From 4a048d8f6f70029141ffe4b6630c5eff4ba672f0 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 15 Mar 2017 09:46:01 +0100 Subject: Static documentation except articles rebuilt by pkgdown --- docs/reference/mkinfit.html | 83 ++++++++++++++++++++++++--------------------- 1 file changed, 44 insertions(+), 39 deletions(-) (limited to 'docs/reference/mkinfit.html') diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 3dd701d3..01c930e2 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -6,7 +6,8 @@ -Fit a kinetic model to data with one or more state variables — mkinfit • mkin + + — mkinfit • mkin @@ -71,6 +72,9 @@ Performance benefit by using compiled model definitions in mkin + +
  • + News
    • @@ -92,7 +96,8 @@
    -

    Fit a kinetic model to data with one or more state variables

    +

    +

    @@ -372,17 +377,17 @@

    Examples

    # Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-summary(fit)
    #> mkin version:    0.9.44.9000 
-#> R version:       3.3.2 
-#> Date of fit:     Thu Dec  8 07:56:46 2016 
-#> Date of summary: Thu Dec  8 07:56:46 2016 
+summary(fit)
    #> mkin version:    0.9.45.1 
+#> R version:       3.3.3 
+#> Date of fit:     Wed Mar 15 09:44:56 2017 
+#> Date of summary: Wed Mar 15 09:44:56 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 0.145 s
+#> Fitted with method Port using 64 model solutions performed in 0.146 s
 #> 
 #> Weighting: none
 #> 
@@ -451,7 +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 
-#>   1.172   1.232   0.904 
    coef(fit)
    #>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>   1.216   1.268   0.942 
    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 
@@ -528,7 +533,7 @@
 #> Model cost at call  152 :  371.2134 
 #> Optimisation by method Port successfully terminated.
 #>    user  system elapsed 
-#>   0.712   0.044   0.709 
    coef(fit.deSolve)
    #>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>   0.712   0.040   0.703 
    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 
@@ -569,10 +574,10 @@
 # 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:    0.9.44.9000 
-#> R version:       3.3.2 
-#> Date of fit:     Thu Dec  8 07:56:57 2016 
-#> Date of summary: Thu Dec  8 07:56:57 2016 
+summary(f.noweight)
    #> mkin version:    0.9.45.1 
+#> R version:       3.3.3 
+#> Date of fit:     Wed Mar 15 09:45:07 2017 
+#> Date of summary: Wed Mar 15 09:45:07 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -580,7 +585,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 185 model solutions performed in 0.77 s
+#> Fitted with method Port using 185 model solutions performed in 0.753 s
 #> 
 #> Weighting: none
 #> 
@@ -690,10 +695,10 @@
 #>   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:    0.9.44.9000 
-#> R version:       3.3.2 
-#> Date of fit:     Thu Dec  8 07:56:59 2016 
-#> Date of summary: Thu Dec  8 07:56:59 2016 
+summary(f.irls)
    #> mkin version:    0.9.45.1 
+#> R version:       3.3.3 
+#> Date of fit:     Wed Mar 15 09:45:09 2017 
+#> Date of summary: Wed Mar 15 09:45:09 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -701,7 +706,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 486 model solutions performed in 2.019 s
+#> Fitted with method Port using 486 model solutions performed in 2.091 s
 #> 
 #> Weighting: none then iterative reweighting method obs
 #> 
@@ -811,10 +816,10 @@
 #>   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:    0.9.44.9000 
-#> R version:       3.3.2 
-#> Date of fit:     Thu Dec  8 07:57:00 2016 
-#> Date of summary: Thu Dec  8 07:57:00 2016 
+summary(f.w.mean)
    #> mkin version:    0.9.45.1 
+#> R version:       3.3.3 
+#> Date of fit:     Wed Mar 15 09:45:10 2017 
+#> Date of summary: Wed Mar 15 09:45:10 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -822,7 +827,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 155 model solutions performed in 0.65 s
+#> Fitted with method Port using 155 model solutions performed in 0.661 s
 #> 
 #> Weighting: mean
 #> 
@@ -933,10 +938,10 @@
 #>   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:    0.9.44.9000 
-#> R version:       3.3.2 
-#> Date of fit:     Thu Dec  8 07:57:01 2016 
-#> Date of summary: Thu Dec  8 07:57:01 2016 
+summary(f.w.value)
    #> mkin version:    0.9.45.1 
+#> R version:       3.3.3 
+#> Date of fit:     Wed Mar 15 09:45:11 2017 
+#> Date of summary: Wed Mar 15 09:45:11 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -944,7 +949,7 @@
 #> 
 #> 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 0.724 s
 #> 
 #> Weighting: manual
 #> 
@@ -1055,10 +1060,10 @@
 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:    0.9.44.9000 
-#> R version:       3.3.2 
-#> Date of fit:     Thu Dec  8 07:57:02 2016 
-#> Date of summary: Thu Dec  8 07:57:02 2016 
+summary(f.w.man)
    #> mkin version:    0.9.45.1 
+#> R version:       3.3.3 
+#> Date of fit:     Wed Mar 15 09:45:12 2017 
+#> Date of summary: Wed Mar 15 09:45:12 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1066,7 +1071,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 316 model solutions performed in 1.322 s
+#> Fitted with method Port using 316 model solutions performed in 1.31 s
 #> 
 #> Weighting: manual
 #> 
@@ -1177,10 +1182,10 @@
 #>   120       m1    25.15 28.760615  -3.610615   2
 #>   120       m1    33.31 28.760615   4.549385   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:    0.9.44.9000 
-#> R version:       3.3.2 
-#> Date of fit:     Thu Dec  8 07:57:05 2016 
-#> Date of summary: Thu Dec  8 07:57:05 2016 
+summary(f.w.man.irls)
    #> mkin version:    0.9.45.1 
+#> R version:       3.3.3 
+#> Date of fit:     Wed Mar 15 09:45:15 2017 
+#> Date of summary: Wed Mar 15 09:45:15 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1188,7 +1193,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 648 model solutions performed in 2.818 s
+#> Fitted with method Port using 648 model solutions performed in 2.766 s
 #> 
 #> Weighting: manual then iterative reweighting method obs
 #> 
-- 
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