From af84d618508d5882072ab7b8de481cb5efc60852 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 21 Feb 2019 15:01:03 +0100 Subject: Make example logistic fit quiet --- docs/articles/FOCUS_D.html | 6 ++-- docs/articles/FOCUS_L.html | 42 ++++++++++++------------ docs/articles/web_only/compiled_models.html | 12 +++---- docs/reference/Extract.mmkin.html | 12 +++---- docs/reference/logistic.solution.html | 50 ++--------------------------- docs/reference/mccall81_245T.html | 12 +++---- docs/reference/mkinfit.html | 42 ++++++++++++------------ docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 4 +-- docs/reference/mmkin.html | 4 +-- docs/reference/summary.mkinfit.html | 4 +-- docs/reference/transform_odeparms.html | 24 +++++++------- man/logistic.solution.Rd | 2 +- 13 files changed, 85 insertions(+), 131 deletions(-) diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index 6a8500a0..4a080ac1 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -163,8 +163,8 @@ 
summary(fit)
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Feb 21 14:32:03 2019 
-## Date of summary: Thu Feb 21 14:32:04 2019 
+## Date of fit:     Thu Feb 21 14:58:25 2019 
+## Date of summary: Thu Feb 21 14:58:26 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -172,7 +172,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.735 s
+## Fitted with method Port using 153 model solutions performed in 0.705 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 265dd96c..b9f72dbe 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -111,15 +111,15 @@
 summary(m.L1.SFO)
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Feb 21 14:32:06 2019 
-## Date of summary: Thu Feb 21 14:32:06 2019 
+## Date of fit:     Thu Feb 21 14:58:27 2019 
+## Date of summary: Thu Feb 21 14:58:27 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.097 s
+## Fitted with method Port using 37 model solutions performed in 0.096 s
 ## 
 ## Weighting: none
 ## 
@@ -202,15 +202,15 @@
 
summary(m.L1.FOMC, data = FALSE)

 
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Feb 21 14:32:08 2019 
-## Date of summary: Thu Feb 21 14:32:08 2019 
+## Date of fit:     Thu Feb 21 14:58:29 2019 
+## Date of summary: Thu Feb 21 14:58:29 2019 
 ## 
 ## 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 1.547 s
+## Fitted with method Port using 611 model solutions performed in 1.507 s
 ## 
 ## Weighting: none
 ## 
@@ -297,15 +297,15 @@
 
summary(m.L2.FOMC, data = FALSE)

 
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Feb 21 14:32:08 2019 
-## Date of summary: Thu Feb 21 14:32:08 2019 
+## Date of fit:     Thu Feb 21 14:58:30 2019 
+## Date of summary: Thu Feb 21 14:58:30 2019 
 ## 
 ## 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 0.201 s
+## Fitted with method Port using 81 model solutions performed in 0.197 s
 ## 
 ## Weighting: none
 ## 
@@ -368,8 +368,8 @@
 
summary(m.L2.DFOP, data = FALSE)

 
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Feb 21 14:32:09 2019 
-## Date of summary: Thu Feb 21 14:32:09 2019 
+## Date of fit:     Thu Feb 21 14:58:31 2019 
+## Date of summary: Thu Feb 21 14:58:31 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -378,7 +378,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 0.86 s
+## Fitted with method Port using 336 model solutions performed in 0.842 s
 ## 
 ## Weighting: none
 ## 
@@ -460,8 +460,8 @@
 
summary(mm.L3[["DFOP", 1]])

 
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Feb 21 14:32:10 2019 
-## Date of summary: Thu Feb 21 14:32:11 2019 
+## Date of fit:     Thu Feb 21 14:58:32 2019 
+## Date of summary: Thu Feb 21 14:58:32 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -470,7 +470,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.351 s
+## Fitted with method Port using 137 model solutions performed in 0.346 s
 ## 
 ## Weighting: none
 ## 
@@ -561,15 +561,15 @@
 
summary(mm.L4[["SFO", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Feb 21 14:32:11 2019 
-## Date of summary: Thu Feb 21 14:32:11 2019 
+## Date of fit:     Thu Feb 21 14:58:32 2019 
+## Date of summary: Thu Feb 21 14:58:33 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.113 s
+## Fitted with method Port using 46 model solutions performed in 0.111 s
 ## 
 ## Weighting: none
 ## 
@@ -621,15 +621,15 @@
 
summary(mm.L4[["FOMC", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.47.6 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Thu Feb 21 14:32:11 2019 
-## Date of summary: Thu Feb 21 14:32:11 2019 
+## Date of fit:     Thu Feb 21 14:58:33 2019 
+## Date of summary: Thu Feb 21 14:58:33 2019 
 ## 
 ## 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 0.168 s
+## Fitted with method Port using 66 model solutions performed in 0.165 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 3a37d114..e1149c67 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -126,14 +126,14 @@
 }

 
## Lade nötiges Paket: rbenchmark

 
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   2.429    1.000     2.427        0
-## 1 deSolve, not compiled            3  17.826    7.339    17.815        0
-## 2      Eigenvalue based            3   2.968    1.222     2.967        0
+## 3     deSolve, compiled            3   2.329    1.000     2.327        0
+## 1 deSolve, not compiled            3  17.556    7.538    17.549        0
+## 2      Eigenvalue based            3   2.863    1.229     2.860        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
 ## 2          0         0

-
We see that using the compiled model is by a factor of around 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 around 8 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.

 
 

 

@@ -157,8 +157,8 @@
 }

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

 
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.234    1.000     4.232        0
-## 1 deSolve, not compiled            3  37.807    8.929    37.785        0
+## 2     deSolve, compiled            3   4.105    1.000     4.101        0
+## 1 deSolve, not compiled            3  37.400    9.111    37.381        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index dd088a0f..fe6fc125 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -280,7 +280,7 @@
 #> 
 #> $time
 #>        User      System verstrichen 
-#>       0.196       0.000       0.196 
+#>       0.199       0.000       0.200 
 #> 
 #> $mkinmod
 #> <mkinmod> model generated with
@@ -469,8 +469,8 @@
 #>     }
 #>     return(mC)
 #> }
-#> <bytecode: 0x555559201470>
-#> <environment: 0x555555ce4640>
+#> <bytecode: 0x555559227548>
+#> <environment: 0x555556ee4048>
 #> 
 #> $cost_notrans
 #> function (P) 
@@ -492,8 +492,8 @@
 #>         scaleVar = scaleVar)
 #>     return(mC)
 #> }
-#> <bytecode: 0x55555a3214d8>
-#> <environment: 0x555555ce4640>
+#> <bytecode: 0x55555a34ddf0>
+#> <environment: 0x555556ee4048>
 #> 
 #> $hessian_notrans
 #>                   parent_0 k_parent_sink
@@ -560,7 +560,7 @@
 #> 99.17407 
 #> 
 #> $date
-#> [1] "Thu Feb 21 14:30:10 2019"
+#> [1] "Thu Feb 21 14:56:32 2019"
 #> 
 #> $version
 #> [1] "0.9.47.6"
diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html
index b0ab72d7..310f1c5a 100644
--- a/docs/reference/logistic.solution.html
+++ b/docs/reference/logistic.solution.html
@@ -202,54 +202,8 @@
     sdfunc = function(x) sigma_twocomp(x, 0.5, 0.07),
     n = 1, reps = 2, digits = 5, LOD = 0.1, seed = 123456)[[1]]
 
-  m <- mkinfit("logistic", d_2_1)
#> Model cost at call  1 :  789.6044 
-#> Model cost at call  2 :  789.6043 
-#> Model cost at call  7 :  716.9934 
-#> Model cost at call  12 :  697.1186 
-#> Model cost at call  15 :  697.1185 
-#> Model cost at call  16 :  697.1184 
-#> Model cost at call  17 :  661.1574 
-#> Model cost at call  20 :  661.1573 
-#> Model cost at call  22 :  620.0542 
-#> Model cost at call  25 :  620.0541 
-#> Model cost at call  29 :  616.6874 
-#> Model cost at call  32 :  616.6874 
-#> Model cost at call  33 :  616.6874 
-#> Model cost at call  34 :  615.1671 
-#> Model cost at call  37 :  615.1671 
-#> Model cost at call  39 :  612.0795 
-#> Model cost at call  42 :  612.0795 
-#> Model cost at call  43 :  612.0795 
-#> Model cost at call  44 :  605.9119 
-#> Model cost at call  45 :  593.0433 
-#> Model cost at call  46 :  548.0815 
-#> Model cost at call  47 :  504.9062 
-#> Model cost at call  50 :  504.9061 
-#> Model cost at call  51 :  504.9061 
-#> Model cost at call  53 :  485.929 
-#> Model cost at call  55 :  485.929 
-#> Model cost at call  56 :  485.929 
-#> Model cost at call  58 :  485.241 
-#> Model cost at call  60 :  485.241 
-#> Model cost at call  61 :  485.2409 
-#> Model cost at call  62 :  485.2409 
-#> Model cost at call  63 :  484.0717 
-#> Model cost at call  69 :  483.9062 
-#> Model cost at call  74 :  483.5646 
-#> Model cost at call  79 :  483.4908 
-#> Model cost at call  84 :  483.4859 
-#> Model cost at call  85 :  483.4859 
-#> Model cost at call  89 :  483.4848 
-#> Model cost at call  90 :  483.4836 
-#> Model cost at call  92 :  483.4836 
-#> Model cost at call  94 :  483.4836 
-#> Model cost at call  97 :  483.4833 
-#> Model cost at call  100 :  483.4833 
-#> Model cost at call  105 :  483.4832 
-#> Model cost at call  108 :  483.4832 
-#> Model cost at call  114 :  483.4832 
-#> Model cost at call  128 :  483.4832 
-#> Optimisation by method Port successfully terminated.
  plot_sep(m)
  summary(m)$bpar
#>              Estimate   se_notrans    t value       Pr(>t)        Lower
+  m <- mkinfit("logistic", d_2_1, quiet = TRUE)
+  plot_sep(m)
  summary(m)$bpar
#>              Estimate   se_notrans    t value       Pr(>t)        Lower
 #> parent_0 1.057896e+02 2.3743105248 44.5559374 6.656664e-16 1.006602e+02
 #> kmax     6.398190e-02 0.0193490291  3.3067243 2.836921e-03 3.329058e-02
 #> k0       1.612775e-04 0.0009640761  0.1672871 4.348592e-01 3.972250e-10
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index dcfc499f..bed8ed8e 100644
--- a/docs/reference/mccall81_245T.html
+++ b/docs/reference/mccall81_245T.html
@@ -160,8 +160,8 @@
                          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 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:30:31 2019 
-#> Date of summary: Thu Feb 21 14:30:31 2019 
+#> Date of fit:     Thu Feb 21 14:56:53 2019 
+#> Date of summary: Thu Feb 21 14:56:53 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 3.822 s
+#> Fitted with method Port using 574 model solutions performed in 3.873 s
 #> 
 #> Weighting: none
 #> 
@@ -249,8 +249,8 @@
                    fixed_parms = "k_phenol_sink", quiet = TRUE)
     summary(fit.2, data = FALSE)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:30:32 2019 
-#> Date of summary: Thu Feb 21 14:30:32 2019 
+#> Date of fit:     Thu Feb 21 14:56:55 2019 
+#> Date of summary: Thu Feb 21 14:56:55 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 1.601 s
+#> Fitted with method Port using 246 model solutions performed in 1.633 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html
index d09b9232..4f071574 100644
--- a/docs/reference/mkinfit.html
+++ b/docs/reference/mkinfit.html
@@ -438,8 +438,8 @@
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
 summary(fit)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:30:35 2019 
-#> Date of summary: Thu Feb 21 14:30:35 2019 
+#> Date of fit:     Thu Feb 21 14:56:58 2019 
+#> Date of summary: Thu Feb 21 14:56:58 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -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 
-#>       1.017       0.004       1.022 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       1.036       0.000       1.036 
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 
-#>       0.845       0.000       0.846 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.830       0.000       0.832 
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 
@@ -628,8 +628,8 @@
                       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 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:30:47 2019 
-#> Date of summary: Thu Feb 21 14:30:47 2019 
+#> Date of fit:     Thu Feb 21 14:57:10 2019 
+#> Date of summary: Thu Feb 21 14:57:10 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -745,8 +745,8 @@
 #>   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 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:30:50 2019 
-#> Date of summary: Thu Feb 21 14:30:50 2019 
+#> Date of fit:     Thu Feb 21 14:57:13 2019 
+#> Date of summary: Thu Feb 21 14:57:13 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 2.529 s
+#> Fitted with method Port using 551 model solutions performed in 2.543 s
 #> 
 #> Weighting: none
 #> 
@@ -867,8 +867,8 @@
 #>   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 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:30:51 2019 
-#> Date of summary: Thu Feb 21 14:30:51 2019 
+#> Date of fit:     Thu Feb 21 14:57:14 2019 
+#> Date of summary: Thu Feb 21 14:57:14 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -876,7 +876,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 155 model solutions performed in 0.707 s
+#> Fitted with method Port using 155 model solutions performed in 0.718 s
 #> 
 #> Weighting: mean
 #> 
@@ -985,8 +985,8 @@
                      quiet = TRUE)
 summary(f.w.value)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:30:52 2019 
-#> Date of summary: Thu Feb 21 14:30:52 2019 
+#> Date of fit:     Thu Feb 21 14:57:15 2019 
+#> Date of summary: Thu Feb 21 14:57:15 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 0.792 s
+#> Fitted with method Port using 174 model solutions performed in 0.8 s
 #> 
 #> Weighting: manual
 #> 
@@ -1105,8 +1105,8 @@
 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 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:30:53 2019 
-#> Date of summary: Thu Feb 21 14:30:53 2019 
+#> Date of fit:     Thu Feb 21 14:57:16 2019 
+#> Date of summary: Thu Feb 21 14:57:16 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 1.243 s
+#> Fitted with method Port using 270 model solutions performed in 1.248 s
 #> 
 #> Weighting: manual
 #> 
@@ -1223,8 +1223,8 @@
                        reweight.method = "obs")
 summary(f.w.man.irls)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:30:57 2019 
-#> Date of summary: Thu Feb 21 14:30:57 2019 
+#> Date of fit:     Thu Feb 21 14:57:19 2019 
+#> Date of summary: Thu Feb 21 14:57:19 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 3.27 s
+#> Fitted with method Port using 692 model solutions performed in 3.287 s
 #> 
 #> Weighting: manual
 #> 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 0710e6de..17d8400d 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -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 file33652d0fd552.c 2> file33652d0fd552.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file522976635fac.c 2> file522976635fac.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 8c5bf22b..414d97a8 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -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 
-#>       0.002       0.000       0.002 
  system.time(
+#>       0.001       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 
-#>       0.047       0.000       0.047 

+#>       0.039       0.000       0.040 

   
    # 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/mmkin.html b/docs/reference/mmkin.html
index 75da28c7..7352fb74 100644
--- a/docs/reference/mmkin.html
+++ b/docs/reference/mmkin.html
@@ -191,8 +191,8 @@
 time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))
 
 time_default
#>        User      System verstrichen 
-#>       0.039       0.040       7.082 
time_1
#>        User      System verstrichen 
-#>      22.650       0.004      22.666 

+#>       0.044       0.036       7.245 
time_1
#>        User      System verstrichen 
+#>      22.796       0.004      22.814 

 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/summary.mkinfit.html b/docs/reference/summary.mkinfit.html
index 242d9f63..53b94948 100644
--- a/docs/reference/summary.mkinfit.html
+++ b/docs/reference/summary.mkinfit.html
@@ -208,8 +208,8 @@
     
Examples

     
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:31:48 2019 
-#> Date of summary: Thu Feb 21 14:31:48 2019 
+#> Date of fit:     Thu Feb 21 14:58:11 2019 
+#> Date of summary: Thu Feb 21 14:58:11 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 939fa7b4..3dbacbe8 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -202,8 +202,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 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 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:31:57 2019 
-#> Date of summary: Thu Feb 21 14:31:57 2019 
+#> Date of fit:     Thu Feb 21 14:58:19 2019 
+#> Date of summary: Thu Feb 21 14:58:19 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 0.849 s
+#> Fitted with method Port using 153 model solutions performed in 0.765 s
 #> 
 #> Weighting: none
 #> 
@@ -278,8 +278,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 
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 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:31:59 2019 
-#> Date of summary: Thu Feb 21 14:31:59 2019 
+#> Date of fit:     Thu Feb 21 14:58:21 2019 
+#> Date of summary: Thu Feb 21 14:58:21 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 1.649 s
+#> Fitted with method Port using 350 model solutions performed in 1.58 s
 #> 
 #> Weighting: none
 #> 
@@ -366,8 +366,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 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 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:32:00 2019 
-#> Date of summary: Thu Feb 21 14:32:00 2019 
+#> Date of fit:     Thu Feb 21 14:58:22 2019 
+#> Date of summary: Thu Feb 21 14:58:22 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 0.976 s
+#> Fitted with method Port using 186 model solutions performed in 0.872 s
 #> 
 #> Weighting: none
 #> 
@@ -450,8 +450,8 @@ The transformation of sets of formation fractions is fragile, as it supposes
 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 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Thu Feb 21 14:32:01 2019 
-#> Date of summary: Thu Feb 21 14:32:01 2019 
+#> Date of fit:     Thu Feb 21 14:58:23 2019 
+#> Date of summary: Thu Feb 21 14:58:23 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -459,7 +459,7 @@ The transformation of sets of formation fractions is fragile, as it supposes
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 104 model solutions performed in 0.512 s
+#> Fitted with method Port using 104 model solutions performed in 0.473 s
 #> 
 #> Weighting: none
 #> 
diff --git a/man/logistic.solution.Rd b/man/logistic.solution.Rd
index 798e78d1..396e09ef 100644
--- a/man/logistic.solution.Rd
+++ b/man/logistic.solution.Rd
@@ -61,7 +61,7 @@ logistic.solution(t, parent.0, kmax, k0, r)
     sdfunc = function(x) sigma_twocomp(x, 0.5, 0.07),
     n = 1, reps = 2, digits = 5, LOD = 0.1, seed = 123456)[[1]]
 
-  m <- mkinfit("logistic", d_2_1)
+  m <- mkinfit("logistic", d_2_1, quiet = TRUE)
   plot_sep(m)
   summary(m)$bpar
 }
-- 
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