system_nm_check_ds: Check NONMEM Dataset for Automatic Definitions

In john-harrold/ubiquity: PKPD, PBPK, and Systems Pharmacology Modeling Tools

Check NONMEM Dataset for Automatic Definitions

Description

Checks the dataset against the information specified by system_define_cohorts_nm for validity

Usage

system_nm_check_ds(
  cfg,
  DS = "DSNAME",
  col_ID = "ID",
  col_CMT = "CMT",
  col_DV = "DV",
  col_TIME = "TIME",
  col_AMT = "AMT",
  col_RATE = "RATE",
  col_EVID = "EVID",
  col_GROUP = NULL,
  filter = NULL,
  INPUTS = NULL,
  OBS = NULL
)

Arguments

cfg	ubiquity system object
DS	Name of the dataset loaded using system_load_data
col_ID	Column of unique subject identifier
col_CMT	Compartment column
col_DV	Column with observations or ’.’ for input
col_TIME	Column with system time of each record
col_AMT	Infusion/dose amounts (these need to be in the same units specified in the system.txt file)
col_RATE	Rate of infusion or ’.’ for bolus
col_EVID	EVID (0 - observation, 1 dose)
col_GROUP	Column name to use for defining similar cohorts when generating figures.
filter	List used to filter the dataset or NULL if the whole dataset is to be used (see filter rules or nm_select_records or a description of how to use this option)
INPUTS	List mapping input information in the dataset to names used in the system.txt file
OBS	List mapping obseravation information in the dataset to names used in the system.txt file

Value

list with the following elements

• "isgood" Boolean variable indicating success (TRUE) or failure (FALSE)

• "mywarning" Boolean variable indicating warnings (TRUE) or no warnings (FALSE)

• "dsraw" Dataframe with the filtered raw data that was used

• "input_records" Rows from dsraw containing the input information

• "obs_records" Rows from dsraw containing the observation information

• "sids" Subject ids found in dsraw

• "TSsys" system time scale used in the dataset

john-harrold/ubiquity documentation built on March 13, 2024, 2:58 a.m.