From 39b6d8b8569801c2957b22d0973b5ad0c9405e7d Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 18 Sep 2018 10:14:40 +0200 Subject: Support maximum twa for HS, test, docs --- docs/reference/mkinfit.html | 62 ++++++++++++++++++++++----------------------- 1 file changed, 31 insertions(+), 31 deletions(-) (limited to 'docs/reference/mkinfit.html') diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index f3c6d595..1ae53f8a 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -71,7 +71,7 @@ mkin - 0.9.47.5 + 0.9.47.6 @@ -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:    0.9.47.5 
+summary(fit)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 20:59:02 2018 
-#> Date of summary: Fri Sep 14 20:59:02 2018 
+#> Date of fit:     Tue Sep 18 09:49:30 2018 
+#> Date of summary: Tue Sep 18 09:49:30 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 0.14 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 
-#>       0.895       0.000       0.897 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.872       0.001       0.874 
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 
-#>       0.726       0.000       0.726 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>       0.690       0.000       0.689 
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:    0.9.47.5 
+summary(f.noweight)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 20:59:13 2018 
-#> Date of summary: Fri Sep 14 20:59:13 2018 
+#> Date of fit:     Tue Sep 18 09:49:40 2018 
+#> Date of summary: Tue Sep 18 09:49:40 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 0.757 s
+#> Fitted with method Port using 186 model solutions performed in 0.725 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:    0.9.47.5 
+summary(f.irls)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 20:59:15 2018 
-#> Date of summary: Fri Sep 14 20:59:16 2018 
+#> Date of fit:     Tue Sep 18 09:49:42 2018 
+#> Date of summary: Tue Sep 18 09:49:42 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 2.329 s
+#> Fitted with method Port using 551 model solutions performed in 2.147 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:    0.9.47.5 
+summary(f.w.mean)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 20:59:16 2018 
-#> Date of summary: Fri Sep 14 20:59:16 2018 
+#> Date of fit:     Tue Sep 18 09:49:43 2018 
+#> Date of summary: Tue Sep 18 09:49:43 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 0.628 s
+#> Fitted with method Port using 155 model solutions performed in 0.603 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:    0.9.47.5 
+summary(f.w.value)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 20:59:17 2018 
-#> Date of summary: Fri Sep 14 20:59:17 2018 
+#> Date of fit:     Tue Sep 18 09:49:44 2018 
+#> Date of summary: Tue Sep 18 09:49:44 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 0.713 s
+#> Fitted with method Port using 174 model solutions performed in 0.69 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:    0.9.47.5 
+summary(f.w.man)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 20:59:18 2018 
-#> Date of summary: Fri Sep 14 20:59:18 2018 
+#> Date of fit:     Tue Sep 18 09:49:45 2018 
+#> Date of summary: Tue Sep 18 09:49:45 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 1.119 s
+#> Fitted with method Port using 270 model solutions performed in 1.133 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:    0.9.47.5 
+summary(f.w.man.irls)
#> mkin version used for fitting:    0.9.47.6 
 #> R version used for fitting:       3.5.1 
-#> Date of fit:     Fri Sep 14 20:59:21 2018 
-#> Date of summary: Fri Sep 14 20:59:21 2018 
+#> Date of fit:     Tue Sep 18 09:49:48 2018 
+#> Date of summary: Tue Sep 18 09:49:48 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 2.955 s
+#> Fitted with method Port using 692 model solutions performed in 2.77 s
 #> 
 #> Weighting: manual
 #> 
-- 
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