remove nm_fdata from this PR

 - opting to separate this into a separate, more focused PR

NAMESPACE

@@ -76,7 +76,6 @@ S3method(print,bbi_nmboot_summary)
 S3method(print,bbi_nonmem_summary)
 S3method(print,bbi_process)
 S3method(print,model_tree_static)
-S3method(print,nmtran_fdata)
 S3method(print,nmtran_process)
 S3method(print_model_files,default)
 S3method(submit_model,bbi_base_model)
@@ -161,7 +160,6 @@ export(new_bootstrap_run)
 export(new_ext)
 export(new_model)
 export(nm_data)
-export(nm_fdata)
 export(nm_file)
 export(nm_file_multi_tab)
 export(nm_grd)

R/aaa.R

@@ -210,7 +210,6 @@ CONF_LOG_CLASS <- "bbi_config_log_df"
 SUM_LOG_CLASS <- "bbi_summary_log_df"
 LOG_DF_CLASS <- "bbi_log_df"
 NMTRAN_PROCESS_CLASS <- "nmtran_process"
-NMTRAN_FDATA_CLASS <- "nmtran_fdata"
 
 # YAML keys that are hard-coded
 YAML_YAML_MD5 <- "yaml_md5"

R/print.R

@@ -502,18 +502,6 @@ print.nmtran_process <- function(x, ...){
 }
 
 
-#' @describeIn print_bbi Prints the `FDATA`, showing key changes from `nm_data`
-#' @export
-print.nmtran_fdata <- function(x, ...){
-  recs_dropped <- attributes(x)$n_records_dropped
-  cli::cat_bullet(
-    paste("Number of records dropped:", col_blue(recs_dropped)),
-    bullet = "en_dash"
-  )
-  cat("\n")
-  NextMethod()
-}
-
 #' @describeIn print_bbi Draw model tree as a static plot
 #' @param x plot to display
 #' @param newpage Logical (T/F). If `TRUE`, draw new (empty) page first.

R/run-nmtran.R

@@ -8,8 +8,7 @@
 #' control stream data and instructions into a form executable by `NONMEM`.
 #'
 #' `run_nmtran()` allows users to test their models ahead of submission to ensure
-#' correct coding, whereas `nm_fdata()` generates and returns the `NM-TRAN`
-#' dataset (`FDATA`) for further analysis and verification.
+#' correct coding.
 #'
 #' @param .mod A `bbr` model object.
 #' @param .config_path Path to a bbi configuration file. If `NULL`, the default,
@@ -28,9 +27,6 @@
 #' # Set the path to an NM-TRAN executable
 #' run_nmtran(mod, nmtran_exe = "/opt/NONMEM/nm75/tr/NMTRAN.exe")
 #'
-#' # Generate and return `FDATA`
-#' fdata <- nm_fdata(mod)
-#'
 #' }
 #' @name nmtran
 NULL
@@ -91,56 +87,6 @@ run_nmtran <- function(
 }
 
 
-#' @describeIn nmtran Executes `run_nmtran` on a `bbi_nonmem_model` and
-#'  returns the `NM-TRAN` dataset (`FDATA`)
-#' @export
-nm_fdata <- function(
-    .mod,
-    .config_path = NULL,
-    nmtran_exe = NULL
-){
-  nmtran_p <- run_nmtran(.mod, .config_path, nmtran_exe, delete_on_exit = FALSE)
-  on.exit(fs::dir_delete(nmtran_p$run_dir))
-
-  if(nmtran_p$status_val != 0){
-    # trim output
-    output_lines <- nmtran_p$output_lines[!grepl("^\\s+$", nmtran_p$output_lines)]
-    rlang::warn(
-      c(
-        "NM-TRAN was unsuccessful and returned the following messages:",
-        paste(output_lines, collapse = "\n")
-      )
-    )
-  }
-
-  # Attempt to read in FDATA (even if status_val is not 0)
-  #  - FDATA can still be read in in _some scenarios_ where NM-TRAN fails
-  fdata_path <- file.path(nmtran_p$run_dir, "FDATA")
-  if(fs::file_exists(fdata_path)){
-    input_data <- nm_data(.mod) %>% suppressMessages()
-    fdata <- tryCatch({
-      nm_file_impl(fdata_path, skip = 0) %>%
-        stats::setNames(names(input_data))
-    }, error = function(cond){
-      rlang::inform(
-        c("FDATA could not be read in:", cond$parent$message)
-      )
-      return(NULL)
-    })
-
-    if(!is.null(fdata)){
-      attr(fdata, "n_records_dropped") <- nrow(input_data) - nrow(fdata)
-    }
-
-    # assign class and return
-    class(fdata) <- c(NMTRAN_FDATA_CLASS, class(fdata))
-    return(fdata)
-  }else{
-    return(invisible(NULL))
-  }
-}
-
-
 #' Search for and validate existence of an `NM-TRAN` executable
 #'
 #' If `nmtran_exe = NULL`, this will look for a `bbi.yaml` file in the same

tests/testthat/test-workflow-bbi.R

@@ -402,17 +402,6 @@ withr::with_options(list(
       expect_equal(nmtran_results$status, "NMTRAN successful")
     })
 
-    it("nm_fdata: integration", {
-      fdata <- nm_fdata(mod1)
-
-      expect_equal(names(fdata), names(nm_data(mod1)))
-
-      # Test dropped/renamed columns
-
-      # Test failure: incorrect data path
-      data_path <- "test/this/path/data.csv"
-      modify_data_path_ctl(mod1, data_path)
-    })
   })
 
 }) # closing withr::with_options