METHOD_OPTIONS
Type: dict_record
method options for gen_script
Example:-
METHOD_OPTIONS:
py_module: gen
rand_seed: 12345
float_format: default
py_module
Type: one_of(gen)
Python module required to process this script file
Example:-
py_module: gen
rand_seed
Option to set seed to make run result reproducible -e.g. when debugging.
Example:-
rand_seed: 12345
float_format
Type: str
Format string for numerical output
Example:-
float_format: default
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
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
DESCRIPTION
Type: dict_record
Description fields for script.
Example:-
DESCRIPTION:
name: my_pkpd_model
title: My PKPD model
author: My Name
abstract: |
Abstract describing the model
keywords: ['pkpd']
name
Type: str
Unique name used to distinguish script
Example:-
name: my_pkpd_model
title
Type: str
A longer text string that could serve as a title
Example:-
title: My PKPD model
abstract
Type: verbatim
Abstract paragraph describing model
Example:-
abstract: |
Abstract describing the model
keywords
Type: list
Keywords list used to categorise models.
Example:-
keywords: ['pkpd']
FILE_PATHS
Type: dict_record
file paths for script
Example:-
FILE_PATHS:
output_folder: auto
temp_folder: auto
log_folder: auto
output_file_ext: ['svg']
delete_old_files_flag: False
output_folder
Type: output_folder / auto
Output folder - results of computation stored here
Example:-
output_folder: auto
temp_folder
Type: output_folder / auto
Temp folder - temporary files stored here
Example:-
temp_folder: auto
log_folder
Type: output_folder / auto
Log folder - log files stored here
Example:-
log_folder: auto
output_file_ext
Type: list_of(pdf,png,svg)
Output file extension - determines graphical output file format.
Example:-
output_file_ext: ['svg']
delete_old_files_flag
Type: bool
Option to delete any existing files before running.
Example:-
delete_old_files_flag: False
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
EFFECTS
Type: repeat_verb_record
EFFECT params to define hierarchical population model
Example:-
EFFECTS:
POP: |
c[AMT] = 100.0
f[KA] = 0.2
f[CL] = 2.0
f[V1] = 50
f[Q] = 1.0
f[V2] = 80
f[KA_isv,CL_isv,V1_isv,Q_isv,V2_isv] = [
[0.1],
[0.01, 0.03],
[0.01, -0.01, 0.09],
[0.01, 0.02, 0.01, 0.07],
[0.01, 0.02, 0.01, 0.01, 0.05],
]
f[PNOISE] = 0.15
ID: |
c[ID] = sequential(50)
t[DOSE] = 2.0
t[OBS] ~ unif(1.0, 50.0; 5)
# t[OBS] = range(1.0, 50.0; 5)
r[KA, CL, V1, Q, V2] ~ mnorm([0,0,0,0,0], f[KA_isv,CL_isv,V1_isv,Q_isv,V2_isv])
PREPROCESS
Type: verbatim
Code that preprocesses the input data. Use this to filter rows and create derived covariates.
Example:-
PREPROCESS: |
MODEL_PARAMS
Type: verbatim
Defines the mapping from c[X], f[X] and r[X] variables to individual model m[X] parameters.
Example:-
MODEL_PARAMS: |
m[KA] = f[KA] * exp(r[KA])
m[CL] = f[CL] * exp(r[CL])
m[V1] = f[V1] * exp(r[V1])
m[Q] = f[Q] * exp(r[Q])
m[V2] = f[V2] * exp(r[V2])
m[ANOISE] = 0.001
m[PNOISE] = f[PNOISE]
STATES
Type: verbatim
Optional section for setting initial values of s[X] variables can also set slabel[X] text labels.
Example:-
STATES: |
DERIVATIVES
Type: verbatim
Define how the covariates and effects determine flows between compartments.
Example:-
DERIVATIVES: |
# s[DEPOT,CENTRAL,PERI] = @dep_two_cmp_cl{dose:@bolus{amt: c[AMT]}}
d[DEPOT] = @bolus{amt: c[AMT]} - m[KA]*s[DEPOT]
d[CENTRAL] = m[KA]*s[DEPOT] - s[CENTRAL]*m[CL]/m[V1] - s[CENTRAL]*m[Q]/m[V1] + s[PERI]*m[Q]/m[V2]
d[PERI] = s[CENTRAL]*m[Q]/m[V1] - s[PERI]*m[Q]/m[V2]
PREDICTIONS
Type: verbatim
Define the final predicted m[X] variables to be output by the compartment model system.
Example:-
PREDICTIONS: |
p[DV_CENTRAL] = s[CENTRAL]/m[V1]
plabel[DV_CENTRAL] = 'Drug conc. (units)'
var = m[ANOISE]**2 + m[PNOISE]**2 * p[DV_CENTRAL]**2
c[DV_CENTRAL] ~ norm(p[DV_CENTRAL], var)
POSTPROCESS
Type: verbatim
Code that postprocesses the output data. Use this to filter rows and create derived covariates, after the main data curves have been generated.
Example:-
POSTPROCESS: |
ODE_SOLVER
Type: one_of_record
one of many possible solvers
Example:-
ODE_SOLVER:
CPPLSODA:
atol: 1e-06
rtol: 1e-06
max_nsteps: 10000000
use_supersections: True
use_sens: True
hmin: 0.0
NO_SOLVER
Type: dict_record
Null method for blank derivatives.
Example:-
NO_SOLVER: {}
ANALYTIC
Type: dict_record
Analytic method for solving ODE
Example:-
ANALYTIC:
use_supersections: auto
use_sens: True
use_supersections
Option to combine sections into supersections, which can make PoPy run faster, however with discontinuous ODE params you may need to turn this off (closer to nonmem approach).
Example:-
use_supersections: auto
use_sens
Type: bool
Option to use sensitivity equations in ode solver.
Example:-
use_sens: True
SCIPY_ODEINT
Type: dict_record
odeint solver record
Example:-
SCIPY_ODEINT:
atol: 1e-06
rtol: 1e-06
max_nsteps: 10000000
use_supersections: auto
use_jacobian: False
use_sens: True
use_tcrit: False
atol
Type: float
Absolute tolerance of ode solver.
Example:-
atol: 1e-06
rtol
Type: float
Relative tolerance of ode solver.
Example:-
rtol: 1e-06
max_nsteps
Type: int
Maximum number of steps allowed in ode solver.
Example:-
max_nsteps: 10000000
use_supersections
Option to combine sections into supersections, which can make PoPy run faster, however with discontinuous ODE params you may need to turn this off (closer to nonmem approach).
Example:-
use_supersections: auto
use_jacobian
Type: bool
Option to use jacobian in ode solver.
Example:-
use_jacobian: False
use_sens
Type: bool
Option to use sensitivity equations in ode solver.
Example:-
use_sens: True
use_tcrit
Type: bool
Option to set lsoda tcrit to start and end of subsection. Note this is an experimental option.
Example:-
use_tcrit: False
CPPLSODA
Type: dict_record
C++ version of original cvode c library.
Example:-
CPPLSODA:
atol: 1e-06
rtol: 1e-06
max_nsteps: 10000000
use_supersections: auto
use_sens: True
hmin: 1e-12
atol
Type: float
Absolute tolerance of ode solver.
Example:-
atol: 1e-06
rtol
Type: float
Relative tolerance of ode solver.
Example:-
rtol: 1e-06
max_nsteps
Type: int
Maximum number of steps allowed in ode solver.
Example:-
max_nsteps: 10000000
use_supersections
Option to combine sections into supersections, which can make PoPy run faster, however with discontinuous ODE params you may need to turn this off (closer to nonmem approach).
Example:-
use_supersections: auto
use_sens
Type: bool
Option to use sensitivity equations in ode solver.
Example:-
use_sens: True
hmin
Type: float
Minimum step size of ode solver.
Example:-
hmin: 1e-12
OUTPUT_SCRIPTS
Type: dict_record
scripts to output for further processing
Example:-
OUTPUT_SCRIPTS:
GRPH: {output_mode: none, grph_list: ['OBS_vs_TIME']}
TABLE: {output_mode: none, tables_list: []}
SIM:
output_mode: run
sim_time_step: 1.0
grph_list: ['OBS_vs_TIME']
tables_list: []
GENSUM: {output_mode: run}
GRPH
Type: dict_record
options to pass to grph script.
Example:-
GRPH:
output_mode: none
grph_list: ['OBS_vs_TIME']
output_mode
Type: one_of(none,create,run)
Output options.
Example:-
output_mode: none
grph_list
Type: list(str)
Graph types to plt
Example:-
grph_list: ['OBS_vs_TIME']
TABLE
Type: dict_record
Options to pass to TAB script.
Example:-
TABLE:
output_mode: none
tables_list: []
output_mode
Type: one_of(none,create,run)
Output options.
Example:-
output_mode: none
tables_list
Type: list_record
List of tables to create.
Example:-
tables_list:
- 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: "*"
input_solution
Type: str
Label of the solution to parse
Example:-
input_solution: final_fit_ipred
output_file
Type: output_file
Destination file for table
Example:-
output_file: my_table.csv
cx_columns
Columns from covariates/observations table to output
Example:-
cx_columns: "*"
mx_columns
Columns from model_params table to output
Example:-
mx_columns: "*"
sx_columns
Columns from states table to output
Example:-
sx_columns: "*"
px_columns
Columns from predictions table to output
Example:-
px_columns: "*"
SIM
Type: dict_record
options to pass to sim script.
Example:-
SIM:
output_mode: none
sim_time_step: -1.0
grph_list: ['OBS_vs_TIME']
tables_list:
- TABLE:
input_solution: final_fit_ipred
output_file: my_table.csv
cx_columns: "*"
mx_columns: "*"
sx_columns: "*"
px_columns: "*"
output_mode
Type: one_of(none,create,run)
Output options.
Example:-
output_mode: none
sim_time_step
Type: float
Size of time step when creating smooth curve predictions note setting this to a negative value, results in simulated predictions for each individual ONLY at time points in the original data set.
Example:-
sim_time_step: -1.0
grph_list
Type: list(str)
Graph types to plt
Example:-
grph_list: ['OBS_vs_TIME']
tables_list
Type: list_record
List of tables to create.
Example:-
tables_list:
- 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: "*"
input_solution
Type: str
Label of the solution to parse
Example:-
input_solution: final_fit_ipred
output_file
Type: output_file
Destination file for table
Example:-
output_file: my_table.csv
cx_columns
Columns from covariates/observations table to output
Example:-
cx_columns: "*"
mx_columns
Columns from model_params table to output
Example:-
mx_columns: "*"
sx_columns
Columns from states table to output
Example:-
sx_columns: "*"
px_columns
Columns from predictions table to output
Example:-
px_columns: "*"
GENSUM
Type: dict_record
options to pass to gensum script.
Example:-
GENSUM:
output_mode: none
output_mode
Type: one_of(none,create,run)
Output options.
Example:-
output_mode: none