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  • News
    • - + @@ -110,8 +116,8 @@ 
    summary(fit)
    ## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Wed Nov  2 16:25:22 2016 
-## Date of summary: Wed Nov  2 16:25:22 2016 
+## Date of fit:     Fri Nov  4 16:56:20 2016 
+## Date of summary: Fri Nov  4 16:56:20 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -119,7 +125,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.665 s
+## Fitted with method Port using 153 model solutions performed in 0.661 s
 ## 
 ## Weighting: none
 ## 
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diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 6a9c6ba5..2244a359 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -24,7 +24,13 @@
 
  • 
   News
 
    • 
-      
      
+      
   
 
 
@@ -57,15 +63,15 @@ FOCUS_2006_L1_mkin <- summary(m.L1.SFO)
      ## mkin version:    0.9.44.9000 
 ## R version:       3.3.2 
-## Date of fit:     Fri Nov  4 15:38:03 2016 
-## Date of summary: Fri Nov  4 15:38:03 2016 
+## Date of fit:     Fri Nov  4 16:56:21 2016 
+## Date of summary: Fri Nov  4 16:56:21 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.089 s
+## Fitted with method Port using 37 model solutions performed in 0.087 s
 ## 
 ## Weighting: none
 ## 
@@ -150,8 +156,8 @@ 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  4 15:38:04 2016 
-## Date of summary: Fri Nov  4 15:38:04 2016 
+## Date of fit:     Fri Nov  4 16:56:21 2016 
+## Date of summary: Fri Nov  4 16:56:21 2016 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -163,7 +169,7 @@ 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  4 15:38:05 2016 
-## Date of summary: Fri Nov  4 15:38:05 2016 
+## Date of fit:     Fri Nov  4 16:56:22 2016 
+## Date of summary: Fri Nov  4 16:56:22 2016 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.19 s
+## Fitted with method Port using 81 model solutions performed in 0.199 s
 ## 
 ## Weighting: none
 ## 
@@ -317,8 +323,8 @@ 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  4 15:38:06 2016 
-## Date of summary: Fri Nov  4 15:38:06 2016 
+## Date of fit:     Fri Nov  4 16:56:23 2016 
+## Date of summary: Fri Nov  4 16:56:23 2016 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -327,7 +333,7 @@ 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  4 15:38:07 2016 
-## Date of summary: Fri Nov  4 15:38:07 2016 
+## Date of fit:     Fri Nov  4 16:56:24 2016 
+## Date of summary: Fri Nov  4 16:56:25 2016 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -416,7 +422,7 @@ 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  4 15:38:07 2016 
-## Date of summary: Fri Nov  4 15:38:08 2016 
+## Date of fit:     Fri Nov  4 16:56:25 2016 
+## Date of summary: Fri Nov  4 16:56:25 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.112 s
+## Fitted with method Port using 46 model solutions performed in 0.109 s
 ## 
 ## Weighting: none
 ## 
@@ -566,15 +572,15 @@ 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  4 15:38:08 2016 
-## Date of summary: Fri Nov  4 15:38:08 2016 
+## Date of fit:     Fri Nov  4 16:56:25 2016 
+## Date of summary: Fri Nov  4 16:56:25 2016 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.148 s
+## Fitted with method Port using 66 model solutions performed in 0.16 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_L_cache/html/__packages b/docs/articles/FOCUS_L_cache/html/__packages
deleted file mode 100644
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--- a/docs/articles/FOCUS_L_cache/html/__packages
+++ /dev/null
@@ -1,8 +0,0 @@
-base
-minpack.lm
-rootSolve
-inline
-mkin
-knitr
-microbenchmark
-ggplot2
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index 09039f62..e1572b17 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -24,7 +24,13 @@
 
    • 
   News
 
      • 
-      
        
+      
   
 
 
@@ -72,21 +78,21 @@ mb.1 <- micr
 print(mb.1)
        
 
        ## Unit: milliseconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 6581.1731 6598.7831 6630.0395 6616.3931 6654.4726
-##       Eigenvalue based  880.1617  890.3517  911.2758  900.5416  926.8328
-##      deSolve, compiled  739.4343  749.6078  753.6543  759.7813  760.7643
+##  deSolve, not compiled 6326.4518 6378.7429 6476.2219 6431.0341 6551.1069
+##       Eigenvalue based  925.7797  935.9924  939.8725  946.2051  946.9189
+##      deSolve, compiled  740.2821  750.0017  767.8440  759.7212  781.6249
 ##        max neval cld
-##  6692.5522     3   c
-##   953.1240     3  b 
-##   761.7474     3 a
        
+##  6671.1797     3   b
+##   947.6327     3  a 
+##   803.5287     3  a
        
 
        autoplot(mb.1)
        
 
        
-
        We see that using the compiled model is by a factor of 8.7 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:
        
+
        We see that using the compiled model is by a factor of 8.5 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:
        
 
        rownames(smb.1) <- smb.1$expr
 smb.1["median"]/smb.1["deSolve, compiled", "median"]
        
 
        ##                         median
-## deSolve, not compiled 8.708286
-## Eigenvalue based      1.185264
+## deSolve, not compiled 8.464993
+## Eigenvalue based      1.245464
 ## deSolve, compiled     1.000000
        
 
 
        
@@ -108,18 +114,18 @@ smb.1["median"]/smbprint(mb.2)
        
 
        ## Unit: seconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 13.756286 13.813205 13.874083 13.870125 13.932982
-##      deSolve, compiled  1.323196  1.372916  1.391915  1.422635  1.426274
+##  deSolve, not compiled 13.619556 13.761382 13.825679 13.903207 13.928741
+##      deSolve, compiled  1.316871  1.322577  1.358847  1.328283  1.379834
 ##        max neval cld
-##  13.995838     3   b
-##   1.429913     3  a
        
+##  13.954275     3   b
+##   1.431386     3  a
        
 
        smb.2["median"]/smb.2["deSolve, compiled", "median"]
        
 
        ##   median
 ## 1     NA
 ## 2     NA
        
 
        autoplot(mb.2)
        
 
        
-
        Here we get a performance benefit of a factor of 9.7 using the version of the differential equation model compiled from C code!
        
+
        Here we get a performance benefit of a factor of 10.5 using the version of the differential equation model compiled from C code!
        
 
        This vignette was built with mkin 0.9.44.9000 on
        
 
        ## R version 3.3.2 (2016-10-31)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
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index 9f7cdd74..cd6a7bea 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -60,7 +60,12 @@
       
       
       
     
   
diff --git a/docs/articles/mkin.html b/docs/articles/mkin.html
index 5f6ae46c..8a24352c 100644
--- a/docs/articles/mkin.html
+++ b/docs/articles/mkin.html
@@ -24,7 +24,13 @@
 
      • 
   News
 
        • 
-      
          
+      
   
 
 
diff --git a/docs/articles/mkin_cache/html/__packages b/docs/articles/mkin_cache/html/__packages
index 03ece635..c8b1e877 100644
--- a/docs/articles/mkin_cache/html/__packages
+++ b/docs/articles/mkin_cache/html/__packages
@@ -1,13 +1,8 @@
 base
-datasets
-utils
-grDevices
-graphics
-stats
 knitr
 minpack.lm
 rootSolve
-methods
 inline
-parallel
 mkin
+microbenchmark
+ggplot2
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-- 
cgit v1.2.1