system_define_cohorts_nm: Define Cohorts from NONMEM Input File

Description

This function allows the user to define cohorts automatically from a NONMEM dataset

Usage

system_define_cohorts_nm(
  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
)

Value

ubiquity system object with cohorts defined.

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 nams used in the system.txt file

Details

NOTE: to use this function it is necessary that a timescale be define for the system time scale. For example, if the system time scale was days, something like the following is needed:

<TS:days> 1

Include all records in the dataset

filter = NULL

Include only records matching the following filter

filter = list()
filter$COLNAME = c()

Mapping information:

The inputs mapping information (INPUTMAP) is alist with a field for each type of input: input:

bolus List with a name for each bolus state in the dataset (<B:?>): each bolus name should have a CMT_NUM field indicating the compartment number for that state
infusion_rates List with a name for each rate in the dataset (<R:?>): each rate name should have a CMT_NUM field indicating the compartment number for that state
covariates List with for each covariate in the dataset (<CV:?>): each covariate name should have a col_COV indicating the column in the database that contains that covariate

From a coding perspective it looks like this:

INPUTMAP = list()
INPUTMAP$bolus$SPECIES$CMT_NUM            =  1
INPUTMAP$infusion_rates$RATE$CMT_NUM      =  1
INPUTMAP$covariates$CVNAME$col_COV        = 'CNAME'

The observation mapping information (OBSMAP) is a list with elements for each output as described in for system_define_cohort. Each output is a list with the following names:

variance Variance model for this output
CMT Compartment number mapping observations for this output
output Name of the output (<O>) corresponding with the observations
missing Value indicating a missing observation or NULL