From 7035cde3a53781721fe15a8893fdf328c789bdd2 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 7 Mar 2022 12:03:40 +0100
Subject: Remove nlmixr interface for release of mkin 1.1.0

I am postponing my attempts to get the nlmixr interface to CRAN, given
some problems with nlmixr using R-devel under Windows, see
https://github.com/nlmixrdevelopment/nlmixr/issues/596
and
https://github.com/r-hub/rhub/issues/512,
which is fixed by the removal of nlmixr from the testsuite.

For the tests to be more platform independent, the biphasic mixed
effects models test dataset was defined in a way that fitting
should be more robust (less ill-defined).
---
 R/tffm0.R | 51 ---------------------------------------------------
 1 file changed, 51 deletions(-)
 delete mode 100644 R/tffm0.R

(limited to 'R/tffm0.R')

diff --git a/R/tffm0.R b/R/tffm0.R
deleted file mode 100644
index 56283a5d..00000000
--- a/R/tffm0.R
+++ /dev/null
@@ -1,51 +0,0 @@
-#' Transform formation fractions as in the first published mkin version
-#'
-#' This transformation was used originally in mkin, in order to implement a
-#' constraint for the sum of formation fractions to be smaller than 1.  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, the original 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.
-#' 
-#' If the transformed formation fractions are restricted to the interval
-#' between 0 and 1, the sum of backtransformed values is restricted
-#' to this interval.
-#'
-#' @param ff Vector of untransformed formation fractions. The sum
-#'   must be smaller or equal to one
-#' @param ff_trans Vector of transformed formation fractions that can be
-#'   restricted to the interval from 0 to 1
-#' @return A vector of the transformed formation fractions
-#' @export
-#' @examples
-#' ff_example <- c(
-#'   0.10983681, 0.09035905, 0.08399383
-#' )
-#' ff_example_trans <- tffm0(ff_example)
-#' invtffm0(ff_example_trans)
-tffm0 <- function(ff) {
-  n <- length(ff)
-  res <- numeric(n)
-  f_remaining <- 1
-  for (i in 1:n) {
-    res[i] <- ff[i]/f_remaining
-    f_remaining <- f_remaining - ff[i]
-  }
-  return(res)
-}
-#' @rdname tffm0
-#' @export
-#' @return A vector of backtransformed formation fractions for natural use in degradation models
-invtffm0 <- function(ff_trans) {
-  n <- length(ff_trans)
-  res <- numeric(n)
-  f_remaining <- 1
-  for (i in 1:n) {
-    res[i] <- ff_trans[i] * f_remaining
-    f_remaining <- f_remaining - res[i]
-  }
-  return(res)
-}
-- 
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