From 6ea7bc3614b9a303f7c38dd63b9f80b8d0ebd95e Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 21 Mar 2018 18:16:52 +0100 Subject: Static documentation rebuilt by pkgdown --- docs/articles/FOCUS_D.html | 2 +- docs/articles/FOCUS_L.html | 56 +++++++++++++++++----------------- docs/articles/FOCUS_Z.html | 2 +- docs/articles/compiled_models.html | 14 ++++----- docs/articles/mkin.html | 2 +- docs/articles/twa.html | 2 +- docs/news/index.html | 6 ++-- docs/reference/Extract.mmkin.html | 14 ++++----- docs/reference/mccall81_245T.html | 8 ++--- docs/reference/mkinfit.html | 10 +++--- docs/reference/mkinpredict.html | 4 +-- docs/reference/mmkin.html | 4 ++- docs/reference/summary.mkinfit.html | 8 ++--- docs/reference/transform_odeparms.html | 8 ++--- 14 files changed, 71 insertions(+), 69 deletions(-) diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index a8002acd..a83c2f44 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -80,7 +80,7 @@

Example evaluation of FOCUS Example Dataset D

Johannes Ranke

-

2018-03-11

+

2018-03-21

diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index a23876ec..08e144bd 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -80,7 +80,7 @@

Example evaluation of FOCUS Laboratory Data L1 to L3

Johannes Ranke

-

2018-03-11

+

2018-03-21

@@ -102,16 +102,16 @@ FOCUS_2006_L1_mkin <- 
m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet = TRUE)
 summary(m.L1.SFO)
## mkin version:    0.9.46.3 
-## R version:       3.4.3 
-## Date of fit:     Sun Mar 11 22:11:58 2018 
-## Date of summary: Sun Mar 11 22:11:58 2018 
+## R version:       3.4.4 
+## Date of fit:     Wed Mar 21 18:16:03 2018 
+## Date of summary: Wed Mar 21 18:16:03 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.235 s
+## Fitted with method Port using 37 model solutions performed in 0.257 s
 ## 
 ## Weighting: none
 ## 
@@ -193,16 +193,16 @@ FOCUS_2006_L1_mkin <- 

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

 
## mkin version:    0.9.46.3 
-## R version:       3.4.3 
-## Date of fit:     Sun Mar 11 22:12:01 2018 
-## Date of summary: Sun Mar 11 22:12:01 2018 
+## R version:       3.4.4 
+## Date of fit:     Wed Mar 21 18:16:05 2018 
+## Date of summary: Wed Mar 21 18:16:05 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 611 model solutions performed in 1.458 s
+## Fitted with method Port using 611 model solutions performed in 1.404 s
 ## 
 ## Weighting: none
 ## 
@@ -288,16 +288,16 @@ FOCUS_2006_L2_mkin <- 

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

 
## mkin version:    0.9.46.3 
-## R version:       3.4.3 
-## Date of fit:     Sun Mar 11 22:12:01 2018 
-## Date of summary: Sun Mar 11 22:12:01 2018 
+## R version:       3.4.4 
+## Date of fit:     Wed Mar 21 18:16:06 2018 
+## Date of summary: Wed Mar 21 18:16:06 2018 
 ## 
 ## 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 0.158 s
+## Fitted with method Port using 81 model solutions performed in 0.168 s
 ## 
 ## Weighting: none
 ## 
@@ -359,9 +359,9 @@ FOCUS_2006_L2_mkin <- 

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

 
## mkin version:    0.9.46.3 
-## R version:       3.4.3 
-## Date of fit:     Sun Mar 11 22:12:02 2018 
-## Date of summary: Sun Mar 11 22:12:02 2018 
+## R version:       3.4.4 
+## Date of fit:     Wed Mar 21 18:16:06 2018 
+## Date of summary: Wed Mar 21 18:16:06 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -370,7 +370,7 @@ FOCUS_2006_L2_mkin <-  
summary(mm.L3[["DFOP", 1]])

 
## mkin version:    0.9.46.3 
-## R version:       3.4.3 
-## Date of fit:     Sun Mar 11 22:12:03 2018 
-## Date of summary: Sun Mar 11 22:12:03 2018 
+## R version:       3.4.4 
+## Date of fit:     Wed Mar 21 18:16:07 2018 
+## Date of summary: Wed Mar 21 18:16:07 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -462,7 +462,7 @@ mm.L3 <-  \(\chi^2\) 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:    0.9.46.3 
-## R version:       3.4.3 
-## Date of fit:     Sun Mar 11 22:12:04 2018 
-## Date of summary: Sun Mar 11 22:12:04 2018 
+## R version:       3.4.4 
+## Date of fit:     Wed Mar 21 18:16:08 2018 
+## Date of summary: Wed Mar 21 18:16:08 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
@@ -612,16 +612,16 @@ mm.L4 <- 
summary(mm.L4[["FOMC", 1]], data = FALSE)

 
## mkin version:    0.9.46.3 
-## R version:       3.4.3 
-## Date of fit:     Sun Mar 11 22:12:04 2018 
-## Date of summary: Sun Mar 11 22:12:04 2018 
+## R version:       3.4.4 
+## Date of fit:     Wed Mar 21 18:16:08 2018 
+## Date of summary: Wed Mar 21 18:16:08 2018 
 ## 
 ## 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 0.13 s
+## Fitted with method Port using 66 model solutions performed in 0.138 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_Z.html b/docs/articles/FOCUS_Z.html
index 78a00062..a2b88caa 100644
--- a/docs/articles/FOCUS_Z.html
+++ b/docs/articles/FOCUS_Z.html
@@ -80,7 +80,7 @@
       
Example evaluation of FOCUS dataset Z

                         
Johannes Ranke

             
-            
2018-03-11

+            
2018-03-21

           
 
     
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index 8923acac..19cb806b 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -80,7 +80,7 @@
       
Performance benefit by using compiled model definitions in mkin

                         
Johannes Ranke

             
-            
2018-03-11

+            
2018-03-21

           
 
     
@@ -118,9 +118,9 @@ SFO_SFO <-  Johannes Ranke
             
-            
2018-03-11

+            
2018-03-21

           
 
     
diff --git a/docs/articles/twa.html b/docs/articles/twa.html
index 7f4c941e..551cf03f 100644
--- a/docs/articles/twa.html
+++ b/docs/articles/twa.html
@@ -80,7 +80,7 @@
       
Calculation of time weighted average concentrations with mkin

                         
Johannes Ranke

             
-            
2018-03-11

+            
2018-03-21

           
 
     
diff --git a/docs/news/index.html b/docs/news/index.html
index f311efe5..c4605ae1 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -107,9 +107,9 @@
     
 
     

-    

+    

 

-mkin 0.9.47.1 (2017-02-06)

+mkin 0.9.47.1 (2018-02-06)
 
    
 
  • Skip some test on CRAN and winbuilder to avoid timeouts
    • 
 
  • ‘test_data_from_UBA_2014’: Added this list of datasets containing experimental data used in the expertise from 2014
    • 
@@ -594,7 +594,7 @@
     
    
       
    Contents
    
       
      
-        
    • 0.9.47.1
      • 
+        
    • 0.9.47.1
      • 
         
    • 0.9.46.3
      • 
         
    • 0.9.46.2
      • 
         
    • 0.9.46.1
      • 
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index e554432f..2a3b1c78 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -263,7 +263,7 @@
 #> 
 #> $time
 #>    user  system elapsed 
-#>   0.234   0.000   0.234 
+#>   0.242   0.000   0.244 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -452,8 +452,8 @@
 #>     }
 #>     return(mC)
 #> }
-#> <bytecode: 0x5555578e66e0>
-#> <environment: 0x555559cd9780>
+#> <bytecode: 0x5555578ff9d0>
+#> <environment: 0x555559a0da40>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -475,8 +475,8 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555acf3f50>
-#> <environment: 0x555559cd9780>
+#> <bytecode: 0x555559b90d60>
+#> <environment: 0x555559a0da40>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -543,13 +543,13 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Sun Mar 11 22:10:21 2018"
+#> [1] "Wed Mar 21 18:14:20 2018"
 #> 
 #> $version
 #> [1] "0.9.47.1"
 #> 
 #> $Rversion
-#> [1] "3.4.3"
+#> [1] "3.4.4"
 #> 
 #> attr(,"class")
 #> [1] "mkinfit" "modFit" 
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 80cac442..cb70e68c 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -150,9 +150,9 @@
                  parms.ini = c(k_phenol_sink = 0),
                  fixed_parms = "k_phenol_sink", quiet = TRUE)
   summary(fit.2, data = FALSE)
    #> mkin version used for fitting:    0.9.47.1 
-#> R version used for fitting:       3.4.3 
-#> Date of fit:     Sun Mar 11 22:10:30 2018 
-#> Date of summary: Sun Mar 11 22:10:30 2018 
+#> R version used for fitting:       3.4.4 
+#> Date of fit:     Wed Mar 21 18:14:30 2018 
+#> Date of summary: Wed Mar 21 18:14:30 2018 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -162,7 +162,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 246 model solutions performed in 1.318 s
+#> Fitted with method Port using 246 model solutions performed in 1.403 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 991df1cc..8ac8295f 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -413,16 +413,16 @@
     
    # Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
 summary(fit)
    #> mkin version used for fitting:    0.9.47.1 
-#> R version used for fitting:       3.4.3 
-#> Date of fit:     Sun Mar 11 22:10:32 2018 
-#> Date of summary: Sun Mar 11 22:10:32 2018 
+#> R version used for fitting:       3.4.4 
+#> Date of fit:     Wed Mar 21 18:14:33 2018 
+#> Date of summary: Wed Mar 21 18:14:33 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 64 model solutions performed in 0.135 s
+#> Fitted with method Port using 64 model solutions performed in 0.14 s
 #> 
 #> Weighting: none
 #> 
@@ -491,7 +491,7 @@
   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 
-#>   0.829   0.000   0.829 
    coef(fit)
    #>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>   0.834   0.000   0.835 
    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/mkinpredict.html b/docs/reference/mkinpredict.html
index 044b2d92..4768215b 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -306,7 +306,7 @@
                 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 
-#>   0.002   0.000   0.003 
      system.time(
+#>   0.003   0.000   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")[201,]))
    #>     time   parent       m1
@@ -316,7 +316,7 @@
                 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 
-#>   0.029   0.000   0.029 
    
+#>   0.033   0.000   0.032