From 88cf130615a6cde0c4e65d14db32fed7f6e43085 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Sat, 12 Jun 2021 11:05:24 +0200
Subject: Small cosmetics

---
 DESCRIPTION                 |  2 +-
 R/dimethenamid_2018.R       | 25 +++++++++++++++++++++++++
 R/nlmixr.R                  | 20 +++++++++-----------
 tests/testthat/test_mixed.R |  2 +-
 4 files changed, 36 insertions(+), 13 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index e81fcb32..c6151839 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: mkin
 Type: Package
 Title: Kinetic Evaluation of Chemical Degradation Data
 Version: 1.0.5
-Date: 2021-06-03
+Date: 2021-06-11
 Authors@R: c(
   person("Johannes", "Ranke", role = c("aut", "cre", "cph"),
     email = "jranke@uni-bremen.de",
diff --git a/R/dimethenamid_2018.R b/R/dimethenamid_2018.R
index 189da618..79018c11 100644
--- a/R/dimethenamid_2018.R
+++ b/R/dimethenamid_2018.R
@@ -18,4 +18,29 @@
 #'   \url{http://registerofquestions.efsa.europa.eu/roqFrontend/outputLoader?output=ON-5211}
 #' @examples
 #' print(dimethenamid_2018)
+#' dmta_ds <- lapply(1:8, function(i) {
+#'   ds_i <- dimethenamid_2018$ds[[i]]$data
+#'   ds_i[ds_i$name == "DMTAP", "name"] <-  "DMTA"
+#'   ds_i$time <- ds_i$time * dimethenamid_2018$f_time_norm[i]
+#'   ds_i
+#' })
+#' names(dmta_ds) <- sapply(dimethenamid_2018$ds, function(ds) ds$title)
+#' dmta_ds[["Borstel"]] <- rbind(dmta_ds[["Borstel 1"]], dmta_ds[["Borstel 2"]])
+#' dmta_ds[["Borstel 1"]] <- NULL
+#' dmta_ds[["Borstel 2"]] <- NULL
+#' dmta_ds[["Elliot"]] <- rbind(dmta_ds[["Elliot 1"]], dmta_ds[["Elliot 2"]])
+#' dmta_ds[["Elliot 1"]] <- NULL
+#' dmta_ds[["Elliot 2"]] <- NULL
+#' dfop_sfo3_plus <- mkinmod(
+#'   DMTA = mkinsub("DFOP", c("M23", "M27", "M31")),
+#'   M23 = mkinsub("SFO"),
+#'   M27 = mkinsub("SFO"),
+#'   M31 = mkinsub("SFO", "M27", sink = FALSE),
+#'   quiet = TRUE
+#' )
+#' f_dmta_mkin_tc <- mmkin(
+#'   list("DFOP-SFO3+" = dfop_sfo3_plus),
+#'   dmta_ds, quiet = TRUE, error_model = "tc")
+#' nlmixr_model(f_dmta_mkin_tc) # incomplete
+#' # nlmixr(f_dmta_mkin_tc, est = "saem") # not supported (yet)
 "dimethenamid_2018"
diff --git a/R/nlmixr.R b/R/nlmixr.R
index 98783ca7..6e0b5128 100644
--- a/R/nlmixr.R
+++ b/R/nlmixr.R
@@ -43,11 +43,11 @@ nlmixr::nlmixr
 #' ds <- lapply(experimental_data_for_UBA_2019[6:10],
 #'  function(x) subset(x$data[c("name", "time", "value")]))
 #' names(ds) <- paste("Dataset", 6:10)
-#' 
+#'
 #' f_mmkin_parent <- mmkin(c("SFO", "FOMC", "DFOP", "HS"), ds, quiet = TRUE, cores = 1)
 #' f_mmkin_parent_tc <- mmkin(c("SFO", "FOMC", "DFOP"), ds, error_model = "tc",
 #'   cores = 1, quiet = TRUE)
-#' 
+#'
 #' f_nlmixr_sfo_saem <- nlmixr(f_mmkin_parent["SFO", ], est = "saem")
 #' f_nlmixr_sfo_focei <- nlmixr(f_mmkin_parent["SFO", ], est = "focei")
 #'
@@ -278,20 +278,18 @@ nlmixr_model <- function(object,
     conf.level = conf.level, random = TRUE)
 
   degparms_optim <- degparms_mmkin$fixed
-
-  degparms_optim <- degparms_mmkin$fixed
+  degparms_optim_back <- backtransform_odeparms(degparms_optim,
+      object[[1]]$mkinmod,
+      object[[1]]$transform_rates,
+      object[[1]]$transform_fractions)
+  degparms_optim_back_names <- names(degparms_optim_back)
+  names(degparms_optim_back_names) <- names(degparms_optim)
 
   if (degparms_start[1] == "auto") {
     degparms_start <- degparms_optim
   }
   degparms_fixed <- object[[1]]$bparms.fixed
 
-  degparms_optim_back_names <- names(backtransform_odeparms(degparms_optim,
-      object[[1]]$mkinmod,
-      object[[1]]$transform_rates,
-      object[[1]]$transform_fractions))
-  names(degparms_optim_back_names) <- names(degparms_optim)
-
   odeini_optim_parm_names <- grep('_0$', names(degparms_optim), value = TRUE)
   odeini_fixed_parm_names <- grep('_0$', names(degparms_fixed), value = TRUE)
 
@@ -307,7 +305,7 @@ nlmixr_model <- function(object,
   ini_block <- "ini({"
 
   # Initial values for all degradation parameters
-  for (parm_name in names(degparms_optim)) {
+  for (parm_name in names(degparms_start)) {
     # As initials for state variables are not transformed,
     # we need to modify the name here as we want to
     # use the original name in the model block
diff --git a/tests/testthat/test_mixed.R b/tests/testthat/test_mixed.R
index 5d15530b..9c8a84d7 100644
--- a/tests/testthat/test_mixed.R
+++ b/tests/testthat/test_mixed.R
@@ -113,7 +113,7 @@ test_that("nlme results are reproducible to some degree", {
 
   expect_known_output(print(test_summary, digits = 1), "summary_nlme_biphasic_s.txt")
 
-  # k1 just fails the first test (lower bound of the ci), so we need to excluded it 
+  # k1 just fails the first test (lower bound of the ci), so we need to exclude it
   dfop_no_k1 <- c("parent_0", "k_m1", "f_parent_to_m1", "k2", "g")
   dfop_sfo_pop_no_k1 <- as.numeric(dfop_sfo_pop[dfop_no_k1])
   dfop_sfo_pop <- as.numeric(dfop_sfo_pop)
-- 
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