METHOD_OPTIONS

method options for TABLE

Example:-

METHOD_OPTIONS:
    py_module: table

py_module

Type: one_of(table)

Python module required to process this script file

Example:-

py_module: table

PARALLEL

Type: one_of_record

one of many possible servers

Example:-

PARALLEL:
    SINGLE: {progress_bar_length: 0}

SINGLE

Type: dict_record

single process server spec.

Example:-

SINGLE:
    progress_bar_length: 0

progress_bar_length

Type: int

Length of progress bar on screen (default=0, off)

Example:-

progress_bar_length: 0

MPI_WORKERS

Type: dict_record

MPI local server spec.

Example:-

MPI_WORKERS:
    n_workers: auto
    cpu_load: 1.0
    progress_bar_length: 0

n_workers

Type: int / auto

Number of workers to use on this machine, defaults to number of processors, but could be more or fewer.

Example:-

n_workers: auto

cpu_load

Type: float

Desired load on CPU as a decimal greater than 0.0 (0%) and less than or equal to 1.0 (100%)

Example:-

cpu_load: 1.0

progress_bar_length

Type: int

Length of progress bar on screen (default=0, off)

Example:-

progress_bar_length: 0

FILE_PATHS

Type: dict_record

file paths

Example:-

FILE_PATHS:
    output_folder: auto
    log_folder: auto
    table_file_ext: ['csv']
    delete_old_files_flag: False
    solutions:
        initial_fit_ipred: sol0/solution.pyml
        final_fit_ipred: solN/solution.pyml

output_folder

Type: output_folder / auto

Output folder - results of computation stored here

Example:-

output_folder: auto

log_folder

Type: output_folder / auto

Log folder - log files stored here

Example:-

log_folder: auto

table_file_ext

Type: list_of(csv)

Output file extension; determines tabular output file format.

Example:-

table_file_ext: ['csv']

delete_old_files_flag

Type: bool

Option to delete any existing files before running.

Example:-

delete_old_files_flag: False

solutions

Type: dict

Solutions to compare

Example:-

solutions:
    initial_fit_ipred: sol0/solution.pyml
    final_fit_ipred: solN/solution.pyml

DATA_FIELDS

Type: dict_record

data fields for popy.dat.fields object

Example:-

DATA_FIELDS:
    type_field: TYPE
    id_field: ID
    time_field: TIME

type_field

Type: str

Field name in data file that contains row type info, e.g. obs/dose etc

Example:-

type_field: TYPE

id_field

Type: str

Field name in data file that contains identity string for each data row e.g. obs/dose etc

Example:-

id_field: ID

time_field

Type: str

Field name in data file that contains time or event for each data row

Example:-

time_field: TIME

PREPROCESS

Type: verbatim

Code that preprocesses the input data. Use this to filter rows and create derived covariates.

Example:-

PREPROCESS: |

OUTPUT_TABLES

Type: list_record

List of tables to create.

Example:-

OUTPUT_TABLES:
    - TABLE:
        input_solution: final_fit_ipred
        output_file: my_table.csv
        cx_columns: "*"
        mx_columns: "*"
        sx_columns: "*"
        px_columns: "*"

TABLE

Type: dict_record

Table properties.

Example:-

TABLE:
    input_solution: final_fit_ipred
    output_file: my_table.csv
    cx_columns: "*"
    mx_columns: "*"
    sx_columns: "*"
    px_columns: "*"