• Language: en

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: []
N2PDat Script
P2NDat Script
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