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/intervals.R | 84 -----------------------------------------------------------
 1 file changed, 84 deletions(-)

(limited to 'R/intervals.R')

diff --git a/R/intervals.R b/R/intervals.R
index 8ab2b7ec..258eb4ad 100644
--- a/R/intervals.R
+++ b/R/intervals.R
@@ -95,87 +95,3 @@ intervals.saem.mmkin <- function(object, level = 0.95, backtransform = TRUE, ...
   attr(res, "level") <- level
   return(res)
 }
-
-#' Confidence intervals for parameters in nlmixr.mmkin objects
-#'
-#' @param object The fitted saem.mmkin object
-#' @param level The confidence level.
-#' @param backtransform Should we backtransform the parameters where a one to
-#'   one correlation between transformed and backtransformed parameters exists?
-#' @param \dots For compatibility with the generic method
-#' @importFrom nlme intervals
-#' @return An object with 'intervals.saem.mmkin' and 'intervals.lme' in the
-#'  class attribute
-#' @export
-intervals.nlmixr.mmkin <- function(object, level = 0.95, backtransform = TRUE, ...)
-{
-
-  # Fixed effects
-  mod_vars <- names(object$mkinmod$diffs)
-
-  conf.int <- confint(object$nm)
-  dpnames <- setdiff(rownames(conf.int), names(object$mean_ep_start))
-  ndp <- length(dpnames)
-
-  confint_trans <- as.matrix(conf.int[dpnames, c(3, 1, 4)])
-  colnames(confint_trans) <- c("lower", "est.", "upper")
-
-  if (backtransform) {
-    bp <- backtransform_odeparms(confint_trans[, "est."], object$mkinmod,
-      object$transform_rates, object$transform_fractions)
-    bpnames <- names(bp)
-
-    # Transform boundaries of CI for one parameter at a time,
-    # with the exception of sets of formation fractions (single fractions are OK).
-    f_names_skip <- character(0)
-    for (box in mod_vars) { # Figure out sets of fractions to skip
-      f_names <- grep(paste("^f", box, sep = "_"), dpnames, value = TRUE)
-      n_paths <- length(f_names)
-      if (n_paths > 1) f_names_skip <- c(f_names_skip, f_names)
-    }
-
-    confint_back <- matrix(NA, nrow = length(bp), ncol = 3,
-      dimnames = list(bpnames, colnames(confint_trans)))
-    confint_back[, "est."] <- bp
-
-    for (pname in dpnames) {
-      if (!pname %in% f_names_skip) {
-        par.lower <- confint_trans[pname, "lower"]
-        par.upper <- confint_trans[pname, "upper"]
-        names(par.lower) <- names(par.upper) <- pname
-        bpl <- backtransform_odeparms(par.lower, object$mkinmod,
-                                              object$transform_rates,
-                                              object$transform_fractions)
-        bpu <- backtransform_odeparms(par.upper, object$mkinmod,
-                                              object$transform_rates,
-                                              object$transform_fractions)
-        confint_back[names(bpl), "lower"] <- bpl
-        confint_back[names(bpu), "upper"] <- bpu
-      }
-    }
-    confint_ret <- confint_back
-  } else {
-    confint_ret <- confint_trans
-  }
-  attr(confint_ret, "label") <- "Fixed effects:"
-
-  # Random effects
-  ranef_ret <- as.matrix(data.frame(lower = NA, 
-      "est." = sqrt(diag(object$nm$omega)), upper = NA))
-  rownames(ranef_ret) <- paste0(gsub("eta\\.", "sd(", rownames(ranef_ret)), ")")
-  attr(ranef_ret, "label") <- "Random effects:"
-
-  # Error model
-  enames <- names(object$nm$sigma)
-  err_ret <- as.matrix(conf.int[enames, c(3, 1, 4)])
-  colnames(err_ret) <- c("lower", "est.", "upper")
-
-  res <- list(
-    fixed = confint_ret,
-    random = ranef_ret,
-    errmod = err_ret
-  )
-  class(res) <- c("intervals.nlmixr.mmkin", "intervals.lme")
-  attr(res, "level") <- level
-  return(res)
-}
-- 
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