Transform formation fractions as in the first published mkin version — tffm0 • mkin

From 255430279d65bfe92093d48c9a586b062a38303d Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 22 Jun 2021 15:15:02 +0200 Subject: Update development version of online docs --- docs/dev/reference/tffm0.html | 226 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 226 insertions(+) create mode 100644 docs/dev/reference/tffm0.html (limited to 'docs/dev/reference/tffm0.html') diff --git a/docs/dev/reference/tffm0.html b/docs/dev/reference/tffm0.html new file mode 100644 index 00000000..d993e8ff --- /dev/null +++ b/docs/dev/reference/tffm0.html @@ -0,0 +1,226 @@ + + + + + + + + +Transform formation fractions as in the first published mkin version — tffm0 • mkin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+

+ + + + +

+ +

+

+ + +

+

The transformed fractions can be restricted between 0 and 1 in model +optimisations. Therefore this transformation was used originally in mkin. It +was later replaced by the ilr transformation because the ilr transformed +fractions can assumed to follow normal distribution. As the ilr +transformation is not available in RxODE and can therefore not be used in +the nlmixr modelling language, this transformation is currently used for +translating mkin models with formation fractions to more than one target +compartment for fitting with nlmixr in nlmixr_model. However, +this implementation cannot be used there, as it is not accessible +from RxODE.

+

+ +

tffm0(ff)
+
+invtffm0(ff_trans)

+ +

Arguments

+ + + + + + + + + + +

ff	Vector of untransformed formation fractions. The sum +must be smaller or equal to one
ff_trans	Vector of transformed formation fractions that can be +restricted to the interval from 0 to 1

+ +

Value

+ +

A vector of the transformed formation fractions

+

A vector of backtransformed formation fractions for natural use in degradation models

+ +

Examples

+

ff_example <- c(
+  0.10983681, 0.09035905, 0.08399383
+)
+ff_example_trans <- tffm0(ff_example)
+invtffm0(ff_example_trans)
+
#> [1] 0.10983681 0.09035905 0.08399383

+

+ +

+ + + +

+ + + + + + + + -- cgit v1.2.1 From 0b754ffa91b9496bdd2f892cf3ca2bd887028dea Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 27 Jul 2021 18:22:01 +0200 Subject: Fix dimethenamid vignette problems and update docs --- docs/dev/reference/tffm0.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'docs/dev/reference/tffm0.html') diff --git a/docs/dev/reference/tffm0.html b/docs/dev/reference/tffm0.html index d993e8ff..67f26b85 100644 --- a/docs/dev/reference/tffm0.html +++ b/docs/dev/reference/tffm0.html @@ -81,7 +81,7 @@ from RxODE." /> -- cgit v1.2.1 From 137612045c23198f10d6e8612c32e266c2a6c00e Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 29 Jul 2021 12:17:56 +0200 Subject: Go back to 1.0.x version, update docs --- docs/dev/reference/tffm0.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'docs/dev/reference/tffm0.html') diff --git a/docs/dev/reference/tffm0.html b/docs/dev/reference/tffm0.html index 67f26b85..d993e8ff 100644 --- a/docs/dev/reference/tffm0.html +++ b/docs/dev/reference/tffm0.html @@ -81,7 +81,7 @@ from RxODE." /> -- cgit v1.2.1 From c41381a961263c28d60976e68923157916c78b15 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 16 Sep 2021 15:31:13 +0200 Subject: Adapt and improve the dimethenamid vignette Adapt to the corrected data and unify control parameters for saemix and nlmixr with saem. Update docs --- docs/dev/reference/tffm0.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'docs/dev/reference/tffm0.html') diff --git a/docs/dev/reference/tffm0.html b/docs/dev/reference/tffm0.html index d993e8ff..67f26b85 100644 --- a/docs/dev/reference/tffm0.html +++ b/docs/dev/reference/tffm0.html @@ -81,7 +81,7 @@ from RxODE." /> -- cgit v1.2.1 From ff83d8b2ba623513d92ac90fac4a1b0ec98c2cb5 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 5 Oct 2021 17:33:52 +0200 Subject: Update docs --- docs/dev/reference/tffm0.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'docs/dev/reference/tffm0.html') diff --git a/docs/dev/reference/tffm0.html b/docs/dev/reference/tffm0.html index 67f26b85..c7b5b6de 100644 --- a/docs/dev/reference/tffm0.html +++ b/docs/dev/reference/tffm0.html @@ -157,7 +157,7 @@ from RxODE." /> optimisations. Therefore this transformation was used originally in mkin. It was later replaced by the ilr transformation because the ilr transformed fractions can assumed to follow normal distribution. As the ilr -transformation is not available in RxODE and can therefore not be used in +transformation is not available in RxODE and can therefore not be used in the nlmixr modelling language, this transformation is currently used for translating mkin models with formation fractions to more than one target compartment for fitting with nlmixr in nlmixr_model. However, -- cgit v1.2.1