Join simulation and input data

Joins the simulation and input data of a bbi_nonmem_model object with an attached simulation.

nm_join_sim(
  .mod,
  .join_col = "NUM",
  .cols_keep = "all",
  add_table_names = FALSE
)

Arguments

.mod: A bbi_nonmem_model with an attached simulation, or a bbi_nmsim_model object.
.join_col: Character column name(s) to use to join table files. Defaults to NUM. See Details.
.cols_keep: Either 'all', or a vector of column name(s) to retain in the final dataset after joining. Defaults to keeping all columns.
add_table_names: Logical (T/F). If TRUE, include a column denoting the table names as specified in the file (e.g., 'TABLE NO. 1').

Value

a tibble

Note

The join column name(s) specified should match what you provided to add_simulation().

Join column

The .join_col is the name of a single column that should appear in both the input data set and any tables you want to join. We recommend you make this column a simple integer numbering the rows in the input data set (for example NUM). When this column is carried into the output table files, there will be unambiguous matching from the table file back to the input data set.

Note also that, when .join_col is carried into table outputs, there is no need to table any other columns from the input data as long as the nm_join() approach is used; any column in the input data set, regardless of whether it is listed in $INPUT or not, will be carried through from the input data and therefore available in the joined result.

Duplicate Rows Warning for Join Column

If there are duplicate rows found in the specified .join_col, a warning will be raised specifying a subset of the repeated rows. Duplicates may be caused by lack of output width. FORMAT may be need to be stated in control stream to have sufficient width to avoid truncating .join_col.

Example: creating a row number `.join_col`

Take the following $INPUT and $DATA records:

$INPUT ID TIME MDV EVID DV AMT SEX WT ETN
$DATA ../../../../extdata/acop.csv

Before submitting a model, read in the data and add a row number column;

library(dplyr)
data <- nm_data(.mod) %>% mutate(NUM = 1:n())
readr::write_csv(data, get_data_path(.mod))

Then add 'NUM' to the list of input columns:

$INPUT ID TIME MDV EVID DV AMT SEX WT ETN *NUM*

Examples

if (FALSE) {

add_simulation(.mod, .join_col = c("NUM", "ID"))

nm_join_sim(.mod, .join_col = c("NUM", "ID"), .cols_keep = "ID")

# These return the same thing (simulation model is automatically read-in):
nm_join_sim(.mod)
nm_join_sim(get_simulation(.mod))
}