Estimation of parameter distributions from mmkin row objects

Performance benefit by using compiled model definitions in mkin

Johannes Ranke

2020-04-02

2020-04-04

"R package rbenchmark is not available"

}

## test replications elapsed relative user.self sys.self -## 3 deSolve, compiled 3 3.239 1.000 3.237 0 -## 1 deSolve, not compiled 3 29.758 9.187 29.739 0 -## 2 Eigenvalue based 3 4.558 1.407 4.554 0 +## 3 deSolve, compiled 3 3.107 1.000 3.105 0 +## 1 deSolve, not compiled 3 28.765 9.258 28.749 0 +## 2 Eigenvalue based 3 4.446 1.431 4.445 0 ## user.child sys.child ## 3 0 0 ## 1 0 0 @@ -170,8 +170,8 @@ }

## Successfully compiled differential equation model from auto-generated C code.

## test replications elapsed relative user.self sys.self -## 2 deSolve, compiled 3 4.984 1.000 4.981 0.000 -## 1 deSolve, not compiled 3 55.358 11.107 55.326 0.003 +## 2 deSolve, compiled 3 4.844 1.000 4.842 0 +## 1 deSolve, not compiled 3 53.833 11.113 53.807 0 ## user.child sys.child ## 2 0 0 ## 1 0 0

Unreleased

‘mean_degparms, nlme_data, nlme_function’: Three new functions to facilitate building nlme models from mmkin row objects

‘endpoints’: Don’t return the SFORB list component if it’s empty. This reduces distraction and complies with the documentation

Article in compiled models: Add some platform specific code and suppress warnings about zero values being removed from the FOCUS D dataset

‘plot.mmkin’: Add the argument ‘standardized’ to avoid warnings that occurred when it was passed as part of the additional arguments captured by the dots (…)

diff --git a/docs/reference/index.html b/docs/reference/index.html index 6ccc9255..a3547e29 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -270,6 +270,12 @@ of an mmkin object

AIC(<mmkin>) BIC(<mmkin>)

Calculate the AIC for a column of an mmkin object

+ + + +

mean_degparms() nlme_data() nlme_function()

+ +

Estimation of parameter distributions from mmkin row objects

diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index e38c153c..b3be7c2c 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -70,7 +70,7 @@ mkinmod." /> @@ -181,10 +181,11 @@ results on other operating systems or system configurations.

SFO_SFO.2 <- mkinmod( parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"))

#> Successfully compiled differential equation model from auto-generated C code.

-# Now supplying full names -SFO_SFO.2 <- mkinmod( - parent = mkinsub("SFO", "m1", full_name = "Test compound"), - m1 = mkinsub("SFO", full_name = "Metabolite M1"))

#> Successfully compiled differential equation model from auto-generated C code.

+# \dontrun{ + # Now supplying full names + SFO_SFO.2 <- mkinmod( + parent = mkinsub("SFO", "m1", full_name = "Test compound"), + m1 = mkinsub("SFO", full_name = "Metabolite M1"))

#> Successfully compiled differential equation model from auto-generated C code.

# }

diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html new file mode 100644 index 00000000..b939d1c3 --- /dev/null +++ b/docs/reference/nlme.html @@ -0,0 +1,199 @@ + + + + + + + + +Estimation of parameter distributions from mmkin row objects — mean_degparms • mkin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + +

+ +

+ + +

This function sets up and attempts to fit a mixed effects model to +an mmkin row object. An mmkin row object is essentially a list of mkinfit +objects that have been obtained by fitting the same model to a list of +datasets.

+ +

mean_degparms(object)
+
+nlme_data(object)
+
+nlme_function(object)

+ +

Arguments

+ + + + + + +

object	An mmkin row object containing several fits of the same model to different datasets

+ +

Value

+ +

A named vector containing mean values of the fitted degradation model parameters

A groupedData data object

A function that can be used with nlme

+ +

Examples

+ +

+ + + +

+ + + + + + + + diff --git a/docs/sitemap.xml b/docs/sitemap.xml index a8d6dfa4..8ba032de 100644 --- a/docs/sitemap.xml +++ b/docs/sitemap.xml @@ -129,6 +129,9 @@ https://pkgdown.jrwb.de/mkin/reference/nafta.html + + https://pkgdown.jrwb.de/mkin/reference/nlme.html + https://pkgdown.jrwb.de/mkin/reference/nobs.mkinfit.html -- cgit v1.2.1

Performance benefit by using compiled model definitions in mkin

Johannes Ranke

2020-04-02

2020-04-04

Estimation of parameter distributions from mmkin row objects

Arguments

Value

Examples

Contents