From 8b7edd4eaf0d196e674a085f744d1a69260a6c91 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 16 Nov 2023 06:02:05 +0100 Subject: Update pkgdown docs to bootstrap 5 with search --- docs/reference/mkinfit.html | 240 +++++++++++++++++++------------------------- 1 file changed, 105 insertions(+), 135 deletions(-) (limited to 'docs/reference/mkinfit.html') diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 865bdc28..7cd4eaa3 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -1,5 +1,13 @@ -Fit a kinetic model to data with one or more state variables — mkinfit • mkinFit a kinetic model to data with one or more state variables — mkinfit • mkin + + Skip to contents -
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Fit a kinetic model to data with one or more state variables

- Source: R/mkinfit.R - +
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Fit a kinetic model to data with one or more state variables

+ Source: R/mkinfit.R +
mkinfit.Rd
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This function maximises the likelihood of the observed data using the Port algorithm stats::nlminb(), and the specified initial or fixed parameters and starting values. In each step of the optimisation, the @@ -128,7 +101,8 @@ degradation model parameters, as both of them are arguments of the likelihood function.

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Usage

mkinfit(
   mkinmod,
   observed,
@@ -158,8 +132,8 @@ likelihood function.

 )
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Arguments

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Arguments

mkinmod

A list of class mkinmod, containing the kinetic model to be fitted to the data, or one of the shorthand names ("SFO", @@ -357,27 +331,27 @@ the error model parameters in IRLS fits.

deSolve::ode().

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Value

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Value

A list with "mkinfit" in the class attribute.

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Details

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Details

Per default, parameters in the kinetic models are internally transformed in order to better satisfy the assumption of a normal distribution of their estimators.

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Note

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Note

When using the "IORE" submodel for metabolites, fitting with "transform_rates = TRUE" (the default) often leads to failures of the numerical ODE solver. In this situation it may help to switch off the internal rate transformation.

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References

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References

Rocke DM and Lorenzato S (1995) A two-component model for measurement error in analytical chemistry. Technometrics 37(2), 176-184.

Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical @@ -385,36 +359,36 @@ Degradation Data. Environments 6(12) 124 doi:10.3390/environments6120124 .

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See also

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See also

summary.mkinfit, plot.mkinfit, parms and lrtest.

Comparisons of models fitted to the same data can be made using AIC by virtue of the method logLik.mkinfit.

Fitting of several models to several datasets in a single call to mmkin.

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Author

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Author

Johannes Ranke

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Examples

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Examples


 # Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
 summary(fit)
 #> mkin version used for fitting:    1.2.6 
-#> R version used for fitting:       4.3.1 
-#> Date of fit:     Mon Oct 30 09:30:09 2023 
-#> Date of summary: Mon Oct 30 09:30:09 2023 
+#> R version used for fitting:       4.3.2 
+#> Date of fit:     Thu Nov 16 04:15:31 2023 
+#> Date of summary: Thu Nov 16 04:15:31 2023 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 222 model solutions performed in 0.031 s
+#> Fitted using 222 model solutions performed in 0.014 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -555,9 +529,9 @@ Degradation Data. Environments 6(12) 124
       solution_type = "analytical"))
 }
 #>               test relative elapsed
-#> 3       analytical    1.000   0.465
-#> 2            eigen    2.260   1.051
-#> 1 deSolve_compiled    2.282   1.061
+#> 3       analytical    1.000   0.223
+#> 2            eigen    1.973   0.440
+#> 1 deSolve_compiled    2.072   0.462
 # }
 
 # Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO
@@ -585,9 +559,9 @@ Degradation Data. Environments 6(12) 124
 #> Warning: NaNs produced
 #> Warning: diag(.) had 0 or NA entries; non-finite result is doubtful
 #> mkin version used for fitting:    1.2.6 
-#> R version used for fitting:       4.3.1 
-#> Date of fit:     Mon Oct 30 09:30:19 2023 
-#> Date of summary: Mon Oct 30 09:30:19 2023 
+#> R version used for fitting:       4.3.2 
+#> Date of fit:     Thu Nov 16 04:15:35 2023 
+#> Date of summary: Thu Nov 16 04:15:35 2023 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -596,7 +570,7 @@ Degradation Data. Environments 6(12) 124
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 4062 model solutions performed in 1.981 s
+#> Fitted using 4062 model solutions performed in 0.768 s
 #> 
 #> Error model: Two-component variance function 
 #> 
@@ -696,26 +670,22 @@ Degradation Data. Environments 6(12) 124
 # }
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Developed by Johannes Ranke.

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Site built with pkgdown 2.0.7.

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- -- cgit v1.2.1 From 6476f5f49b373cd4cf05f2e73389df83e437d597 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 13 Feb 2025 16:30:31 +0100 Subject: Axis legend formatting, update vignettes --- docs/reference/mkinfit.html | 191 +++++++++++++++++++++----------------------- 1 file changed, 89 insertions(+), 102 deletions(-) (limited to 'docs/reference/mkinfit.html') diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 7cd4eaa3..5af8eaaf 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -1,5 +1,5 @@ -Fit a kinetic model to data with one or more state variables — mkinfit • mkinFit a kinetic model to data with one or more state variables — mkinfit • mkin +likelihood function."> Skip to contents - -