Method to get the names of ill-defined parameters — illparms • mkin

From 9ee3d9f025ec7f5effddb0bcf9cf6e054c99794b Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 10 Aug 2022 13:21:34 +0200 Subject: Update static docs --- _pkgdown.yml | 14 +- docs/404.html | 2 +- docs/articles/index.html | 2 +- docs/authors.html | 2 +- docs/index.html | 2 +- docs/news/index.html | 11 +- docs/pkgdown.yml | 4 +- docs/reference/Rplot001.png | Bin 1011 -> 18718 bytes docs/reference/Rplot003.png | Bin 48687 -> 49705 bytes docs/reference/illparms.html | 48 ++++++- docs/reference/index.html | 46 ++++--- docs/reference/mhmkin.html | 213 ++++++++++++++++++++++++++++++ docs/reference/mkinfit.html | 304 +++++++++++++++++++++++++------------------ docs/reference/saem-3.png | Bin 128609 -> 128227 bytes docs/reference/saem.html | 295 ++++++++++++++++++++++++----------------- docs/sitemap.xml | 3 + 16 files changed, 664 insertions(+), 282 deletions(-) create mode 100644 docs/reference/mhmkin.html diff --git a/_pkgdown.yml b/_pkgdown.yml index 787fb371..1f6ba2fa 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -17,7 +17,13 @@ reference: - mkinmod - mkinfit - mmkin - - nafta + - mhmkin + - title: Generics + desc: Generic functions introduced by the package + contents: + - convergence + - illparms + - endpoints - title: Show results desc: Functions working with mkinfit objects contents: @@ -29,7 +35,6 @@ reference: - lrtest.mkinfit - loftest - mkinerrmin - - endpoints - aw - CAKE_export - title: Work with mmkin objects @@ -38,14 +43,13 @@ reference: - "`[.mmkin`" - plot.mmkin - AIC.mmkin - - convergence - - illparms - summary.mmkin - title: Mixed models - desc: Create and work with nonlinear mixed effects models + desc: Create and work with nonlinear hierarchical models contents: - nlme.mmkin - saem.mmkin + - "`[.mhmkin`" - plot.mixed.mmkin - summary.nlme.mmkin - summary.saem.mmkin diff --git a/docs/404.html b/docs/404.html index 750f0ae7..89c41d21 100644 --- a/docs/404.html +++ b/docs/404.html @@ -124,7 +124,7 @@ Content not found. Please use links in the navbar.

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/articles/index.html b/docs/articles/index.html index 9a014b09..c3a39708 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -112,7 +112,7 @@

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/authors.html b/docs/authors.html index 9daad578..ab436c86 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -130,7 +130,7 @@ R package version 1.1.2, https://pkgdown

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/index.html b/docs/index.html index 6118572b..67e1702a 100644 --- a/docs/index.html +++ b/docs/index.html @@ -276,7 +276,7 @@

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/news/index.html b/docs/news/index.html index d5c30552..faaab288 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -83,12 +83,15 @@

-

‘R/convergence.R’: New generic to show convergence information with a method for ‘mmin’ objects.
‘R/illparms.R’: New generic to show ill-defined parameters with methods for ‘mkinfit’ and ‘mmkin’ objects.

‘R/mhmkin.R’: New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel.
‘R/saem.R’: Implement and test saemix transformations for FOMC and HS. Also, error out if saemix transformations are requested but not supported.
‘R/saem.R’: ‘logLik’ and ‘update’ methods for ‘saem.mmkin’ objects.
‘R/convergence.R’: New generic to show convergence information with methods for ‘mmkin’ and ‘mhmkin’ objects.
‘R/illparms.R’: New generic to show ill-defined parameters with methods for ‘mkinfit’, ‘mmkin’, ‘saem.mmkin’ and ‘mhmkin’ objects.
‘R/summary.mmkin.R’: Summary method for mmkin objects.

- +

’R/{mkinmod,mkinpredict}.R: Store DLL information in mkinmod objects and use that information in mkinpredict to avoid a performance regression brought by a bugfix in R 4.2.x. Thanks to Tomas Kalibera for his analysis of the problem on the r-package-devel list and his suggestion on how to fix it.
‘vignettes/FOCUS_L.rmd’: Remove an outdated note referring to a failure to calculate the covariance matrix for DFOP with the L2 dataset. Since 0.9.45.5 the covariance matrix is available
‘vignettes/web_only/benchmarks.rmd’: Add the first benchmark data using my laptop system, therefore add the CPU when showing the benchmark results.

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 9c5ace2f..b3090f05 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,5 +1,5 @@ pandoc: 2.9.2.1 -pkgdown: 2.0.5 +pkgdown: 2.0.6 pkgdown_sha: ~ articles: FOCUS_D: FOCUS_D.html @@ -11,7 +11,7 @@ articles: benchmarks: web_only/benchmarks.html compiled_models: web_only/compiled_models.html dimethenamid_2018: web_only/dimethenamid_2018.html -last_built: 2022-07-22T09:39Z +last_built: 2022-08-10T11:14Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png index 17a35806..1ec32c4a 100644 Binary files a/docs/reference/Rplot001.png and b/docs/reference/Rplot001.png differ diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png index f8bf10bb..1af5d4b4 100644 Binary files a/docs/reference/Rplot003.png and b/docs/reference/Rplot003.png differ diff --git a/docs/reference/illparms.html b/docs/reference/illparms.html index 037d7a8c..cbdbfde2 100644 --- a/docs/reference/illparms.html +++ b/docs/reference/illparms.html @@ -1,5 +1,9 @@ -Method to get the names of ill-defined parameters — illparms • mkinMethod to get the names of ill-defined parameters — illparms • mkin @@ -83,7 +87,11 @@

-

Method to get the names of ill-defined parameters

+

The method for generalised nonlinear regression fits as obtained +with mkinfit and mmkin checks if the degradation parameters +pass the Wald test (in degradation kinetics often simply called t-test) for +significant difference from zero. For this test, the parameterisation +without parameter transformations is used.

@@ -96,6 +104,15 @@ illparms(object, conf.level = 0.95, ...) # S3 method for illparms.mmkin +print(x, ...) + +# S3 method for saem.mmkin +illparms(object, conf.level = 0.95, random = TRUE, errmod = TRUE, ...) + +# S3 method for mhmkin +illparms(object, conf.level = 0.95, random = TRUE, errmod = TRUE, ...) + +# S3 method for illparms.mhmkin print(x, ...)

@@ -116,14 +133,33 @@

x

The object to be printed

+ +

random

+

For hierarchical fits, should random effects be tested?

+ + +

errmod

+

For hierarchical fits, should error model parameters be +tested?

+

Value

-

For mkinfit objects, a character vector of parameter names -For mmkin objects, an object of class 'illparms.mmkin' with a -suitable printing method.

+

For mkinfit or saem objects, a character vector of parameter +names. For mmkin or mhmkin objects, a matrix like object of class +'illparms.mmkin' or 'illparms.mhmkin'. The latter objects have a suitable +printing method.

+

+

+

Details

+

The method for hierarchical model fits, also known as nonlinear +mixed-effects model fits as obtained with saem and mhmkin +checks if any of the confidence intervals for the random +effects expressed as standard deviations include zero, and if +the confidence intervals for the error model parameters include +zero.

@@ -157,7 +193,7 @@ suitable printing method.

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/reference/index.html b/docs/reference/index.html index 482edf08..956648d2 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -98,9 +98,27 @@

Fit one or more kinetic models with one or more state variables to one or more datasets

-

nafta() print(<nafta>)

+

mhmkin() `[`(<mhmkin>) print(<mhmkin>)

-

Evaluate parent kinetics using the NAFTA guidance

+

Fit nonlinear mixed-effects models built from one or more kinetic +degradation models and one or more error models

+ +

Generics

+

Generic functions introduced by the package

+ + +

convergence() print(<convergence.mmkin>)

+ +

Method to get convergence information

+ +

illparms() print(<illparms.mmkin>) print(<illparms.mhmkin>)

+ +

Method to get the names of ill-defined parameters

+ +

+ +

Function to calculate endpoints for further use from kinetic models fitted +with mkinfit

Show results

Functions working with mkinfit objects

@@ -137,11 +155,6 @@ more datasets

Calculate the minimum error to assume in order to pass the variance test

- -

- -

Function to calculate endpoints for further use from kinetic models fitted -with mkinfit

@@ -167,21 +180,13 @@ of an mmkin object

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

Calculate the AIC for a column of an mmkin object

- -

convergence() print(<convergence.mmkin>)

- -

Method to get convergence information

- -

illparms() print(<illparms.mmkin>)

- -

Method to get the names of ill-defined parameters

summary(<mmkin>) print(<summary.mmkin>)

Summary method for class "mmkin"

Mixed models

-

Create and work with nonlinear mixed effects models

+

Create and work with nonlinear hierarchical models

nlme(<mmkin>) print(<nlme.mmkin>) update(<nlme.mmkin>)

@@ -191,6 +196,11 @@ of an mmkin object

saem() print(<saem.mmkin>) saemix_model() saemix_data()

Fit nonlinear mixed models with SAEM

+ +

mhmkin() `[`(<mhmkin>) print(<mhmkin>)

+ +

Fit nonlinear mixed-effects models built from one or more kinetic +degradation models and one or more error models

plot(<mixed.mmkin>)

@@ -216,7 +226,7 @@ of an mmkin object

Create a mixed effects model from an mmkin row object

-

+

reexports intervals lrtest nlme

Objects exported from other packages

@@ -441,7 +451,7 @@ kinetic models fitted with mkinfit

-

Site built with pkgdown 2.0.5.

+

Site built with pkgdown 2.0.6.

diff --git a/docs/reference/mhmkin.html b/docs/reference/mhmkin.html new file mode 100644 index 00000000..25be0af6 --- /dev/null +++ b/docs/reference/mhmkin.html @@ -0,0 +1,213 @@ + +Fit nonlinear mixed-effects models built from one or more kinetic +degradation models and one or more error models — mhmkin • mkin + + +

+

+ + + +

+

+ + +

+

The name of the methods expresses that (multiple) hierarchichal +(also known as multilevel) multicompartment kinetic models are +fitted. Our kinetic models are nonlinear, so we can use various nonlinear +mixed-effects model fitting functions.

+

+ +

+

mhmkin(objects, backend = "saemix", algorithm = "saem", ...)
+
+# S3 method for list
+mhmkin(
+  objects,
+  backend = "saemix",
+  ...,
+  cores = if (Sys.info()["sysname"] == "Windows") 1 else parallel::detectCores(),
+  cluster = NULL
+)
+
+# S3 method for mhmkin
+[(x, i, j, ..., drop = FALSE)
+
+# S3 method for mhmkin
+print(x, ...)

+

+ +

+

Arguments

+

objects: A list of mmkin objects containing fits of the same +degradation models to the same data, but using different error models.
backend: The backend to be used for fitting. Currently, only saemix is +supported
algorithm: The algorithm to be used for fitting (currently not used)
...: Further arguments that will be passed to the nonlinear mixed-effects +model fitting function.
cores: The number of cores to be used for multicore processing. This +is only used when the cluster argument is NULL. On Windows +machines, cores > 1 is not supported, you need to use the cluster +argument to use multiple logical processors. Per default, all cores detected +by parallel::detectCores() are used, except on Windows where the default +is 1.
cluster: A cluster as returned by makeCluster to be used for +parallel execution.
x: An mhmkin object.
i: Row index selecting the fits for specific models
j: Column index selecting the fits to specific datasets
drop: If FALSE, the method always returns an mhmkin object, otherwise +either a list of fit objects or a single fit object.

+

+

Value

+ + +

A two-dimensional array of fit objects and/or try-errors that can +be indexed using the degradation model names for the first index (row index) +and the error model names for the second index (column index), with class +attribute 'mhmkin'.

+ + +

An object of class mhmkin.

+

+

+

See also

+

[.mhmkin for subsetting mhmkin objects

+

+

+

Author

+

Johannes Ranke

+

+ +

+ +

+ + +

+ + + + + + + + diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index e5bf1203..3b27ac7f 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -25,7 +25,7 @@ likelihood function.">