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b/docs/articles/FOCUS_D.html index f32d7f82..1c4edbd0 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -24,7 +24,13 @@
  • 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 @@
 
      • 
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        • 
-      
          
+      
   
 
 
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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+++ b/docs/news/index.html
@@ -60,7 +60,12 @@
       
       
       
     
   
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index 7d036804..c0690f41 100644
--- a/docs/reference/DFOP.solution.html
+++ b/docs/reference/DFOP.solution.html
@@ -6,8 +6,7 @@
 
 
 
-
- — DFOP.solution • mkin
+Double First-Order in Parallel kinetics — DFOP.solution • mkin
 
 
 
@@ -61,7 +60,12 @@
       
       
       
     
   
@@ -73,8 +77,7 @@
       
          
   
          
     
          
-    
          
-
          
+    
          Double First-Order in Parallel kinetics
          
     
          
 
     
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index cfe6329b..ad4614fb 100644
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+++ b/docs/reference/Extract.mmkin.html
@@ -60,7 +60,12 @@
       
       
       
     
          
   
          
@@ -188,7 +193,7 @@
 #> 
 #> $time
 #>    user  system elapsed 
-#>   0.316   0.000   0.317 
+#>   0.264   0.000   0.262 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -374,7 +379,7 @@
 #>     }
 #>     return(mC)
 #> }
-#> <environment: 0x5d4a3b0>
+#> <environment: 0x50d32d0>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -396,7 +401,7 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <environment: 0x5d4a3b0>
+#> <environment: 0x50d32d0>
 #> 
 #> $hessian_notrans
 #>            parent_0     alpha       beta
@@ -462,7 +467,7 @@
 #> 99.66619 
 #> 
 #> $date
-#> [1] "Fri Nov  4 15:36:31 2016"
+#> [1] "Fri Nov  4 17:08:52 2016"
 #> 
 #> attr(,"class")
 #> [1] "mkinfit" "modFit" 
            fits["SFO", "B"]
          #>      dataset
@@ -541,7 +546,7 @@
 #> 
 #> $time
 #>    user  system elapsed 
-#>   0.076   0.000   0.077 
+#>   0.068   0.000   0.067 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -728,7 +733,7 @@
 #>     }
 #>     return(mC)
 #> }
-#> <environment: 0x5d98970>
+#> <environment: 0x4f17408>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -750,7 +755,7 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <environment: 0x5d98970>
+#> <environment: 0x4f17408>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -813,7 +818,7 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Fri Nov  4 15:36:30 2016"
+#> [1] "Fri Nov  4 17:08:51 2016"
 #> 
 #> attr(,"class")
 #> [1] "mkinfit" "modFit" 
            fits["SFO", "B", drop = TRUE]
          #> [[1]]
@@ -889,7 +894,7 @@
 #> 
 #> $time
 #>    user  system elapsed 
-#>   0.076   0.000   0.077 
+#>   0.068   0.000   0.067 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -1076,7 +1081,7 @@
 #>     }
 #>     return(mC)
 #> }
-#> <environment: 0x5d98970>
+#> <environment: 0x4f17408>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -1098,7 +1103,7 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <environment: 0x5d98970>
+#> <environment: 0x4f17408>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -1161,7 +1166,7 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Fri Nov  4 15:36:30 2016"
+#> [1] "Fri Nov  4 17:08:51 2016"
 #> 
 #> attr(,"class")
 #> [1] "mkinfit" "modFit" 
diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
index 97af2f9c..13dfa186 100644
--- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
+++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html
@@ -6,8 +6,7 @@
 
 
 
-
- — FOCUS_2006_DFOP_ref_A_to_B • mkin
+Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B • mkin
 
 
 
@@ -61,7 +60,12 @@
       
       
       
     
          
   
@@ -73,8 +77,7 @@
       
          
   
          
     
          
-    
          
-
          
+    
          Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)
          
     
          
 
     
diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
index 1487e2c9..5b36ac74 100644
--- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html
@@ -6,8 +6,7 @@
 
 
 
-
- — FOCUS_2006_FOMC_ref_A_to_F • mkin
+Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F • mkin
 
 
 
@@ -61,7 +60,12 @@
       
       
       
     
          
   
          
@@ -73,8 +77,7 @@
       
          
   
          
     
          
-    
          
-
          
+    
          Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)
          
     
          
 
     
diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
index 4571c175..446ce4d7 100644
--- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html
@@ -6,8 +6,7 @@
 
 
 
-
- — FOCUS_2006_HS_ref_A_to_F • mkin
+Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F • mkin
 
 
 
@@ -61,7 +60,12 @@
       
       
       
     
          
   
          
@@ -73,8 +77,7 @@
       
          
   
          
     
          
-    
          
-
          
+    
          Results of fitting the HS model to Datasets A to F of FOCUS (2006)
          
     
          
 
     
diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
index 7003fa0e..db462f10 100644
--- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
+++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html
@@ -6,8 +6,7 @@
 
 
 
-
- — FOCUS_2006_SFO_ref_A_to_F • mkin
+Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F • mkin
 
 
 
@@ -61,7 +60,12 @@
       
       
       
     
          
   
          
@@ -73,8 +77,7 @@
       
          
   
          
     
          
-    
          
-
          
+    
          Results of fitting the SFO model to Datasets A to F of FOCUS (2006)
          
     
          
 
     
diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html
index 83edd323..ffc7558e 100644
--- a/docs/reference/FOCUS_2006_datasets.html
+++ b/docs/reference/FOCUS_2006_datasets.html
@@ -6,8 +6,7 @@
 
 
 
-
- — FOCUS_2006_datasets • mkin
+Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets • mkin
 
 
 
@@ -61,7 +60,12 @@
       
       
       
     
          
   
          
@@ -73,8 +77,7 @@
       
          
   
          
     
          
-    
          
-
          
+    
          Datasets A to F from the FOCUS Kinetics report from 2006
          
     
          
 
     
diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html
index 83bca886..fdbf0d1f 100644
--- a/docs/reference/FOMC.solution.html
+++ b/docs/reference/FOMC.solution.html
@@ -6,7 +6,7 @@
 
 
 
- First-Order Multi-Compartment kinetics  — FOMC.solution • mkin
+First-Order Multi-Compartment kinetics — FOMC.solution • mkin
 
 
 
@@ -60,7 +60,12 @@
       
       
       
     
          
   
          
@@ -72,7 +77,7 @@
       
          
   
          
     
          
-    
           First-Order Multi-Compartment kinetics 
          
+    
          First-Order Multi-Compartment kinetics
          
     
          
 
     
diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html
index 13db29aa..fbe0b590 100644
--- a/docs/reference/HS.solution.html
+++ b/docs/reference/HS.solution.html
@@ -6,7 +6,7 @@
 
 
 
- Hockey-Stick kinetics  — HS.solution • mkin
+Hockey-Stick kinetics — HS.solution • mkin
 
 
 
@@ -60,7 +60,12 @@
       
       
       
     
          
   
          
@@ -72,7 +77,7 @@
       
          
   
          
     
          
-    
           Hockey-Stick kinetics 
          
+    
          Hockey-Stick kinetics
          
     
          
 
     
diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html
index 56c2b48e..553c38b0 100644
--- a/docs/reference/IORE.solution.html
+++ b/docs/reference/IORE.solution.html
@@ -6,7 +6,7 @@
 
 
 
- Indeterminate order rate equation kinetics  — IORE.solution • mkin
+Indeterminate order rate equation kinetics — IORE.solution • mkin
 
 
 
@@ -60,7 +60,12 @@
       
       
       
     
          
   
          
@@ -72,7 +77,7 @@
       
          
   
          
     
          
-    
           Indeterminate order rate equation kinetics 
          
+    
          Indeterminate order rate equation kinetics
          
     
          
 
     
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index 8ff5b5ba..2ead8f24 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.html
@@ -6,7 +6,7 @@
 
 
 
- Single First-Order kinetics  — SFO.solution • mkin
+Single First-Order kinetics — SFO.solution • mkin
 
 
 
@@ -60,7 +60,12 @@
       
       
       
     
          
   
          
@@ -72,7 +77,7 @@
       
          
   
          
     
          
-    
           Single First-Order kinetics 
          
+    
          Single First-Order kinetics
          
     
          
 
     
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
index 43b6028a..be425d83 100644
--- a/docs/reference/SFORB.solution.html
+++ b/docs/reference/SFORB.solution.html
@@ -6,7 +6,7 @@
 
 
 
- Single First-Order Reversible Binding kinetics  — SFORB.solution • mkin
+Single First-Order Reversible Binding kinetics — SFORB.solution • mkin
 
 
 
@@ -60,7 +60,12 @@
       
       
       
     
          
   
          
@@ -72,7 +77,7 @@
       
          
   
          
     
          
-    
           Single First-Order Reversible Binding kinetics 
          
+    
          Single First-Order Reversible Binding kinetics
          
     
          
 
     
diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html
index 8e491bc9..0a126c5c 100644
--- a/docs/reference/add_err.html
+++ b/docs/reference/add_err.html
@@ -6,8 +6,7 @@
 
 
 
-
- — add_err • mkin
+Add normally distributed errors to simulated kinetic degradation data — add_err • mkin
 
 
 
@@ -61,7 +60,12 @@
       
       
       
     
          
   
          
@@ -73,8 +77,7 @@
       
          
   
          
     
          
-    
          
-
          
+    
          Add normally distributed errors to simulated kinetic degradation data
          
     
          
 
     
diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html
index a3716060..44a8f4c4 100644
--- a/docs/reference/endpoints.html
+++ b/docs/reference/endpoints.html
@@ -6,8 +6,7 @@
 
 
 
-
- — endpoints • mkin
+Function to calculate endpoints for further use from kinetic models fitted with mkinfit — endpoints • mkin
 
 
 
@@ -61,7 +60,12 @@
       
       
       
     
          
   
          
@@ -73,8 +77,7 @@
       
          
   
          
     
          
-    
          
-
          
+    
          Function to calculate endpoints for further use from kinetic models fitted with mkinfit
          
     
          
 
     
diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html
index 633e0865..97352ff8 100644
--- a/docs/reference/geometric_mean.html
+++ b/docs/reference/geometric_mean.html
@@ -6,7 +6,7 @@
 
 
 
- Calculate the geometric mean  — geometric_mean • mkin
+Calculate the geometric mean — geometric_mean • mkin
 
 
 
@@ -60,7 +60,12 @@
       
       
       
     
          
   
          
@@ -72,7 +77,7 @@
       
          
   
          
     
          
-    
           Calculate the geometric mean 
          
+    
          Calculate the geometric mean
          
     
          
 
     
diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html
index 955b5c58..95fed72e 100644
--- a/docs/reference/ilr.html
+++ b/docs/reference/ilr.html
@@ -6,8 +6,7 @@
 
 
 
-
- — ilr • mkin
+Function to perform isometric log-ratio transformation — ilr • mkin
 
 
 
@@ -61,7 +60,12 @@
       
       
       
     
          
   
          
@@ -73,8 +77,7 @@
       
          
   
          
     
          
-    
          
-
          
+    
          Function to perform isometric log-ratio transformation
          
     
          
 
     
diff --git a/docs/reference/index.html b/docs/reference/index.html
index b7d59a21..32455baa 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -60,7 +60,12 @@
       
       
       
     
          
   
          
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index d32acb5b..6eb4741b 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -6,8 +6,7 @@
 
 
 
-
- — mccall81_245T • mkin
+Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T • mkin
 
 
 
@@ -61,7 +60,12 @@
       
       
       
     
   
@@ -73,8 +77,7 @@
       
          
   
          
     
          
-    
          
-
          
+    
          Datasets on aerobic soil metabolism of 2,4,5-T in six soils
          
     
          
 
     
@@ -119,8 +122,8 @@
                  fixed_parms = "k_phenol_sink", quiet = TRUE)
   summary(fit.2, data = FALSE)
          #> mkin version:    0.9.44.9000 
 #> R version:       3.3.2 
-#> Date of fit:     Fri Nov  4 15:36:38 2016 
-#> Date of summary: Fri Nov  4 15:36:38 2016 
+#> Date of fit:     Fri Nov  4 17:08:59 2016 
+#> Date of summary: Fri Nov  4 17:08:59 2016 
 #> 
 #> Equations:
 #> d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -130,7 +133,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 246 model solutions performed in 1.886 s
+#> Fitted with method Port using 246 model solutions performed in 1.497 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html
index 21a8a8f8..fa131a6d 100644
--- a/docs/reference/mkin_long_to_wide.html
+++ b/docs/reference/mkin_long_to_wide.html
@@ -6,8 +6,7 @@
 
 
 
-
- — mkin_long_to_wide • mkin
+Convert a dataframe from long to wide format — mkin_long_to_wide • mkin
 
 
 
@@ -61,7 +60,12 @@
       
       
       
     
          
   
          
@@ -73,8 +77,7 @@
       
          
   
          
     
          
-    
          
-
          
+    
          Convert a dataframe from long to wide format
          
     
          
 
     
diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html
index fe6e47e4..077c0b7d 100644
--- a/docs/reference/mkin_wide_to_long.html
+++ b/docs/reference/mkin_wide_to_long.html
@@ -6,8 +6,7 @@
 
 
 
-
- — mkin_wide_to_long • mkin
+Convert a dataframe with observations over time into long format — mkin_wide_to_long • mkin
 
 
 
@@ -61,7 +60,12 @@
       
       
       
     
          
   
          
@@ -73,8 +77,7 @@
       
          
   
          
     
          
-    
          
-
          
+    
          Convert a dataframe with observations over time into long format
          
     
          
 
     
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
index f5dd4c88..522aab33 100644
--- a/docs/reference/mkinds.html
+++ b/docs/reference/mkinds.html
@@ -60,7 +60,12 @@
       
       
       
     
          
   
          
diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html
index 8d420165..d212e3b2 100644
--- a/docs/reference/mkinerrmin.html
+++ b/docs/reference/mkinerrmin.html
@@ -6,8 +6,7 @@
 
 
 
-
- — mkinerrmin • mkin
+Calculate the minimum error to assume in order to pass the variance test — mkinerrmin • mkin
 
 
 
@@ -61,7 +60,12 @@
       
       
       
     
   
@@ -73,8 +77,7 @@
       
          
   
          
     
          
-    
          
-
          
+    
          Calculate the minimum error to assume in order to pass the variance test
          
     
          
 
     
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index b298d90a..93185eff 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -6,8 +6,7 @@
 
 
 
-
- — mkinfit • mkin
+Fit a kinetic model to data with one or more state variables — mkinfit • mkin
 
 
 
@@ -61,7 +60,12 @@
       
       
       
     
          
   
          
@@ -73,8 +77,7 @@
       
          
   
          
     
          
-    
          
-
          
+    
          Fit a kinetic model to data with one or more state variables
          
     
          
 
     
@@ -356,8 +359,8 @@
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
 summary(fit)
          #> mkin version:    0.9.44.9000 
 #> R version:       3.3.2 
-#> Date of fit:     Fri Nov  4 15:36:41 2016 
-#> Date of summary: Fri Nov  4 15:36:41 2016 
+#> Date of fit:     Fri Nov  4 17:09:01 2016 
+#> Date of summary: Fri Nov  4 17:09:01 2016 
 #> 
 #> Equations:
 #> d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -433,7 +436,7 @@
   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 
-#>   1.244   1.208   0.933 
          coef(fit)
          #>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>   1.256   1.216   0.946 
          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/mkinmod.html b/docs/reference/mkinmod.html
index 7dba1b6d..f328c34a 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -6,8 +6,7 @@
 
 
 
-
- — mkinmod • mkin
+Function to set up a kinetic model with one or more state variables — mkinmod • mkin
 
 
 
@@ -61,7 +60,12 @@
       
       
       
     
          
   
          
@@ -73,8 +77,7 @@
       
          
   
          
     
          
-    
          
-
          
+    
          Function to set up a kinetic model with one or more state variables
          
     
          
 
     
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index 923abc6d..764f1ab4 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -6,8 +6,8 @@
 
 
 
-
- — mkinparplot • mkin
+Function to plot the confidence intervals obtained using
+  list(list("mkinfit")) — mkinparplot • mkin
 
 
 
@@ -61,7 +61,12 @@
       
       
       
     
          
   
          
@@ -73,8 +78,8 @@
       
          
   
          
     
          
-    
          
-
          
+    
          Function to plot the confidence intervals obtained using
+  list(list("mkinfit"))
          
     
          
 
     
diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html
index 5fe94a8a..921affdc 100644
--- a/docs/reference/mkinplot.html
+++ b/docs/reference/mkinplot.html
@@ -6,8 +6,7 @@
 
 
 
-
- — mkinplot • mkin
+Plot the observed data and the fitted model of an mkinfit object — mkinplot • mkin
 
 
 
@@ -61,7 +60,12 @@
       
       
       
     
          
   
          
@@ -73,8 +77,7 @@
       
          
   
          
     
          
-    
          
-
          
+    
          Plot the observed data and the fitted model of an mkinfit object
          
     
          
 
     
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index f7eb950a..9f00dab7 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -6,8 +6,7 @@
 
 
 
-
- — mkinpredict • mkin
+Produce predictions from a kinetic model using specific parameters — mkinpredict • mkin
 
 
 
@@ -61,7 +60,12 @@
       
       
       
     
          
   
          
@@ -73,8 +77,7 @@
       
          
   
          
     
          
-    
          
-
          
+    
          Produce predictions from a kinetic model using specific parameters
          
     
          
 
     
@@ -272,7 +275,7 @@
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "eigen")[201,]))
          #>     time   parent       m1
 #> 201   20 4.978707 27.46227
          #>    user  system elapsed 
-#>   0.008   0.024   0.005 
            system.time(
+#>   0.004   0.028   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
@@ -282,7 +285,7 @@
                 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 
-#>   0.036   0.000   0.037 
          
+#>   0.052   0.000   0.052 
          
   
   
   
@@ -73,8 +77,7 @@
       
          
   
          
     
          
-    
          
-
          
+    
          Function to plot residuals stored in an mkin object
          
     
          
 
     
diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html
index 8424eaab..8bb2ce1c 100644
--- a/docs/reference/mkinsub.html
+++ b/docs/reference/mkinsub.html
@@ -6,8 +6,7 @@
 
 
 
-
- — mkinsub • mkin
+Function to set up a kinetic submodel for one state variable — mkinsub • mkin
 
 
 
@@ -61,7 +60,12 @@
       
       
       
     
          
   
          
@@ -73,8 +77,7 @@
       
          
   
          
     
          
-    
          
-
          
+    
          Function to set up a kinetic submodel for one state variable
          
     
          
 
     
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 5613a720..a21a980b 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -6,8 +6,7 @@
 
 
 
-
- — mmkin • mkin
+Fit one or more kinetic models with one or more state variables to one or more datasets — mmkin • mkin
 
 
 
@@ -61,7 +60,12 @@
       
       
       
     
          
   
          
@@ -73,8 +77,7 @@
       
          
   
          
     
          
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          Fit one or more kinetic models with one or more state variables to one or more datasets
          
     
          
 
     
diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index e7158180..52db9bc6 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -6,8 +6,7 @@
 
 
 
-
- — plot.mkinfit • mkin
+Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit • mkin
 
 
 
@@ -61,7 +60,12 @@
       
       
       
     
          
   
          
@@ -73,8 +77,7 @@
       
          
   
          
     
          
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          Plot the observed data and the fitted model of an mkinfit object
          
     
          
 
     
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index ef5c04b7..eac31273 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -6,8 +6,7 @@
 
 
 
-
- — plot.mmkin • mkin
+Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object — plot.mmkin • mkin
 
 
 
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@@ -73,8 +77,7 @@
       
          
   
          
     
          
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          Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object
          
     
          
 
     
diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html
index c578f4ee..9057114d 100644
--- a/docs/reference/print.mkinds.html
+++ b/docs/reference/print.mkinds.html
@@ -6,8 +6,7 @@
 
 
 
-
- — print.mkinds • mkin
+Print mkinds objects — print.mkinds • mkin
 
 
 
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          Print mkinds objects
          
     
          
 
     
diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html
index 3f653971..2034ea10 100644
--- a/docs/reference/print.mkinmod.html
+++ b/docs/reference/print.mkinmod.html
@@ -6,8 +6,7 @@
 
 
 
-
- — print.mkinmod • mkin
+Print mkinmod objects — print.mkinmod • mkin
 
 
 
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          Print mkinmod objects
          
     
          
 
     
diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index c63ba490..e2f845d9 100644
--- a/docs/reference/schaefer07_complex_case.html
+++ b/docs/reference/schaefer07_complex_case.html
@@ -6,8 +6,7 @@
 
 
 
-
- — schaefer07_complex_case • mkin
+Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case • mkin
 
 
 
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@@ -73,8 +77,7 @@
       
          
   
          
     
          
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          Metabolism data set used for checking the software quality of KinGUI
          
     
          
 
     
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 241964a7..f67bc1d1 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -6,8 +6,7 @@
 
 
 
-
- — summary.mkinfit • mkin
+Summary method for class "mkinfit" — summary.mkinfit • mkin
 
 
 
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          Summary method for class "mkinfit"
          
     
          
 
     
@@ -139,8 +142,8 @@
     
          Examples
          
     
            summary(mkinfit(mkinmod(parent = list(type = "SFO")), FOCUS_2006_A, quiet = TRUE))
          #> mkin version:    0.9.44.9000 
 #> R version:       3.3.2 
-#> Date of fit:     Fri Nov  4 15:36:49 2016 
-#> Date of summary: Fri Nov  4 15:36:49 2016 
+#> Date of fit:     Fri Nov  4 17:09:10 2016 
+#> Date of summary: Fri Nov  4 17:09:10 2016 
 #> 
 #> Equations:
 #> d_parent = - k_parent_sink * parent
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index 333b3dbf..c6f29582 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -6,8 +6,7 @@
 
 
 
-
- — synthetic_data_for_UBA_2014 • mkin
+Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014 • mkin
 
 
 
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@@ -73,8 +77,7 @@
       
          
   
          
     
          
-    
          
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+    
          Synthetic datasets for one parent compound with two metabolites
          
     
          
 
     
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 5ee1e9cc..60208ff4 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -6,8 +6,7 @@
 
 
 
-
- — transform_odeparms • mkin
+Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms • mkin
 
 
 
@@ -61,7 +60,12 @@
       
       
       
     
          
   
          
@@ -73,8 +77,7 @@
       
          
   
          
     
          
-    
          
-
          
+    
          Functions to transform and backtransform kinetic parameters for fitting
          
     
          
 
     
@@ -146,8 +149,8 @@
 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:       3.3.2 
-#> Date of fit:     Fri Nov  4 15:36:50 2016 
-#> Date of summary: Fri Nov  4 15:36:50 2016 
+#> Date of fit:     Fri Nov  4 17:09:11 2016 
+#> Date of summary: Fri Nov  4 17:09:11 2016 
 #> 
 #> Equations:
 #> d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -155,7 +158,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 153 model solutions performed in 0.663 s
+#> Fitted with method Port using 153 model solutions performed in 0.638 s
 #> 
 #> Weighting: none
 #> 
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