From 4596667b19f032232ceb8f3f762aaad5d69c15be Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 5 Jul 2019 15:57:24 +0200 Subject: Static documentation rebuilt by pkgdown --- docs/reference/mkinfit.html | 51 ++++++++++++++++++++++++++------------------- 1 file changed, 29 insertions(+), 22 deletions(-) (limited to 'docs/reference/mkinfit.html') diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 0983007e..e9ad9343 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -71,7 +71,7 @@ Per default, parameters in the kinetic models are internally transformed in mkin - 0.9.49.5 + 0.9.49.6 @@ -327,7 +327,8 @@ Per default, parameters in the kinetic models are internally transformed in error_model_algorithm

If the error model is "const", the error model algorithm is ignored, because no special algorithm is needed and unweighted (also known as - ordinary) least squares fitting can be applied.

+ ordinary) least squares fitting (listed as "OLS" in the summary) can be + applied.

The default algorithm "d_3" will directly minimize the negative log-likelihood and - independently - also use the three step algorithm described below. The fit with the higher likelihood is returned.

@@ -397,21 +398,21 @@ Per default, parameters in the kinetic models are internally transformed in

Examples

# Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-summary(fit)
#> mkin version used for fitting:    0.9.49.5 
+summary(fit)
#> mkin version used for fitting:    0.9.49.6 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Thu Jul  4 08:02:21 2019 
-#> Date of summary: Thu Jul  4 08:02:21 2019 
+#> Date of fit:     Fri Jul  5 15:50:49 2019 
+#> Date of summary: Fri Jul  5 15:50:49 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 222 model solutions performed in 0.464 s
+#> Fitted using 222 model solutions performed in 0.455 s
 #> 
 #> Error model: Constant variance 
 #> 
-#> Error model algorithm: d_3 
+#> Error model algorithm: OLS 
 #> 
 #> Starting values for parameters to be optimised:
 #>              value   type
@@ -481,7 +482,10 @@ Per default, parameters in the kinetic models are internally transformed in
   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)))
#> Warning: Observations with value of zero were removed from the data
#>        User      System verstrichen 
-#>       1.507       0.004       1.511 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
+#>       1.502       0.000       1.503 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>         99.598483         -3.038220         -2.980300         -5.247500 
+#>             sigma 
+#>          3.125504 
endpoints(fit)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
@@ -553,7 +557,10 @@ Per default, parameters in the kinetic models are internally transformed in
 #> Sum of squared residuals at call 126: 371.2134
 #> Sum of squared residuals at call 135: 371.2134
 #> Negative log-likelihood at call 145: 97.22429
#> Optimisation successfully terminated.
#>        User      System verstrichen 
-#>       1.078       0.000       1.078 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
+#>       1.089       0.000       1.089 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>         99.598483         -3.038220         -2.980300         -5.247500 
+#>             sigma 
+#>          3.125504 
endpoints(fit.deSolve)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
@@ -583,10 +590,10 @@ Per default, parameters in the kinetic models are internally transformed in
 fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode, quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data

 
# 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)
#> Warning: Observations with value of zero were removed from the data
summary(f.noweight)
#> mkin version used for fitting:    0.9.49.5 
+                      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)
#> Warning: Observations with value of zero were removed from the data
summary(f.noweight)
#> mkin version used for fitting:    0.9.49.6 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Thu Jul  4 08:02:37 2019 
-#> Date of summary: Thu Jul  4 08:02:37 2019 
+#> Date of fit:     Fri Jul  5 15:51:05 2019 
+#> Date of summary: Fri Jul  5 15:51:05 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -594,11 +601,11 @@ Per default, parameters in the kinetic models are internally transformed in
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 421 model solutions performed in 1.096 s
+#> Fitted using 421 model solutions performed in 1.08 s
 #> 
 #> Error model: Constant variance 
 #> 
-#> Error model algorithm: d_3 
+#> Error model algorithm: OLS 
 #> 
 #> Starting values for parameters to be optimised:
 #>                     value   type
@@ -702,10 +709,10 @@ Per default, parameters in the kinetic models are internally transformed in
 #>   100       m1    31.04  31.98163 -9.416e-01
 #>   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.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.obs)
#> mkin version used for fitting:    0.9.49.5 
+#>   120       m1    33.31  28.78984  4.520e+00
f.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.obs)
#> mkin version used for fitting:    0.9.49.6 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Thu Jul  4 08:02:40 2019 
-#> Date of summary: Thu Jul  4 08:02:40 2019 
+#> Date of fit:     Fri Jul  5 15:51:08 2019 
+#> Date of summary: Fri Jul  5 15:51:08 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -713,7 +720,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 979 model solutions performed in 2.574 s
+#> Fitted using 979 model solutions performed in 2.623 s
 #> 
 #> Error model: Variance unique to each observed variable 
 #> 
@@ -834,10 +841,10 @@ Per default, parameters in the kinetic models are internally transformed in
 #>   100       m1    31.04  31.98773 -9.477e-01
 #>   100       m1    33.13  31.98773  1.142e+00
 #>   120       m1    25.15  28.80429 -3.654e+00
-#>   120       m1    33.31  28.80429  4.506e+00
f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.tc)
#> mkin version used for fitting:    0.9.49.5 
+#>   120       m1    33.31  28.80429  4.506e+00
f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.tc)
#> mkin version used for fitting:    0.9.49.6 
 #> R version used for fitting:       3.6.0 
-#> Date of fit:     Thu Jul  4 08:02:49 2019 
-#> Date of summary: Thu Jul  4 08:02:49 2019 
+#> Date of fit:     Fri Jul  5 15:51:17 2019 
+#> Date of summary: Fri Jul  5 15:51:17 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -845,7 +852,7 @@ Per default, parameters in the kinetic models are internally transformed in
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 2289 model solutions performed in 9.379 s
+#> Fitted using 2289 model solutions performed in 9.215 s
 #> 
 #> Error model: Two-component variance function 
 #> 
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