Remove nlmixr_data_simplify() in favor of rxode2::etTrans()

NAMESPACE

@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export(nlmixr_data_simplify)
 export(nlmixr_object_simplify)
 export(tar_nlmixr)
 export(tar_nlmixr_multimodel)

R/simplify.R

@@ -52,75 +52,3 @@ nlmixr_object_simplify_zero_initial_helper <- function(object) {
   }
   object
 }
-
-#' Standardize and simplify data for nlmixr2 estimation
-#'
-#' This function is typically not needed by end users.
-#'
-#' The standardization keeps columns that rxode2 and nlmixr2 use along with the
-#' covariates.  Column order is standardized (rxode2 then nlmixr2 then
-#' alphabetically sorted covariates), and rxode2 and nlmixr2 column names are
-#' converted to lower case.
-#'
-#' @inheritParams nlmixr2est::nlmixr
-#' @param object an nlmixr_ui object (e.g. the output of running
-#'   \code{nlmixr(object = model)}
-#' @return The data with the nlmixr2 column lower case and on the left and the
-#'   covariate columns on the right and alphabetically sorted.
-#' @family Simplifiers
-#' @export
-nlmixr_data_simplify <- function(data, object, table = list()) {
-  nlmixr_cols <-
-    c(
-      # rxode2 columns
-      c("id", "time", "amt", "rate", "dur", "evid", "cmt", "dvid", "ss", "ii", "addl"),
-      # nlmixr2 columns
-      c("dv", "mdv", "cens", "limit")
-    )
-  # nlmixr pays attention to the columns in a case-insensitive way for the
-  # standard columns.  Verify that the data has case-insensitive column names
-  # for these columns (for example not "ADDL" and "addl").
-  mask_nlmixr_cols <- tolower(names(data)) %in% nlmixr_cols
-  nlmixr_names <- names(data)[mask_nlmixr_cols]
-  mask_duplicated <- duplicated(tolower(nlmixr_names))
-  if (any(mask_duplicated)) {
-    stop(
-      "The following column(s) are duplicated when lower case: ",
-      paste0("'", nlmixr_names[mask_duplicated], "'", collapse = ", ")
-    )
-  }
-  if (!is.null(object$ui)) {
-    covVec <- object$ui$all.covs
-  } else {
-    covVec <- object$all.covs
-  }
-  cov_names <- nlmixr_data_simplify_cols(data, cols = covVec, type = "covariate")
-  keep_names <- nlmixr_data_simplify_cols(data, cols = table$keep, type = "keep")
-  # Simplifying the nlmixr_names column names to always be lower case ensures
-  # that upper/lower case column name changes will not affect the need to rerun.
-  # Also, standardizing the column name order to always be the same will prevent
-  # the need to rerun, so cov_names is sorted.
-
-  # Sorting so that they are in order, unique so that duplication between
-  # covariates and keep do not try to duplicate columns in the output data.
-  add_col_names <- sort(unique(c(cov_names, keep_names)))
-
-  # Drop names from nlmixr_names from the added names
-  add_col_names <- setdiff(add_col_names, nlmixr_names)
-
-  stats::setNames(
-    object = data[, c(nlmixr_names, add_col_names), drop = FALSE],
-    nm = c(tolower(nlmixr_names), add_col_names)
-  )
-}
-
-nlmixr_data_simplify_cols <- function(data, cols, type) {
-  missing_col <- setdiff(cols, names(data))
-  if (length(missing_col) > 0) {
-    stop(
-      "The following ", type, " column(s) are missing from the data: ",
-      paste0("'", missing_col, "'", collapse = ", ")
-    )
-  }
-  cols
-}

R/tar_nlmixr.R

@@ -6,9 +6,9 @@
 #' `paste(name, "data_simple", sep = "_tar_")` (e.g. "pheno_tar_data_simple") as
 #' the simplified data object.
 #'
-#' For the way that the objects are simplified, see `nlmixr_object_simplify()`
-#' and `nlmixr_data_simplify()`.  To see how to write initial conditions to work
-#' with targets, see `nlmixr_object_simplify()`.
+#' For the way that the objects are simplified, see `nlmixr_object_simplify()`.
+#' To see how to write initial conditions to work with targets, see
+#' `nlmixr_object_simplify()`.
 #'
 #' @inheritParams nlmixr2est::nlmixr
 #' @inheritParams targets::tar_target
@@ -86,7 +86,7 @@ tar_nlmixr_raw <- function(name, object, data, est, control, table, object_simpl
       name = data_simple_name,
       command =
         substitute(
-          nlmixr_data_simplify(object = object_simple, data = data, table = table),
+          rxode2::etTrans(inData = data, obj = object_simple, keep = table$keep),
           list(
             object_simple = as.name(object_simple_name),
             data = data,

tests/testthat/test-simplify.R

@@ -21,60 +21,6 @@ model_simple <-
     nlmixr_object_simplify(pheno)
   ))
 
-test_that("nlmixr_data_simplify", {
-  # Columns are kept in the correct order
-  expect_equal(
-    names(nlmixr_data_simplify(data = nlmixr2data::pheno_sd, object = model_simple)),
-    c("id", "time", "amt", "dv", "mdv", "evid", "WT")
-  )
-  # table's 'keep' argument is respected
-  expect_equal(
-    names(nlmixr_data_simplify(
-      data = nlmixr2data::pheno_sd,
-      object = model_simple,
-      table = nlmixr2est::tableControl(keep = "APGR")
-    )),
-    c("id", "time", "amt", "dv", "mdv", "evid", "APGR", "WT")
-  )
-  # duplication between table's 'keep' argument and covariates does not
-  # duplicate columns
-  expect_equal(
-    names(nlmixr_data_simplify(
-      data = nlmixr2data::pheno_sd,
-      object = model_simple,
-      table = nlmixr2est::tableControl(keep = "WT")
-    )),
-    c("id", "time", "amt", "dv", "mdv", "evid", "WT")
-  )
-  # duplication between table's 'keep' argument and nlmixr2 columns does not add
-  # them
-  expect_equal(
-    names(nlmixr_data_simplify(
-      data = nlmixr2data::pheno_sd,
-      object = model_simple,
-      table = nlmixr2est::tableControl(keep = "EVID")
-    )),
-    c("id", "time", "amt", "dv", "mdv", "evid", "WT")
-  )
-})
-
-test_that("nlmixr_data_simplify expected errors", {
-  bad_data_lower_case <- nlmixr2data::pheno_sd
-  bad_data_lower_case$id <- bad_data_lower_case$ID
-  expect_error(
-    nlmixr_data_simplify(data = bad_data_lower_case, object = model_simple),
-    regexp = "The following column(s) are duplicated when lower case: 'id'",
-    fixed = TRUE
-  )
-  bad_data_no_cov <- nlmixr2data::pheno_sd
-  bad_data_no_cov$WT <- NULL
-  expect_error(
-    nlmixr_data_simplify(data = bad_data_no_cov, object = model_simple),
-    regexp = "The following covariate column(s) are missing from the data: 'WT'",
-    fixed = TRUE
-  )
-})
-
 test_that("nlmixr_object_simplify_zero_initial", {
   pheno <- function() {
     ini({
@@ -115,20 +61,3 @@ test_that("nlmixr_object_simplify_zero_initial", {
   new_model <- nlmixr_object_simplify_zero_initial(pheno)
   expect_equal(body(new_model), body(pheno_0))
 })
-
-test_that("re-estimating a model works with covariates (#9)", {
-  bad_data_lower_case <- nlmixr2data::pheno_sd
-  bad_data_lower_case$id <- bad_data_lower_case$ID
-  fit_estimated <-
-    suppressMessages(
-      nlmixr2est::nlmixr(
-        object = model_simple,
-        data = nlmixr2data::pheno_sd,
-        est = "focei",
-        control = list(eval.max = 1)
-      )
-    )
-  expect_true(
-    "WT" %in% names(nlmixr_data_simplify(data = nlmixr2data::pheno_sd, object = fit_estimated))
-  )
-})