From d852e9e000f57f280deb84611ae1af58daa883cc Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 18 Nov 2016 23:08:45 +0100 Subject: Fix links in README, configure navbar, rebuild docs --- docs/articles/FOCUS_D.R | 20 +++++++++ docs/articles/FOCUS_D.html | 2 +- docs/articles/FOCUS_L.html | 44 +++++++++---------- docs/articles/FOCUS_Z.pdf | Bin 239558 -> 239561 bytes docs/articles/compiled_models.html | 32 +++++++------- .../figure-html/benchmark_FOMC_SFO-1.png | Bin 9843 -> 9618 bytes .../figure-html/benchmark_SFO_SFO-1.png | Bin 11615 -> 10679 bytes docs/articles/index.html | 2 +- docs/articles/mkin.html | 2 +- docs/authors.html | 2 +- docs/index.html | 10 ++--- docs/news/index.html | 2 +- docs/reference/DFOP.solution.html | 2 +- docs/reference/Extract.mmkin.html | 10 ++--- docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 2 +- docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 2 +- docs/reference/FOCUS_2006_HS_ref_A_to_F.html | 2 +- docs/reference/FOCUS_2006_SFO_ref_A_to_F.html | 2 +- docs/reference/FOCUS_2006_datasets.html | 2 +- docs/reference/FOMC.solution.html | 2 +- docs/reference/HS.solution.html | 2 +- docs/reference/IORE.solution.html | 2 +- docs/reference/SFO.solution.html | 2 +- docs/reference/SFORB.solution.html | 2 +- docs/reference/add_err.html | 2 +- docs/reference/endpoints.html | 2 +- docs/reference/geometric_mean.html | 2 +- docs/reference/ilr.html | 2 +- docs/reference/index.html | 2 +- docs/reference/mccall81_245T.html | 14 +++--- docs/reference/mkin_long_to_wide.html | 2 +- docs/reference/mkin_wide_to_long.html | 2 +- docs/reference/mkinds.html | 2 +- docs/reference/mkinerrmin.html | 2 +- docs/reference/mkinfit.html | 48 ++++++++++----------- docs/reference/mkinmod.html | 4 +- docs/reference/mkinparplot.html | 2 +- docs/reference/mkinplot.html | 2 +- docs/reference/mkinpredict.html | 8 ++-- docs/reference/mkinresplot.html | 2 +- docs/reference/mkinsub.html | 2 +- docs/reference/mmkin.html | 6 +-- docs/reference/plot.mkinfit.html | 2 +- docs/reference/plot.mmkin.html | 2 +- docs/reference/print.mkinds.html | 2 +- docs/reference/print.mkinmod.html | 2 +- docs/reference/schaefer07_complex_case.html | 2 +- docs/reference/summary.mkinfit.html | 8 ++-- docs/reference/synthetic_data_for_UBA.html | 8 ++-- docs/reference/transform_odeparms.html | 26 +++++------ 50 files changed, 163 insertions(+), 143 deletions(-) (limited to 'docs') diff --git a/docs/articles/FOCUS_D.R b/docs/articles/FOCUS_D.R index 9eaf41f7..51723496 100644 --- a/docs/articles/FOCUS_D.R +++ b/docs/articles/FOCUS_D.R @@ -2,3 +2,23 @@ library(knitr) opts_chunk$set(tidy = FALSE, cache = TRUE) +## ----data---------------------------------------------------------------- +library("mkin") +print(FOCUS_2006_D) + +## ----model--------------------------------------------------------------- +SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")) +print(SFO_SFO$diffs) + +## ----fit----------------------------------------------------------------- +fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE) + +## ----plot, fig.height = 6, fig.width = 8--------------------------------- +plot_sep(fit, lpos = c("topright", "bottomright")) + +## ----plot_2, fig.height = 4, fig.width = 8------------------------------- +mkinparplot(fit) + +## ------------------------------------------------------------------------ +summary(fit) + diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index ad53126e..782a789d 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -16,7 +16,7 @@ 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov 18 16:48:11 2016 
-## Date of summary: Fri Nov 18 16:48:11 2016 
+## Date of fit:     Fri Nov 18 22:54:43 2016 
+## Date of summary: Fri Nov 18 22:54:43 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.085 s
+## Fitted with method Port using 37 model solutions performed in 0.09 s
 ## 
 ## Weighting: none
 ## 
@@ -169,8 +169,8 @@ FOCUS_2006_L1_mkin <- 
summary(m.L1.FOMC, data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov 18 16:48:12 2016 
-## Date of summary: Fri Nov 18 16:48:12 2016 
+## Date of fit:     Fri Nov 18 22:54:44 2016 
+## Date of summary: Fri Nov 18 22:54:44 2016 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -182,7 +182,7 @@ FOCUS_2006_L1_mkin <-  
summary(m.L2.FOMC, data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov 18 16:48:13 2016 
-## Date of summary: Fri Nov 18 16:48:13 2016 
+## Date of fit:     Fri Nov 18 22:54:44 2016 
+## Date of summary: Fri Nov 18 22:54:44 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.196 s
+## Fitted with method Port using 81 model solutions performed in 0.184 s
 ## 
 ## Weighting: none
 ## 
@@ -336,8 +336,8 @@ FOCUS_2006_L2_mkin <- 
summary(m.L2.DFOP, data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov 18 16:48:14 2016 
-## Date of summary: Fri Nov 18 16:48:14 2016 
+## Date of fit:     Fri Nov 18 22:54:45 2016 
+## Date of summary: Fri Nov 18 22:54:46 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -346,7 +346,7 @@ FOCUS_2006_L2_mkin <-  
summary(mm.L3[["DFOP", 1]])

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov 18 16:48:15 2016 
-## Date of summary: Fri Nov 18 16:48:15 2016 
+## Date of fit:     Fri Nov 18 22:54:47 2016 
+## Date of summary: Fri Nov 18 22:54:47 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -435,7 +435,7 @@ mm.L3 <-  
summary(mm.L4[["SFO", 1]], data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov 18 16:48:15 2016 
-## Date of summary: Fri Nov 18 16:48:16 2016 
+## Date of fit:     Fri Nov 18 22:54:47 2016 
+## Date of summary: Fri Nov 18 22:54:48 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.107 s
+## Fitted with method Port using 46 model solutions performed in 0.108 s
 ## 
 ## Weighting: none
 ## 
@@ -585,15 +585,15 @@ mm.L4 <- 
summary(mm.L4[["FOMC", 1]], data = FALSE)

 
## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov 18 16:48:16 2016 
-## Date of summary: Fri Nov 18 16:48:16 2016 
+## Date of fit:     Fri Nov 18 22:54:47 2016 
+## Date of summary: Fri Nov 18 22:54:48 2016 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.15 s
+## Fitted with method Port using 66 model solutions performed in 0.145 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_Z.pdf b/docs/articles/FOCUS_Z.pdf
index 6f8929ea..d8bfd68c 100644
Binary files a/docs/articles/FOCUS_Z.pdf and b/docs/articles/FOCUS_Z.pdf differ
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index 31340867..87913685 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -16,7 +16,7 @@