From e1ccb85d60802be5e4848ceec0637483753ad8c3 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 6 Sep 2018 13:38:06 +0200 Subject: Fixed publication date in NEWS, docs rebuilt --- NEWS.md | 2 +- docs/articles/FOCUS_L.html | 38 +++++++++++++++++----------------- docs/articles/compiled_models.html | 10 ++++----- docs/news/index.html | 6 +++--- docs/reference/Extract.mmkin.html | 12 +++++------ docs/reference/mccall81_245T.html | 6 +++--- docs/reference/mkinfit.html | 8 +++---- docs/reference/mkinpredict.html | 4 ++-- docs/reference/summary.mkinfit.html | 6 +++--- docs/reference/transform_odeparms.html | 6 +++--- 10 files changed, 49 insertions(+), 49 deletions(-) diff --git a/NEWS.md b/NEWS.md index e67fe7b7..62b6038e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# mkin 0.9.47.2 (2018-07-09) +# mkin 0.9.47.2 (2018-07-19) - 'sigma_twocomp': Rename 'sigma_rl' to 'sigma_twocomp' as the Rocke and Lorenzato model assumes lognormal distribution for large y. Correct references to the Rocke and Lorenzato model accordingly. diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html index 4b324b7e..a42c6e38 100644 --- a/docs/articles/FOCUS_L.html +++ b/docs/articles/FOCUS_L.html @@ -110,15 +110,15 @@ summary(m.L1.SFO) 
## mkin version used for fitting:    0.9.47.2 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Thu Sep  6 11:51:22 2018 
-## Date of summary: Thu Sep  6 11:51:22 2018 
+## Date of fit:     Thu Sep  6 13:35:50 2018 
+## Date of summary: Thu Sep  6 13:35:50 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 0.085 s
+## Fitted with method Port using 37 model solutions performed in 0.086 s
 ## 
 ## Weighting: none
 ## 
@@ -201,15 +201,15 @@
 
 
## mkin version used for fitting:    0.9.47.2 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Thu Sep  6 11:51:24 2018 
-## Date of summary: Thu Sep  6 11:51:24 2018 
+## Date of fit:     Thu Sep  6 13:35:52 2018 
+## Date of summary: Thu Sep  6 13:35:52 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 1.348 s
+## Fitted with method Port using 611 model solutions performed in 1.35 s
 ## 
 ## Weighting: none
 ## 
@@ -296,15 +296,15 @@
 
 
## mkin version used for fitting:    0.9.47.2 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Thu Sep  6 11:51:25 2018 
-## Date of summary: Thu Sep  6 11:51:25 2018 
+## Date of fit:     Thu Sep  6 13:35:52 2018 
+## Date of summary: Thu Sep  6 13:35:53 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 0.182 s
+## Fitted with method Port using 81 model solutions performed in 0.175 s
 ## 
 ## Weighting: none
 ## 
@@ -367,8 +367,8 @@
 
 
## mkin version used for fitting:    0.9.47.2 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Thu Sep  6 11:51:26 2018 
-## Date of summary: Thu Sep  6 11:51:26 2018 
+## Date of fit:     Thu Sep  6 13:35:53 2018 
+## Date of summary: Thu Sep  6 13:35:53 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -377,7 +377,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 0.749 s
+## Fitted with method Port using 336 model solutions performed in 0.746 s
 ## 
 ## Weighting: none
 ## 
@@ -459,8 +459,8 @@
 
 
## mkin version used for fitting:    0.9.47.2 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Thu Sep  6 11:51:27 2018 
-## Date of summary: Thu Sep  6 11:51:27 2018 
+## Date of fit:     Thu Sep  6 13:35:54 2018 
+## Date of summary: Thu Sep  6 13:35:55 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -469,7 +469,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.329 s
+## Fitted with method Port using 137 model solutions performed in 0.324 s
 ## 
 ## Weighting: none
 ## 
@@ -560,8 +560,8 @@
 
 
## mkin version used for fitting:    0.9.47.2 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Thu Sep  6 11:51:27 2018 
-## Date of summary: Thu Sep  6 11:51:27 2018 
+## Date of fit:     Thu Sep  6 13:35:55 2018 
+## Date of summary: Thu Sep  6 13:35:55 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
@@ -620,8 +620,8 @@
 
 
## mkin version used for fitting:    0.9.47.2 
 ## R version used for fitting:       3.5.1 
-## Date of fit:     Thu Sep  6 11:51:27 2018 
-## Date of summary: Thu Sep  6 11:51:27 2018 
+## Date of fit:     Thu Sep  6 13:35:55 2018 
+## Date of summary: Thu Sep  6 13:35:55 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
diff --git a/docs/articles/compiled_models.html b/docs/articles/compiled_models.html
index 17387187..16059fcb 100644
--- a/docs/articles/compiled_models.html
+++ b/docs/articles/compiled_models.html
@@ -125,9 +125,9 @@
 }

 
## Lade nötiges Paket: rbenchmark

 
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   2.112    1.000     2.110        0
-## 1 deSolve, not compiled            3  16.633    7.875    16.624        0
-## 2      Eigenvalue based            3   2.637    1.249     2.635        0
+## 3     deSolve, compiled            3   2.218    1.000     2.217        0
+## 1 deSolve, not compiled            3  16.654    7.509    16.646        0
+## 2      Eigenvalue based            3   2.724    1.228     2.722        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -156,8 +156,8 @@
 }

 
## Successfully compiled differential equation model from auto-generated C code.

 
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   3.720    1.000     3.718        0
-## 1 deSolve, not compiled            3  34.677    9.322    34.661        0
+## 2     deSolve, compiled            3   3.780    1.000     3.777        0
+## 1 deSolve, not compiled            3  35.169    9.304    35.152        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

diff --git a/docs/news/index.html b/docs/news/index.html
index 95995810..71390917 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -117,9 +117,9 @@
       
     
 
-    

+    

 

-mkin 0.9.47.2 (2018-07-09) 2018-07-19 
+mkin 0.9.47.2 (2018-07-19) 2018-07-19 
 

 
    
 
  • ‘sigma_twocomp’: Rename ‘sigma_rl’ to ‘sigma_twocomp’ as the Rocke and Lorenzato model assumes lognormal distribution for large y. Correct references to the Rocke and Lorenzato model accordingly.
    • 
@@ -639,7 +639,7 @@
     
    
       
    Contents
    
       
      
-        
    • 0.9.47.2
      • 
+        
    • 0.9.47.2
      • 
         
    • 0.9.47.1
      • 
         
    • 0.9.46.3
      • 
         
    • 0.9.46.2
      • 
diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 982363a1..8771b53b 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -278,7 +278,7 @@
 #> 
 #> $time
 #>        User      System verstrichen 
-#>       0.183       0.000       0.184 
+#>       0.171       0.001       0.171 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -467,8 +467,8 @@
 #>     }
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555bd7d1a0>
-#> <environment: 0x55555bc8d4d8>
+#> <bytecode: 0x55555bd7f970>
+#> <environment: 0x55555bc8fca8>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -490,8 +490,8 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555ca81b68>
-#> <environment: 0x55555bc8d4d8>
+#> <bytecode: 0x55555ca84338>
+#> <environment: 0x55555bc8fca8>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -558,7 +558,7 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Thu Sep  6 11:50:56 2018"
+#> [1] "Thu Sep  6 13:35:24 2018"
 #> 
 #> $version
 #> [1] "0.9.47.2"
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index cdfc4b5d..9894f8eb 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -166,8 +166,8 @@
                  fixed_parms = "k_phenol_sink", quiet = TRUE)
   summary(fit.2, data = FALSE)
    #> mkin version used for fitting:    0.9.47.2 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Thu Sep  6 11:51:05 2018 
-#> Date of summary: Thu Sep  6 11:51:05 2018 
+#> Date of fit:     Thu Sep  6 13:35:34 2018 
+#> Date of summary: Thu Sep  6 13:35:34 2018 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -177,7 +177,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 246 model solutions performed in 1.51 s
+#> Fitted with method Port using 246 model solutions performed in 1.549 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index e99e7d9e..f9c6c117 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -433,15 +433,15 @@
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
 summary(fit)
    #> mkin version used for fitting:    0.9.47.2 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Thu Sep  6 11:51:08 2018 
-#> Date of summary: Thu Sep  6 11:51:08 2018 
+#> Date of fit:     Thu Sep  6 13:35:36 2018 
+#> Date of summary: Thu Sep  6 13:35:36 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 0.142 s
+#> Fitted with method Port using 64 model solutions performed in 0.144 s
 #> 
 #> Weighting: none
 #> 
@@ -510,7 +510,7 @@
   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 verstrichen 
-#>       0.895       0.000       0.898 
    coef(fit)
    #>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.919       0.000       0.920 
    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 5e2e5449..59b67a5d 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -326,12 +326,12 @@
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve")[201,]))
    #>     time   parent       m1
 #> 201   20 4.978707 27.46227
    #>        User      System verstrichen 
-#>       0.002       0.000       0.001 
      system.time(
+#>       0.002       0.000       0.002 
      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", use_compiled = FALSE)[201,]))
    #>     time   parent       m1
 #> 201   20 4.978707 27.46227
    #>        User      System verstrichen 
-#>       0.035       0.000       0.034 

+#>       0.037       0.000       0.038