkinmod> model generated with @@ -1083,7 +1083,7 @@ #> } #> return(mC) #> } -#> <environment: 0x4da08d0> +#> <environment: 0x3c1a660> #> #> $cost_notrans #> function (P) @@ -1105,7 +1105,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x4da08d0> +#> <environment: 0x3c1a660> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -1168,7 +1168,7 @@ #> 99.17407 #> #> $date -#> [1] "Thu Oct 6 09:39:06 2016" +#> [1] "Thu Oct 6 10:47:28 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit" diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 17e900a4..63635f9a 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -122,8 +122,8 @@ fixed_parms = "k_phenol_sink", quiet = TRUE) summary(fit.2, data = FALSE)
#> mkin version: 0.9.44.9000 #> R version: 3.3.1 -#> Date of fit: Thu Oct 6 09:39:12 2016 -#> Date of summary: Thu Oct 6 09:39:12 2016 +#> Date of fit: Thu Oct 6 10:47:34 2016 +#> Date of summary: Thu Oct 6 10:47:34 2016 #> #> Equations: #> d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -133,7 +133,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.544 s +#> Fitted with method Port using 246 model solutions performed in 1.492 s #> #> Weighting: none #> diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 14c1b364..7acbbe5a 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -363,15 +363,15 @@ fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)
#> mkin version: 0.9.44.9000 #> R version: 3.3.1 -#> Date of fit: Thu Oct 6 09:39:14 2016 -#> Date of summary: Thu Oct 6 09:39:14 2016 +#> Date of fit: Thu Oct 6 10:47:36 2016 +#> Date of summary: Thu Oct 6 10:47:36 2016 #> #> Equations: #> d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted with method Port using 64 model solutions performed in 0.16 s +#> Fitted with method Port using 64 model solutions performed in 0.152 s #> #> Weighting: none #> @@ -441,7 +441,7 @@ 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 -#> 1.204 1.224 0.917 +#> 1.240 1.280 0.973 #>
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 diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index b0899a3e..5b7cdb32 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -284,21 +284,21 @@ solution_type = "eigen")[201,]))
#> time parent m1 #> 201 20 4.978707 27.46227 #>
#> user system elapsed -#> 0.008 0.024 0.004 +#> 0.008 0.020 0.004 #>
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 -#> 0.016 0.004 0.002 +#> 0.016 0.004 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", use_compiled = FALSE)[201,]))
#> time parent m1 #> 201 20 4.978707 27.46227 #>
#> user system elapsed -#> 0.032 0.000 0.033 +#> 0.032 0.000 0.034 #>
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 001852a5..acbf36dc 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -142,15 +142,15 @@

Examples

  summary(mkinfit(mkinmod(parent = list(type = "SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version:    0.9.44.9000 
 #> R version:       3.3.1 
-#> Date of fit:     Thu Oct  6 09:39:22 2016 
-#> Date of summary: Thu Oct  6 09:39:22 2016 
+#> Date of fit:     Thu Oct  6 10:47:44 2016 
+#> Date of summary: Thu Oct  6 10:47:44 2016 
 #> 
 #> Equations:
 #> d_parent = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 35 model solutions performed in 0.078 s
+#> Fitted with method Port using 35 model solutions performed in 0.079 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 2b736098..66253bba 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -147,8 +147,8 @@
 fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
 summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version:    0.9.44.9000 
 #> R version:       3.3.1 
-#> Date of fit:     Thu Oct  6 09:39:23 2016 
-#> Date of summary: Thu Oct  6 09:39:23 2016 
+#> Date of fit:     Thu Oct  6 10:47:45 2016 
+#> Date of summary: Thu Oct  6 10:47:45 2016 
 #> 
 #> Equations:
 #> d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -156,7 +156,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 153 model solutions performed in 0.63 s
+#> Fitted with method Port using 153 model solutions performed in 0.638 s
 #> 
 #> Weighting: none
 #> 
-- 
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