# METHOD_OPTIONS

Type: dict_record

method options for nm.input_data

Example:-

    METHOD_OPTIONS:
        py_module: n2pdat

## py_module

Type: one_of(n2pdat)

Python module required to process this script file

Example:-

    py_module: n2pdat

# FILE_PATHS

Type: dict_record

File path options for n2pdat program.

Example:-

    FILE_PATHS:
        input_nonmem_file: input_nonmem_data.csv
        output_popy_file: output_popy_data.csv

## input_nonmem_file

Type: input_file

path to input comma separated value file in nonmem data format

Example:-

    input_nonmem_file: input_nonmem_data.csv

## output_popy_file

Type: output_file

path to output popy data file to be created by script

Example:-

    output_popy_file: output_popy_data.csv

# INPUT_NONMEM_FIELDS

Type: dict_record

Details for input popy data.

Example:-

    INPUT_NONMEM_FIELDS:
        comment_prefix: '#'
        column_names: auto
        date_field: none
        date_format: none
        time_field: TIME
        id_field: ID
        evid_field: EVID
        dv_field: DV
        mdv_field: none
        amt_field: AMT
        rate_field: none
        dur_field: none
        cmt_field: CMT
        obs_cmt_numbers: [1]
        dose_cmt_numbers: [1]

## comment_prefix

Type: str

Characters used to indicate a comment line

Example:-

    comment_prefix: '#'

## column_names

Type: list / auto

List of column names. “auto” takes names from first row of dataset

Example:-

    column_names: auto

## date_field

Type: str

Name of input nonmem date field

Example:-

    date_field: none

## date_format

Type: str

Name of input nonmem date format (e.g. yyyy/mm/dd)

Example:-

    date_format: none

## time_field

Type: str

Name of input nonmem time field

Example:-

    time_field: TIME

## id_field

Type: str

Name of input nonmem id field

Example:-

    id_field: ID

## evid_field

Type: str

Name of input nonmem evid field

Example:-

    evid_field: EVID

## dv_field

Type: str

Name of input nonmem dependent value field

Example:-

    dv_field: DV

## mdv_field

Type: str

Name of input nonmem missing dependent value column

Example:-

    mdv_field: none

## amt_field

Type: str

Name of input nonmem dose amount column

Example:-

    amt_field: AMT

## rate_field

Type: str

Name of input nonmem infusion rate column (e.g. RATE)

Example:-

    rate_field: none

## dur_field

Type: str

Name of input nonmem infusion duration column (e.g. DUR)

Example:-

    dur_field: none

## cmt_field

Type: str

Name of input nonmem compartment column

Example:-

    cmt_field: CMT

## obs_cmt_numbers

Type: list(int)

For each input nonmem dv field specify a compartment number has to be same length as PoPy dv_fields list

Example:-

    obs_cmt_numbers: [1]

## dose_cmt_numbers

Type: list(int)

For each input nonmem amt field specify a compartment number, has to be same length as PoPy amt_fields list

Example:-

    dose_cmt_numbers: [1]

# OUTPUT_POPY_FIELDS

Type: dict_record

Details for output popy data.

Example:-

    OUTPUT_POPY_FIELDS:
        time_field: ABSTIME
        id_field: ID
        type_field: TYPE
        dv_fields: ['DRUG_CONC']
        amt_fields: ['AMT']
        rate_fields: []
        dur_fields: []
        dose_labels: ['']

## time_field

Type: str

Name of output popy time field

Example:-

    time_field: ABSTIME

## id_field

Type: str

Name of output popy id field

Example:-

    id_field: ID

## type_field

Type: str

Name of output popy type field

Example:-

    type_field: TYPE

## dv_fields

Type: list(str)

List of output popy fields containing dependent value information

Example:-

    dv_fields: ['DRUG_CONC']

## amt_fields

Type: list(str)

List of output popy columns containing dosing amount information

Example:-

    amt_fields: ['AMT']

## rate_fields

Type: list(str)

List of output popy columns containing infusion rate information

Example:-

    rate_fields: []

## dur_fields

Type: list(str)

List of output popy columns containing infusion duration information

Example:-

    dur_fields: []

## dose_labels

Type: list(str)

List of output popy dose label values within the TYPE field that define different types of dose i.e if entry is dose:X then put X in listif entry is dose then put “” in list

Example:-

    dose_labels: ['']

# OUTPUT_OPTIONS

Type: dict_record

Output options for n2pdat/p2ndat programs.

Example:-

    OUTPUT_OPTIONS:
        drop_fields: []

## drop_fields

Type: list(str)

Columns to remove from the output

Example:-

    drop_fields: []