From 70d158c4dd919f4f77bc12f8ace333d29d249b79 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 14 Sep 2018 16:57:17 +0200 Subject: Remove two vignettes from the package but not from docs - Rebuild static documentation - Adapt test to new approach to two component error model where the model is inadequate --- docs/reference/mkinfit.html | 66 ++++++++++++++++++++++----------------------- 1 file changed, 33 insertions(+), 33 deletions(-) (limited to 'docs/reference/mkinfit.html') diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 13029e91..0f2bb875 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -71,7 +71,7 @@ mkin - 0.9.47.4 + 0.9.47.5 @@ -97,10 +97,10 @@ Example evaluation of FOCUS Laboratory Data L1 to L3
  • - Example evaluation of FOCUS Example Dataset Z + Example evaluation of FOCUS Example Dataset Z
  • - Performance benefit by using compiled model definitions in mkin + Performance benefit by using compiled model definitions in mkin
  • Calculation of time weighted average concentrations with mkin @@ -432,17 +432,17 @@

    Examples

    # Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-summary(fit)
    #> mkin version used for fitting:    0.9.47.4 
+summary(fit)
    #> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 11:34:54 2018 
-#> Date of summary: Fri Sep 14 11:34:54 2018 
+#> Date of fit:     Fri Sep 14 16:53:29 2018 
+#> Date of summary: Fri Sep 14 16:53:29 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 0.141 s
+#> Fitted with method Port using 64 model solutions performed in 0.158 s
 #> 
 #> Weighting: none
 #> 
@@ -511,7 +511,7 @@
   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 
-#>       0.906       0.000       0.907 
    coef(fit)
    #>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.909       0.000       0.910 
    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 
@@ -586,7 +586,7 @@
 #> Model cost at call  146 :  371.2134 
 #> Optimisation by method Port successfully terminated.
 #>        User      System verstrichen 
-#>       0.714       0.000       0.715 
    coef(fit.deSolve)
    #>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.749       0.000       0.749 
    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 
@@ -622,10 +622,10 @@
 
    # 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:    0.9.47.4 
+summary(f.noweight)
    #> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 11:35:05 2018 
-#> Date of summary: Fri Sep 14 11:35:05 2018 
+#> Date of fit:     Fri Sep 14 16:53:40 2018 
+#> Date of summary: Fri Sep 14 16:53:40 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -633,7 +633,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 186 model solutions performed in 0.763 s
+#> Fitted with method Port using 186 model solutions performed in 0.79 s
 #> 
 #> Weighting: none
 #> 
@@ -739,10 +739,10 @@
 #>   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:    0.9.47.4 
+summary(f.irls)
    #> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 11:35:07 2018 
-#> Date of summary: Fri Sep 14 11:35:07 2018 
+#> Date of fit:     Fri Sep 14 16:53:43 2018 
+#> Date of summary: Fri Sep 14 16:53:43 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -750,7 +750,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 551 model solutions performed in 2.297 s
+#> Fitted with method Port using 551 model solutions performed in 2.278 s
 #> 
 #> Weighting: none
 #> 
@@ -861,10 +861,10 @@
 #>   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:    0.9.47.4 
+summary(f.w.mean)
    #> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 11:35:08 2018 
-#> Date of summary: Fri Sep 14 11:35:08 2018 
+#> Date of fit:     Fri Sep 14 16:53:43 2018 
+#> Date of summary: Fri Sep 14 16:53:43 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -872,7 +872,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 155 model solutions performed in 0.618 s
+#> Fitted with method Port using 155 model solutions performed in 0.643 s
 #> 
 #> Weighting: mean
 #> 
@@ -979,10 +979,10 @@
 #>   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:    0.9.47.4 
+summary(f.w.value)
    #> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 11:35:09 2018 
-#> Date of summary: Fri Sep 14 11:35:09 2018 
+#> Date of fit:     Fri Sep 14 16:53:44 2018 
+#> Date of summary: Fri Sep 14 16:53:44 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -990,7 +990,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 174 model solutions performed in 0.704 s
+#> Fitted with method Port using 174 model solutions performed in 0.722 s
 #> 
 #> Weighting: manual
 #> 
@@ -1099,10 +1099,10 @@
 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:    0.9.47.4 
+summary(f.w.man)
    #> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 11:35:10 2018 
-#> Date of summary: Fri Sep 14 11:35:10 2018 
+#> Date of fit:     Fri Sep 14 16:53:45 2018 
+#> Date of summary: Fri Sep 14 16:53:45 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1110,7 +1110,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 270 model solutions performed in 1.109 s
+#> Fitted with method Port using 270 model solutions performed in 1.11 s
 #> 
 #> Weighting: manual
 #> 
@@ -1217,10 +1217,10 @@
 #>   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:    0.9.47.4 
+summary(f.w.man.irls)
    #> mkin version used for fitting:    0.9.47.5 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 11:35:13 2018 
-#> Date of summary: Fri Sep 14 11:35:13 2018 
+#> Date of fit:     Fri Sep 14 16:53:49 2018 
+#> Date of summary: Fri Sep 14 16:53:49 2018 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1228,7 +1228,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 692 model solutions performed in 2.903 s
+#> Fitted with method Port using 692 model solutions performed in 2.945 s
 #> 
 #> Weighting: manual
 #> 
-- 
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