From 20d7834a633d32b663c6bcc1a7f7b0300aa65d5b Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 29 Jul 2017 15:15:41 +0200 Subject: Bump version, update NEWS and rebuild pkdown docs --- docs/reference/mkinfit.html | 72 ++++++++++++++++++++++----------------------- 1 file changed, 36 insertions(+), 36 deletions(-) (limited to 'docs/reference/mkinfit.html') diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 875bd1dd..cdf7c7ef 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -377,17 +377,17 @@

Examples

# Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-summary(fit)
#> mkin version:    0.9.45.2 
-#> R version:       3.4.0 
-#> Date of fit:     Fri May  5 12:45:06 2017 
-#> Date of summary: Fri May  5 12:45:06 2017 
+summary(fit)
#> mkin version:    0.9.46 
+#> R version:       3.4.1 
+#> Date of fit:     Sat Jul 29 15:14:18 2017 
+#> Date of summary: Sat Jul 29 15:14:18 2017 
 #> 
 #> 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 0.206 s
+#> Fitted with method Port using 64 model solutions performed in 0.141 s
 #> 
 #> Weighting: none
 #> 
@@ -456,7 +456,7 @@
   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 elapsed 
-#>   0.912   0.000   0.915 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>   0.888   0.000   0.890 
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 
@@ -535,7 +535,7 @@
 #> Model cost at call  153 :  371.2134 
 #> Optimisation by method Port successfully terminated.
 #>    user  system elapsed 
-#>   0.792   0.000   0.793 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>   0.728   0.000   0.729 
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 
@@ -576,10 +576,10 @@
 # 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:    0.9.45.2 
-#> R version:       3.4.0 
-#> Date of fit:     Fri May  5 12:45:17 2017 
-#> Date of summary: Fri May  5 12:45:17 2017 
+summary(f.noweight)
#> mkin version:    0.9.46 
+#> R version:       3.4.1 
+#> Date of fit:     Sat Jul 29 15:14:28 2017 
+#> Date of summary: Sat Jul 29 15:14:28 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -697,10 +697,10 @@
 #>   100       m1    33.13 3.198e+01  1.148e+00
 #>   120       m1    25.15 2.879e+01 -3.640e+00
 #>   120       m1    33.31 2.879e+01  4.520e+00
f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs", quiet = TRUE)
-summary(f.irls)
#> mkin version:    0.9.45.2 
-#> R version:       3.4.0 
-#> Date of fit:     Fri May  5 12:45:19 2017 
-#> Date of summary: Fri May  5 12:45:19 2017 
+summary(f.irls)
#> mkin version:    0.9.46 
+#> R version:       3.4.1 
+#> Date of fit:     Sat Jul 29 15:14:30 2017 
+#> Date of summary: Sat Jul 29 15:14:30 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -708,7 +708,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 468 model solutions performed in 1.925 s
+#> Fitted with method Port using 468 model solutions performed in 1.914 s
 #> 
 #> Weighting: none then iterative reweighting method obs
 #> 
@@ -818,10 +818,10 @@
 #>   100       m1    33.13 3.199e+01  1.140e+00 2.722
 #>   120       m1    25.15 2.881e+01 -3.659e+00 2.722
 #>   120       m1    33.31 2.881e+01  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:    0.9.45.2 
-#> R version:       3.4.0 
-#> Date of fit:     Fri May  5 12:45:20 2017 
-#> Date of summary: Fri May  5 12:45:20 2017 
+summary(f.w.mean)
#> mkin version:    0.9.46 
+#> R version:       3.4.1 
+#> Date of fit:     Sat Jul 29 15:14:31 2017 
+#> Date of summary: Sat Jul 29 15:14:31 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -829,7 +829,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 155 model solutions performed in 0.699 s
+#> Fitted with method Port using 155 model solutions performed in 0.692 s
 #> 
 #> Weighting: mean
 #> 
@@ -940,10 +940,10 @@
 #>   120       m1    25.15 28.824128  -3.674128
 #>   120       m1    33.31 28.824128   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:    0.9.45.2 
-#> R version:       3.4.0 
-#> Date of fit:     Fri May  5 12:45:21 2017 
-#> Date of summary: Fri May  5 12:45:21 2017 
+summary(f.w.value)
#> mkin version:    0.9.46 
+#> R version:       3.4.1 
+#> Date of fit:     Sat Jul 29 15:14:32 2017 
+#> Date of summary: Sat Jul 29 15:14:32 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -951,7 +951,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 174 model solutions performed in 0.767 s
+#> Fitted with method Port using 174 model solutions performed in 0.701 s
 #> 
 #> Weighting: manual
 #> 
@@ -1062,10 +1062,10 @@
 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:    0.9.45.2 
-#> R version:       3.4.0 
-#> Date of fit:     Fri May  5 12:45:22 2017 
-#> Date of summary: Fri May  5 12:45:22 2017 
+summary(f.w.man)
#> mkin version:    0.9.46 
+#> R version:       3.4.1 
+#> Date of fit:     Sat Jul 29 15:14:33 2017 
+#> Date of summary: Sat Jul 29 15:14:33 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1073,7 +1073,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 297 model solutions performed in 1.276 s
+#> Fitted with method Port using 297 model solutions performed in 1.223 s
 #> 
 #> Weighting: manual
 #> 
@@ -1184,10 +1184,10 @@
 #>   120       m1    25.15 28.760616  -3.610616   2
 #>   120       m1    33.31 28.760616   4.549384   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:    0.9.45.2 
-#> R version:       3.4.0 
-#> Date of fit:     Fri May  5 12:45:25 2017 
-#> Date of summary: Fri May  5 12:45:25 2017 
+summary(f.w.man.irls)
#> mkin version:    0.9.46 
+#> R version:       3.4.1 
+#> Date of fit:     Sat Jul 29 15:14:36 2017 
+#> Date of summary: Sat Jul 29 15:14:36 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1195,7 +1195,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 628 model solutions performed in 2.626 s
+#> Fitted with method Port using 628 model solutions performed in 2.578 s
 #> 
 #> Weighting: manual then iterative reweighting method obs
 #> 
-- 
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