From 1511ed0a775e15ec2158e22d08a4da00cdd834aa Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 16 Nov 2017 17:13:35 +0100 Subject: Use html_vignette for FOCUS_D vignette, fix address Static documentation articles rebuilt by pkgdown::build_articles() --- docs/articles/FOCUS_D.html | 11 +-- docs/articles/FOCUS_D_files/figure-html/plot-1.png | Bin 98934 -> 39955 bytes .../FOCUS_D_files/figure-html/plot_2-1.png | Bin 14308 -> 6454 bytes docs/articles/FOCUS_L.html | 79 ++++++++++----------- docs/articles/FOCUS_Z.R | 33 +++++---- docs/articles/FOCUS_Z.html | 13 +--- docs/articles/compiled_models.html | 36 ++++------ docs/articles/index.html | 9 +-- docs/articles/mkin.html | 15 ++-- docs/articles/twa.html | 11 +-- 10 files changed, 77 insertions(+), 130 deletions(-) (limited to 'docs') diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 6607d614..d6941019 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -62,14 +62,7 @@ News - + @@ -84,7 +77,7 @@

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

2017-09-14

+

2017-11-16

diff --git a/docs/articles/FOCUS_D_files/figure-html/plot-1.png b/docs/articles/FOCUS_D_files/figure-html/plot-1.png index c0fab72d..75c4c299 100644 Binary files a/docs/articles/FOCUS_D_files/figure-html/plot-1.png and b/docs/articles/FOCUS_D_files/figure-html/plot-1.png differ diff --git a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png index 47916477..94e7e2b3 100644 Binary files a/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png and b/docs/articles/FOCUS_D_files/figure-html/plot_2-1.png differ diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index b89c7b20..7cef7abd 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -62,14 +62,7 @@ News - + @@ -84,7 +77,7 @@

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

-

2017-09-14

+

2017-11-16

@@ -105,17 +98,17 @@ FOCUS_2006_L1_mkin <- for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.

m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet = TRUE)
 summary(m.L1.SFO)
-
## mkin version:    0.9.46.1 
-## R version:       3.4.1 
-## Date of fit:     Thu Sep 14 12:15:03 2017 
-## Date of summary: Thu Sep 14 12:15:03 2017 
+
## mkin version:    0.9.46.2 
+## R version:       3.4.2 
+## Date of fit:     Thu Nov 16 17:12:46 2017 
+## Date of summary: Thu Nov 16 17:12:46 2017 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.255 s
+## Fitted with method Port using 37 model solutions performed in 0.253 s
 ## 
 ## Weighting: none
 ## 
@@ -198,10 +191,10 @@ FOCUS_2006_L1_mkin <- 
plot(m.L1.FOMC, show_errmin = TRUE, main = "FOCUS L1 - FOMC")

 

 
summary(m.L1.FOMC, data = FALSE)

-
## mkin version:    0.9.46.1 
-## R version:       3.4.1 
-## Date of fit:     Thu Sep 14 12:15:05 2017 
-## Date of summary: Thu Sep 14 12:15:05 2017 
+
## mkin version:    0.9.46.2 
+## R version:       3.4.2 
+## Date of fit:     Thu Nov 16 17:12:47 2017 
+## Date of summary: Thu Nov 16 17:12:47 2017 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -213,7 +206,7 @@ FOCUS_2006_L1_mkin <-  main = "FOCUS L2 - FOMC")

 

 
summary(m.L2.FOMC, data = FALSE)

-
## mkin version:    0.9.46.1 
-## R version:       3.4.1 
-## Date of fit:     Thu Sep 14 12:15:06 2017 
-## Date of summary: Thu Sep 14 12:15:06 2017 
+
## mkin version:    0.9.46.2 
+## R version:       3.4.2 
+## Date of fit:     Thu Nov 16 17:12:48 2017 
+## Date of summary: Thu Nov 16 17:12:48 2017 
 ## 
 ## 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 0.176 s
+## Fitted with method Port using 81 model solutions performed in 0.183 s
 ## 
 ## Weighting: none
 ## 
@@ -369,10 +362,10 @@ FOCUS_2006_L2_mkin <- main = "FOCUS L2 - DFOP")

 

 
summary(m.L2.DFOP, data = FALSE)

-
## mkin version:    0.9.46.1 
-## R version:       3.4.1 
-## Date of fit:     Thu Sep 14 12:15:07 2017 
-## Date of summary: Thu Sep 14 12:15:07 2017 
+
## mkin version:    0.9.46.2 
+## R version:       3.4.2 
+## Date of fit:     Thu Nov 16 17:12:49 2017 
+## Date of summary: Thu Nov 16 17:12:49 2017 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -381,7 +374,7 @@ FOCUS_2006_L2_mkin <-  
summary(mm.L3[["DFOP", 1]])

-
## mkin version:    0.9.46.1 
-## R version:       3.4.1 
-## Date of fit:     Thu Sep 14 12:15:08 2017 
-## Date of summary: Thu Sep 14 12:15:08 2017 
+
## mkin version:    0.9.46.2 
+## R version:       3.4.2 
+## Date of fit:     Thu Nov 16 17:12:50 2017 
+## Date of summary: Thu Nov 16 17:12:50 2017 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -473,7 +466,7 @@ mm.L3 <-  

 
The \(\chi^2\) error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the \(\chi^2\) test passes is slightly lower for the FOMC model. However, the difference appears negligible.

 
summary(mm.L4[["SFO", 1]], data = FALSE)

-
## mkin version:    0.9.46.1 
-## R version:       3.4.1 
-## Date of fit:     Thu Sep 14 12:15:08 2017 
-## Date of summary: Thu Sep 14 12:15:09 2017 
+
## mkin version:    0.9.46.2 
+## R version:       3.4.2 
+## Date of fit:     Thu Nov 16 17:12:50 2017 
+## Date of summary: Thu Nov 16 17:12:51 2017 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
@@ -622,17 +615,17 @@ mm.L4 <- 
summary(mm.L4[["FOMC", 1]], data = FALSE)

-
## mkin version:    0.9.46.1 
-## R version:       3.4.1 
-## Date of fit:     Thu Sep 14 12:15:08 2017 
-## Date of summary: Thu Sep 14 12:15:09 2017 
+
## mkin version:    0.9.46.2 
+## R version:       3.4.2 
+## Date of fit:     Thu Nov 16 17:12:51 2017 
+## Date of summary: Thu Nov 16 17:12:51 2017 
 ## 
 ## 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 0.151 s
+## Fitted with method Port using 66 model solutions performed in 0.136 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_Z.R b/docs/articles/FOCUS_Z.R
index 5c70b57e..a77441cf 100644
--- a/docs/articles/FOCUS_Z.R
+++ b/docs/articles/FOCUS_Z.R
@@ -1,10 +1,9 @@
-## ----include=FALSE--------------------------------------------------
+## ---- include = FALSE----------------------------------------------------
 require(knitr)
-opts_chunk$set(engine='R', tidy = FALSE, cache = TRUE)
-options(width=70)
+opts_chunk$set(engine='R', tidy = FALSE)
 
-## ----FOCUS_2006_Z_data, echo=TRUE, eval=TRUE------------------------
-require(mkin)
+## ---- echo = TRUE, fig = TRUE, fig.width = 8, fig.height = 7-------------
+library(mkin, quiet = TRUE)
 LOD = 0.5
 FOCUS_2006_Z = data.frame(
   t = c(0, 0.04, 0.125, 0.29, 0.54, 1, 2, 3, 4, 7, 10, 14, 21,
@@ -20,14 +19,14 @@ FOCUS_2006_Z = data.frame(
 
 FOCUS_2006_Z_mkin <- mkin_wide_to_long(FOCUS_2006_Z)
 
-## ----FOCUS_2006_Z_fits_1, echo=TRUE, fig.height=6-------------------
+## ----FOCUS_2006_Z_fits_1, echo=TRUE, fig.height=6------------------------
 Z.2a <- mkinmod(Z0 = mkinsub("SFO", "Z1"),
                 Z1 = mkinsub("SFO"))
 m.Z.2a <- mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE)
 plot_sep(m.Z.2a)
 summary(m.Z.2a, data = FALSE)$bpar
 
-## ----FOCUS_2006_Z_fits_2, echo=TRUE, fig.height=6-------------------
+## ----FOCUS_2006_Z_fits_2, echo=TRUE, fig.height=6------------------------
 Z.2a.ff <- mkinmod(Z0 = mkinsub("SFO", "Z1"),
                    Z1 = mkinsub("SFO"),
                    use_of_ff = "max")
@@ -36,21 +35,21 @@ m.Z.2a.ff <- mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE)
 plot_sep(m.Z.2a.ff)
 summary(m.Z.2a.ff, data = FALSE)$bpar
 
-## ----FOCUS_2006_Z_fits_3, echo=TRUE, fig.height=6-------------------
+## ----FOCUS_2006_Z_fits_3, echo=TRUE, fig.height=6------------------------
 Z.3 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
                Z1 = mkinsub("SFO"), use_of_ff = "max")
 m.Z.3 <- mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE)
 plot_sep(m.Z.3)
 summary(m.Z.3, data = FALSE)$bpar
 
-## ----FOCUS_2006_Z_fits_5, echo=TRUE, fig.height=7-------------------
+## ----FOCUS_2006_Z_fits_5, echo=TRUE, fig.height=7------------------------
 Z.5 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
                Z1 = mkinsub("SFO", "Z2", sink = FALSE),
                Z2 = mkinsub("SFO"), use_of_ff = "max")
 m.Z.5 <- mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE)
 plot_sep(m.Z.5)
 
-## ----FOCUS_2006_Z_fits_6, echo=TRUE, fig.height=8-------------------
+## ----FOCUS_2006_Z_fits_6, echo=TRUE, fig.height=8------------------------
 Z.FOCUS <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
                    Z1 = mkinsub("SFO", "Z2", sink = FALSE),
                    Z2 = mkinsub("SFO", "Z3"),
@@ -63,7 +62,7 @@ plot_sep(m.Z.FOCUS)
 summary(m.Z.FOCUS, data = FALSE)$bpar
 endpoints(m.Z.FOCUS)
 
-## ----FOCUS_2006_Z_fits_7, echo=TRUE, fig.height=8-------------------
+## ----FOCUS_2006_Z_fits_7, echo=TRUE, fig.height=8------------------------
 Z.mkin.1 <- mkinmod(Z0 = mkinsub("SFO", "Z1", sink = FALSE),
                     Z1 = mkinsub("SFO", "Z2", sink = FALSE),
                     Z2 = mkinsub("SFO", "Z3"),
@@ -72,14 +71,14 @@ m.Z.mkin.1 <- mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE)
 plot_sep(m.Z.mkin.1)
 summary(m.Z.mkin.1, data = FALSE)$cov.unscaled
 
-## ----FOCUS_2006_Z_fits_9, echo=TRUE, fig.height=8-------------------
+## ----FOCUS_2006_Z_fits_9, echo=TRUE, fig.height=8------------------------
 Z.mkin.3 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
                     Z1 = mkinsub("SFO", "Z2", sink = FALSE),
                     Z2 = mkinsub("SFO"))
 m.Z.mkin.3 <- mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE)
 plot_sep(m.Z.mkin.3)
 
-## ----FOCUS_2006_Z_fits_10, echo=TRUE, fig.height=8------------------
+## ----FOCUS_2006_Z_fits_10, echo=TRUE, fig.height=8-----------------------
 Z.mkin.4 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
                     Z1 = mkinsub("SFO", "Z2", sink = FALSE),
                     Z2 = mkinsub("SFO", "Z3"),
@@ -89,7 +88,7 @@ m.Z.mkin.4 <- mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin,
                       quiet = TRUE)
 plot_sep(m.Z.mkin.4)
 
-## ----FOCUS_2006_Z_fits_11, echo=TRUE, fig.height=8------------------
+## ----FOCUS_2006_Z_fits_11, echo=TRUE, fig.height=8-----------------------
 Z.mkin.5 <- mkinmod(Z0 = mkinsub("SFORB", "Z1", sink = FALSE),
                     Z1 = mkinsub("SFO", "Z2", sink = FALSE),
                     Z2 = mkinsub("SFO", "Z3"),
@@ -99,7 +98,7 @@ m.Z.mkin.5 <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin,
                       quiet = TRUE)
 plot_sep(m.Z.mkin.5)
 
-## ----FOCUS_2006_Z_fits_11a, echo=TRUE-------------------------------
+## ----FOCUS_2006_Z_fits_11a, echo=TRUE------------------------------------
 m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin,
                        parms.ini = c(m.Z.mkin.5$bparms.ode[1:7],
                                      k_Z3_bound_free = 0),
@@ -107,9 +106,9 @@ m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin,
                        quiet = TRUE)
 plot_sep(m.Z.mkin.5a)
 
-## ----FOCUS_2006_Z_fits_11b, echo=TRUE-------------------------------
+## ----FOCUS_2006_Z_fits_11b, echo=TRUE------------------------------------
 mkinparplot(m.Z.mkin.5a)
 
-## ----FOCUS_2006_Z_fits_11b_endpoints, echo=TRUE---------------------
+## ----FOCUS_2006_Z_fits_11b_endpoints, echo=TRUE--------------------------
 endpoints(m.Z.mkin.5a)
 
diff --git a/docs/articles/FOCUS_Z.html b/docs/articles/FOCUS_Z.html
index c3bb5180..d16299ca 100644
--- a/docs/articles/FOCUS_Z.html
+++ b/docs/articles/FOCUS_Z.html
@@ -62,14 +62,7 @@
   News
 
       
-
+
    
 
 
   
@@ -84,13 +77,13 @@
       
    Example evaluation of FOCUS dataset Z
    
                         
    Johannes Ranke
    
             
-            
    2017-09-14
    
+            
    2017-11-16
    
           
 
     
     
 
    
-
    Wissenschaftlicher Berater, Kronacher Str. 8, 79639 Grenzach-Wyhlen, Germany
    Privatdozent at the University of Bremen
    
+
    Wissenschaftlicher Berater, Kronacher Str. 12, 79639 Grenzach-Wyhlen, Germany
    Privatdozent at the University of Bremen
    
 
    
 
    
 The data
    
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index af47841b..68aa1bac 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -62,14 +62,7 @@
   News
 
       
-
+
      
 
      
 
   
      
@@ -84,7 +77,7 @@
       
      Performance benefit by using compiled model definitions in mkin
      
                         
      Johannes Ranke
      
             
-            
      2017-09-14
      
+            
      2017-11-16
      
           
 
     
@@ -98,13 +91,8 @@
 
      ##            gcc 
 ## "/usr/bin/gcc"
      
 
      First, we build a simple degradation model for a parent compound with one metabolite.
      
-
      library("mkin")
      
-
      ## Lade nötiges Paket: minpack.lm
      
-
      ## Lade nötiges Paket: rootSolve
      
-
      ## Lade nötiges Paket: inline
      
-
      ## Lade nötiges Paket: methods
      
-
      ## Lade nötiges Paket: parallel
      
-
      SFO_SFO <- mkinmod(
+
      library("mkin")
+SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"))
      
 
      ## Successfully compiled differential equation model from auto-generated C code.
      
@@ -127,9 +115,9 @@
 }
      
 
      ## Lade nötiges Paket: rbenchmark
      
 
      ##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   2.038    1.000     2.036        0
-## 1 deSolve, not compiled            3  14.822    7.273    14.824        0
-## 2      Eigenvalue based            3   2.543    1.248     2.544        0
+## 3     deSolve, compiled            3   2.029    1.000     2.028        0
+## 1 deSolve, not compiled            3  14.237    7.017    14.236        0
+## 2      Eigenvalue based            3   2.700    1.331     2.700        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -158,14 +146,14 @@
 }
      
 
      ## Successfully compiled differential equation model from auto-generated C code.
      
 
      ##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   3.488    1.000     3.488        0
-## 1 deSolve, not compiled            3  30.604    8.774    30.600        0
+## 2     deSolve, compiled            3   3.495    1.000     3.496        0
+## 1 deSolve, not compiled            3  29.264    8.373    29.260        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0
      
-
      Here we get a performance benefit of a factor of 9 using the version of the differential equation model compiled from C code!
      
-
      This vignette was built with mkin 0.9.46.1 on
      
-
      ## R version 3.4.1 (2017-06-30)
+
      Here we get a performance benefit of a factor of 8 using the version of the differential equation model compiled from C code!
      
+
      This vignette was built with mkin 0.9.46.2 on
      
+
      ## R version 3.4.2 (2017-09-28)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 9 (stretch)
      
 
      ## CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz
      
diff --git a/docs/articles/index.html b/docs/articles/index.html
index d02bfe80..0a355e17 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -86,12 +86,7 @@
       
       
       
     
   
@@ -101,7 +96,7 @@
       
 
       
      
-  
      Articles version 0.9.46.1
      
+  
      Articles version 0.9.46.3
      
 
      
 
 
      
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 92bd2bb4..14349e53 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -62,14 +62,7 @@
   News
 
       
-
+
        
 
        
 
   
@@ -84,13 +77,13 @@
       
        Introduction to mkin
        
                         
        Johannes Ranke
        
             
-            
        2017-09-14
        
+            
        2017-11-16
        
           
 
     
     
 
        
-
        Wissenschaftlicher Berater, Kronacher Str. 8, 79639 Grenzach-Wyhlen, Germany
        Privatdozent at the University of Bremen
        
+
        Wissenschaftlicher Berater, Kronacher Str. 12, 79639 Grenzach-Wyhlen, Germany
        Privatdozent at the University of Bremen
        
 
        
 
        
 Abstract
        
@@ -147,7 +140,7 @@ f_SFO_SFO_SFO <- documentation page and manual for further information.
        
+
        A further graphical user interface (GUI) that has recently been brought to a decent degree of maturity is the browser based GUI named gmkin. Please see its documentation page and manual for further information.
        
 
        
 
        
 
        
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 3a1d5731..0a4df0ff 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -62,14 +62,7 @@
   News
 
       
-
+
          
 
          
 
   
          
@@ -84,7 +77,7 @@
       
          Calculation of time weighted average concentrations with mkin
          
                         
          Johannes Ranke
          
             
-            
          2017-09-14
          
+            
          2017-11-16
          
           
 
     
-- 
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