From ad42e8870803335a549784888ddda80e4662f441 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 21 Feb 2019 15:16:14 +0100 Subject: Static documentation rebuilt by pkgdown --- docs/reference/AIC.mmkin.html | 2 +- docs/reference/CAKE_export.html | 2 +- docs/reference/DFOP.solution.html | 2 +- docs/reference/Extract.mmkin.html | 16 +++---- docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 2 +- docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 2 +- docs/reference/FOCUS_2006_HS_ref_A_to_F.html | 2 +- docs/reference/FOCUS_2006_SFO_ref_A_to_F.html | 2 +- docs/reference/FOCUS_2006_datasets.html | 2 +- docs/reference/FOMC.solution.html | 2 +- docs/reference/HS.solution.html | 2 +- docs/reference/IORE.solution.html | 2 +- docs/reference/SFO.solution.html | 2 +- docs/reference/SFORB.solution.html | 2 +- docs/reference/add_err.html | 2 +- docs/reference/endpoints.html | 2 +- docs/reference/geometric_mean.html | 2 +- docs/reference/ilr.html | 2 +- docs/reference/index.html | 2 +- docs/reference/logLik.mkinfit.html | 2 +- docs/reference/logistic.solution.html | 3 +- docs/reference/max_twa_parent.html | 2 +- docs/reference/mccall81_245T.html | 18 ++++---- docs/reference/mkin_long_to_wide.html | 2 +- docs/reference/mkin_wide_to_long.html | 2 +- docs/reference/mkinds.html | 2 +- docs/reference/mkinerrmin.html | 2 +- docs/reference/mkinfit.html | 60 +++++++++++++------------- docs/reference/mkinmod.html | 4 +- docs/reference/mkinparplot.html | 2 +- docs/reference/mkinplot.html | 2 +- docs/reference/mkinpredict.html | 6 +-- docs/reference/mkinresplot.html | 2 +- docs/reference/mkinsub.html | 2 +- docs/reference/mmkin.html | 6 +-- docs/reference/plot.mkinfit.html | 2 +- docs/reference/plot.mmkin.html | 2 +- docs/reference/print.mkinds.html | 2 +- docs/reference/print.mkinmod.html | 2 +- docs/reference/schaefer07_complex_case.html | 2 +- docs/reference/sigma_twocomp.html | 2 +- docs/reference/summary.mkinfit.html | 10 ++--- docs/reference/synthetic_data_for_UBA.html | 2 +- docs/reference/test_data_from_UBA_2014.html | 2 +- docs/reference/transform_odeparms.html | 32 +++++++------- 45 files changed, 113 insertions(+), 114 deletions(-) (limited to 'docs/reference') diff --git a/docs/reference/AIC.mmkin.html b/docs/reference/AIC.mmkin.html index d90b325f..3d10d36e 100644 --- a/docs/reference/AIC.mmkin.html +++ b/docs/reference/AIC.mmkin.html @@ -64,7 +64,7 @@ mkin - 0.9.47.6 + 0.9.48.1 diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index 21dd46a9..886c1922 100644 --- a/docs/reference/CAKE_export.html +++ b/docs/reference/CAKE_export.html @@ -64,7 +64,7 @@ mkin - 0.9.47.6 + 0.9.48.1 diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 7f17e421..9bc215f0 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -64,7 +64,7 @@ mkin - 0.9.47.6 + 0.9.48.1 diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index fe6fc125..39228ba7 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -63,7 +63,7 @@ mkin - 0.9.47.6 + 0.9.48.1 @@ -280,7 +280,7 @@ #> #> $time #> User System verstrichen -#> 0.199 0.000 0.200 +#> 0.197 0.000 0.197 #> #> $mkinmod #> <mkinmod> model generated with @@ -469,8 +469,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x555559227548> -#> <environment: 0x555556ee4048> +#> <bytecode: 0x55555920c328> +#> <environment: 0x555555b0eb48> #> #> $cost_notrans #> function (P) @@ -492,8 +492,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x55555a34ddf0> -#> <environment: 0x555556ee4048> +#> <bytecode: 0x55555a39faa0> +#> <environment: 0x555555b0eb48> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -560,10 +560,10 @@ #> 99.17407 #> #> $date -#> [1] "Thu Feb 21 14:56:32 2019" +#> [1] "Thu Feb 21 15:11:41 2019" #> #> $version -#> [1] "0.9.47.6" +#> [1] "0.9.48.1" #> #> $Rversion #> [1] "3.5.2" 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 8565c1e6..9a43e010 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -67,7 +67,7 @@ in this fit." /> mkin - 0.9.47.6 + 0.9.48.1 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 96329ca3..663600dd 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -67,7 +67,7 @@ in this fit." /> mkin - 0.9.47.6 + 0.9.48.1 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 e1f9ae2b..58cab325 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -67,7 +67,7 @@ in this fit." /> mkin - 0.9.47.6 + 0.9.48.1 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 1d039652..f9cf0e11 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -67,7 +67,7 @@ in this fit." /> mkin - 0.9.47.6 + 0.9.48.1 diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index e3c366b5..56f58d03 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -63,7 +63,7 @@ mkin - 0.9.47.6 + 0.9.48.1 diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 3ece2c08..fe6944d3 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -67,7 +67,7 @@ The form given here differs slightly from the original reference by Gustafson mkin - 0.9.47.6 + 0.9.48.1 diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 0d8751e1..6997ebae 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -64,7 +64,7 @@ mkin - 0.9.47.6 + 0.9.48.1 diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 2ad38a16..103a1ae3 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -64,7 +64,7 @@ mkin - 0.9.47.6 + 0.9.48.1 diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 55ff216c..325a4285 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -63,7 +63,7 @@ mkin - 0.9.47.6 + 0.9.48.1 diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 81ed61aa..f22b3af5 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -67,7 +67,7 @@ mkin - 0.9.47.6 + 0.9.48.1 diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index c8024d66..c2db5b52 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -65,7 +65,7 @@ mkin - 0.9.47.6 + 0.9.48.1 diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 9952f7ad..e241c7b9 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -66,7 +66,7 @@ with the advantage that the SFORB model can also be used for metabolites." /> mkin - 0.9.47.6 + 0.9.48.1 diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index ca3d8808..e52ac866 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -63,7 +63,7 @@ mkin - 0.9.47.6 + 0.9.48.1 diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 760dd3aa..4c8af606 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -63,7 +63,7 @@ mkin - 0.9.47.6 + 0.9.48.1 diff --git a/docs/reference/index.html b/docs/reference/index.html index 78eb0337..f31a72fe 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -60,7 +60,7 @@ mkin - 0.9.47.6 + 0.9.48.1 diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index a23ea52b..1e3b5702 100644 --- a/docs/reference/logLik.mkinfit.html +++ b/docs/reference/logLik.mkinfit.html @@ -80,7 +80,7 @@ In the case of iterative reweighting, the variances obtained by this mkin - 0.9.47.6 + 0.9.48.1 diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html index 310f1c5a..1894ed0e 100644 --- a/docs/reference/logistic.solution.html +++ b/docs/reference/logistic.solution.html @@ -64,7 +64,7 @@ mkin - 0.9.47.6 + 0.9.48.1 @@ -194,7 +194,6 @@ sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) parms_logistic <- c(kmax = 0.08, k0 = 0.0001, r = 0.2) - parms_logistic_optim <- c(parent_0 = 100, parms_logistic) d_logistic <- mkinpredict(logistic, parms_logistic, c(parent = 100), sampling_times) diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 320bdd46..2c10b624 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -67,7 +67,7 @@ guidance." /> mkin - 0.9.47.6 + 0.9.48.1 diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index bed8ed8e..ce1c88e9 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -65,7 +65,7 @@ mkin - 0.9.47.6 + 0.9.48.1 @@ -158,10 +158,10 @@ 
  SFO_SFO_SFO <- mkinmod(T245 = list(type = "SFO", to = "phenol"),
                          phenol = list(type = "SFO", to = "anisole"),
                          anisole = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
  
    fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
-    summary(fit.1, data = FALSE)
#> mkin version used for fitting:    0.9.47.6 
+    summary(fit.1, data = FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:56:53 2019 
-#> Date of summary: Thu Feb 21 14:56:53 2019 
+#> Date of fit:     Thu Feb 21 15:12:02 2019 
+#> Date of summary: Thu Feb 21 15:12:02 2019 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -171,7 +171,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 574 model solutions performed in 3.873 s
+#> Fitted with method Port using 574 model solutions performed in 3.856 s
 #> 
 #> Weighting: none
 #> 
@@ -247,10 +247,10 @@
     fit.2 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"),
                    parms.ini = c(k_phenol_sink = 0),
                    fixed_parms = "k_phenol_sink", quiet = TRUE)
-    summary(fit.2, data = FALSE)
#> mkin version used for fitting:    0.9.47.6 
+    summary(fit.2, data = FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:56:55 2019 
-#> Date of summary: Thu Feb 21 14:56:55 2019 
+#> Date of fit:     Thu Feb 21 15:12:04 2019 
+#> Date of summary: Thu Feb 21 15:12:04 2019 
 #> 
 #> Equations:
 #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -260,7 +260,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 246 model solutions performed in 1.633 s
+#> Fitted with method Port using 246 model solutions performed in 1.607 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html
index 290d3e76..f8849a3e 100644
--- a/docs/reference/mkin_long_to_wide.html
+++ b/docs/reference/mkin_long_to_wide.html
@@ -65,7 +65,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     

 
diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html
index d7438fcf..04eaff8b 100644
--- a/docs/reference/mkin_wide_to_long.html
+++ b/docs/reference/mkin_wide_to_long.html
@@ -64,7 +64,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html
index bf90726d..7a87c11e 100644
--- a/docs/reference/mkinds.html
+++ b/docs/reference/mkinds.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html
index 35086a61..c155a838 100644
--- a/docs/reference/mkinerrmin.html
+++ b/docs/reference/mkinerrmin.html
@@ -64,7 +64,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006." />
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index 4f071574..369d7bbe 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -73,7 +73,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
@@ -436,17 +436,17 @@
     
Examples

     
# Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-summary(fit)
#> mkin version used for fitting:    0.9.47.6 
+summary(fit)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:56:58 2019 
-#> Date of summary: Thu Feb 21 14:56:58 2019 
+#> Date of fit:     Thu Feb 21 15:12:07 2019 
+#> Date of summary: Thu Feb 21 15:12:07 2019 
 #> 
 #> 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 0.16 s
+#> Fitted with method Port using 64 model solutions performed in 0.164 s
 #> 
 #> Weighting: none
 #> 
@@ -515,7 +515,7 @@
   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 
-#>       1.036       0.000       1.036 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       1.045       0.000       1.046 
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 
@@ -590,7 +590,7 @@
 #> Model cost at call  146 :  371.2134 
 #> Optimisation by method Port successfully terminated.
 #>        User      System verstrichen 
-#>       0.830       0.000       0.832 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.835       0.000       0.835 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
 #>          99.59848          -3.03822          -2.98030          -5.24750 
endpoints(fit.deSolve)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
@@ -626,10 +626,10 @@
 
# Weighted fits, including IRLS
 SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"),
                       m1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
-summary(f.noweight)
#> mkin version used for fitting:    0.9.47.6 
+summary(f.noweight)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:57:10 2019 
-#> Date of summary: Thu Feb 21 14:57:10 2019 
+#> Date of fit:     Thu Feb 21 15:12:19 2019 
+#> Date of summary: Thu Feb 21 15:12:19 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -637,7 +637,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 186 model solutions performed in 0.86 s
+#> Fitted with method Port using 186 model solutions performed in 0.853 s
 #> 
 #> Weighting: none
 #> 
@@ -743,10 +743,10 @@
 #>   100       m1    33.13  31.98163  1.148e+00
 #>   120       m1    25.15  28.78984 -3.640e+00
 #>   120       m1    33.31  28.78984  4.520e+00
f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs", quiet = TRUE)
-summary(f.irls)
#> mkin version used for fitting:    0.9.47.6 
+summary(f.irls)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:57:13 2019 
-#> Date of summary: Thu Feb 21 14:57:13 2019 
+#> Date of fit:     Thu Feb 21 15:12:22 2019 
+#> Date of summary: Thu Feb 21 15:12:22 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -754,7 +754,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 551 model solutions performed in 2.543 s
+#> Fitted with method Port using 551 model solutions performed in 2.573 s
 #> 
 #> Weighting: none
 #> 
@@ -865,10 +865,10 @@
 #>   100       m1    33.13  31.98971  1.140e+00 2.722
 #>   120       m1    25.15  28.80898 -3.659e+00 2.722
 #>   120       m1    33.31  28.80898  4.501e+00 2.722
f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", quiet = TRUE)
-summary(f.w.mean)
#> mkin version used for fitting:    0.9.47.6 
+summary(f.w.mean)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:57:14 2019 
-#> Date of summary: Thu Feb 21 14:57:14 2019 
+#> Date of fit:     Thu Feb 21 15:12:22 2019 
+#> Date of summary: Thu Feb 21 15:12:22 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -983,10 +983,10 @@
 #>   120       m1    25.15  28.82413  -3.674128
 #>   120       m1    33.31  28.82413   4.485872
f.w.value <- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), err = "value",
                      quiet = TRUE)
-summary(f.w.value)
#> mkin version used for fitting:    0.9.47.6 
+summary(f.w.value)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:57:15 2019 
-#> Date of summary: Thu Feb 21 14:57:15 2019 
+#> Date of fit:     Thu Feb 21 15:12:23 2019 
+#> Date of summary: Thu Feb 21 15:12:23 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -994,7 +994,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 174 model solutions performed in 0.8 s
+#> Fitted with method Port using 174 model solutions performed in 0.802 s
 #> 
 #> Weighting: manual
 #> 
@@ -1103,10 +1103,10 @@
 errors <- c(parent = 2, m1 = 1)
 dw$err.man <- errors[FOCUS_2006_D$name]
 f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE)
-summary(f.w.man)
#> mkin version used for fitting:    0.9.47.6 
+summary(f.w.man)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:57:16 2019 
-#> Date of summary: Thu Feb 21 14:57:16 2019 
+#> Date of fit:     Thu Feb 21 15:12:25 2019 
+#> Date of summary: Thu Feb 21 15:12:25 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1114,7 +1114,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 270 model solutions performed in 1.248 s
+#> Fitted with method Port using 270 model solutions performed in 1.251 s
 #> 
 #> Weighting: manual
 #> 
@@ -1221,10 +1221,10 @@
 #>   120       m1    25.15  28.76062  -3.610621   2
 #>   120       m1    33.31  28.76062   4.549379   2
f.w.man.irls <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE,
                        reweight.method = "obs")
-summary(f.w.man.irls)
#> mkin version used for fitting:    0.9.47.6 
+summary(f.w.man.irls)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:57:19 2019 
-#> Date of summary: Thu Feb 21 14:57:19 2019 
+#> Date of fit:     Thu Feb 21 15:12:28 2019 
+#> Date of summary: Thu Feb 21 15:12:28 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1232,7 +1232,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 692 model solutions performed in 3.287 s
+#> Fitted with method Port using 692 model solutions performed in 3.31 s
 #> 
 #> Weighting: manual
 #> 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 17d8400d..e4509e8a 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -68,7 +68,7 @@ For the definition of model types and their parameters, the equations given
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     

 
@@ -231,7 +231,7 @@ For the definition of model types and their parameters, the equations given
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"), verbose = TRUE)
#> Compilation argument:
-#>  /usr/lib/R/bin/R CMD SHLIB file522976635fac.c 2> file522976635fac.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file6490632228a0.c 2> file6490632228a0.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html
index 93aa4b41..7438e0e0 100644
--- a/docs/reference/mkinparplot.html
+++ b/docs/reference/mkinparplot.html
@@ -64,7 +64,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     

 
diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html
index 7e832f97..2f386d45 100644
--- a/docs/reference/mkinplot.html
+++ b/docs/reference/mkinplot.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 414d97a8..deb1335a 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -65,7 +65,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
@@ -330,12 +330,12 @@
                 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 
-#>       0.001       0.000       0.002 
  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 
-#>       0.039       0.000       0.040 

+#>       0.039       0.000       0.039 

   
    # Predict from a fitted model
     f <- mkinfit(SFO_SFO, FOCUS_2006_C)
#> Model cost at call  1 :  552.5739 
 #> Model cost at call  3 :  552.5739 
diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html
index d088cfc9..702e50eb 100644
--- a/docs/reference/mkinresplot.html
+++ b/docs/reference/mkinresplot.html
@@ -66,7 +66,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     

 
diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html
index 135c0325..95689f48 100644
--- a/docs/reference/mkinsub.html
+++ b/docs/reference/mkinsub.html
@@ -64,7 +64,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html
index 7352fb74..af52e38a 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -64,7 +64,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
@@ -191,8 +191,8 @@
 time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))
 
 time_default
#>        User      System verstrichen 
-#>       0.044       0.036       7.245 
time_1
#>        User      System verstrichen 
-#>      22.796       0.004      22.814 

+#>       0.036       0.050       7.160 
time_1
#>        User      System verstrichen 
+#>      22.888       0.000      22.902 

 endpoints(fits.0[["SFO_lin", 2]])
#> $ff
 #>   parent_M1 parent_sink       M1_M2     M1_sink 
 #>   0.7340480   0.2659520   0.7505686   0.2494314 
diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html
index ab94d61b..b46da2f1 100644
--- a/docs/reference/plot.mkinfit.html
+++ b/docs/reference/plot.mkinfit.html
@@ -68,7 +68,7 @@ If the current plot device is a tikz device,
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     

 
diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html
index 689fd488..acea2def 100644
--- a/docs/reference/plot.mmkin.html
+++ b/docs/reference/plot.mmkin.html
@@ -67,7 +67,7 @@ If the current plot device is a tikz device,
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html
index 0cab1051..e4e142d7 100644
--- a/docs/reference/print.mkinds.html
+++ b/docs/reference/print.mkinds.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html
index 0c78b6fb..d5e128a7 100644
--- a/docs/reference/print.mkinmod.html
+++ b/docs/reference/print.mkinmod.html
@@ -63,7 +63,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html
index d1c89770..410c95d8 100644
--- a/docs/reference/schaefer07_complex_case.html
+++ b/docs/reference/schaefer07_complex_case.html
@@ -65,7 +65,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/sigma_twocomp.html b/docs/reference/sigma_twocomp.html
index 00b463e8..01b0d542 100644
--- a/docs/reference/sigma_twocomp.html
+++ b/docs/reference/sigma_twocomp.html
@@ -68,7 +68,7 @@ This is the error model used for example by Werner et al. (1978). The model
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 53b94948..80298bb4 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -66,7 +66,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
@@ -206,17 +206,17 @@
     
 
     
Examples

-    
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.47.6 
+    
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:58:11 2019 
-#> Date of summary: Thu Feb 21 14:58:11 2019 
+#> Date of fit:     Thu Feb 21 15:13:20 2019 
+#> Date of summary: Thu Feb 21 15:13:20 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 35 model solutions performed in 0.085 s
+#> Fitted with method Port using 35 model solutions performed in 0.087 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index 14db4358..b2b55805 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -78,7 +78,7 @@ Compare also the code in the example section to see the degradation models." />
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     

 
diff --git a/docs/reference/test_data_from_UBA_2014.html b/docs/reference/test_data_from_UBA_2014.html
index 1999de8d..39f6d364 100644
--- a/docs/reference/test_data_from_UBA_2014.html
+++ b/docs/reference/test_data_from_UBA_2014.html
@@ -64,7 +64,7 @@
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     

 
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 3dbacbe8..088ea9d0 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -71,7 +71,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
       
       
         mkin
-        0.9.47.6
+        0.9.48.1
       
     
 
@@ -200,10 +200,10 @@ The transformation of sets of formation fractions is fragile, as it supposes
   parent = list(type = "SFO", to = "m1", sink = TRUE),
   m1 = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
 fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
-summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version used for fitting:    0.9.47.6 
+summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:58:19 2019 
-#> Date of summary: Thu Feb 21 14:58:19 2019 
+#> Date of fit:     Thu Feb 21 15:13:29 2019 
+#> Date of summary: Thu Feb 21 15:13:29 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -211,7 +211,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 153 model solutions performed in 0.765 s
+#> Fitted with method Port using 153 model solutions performed in 0.84 s
 #> 
 #> Weighting: none
 #> 
@@ -276,10 +276,10 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> parent   7.023  23.33
 #> m1     131.761 437.70

 
fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
-summary(fit.2, data=FALSE)
#> mkin version used for fitting:    0.9.47.6 
+summary(fit.2, data=FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:58:21 2019 
-#> Date of summary: Thu Feb 21 14:58:21 2019 
+#> Date of fit:     Thu Feb 21 15:13:30 2019 
+#> Date of summary: Thu Feb 21 15:13:30 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -287,7 +287,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 350 model solutions performed in 1.58 s
+#> Fitted with method Port using 350 model solutions performed in 1.631 s
 #> 
 #> Weighting: none
 #> 
@@ -364,10 +364,10 @@ The transformation of sets of formation fractions is fragile, as it supposes
   m1 = list(type = "SFO"),
   use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

 fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
-summary(fit.ff, data = FALSE)
#> mkin version used for fitting:    0.9.47.6 
+summary(fit.ff, data = FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:58:22 2019 
-#> Date of summary: Thu Feb 21 14:58:22 2019 
+#> Date of fit:     Thu Feb 21 15:13:32 2019 
+#> Date of summary: Thu Feb 21 15:13:32 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -375,7 +375,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 186 model solutions performed in 0.872 s
+#> Fitted with method Port using 186 model solutions performed in 0.852 s
 #> 
 #> Weighting: none
 #> 
@@ -448,10 +448,10 @@ The transformation of sets of formation fractions is fragile, as it supposes
   use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

 
 fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE)
-summary(fit.ff.2, data = FALSE)
#> mkin version used for fitting:    0.9.47.6 
+summary(fit.ff.2, data = FALSE)
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:58:23 2019 
-#> Date of summary: Thu Feb 21 14:58:23 2019 
+#> Date of fit:     Thu Feb 21 15:13:32 2019 
+#> Date of summary: Thu Feb 21 15:13:32 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
-- 
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