modify_records: Modify or retrieve options and records from a 'NONMEM'...
In metrumresearchgroup/bbr: R package for bbi

modify_records

R Documentation

Modify or retrieve options and records from a `NONMEM` control stream file

Description

Modify or retrieve options and records from a NONMEM control stream file

Usage

get_model_ctl(.mod)

get_records(.mod, type, get_lines = FALSE)

mod_has_record(.mod, type)

remove_records(.mod, type)

add_new_record(
  .mod,
  type,
  rec_name = paste0("$", toupper(type), " "),
  lines = NULL,
  after = NULL
)

modify_data_path_ctl(.mod, data_path)

modify_prob_statement(.mod, prob_text = NULL)

get_input_columns(.mod, from_data = TRUE)

get_table_columns(.mod, from_data = TRUE)

Arguments

`.mod`	a bbr model object
`type`	record type. This may be spelled any way that's accepted in a `NONMEM` control stream.
`get_lines`	Logical (T/F). If `TRUE`, return the lines as character vectors (based on how they were defined in the control stream).
`rec_name`	a character string defining the record name (e.g., `⁠$THETA⁠`)
`lines`	a character string or vector of lines to append to the new record. If passing a vector, creates a new line per index. Defaults to `NULL`.
`after`	add new record after this record type. This may be spelled any way that's accepted in a `NONMEM` control stream. If `NULL`, append to the end of the control stream. If multiple records are found, uses the last index
`data_path`	Data path to set in a `⁠$DATA⁠` record.
`prob_text`	If `NULL` return the current `⁠$PROBLEM⁠` statement. If a character string, set the problem statement to that value.
`from_data`	Logical (T/F). If `TRUE`, the default, get the column names from the first line of the referenced dataset (input data or table file). If `FALSE`, parse the control stream and retrieve from the relevant record type (`⁠$INPUT⁠` or `⁠$TABLE⁠`).

Details

get_model_ctl() is called internally within the other functions, though it can also be used outside of that context.
modify_prob_statement(), modify_data_path_ctl(), remove_records(), and add_new_record() read in the control stream, make any modifications, and then save out the updated control stream.
- modify_prob_statement() also returns a character string defining the ⁠$PROBLEM⁠ text (see prob_text argument).
mod_has_record() will return a logical value denoting whether a bbr model has a given record type.
get_records() extracts all records of a given type. Note that it is not meant to be used to modify existing records.
get_input_columns() and get_table_columns() extract the column names of the input data and all table files respectively. They can either be parsed from a NONMEM control stream file, or determined from reading in the csvs/table files. See from_data argument for more details.

Functions

get_model_ctl(): Read in a NONMEM control stream file, parsed via nmrec
get_records(): Pull all records of a given record type from a bbr model
mod_has_record(): Check if a bbr model has a given record type
remove_records(): Remove all records of a given type from a NONMEM control stream file
add_new_record(): Add a new record of a given type from a NONMEM control stream file
modify_data_path_ctl(): Modify the specified data path in a NONMEM control stream file
modify_prob_statement(): Modify or retrieve the ⁠$PROBLEM⁠ statement from a NONMEM control stream file.
get_input_columns(): Retrieve input data column names from either the ⁠$INPUT⁠ record in a NONMEM control stream file or the input dataset.
get_table_columns(): Retrieve table columns names from either ⁠$TABLE⁠ record(s) in a NONMEM control stream file or the tabled out files

Note

Run the following command to see what record types are available/supported by nmrec:

`ls(nmrec:::record_names)`

Examples

## Not run: 

# Adding a new record
seed <- 1234; n <- 100
sim_lines <- glue("({seed}) SUBPROBLEMS={n} TRUE=FINAL ONLYSIMULATION")
add_new_record(.mod, "simulation", lines = sim_lines, after = "pred")


# Remove all records of a given type
if(mod_has_record(.mod, "table")) remove_records(.mod, "table")


# Modify or extract a problem statement
modify_prob_statement(.mod, prob_text = NULL)
#> [1] "PK model 1 cmt base"
modify_prob_statement(.mod, prob_text = "new problem")
#> [1] "new problem"


## End(Not run)

metrumresearchgroup/bbr documentation built on March 29, 2025, 1:08 p.m.